Weekend reads: Trying unsuccessfully to correct the scientific record; drug company funding and research

There were lots of pieces about scientific misconduct, publishing, and related issues posted around the web this week, so without further ado:

The News & Observer has a great two-part series about a Stefan Franzen, a chemistry professor at North Carolina State University who has been trying unsuccessfully to correct the scientific record, including a paper in Science. (Here’s a 2011 report on the case from Nature.) The reporter, Joseph Neff, puts the series into context here.
Pacific Standard and Slate have corrected pieces on what happens when women take their husbands’ names because they both relied on retracted research by Diederik Stapel.
“It’s not often that a journal will call attention to unreliable findings that it publishes…” But the editor of Human Reproduction did. And the Journal of Clinical Endocrinology & Metabolism may walk back a policy under which they “would no longer publish work that used immunoassays to measure steroid levels for primary outcomes,” following strong reader reaction.
Following our coverage of a silent retraction in Cureus of a paper by a researcher who has threatened to sue us, the journal explains how it deals with retractions.
The Guardian details the story of Nick Brown, the “British amateur who debunked the mathematics of happiness” and whose work we covered in September. Narrative.ly wrote about Brown in October.
Benjamin Schwessinger, a colleague of Pamela Ronald’s, gives a behind-the-scenes look at what led to the lab’s two retractions.
Julia Belluz sits in on a class by John Ioannidis, who has made a career out of showing how many studies don’t hold up. Ioannidis also features prominently in a New York Times essay on reproducibility by George Johnson.
The University of Queensland offered an update on their investigation of ~~Levon Khachigian, who has had four papers retracted~~ Bruce Murdoch, who has had one paper retracted.
Here’s what MIT was teaching about the responsible conduct of research before fraudster Luk Van Parijs joined the faculty.
“Should journals stop publishing research funded by the drug industry?”
At the Scholarly Kitchen, Kent Anderson says an analysis of advertising in medical journals — which we highlighted in a recent Weekend Reads — is “fatally flawed.”
For some scientists, it’s unclear what’s new about a recently published paper on “quilt plots.”
JAMA has posted an oral history of the evidence-based medicine movement.
“I need to stay alert to one of the most corrupting forms of temptation, stopping myself from selecting evidence for no better reason than that it confirms my prior thinking.”
Genome Web adds a lot of detail (sub req’d) to the story of a former NIH researcher who falsified images that we covered last month.
What scientific ideas are ready for retirement? That’s the question Edge asked. Tabitha Powledge has a roundup.
As part of its Supplement Shell Game series, USA Today finds that one of the main authors of a study supposedly showing the value of Craze is a doctor who has been disciplined in two states.
Here’s a groaner of a comic about plagiarism, featuring DNA.

399 thoughts on “Weekend reads: Trying unsuccessfully to correct the scientific record; drug company funding and research”

Jaime A. Teixeira da Silva says:

January 25, 2014 at 2:25 pm

Frustration in dealing with errors in the plant (and allied sciences) science literature

These are all important stories, but I would say that the one that relates most to plant scientists – except for the story on the Ronald lab – is in fact the story by Stefan Franzen. I wish to echo his frustration in my own attempts to show how the plant science literature is fraught with errors, but that there is currently little appetite to correct the literature for a few reasons. Many of my own colleagues and friends have been critical of me, even asking me “why” or “for what purpose”, and thus exposing oneself (and ones work and legacy) to critique is one of the greatest challenges that plant scientists face.

a) Arrogance and fear among editors and editors-in-chief (EICs) who do not want to admit that their quality control (QC) – personal, professional or system-related – failed during the traditional peer review process. A corrigendum under their name would reflect poorly on their management and their legacy would be stained. Which editor wants to, frankly speaking, have a stain on their CV even long after they have left this earth?

b) The failure to convince such editors and EICs that issuing an erratum (if the author brings forth the claim), a corrigendum (if the publisher recognizes that the error was theirs) is the morally and ethically correct thing to do. There seems to be a serious case of serial and wide-spread denial among plant scientists, or, even worse, a passive lack of will for change.

c) The lack of desire by publishers to expose that their peer review systems have been fallible and weak, with inherent weaknesses, simply because perfection can only be achieved (if ever), where sample size tends towards infinity. And since most peer reviews in moderate to high IF journals in the plant sciences (IF = 1.0 to 3.5) rely on the “expert” opinion of usually not more than three individuals in a pool that probably contains several million, it is quite easy to understand how the system of traditional peer review is broken, imperfect, and open to abuse, errors and fraud. The current climate of retractions is trying to focus on the authors and scientists, while protecting their own backs and images, thus skirting deeper scrutiny of the current publishing model, which is fundamentally highly flawed.

d) The real “crime” occurs when there are errors that have been pointed out by the academic community as factual, evidence-based information and critical analysis [1], but which the editors then fail to take into consideration, i.e., the active ignoring of the advice, the facts and the warning signals. Failure to act will be the ultimate down-fall of the reputation of an editor, of the fame of the journal, and the trust of a publisher. Unfortunately, however, if in fact an erratum, corrigendum, or retraction were to be issued for the level that I am personally observing in the plant sciences, then I am afraid that this could potentially wipe out an entire slice of the plant science literature, calling into question the validity of studies that referenced such flawed or erroneous studies. In some cases, the decision is made by the EIC, or by two or three editors. In other words, the fate of the correction of science lies in the hands of a tiny elite and dangerously powerful status quo. Such ego-centric decisions are fundamentally wrong, self-centered, and of course, fraught with bias. But this is one large reality that explains the resistance we are facing in the plant sciences.

e) The fear by the community of the down-stream effects. No scientist wants their work to be remembered by an erratum, correction or in the worst case, retraction. But these three aspects need to form part of the quotidian landscape of science publishing. And retro-active analysis, and punishment – where merited – should be the mainstay of science moving forward. The equivalent of not assuming this position, no matter how unpalatable it is, is like using the internet thinking that one would be free of virus attacks, hacking, or spying. Naivety, ignorance, and inaction are making corrections to the plant science literature much more than just an uphill climb. In some cases, they are making corrections impossible. The human, intellectual and psychological firewall in place is massive.

f) There is a lack of understanding of a basic principle that science is a constant conversation. A theory that was established 50 or 80 years ago, if valid at that time, should form part of the discussion even now. In some ways, I am very concerned about the aggressive wave of anti-science activists who are blindly looking at all problems, big and small, as being valid targets for retractions. Those that hate science will seek every means possible to retract anything related to science. Those that care about science want to see the issues resolved correctly, and fairly. Therefore, clear fraud should be punished with a retraction (and more), but “relatively minor” issues should face more lenient or rational punishment, such as an erratum or corrigendum. We are in a historical phase in science, I believe in which retractions seem to be as fashionable as the iPAD or Twitter, and everyone is trying to jump on the band-wagon, especially the skeptics and the critics who have now found a valid avenue to vent their frustrations. However, when we retract a piece of literature, in some ways, it is gone forever. So, we need to inculcate among our peers and editors, a new culture of change. If we can accept that errors are fundamental parts of – if not the essence of – science, then there is hope. And if we can accept that talking about errors, corrections and retractions as part of the everyday conversation [2], even in the literature, then this solidifies hope and breeds change.

g) The lack of a solid support framework that involves an advice hub, a claims center, a counseling center, the acceptance of anonymity, and the decentralization of power. Although this may sound perfect, in fact it is extremely easy, and cheap, to achieve. This is because it only requires the consciousness of scientists, their time and their willingness to do what is right. Unfortunately, most scientists face that thing called reality! Long work hours and increasingly reduced pay and grants/funding, greater pressure for productivity, and increase scrutiny. Thus, there is little desire to offer their time, intellect and effort to conduct post-publication peer review (PPPR) [1] because it’s simply not convenient. From personal experience, I can say that PPPR is painful, time-consuming, exasperating, frustrating, and damaging (to others and to ourselves). The peer pool is already excessively squeezed, with few drops of additional effort and time to add to the need for precise scrutiny in PPPR. Thus, I believe that we have a real crisis in plant science in which the call for the need is not being met by the correct attitude of the base it is meant to be correcting (and assisting). The crisis is being further fueled by an aggressive attitude by retraction hard-liners that any error, small or large, is something that should be subjected to a retraction. I suspect that there is an underground agenda (but not yet reported on) that is using retractions, and the twisting of ethical values and guidelines, to achieve permanent damage to science, and to undermine its importance in society. This “underground” movement (hypothesis) would be counterproductive to the genuine efforts by real scientists, and real academics, who simply want to see unfairness in science and science publishing eliminated (or reduced as much as possible), and that recognize that one effective way of achieving this is through PPPR.

The frustrations I feel about plant science relate not so much to the lack of retractions, but to the lack of acceptance that the literature has problems, and needs to be corrected. I was going to substantiate my claims with real examples, as I usually do, but I have decided to reduce them to two references only (to passive my critics who dislike my verbosity). When the time is right, more factual evidence will be released into the blogosphere. PubPeer and PubMed commons are useful tools, but when push comes to shove, the final message to our peers should be one of encouragement and active participation, and not one of fear.

[1] http://www.frontiersin.org/Journal/10.3389/fpls.2013.00485/full
[2] See a simple model for reporting publically on errors in the chrysanthemum literature, some of which merit retractions: http://retractionwatch.com/2014/01/07/journal-dumps-grain-paper-for-controversial-data/#comments

Reply
1. O Baptista says:
  
  March 30, 2014 at 10:33 pm
  
  Report of apparent data/paper duplication: Acta Horticulturae (International Society for Horticultural Science)
  
  Miguel, M.G., Duarte, F., Venâncio, F. and Tavares, R. 2002. CHEMICAL COMPOSITION OF THE ESSENTIAL OILS FROM THYMUS MASTICHINA OVER A DAY PERIOD. Acta Hort. (ISHS) 576:87-90
  http://www.actahort.org/books/576/576_15.htm
  http://wwwlib.teiep.gr/images/stories/acta/Acta%20576/576_15.pdf
  
  Miguel, M.G., Duarte, F., Venãncio, F. and Tavares, R. 2003. CHEMICAL COMPOSITION OF THE ESSENTIAL OILS FROM THYMUS MASTICHINA OVER A DAY PERIOD. Acta Hort. (ISHS) 597:75-78
  http://www.actahort.org/books/597/597_8.htm
  http://wwwlib.teiep.gr/images/stories/acta/Acta%20597/597_8.pdf
  
  Reply
  1. O Baptista says:
    
    April 18, 2014 at 3:01 pm
    
    An update. The 2003 copy has been retracted. The official e-mail follows (e-mails redacted):
    
    From: Jozef Van Assche
    Sent: 04/01/14 04:10 PM
    To:
    Subject: Miguel (UALG): duplication report
    
    Dear Sir,
    Dear Dr. Paulo Baptista,
    
    I have been informed about your complaint to the ISHS President, Prof. Antonio Monteiro, on a so called duplicate publication of the article entitled ‘Chemical Composition of the Essential Oils from Thymus mastichina over a Day Period’, by M.G. Miguel, F. Duarte, F. Venâncio and R. Tavares.
    
    I hereby wish to inform you that this happened outside of the will of the authors.
    
    The contributions of the International Conference on Medicinal and Aromatic Plants, Budapest, Hungary, 8-11 July, 2001, were published in two volumes of Acta Horticulturae, AH 576 Volume I and AH 597 Volume II. The first Volume was published soon after the meeting as Acta Horticulturae 576, the second batch of papers was published as Volume II as Acta Horticulturae 597 some time later, and containing additional contributions of the symposium.
    
    For one reason or another, the Editors did not noticed that the paper of Dr. M.G. Miguel et al, was published in 576, and they also included it in the batch for 597. All this just by accident. This is this a human failure were the same article was published twice in the set of proceedings on the same meeting.
    
    We hereby are pleased to inform you that the article has been retracted from AH 597, and that the original stands in AH 576.
    
    We wish to thank you for bringing this to our attention and remain.
    Faithfully
    
    Jozef
    —
    Jozef Van Assche
    Executive Director
    
    International Society for Horticultural Science
    PO Box 500 – 3001 Leuven 1 – Belgium
    Phone: +32 16229427 Fax: +32 16229450
    
    Visit our website at http://www.ishs.org
    The ISHS, dating from 1864 and formally constituted in 1959, has more than 7000 members representing over 140 countries. It is the world’s leading independent organization of horticultural scientists. ISHS publishes Acta Horticulturae, Chronica Horticulturae, and Scripta Horticulturae.
    
    Reply
Jeanette Garwood says:

January 25, 2014 at 2:29 pm

Hi,

Thank you so much for all the brilliant posts you guys send out. I have a professional interest in bad behaviour, and Integrity officer status at my university, and Retraction Watch is so educative.

Thank you so much for all your hard work 🙂

Jeanette (Oxford D.Phil 1991)

Reply
Nurse Dina says:

January 26, 2014 at 1:23 am

Stay on it guys. You are the only encouragement to me, a victim of plagiarism. Just when I think I can’t fight anymore, one of your posts will appear and keep me going.

Reply
1. Qui? says:
  
  February 7, 2014 at 8:46 am
  
  Report of apparent figure duplication: for EMBRAPA, SIVB, IVCDB, Acta Scientiarum, Authors, other parties
  
  Paper 1: Pinto de Carvalho ACP, Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Otoni WC. Produção de mudas micropropagadas de antúrio (Anthurium andraeanum) cv. Eidibel por embriogênese somática. Embrapa Circular Técnica (Fortaleza) 2012;41:1-14
  Paper 2: Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Pinto de Carvalho ACP, Jardim de Oliveira E, Otoni WC. Somatic embryogenesis in anthurium (Anthurium andraeanum cv. Eidibel) as affected by different explants. Acta Scientiarum Agronomy 2014;36:87-98.
  Paper 3: Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Pinto de Carvalho ACP, Ventrella MC, Otoni WC. Maturation of Anthurium andraeanum cv. Eidibel somatic embryos from nodal segments. In Vitro Cellular & Developmental Biology – Plant 2013;49( 3):304-312.
  
  We wish to make an anonymous report of potential figure duplication.
  Fig 2B, C and E of paper 1 seem identical to Fig. 3A, B and K of paper 2.
  Fig. 3B seems identical to Fig. 4A in paper 2 (rotated 90°)
  Fig. 3A, B, C and D of paper 1 seem identical to Fig. 4B, C, D and G of paper 2, with B and D of the former being cropped and size/proportion manipulated.
  Fig. Fig 6B in paper 1 seems identical to 4I in paper 2.
  Fig. 5E, F, G, H, J in paper 1 seem identical to Fig. 5E, F, G, H, J in paper 3.
  
  Paper 1 was not reported in paper 2 or paper 3, even though paper 1 appears as open access online and even though it is a formal publication of Embrapa Agroindústria Tropical. Figure duplication would thus also possibly constitute copyright infringement.
  
  Figure duplication and manipulation is a serious academic offense that distorts the accuracy of the academic record and we call on the retraction of the 2014 paper from Acta Scientiarum and the 2013 paper from In Vitro Cellular & Developmental Biology – Plant. We call on the authors, editors and publishers to take responsible action.
  
  See sections 4.1, 4.2 and 4.3 of Springer 2013 Publication Ethics Manual for Editor and Authors:
  http://static.springer.com/sgw/documents/1393202/application/pdf/Publication_Ethics_Guide_for_Editors_from_Springer_27052013.pdf
  
  See clause 3 of Acta Scientiarum Agronomy:
  http://www.scielo.br/revistas/asagr/iinstruc.htm (“Author(s) should state that the manuscript, reporting original work, was not sent, in part or in whole, for publication to another scientific journal.”)
  
  AR Qui
  
  Reply
  1. Qui? says:
    
    February 18, 2014 at 12:29 pm
    
    Case 30
    
    Kalimuthu K, Prabakaran R (2013b) In vitro flowering from nodal explants of Ceropegia pusilla Wight and Arn. International Journal of Botany and Research 3(3), 35-42
    http://tjprc.org/journals.php?jtype=2&id=46 (no editor board)
    Kalimuthu K, Prabakaran R (2013c) In vitro and micropropagation for conservation of rare and threatened medicinal plant Ceropegia species – a review. International Journal of Biological Technology 4(2), 23-36
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204(2).htm
    Kalimuthu K, Prabakaran R, Paulsamy S, Jeyaraman S (2014) Microtuberization of Ceropegia pusilla Wight and Arn. an endangered medicinal plant. European Journal of Medicinal Plants 4(1), 64-74
    http://www.sciencedomain.org/issue.php?iid=383&id=14
    Prabakaran R., Sasikala T., Kalimuthu K. (2013) Regeneration of shoots from callus of Ceropegia pusilla Wight and ARN. British Biotechnology Journal 3(3), 416-423
    http://www.sciencedomain.org/journal-home.php?id=11
    
    Apparent data duplication
    data in Table 2 of 2014 = data in Table 1 of Prabakharan et al. 2013
    data in Table 3 of 2014 = data in Table 4 of Prabakharan et al. 2013
    Notice how micromolar amounts are used by Prabakharan et al. 2013 and mg/l amounts in 2014
    
    Apparent figure duplication and manipulation
    1F of 2013b = 1E of 2013c = 1G of 2014
    1A of 2013c = 1A of Prabakharan et al. 2013
    1B of 2013c = 1B of Prabakharan et al. 2013
    1F of 2013c = 1F of Prabakharan et al. 2013
    1D of 2014 = 1C of 2013b
    1E of 2014 = 1C of 2013c
    1B of 2013b = 1D of Prabakharan et al. 2013 (tilted and twisted)
    
    Apparent plagiarism:
    2013 review copies the abstracts of most studies in the literature, and presents this as a review, listing the studies chronologically. Subsequently, this paper has already been retracted, 24 hours after we issued our report:
    IJBT Biotek Editor writes “Thank you for your advice. As the plagiarism is serious, we have retracted the article now on consulting with the consent editor and corresponding author. The retracted article link is given below for your reference.”
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29kalimuthu%20abs.htm
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29/ijbt150813104.pdf
    
    Apparent salami slicing and data/method duplication
    in vitro tuberization, shoot and flower induction already reported in 2013b (classical salami slice adding information to text in 2013b and data in tables in 2014 to feign originality; self-plagiarism exact text copied, see M&M section; values reported in molar amounts in 2013b and then in g/l amounts in 2014 to appear original, but are identical concentrations.
    
    Reply
    1. Qui? says:
      
      February 18, 2014 at 12:30 pm
      
      Case 31
      
      Kondamudi R, Murthy, K.S.R. 2011. Micropropagation of Ceropegia pusilla Wt. & Arn. – an endangered and rare medicinal Asclepiad. Journal of Tropical Medicinal Plants 12: 41-48
      http://tropmedplants.com/article.php?aid=464 (no editor board)
      Kondamudi R, Vijayalakshmi V, Murthy, K.S.R. (2010) Induction of morphogenetic callus and multiple shoot regeneration in Ceropegia pusilla Wight and Arn. Biotechnology, 9: 141-148
      http://scialert.net/qredirect.php?doi=biotech.2010.141.148&linkid=pdf (ANSI; no editor-in-chief; http://scialert.net/eboard.php?issn=1682-296x)
      Murthy KSR, Kondamudi R (2010) Effect of cytokinins and auxins on in vitro flowering of endangered Ceropegia spiralis Wight and C. pusilla Wight & Arn. Phytomorphology. 60: 32-37
      Murthy KSR, Kondamudi R, Vijayalakshmi V (2010a) Micropropagation of an endangered medicinal plant Ceropegia spiralis Wight. J Agric. Tech 6: 179-191
      Murthy KSR, Kondamudi R, Pullaiah T (2010b) High frequency somatic embryogenesis in Ceropegia spiralis Wight – an endemic and endangered medicinal plant. Indian J. Biotechnol. 9, 414-418
      http://nopr.niscair.res.in/bitstream/123456789/10441/1/IJBT%209%284%29%20414-418.pdf (NISCAIR; IF = 0.477)
      Murthy KSR, Kondamudi R (2011) Rapid shoot regeneration from thin cell layer explants of an endangered medicinal asclepiad Ceropegia spiralis L. Plant Tissue Cult. Biotech. 21(1): 63-73
      http://www.banglajol.info/index.php/PTCB/article/view/9564 (BAPTC&B)
      Murthy KSR, Kondamudi R, Karuppusamy S. (2012) Microtuberization of Ceropegia spiralis Wight and Ceropegia pusilla Wt. and Arn. African J. Plant Sci. 6: 321-327
      http://academicjournals.org/article/article1380125590_Murthy%20%20et%20al.pdf (Academic Journals)
      
      Apparent data duplication
      20 shoot-related data points in Table 2 of Kondamudi and Murthy 2011 are identical to data in Table 3 of Kondamudi et al. 2010
      Data in Table 2 of Murthy and Kondamudi 2010 identical to data in Table 3 of Kondamudi and Murthy 2011
      Table 2 data of Murthy et al. 2010a = Table 1 data of Murthy et al. 2011
      Table 4 data of Murthy et al. 2010a = Table 1 data of Murthy et al. 2012
      
      Apparent figure duplication and/or manipulation
      Fig 1D of Kondamudi et al. 2010 identical to Fig. 1F of Kondamudi and Murthy 2011
      Fig. 1B of Murthy and Kondamudi 2010 identical to Fig. 1E of Kondamudi and Murthy 2011
      Fig 1B of Murthy and Kondamudi 2011 = Fig. 1B of Murthy et al. 2010a = Fig. 1Ce of Murthy et al. 2012
      Fig 1A of Murthy and Kondamudi 2011 = Fig. 1Cb of Murthy et al. 2012
      Fig 1D of Murthy and Kondamudi 2011 = Fig. 1Cc of Murthy et al. 2012
      Fig. 1G of Murthy et al. 2010a rotated 90° = Fig. 1i of Murthy et al. 2010b
      Fig 1A of Murthy et al. 2010a = Fig. 1A of Murthy et al. 2012
      Fig. 1F of Murthy et al. 2012 = Fig. 1D of Kondamudi et al. 2010
      Fig. 1E of 2012 repeated twice (self-plagiarism)
      
      This would also directly influence the claims of originality in the review written by this group:
      Murthy, K.S.R., Kondamudi, R., Reddy, M.C., Karuppusamy, S., Pullaiah, T., 2012b. Check-list and conservation strategies of the genus Ceropegia in India. Int. J. Biodivers. Conserv. 4(8), 304-315 (Academic Journals)
      
      Reply
      1. Qui? says:
        
        March 3, 2014 at 5:56 pm
        
        We reported this case on February 11, 2014. By March 3, 2014, the 2012b paper had been retracted, but without any notice. The paper just vanished.
        
        Raad MK, Zanjani SB, Shoor M, Hamidoghli Y, Sayyad AR, Kharabian-Masouleh A, Kaviani B. Callus induction and organogenesis capacity from lamina and petiole explants of Anthurium andraeanum Linden (Casino and Antadra). Australian J Crop Sci 2012a;6(5):928-937. (Southern Cross Publishing Group, Australia, listed at http://scholarlyoa.com/publishers/)
        
        Raad MK, Zanjani SB, Sayyad AR, Maghsudi M, Kaviani B. Effect of cultivar, type and age of explants, light conditions and plant growth regulators on callus formation of anthurium. American-Eurasian J Agric Environ. Sci 2012b;12(6):706-712. (IDOSI Publications, Dubai, listed at http://scholarlyoa.com/publishers/)
        
        Fig. 1 data of 2012a is identical to “Callus weight” column of Table 1 (2012b)
        Fig. 2 of 2012a is identical to Fig. 1 of 2012b
        Fig. 3 data of 2012a is identical to “Days to callus induction” column of Table 1 (2012b)
        Table 1 data of 2012a is repeated in Fig. 2 and Fig. 3
        
        Neither paper acknowledged the existence of the other paper.
        
        We wish to deposit this case here as a public record.
      2. Qui? says:
        
        March 3, 2014 at 5:59 pm
        
        We wish to report an apparent partial duplication.
        
        Javad Sharifi Rad, Majid Sharifi Rad, Abdolhossein Miri (2013) Regulation of the Expression of Nitrate Reductase genes in Leaves of Medical plant, Foeniculum vulgare by Different Nitrate Sources. International Journal of Agriculture and Crop Sciences 5 (24), 2911-2916
        http://ijagcs.com/wp-content/uploads/2013/09/2911-2916.pdf
        
        Javad Sharifi Rad, Majid Sharifi Rad (2013) Regulation of the Expression of Nitrate Reductase Genes in Leaves of Medical Plant, Foeniculum vulgare by Different Nitrate Sources. World Applied Sciences Journal 28 (9): 1311-1315
        http://www.idosi.org/wasj/wasj28(9)13/18.pdf
        
        Fig. 4 of IJCAS = Fig. 1 WASJ
        Fig. 1 WASJ = Fig. 2 WASJ = Fig. 3 WASJ = Fig. 4 WASJ
        
        This serves as a public record.
      3. ABV Prasad says:
        
        March 3, 2014 at 6:04 pm
        
        I want to report a possible partial duplication.
        
        Sule WF, Okonko IO, Joseph TA, Ojezele MO, Nwanze JC, Alli JA, Adewale OG, Ojezele OJ (2010a) In vitro antifungal activity of Senna alata Linn. crude leaf extract. Research Journal of Biological Sciences 5 (3): 275-284 (Publisher: Medwell Journals)
        http://www.medwelljournals.com/fulltext/?doi=rjbsci.2010.275.284
        http://docsdrive.com/pdfs/medwelljournals/rjbsci/2010/275-284.pdf
        
        Sule WF, Okonko IO, Joseph TA, Ojezele MO, Nwanze JC, Alli JA, Adewale OG, Ojezele OJ (2010b) In-vitro antifungal activity of Senna Alata Linn. Crude leaf extract. Advances in Applied Science Research 1 (2): 14-26 (Publisher: Pelagia Research Library)
        http://www.pelagiaresearchlibrary.com/advances-in-applied-science/vol1-iss2/AdSSR-2010-1-2-14-26.pdf
        
        A third paper, 2011 published on the bark, has identical results (Tables 1, 3 and 4) as the 2010a and 2010b paper about leaves. Table 2 has similar data to the 2010a and 2010b papers:
        
        Sule W. F., Okonko I. O., Omo-Ogun S., Nwanze J. C., Ojezele M. O., Ojezele O. J., Alli J. A., Soyemi E. T., Olaonipekun T. O. (2011) Phytochemical properties and in-vitro antifungal activity of Senna alata Linn. crude stem bark extract. Journal of Medicinal Plants Research 5(2), 176-183 (Academic Journals)
        http://www.academicjournals.org/article/article1380554162_Sule%20et%20al.pdf
        
        All three publishers are listed on Jeffrey Beall’s http://www.scholarlyoa.com
      4. T-bone steak says:
        
        March 27, 2014 at 1:29 am
        
        Mr. Prasad, I followed up on your lead. I contacted the editor boards of all three publishers and early in March, Pelagia Research Library retracted the Sule et al. 2010b paper. Not only does clicking the link above lead to an HTTP error, the journal issue web-page lists a gap: http://pelagiaresearchlibrary.com/advances-in-applied-science/vol1-iss2.html
        Unfortunately, this gap is not useful, or instructive about the problem, and the research community has no idea why the paper was retracted, so I indicated one clear case of a good, informative retraction notice, with a red stamp RETRACTED on the original PDF. I am not sure that they will take the trouble of making this change, but if they do, this would be a positive sign that we may start to be able to correct the literature, by placing pressure on authors and publishers simultaneously.
      5. Bhavin says:
        
        July 24, 2014 at 10:09 am
        
        Dear Qyi?,
        Excellent detection, many of Murthy publications are from predatory journals
  2. Qui? says:
    
    November 19, 2014 at 1:42 am
    
    There are now two PubPeer entries for this case:
    https://pubpeer.com/publications/AFD78E3F00791586BA5D65DDC24E2F (paper 3)
    https://pubpeer.com/publications/625423731873AA049FEAD97C824708 (paper 2)
    
    Reply
    1. Dendrobium concerns says:
      
      November 19, 2014 at 10:21 am
      
      There is now a PubPeer entry for the Sule et al. Senna alata case:
      https://pubpeer.com/publications/4833F47FEE80273B000008C1069022
      
      Reply
Nasraoui, Bouzid says:

April 15, 2014 at 12:46 pm

As the Editor-in-Chief of Tunisian Journal of Plant Protection (TJPP), I discover via a colleague of mine, that one scientific paper was published in 2009 at the same time in TJPP and in Journal of Biopesticides. The paper dealt with the “Efficiency of Spinetoram as a biopesticide to Onion Thrips (Thrips tabaci Lindeman) and Green Peach Aphid (Myzus persicae Sulzer) under laboratory and field conditions” with the first author “Mahmoud Farag Mahmoud”. Noting that is a case of a flagrante delicto of scientific honesty lack, TJPP withdraw from its website this paper simultaneously published in Tunisian Journal of Plant Protection 4 (2): 221-227 (2009) and Journal of Biopesticides, 2(2): 223- 227 (2009).

Reply
1. JATdS says:
  
  April 15, 2014 at 9:53 pm
  
  The TJPP web-site for that paper is:
  http://www.iresa.agrinet.tn/tjpp/tjpp8/TJPP8.htm
  The JoB web-site for that paper is:
  http://www.jbiopest.com/users/LW8/page.php?intPageId=199
  
  It would have been useful if TPJJ had provided more information about the problem, and posted a retraction using a style similar to this one, including the full text of the retracted article:
  http://ptno.ogr.ar.krakow.pl/Wydawn/FoliaHorticulturae/Spisy/FH2006/PDF18012006/fh1801p08.pdf
  http://www.ptno.ogr.ar.krakow.pl/Wydawn/FoliaHorticulturae/Spisy/FH2006/PDF18012006/fh1801p08-R.pdf
  
  Incidentally, RW readers’ attention is drawn to the DeGruyter policies on authorship, corrigenda, retractions and author complaints:
  http://degruyteropen.com/you/journal-author/editorial-policies/other-stm/
  
  Reply
  1. JATdS says:
    
    April 17, 2014 at 2:11 pm
    
    Apparent figure duplication / manipulation.
    
    Pejman Azadi, Dong Poh Chin, Kiyo Kuroda, Raham Sher Khan, Masahiro Mii (2010) Macro elements in inoculation and co-cultivation medium strongly affect the efficiency of Agrobacterium-mediated transformation in Lilium. Plant Cell, Tissue and Organ Culture (PCTOC) Volume 101, Issue 2, pp 201-209
    http://link.springer.com/article/10.1007/s11240-010-9677-9
    
    Pejman Azadi, Ntui Valentaine Otang, Hasthanasombut Supaporn, Raham Sher Khan, Dong Poh Chin, Ikuo Nakamura, Masahiro Mii (2011) Increased resistance to cucumber mosaic virus (CMV) in Lilium transformed with a defective CMV replicase gene. Biotechnology Letters Volume 33, Issue 6, pp 1249-1255
    http://link.springer.com/article/10.1007%2Fs10529-011-0550-7
    
    Fig. 2a of the 2011 paper appears to be the same as Fig. 1a of the 2010 paper, just cropped, focusing in on one part of the Petri dish.
    
    Reply
    1. Bhavin says:
      
      July 24, 2014 at 5:53 am
      
      I found a little mistake in a published paper: Davies et al. “A preliminary evaluation of matricaria maritimum fibres for polymer reinforcement.” Industrial Crops and Products 34.3 (2011): 1652-1654*. The first name of the plant should be capitalized, i.e., Matricaria maritimum. I queried the corresponding author, Naceur BELGACEM, about this. He responded: “Thank you. Unfortunately, there is no way of correcting anything in a published paper. The last possibility is the proof corrections. Thank you again. I will do my best in the future.” Dr. Belgacem is the Director of The International School of Paper, Print Media and Biomaterials (France). My question is, is he correct, can such errors not be corrected by Elsevier if reported by authors if the corresponding author decides that no erratum can be published? The other question I have is: Should errata be issued for minor errors that are detected? If no, why not?
      * http://www.sciencedirect.com/science/article/pii/S0926669011001889
      
      Reply
      1. Jaime A. Teixeira da Silva says:
        
        July 26, 2014 at 10:25 am
        
        Letter sent on March 12, 2014, to the entire staff at The Hebrew University of Jerusalem. That e-mail was copied to RW. 4 months later, the largely duplicated text remains intact, unretracted. To date, 4 months later, not a single e-mail by the ISHS or by The Hebrew University of Jerusalem.
        
        It is time to start documenting these acts of lack of responsibility publically.
        “Dear Prof. Zach Adam and colleagues at The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture
        http://departments.agri.huji.ac.il/plantscience/people.php
        
        Duplication is a serious academic offense*.
        
        I wish to report my concern about two papers (files available upon request) that duplicate text of approximately 60-70% of the paper content. The author is Prof. Abraham H. Halevy, who is now deceased.
        
        The original (possibly): Halevy, A.H. 2003. THE USE OF NATIVE ISRAELI FLORA FOR INTRODUCTION OF NEW ORNAMENTAL CROPS. Acta Hort. (ISHS) 598:55-58: http://www.actahort.org/books/598/598_6.htm
        
        The duplicate paper (text almost identical with some re-shuffling):
        
        Halevy, A.H. 2005. EXPLORING ISRAELI FLORA FOR NEW FLORICULTURE CROPS. Acta Hort. (ISHS) 683:33-36: http://www.actahort.org/books/683/683_2.htm
        
        This case should be reported to the person in charge of the academic affairs of Acta Horticulturae, Prof. Yves Desjardins ([e-mails redacted]), who had already formally indicated that duplicate papers will be retracted and that the ISHS will follow the highest international standards of publishing ethics.
        
        The example of Prof. Johan Van Huylenbroeck and Dr. Tom Eeckhaut, who responsibly retracted their duplicated paper from Acta Horticulturae (http://www.actahort.org/books/961/961_15.htm), should be followed, and the initiative should come from you, Prof. Adam, as head of department, in this case where the author is now deceased.
        
        It is essential to correct the literature and remove redundant information to ensure the academic and scientific integrity of the horticultural literature. A second concern involves the listing of only a few dozen papers on Prof. Halevy’s profile (http://www.huji.ac.il/dataj/controller/ihoker/MOP-STAFF_LINK?sno=750384&Save_t=horticulture) when in fact his site claims that he has published “Over 350 publications in international refereed journals.” Is there a particular reason for The Hebrew University of Jerusalem not providing a full list of these 350+ papers?
        
        I look forward to seeing the paper retracted soon. May I also recommend that the staff at your institute review its publication profiles and ensure that no additional duplicate publications exist as a wide-spread post-publication peer review of the plant (and horticultural) science literature is now in effect: http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00485/full. The Hebrew University of Jerusalem has some extremely respectable plant scientists, current and emeriti, but the recent shocking discovery of this ethical infringement by one of the great leaders, Prof. Halevy, and other leading horticultural scientists from around the world, for example, Prof. Johan Van Huylenbroeck (http://www.actahort.org/books/961/961_15.htm), has not raised red flags and alarm bells that perhaps the horticultural and plant science literature is much more corrupted than has been led to believe.
        
        Sincerely,
        
        Jaime A. Teixeira da Silva
        
        *References
        http://www.radford.edu/spj/pubethics.html
        http://www.ncbi.nlm.nih.gov/pubmed/12786648
        http://healthydebate.ca/2013/10/topic/quality/research-ethics-bureaucracy
        http://publicationethics.org/case/duplicate-publication-possibly-four-papers
        http://www.waisman.wisc.edu/events/ethics/spring06-sem3-ethical-scientific-writing.pdf
        http://advan.physiology.org/content/29/2/59.full
        http://www.nature.com/nature/journal/v451/n7177/full/451397a.html
        http://www.jkscience.org/archive/Volume83/unethic.pdf
        http://www.ifcc.org/media/161822/IFCC%20Ethics%20in%20Science.pdf
        http://www.medicaldaily.com/two-thirds-scientific-papers-retracted-due-misconduct-242854
        http://www.academia.edu/5027331/Ethical_abuses_in_the_authorship_of_scientific_papers
        and much more”
    2. JATdS says:
      
      November 19, 2014 at 7:38 am
      
      Azadi et al. papers have two PubPeer entries:
      Paper 1: https://pubpeer.com/publications/B3161A9A5157B83F1A08506CD22966#fb16666
      Paper 2: https://pubpeer.com/publications/5740E043753A1CEC14D4494FD2EAA8#fb16667
      
      Reply
Science Society says:

November 7, 2014 at 3:38 pm

We wish to report a case of potential plagiarism.
Thulasi Muneppa Sridhar, Chenna Reddy Aswath
Department of Biotechnology, Indian Institute of Horticultural Research (IIHR), Bangalore, India
Review on Medicinal Plants Propagation: A Comprehensive Study on Role of Natural Organic Extracts in Tissue Culture Medium
American Journal of Plant Sciences, 5, 3073-3088. doi: 10.4236/ajps.2014.520324
http://www.scirp.org/journal/PaperInformation.aspx?paperID=50185&

The following sections are text that has been copied from the four sets of sources below, word for word, without attribution to the source, or without quotation marks, as follows:
From [1], 707 words (or 10.9% of total)
From [2], 373 words (or 5.7% of total)
From [3], 960 words (or 14.8% of total)
From [4], 192 words (or 3% of total) (including some self-plagiarism)

[1] Molnár Z, Virág E, Ordog V (2011) Natural substances in tissue culture media of higher plants. Acta Biol Szeged 55:123–127.
[2] George EF, Hall MA, Klerk G-J De (2007b) The components of plant Tissue culture media ll: organic additions, osmotic and pH effects, and support systems. In: George EF, Hall MA, Klerk G-J De (eds) Plant Propag. by Tissue Cult. Springer Netherlands, Dordrecht, pp 115–173 + George EF, Hall MA, Klerk G-J De (2007a) The components of plant tissue culture media I: macro- and micro-nutrient. In: George EF, Hall MA, Klerk G-J De (eds) Plant Propag. by Tissue Cult. Springer Netherlands, Dordrecht, pp 65–113
[3] Yong JWH, Ge L, Ng YF, Tan SN (2009) The chemical composition and biological properties of coconut (Cocos nucifera L.) water. Molecules 14:5144–64. doi: 10.3390/molecules14125144
[4] Other sources:
Anonymous (2014) Plant Tissue Culture- Mavens Biotech Limited. http://www.mavensbiotech.com/Biotechnology/Plant Tissue Culture.html. Accessed 15 Oct 2014
Lakshmi S, Benjamin J (2010) In vitro propagation of Hoya wightii ssp. palniensis KT Mathew, a highly vulnerable and endemic species of Western Ghats of Tamil Nadu, India. African J Biotechnol 9:620–627. doi: 10.5897/AJB09.846
Mehta J, Kumar V, Syedy M, et al (2012) In vitro shoot regeneration of Bacopa monnieri ( L .) using cyanobacterial media- a novel approach and effect of phytoregulators on in vitro micropropagation. Asian J Plant Sci Res 2:699–706.
Sivanesan I, Jeong BR (2007) Direct shoot regeneration from nodal explants of Sida cordifolia Linn. In Vitr Cell Dev Biol – Plant 43:436–441. doi: 10.1007/s11627-007-9090-1
Sridhar TM, Aswath CR (2014) Influence of additives on enhanced in vitro shoot multiplication of Stevia rebaudiana (Bert.)—An important anti diabetic medicinal plant. Am J Plant Sci 05:192–199. doi: 10.4236/ajps.2014.51025
Tanwer BS, Choudhary R, Vijayvergia R (2010) In-vivo and in-vitro comparative study of primary metabolites and antioxidant activity of Andrographis paniculata. J Chem Pharm Res 2:489–495.

The publisher of American Journal of Plant Sciences, SCIRP, is listed on Jeffrey Beall’s list of “possible” predatory OA journals: http://scholarlyoa.com/publishers/

Finally, this study received the following funding: “The authors are thankful to Department of Biotechnology for providing financial assistance in the form of DBT sponsored Post Doctoral Fellowship (Dr .T. M. Sridhar).”

Reply
1. Tehran says:
  
  November 18, 2014 at 6:13 pm
  
  There is now a PubPeer entry for this case:
  https://pubpeer.com/publications/B714C857CF4ED385A4B9E2DC37DFA5
  
  Reply
2. Medicinal Plants Propagation retracted says:
  
  April 7, 2016 at 5:09 am
  
  This paper is now retracted.
  
  “Short Retraction Notice The following article has been retracted due to the investigation of complaints received against it. The Editorial Board found that substantial portions of the text came from other published papers without appropriate attribution to the source. This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE’s Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Prof. Sukumar Saha (EiC of AJPS). Please see the article page for more details. The full retraction notice in PDF is preceding the original paper which is marked “RETRACTED”.”
  
  Reply
Tehran says:

November 8, 2014 at 12:27 pm

A case of apparent duplicate papers:
Salwee, Y., Nehvi, F.A. (2014) Effect of Plant Growth Regulators on Microcorm Formation in Saffron (Crocus sativus L.). International Journal of Current Microbiology and Applied Sciences Volume 3, Number 7, pp. 702-712
ISSN: 2319-7706 http://www.ijcmas.com/Archives-20.php
http://www.ijcmas.com/vol-3-7/Salwee%20Yasmin%20and%20F.A.Nehvi.pdf

Salwee, Y., Nehvi, F.A. (2014) In Vitro Microcorm Formation in Saffron (Crocus sativus L.). Journal of Cell and Tissue Research Vol. 14(2), 4463-4470
Received June 2014; No DOI
ISSN: 0973-0028; E-ISSN: 0974-0910
http://tcrjournals.com/tr_currentabstract.php?vid=57
http://tcrjournals.com/uploads/7314136._Salvee.pdf

Dr. Salwee Yasmin is at Baba Ghulam Shah Badshah University, Jammu and Kashmir, Rajouri, India, and Prof. Firdos Ahmad Nehvi is Senior Scientist, Saffron Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST) of Kashmir, India.

There is a separate case of retraction caused by plagiarism by SKUAST researchers (Mushtaq Ahmad, Gul Zaffar, S.D. Mir, S.M. Razvi, M.A. Rather and M.R. Mir):
http://scialert.net/abstract/?doi=rjmp.2011.630.649
http://scialert.net/qredirect.php?doi=rjmp.2011.630.649&linkid=pdf
The retraction notice states “Science Alert considers misappropriation of intellectual property and duplication of text from other authors or publications without clear and unambiguous attribution totally unacceptable. Plagiarism is a violation of copyright and a serious breach of scientific ethics. The Editors and Publisher have agreed to officially retract this article.”

Reply
1. Tehran says:
  
  November 18, 2014 at 6:12 pm
  
  There is now a PubPeer entry for this case:
  https://pubpeer.com/publications/8D6BC53D18D77C4D5855404CB9E383
  
  Reply
Hyderabad says:

November 9, 2014 at 3:22 pm

I report a retraction of an onion study:
J.I. Córcoles, J.F. Ortega, D. Hernández, M.A. Moreno
Use of digital photography from unmanned aerial vehicles for estimation of leaf area index in onion (Allium cepa L.)
European Journal of Agronomy, Volume 45, February 2013, Pages 96-104
http://www.sciencedirect.com/science/article/pii/S116103011300124X
http://ac.els-cdn.com/S1161030112001463/1-s2.0-S1161030112001463-main.pdf?_tid=fc3cc9c0-684d-11e4-ac8a-00000aab0f26&acdnat=1415564668_7549d27073690fbb43946bd637c897f3
The notice writes: “This paper has been retracted because a near identical version of this paper was published in the Journal Biosystems Engineering: J.I. Córcoles, J.F. Ortega, D. Hernández, & M.A. Moreno (2013). Estimation of leaf area index in onion (Allium cepa L.) using an unmanned aerial vehicle. Biosystems Engineering. 115: 31–42; http://dx.doi.org/10.1016/j.biosystemseng.2013.02.002. This article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.”

Reply
Strelitzia Watch says:

November 15, 2014 at 1:12 pm

Title: Genus: Strelitzia
Authors: Marcos Ribeiro da Silva Vieira, Giuseppina Pace Pereira Lima, Damiana Cleuma de Medeiros, Ângela Vacaro de Souza, Emídio Cantidio Almeida de Oliveira
Journal of Horticulture and Forestry Vol. 4(11), pp. 178-180, November 2012
DOI: 10.5897/JHF12.025
http://www.academicjournals.org/article/article1379513573_Vieira%20et%20al.pdf

There are two queries. First, the source of the photos in the four figures. Three of the photos / figures (2-4) are identical to images from the internet, without attribution to the source. To verify, simply add the Latin names of the three Strelitzia species into Google and Yahoo, click on images, and scroll down. Secondly, why does it require 5 individuals to write a 3-page review?

Reply
1. Strelitzia Watch says:
  
  November 18, 2014 at 6:20 pm
  
  There is now a PubPeer entry for this case:
  https://pubpeer.com/publications/C0122881E5A6815F9FA54CB2277C5E
  
  Reply
Vivek Kumar query says:

November 17, 2014 at 1:08 am

A case of potential partial (self-)plagiarism.

Paper 1: Vivek Kumar (2014) Nanobiotechnology and its implementation in Agriculture. Journal of Advanced Botany and Zoology V1-I1.
(research article on the PDF; editorial online) DOI 10.15297/JABZ.V1I1.02
Received: December 28, 2013, Accepted: December 30, 2013, Published: January 3, 2014
http://scienceq.org/archive.php?jname=abz&jid=abz0114462&tit=Nanobiotechnology and its implementation in Agriculture#.VGmFNJVxnIU
http://scienceq.org/archive_user.php?jname=abz#.VGl9mpVxnIU (Publisher: ScienceQ*)

Paper 2: Ram Prasad 1*, Vivek Kumar 1, Kumar Suranjit Prasad 2 (2014) Nanotechnology in sustainable agriculture: Present concerns and future aspects. African Journal of Biotechnology 13(6), 705-713 (review)
DOI: 10.5897/AJBX2013.13554; Article Number – 1C0ABA342977
1 Amity institute of Microbial Technology, Amity University Uttar Pradesh, Sector 125, Noida- 201303, UP, India
2 Department of Environmental Biotechnology, Ashok & Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New Vallabh Vidyanagar, Anand-388121, Gujarat, India
Received: 12 November 2013, Accepted: 16 January 2014; Published: 05 February 2014
http://www.academicjournals.org/journal/AJB/article-abstract/1C0ABA342977
http://www.academicjournals.org/journal/AJB/article-stat/1C0ABA342977 (total views: 603; downloaded: 2202)

Problem/concern:
The entire introduction of paper 2 (pp. 705-706) and parts of the conclusions (pp. 711-712) is identical, in most parts, word for word, to paper 1. Neither paper references the other, nor indicates the existence of the other.

Paper 1 states “Vivek Kumar is working as Associate. Professor, Amity Institute of Microbial Technology, AMITY University, Noida, India. He did his Master’s and Doctoral degree in Microbiology. He has served as Microbiologist in Public Authority of Agricultural Affairs, Kuwait for 8 years. Guided many M.Sc/M.Tech students and guiding two doctoral degree students. Has published 51 research papers, 7 book chapters, 4 review articles and one book. He has delivered many research related lectures in conferences in India and abroad. He is recipient of “Young Scientist ward” in Agricultural Microbiology by Association of Microbiologists of India. His area of research interests are; plant-microbe-interactions, bioremediation, environmental microbiology and nanotechnology.”

Dr. Kumar is on the board of editors at JABZ, the journal in which paper 1 was published:
http://scienceq.org/editormenu.php?jname=abz#.VGmLl5VxnIU

* Listed as predatory open access publishers on Jeffrey Beall’s blog. Both journals/publishers consider plagiarism to be a serious academic offense:
http://www.academicjournals.org/publication_ethics
http://scienceq.org/instruction_author.php#.VGmOqJVxnIU

Reply
1. Vivek Kumar query says:
  
  November 18, 2014 at 2:59 pm
  
  There is now a PubPeer entry for this case:
  https://pubpeer.com/publications/5CA64C2F1901791084669D498E07EE
  
  Reply
Dendrobium crisis says:

November 18, 2014 at 2:37 am

There are now 4 PubPeer entires corresponding to Papers 1 to 4:
Paper 1: https://pubpeer.com/publications/8448D8CF8D1F69936CDC1A35D9BBCC
Paper 2: https://pubpeer.com/publications/1CE3174266AF780AD6AB8EC0ABADE1
Paper 3: https://pubpeer.com/publications/1801EC08556E90F5026575FA1431B2
Paper 4: https://pubpeer.com/publications/C7D8632E7ED6D6F852A93D9A516A49

Reply
Dendrobium concerns says:

November 19, 2014 at 9:54 am

Paper A (Springer)
Padmaja Mohanty, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) Cryopreservation of pharmaceutically important orchid Dendrobium chrysanthum Wall. ex Lindl. using vitrification based method. Acta Physiologia Plantarum 35: 1373–1379
Plant Biotechnology Laboratory, Centre for Advanced Studies in Botany North Eastern Hill University, Shillong, India
http://www.nehu.ac.in/
DOI 10.1007/s11738-012-1163-z
http://link.springer.com/article/10.1007/s11738-012-1163-z
No citations

Paper B (Springer)
Padmaja Mohanty, Pynbeitsyon Nongkling, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) Short-term storage of alginate-encapsulated protocorm-like bodies of Dendrobium nobile Lindl.: an endangered medicinal orchid from North-east India. 3 Biotech 3: 235–239
DOI 10.1007/s13205-012-0090-4
http://link.springer.com/article/10.1007/s13205-012-0090-4 (open access)
No citations

Paper C (Springer)
Padmaja Mohanty 1, J. Das 2 (2013) Synthetic seed technology for short term conservation of medicinal orchid Dendrobium densiflorum Lindl. Ex Wall and assessment of genetic fidelity of regenerants. Plant Growth Regulation 70(3):297–303
1. National Research Centre for Orchids, Pakyong, 737106, Sikkim, India (http://www.nrcorchids.nic.in/)
2. Plant Bioresources Division, Institute of Bioresources and Sustainable Development (IBSD), Sikkim Centre, Tadong, 737102, Gangtok, India (http://www.ibsd.gov.in/currentResearch.htm)
DOI 10.1007/s10725-013-9801-z
Erratum: http://link.springer.com/article/10.1007/s10725-013-9831-6
http://download.springer.com/static/pdf/652/art%253A10.1007%252Fs10725-013-9831-6.pdf?auth66=1416229592_ab8f79c7a260625e009a76ff46ab3d55&ext=.pdf states “Due to an institutional conflict on research program, the corresponding author of the article would like to remove the fig 1 from the original publication of the article.” (Published online: 6 June 2013)
Retraction: http://link.springer.com/article/10.1007/s10725-013-9801-z states “This article has been retracted at the request of the Publisher due to a violation of Springer’s publishing integrity. The figure 1 of the article has been duplicated from different research papers and led to some serious scientific flaw in the article.”
Retraction notice: http://link.springer.com/article/10.1007/s10725-013-9871-y
http://download.springer.com/static/pdf/883/art%253A10.1007%252Fs10725-013-9871-y.pdf?auth66=1416229764_7b3d67ec9fdd98a8796cff5a05661142&ext=.pdf
No citations

Paper D (Springer)
Padmaja Mohanty, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) High-efficiency cryopreservation of the medicinal orchid Dendrobium nobile Lindl. Plant Cell Tissue and Organ Culture 109(2):297–305
DOI 10.1007/s11240-011-0095-4
http://link.springer.com/article/10.1007/s11240-011-0095-4
No citations

Six apparent figure duplications

1) Fig 3D of Paper A is identical to Fig. 1B of Paper C
False (unintended) conclusion: Dendrobium chrysanthum = Dendrobium densiflorum

2) Fig. 3E of Paper B is identical to Fig 1A of Paper C
Fig. 3B of Paper B is identical to Fig 1D of Paper C
False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

3) Fig. 3A of Paper B is identical to Fig 1C of Paper C
False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

4) Fig. 7G of Paper D is identical to Fig 3H of Paper B
Fig. 7E of Paper D is identical to Fig 1E of Paper C
False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

Several figures have been duplicated across four manuscripts. This raises doubts about the correct plant material used in any of the in vitro experiments described in all four papers. Since several photos are duplicated and/or mixed up, there are also doubts about the validity of the interpretation of the data sets, and if they in fact refer to the plant that is being referred to in each title. The integrity of all four papers is thus in doubt, and a key question arises: which manuscript actually represents which Dendrobium species?

Institutional profile (Tandon, Kumaria, Das):
http://nehu.ac.in/Schools/Life%20Sciences/Botany/faculty.php
Professional profiles:
Pramod Tandon (Professor): http://nac.nic.in/members/pramod.php
Suman Kumaria (Professor): http://www.researchgate.net/profile/Suman_Kumaria/publications?pubType=dataset
Meera C. Das (Lecturer): http://www.researchgate.net/profile/Meera_Das/topics
Padmaja Mohanty: not listed at NRCO: http://www.nrcorchids.nic.in/Personnel.html
Pynbeitsyon Nongkling: after MSc (2008-2010) at NEHU, PhD candidate 2011-2012 (candidate no. 5):
http://www.nehu.ac.in/Schools/Life%20Sciences/Botany/bot_151111.pdf (supervisor = H. Kayang)
The institutional web-page of J. Das cannot be identified.

There are now four PubPeer entries corresponding to Papers A to D:
Paper A: https://pubpeer.com/publications/8448D8CF8D1F69936CDC1A35D9BBCC
Paper B: https://pubpeer.com/publications/1CE3174266AF780AD6AB8EC0ABADE1
Paper C: https://pubpeer.com/publications/1801EC08556E90F5026575FA1431B2
Paper D: https://pubpeer.com/publications/C7D8632E7ED6D6F852A93D9A516A49

Reply
1. Meera C. Das says:
  
  November 20, 2014 at 4:32 am
  
  The following is my response to the commentary posts:
  
  Similar allegations were made earlier by the anonymous whistleblower to Springer Publications.
  
  I reproduce the decision of Springer:
  
  [Dear Dr. Das,
  
  I would like to inform you that the anonymous whistleblower has received the following response by my colleague Jacco Flipsen:
  
  “Following up to COPE standards, we have evaluated your retraction request related to duplication of figures. The case also has been evaluated by the Ethics group at Springer. We have come to the conclusion that the article in Plant Growth Regulation should not have been published because of figure duplication. This article will be retracted shortly; the authors have been informed. […]”
  
  So the article in Plant Growth Regulation will be retracted, all other papers are not affected.
  
  Kind regards
  Christina Eckey
  —  Christina Eckey, PhD
  Springer Senior Editor, Plant Sciences]
  
  I wish to put the matter straight. In fact I had complained to all the concerned Editors of Springer and officials of Institute of Bioresource Development (place of work of J. Das) and National Research Centre on Orchids (place of work of P. Mohanty) about the use of photographs from our earlier published work in the following publication:
  
  Paper C: Mohanty, P. and J. Das (2013)
  Plant Growth Regulation 70:297–303
  DOI 10.1007/s10725-013-9801-z
  
  Healthy criticism is always welcome, but a matter already decided by Springer needs no further clarification from my end. I will not engage in any form of correspondence in this matter henceforth.
  
  Meera C Das, Botany Department, North-Eastern Hill University, Shillong 793022, India
  
  Reply
Dendrobium concerns says:

November 19, 2014 at 10:09 am

Concerns about Vyas et al. 2009, 2011 and 2012 Dendrobium papers

2009 paper
Vyas, S., Guha, S., Bhattacharya M, Usha Rao, I. 2009. Rapid regeneration of plants of Dendrobium lituiflorum Lindl. (Orchidaceae) by using banana extract. Scientia Horticulturae 121:32-37 (Elsevier)
Department of Botany, University of Delhi, Delhi, 110007, India
http://www.sciencedirect.com/science/article/pii/S0304423809000107
DOI: 10.1016/j.scienta.2009.01.012

2011 paper
S. Vyas, P. Kapoor-Pandey, S.Guha, I. Usha Rao. 2011. Synchronous plantlet formation by using banana extract and in vitro hardening in orchid, Dendrobium lituiflorum Lindl. Journal of Ornamental and Horticultural Plants 1(3): 175-184
http://webzoom.freewebs.com/jornamental/vol%203/Shivani2.pdf
No DOI

2012 paper
Vyas, S., Kapai, V.Y., Kapoor, P., Guha, S., Usha Rao, I. 2012. In vitro plantlet regeneration from protocorms of Dendrobium lituiflorum Lindl. and Cymbidium bicolor Lindl. and their acclimatization: effect of salts, sucrose, and banana extract. Journal of Horticultural Science and Biotechnology 87(5): 485-492
http://www.jhortscib.org/Vol87/87_5/15.htm
No DOI

Similarities (suggesting partial duplication and salami publication):
a) same orchid: Dendrobium lituiflorum
b) same plant material: seed-derived protocorms
c) same parameters assessed: banana extract
d) same medium: Knudson’s C
e) same acclimatization protocol: 9:1 (cocopeat : perlite)
f) same stats analyses.
g) The 1st line of the 2012 R&D paper states: “The present study indicated that the natural additive, BE, promoted plantlet regeneration and subsequent growth.” This fact alone nullifies the originality of this manuscript since this fact was already proved in the 2009 and 2011 papers.

Concerns:
a) Fig. 3E of the 2011 paper appears to be a photo of the same plants photographed in Fig. 7H of the 2009 paper (2009 paper in oblique view, 2011 paper in top view).
b) For best protocorm development, in the 2009 paper, the authors recommend 10% BE, in the 2011 paper, 20% BE and in the 2012 paper 10% or 20% BE. Given the fact that this is identical plant material, why are different optimal levels recommended? Which concentration should orchid scientists use, and average of 15% BE? In the 2009 paper, the authors stated “A significant increase (p < 0.05) in protocorms with developing leaves and rhizoids (stage 4) with higher percentages of BE up to 10% (v/v) BE in KC medium was observed (Figs 3 and 7A).” However, studying Fig 3 it is clear that there was no significant difference between the effects of BE at 2.5, 5 or 10% on the percentage of protocorms in stage 4. Moreover they stated, that “The higher concentrations [of BA] proved to be inhibitory”. However, studying Fig. 2 it is clear that BA had no effect on germination, either stimulatory or inhibitory, because no significant differences were presented between the treatments or even relative to the control. If the data has not been correctly interpreted, then how accurate are the subsequent claims made in the subsequent 2011 and 2012 papers?
c) For best plantlet development, in the 2009 paper, the authors recommend 12.5% BE, in the 2011 paper, 20% BE and in the 2012 paper 20% BE. Which concentration should orchid scientists use, considering that it is identical plant material?
d) In all three papers, the English is very poor and riddled with serious grammatical errors. This makes interpretation of the data a little difficult to understand.
e) In the 2011 paper, Figures 1A and 1C indicate the exact same parameters with completely different data. This is a serious fault that casts doubt on the validity of the data set. The negative values on the Y-axis make absolutely no sense (just as the paper from 2012). Most likely Fig 1A was about root and shoot number. In the 2010 and 2011 papers, the authors reference the Vyas et al (2009) paper in the text several times, but no paper is listed under Vyas et al (2009) in the reference list. What study and paper exactly were the authors referring to? Is there a fourth, unknown paper? The authors use a confusing term in their 2011 paper “the root length was clubbed into two categories”: what does this mean?
f) The data on root and shoot length and number has been stretched over 2-3 papers (i.e., possible salami publication).
g) In all three papers, it is not indicated if percentage values were transformed prior to analyses. What version of SPSS was used?
h) Why are the authors so different despite almost the same parameters having been studied? This shows why it is important for journals to indicate clearly the authors’ contributions. In particular, the authors Kapai and Bhattacharya. Why is one author indicated as Kapoor-Pandey in the 2011 paper but only as Kapoor in the 2012 paper? Are these in fact the same individual? If yes, then this confuses metrics and accurate referencing.
i) Finally, in the conclusion of the 2009 paper, the authors state “conservation of biodiversity.” However, biodiversity is not an issue in this paper. Surely, the authors meant “germplasm conservation” since the in vitro protocol generates clonal material which is the antithesis of biodiversity?

Although the three papers do describe additional analyses and some differences (e.g. testing BA in the 2009 paper, data on Luffa sponge and agar-agar in the 2011 paper, or some new additives and another orchid, Cymbidium bicolor, in the 2012 paper), the similarities between all three papers are substantial (abstract, introduction, M&M, and R&D sections) and the main findings have already been published in the 2009 paper and thus should not, in my opinion, have appeared in the 2011 or 2012 papers as “original data”, which it is not. It is redundant data. At minimum, the authors had the responsibility of declaring the 2009 paper in the 2011 references, and the 2011 paper in the 2012 references, but they did not. Why did the authors not indicate the existence of these previous papers?

Reply
1. Dendrobium concerns says:
  
  November 26, 2014 at 1:54 am
  
  A PubPeer entry now exists for this case, listed under paper 1:
  https://pubpeer.com/publications/3359C634C9DB90057A38A4A4E461C0#fb17158
  
  Reply
Qui? says:

November 19, 2014 at 2:32 pm

An update on the following case, and insight into why the 2012b paper suddenly vanished from the IDOSI web-site. Note that even though Dr. Hamidoghli claims that he was not aware of both of these papers, that the 2012a paper continues intact, without any notice, or expression of concern.

Raad MK, Zanjani SB, Shoor M, Hamidoghli Y, Sayyad AR, Kharabian-Masouleh A, Kaviani B. Callus induction and organogenesis capacity from lamina and petiole explants of Anthurium andraeanum Linden (Casino and Antadra). Australian J Crop Sci 2012a;6(5):928-937.

Raad MK, Zanjani SB, Sayyad AR, Maghsudi M, Kaviani B. Effect of cultivar, type and age of explants, light conditions and plant growth regulators on callus formation of anthurium. American-Eurasian J Agric Environ. Sci 2012b;12(6):706-712.

Dr. Y. Hamidoghli, Dept. of Horticulture, University of Guilan, Rasht, Iran, provided a formal explanation:
“I shall thank you for your e-mail and notification, because I was not aware of the tow published articles. In 2011, Mr. Raad MK, Zanjani finished his Msc. thesis with me and Dr. M. Shoor as supervisors. According to your e-mail, Dr. Kavyani (I don,t know him) wrote! an article from this dissertation (in 2012) and added some other names as ”Authors” in the article. This article was published in AJCS. In the same year, he published another copy of this article, with some other names as authors, in American-Eurasian J Agric Environ. Sci Journal. Please be aware that all these publications were without my permission or awareness. Due to this plagiarism, I request the deletion of both articles from stated journals. Please include Dr. Kavyani and Dr. Ardashir Kharabian-Masouleh’s names in the black list so that this would not be repeated. Thank you for your cooperation sincerely Dr. Y. Hamidoghli”

Reply
Anthurium query says:

November 19, 2014 at 3:50 pm

Gantait S, Mandal N, Bhattacharyya S, Das PK. In vitro mass multiplication with pure genetic identity in Anthurium andraeanum Lind. Plant Tissue Culture and Biotechnology 2008;18(2):113-122. (Publisher: Bangladesh Association for Plant Tissue Culture and Biotechnology)
Department of Biotechnology, Instrumentation and Environmental Science, B.C.K.V., Mohanpur, W.B.‐741252, India
http://www.baptcb.org/ptc/Full_article/ptc18_2_03.pdf (open access)
No DOI

Saikat Gantait, Nirmal Mandal. Tissue culture of Anthurium andraeanum: a significant review and future prospective. International Journal of Botany 2010;6(3):207-219. (Publisher: Science Alert*)
Institutional address: as above.
http://scialert.net/fulltext/?doi=ijb.2010.207.219 (open access)
DOI: 10.3923/ijb.2010.207.219

Saikat Gantait, Uma Rani Sinniah. Morphology, flow cytometry and molecular assessment of ex-vitro grown micropropagated anthurium in comparison with seed germinated plants. African Journal of Biotechnology 2011;10(64):13991-13998. (Publisher: Academic Journals*)
Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
http://www.academicjournals.org/article/article1380884655_Gantait%20and%20Sinniah.pdf
DOI: 10.5897/AJB11.1855 (valid DOI?)

Saikat Gantait 1, Uma Rani Sinniah 1, Nirmal Mandal 2, Prakash Kanti Das 3. Direct induction of protocorm-like bodies from shoot tips, plantlet formation, and clonal fidelity analysis in Anthurium andreanum cv. CanCan. Plant Growth Regulation 2012;67(3):257-270. (Publisher: Springer Science + Business Media)
1. Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
2. Department of Biotechnology, Instrumentation and Environmental Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, WB, 741252, India
3. Department of Genetics, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, WB, 741252, India
http://link.springer.com/article/10.1007/s10725-012-9684-4
DOI: 10.1007/s10725-012-9684-4

In the 2012 paper, figure 3e of the acclimatized plants is identical to Fig. 1a of the 2011 paper

Of concern is that the first five lanes of Fig. 1f of the 2010 paper are identical to the full gel indicated in Fig. 2A of the 2008 paper. The 2010 paper does not indicate whether it has used the same gel image from the 2008 paper. The first sample lane of the 2008 gel, labelled as P, refers to the mother plant. The first sample lane of the 2010 gel, labelled as C1, refers to a clone. The 2008 P lane appears to be identical to the C1 lane of the 2010 gel. It is evident that identical lanes cannot represent different samples.

Authors and all journals were anonymously notified of these concerns in February, 2014.

* Open access publishers considered to be “predatory” by Jeffrey Beall: http://scholarlyoa.com/publishers/

There is a PubPeer entry for this case:
https://pubpeer.com/publications/7D433CBB6E3CF846EF798FA747B0F0#fb16726

Reply
Ceropegia query says:

November 19, 2014 at 11:40 pm

Paper 1 (P-1)
Publisher: Trans Stellar*
Kalimuthu K, Prabakaran R (2013) In vitro flowering from nodal explants of Ceropegia pusilla Wight and Arn. International Journal of Botany and Research 3(3), 35-42
Plant Tissue Culture Division, PG and Research, Department of Botany, Government Arts College (Autonomous), Coimbatore, Tamil Nadu, India
http://tjprc.org/journals.php?jtype=2&id=46 (no editor board)
http://tjprc.org/view-archives.php?year=2013_14_2&id=46&jtype=2&page=2
No DOI (open access)
No submission, acceptance or publication dates.
Funding: “The authors extend their gratitude to the University Grants Commission (UGC File No 35-35/2008(SR) dt.19.03.2009), New Delhi of their financial assistance.”

Paper 2 (P-2) (PDF watermarked “RETRACTED”)
Publisher: Gyathri Publishers
Kalimuthu K, Prabakaran R (2013) In vitro and micropropagation for conservation of rare and threatened medicinal plant Ceropegia species – a review. International Journal of Biological Technology 4(2), 23-36
Institutional address as for P-1.
http://www.gbtrp.com/journal/ijbt%20volume%20no%204(2).htm (if links problematic, search from root menu: http://gbtrp.com/ijbt.htm)
No DOI (open access)
No funding statement.
Published: 15, August, 2013. No submission or acceptance dates.

Paper 3 (P-3)
Publisher: ScienceDomain International*
Kalimuthu K 1, Prabakaran R 1, Paulsamy S 2, Jeyaraman S 1 (2014) Microtuberization of Ceropegia pusilla Wight and Arn. an endangered medicinal plant. European Journal of Medicinal Plants 4(1), 64-74
1 Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
2 Department of Botany, Government Arts College (Autonomous), Salem-636007, India.
http://www.sciencedomain.org/issue.php?iid=281&id=13?aid=729
http://www.sciencedomain.org/abstract.php?id=13?aid=729&aid=2256
DOI: 10.9734/EJMP/2014/5266 (open access)
Funding: “The authors extend their gratitude to the University Grand Commission (UGC), New Delhi for their financial assistance.”
Received 12th June 2013; Accepted 14th September 2013; Published 11th October 2013
“Authors’ contributions: All the authors have cordially supported to the work and preparation of manuscript. Authors KK and RP have designed the entire study and protocols with interpretations of the results and prepared the first draft of the manuscript. Author SJ managed the analyses of the study and computational work respectively. Author SP guided in the entire research and documented the final draft of the manuscript. All the authors have read and approved the final manuscript.”

Paper 4 (P-4) (PDF watermarked “UNDER INVESTIGATION”)
Publisher: ScienceDomain International*
Prabakaran R 1, Sasikala T 2, Kalimuthu K 1 (2013) Regeneration of shoots from callus of Ceropegia pusilla Wight and ARN. British Biotechnology Journal 3(3), 416-423
1 Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
2 Department of Botany, Government Arts College (Autonomous), Salem-636007, India.
http://www.sciencedomain.org/issue.php?iid=217&id=11
http://www.sciencedomain.org/abstract.php?iid=217&id=11&aid=1596
DOI: 10.9734/BBJ/2013/4048 (open access)
Funding: “The authors extend their gratitude to the University Grand Commission (UGC), New Delhi for their financial assistance.”
Received 25th March 2013; Accepted 10th June 2013; Published 29th June 2013
“Authors’ contributions: This work was carried out in collaboration between the three authors. Author KK designed the study, performed the statistical analysis, and made the final draft of the manuscript. Authors RP and TS managed the literature searches, carried out the study under the supervision of author KK and wrote the protocol. All authors read and approved the final manuscript.”

Apparent data duplication
data in Table 2 of P-3 = data in Table 1 of P-4
data in Table 3 of P-3 = data in Table 4 of P-4
Notice how micromolar amounts are used by P-4 and mg/l amounts in P-3

Apparent figure duplication and manipulation
1F of P-1 = 1E of P-2 = 1G of P-3
1A of P-2 = 1A of P-4
1B of P-2 = 1B of P-4
1F of P-2 = 1F of P-4
1D of P-3 = 1C of P-1
1E of P-3 = 1C of P-2
1B of P-1 = 1D of P-4 (tilted and twisted)

Apparent plagiarism:
2013 review (P-2) copies the abstracts of most studies in the literature, and presents this as a review, listing the studies chronologically. Subsequently, this paper has already been retracted, 24 hours after we issued our report:
IJBT Biotek Editor writes “Thank you for your advice. As the plagiarism is serious, we have retracted the article now on consulting with the consent editor and corresponding author. The retracted article link is given below for your reference.”
http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29kalimuthu%20abs.htm
http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29/ijbt150813104.pdf

Apparent salami slicing and data/method duplication
in vitro tuberization, shoot and flower induction already reported in P-1 (classical salami slice adding information to text in P-1 and data in tables in P-3 to feign originality; self-plagiarism exact text copied, see M&M section; values reported in molar amounts in P-1 and then in g/l amounts in P-3 to appear original, but are identical concentrations.

Paper 5 (P-5) (PDF watermarked “UNDER INVESTIGATION”)
Publisher: ScienceDomain International*
Interestingly, another paper by the same authors, on the same plant, but on another aspect and in another journal by the same publisher, Sciencedomain.
R. Prabakaran1, K. Kalimuthu1*, C. Vani2 and C. Brindha3 (2014) Angiogenesis and Antioxidant Activity of in vitro and in vivo Tuber of Ceropegia pusilla Wight and Arn. British Journal of Pharmaceutical Research 4(5), 608-616
1Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
2Department of Biotechnology, Karunya University, Coimbatore-641 114, India.
3Department of Microbiology PSG College of Arts and Science Coimbatore-641 014, India.
http://www.sciencedomain.org/issue.php?iid=383&id=14
http://www.sciencedomain.org/abstract.php?iid=383&id=14&aid=3262
DOI: 10.9734/BJPR/2014/7481
Funding: None declared.
Received 18th October 2013; Accepted 24th December 2013; Published 12th January 2014
“Authors’ contributions: This work was carried out in collaboration between all authors. Authors RP and C.B conducted the plant extraction, antioxidant assays, performed the statistical analysis and wrote the manuscript. Author KK participated in designing the experimental details and interpreting the work and revising the paper. Author CV conducted the in vivo CAM assay and critically revised the paper. All authors read, edited and approved the final manuscript.”

There are three PubPeer entries:
P-3: https://pubpeer.com/publications/465647BF634B1332302F3A5FFF4382
P-4: https://pubpeer.com/publications/0878DCF9FB46DF7AE12D59B6F730A4
P-5: https://pubpeer.com/publications/937ED73ED01C18847EE9F4A9256E42

* Publishers listed as “predatory” by Jeffrey Beall at http://scholarlyoa.com/publishers/

Reply
Das Eckey query says:

November 20, 2014 at 7:17 am

Dear Prof. Meera Das. You are kind and courageous to respond. It is healthy to have an open and frank discussion about your three papers. However, it appears as if there are about 150 errors and concerns with these three papers. How do you plan to address those errors? Also, can you or Christina Eckey kindly indicate who forms part of this “ethics group” at Springer that oversees such important decisions? Will Springer request you to address the approximately 150 comments, questions and concerns related to your three papers, and will a comprehensive erratum be published that addresses all the issues? Or will you and your co-authors voluntarily come forward to address the comments, and then request an erratum, or even an expression of concern?

Does your statement “I will not engage in any form of correspondence in this matter henceforth” indicate that you are not prepared to respond to the concerns and queries and to correct the academic record? Do you feel that this would be the most responsible attitude towards the plant science community, especially orchidologists who would need to rely on accurate, clear and well-explained protocols to complete work on Dendrobium?

Finally, your note was very curious. If we enter the name, Christina Eckey*, into the main scientific data-bases (Elsevier’s sciencedirect.com, Springer’s SpringerLink, Taylor and Francis Online, Wiley Online, PubMed, Walter deGryter), the data-bases turn up two very respectable papers from 2004** and 2005*** related to molecular phytopathology, when it appears as if Dr. Eckey appears to have obtained her PhD from Justus-Liebig-University. I am assuming that this experience in plant science is what allowed her to be given the position of Springer Senior Editor, Plant Sciences. What experience has Dr. Eckey had in the past 8 years in plant science research that would then qualify her to make a scientifically validated judgment about orchid biotechnology? And what criteria are required to form part of the Springer “ethics group”? Perhaps Christina Eckey might like to come forward to explain these important issues since transparency underlies not only the peer review process, but also the decisions regarding retractions and errata. As equally as scientists are expected to trust the transparency of an editor board, so too, surely, should the scientific pool also request more transparency from Springer?

* http://www.springer.com/biomed/contact?SGWID=0-1755214-0-0-0
** http://link.springer.com/article/10.1007/s11103-004-0275-2
Christina Eckey, Michael Korell, Katja Leib, Dagmar Biedenkopf, Carin Jansen, Gregor Langen, Karl-Heinz Kogel Identification of powdery mildew-induced barley genes by cDNA-AFLP: functional assessment of an early expressed MAP kinase Plant Molecular Biology May 2004, Volume 55, Issue 1, pp 1-15
*** http://www.sciencedirect.com/science/article/pii/S0168945204003814
Carin Jansen, Michael Korell, Christina Eckey, Dagmar Biedenkopf, Karl-Heinz Kogel Identification and transcriptional analysis of powdery mildew-induced barley genes. Plant Science, Volume 168, Issue 2, February 2005, Pages 373-380
Department of Phytopathology and Applied Zoology, Interdisciplinary Research Centre for Environmental Sciences, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany

Reply
Wheat query says:

November 21, 2014 at 4:51 am

C. L. Olliver, A. Grobler-Rabie, C. D. Boyd (1984) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: Nucleic Acids Methods in Molecular Biology Volume 2, pp 137-144
Affiliation for all three authors: MRC Unit for Molecular and Cellular Cardiology, University of Stellenbosch Medical School, Tygerberg, South Africa
Editor: John M. Walker
DOI: 10.1385/0-89603-064-4:137
Publisher and copyright holder: Humana Press
http://link.springer.com/protocol/10.1385/0-89603-064-4%3A137

Louise Olliver, Anne Grobler-Rabie, Charles D. Boyd (1998) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: RNA Isolation and Characterization Protocols Methods in Molecular Biology™ Volume 86, pp 229-233
Ollivier and Grobler-Rabie: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
No affiliation for Boyd.
Editors: Ralph Rapley and David L. Manning
DOI: 10.1385/0-89603-494-1:229
Publisher and copyright holder: Humana Press
http://link.springer.com/protocol/10.1385/0-89603-494-1%3A229

An estimated 90-95% of the whole book chapter is identical. Only tiny fractions of the introduction (page 229, 1998 paper) and the notes (page 232, 1998 paper) are different. For the remainder, it is a word-by-word copy. The 1998 paper does not reference or acknowledge the 1984 chapter.

When DOIs are entered into PubPeer, they reveal a “null” result, so unfortunately PubPeer entries cannot be created. Are these real or registered DOIs?

Reply
Wheat query 2 says:

November 21, 2014 at 12:11 pm

There is an update to the above post (Wheat query: 1984 and 1998 book chapters). Another two identical book chapters were discovered on the DOI/CrossRef web-site and have been analyzed. This comment complements the above one and also adds more details about the comparisons.

C. L. Olliver, A. Grobler-Rabie, C. D. Boyd (1996) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: Basic DNA and RNA Protocols. Methods in Molecular Biology™ Volume 58, 1996, pp 485-490
Ollivier and Grobler-Rabie: MRC Unit for Molecular and Cellular Cardiology, University of Stellenbosch Medical School, Tygerberg, South Africa
Boyd: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
Editor: Adrian J. Harwood
DOI: 10.1385/0-89603-402-X:485
Publisher and copyright holder: Humana Press
http://link.springer.com/protocol/10.1385/0-89603-402-X%3A485

Louise Olliver, Anne Grobler-Rabie, Charles D. Boyd (2000) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: The Nucleic Acid Protocols Handbook 2000, pp 891-894
Ollivier, Grobler-Rabie, Boyd: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
Editor: Ralph Rapley
DOI: 10.1385/1-59259-038-1:891
Publisher and copyright holder: Humana Press
http://link.springer.com/protocol/10.1385/1-59259-038-1%3A891

The 1996, 1998 and 2000 chapters are 100% identical. The older chapters do not acknowledge the existence of any of the previously published chapters.

An estimated 90-95% of the 1984 vs 1996/1998/2000 book chapters are identical. Only tiny fractions of the introduction (page 229, 1998 paper) and the notes (page 232, 1998 paper) are different. For the remainder, it is a word-by-word copy. The 1996/1998/2000 chapters do not reference or acknowledge each other, or the 1984 chapter.

When the DOIs of the 1996/1998/2000 book chapters are entered into PubPeer, they reveal a “null” result, so unfortunately PubPeer entries cannot be created. However, a PubPeer entry was created for the 1984 chapter:
https://pubpeer.com/publications/083EB54A0D6E64C345340CA4C8564D#fb16836

Reply
Plant tissue culture query says:

November 21, 2014 at 9:21 pm

P-1
Trevor A. Thorpe History of Plant Tissue Culture. Plant Cell Culture Protocols Methods in Molecular Biology™ Volume 318, 2006, pp 9-32
Editors: Victor M. Loyola-Vargas, Felipe Vázquez-Flota
Publisher and Copyright Holder: Humana Press
http://link.springer.com/protocol/10.1385/1-59259-959-1%3A009
DOI: 10.1385/1-59259-959-1:009

P-2
Trevor A. Thorpe History of plant tissue culture. Molecular Biotechnology October 2007, Volume 37, Issue 2, pp 169-180 Date: 27 Jun 2007
http://link.springer.com/article/10.1007/s12033-007-0031-3
Publisher: Humana Press Inc.; Copyright Holder: not indicated.
DOI: 10.1007/s12033-007-0031-3
23 citations

P-3
Trevor Thorpe History of Plant Tissue Culture. Plant Cell Culture Protocols Methods in Molecular Biology Volume 877, 2012, pp 9-27 Date: 02 Apr 2012
Editors: Víctor M. Loyola-Vargas, Neftalí Ochoa-Alejo
Publisher: Humana Press; Copyright Holder: Springer Science+Business Media, LLC
http://link.springer.com/protocol/10.1007/978-1-61779-818-4_2
DOI: 10.1007/978-1-61779-818-4_2

P-4
Trevor A. Thorpe Chapter 1 – History of Plant Cell Culture. Plant Tissue Culture (Third Edition), 2013, Pages 1-22
Publisher and Copyright Holder: Elsevier Inc.
http://www.sciencedirect.com/science/article/pii/B9780124159204000013
DOI: 10.1016/B978-0-12-415920-4.00001-3

P-1, p. 11: “This current article is based on an earlier review by the author (24) (used with permission from Elsevier).”
P-2, p. 170: “This current article is based on an earlier review by the author [24] (used with permission from Elsevier).”
P-3, p. 10: “This current article is based on an earlier review by the author ( 24 ) (used with permission from Elsevier).”
P-4: no statement indicating any permission or reference to any of the previous chapters.

In P-1, P-2 and P-3, reference 24 is referring to the following 2000 book chapter (extremely difficult to access):
Thorpe, T. A. (2000). History of plant cell culture. Chap. 1. In R. H. Smith (Ed.), Plant tissue culture: Techniques and Experiments (2nd ed., pp. 1–32). California: Academic Press

The concern:
Except for the very brief, approximately 1 page introduction in all 4 chapters, the remainder of the chapter is identical, in most parts (estimated at 90-95%) word-for-word identical. Even section titles and sub-sections are identical. The slight differences that exist most likely reflect edits that each editor requested as the chapters got updated along the way.

The requests/queries:
1) Can the term “based on” be equated with the copying word for word?
2) The author is kindly requested to publicly provide a copy of the three copyright permissions for P-1, P-2 and P-3.
3) The author is kindly requested to indicate if the content of P-4, which is almost identical to that of P1, P-2 and P-3, is also identical, or similar in parts, to the 2000 book chapter.
4) The author is kindly requested to make available, a copy of the 2000 chapter, without breaking any copyright laws (perhaps Academic Press could be so kind as to make the copy available in open access at PubPeer, for the purpose of verification of this case).
5) The author is kindly requested to explain why the list of papers on his professional web-site listed below is incomplete, and does not list these apparent partial chapter duplications.
6) The editors are kindly requested to also join in the conversation and provide their perspectives.
7) If a scientist would like to reference a/the chapter entitled “History of plant cell culture”, but the content of the latter 4 (P-1, P-2, P-3, P-4) is almost identical, which of the four copies does the author recommend be used in the citation?
8) The last part of the four duplicated chapters, entitled “The present” is “interesting” because the chapters span from 2006-2013, yet they say the exact same thing, except for P-2 and P-4 which provide a one sentence and a few-sentences update. See excerpt below of P-1(2006) vs P-3 (2012).*

Prof. Trevor A. Thorpe:
Biological Sciences Department, University of Calgary, Calgary, AB, Canada, T2N 1N4
http://www.bio.ucalgary.ca/contact/faculty/thorpe.html
B.Sc. Agriculture (Pomology), University of Allahabad, India, 1961
M.Sc. Horticultural Science, University of California, Riverside, USA, 1964
Ph.D. Plant Science – Plant Physiology, University of California, Riverside, USA, 1968

Abstracts

P-1: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the beginning of the 20th century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogen-free plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology. The historical development of these in vitro technologies and their applications are the focus of this chapter.”

P-2: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the begining of the 20th century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those that were already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogenfree plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology. The historical development of these in vitro technologies and their applications are the focus of this chapter.”

P-3: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the beginning of the twentieth century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those that were already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogen-free plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology in the twenty-first century. The historical development of these in vitro technologies and their applications is the focus of this chapter.”

* Excerpt from “The present”
P-1, p. 20: “The current emphasis and importance of plant biotechnology can be gleamed from the last two International Congresses on Plant Tissue and Cell Culture and Biotechnology held in Israel in June 1998, and in the United States in June 2002. The theme of the Israeli Congress was Plant Biotechnology and In Vitro Biology in the 21st Century and the theme of the last Congress was Plant Biotechnology 2002 and Beyond. The proceedings for these two congresses (194, 195) were developed through a scientific program that focused on the most important developments, both basic and applied, in the areas of plant tissue culture and molecular biology and their impact on plant improvement and biotechnology. They clearly show where tissue culture is today and where it is heading (i.e., as an equal partner with molecular biology), as a tool in basic plant biology and in various areas of application. In fact, progress in applied plant biotechnology is fully matching and is without doubt stimulating fundamental scientific progress, which remains the best hope for achieving sustainable and environmentally stable agriculture (196). Indeed, the advancements made in the last 100 yr with in vitro technology have gone well beyond what Haberlandt and the other pioneers could have imagined.”

P-3, p. 19-20: “The current emphasis and importance of plant biotechnology can be gleamed from the last three International Congresses on Plant Tissue and Cell Culture and Biotechnology held in Israel in June 1998, in the USA in June 2002, and in China in August 2006. The theme of the Israeli Congress was Plant Biotechnology and In Vitro Biology in the 21st Century ; the theme of the 2002 Congress was Plant Biotechnology 2002 and Beyond , while the theme of the 2006 Congress was Biotechnology and Sustainable Agriculture 2006 and Beyond. The proceedings for these three congresses ( 194– 196 ) were developed through scientific programs that focused on the most important developments, both basic and applied, in the areas of plant tissue culture and molecular biology and their impact on plant improvement and biotechnology. They clearly show where tissue culture is today and where it is heading (i.e., as an equal partner with molecular biology) as a tool in basic plant biology and in various areas of application. In fact, progress in applied plant biotechnology is fully matching and is without doubt stimulating fundamental scientific progress, which remains the best hope for achieving sustainable and environmentally stable agriculture ( 197 ) . Indeed, the advancements made in the last 100 years with in vitro technology have gone well beyond what Haberlandt and other pioneers could have imagined.”

There are two PubPeer entries (the other two papers’ DOIs could not be linked to PubPeer):
P-2: https://pubpeer.com/publications/5E8393A80298AD8B1FEA9210CC368D#fb16846
P-4: https://pubpeer.com/publications/19294ED07445E31E5855FB46F8786E#fb16847　

Reply
Balanites query says:

November 23, 2014 at 8:15 am

Paper 1
Siddique, I., Anis, M., 2009. Direct plant regeneration from nodal explants of Balanites aegyptiaca L. (Del.): a valuable medicinal tree. New Forests 37:53–62. doi:10.1007/s11056-008-9110-y (Springer Science + Business Media)
http://link.springer.com/article/10.1007/s11056-008-9110-y
20 citations

Paper 2
Anis, M., Varshney, A., Siddique, I. 2010. In vitro clonal propagation of Balanites aegyptiaca (L.) Del. Agroforestry Systems 78:151–158. DOI: 10.1007/s10457-009-9238-6 (Springer Science + Business Media)
http://link.springer.com/article/10.1007/s10457-009-9238-6
6 citations

Paper 3
Varshney A. 2012. PhD thesis (Studies on micropropagation and biochemical analysis in Balanites aegyptiaca Del)
Open access (all thesis chapters): http://ir.inflibnet.ac.in:8080/jspui/handle/10603/11369
(issued September, 2013)

Paper 4
Varshney, A., Anis, M., 2013a. Evaluation of clonal integrity in desert date tree (Balanites aegyptiaca Del.) by inter-simple sequence repeat marker assay. Acta Physiologiae Plantarum 35:2559–2565. DOI:10.1007/s11738-013-1292-z (Springer Science + Business Media)
http://link.springer.com/article/10.1007/s11738-013-1292-z
2 citations

Paper 5
Varshney, A., Anis, M., 2013b. Direct plantlet regeneration from segment of root of Balanites aegyptiaca Del. (L.)- A biofuel arid tree. International Journal of Pharma and Bio Sciences 4(2):987–999 (section biological science, paper No. 117).*
http://www.ijpbs.net/archive-issue.php?issueid=22
http://www.ijpbs.net/cms/php/upload/2343_pdf.pdf

Paper 6
Varshney, A., Anis, M., Aref, I.. M., 2013. Control of bioregulants on plant resurgence in vitro from mature seeds of Egyptian Myrobalan Tree (Balanites aegyptiaca Del.)- a plant affluent in saponins. International Journal of Pharmaceutical Sciences Review and Research 22:23–28. (Global Research Online**)
http://globalresearchonline.net/journalcontents/v22-1/05.pdf

Paper 7
Varshney, A., Anis, M., 2014a. Synseed conception for short-term storage, germplasm exchange and potentialities of regeneration genetically stable plantlets of desert date tree (Balanites aegyptiaca Del.). Agroforestry Systems 88:321–329. DOI: 10.1007/s10457-014-9685-6 (Springer Science + Business Media)
http://link.springer.com/article/10.1007/s10457-014-9685-6
No citations

Paper 8
Varshney, A., Anis, M., 2014b. Trees: Propagation and Conservation: Biotechnological Approaches for Propagation of a Multipurpose Tree, Balanites aegyptiaca Del. Springer, New Delhi, India, p. 116. DOI:10.1007/978-81-322-1701-5 (Springer Science + Business Media)
http://link.springer.com/book/10.1007/978-81-322-1701-5

* Listed as “predatory open access publishers” by Jeffrey Beall: http://scholarlyoa.com/individual-journals/
** Listed as “predatory open access publishers” by Jeffrey Beall: http://scholarlyoa.com/publishers/

The symbol = is used next to denote “identical to”.

Fig. 2C (paper 5) = Fig. 1C (paper 6) = Fig. 1E (paper 4) = Fig. 4.18c (paper 8)
Table 4 (paper 5) = Table 4 (paper 6) = Table 4.28 (paper 8)
Problem: shoots are from root segments in the presence of 5 µM BA + 1 µM NAA (Fig. 2C), those from Fig. 1C are from seeds germinated in the presence of GA3, those in Fig. 1E are from nodal explants from mature trees in the presence of 12.5 µM BA + 1 µM NAA, while those in Fig. 4.18c are rooted shoots in the presence of 2 µM IBA.
Issue 1: how is it possible for the exact same shoots to be derived from three completely different and distinct biological tissues and sources and in response to completely different plant growth regulators?
Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in any of the other sources.
Issue 3: Materials and method section. Paper 8 used 3-4 cm shoots while in paper 5, 4-5 cm shoots and in paper 6, shoots with expanded leaves are used (but no size specified).

Fig. 1D (paper 6) = Fig. 1F (paper 4) = Fig. 4.20b (paper 8)
Problem: plants are from seedlings (Fig. 1D), but those from Fig. 1F are from nodal segments. The source of plants in Fig. 4.20b is not specified, only the age (four-month-old plantlets).
Issue 1: how is it possible for the exact same plants to be derived from at least two completely different and distinct biological tissues?
Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in any of the other sources.

Fig. 1C (paper 4) = Fig. 4.2a (paper 8)
Problem: shoots from nodal explants derived from mature trees (Fig. 1C), but those from Fig. 4.2a are from cotyledonary nodes (i.e., from seed-derived shoots).
Issue 1: how is it possible for the exact same shoots to be derived from two completely different and distinct biological tissues?
Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

Fig. 1B (paper 6) = Fig. 4.6a (paper 8)
Problem: intact seedlings from seeds (Fig. 1B) are also shoots from seedling-derived nodal explants (Fig. 4.6a).
Issue 1: how is it possible for the exact same plants to be derived from two completely different and distinct biological tissues?
Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

Fig. 1A-D (paper 5) = Fig. 4.8a-d (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Fig. 2A (paper 5) = Fig. 4.9a (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Fig. 2B (paper 5) = Fig. 4.10a (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Fig. 1A (paper 6) = Fig. 4.12b (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Fig. 1B (paper 2) = Fig. 4.16a (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 2.

Fig. 3B,C,D (paper 7) = Fig. 4.21b,c,d (paper 8)
Issue: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

Fig. 1E (paper 1) = Fig. 4.18b (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 1.

Fig. 2D (paper 5) = Fig. 4.19b (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Fig. 1E (paper 5) = Fig. 4.22d (paper 8)
Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

Other queries and concerns about this set of 8 closely-linked papers:
a) Why are the ISSR banding patterns in Fig. 2 of paper 4 so different from those in Fig. 4.27 (paper 8) when the exact same primers have been used? Admittedly, the samples may be different, but these are not clearly explained in paper 8.
b) Why has paper 8 not referenced paper 4 and paper 6, even though paper 8 was published in 2014 while papers 4 and 6 were published in 2013?
c) In Fig. 1E of paper 1, the figure legend states “in vitro rooted plantlet on MS + IBA (1.0 µM) + activated charcoal (0.5%)”. However, the use of activated charcoal at this concentration would clearly stain the medium black. There is thus clearly a problem with the description of the medium, or of the results. In the PhD thesis (paper 3), the description for the exact same figure states “In vitro rooted shoots cultured on half strength MS medium with 2.0 μM IBA after 4 weeks” (chapter 4, p. 71).
d) In paper 4, the materials and method section clearly states that the medium is “half-strength MS medium supplemented with IBA (1 µM)” but in the figure 1E caption this is specified as “MS + IBA (1 µM)”. The same figure in paper 5 states that the rooting medium is “half strength MS medium with 2.0 µM IBA”. That indicates clearly a discrepancy between the media used, and thus an error in the methods reported.
e) See materials and method section of paper 2. “Healthy, small twigs (3–4 cm) of B. aegyptiaca were collected from 20 years old healthy mature tree growing at Arid Forest Research Institute (AFRI) campus Jodhpur, India.” Distance from Jodhpur to Aligarh (authors’ institute) by air is 528 Km and by road 648 Km according to a trip website http://www.makemytrip.com/routeplanner/jodhpur-aligarh.html. It is surprising how only 3-4 cm small twigs can be preserved for long and over such a great distance, although how the material was preserved over this period is not explained. In this case, experience indicates that generally fresh samples of explants are used and experiments are performed in the early morning. However, it is possible to keep material on ice, but regeneration efficacy is poor in comparison with freshly collected plant material and the chance of contamination by endophytes is higher. Or, if a sample is collected from far away, 2 to 2.5 meter branch (for tree species) and 20 to 50 cm twig (for shrub) from same mother plant and placed in 200 mg/l IAA for 5 h, for rooting, then transplanted. Only mother plants that regenerate (after about 4 months) are used as the source of explants, not freshly collected material. Regrettably, none of these fine-scale but essential details are indicated in the materials and method section, which only mentions that the experiment is repeated in triplicate but the number of replicates are not mentioned anywhere in the text.
f) Chapters 2 and 3 of the thesis (paper 3) are identical to chapters 2 and 3 of the book (paper 8), without attribution. The reference list at the end of both book chapters does not reference paper 3, the Varshney thesis. Paper 3, chapter 1 is approx. 90% identical to paper 8, chapter 1. Paper 3, chapter 2 is approx. 90% identical to paper 8, chapter 2. Vast tracts of text in the thesis (paper 3, chapter 2) as well as in paper 8, chapter 2 (estimated at about 30%) appear to be copied from George et al. (2007), without acknowledgement. Paper 3, chapter 3 is almost identical to paper 8, chapter 3, the same for chapter 4 and chapter 5.
g) Plagiarism software was not used, and values represent rough estimates by crude line-by-line comparisons.

Funding:
a) Paper 1: “Authors gratefully acknowledge the University Grants Commission, New Delhi for financial assistance and the Department of Science and Technology, Govt. of India, New Delhi, for providing research support under DST-FIST Program.”
b) Paper 2: “This research is supported by a Grant from the University Grants Commission (2006–2009), New Delhi. Authors gratefully acknowledge the Department of Science and Technology, Govt. of India, New Delhi for providing research support under DST-FIST (2005) Program.”
c) Paper 3: “Financial support from UGC in the form of Project Fellow in a major research project on Balanites aegyptiaca (2007-2009) and Non-Net fellowship (2011-2012) is greatly acknowledged.”
d) Paper 4: “Authors gratefully acknowledge the Department of Science and Technology, and the University Grant Commission, Govt. of India, New Delhi for providing research support under DST-FIST (2005) and UGC-SAP DRS-I (2009) Programs, respectively.”
e) Paper 5: “Authors also gratefully acknowledge the Department of Science and Technology, Govt. of India, New Delhi for providing research support under DST- FIST (2005), UGC – SAP DRS-I (2009) Programs respectively.”
f) Paper 6: “Authors gratefully acknowledge the Department of Science and Technology, and the University Grant Commission, Govt. of India, New Delhi for providing research support under DST-FIST (2005) and UGC-SAP DRS-I (2009) Programs, respectively.”
g) Paper 7: “Research support from the Department of Science and Technology (Govt. of India) New Delhi under the DST-FIST (2011) and UGC-SAP (2009) Programmes are duly acknowledged.”
h) Paper 8: “The research support and assistance rendered by the Department of Science and Technology and the University Grant Commission, Govt. of India, New Delhi, in the form of DST-FIST (2011–2016) and UGC-DRS-I (2009–2014) programs is duly acknowledged. The award of Young Scientist under DSTFAST TRACK scheme to Ankita Varshney is also gratefully acknowledged.”

Mohammad Anis 1,2; Ankita Varshney 1; I. Siddique (not listed at 1); I. M. Aref 2.
1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
2. Department of Plant Production, College of Food & Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia

1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
http://www.amu.ac.in/dfacultylist.jsp?did=40
2. College of Food & Agricultural Sciences, King Saud University
http://ksu.edu.sa/Deanships/DeanshipofGraduateStudies/Pages/CollegeofFoodSciencesandAgriculture.aspx

There are four PubPeer entries:
Paper 1: https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
Paper 2: https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878　
Paper 4: https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879　
Paper 7: https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880　

Paper 8 DOI could not be read by PubPeer.

Reply
1. Balanites query says:
  
  December 3, 2014 at 3:45 pm
  
  Update.
  
  Dr. Ankita Varshney has responded to an anonymous request to comment on this case but does not understand the concept of anonymity. What the authors also do not appear to understand is that this is a public case that affects the entire plant science literature and all plant scientists, and may have wider consequences and repercussions on academic integrity in plant science journals. Rather than skirting the issue, surely it is best to address them publically at PubPeer as well as directly with the journals, journal editors and publishers? Public accountability for one’s research and publications is not a matter of negotiation, it is a matter of scientific responsibility.
  
  12/3/14 at 8:19 PM “Thanks for your mail dated 23 Nov. 2014. Sir, before reponding publically to queries and concerns about some of our publications at PubPeer, we would like to have your brief introduction. I have seen an unregistered submission at PubPeer for the same. I request you to please tell your designation and credentials to us. Looking for your reply. Thanking You. Dr. Ankita varshney. DST Young Scientist. Plant Biotechnology Lab. Dept. of Botany, AMU Aligarh.” And, one day earlier, 12/2/14 at 6:34 PM “We will shortly submit our clarification at PubPeer. Regards, Dr. Ankita Varshney.”
  
  Reply
Ceropegia query says:

November 25, 2014 at 5:00 pm

“Original” research papers

P-1
Kondamudi R, Murthy, K.S.R. 2011. Micropropagation of Ceropegia pusilla Wt. & Arn. – an endangered and rare medicinal Asclepiad. Journal of Tropical Medicinal Plants 12: 41-48
http://tropmedplants.com/article.php?aid=464 (no editor board)
No DOI. (paid access)

P-2
Kondamudi R, Vijayalakshmi V, Murthy, K.S.R. (2010) Induction of morphogenetic callus and multiple shoot regeneration in Ceropegia pusilla Wight and Arn. Biotechnology 9(2): 141-148
http://scialert.net/qredirect.php?doi=biotech.2010.141.148&linkid=pdf
(Asian Network for Scientific Information, ANSI*; http://scialert.net/eboard.php?issn=1682-296x)
DOI: 10.3923/biotech.2010.141.148 (open access)

P-3
Murthy KSR, Kondamudi R (2010) Effect of cytokinins and auxins on in vitro flowering of endangered Ceropegia spiralis Wight and C. pusilla Wight & Arn. Phytomorphology 60: 32-37.
(Publisher: International Society of Plant Morphologists)
No DOI. (paid access)

P-4
Murthy KSR, Kondamudi R, Vijayalakshmi V (2010a) Micropropagation of an endangered medicinal plant Ceropegia spiralis Wight. Journal of Agricultural Technology 6: 179-191.
http://www.ijat-aatsea.com/past_v6_n1.html
http://www.ijat-aatsea.com/pdf/Jan_v6_n1_10/19-55-IJAT2009_35R.pdf
(Publisher: Association of Agricultural Technology in Southeast Asia (AATSEA))
No DOI. (open access)

P-5
Murthy KSR, Kondamudi R, Pullaiah T (2010b) High frequency somatic embryogenesis in Ceropegia spiralis Wight – an endemic and endangered medicinal plant. Indian Journal of Biotechnology 9, 414-418.
http://nopr.niscair.res.in/bitstream/123456789/10441/1/IJBT%209%284%29%20414-418.pdf
(NISCAIR; IF = 0.477) (open access)

P-6
Murthy KSR, Kondamudi R (2011) Rapid shoot regeneration from thin cell layer explants of an endangered medicinal asclepiad Ceropegia spiralis L. Plant Tissue Culture and Biotechnology 21(1): 63-73.
http://www.banglajol.info/index.php/PTCB/article/view/9564
(Publisher: Bangladesh Association for Plant Tissue Culture and Biotechnology (BAPTC&B))
(Banglajol: http://www.banglajol.info/index.php/index)
DOI: 10.3329/ptcb.v21i1.9564 (open access)

P-7
Murthy KSR, Kondamudi R, Karuppusamy S (2012a) Microtuberization of Ceropegia spiralis Wight and Ceropegia pusilla Wt. and Arn. African Journal of Plant Science 6: 321-327.
http://academicjournals.org/article/article1380125590_Murthy%20%20et%20al.pdf
Total views: 221: downloaded: 345
(Academic Journals*)
DOI: 10.5897/AJPS12.107 (open access)

P-8
Murthy, K.S.R., Kondamudi, R., Reddy, M.C., Karuppusamy, S., Pullaiah, T., 2012b. Check-list and conservation strategies of the genus Ceropegia in India. International Journal of Biodiversity and Conservation 4(8), 304-315.
http://www.academicjournals.org/article/article1380023122_Murthy%20et%20al.pdf
Total views: 241: downloaded: 176
(Academic Journals*)
DOI: 10.5897/IJBC12.011 (open access)

P-9
KSR Murthy, MC Reddy, R Kondamudi (2013) Synthetic seeds – A novel approach for the conservation of endangered C. spiralis wt. and C. pusilla. Bangladesh Journal of Scientific and Industrial Research 48(1), 39-42. (Banglajol: http://www.banglajol.info/index.php/index)
http://www.banglajol.info/index.php/BJSIR/article/view/15412
No DOI. (open access)

The symbol = denotes “identical to” in the following lists.

Tables:
20 shoot-related data points in Table 2 of P-1 are identical to data in Table 3 of P-2
Table 2 data of P-3 = Table 3 data of P-1
Table 2 data of P-4 = Table 1 data of P-6
Table 4 data of P-4 = Table 1 data of P-7 (the latter does, however, include additional information and all negative results in treatments, but 19 identical data points, nonetheless)

Figures:
Fig. 1D of P-2 identical to Fig. 1F of P-1
Fig. 1B of P-3 identical to Fig. 1E of P-1 (slightly rotated)
Fig. 1B of P-6 = Fig. 1B of P-4 = Fig. 1Ce of P-7
Fig. 1A of P-6 = Fig. 1Cb of P-7 (rotated ~90°)
Fig. 1D of P-6 (slightly squashed) = Fig. 1Cc of P-7
Fig. 1G of P-4 (rotated ~45° and tilted) = Fig. 1i of P-5
Fig 1A of P-4 = Fig. 1A of P-7 (slightly rotated)
Fig. 1F of P-7 (left test-tube removed) = Fig. 1D of P-2
Fig. 1E of P-7 repeated twice (in Fig. 1E and Fig. 1C)

These concerns would surely also directly influence the claims in the review written by this group in P-8. Moreover, several of these papers have been referenced in P-9.

Affiliations:
K Sri Rama Murthy, R Kondamudi, MC Reddy, V Vijayalakshmi: School of Conservation Biology and Plant Biotechnology, Department of Biotechnology, Montessori Mahila Kalasala, Vijayawada, 520 010, Andhra Pradesh, India.
http://www.researchgate.net/profile/K_Sri_Rama_Murthy (Head of Department, Department of Biotechnology)
http://www.minglebox.com/college/Montessori-Mahila-Kalasala-College-Vijayawada (actual web-site difficult to trace)
S Karuppusamy: Department of Botany, the Madura College, Madurai, Tamil Nadu – 625 011, India.
http://www.maduracollege.org/botany.php
T Pullaiah: Departent of Botany, Sri Krishnadevaraya University, Anantapur 515 003, Andhra Pradesh, India
http://www.htcampus.com/college/department-botanysri-krishnadevaraya-university/

Financial assistance:
P-1: “The authors extend their gratitude to the Council of Scientific and Industrial Research, New Delhi for financial assistance.”
P-2: “The authors extend their gratitude to the Council of Scientific and Industrial Research, New Delhi of their financial assistance.”
P-3: “The authors are thankful to the Council of Scientific and Industrial Research (CSIR), New Delhi, India for providing the financial assistance.”
P-4: “The receipt of financial assistance from the Council of Scientific and Industrial Research (CSIR), New Delhi, is gratefully acknowledged.”
P-5: “The financial assistance received from Council of Scientific and Industrial Research, New Delhi, is gratefully acknowledged.”
P-6: “The authors thank the authority of The Council of Scientific and Industrial Research (CSIR), New Delhi for providing financial assistance to carry our the present work.”
P-7: “The receipt of financial assistance from the Council of Scientific and Industrial Research (CSIR), New Delhi, is gratefully acknowledged.”
P-8: “One of the authors (KSM) received financial support from the Council of Scientific and Industrial Research, New Delhi, for this study.”

* Publisher listed as “predatory” by Jeffrey Beall at http://scholarlyoa.com/publishers/

Even though the corresponding author, one other author, and all publishers (except for P-9) were anonymously notified of these problems on February 19, 2014, the entire literature listed above remains untouched, and uncorrected.

There are four PubPeer entries for this case:
P-2: https://pubpeer.com/publications/19CF7D9BE88DB147E132A284ECF9AC#fb17111
P-6: https://pubpeer.com/publications/0955F74AA995CED3982A2EB55880F5#fb17110
P-7: https://pubpeer.com/publications/5CC152B8CBCF256457B718A51F1399#fb17112
P-8: https://pubpeer.com/publications/9D91F963C8EFFC96AB2C2D3710E556#fb17113

Reply
Ceropegia concerns says:

November 26, 2014 at 1:58 am

There are now 7 PubPeer entries for the Ceropegia-related cases posted to RW on February 18, 2014.
Case 1:
https://pubpeer.com/publications/465647BF634B1332302F3A5FFF4382
https://pubpeer.com/publications/0878DCF9FB46DF7AE12D59B6F730A4
https://pubpeer.com/publications/937ED73ED01C18847EE9F4A9256E42
Case 2:
https://pubpeer.com/publications/19CF7D9BE88DB147E132A284ECF9AC#fb17111
https://pubpeer.com/publications/0955F74AA995CED3982A2EB55880F5#fb17110
https://pubpeer.com/publications/5CC152B8CBCF256457B718A51F1399#fb17112
https://pubpeer.com/publications/9D91F963C8EFFC96AB2C2D3710E556#fb17113

Reply
Cotton concerns says:

November 26, 2014 at 3:14 am

Cotton 1
Eltayb Abdellatef, Mutasim M. Khalafalla (2008) Influence of growth regulators on callus induction from hypocotyls of medium staple cotton (Gossypium hirsutum L). cultivar Barac B -67. Journal of Soil and Nature 2(1): 17-22
Commission for Biotechnology and Genetic Engineering, National Centre for Research, Khartoum, Sudan
Publisher: Green Global Foundation (GGF) (formerly Green World Foundation (GWF)): http://ggfjournals.com/ *
Accepted for publication: February 03, 2008. No submission or publication dates.
http://ggfjournals.com/content/issue/jsn-v2-is1
http://ggfjournals.com/content/papers/v2i117-22
http://ggfjournals.com/assets/uploads/4.17-22_.pdf (open access)
No DOI.

Cotton 2
Eltayb Abdellatef, Mutasim M. Khalafalla (2008) Ethylene inhibitors promote in vitro regeneration of medium staple cotton (Gossypium hirsutum L.) cultivar Barac B- 67. Advances in Natural and Applied Sciences 2(3): 178-184.
Publisher: American Eurasian Network for Scientific Information (AENSI, Jordan) *
No submission, acceptance or publication dates.
PDF states: “This is a refereed journal and all articles are professionally screened and reviewed.”
http://www.aensiweb.com/old/anas_sept-dec_2008.html
http://www.aensiweb.com/old/anas/2008/178-184.pdf (open access)
No DOI.

Cotton 3
Eltayb Abdellatef, Mutasim M. Khalafalla (2007) Adventitious shoot and plantlet formation in medium staple cotton cultivar (Gossypium hirsutum L. cv Barac [67] B). International Journal of Agriculture and Biology 9(6): 913-916.
Publisher: Friends Science Publishers, Pakistan (http://www.fspublishers.org) *
Received 31 May 2007; Accepted 06 August 2007. No publication date.
http://www.fspublishers.org/Issue.php?categoryID=109
http://www.fspublishers.org/published_papers/35232_..pdf (open access)
No DOI.

Fig 1C of Cotton 1 = Fig 1A of Cotton 2
Fig. 1D of Cotton 2 = Fig. 1F of Cotton 3
Table 1 data of Cotton 1 is identical to Table 1 data of Cotton 3.
The protocols are almost identical, with only small tweaks.

* Listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/).

Authors and publishers were alerted anonymously to this case on 12 February 2014. No action has yet been taken.

Funding:
Cotton 1: “We gratefully acknowledge the financial support of the National Center for Research, Ministry of Science and Technology, Sudan.”
Cotton 2: “We gratefully acknowledge the financial support of the National Center for Research, Ministry of Science and Technology, Sudan.”
Cotton 3: “We thank National Center for Research, Ministry of Science and Technology, Sudan for financial support.”

As there are no DOIs, the case cannot be linked to PubPeer.

Reply
Moringa concerns says:

November 26, 2014 at 3:18 am

Mutasim M. Khalafalla 1, Hussein M. Dafalla 1, A. Nassrallah 2, Khalid M. Aboul-Enein 3, Hany A. El-Shemy 2, Eltayb Abdellatef 1 (2011) Dedifferentiation of leaf explants and antileukemia activity of an ethanolic extract of cell cultures of Moringa oleifera. African Journal of Biotechnology 10(14), 2746-2750, 4 April, 2011 (Academic Journals*)
1 Commission for Biotechnology and Genetic Engineering, P. O. Box 2404 Khartoum, Sudan.
2 Faculty of Agriculture Research Park (FARP) and Department of Biochemistry, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt.
3 Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt.
http://www.academicjournals.org/journal/AJB/cited-by-article/E47D15925665
http://www.academicjournals.org/article/article1380729752_Khalafalla%20et%20al.pdf (open access)
http://www.ms.academicjournals.org/article/article1380729752_Khalafalla%20et%20al.pdf
DOI: 10.5897/AJB10.2099
Total views: 146; Downloaded: 199
Accepted: 30 December 2010; Published: 04 April 2011; Submission date not indicated.

Eltayb Abdellatef, Mutasim M. Khalafalla (2010) In vitro morphogenesis studies on Moringa olifera L. an important medicinal tree. International Journal of Microbiological Research 2010; 1(2): 85-89
(Publisher: Medicobiological Research Publications)
http://www.ijmedres.com/issue2.php
http://www.ijmedres.com/article/013_In_vitro_morphogenesis_studies_on_Moringa_olifera_L_An_important_medicinal_tree_Eltayb_adbedllatef_Mutasim.pdf (this link now apparently dead)
https://app.box.com/s/15e8gfaty3x58fom3jbv (open access)
Received on: 09.08.2010; Revised on: 15.08.2010; Accepted on: 18.10.2010; Published: date not indicated.
No DOI.

5 data points in Table 1 data of the 2011 paper duplicate the same data in Table 2 of the 2010 paper.
Fig. 1A in both papers is identical.
The 2011 paper does not acknowledge the existence of the 2010 paper in its reference list, nor does it indicate that the table data or figure are identical.

*AJB, listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/), claims to follow the COPE ethics (http://www.academicjournals.org/journal/AJB/publication-ethics), which would also automatically imply the implementation of the COPE guidelines for retractions in the case of duplications.

Authors and publishers were alerted to this case on 12 February 2014. No action has yet been taken. Neither paper acknowledges any funding. Even though the AJB paper has a DOI, it cannot be read by PubPeer.

Reply
Anthurium retraction report says:

November 26, 2014 at 4:20 am

Jagan Mohan Reddy, A. K. Bopaiah (2012) Studies on the intiation of callusing and regeneration of plantlets in three different basal media with varied plant growth regulators for the micropropagation of Anthurium scherzeriaum using leaf and spathe as explants. African Journal of Biotechnology 11(23), 6259-6268. (the duplicate paper) (Publisher: Academic Journals, Nigeria*)
Accepted: 27 January 2012. Published: 20 March 2012. Submission date not indicated.
http://www.academicjournals.org/article/article1381128672_Reddy%20and%20Bopaiah.pdf
DOI: 10.5897/AJB10.1292
Total views: 259; Downloads: 109

Jagan Mohan Reddy, A. K. Bopaiah, Abhilash M (2011) In vitro micropropagation of Anthurium digitatum, using leaf as explant. Asian Journal of Pharmaceutical and Health Sciences 1(2): 70-74 (the original paper)* (listed at http://scholarlyoa.com/individual-journals/)
Received: 11 February, 2011; Accepted: 11 March, 2011; Available online: 11 May, 2011.
http://ajphs.com/archives-sub/?id=45 (the paper was retracted and appears on the web-site as “null”):
http://ajphs.com/archives-details/?post_id=582&cat_id=45 (small note reads: “article retracted due to plagiarism…”)

*AJB, listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/), claims to follow the COPE ethics (http://www.academicjournals.org/journal/AJB/publication-ethics), which would also automatically imply the implementation of the COPE guidelines for retractions. AJB and the authors were alerted to this case on June 1, 2013, with a follow-up reminder on July 2, 2013. What is extremely odd about this case is why the earlier paper was retracted, and not the later paper. Does the fact that the remaining paper in AJB, with other concerns (see below), reflect something about peer review and editorial oversight in this journal, or by this publisher?

Even though the one paper was retracted, there is no history of the problems that had been encountered that led to the retraction. This deposit at PubPeer aims to provide a listing of some of the problems.

In the 2011 AJPHS paper, the authors describe an in vitro protocol for Anthurium digitatum.
In the 2012 AJB paper, the authors describe an in vitro protocol for Anthurium scherzeriaum.

Concerns about the papers:
a) Fig 1 in AJPHS is identical to Fig. 9 in AJB. Naturally, the same figure cannot represent two different plant species. This immediately calls into question whether all other figures of both papers are valid and what photos truly represent A. digitatum and which truly represent A. sherzerianum.
b) In the AJB paper, the wrong spelling is used throughout the entire manuscript for Anthurium scherzerianum: it is reported as Anthurium scherzeriaum. This plant does in fact not exist and thus invalidates the entire manuscript.
c) The language of the AJPHS paper is barely English. It is full of grammatical errors that many statements leave open the possibility for multiple interpretations. Ambiguous language implies ambiguous data sets and unreliable data that cannot be used with confidence in the laboratory. The English of the AJB paper is also borderline.
d) In all tables of AJB, 2,4-D is written in almost every possible way (at least 5 variations). Are we dealing with 5 different chemical compounds?
e) Table 9, AJB paper. How can you represent a range of values for the parameters? No sample sizes are given, no statistical analyses exist. How can you have 3-4 roots, for example? Is it 3? Is it 4? Is it an average of 3.4?
f) AJB paper. Figure 2 is identical to Fig. 3, only that Fig 3 is tilted about 30 degrees clockwise and the tone/hue/brightness have been manipulated to give it the impression of a different figure.
g) AJB paper, Figure 8 legend. What is the difference between leaf lamina and leaf size? The figure legend makes no sense as the figure is uninformative.
h) In the AJB paper, only 6 references are listed. Yet, the Anthurium in vitro literature had at least, until 2012, approximately 30-40 studies. Why was the literature so grossly under-represented? The exact same references were used for the AJPHS paper.
i) The exact same experimental design and the exact same explants were used in both studies, except for the spathe in the AJB paper. The plants in vitro look remarkably similar, suggesting that in fact the exact same Anthurium species was used. It is impossible for a reader to verify the actual species and the actual cultivars.
j) The Introduction of the AJB paper does not have a single reference. Yet, it makes many factual claims that are not supported by the literature. Thus, the AJB paper can be considered to be plagiaristic as it does not appropriately list the literature from which this information has arisen.
k) The Introduction of the AJPHS paper is equally unscientific in nature. Not only does it not explore the wide literature on Anthurium in vitro, it makes unsupported statements as indicated at the end of the first paragraph regarding the locations of commercial production.
l) In the AJPHS paper, the authors use non-standard scientific English. For example, what is transflasking? What is 6/6H2O2? These are transcendental errors.
m) In the AJB paper, what is White’s medium? Why is there no reference for this medium? What is Nitsch’ (why the apostrophe?). What are medias?
n) In the AJPHS paper, what are these “secretory products” mentioned in the Introduction?

Requests to the authors on May 30, 2013 for a PDF file of another of their papers remained unanswered:
Jaganmohan Reddy and A.K. Bopaiah
Studies on the Potentiality of Inflorescence Spathe in the Formation of Callus and Regeneration of Plantlets in Ornamentally Important Anthurium andraeanum rubum in Vitro pp. 219-229
http://www.ripublication.com/Volume/ijbbrv2n2.htm

Affiliations:
Jagan Mohan Reddy: Department of Biotechnology, Acharya Institute of Technology, Soladevanahally, Bangalore-560 090, Karnataka, India.
http://www.acharya.ac.in/ait.php
A. K. Bopaiah: Department of Botany, St. Joseph’s College, Bangalore-560 001, Karnataka, India.
http://www.sjc.ac.in/dep_botany.html
M. Abhilash: UST Global, Technopark, Trivandrum, India.
http://www.ust-global.com/en/

Neither paper acknowledges any funding.

The authors published another very weak paper on this ornamental:
http://ijiit.webs.com/documents/120104-03.pdf

There is a PubPeer entry associated with this case:
https://pubpeer.com/publications/2FA8EA21F3078386552B1B4A71C6C3#fb17166

Reply
Rare earth elements + plants report says:

November 26, 2014 at 4:26 am

In this case, none of the three DOIs of the three papers under discussion, published by Springer Science+Business Media, link to PubPeer.

Concerns about statistical analyses (and thus conclusions) in three Biological Trace Element Research (BTER) papers by the same group of authors. An anonymous report was made to Springer, and the Editor-in-Chief, BTER, Prof. Gerhard N. Schrauzer, on 31 July, 2013. This resulted in an expression of concern, but the background concerns were not listed in detail by the Editor-in-Chief, by the journal, or by the publisher, which is as concerning as the three papers themselves because the readers cannot appreciate the actual problems. For this reason, it is important to detail the concerns at PubPeer and RW.

Paper 1: http://link.springer.com/article/10.1385/BTER%3A89%3A3%3A277
Biological Trace Element Research December 2002, Volume 89, Issue 3, pp 277-284
Effects of lanthanum element on the rooting of loquat plantlet in vitro
Weiping Song, Fashui Hong, Zhigang Wan
All authors: Department of Biology, Life Sciences College, Suzhou University, Suzhou, People’s Republic of China
DOI: 10.1385/BTER:89:3:277 (this DOI leads to a different paper on PubPeer)
Publisher and copyright holder: Humana Press Inc.
Citations: 2

Paper 2: http://link.springer.com/article/10.1385/BTER%3A104%3A2%3A185
Biological Trace Element Research 1-May-2005, Volume 104, Issue 2, pp 185-191
Effect of La(III) on the growth and aging of root of loquat plantlet in vitro
Hong Fashui, Song Weiping, Wan Zhigang, Yu Mingliang, Yu Jia, Liu Jiajia, Sheng Ye, Xi Qunhua
Minglinang Yu: Agriculture Academy of Jiangsu Province, 210049, Nanjing, People’s Republic of China
All other authors: Life Sciences College, Suzhou University, 215006, Suzhou, People’s Repubilic of China
DOI: 10.1385/BTER:104:2:185 (this DOI leads to the same incorrect paper on PubPeer)
Publisher and copyright holder: Humana Press Inc.
Citations: 1

Paper 3: http://link.springer.com/article/10.1385/BTER%3A95%3A3%3A259
Biological Trace Element Research December 2003, Volume 95, Issue 3, pp 259-268
Effects of cerium on nitrogen metabolism of peach plantlet in vitro
Song Weiping 1, Hong Fashui 1, Wan Zhigang 1, Zhou Yuzhen 2, Gu Fugen 1, Xu Hongoing 1, Yu Mingliang 2, Chang Youhong 2, Zhao Mizhen 2, Su Jiale 2
1. College of Life Sciences, Suzhou University, 215006, Suzhou, People’s Republic of China
2. Agriculture Academy of Jiangsu Province, 210049, Nangjing, People’s Republic of China
DOI: 10.1385/BTER:95:3:259 (this DOI leads to the same incorrect paper on PubPeer)
Publisher and copyright holder: Humana Press Inc.
Citations: 8

Paper 1
1. Statistical analyses not described.
2. Experimental design, randomization and sampling not described.
3. p. 278 “The relationship between La(NO3)3 concentration and the number of roots was studied. The results are shown in Table 1. The rate of rooting was 41–42% more than that of the control when the La(NO3)3 concentration in the rooting medium was 0.5–5.0 μmol/L, and is significantly different between concentration and control (p ≤ 0.05 level). The average number of roots was 1 to 2.3 times greater than that of the control, and 0.5–3.0 μmol/L concentration of La(NO3)3 was better than the others (p ≤ 0.05 level).” The second statement is false.
4. p. 279. In Table 1, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable.
5. p. 280. Why are no statistical analyses provided to show differences between treatments in Figures 1 and 2?
6. In all analyses, sample sizes are not indicated.
7. In all analyses, it is not indicated whether error bars are SE or SD.
8. It appears as if the study was not repeated, i.e., a single trial. No indication of replicates, sample sizes per treatment or repetitions.

Paper 2
1. The exact cultivar or variety was not described. Such experiments are always genotype-dependent.
2. Experimental design, randomization and sampling not described.
3. p. 187 (Table 1) and p. 189 (Tables 2 and 3). In all three Tables, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable. It appears as if the authors simply assigned the letter a to the table’s upper-most value and then simply pasted ensuing letters of the alphabet for other values in the table going down the table.
4. Table 1 describes the number of explants as being 50. However, a description of the cultures on p. 186 indicates that 50 bottles were cultured for each treatment, and that each bottle contained 4 shoots each. The sample size should therefore be 200 in Table 1. Is 50 correct, or is it 200?
5. Why are the rooting results in Table 1 of Paper 1 so radically different from the results reported in Table 1 of paper 2? This is the exact same plant, the exact same concentrations of La(NO3)3. Therefore, strictly speaking, there should be little variation. However, the data indicates extremely different results. The results of both studies are thus questionable.
6. p. 188. If the authors claim that statistical analyses were conducted, then where are the analyses for Fig. 1?
7. Why are the POD results reported in Table 3 totally different to the analyses also already conducted in Fig. 3 of Paper 1? Why are the units different? Completely different results and analyses when the exact same parameter (POD) and plant material are used invalidate both data sets.

Paper 3
1. p. 260 “We tried to find the best rooting concentration of Ce3+ and also did some research on the relationship between root growth and nitrogen metabolism. We hope that it will supply the theoretical basis and be a technological guide for the application of REEs in a wood plant cultured in vitro.” Poor grammar, typical of all three papers, and highly unscientific description of the hypotheses being tested.
2. Peach variety not defined.
3. Murashige and Skoog medium is claimed to be used, but the 1962 reference for Murashige and Skoog (Physiologia Plantarum) is not provided.
4. Choice of concentrations tested inappropriate. After 5 μmol/L CeCl3, the next concentration was 50. This is incorrect. It should be 10.
5. The authors claim that plant growth was assessed after 15 days in vitro. 15 days for hardwood species is hardly enough time for even root initials to form, let alone assess in vitro plant growth. The observation period is thus too short and thus conclusions based on it are unreliable or unrealistic.
6. Statistical analyses not described.
7. Experimental design, randomization and sampling not described.
8. p. 261. In Table 1, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable.
9. p. 262. Figure 1 stats analyses unclear, in some cases, covered, and the control treatment is missing.
10. Figures 2-8 lack statistical analyses, thus the data sets are unreliable and inconclusive. Without statistical analyses, the authors cannot claim that treatment X is better or worse than treatment Y (at least not with any level of confidence).

These questionable (incomplete, incorrect, inaccurate) statistical analyses may nullify the validity of the data set and thus all conclusions drawn by these three papers.

A collective expression of concern was published for the three papers on January 10, 2014, but the expression of concern is not linked to the top page of the three manuscripts on SpringerLink. Consequently, the readership that accesses any of these three papers is unaware of the expression of concern. Springer and Prof. Schrauzer have been alerted to this point. The expression of concern was published here:
http://link.springer.com/article/10.1007/s12011-013-9881-7
DOI: 10.1007/s12011-013-9881-7 (this DOI cannot be linked to PubPeer)
(http://download.springer.com/static/pdf/283/art%253A10.1007%252Fs12011-013-9881-7.pdf?auth66=1416982954_e0113e14befce561566c2d968c987df7&ext=.pdf) (open access)

Funding:
Paper 1: “This work was funded by a Person of Ability Recommended Foundation of Suzhou University (XQ316011).”
Paper 2: “This work was supported by the Natural Science Fund of Jiangsu Province (no. BK2002501).”
Paper 3: “This work was funded by the Natural Science Foundation of Jiangsu Provice (BK2002501).”

Of note, Prof. Gerhard N. Schrauzer is now Editor-in-Chief Emeritus:
http://www.springer.com/life+sciences/biochemistry+%26+biophysics/journal/12011
It appears as if Prof. Schrauzer was the EIC for at least two decades, or at least associated with BTER for such a long period, including the period in which these three papers were published.

Incidentally, there is an erratum within the same journal, for one of Prof. Schrauzer’s papers:
Original:
http://link.springer.com/article/10.1007/s12011-010-8608-2
http://download.springer.com/static/pdf/415/art%253A10.1007%252Fs12011-010-8608-2.pdf?auth66=1416983999_00ac1df5f365cdf52e3114aaa7df1372&ext=.pdf
DOI: 10.1007/s12011-010-8608-2
Erratum:
http://link.springer.com/article/10.1007/s12011-010-8811-1
http://download.springer.com/static/pdf/310/art%253A10.1007%252Fs12011-010-8811-1.pdf?auth66=1416983962_ce09c2764487133334a77ae6a1f1ad09&ext=.pdf

There is a PubPeer entry for this case:
https://pubpeer.com/publications/07BBFCFFAC98395499B34DE77D3BF8#fb17161

Reply
Dendrobium query says:

November 27, 2014 at 1:49 am

Yifeng Xu, Hao Yu, Prakash P. Kumar (2010) Characterization of floral organ identity genes of the orchid Dendrobium crumenatum. Asia Pacific Journal for Molecular Biology and Biotechnology 18 (1) : 185-187
Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543
http://www.msmbb.org.my/apjmbb/html181/181cont.htm
http://www.msmbb.org.my/apjmbb/html181/181ar.pdf (open access)
No DOI.

Yifeng Xu, Lai Lai Teo, Jing Zhou, Prakash P. Kumar, Hao Yu (2006) Floral organ identity genes in the orchid Dendrobium crumenatum. The Plant Journal, 46: 54–68.
1 Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Science Drive 4, 117543 Singapore, and 2 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02669.x/full
http://www.ncbi.nlm.nih.gov/pubmed/16553895
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02669.x/pdf (open access)
DOI: 10.1111/j.1365-313X.2006.02669.x

2010 paper, Fig. 1ABCD identical to 2006 paper, Fig. 6abcd. The 2010 paper references the 2006 paper, but does not explicitly indicate that these four photos are taken from the 2006 paper, i.e., no attribution to the source. Both papers are considered to be original research papers.

Funding:
2006: “This work was supported by Research Grants R-154-000-232-101 and R-154-000-125-112 and PhD scholarships (to YX, LLT and JZ) from the National University of Singapore, and the intramural research funds from Temasek Life Sciences Laboratory.”
2010: “This work was supported by Research Grants from the National University of Singapore.”

There is a PubPeer entry for this case:
https://pubpeer.com/publications/1B16E05C482DF6EEF2AFD3C3F18715#fb17213

Reply
Ipomoea query says:

November 27, 2014 at 1:40 pm

Original Article
Anwesha M. Bhaduri, M. H. Fulekar (2012) Assessment of arbuscular mycorrhizal fungi on the phytoremediation potential of Ipomoea aquatica on cadmium uptake. 3 Biotech 2:193–198
Environmental Biotechnology Laboratory, Department of Life Sciences, University of Mumbai, Santacruz (E), Mumbai, 400098, India
Received: 14 November 2011; Accepted: 24 January 2012; Published online: 16 February 2012
Publisher: Springer-Verlag
DOI: 10.1007/s13205-012-0046-8
http://link.springer.com/article/10.1007/s13205-012-0046-8/fulltext.html
http://link.springer.com/article/10.1007%2Fs13205-012-0046-8
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433885/
http://download.springer.com/static/pdf/94/art%253A10.1007%252Fs13205-012-0046-8.pdf?auth66=1417058799_4d0d93bc31ab79d4a9770b7a88ac9c13&ext=.pdf (open access)

Concerns:
1) The statistical analysis section states: “Significant differences of measured parameters between AMF, non-AMF were determined by one way ANOVA at p < 0.05 and p < 0.1.” (p. 194) The exact test used to assess significant differences between means, or what software was used to conduct such tests, is not indicated anywhere in the manuscript.
2) The text states, in many places*, that statistically significant differences were observed, referring constantly to the figures. However, not a single figure shows any statistical analyses, or any indication of what treatments are significantly to which others.
3) In one case (2 below), claims of significance are made without a shred of data.
4) In case 3 below, this indicates that a broad claim is made characterizing the trend as being the same across all four enzymes tested (SOD, GPX, CAT, APX), although it is absolutely unclear from the graphs exactly which Cd treatments are significantly different to which other Cd treatments (Fig. 3).
5) Page 197: “The results in (Fig. 4) clearly show that soil microorganisms played a major role in combating toxic effect of Cd.” Does Fig. 4 really show this?
6) There is thus little confidence about the analyses, and considerable lack of clarity about the interpretation of the data, since the reader has simply no way of verifying the veracity of the claims.

* Some examples:
1) “Growth parameters in terms of total biomass, and root and shoot length were significantly (p<0.05), (p<0.1) affected by Cd concentration in both the conditions. In broad-spectrum AMF association exhibited higher growth in terms of fresh biomass, and root and shoot length (Fig. 2a, b).” (p. 195) Fig. 2a and 2b, however, only show relative percentage data.
2) “Phosphorous showed a significant (p<0.05) amount in AMF plants as compared to non-AMF.” and “Phosphorous and potassium were significantly (p<0.05) high in AMF in all concentration as compared to non-AMF. Moreover, nitrogen content in plants was significantly (p<0.1) higher in AMF as compared non-AMF.” appear within the same paragraph (p. 196) Problem is that not a single graph, figure or table contain any data about P, K or N concentrations. So, are the authors referring to unpublished data, or did they forget, perhaps, to submit the respective graphs, tables or data with the manuscript to support these large claims?
3) “Although variations of plant enzymes expressed similar relations in both the conditions, AMF showed significantly (p<0.05) higher enzyme activity than non-AMF with increasing concentrations (Fig. 3).” (p. 197) Unfortunately, the statement is unclear. Are the authors referring to SOD, GPX, CAT, APX? And to which concentrations of Cd? And relative to what? Are comparisons being made across treatments, of between AMF vs non-AMF for each treatment?

Request:
The authors should kindly provide the original data sets for verification, and also request the publisher to publish an erratum, or online supplement that shows clearly, in each figure, the statistical analyses.

Note:
“3 Biotech is supported by King Abdulaziz City for Science and Technology (KACST) in Saudi Arabia and is currently evaluated by Thomson Reuters editors for coverage in Web of Science.”
http://www.springer.com/chemistry/biotechnology/journal/13205

There is a PubPeer entry for this case:
https://pubpeer.com/publications/C7148CDEBC1130EEBD5419B3ABB46A#fb17214　

Reply
Prof. Deepak Pental says:

November 28, 2014 at 4:35 pm

BREAKING NEWS:
Professor Deepak Pental, 63, a “respected” plant geneticist, and the former Delhi University vice chancellor [1], was arrested on two charges, and has been jailed, without bail [2], although there are conflicing stories about the bail. The charges are:
a) plagiarising a fellow professor’s work;
b) theft of cobalt from a laboratory.

[1] http://en.wikipedia.org/wiki/Deepak_Pental
[2] http://www.ndtv.com/article/india/ex-delhi-university-vice-chancellor-deepak-pental-sent-to-tihar-jail-on-plagiarism-complaint-625613

He has some very good papers which now merit closer examination following the accusations by the other professor, especially considering that he is active “real time”:
Journal of Plant Biochemistry and Biotechnology November 2014
Date: 13 Nov 2014
Effective restoration of male-sterile (barnase) lines requires overlapping and higher levels of barstar expression: A multi-generation field analysis in Brassica juncea
Naveen C. Bisht, Arun Jagannath, Rehna Augustine, Pradeep K. Burma, Vibha Gupta, Akshay K. Pradhan, Deepak Pental
http://link.springer.com/article/10.1007/s13562-014-0289-z

For example, was the stolen cobalt or any other stolen chemicals used in this paper or in any other research he published? Surely, the use of stolen chemicals should be subject to at least an expression of concern if not a downright retraction? Springer should be alerted.

This story provides a bit more insight:
http://timesofindia.indiatimes.com/City/Delhi/Delhi-court-gave-ex-DU-vice-chancellor-bail-yet-he-landed-in-jail/articleshow/45290356.cms
“In 2009, Saradhi had filed the private complaint before a Delhi court under various sections of IPC, including forgery, criminal conspiracy and criminal breach of trust. Saradhi, who now teaches in DU’s Environmental Studies Centre, alleged Pental had plagiarised his work on genetically-modified Indian mustard, with the help of Prasad, then a research scholar. Saradhi had alleged that Prasad worked under him on his PhD thesis and went on to conduct research under Pental and, in connivance with Pental, the scholar took the seed of codA transgenic Indian mustard developed by Saradhi’s team under India-Japan Cooperate Science Programme. Pental allegedly allowed Prasad to show this work, carried in his lab during 2001-04, and the data of submitted by Saradhi’s team to the science and technology department.”

This now suggests that a detailed post-publication peer review of his entire published literaure on Indian mustard, and other BRassica species, for example [3], need to be extremely closely examined:
http://www.biomedcentral.com/content/pdf/1471-2164-14-463.pdf

Reply
1. Anonymous says:
  
  November 28, 2014 at 5:13 pm
  
  The Wikipedia page states: “In 2007 he was awarded ‘Officier Des Palmes Academiques‘ for contributions to Research and Education by the Government of Republic of France.” Funny, that’s the same body that knighted Claude Fauquet, the subject of another RW story:
  http://retractionwatch.com/2012/10/09/the-domino-effect-more-retractions-of-papers-that-cited-retracted-plos-one-gmo-cassava-study/
  
  Reply
Vitex negundo concerns says:

December 1, 2014 at 4:28 am

Paper 1:
Naseem Ahmad, Mohammad Anis. 2007. Rapid clonal multiplication of a woody tree, Vitex negundo L. through axillary shoots proliferation. Agroforestry Systems 71(3), 195–200.
Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, UP, India
http://link.springer.com/article/10.1007%2Fs10457-007-9078-1
DOI: 10.1007/s10457-007-9078-1 (PubPeer cannot read this DOI)
Publisher: Springer Netherlands
27 citations

Paper 2:
Naseem Ahmad, S. A. Wali, Mohammad Anis. 2008. In vitro production of true-to-type plants of Vitex negundo from nodal explants. The Journal of Horticultural Science and Biotechnology 83(3): 313-317.
Publisher: The Invicta Press
http://www.jhortscib.org/Vol83/83_3/index.htm
http://www.jhortscib.org/Vol83/83_3/4.htm
No DOI.

Paper 3:
Naseem Ahmad (1), Mohammad Anis (1,2). 2011. An efficient in vitro process for recurrent production of cloned plants of Vitex negundo L. European Journal of Forest Research 130(2): 135–144.
1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, UP, 202 002, India
2. Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
http://link.springer.com/article/10.1007%2Fs10342-010-0415-y
DOI: 10.1007/s10342-010-0415-y
Publisher: Springer-Verlag
13 citations.

Concern 1: data duplication

Table I Ahmad et al. 2008 BA and Kin regeneration frequency data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1A (table vs figure representation). = 13 data points identical
Table 1 Ahmad et al. 2008 BA and Kin number of shoots per explant data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1B (table vs figure representation). = 13 data points identical
Table 1 Ahmad et al. 2008 BA and Kin mean shoot length data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1C (table vs figure representation). = 13 data points identical
Total = 39 identical data points

Table II Ahmad et al. 2008 BAxNAA regeneration frequency data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2A percentage response (table vs figure representation, parameter name changed). = 4 data points identical
Table II Ahmad et al. 2008 BAxNAA number of shoots per explant data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2B mean number of shoot (table vs figure representation, parameter name changed). = 4 data points identical
Table II Ahmad et al. 2008 BAxNAA mean shoot length data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2C (table vs figure representation). = 4 data points identical
Total = 12 identical data points

Table II Ahmad et al. 2008 KinxNAA regeneration frequency data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3A percentage response (table vs figure representation, parameter name changed). = 4 data points identical
Table II Ahmad et al. 2008 KinxNAA number of shoots per explant data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3B mean number of shoot (table vs figure representation, parameter name changed). = 4 data points identical
Table II Ahmad et al. 2008 KinxNAA mean shoot length data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3C (table vs figure representation). = 4 data points identical
Total = 12 identical data points

Table III data Ahmad et al. 2008 (IBA and NAA), 4 concentrations each + control data identical to Table 1 data of Ahmad and Anis 2011 for three parameters: % Rooting, number of shoots/root (and Mean number of roots), mean root length.
Total = 27 identical data points

Grand total of 90 identical data points in Ahmad et al. 2008 and Ahmad and Anis 2011.

Concern 2:
“Few attempts for direct in vitro regeneration of Vitex negundo have been made earlier (Sahoo and Chand 1998; Chandramu et al. 2003b; Rani and Nair 2006; Ahmad and Anis 2007a).” Comment made in Ahmad and Anis 2011 EJFR p 136. But this comment is extremely misleading because the basal protocol for the 2011 paper was based almost exclusively on an identical protocol published in 2007. No other mention of the 2007 paper occurs throughout the whole manuscript.

Concern 3:
How can 2 µM IBA form 4.6 roots/shoot in Ahmad et al. 2008 but 4.6 at 200 µM IBA in Ahmad and Anis 2007? In other words, a 10-fold difference in concentration of the exact same auxin gives the exact same root number? Given the fluctuations shown in the values of this growth parameter caused by other concentrations of this same auxin, this result is simply impossible.

These concerns would immediately cause doubt about the claims made in paper 4:
Naseem Ahmad 1, Md Imran Khan 1, Sarfaraz Ahmed 2, Saad Bin Javed 1, Mohammad Faisal 3, Mohammad Anis 1, Sumbul Rehman 4, Syed Mohammad Umair 4. 2013. Change in total phenolic content and antibacterial activity in regenerants of Vitex negundo L. Acta Physiologiae Plantarum 35(3): 791–800.
1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
2. Natural Product Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202 002, India
3. Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
4. Department of Ilmul Advia, Faculty of Unani Medicine, Aligarh Muslim University, Aligarh, 202 002, India
http://link.springer.com/article/10.1007/s11738-012-1120-x
DOI: 10.1007/s11738-012-1120-x (PubPeer cannot read this DOI)
Publisher: Springer-Verlag

Funding
Paper 1: “The award of a Senior Research Fellowship to N A by the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, is greatly acknowledged. Research support from The Department of Science and Technology (Govt. of India) New Delhi under the FIST-DST Programme, is also acknowledged.”
Paper 2: “Financial assistance, in the form of a Senior Research Fellowship to N. A. from the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, is gratefully acknowledged. We also acknowledge the Department of Science & Technology, (Government of India), New Delhi for rendering assistance to the Department under DST-FIST Programme 2005.”
Paper 3: “N. Ahmad is thankful to the Department of Science and Technology (DST), Govt. of India, New Delhi, for its award of a SERC Fast Track Young Scientist Scheme (SR/FT/LS-014/2009). The authors acknowledge the Department of Science and Technology (DST) and the University Grants Commission (UGC), Govt. of India, New Delhi, for rendering assistance to the Department under DST-FIST (2005) and UGC-DRS (2009) programmes, respectively.”
Paper 4: “The award of DST, Young Scientist (SR/FT/LS-014/2009) Scheme to Naseem Ahmad by the Department of Science and Technology (DST), Government of India, New Delhi, is greatly acknowledged. Research support from the Department of Science and Technology (Govt. of India) New Delhi under the DST-FIST (2011) and UGC-SAP (2009) Programme, is also acknowledged.”

Incidentally, Prof. Mohammad Anis has been the subject of another large query regarding Egyptian Myrobalan Tree (Balanites aegyptiaca Del.) with 4 PubPeer entries:
https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878　
https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879　
https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880　

The authors, who have been contacted, are kindly requested to address these issues publically and to correct the literature.

This case has a PubPeer entry for paper 3:
https://pubpeer.com/publications/228844D355BBACF479209E2D15459E#fb17547

Reply
1. Vitex negundo concerns says:
  
  December 1, 2014 at 1:51 pm
  
  Erratum: Concern 3 should read 100-fold instead of 10-fold.
  
  Reply
  1. Vitex negundo concerns says:
    
    December 3, 2014 at 3:36 pm
    
    Update. A formal response has been received from the authors and AMU.
    
    Naseem Ahmad has responded to an anonymous request to comment on this case but do not understand the concept of anonymity. What the authors also do not appear to understand is that this is a public case that affects the entire plant science literature and all plant scientists, and may have wider consequences and repercussions on academic integrity in plant science journals. Rather than skirting the issue, surely it is best to address them publically at PubPeer as well as directly with the journals, journal editors and publishers? Public accountability for one’s research and publications is not a matter of negotiation, it is a matter of scientific responsibility.
    
    12/3/14 at 6:02 PM “Thanks for your mail dated 30.11.2014 on the subject of “data duplication” in our papers of Vitex negundo. I appreciate your concern about the issue of “data duplication”. As you are working for a noble cause, therefore it should be in a proper way. Comments were raised by an unregistered person on the public platform. Therefore, I request you please register yourself properly on this blog with your correct name, designation, affiliation, email, contact numbers and most importantly your area of expertise as it is most important for understanding the findings of the research. I assure you that I will answer each of your queries one by one on any public platform, if you comply.”
    
    Reply
Of mice and maize says:

December 3, 2014 at 4:32 am

A startling development in maize genomic research. The story just broke at PubPeer:
https://pubpeer.com/publications/89407FFD3DC7905BA81AA548B3FD1B#fb17718
How does one confuse a rat with corn? This is astonishing. If Diego at PubPeer has intel, he should share. Also, he should indicate exactly which GenBank entries are being removed. How will this affect papers that used, relied on, or referenced those incorrect sequences? The authors are strongly encouraged to explain how mice were confused with maize.

Reply
1. herr doktor bimler says:
  
  December 3, 2014 at 6:07 pm
  
  Obviously a misspelling. Someone confused a rat with a maze.
  
  Reply
Parthenium hysterophorus queries says:

December 5, 2014 at 2:20 am

3 Biotech July 2011, Volume 1, Issue 1, pp 1-9,
Open Access. Date: 27 Apr 2011
Harmful and beneficial aspects of Parthenium hysterophorus: an update
Seema Patel
Department of Biotechnology, Lovely Professional University, Jalandhar, 144402, Punjab, India
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339593/
http://link.springer.com/journal/13205/1/1/page/1
http://link.springer.com/article/10.1007/s13205-011-0007-7
http://download.springer.com/static/pdf/779/art%253A10.1007%252Fs13205-011-0007-7.pdf?auth66=1417733929_94de5d29a6f9c08fe755facddb75451b&ext=.pdf
DOI: 10.1007/s13205-011-0007-7
Publisher: Springer-Verlag

Concerns about the source of images used in this review.

Acknowledgements: “The author acknowledges the internet website http://www.wikipedia.org/ for providing with the figures.” If any of the key-words for these images are entered into Wikipedia, these images do not appear. What then is the source. Some web-trawling revealed the following (already back in July, 2013).

NONE OF THESE FIGURES, EITHER IN THE TEXT, FIGURE LEGENDS OR ANYWHERE WITHIN THE MANUSCRIPT, INDICATE ANY OF THE SOURCES THAT MAY BE THE ORIGINAL SOURCES OF THE FIGURES.

Figure 1A of Parthenium hysterophorus from http://www.ecoport.org ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

Figure 1B: The world map. From the Weed Science Society of Pakistan (www.wssp.org.pk) ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

The styles of the chemical structures in Figure 2 are very different, some stretched, some perfect, some blurred. It is thus likely that the source is different and that the author did not use software like ChemDraw to design each compound. What then is the source(s) of these compound images?

Figure 3A: photo of Zygogramma bicolorata from http://www.texasento.net ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

Figure 3B: photo of Epiblema strenuana appears to be taken from the Moth Photographer’s Group of the Mississippi Entomological Museum at MSU (http://mothphotographersgroup.msstate.edu/species.php?hodges=3172), then squashed. The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

Figure 3C: photo of Listronotus setosipennis from old.padil.gov.au ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

Figure 3D: photo of Carmenta ithacae from http://www.discoverlife.org ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

Other concerns:
a) The entire first paragraph of the Introduction lists many facts, but not supported by a single reference.
b) Is it usual for a journal to only accept reviews if the authors are not apparent professionals or specialists in their fields of study? The name of Dr. Patel cannot be found in the reference list. Is Dr. Patel qualified to write a review on this noxious weed?
c) The review itself fails to address the literature accurately, making this review incomplete. Why were other reviews not referenced, or mentioned, and why did the “peer” reviewers and editors not detect this issue, as well as the image concerns during peer review? A review by the Australian Government in 2001 (http://www.daff.qld.gov.au/documents/Biosecurity_EnvironmentalPests/IPA-Parthenium-Nsplan.pdf) is also not mentioned. A review by Javaid, A. and T. Anjum (2005). Parthenium hysterophorus L. – a noxious alien weed. Pak. J. Weed Sci. Res. 11: 1-6 was not mentioned. A review by Javaid, A., S. Shafique and S. Shafique. (2006). Parthenium weed – an emerging threat to plant biodiversity in Pakistan. Int. J. Biol. Biotech. 3(3): 619-622 was not mentioned. A paper by Javaid, A., T. Anjum and R. Bajwa (2005). Biological control of Parthenium II: Allelopathic effect of Desmostachya bipinnata on distribution and early seedling growth of Parthenium hysterophorus L. Int. J. Biol. Biotech. 2: 459-463 was not mentioned. A review by VR Paudel in 2009 http://nepjol.info/index.php/BOTOR/article/viewFile/2915/2954 is not mentioned. A review by Ramamoorthy, K.; Radhamani, S.; Amanullah, M. M.; Subbian, P. (Biology and integrated management of congress grass (Parthenium hysterophorus L.) – a review.) Green Farming 2009 Vol. 2 No. 10 pp. 702-706 is also not referenced or mentioned. An important study in 2010 by Shreshtha et al was not referenced: http://www.forestrynepal.org/images/publications/2010_Shrestha%20et%20al_Fortuitous%20biocontrol%20of%20Parthenium.pdf.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/28076B5AAF504B0E3720D9F53BB159#fb17924

Reply
Kailash C. Bansal query says:

December 6, 2014 at 8:10 pm

Transgenic or GM crops has seen a fair bit of scandal and controversy in India. One of those as-yet unclarified scandals involves Dr. Kailash C Bansal, who is a Professor listed on the Scientific Advisory Committee at the National Institute of Plant Genome Research (NIPGR) [1].

However, he is listed on this 2014 paper on transgenic chickpea as being at the National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India [2, 3]:
Maneesha S. Saxena, Deepak Bajaj, Alice Kujur, Shouvik Das, Saurabh Badoni, Vinod Kumar, Mohar Singh, Kailash C. Bansal, Akhilesh K. Tyagi, Swarup K. Parida (2014) Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea. PLoS ONE 9(9): e107484. DOI: 10.1371/journal.pone.0107484

These facts in themselves might not be newsworthy or even strange to the untrained eye. However, given the fact that two news stories emerged in 2012 of concern [4, 5], claiming the following: “The scientist, Dr Kailash C. Bansal, was given the prestigious Rafi Ahmed Kidwai Award for “outstanding research” in transgenic crops for the year 2007-2008 on the basis of claims that he had “filed three patents for novel gene discovery”, including one on transgenic brinjal. In reality, no such patent application or patent existed when he was given the award on July 16, 2009. Documents obtained under RTI and investigation made by Mail Today show that no patent application had been filed for brinjal discovery in October 2008 when Bansal was nominated for the award or in July 2009 when he was presented the award. Bansal holds top positions in the research hierarchy of the Indian Council of Agriculture Research (ICAR). When he got the Kidwai award he was a professor at the National Research Centre on Plant Biotechnology (NRCPB) and presided over ICAR’s transgenic research programme involving about 20 institutes all over the country and five-year budget exceeding Rs.135 core. Top brass in ICAR have not only ignored the patent goof-up but has also rewarded Bansal by making him director of India’s plant gene bank, officially known as National Bureau of Plant Genetic Resources.”

This then makes the listing in the PLOS ONE paper of great significance because apparently an unresolved and serious issue that led to his rise to the director of that institute, and which also allowed him to obtain a prestigious science prize, remains unresolved. Is this then not a serious conflict of interest that was not disclosed to PLOS ONE when the paper was published? This is somewhat odd, given the fact that the PLOS ONE paper states, under competing interests: “The authors have declared that no competing interests exist.”

A very recent chapter on the topic of the controversy, transgenic brinjal (British for eggplant, or Solanum melongena L.), was published in a Springer Science + Business Medium book [6]:
Chloroplast Biotechnology Methods in Molecular Biology Volume 1132, 2014, pp 305-316
Date: 03 Feb 2014; DOI: 10.1007/978-1-62703-995-6_19
Plastid Transformation in Eggplant
Kailash C. Bansal, Ajay K. Singh
In this paper, Dr. Bansal lists himself as being at the National Bureau of Plant Genetic Resources (ICAR), New Delhi, India.

This is odd. Why does Dr. Bansal list two very different institutional addresses for two different papers published at almost the exact same time? There are three possibilities here:
a) He works at both, but failed to disclose the second working position in both papers, which would constitute an important omission of information, or of a COI.
b) He only works at one, but has used another address inappropriately.
c) None of the above two.

In that chapter, a reference to a 2010 paper [7] might lead to clues on the genetic brinjal the story is referring to:
Singh A, Verma SS, Bansal KC (2010) Plastid transformation in eggplant (Solanum melongena L.). Transgenic Res 19:113–119:
Strangely, there is no mention of a patent in either paper.
At that time, Dr. Bansal was listed as being at the National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India.

To complicate the case a notch further, the news paper stories [4, 5] state, referring to Dr. Bansal: “His boss in ICAR, Dr Swapan K. Datta, also echoed the same line, “ICAR has taken official response on this matter. Dr Bansal is still working within ICAR”. He did not reply when asked specifically what the official stand of the council was.”

Dr. Datta, Dr. Bansal’s boss, is a member of the editor board of Taylor and Francis’ GM Crops and Food.

Despite wide-spread calls for the resignation of Dr. Bansal [9], he appears to retain his position (as the head?) at NBPGR. That decision appears to have been heavily influenced by politics, as the article indicates: “Stressing on the need to introduce GM crops, the Centre has said it would not be able to meet the First Millennium Development Goal of cutting the proportion of hungry people by half with such technologies. A moratorium of 10 years would put the country 20 years back in scientific research, it added.”

It would be important to get a full clarification of this case since there has been a burst of papers in 2014 with Dr. Bansal as co-author, thus any unresolved issues could have an influence on a wide range of individuals.

[1] http://www.nipgr.res.in/about_us/committees.php#governing
[2] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107484
[3] http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0107484&representation=PDF
Received May 1, 2014; Accepted August 11, 2014; Published September 15, 2014
[4] http://indiatoday.intoday.in/story/genetically-modified-food-crops-researcher-kailash-c-bansal-grabbed-rafi-ahmed-kidwai-award-for-patent-claim/1/226654.html
[5] http://www.dailymail.co.uk/indiahome/indianews/article-2224489/Top-GM-food-scientist-false-patent-claim.html
[6] http://link.springer.com/protocol/10.1007/978-1-62703-995-6_19
[7] http://link.springer.com/article/10.1007%2Fs11248-009-9290-z
[8] http://indiatoday.intoday.in/story/association-of-scientists-activists-and-farmers-demand-removal-of-top-gm-researcher/1/228522.html

Reply
1. Kailash C. Bansal query says:
  
  December 7, 2014 at 10:58 pm
  
  There are now two PubPeer entries for this query:
  PLOS ONE paper:
  https://pubpeer.com/publications/A11CF63AF8871AD3885CC1529C8F2C#fb18082
  Springer book chapter:
  https://pubpeer.com/publications/9F685A7C892EA3302AC6E5CC72C410#fb18081
  
  Reply
Cymbidium CryoLetters concern says:

December 8, 2014 at 3:21 pm

Concerns about this paper were linked on PubPeer to other papers of concern by Prof. Pramod Tandon, because this paper does not have a DOI:
https://pubpeer.com/publications/8448D8CF8D1F69936CDC1A35D9BBCC
https://pubpeer.com/publications/1CE3174266AF780AD6AB8EC0ABADE1
https://pubpeer.com/publications/C7D8632E7ED6D6F852A93D9A516A49

It should be noted that Prof. Tandon has still not come forward with a suitable public explanation for these concerns in his publications, and we would hope that he will address the concerns about his Dendrobium and Cymbidium papers. He is also called upon to release the original data-sets and statistical analyses that correspond to this Cymbidium paper.

Gogoi K, Kumaria S, Tandon P (2012) A comparative study of vitrification and encapsulation-vitrification for cryopreservation of protocorms of Cymbidium eburneum L., a threatened and vulnerable orchid of India. CryoLetters 33:443–452.
http://www.cryoletters.org/Abstracts/vol__33_6_2012.htm
http://www.cryoletters.org/Abstracts/vol__33_6_2012.htm#443
Plant Biotechnology Laboratory, Department of Botany, North-Eastern Hill University, Shillong 793 022, India.
Funding: UPE–Biosciences programme, University Grants Commission, New Delhi, India

There is concern about this manuscript published in CryoLetters in 2012. An anonymous report was made to the senior management of the company that publishes this journal, CryoLetters LLP, and approximately half a dozen editors of the editor board. That report was submitted on the 9th August, 2013. More than one year later, not a single note, erratum, expression of concern, or retraction appears which itself is of concern. These issues affect the plant science community and thus deserve to be discussed openly, in public, since the authors and the publisher, and its editors, are not forthcoming. PubPeer has thus been selected for this purpose.

Concerns involve primarily incomplete experimental design, and incorrect of flawed statistical analyses:
a) The first sentence of the Introduction makes factual claims but is not supported by any literature.
b) Characterization of a plant should never be made in the title (i.e., the threatened and vulnerable status).
c) “Due to loss of habitats and heavy anthropogenic pressure for commercial purposes, the species is on the verge of extinction. According to the Red Data Book of Plants of India, C. eburneum is regarded as vulnerable and hence this urgently calls for its conservation (25).” Verge of extinction and vulnerable are completely different concepts in conservation, and are very distant from each other in terms of how close a species is to extinction. Was the former claim made by the authors to exaggerate the status of the plant and maximize the chance of acceptance?
d) “Ex situ conservation of endangered and threatened plants through in vitro cultured plants also requires high maintenance costs and there is a risk of somaclonal variation and genetic instability, due to continuous subculturing of the in vitro raised plantlets.” Claims are made but no literature support is provided.
e) “Encapsulation-vitrification is a combination of both vitrification and encapsulation-dehydration methods. For encapsulation-vitrification, explants are encapsulated in alginate beads and then submitted to highly concentrated vitrification solutions. Encapsulation-vitrification combines advantages of these two techniques, the rapidity of implementation for vitrification and the ease of manipulation of explants for encapsulation.” Claims are made but no literature support is provided.
f) Materials and Methods, Plant material: Why are protocorms used? Protocorms are seed-derived and thus are not clonal material. Therefore, the use of this tissue is inherently flawed in that variation caused by seed-derived material (i.e., protocorms) may also influence the response to treatments and thus the quantitative outcome of data. The idea material that should have been used would have been clonal protocorm-like bodies (PLBs) derived from protocorms. The use of clonal PLBs would have eliminated the inherent variation caused by the biological material.
g) Materials and Methods, Plant material: “agar-gelled Murashige and Skoog medium”. The concentration of agar and the commercial source are not clearly indicated. How can this step be repeated?
h) Materials and Methods, Plant material: “were used for cryopreservation experiments (Fig. 5 A-B).” Why is Figure 5 mentioned first in the text and not Figure 1?
i) Materials and Methods, Plant material: The authors fail to describe the following about the plant material: a) the source of the seeds (commercial or wild) and if the protocorms are of the same size (size in fact not defined, only the age); b) if wild plants, the exact location from which plants were collected and permission from Indian authorities with license numbers to collect red-listed rare orchid plants from the wild; c) the growth conditions of the protocorms during asymbiotic seed germination are totally ignored, including temperature, light vs dark, relative humidity. Is the reader supposed to guess the conditions? How are other scientists supposed to repeat this protocol?
j) Materials and Methods, Cryopreservation procedure: A) “12 h light/12 h dark photoperiod” is incorrect, it should be a 12-h photoperiod (the use of the words light and dark and photoperiod make the words light and dark redundant). Exact same problem in the next section of the M&M. B) “60 µmol m-2 s-1 light intensity” is incorrect. Light intensity would be in lux. µmol m-2 s-1 refers to photosynthetic photon flux density or PPFD. C) The city and country of the cryovials maker is not indicated. D) The authors fail to disclose the commercial source of any of their equipment and chemicals (which is an important aspect for these companies). E) Why is DMSO abbreviation defined if it is not used again? F) “different time periods (5 – 60 min)”. This information is useless. The exact time period tested should have been indicated. G) “different concentrations of sucrose (0.0 – 0.7 M)” . This information is useless. The exact sucrose concentrations tested should have been indicated.
k) Materials and Methods, Protocorm survival and plant regeneration: A) “Petri plates”. The correct term is Petri dishes. The size, diameter and depth as well as the maker are not defined. B) “provided by cool fluorescent tubes”. The maker of the light bulbs, the strength of the bulbs in Watts, and the distance from cultures have all been omitted. These are all important aspects of tissue culture that can affect the effectiveness of the culture. C) “after 8 weeks in culture” unclear whether this is over and above the previous 6 weeks in culture, so in fact, 14 weeks after the beginning of culture. These ambiguities do not make this protocol repeatable.
l) Materials and Methods, Statistical analyses: A) The randomness or design of the experiment were not indicated. B) “Statistical analysis was done by ANOVA at P<0.05 and the means compared using Tukey’s test” There are two serious inaccuracies and incorrect description of the statistics. ANOVA is not a statistical test. ANOVA is used merely to separate the means. Tukey’s test does not exist. It is Tukey’s multiple range test. Where is the reference for the test? C) “PC version Origin 7.0 Northampton, MA, USA).” Something sounds extremely wrong here. It sounds as if the authors are actually describing Windows version 2007, but have represented it incorrectly as if it were a statistical software. What is the name of the statistical software? Who is the manufacturer of this software? This information is absolutely unclear. If statistical analyses are described so incorrectly/inaccurately, what confidence is there that the analyses are actually accurate? The answer may lie in the next three points.
m) Results: Fig 1. For Vit treatments, the stats analyses appear to be sound (i.e. highest value represented with a, lowest by b), but when we observe the E-V treatments, the statistical analyses are completely incorrect. The highest value is represented by c, the intermediate value by a, and the lowest value by c. The statistical analysis is completely wrong. Therefore, any conclusion made in the text based on these statistical analyses is by association debatable. The first incorrect claim comes in this statement “When using the vitrification technique, the lower sucrose concentrations (0.1 – 0.3 M) employed during preculture led to higher regeneration of non-cryopreserved protocorms, with an optimum of 60% for 0.2 M sucrose (Fig. 1). Higher sucrose concentrations (0.4 – 0.8 M) produced lower regeneration percentages, between 34 and 20%.” In fact, the 0.3 M sucrose treatment is significantly similar to 0.1 and 0.2 and also to 0.4-0.8. That is why it is represented by the letters ab. The comment made is incorrect and thus misleading. The next statement is even more serious: “By contrast, with the encapsulation-vitrification technique, higher sucrose concentrations (0.7 – 0.8 M) in the preculture medium gave higher regeneration, with an optimum of 70% for 0.7 M sucrose. Lower sucrose concentrations (0.1 – 0.5 M) produced lower regeneration, between 20 and 34%. Intermediate regeneration (54 %) was achieved after preculture with 0.6 M sucrose.” This entire conclusion is totally invalid since the statistical analyses are incorrect, the representation of the statistical analyses is incorrect, and thus any conclusions drawn from incorrect statistics are also automatically incorrect.
n) Results: Fig 1. On the Y-axis, the parameter measured is regeneration. What exactly is regeneration? Is it callus formation? PLB production? Protocorm growth? Leaf formation? Plantlet growth? The term is so broad that it makes the parameter being measured totally redundant. The entire figure and what it actually teaches the reader is useless because “regeneration” is not defined.
o) Results: Fig 2 and 4. The statistics representation and/or analyses of both vitrification and E-V are completely incorrect with exactly the same problems as listed in m) for the E-V statistics. Consequently, all text in the results related to this figure is invalid.
p) Results: Fig 2, 3, 4. The same problem related to the term Regeneration (%) on the Y-axis as found for Fig. 1 exists (see n) above).
q) Results: Fig 1, 2, 3 and 4 legends. “Means followed by the same letter are not significantly different according to Tukeys’s test”. In fact, an extremely important aspect has been omitted from this description: the fact that analyses were not conducted across treatments. Therefore, the correct way in which the figure legends should have read would have been: Means followed by the same letter within each treatment are not significantly different according to Tukey’s multiple range test. Within each treatment refers to vitrification and encapsulation-vitrification. Incidentally, it should be Tukey’s and not Tukeys’s.
r) Discussion: this section was not analysed since it lost its value in the light of the incorrect statistical analyses of the Results section. However, several very important key orchid cryopreservation studies were omitted.
s) Conclusions: “This is the first report for long-term conservation of protocorms of” This is a false statement. The M&M section clearly states the storage period “These cryocanes were rapidly dipped in a 35 1 narrow neck liquid nitrogen (LN) storage Dewar-flask and stored at -196°C for 1 h.” 1 hour is NOT long-term.

These errors and oversight then also call into question the quality of the peer review at CryoLetters.

Why has no erratum, expression of concern or retraction not appeared on the CryoLetters web-site to alert readers?

Reply
Welbaum and Tay query says:

December 8, 2014 at 9:26 pm

AH paper
Mweetwa, A.M., Welbaum, G.E. and Tay, D. 2008. A PRELIMINARY INVESTIGATION ON THE EFFECT OF SEED PHYSIOLOGICAL STAGE, CONCENTRATION AND DURATION OF EXPOSURE TO CALCIUM HYPOCHLORITE ON IN VITRO GERMINABILITY AND SEEDLING DEVELOPMENT OF PHALAENOPSIS AMABILIS ORCHIDS. Acta Hort. (ISHS) 782:99-106.
http://www.actahort.org/books/782/782_9.htm
No DOI.
Copyright holder: International Society for Horticultural Science
No received, revised or publication dates.
Financial support: J. Harper and the Mid-American Orchid Congress

SH paper
Scientia Horticulturae Volume 117, Issue 3, 23 July 2008, Pages 257–262
Effects of development, temperature, and calcium hypochlorite treatment on in vitro germinability of Phalaenopsis seeds
A.M. Mweetwa, Gregory E. Welbaum, David Tay
Mweetwa, Welbaum: Department of Horticulture, Saunders Hall Virginia Tech, Blacksburg, VA 24061, USA
Tay: USDA-ARS, Ornamental Plant Germplasm Center, 670 Tharp Street, The Ohio State University, Columbus, OH 43210, USA
http://www.sciencedirect.com/science/article/pii/S0304423808001015
DOI: 10.1016/j.scienta.2008.03.035
Copyright holder: Elsevier Ltd.
Received 17 August 2007; Received in revised form 21 March 2008; Accepted 27 March 2008
Financial support: J. Harper and the Mid-American Orchid Congress

The following is duplicated:
A) Large tracts of text, for example the first few paragraphs of the introduction and most of the methodology, in both manuscripts.
B) Table 1 of both papers is identical.
C) Fig. 1 of both papers is identical.
D) Fig. 2 of both papers is identical.
E) Fig. 3 of AH is identical to Fig. 5 of SH.
F) Fig. 4 of AH is identical to Fig. 6 of SH.
G) Neither paper references the other nor indicates the existence of the other.

There is a PubPeer entry associated with this case:
https://pubpeer.com/publications/CA87E4627D35A037995FC65384B8E2#fb18138

Reply
ISHS query says:

December 9, 2014 at 5:10 am

Professor Pierre Debergh, University of Gent, Belgium
https://biblio.ugent.be/person/801000185165
Now deceased following communications with the University of Ghent since October 24, 2013.

The author is thus not available for comment, nor can his co-authors be tracked. The academic responsibility for this paper thus should lie squarely on the shoulders of the International Society for Horticultural Science (ISHS).

Hamidah et al. (1995, 1997a, 1997b). The Hamidah et al. (1997a) paper describes a protocol for the induction of somatic embryos from leaves of A. scherzerianum. The authors determine that 18 µM 2,4-dichlorophenoxyacetic acid and a high sucrose concentration (6%) are the ideal conditions. However, 6% is not tested in the protocol and in fact, the ideal carbohydrate concentration is not clear, although in Hamidah et al. (1997b), the authors claim it to be 2% sucrose + 4% fructose, which corresponds to medium B in Table 1 of Hamidah et al. (1997a). It is unclear why so many PGR combinations in Table 1 were only tested on medium A, and not medium B or C, and it is not clear why the authors made this statement on p. 190: “Medium A was used in the beginning; based on literature review and preliminary experiments (not presented)”. A search of the literature in fact reveals that the Hamidah et al. (1995) paper already reported the data of the 1997a paper. Thus, the 1997a paper is a partial data duplication of the 1995 paper. The 1997b paper has no data, no figures and reports the exact same conclusions about the results as the 1995 and 1997a papers, making it a duplicate and a redundant paper in the anthurium literature. The 1997b paper only has two pages, with absolutely no figures to prove somatic embryogenesis or secondary somatic embryogenesis, and no data or tables to prove absolutely any claims made in the text regarding somatic embryogenesis, secondary somatic embryogenesis or in vitro regeneration. In the 1997b paper, the authors claim to use media that are original, but which are not since the exact same parameters and ideal medium concentrations, related to basal medium, the level of 2,4-D and the very specific concentration of 4% sucrose and 2% glucose are not original ideas, the latter having already been devised by Kuehnle et al. (1992) while the ideal method was simultaneously reported in Hamidah et al. (1997a; PCTOC; M&M section + p. 193).

References:

Hamidah M, Abdul Karim AG, Debergh PC (1995) Somatic embryogenesis of Anthurium scherzerianum Schott. Med. Fac. Landbouw, Univ. Ghent 60/4a: 1671–1673

Hamidah Musa (1), Abdul Ghani Abdul Karim (2), Pierre Debergh (1) (1997a) Somatic embryogenesis and plant regeneration in Anthurium scherzerianum. Plant Cell, Tissue and Organ Culture 48: 189–193.
1. Dept. Plant Production – Horticulture, University Gent, Coupure Links 653, B9000, Gent, Belgium
2. Dept. Botany, Faculty of life Sciences, National University of Malaysia, 43600, Bangi, Selangor, Malaysia
Received 12 June 1995; accepted in revised form 14 March 1997.
http://link.springer.com/article/10.1023%2FA%3A1005834131478
DOI: 10.1023/A:1005834131478
Publisher: Kluwer Academic Publishers
Copyright holder: Springer Science + Business Medium

Hamidah, M., Debergh, P., Ghani, A. and Karim, A. 1997b. CYCLIC SOMATIC EMBRYOGENESIS OF ANTHURIUM SCHERZERIANUM SCHOTT. Acta Hort. (ISHS) 447:123-124
http://www.actahort.org/books/447/447_15.htm
No DOI, and is thus linked to the 1997a paper by the authors on PubPeer.

Kuehnle AR, Chen F & Sugii N (1992) Somatic embryogenesis and plant regeneration in Anthurium andraeanum hybrids. Plant Cell Rep. 11: 438–442

The Acta Horticulturae instructions for authors (http://www.ishs.org/authors) clearly states that “Submission of a manuscript implies: that the work described has not been published before” and “Important elements of the publisher’s role in the scientific communication process are reviewing, recognition and consistent quality assurance.” Online http://www.ishs.org/publications, it is stated that “Acta Horticulturae (ISSN 0567-7572) is a peer reviewed series”. Finally, on the Q&A page, in response to the question “Is Acta Horticulturae a sound peer reviewed journal?” http://www.ishs.org/faq/acta-horticulturae-sound-peer-reviewed-journal, the ISHS states the following: “Acta Horticulturae exclusively contains research which has been presented at an ISHS symposium or at the ISHS Congress”. “Final contributions are submitted by the Editor(s) to the Editorial Board for scientific review.” “Each symposium has an Editorial Board. The Editorial Board includes the most eminent researchers in that particular field of research and this to guarantee a consistent quality of the scientific review process.” “Acta Horticulturae is a sound scientifically reviewed proceedings series.”

The two editors of this volume of Acta Horticulturae (http://www.actahort.org/books/447/index.htm), Prof. Arie Altman, and Prof. Meira Ziv, the management of the ISHS, as well as the University of Gent have yet to correct the literature, even 14 months after a formal report.

There is a PubPeer entry for this case:
https://pubpeer.com/publications/773785209C305926E01A2F28265C3F#fb18158

Reply
Cymbidium stealth retraction says:

December 10, 2014 at 12:22 pm

The original
Naruemol Kaewjampa, Kazuhiko Shimasaki, Syeda Jabun Nahar (June, 2012) Hyaluronic Acid Can be a New Plant Growth Regulator for Hybrid Cymbidium Micropropagation. Plant Tissue Culture and Biotechnology 22(1): 59-64
The United Graduate School of Agriculutral Sciences, Ehime Unversity, 3‐5‐7 Tarumi, Matsuyama, Ehime, 790‐8556 Japan
DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11261
http://www.banglajol.info/index.php/PTCB/article/view/11261
http://www.baptcb.org/ptc/Full_article/ptc22_1_07.pdf (open access)

The duplicate
Full Length Research Paper (was open access)
Naremol Kaewjampa 1, Kazuhiko Shimasaki 2, Nahar Syeda Jabun 1 (2013) Hyaluronic acid can be an alternative plant growth regulator for hybrid Cymbidium micropropagation. African Journal of Agricultural Research Vol. 8(28), pp. 3731-3734
1The United Graduate School of Agriculutral Sciences, Ehime Unversity, 3-5-7 Tarumi, Matsuyama, Ehime,
790-8556 Japan.
2Faculty of Agricuture, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502 Japan.
DOI: 10.5897/AJAR12.564
ISSN 1991-637X ©2013 Academic Journals*
http://www.academicjournals.org/AJAR
Accepted 24 July, 2013
The original site where the paper existed:
http://www.academicjournals.org/journal/AJAR/edition/26_July,_2013

The duplicate paper was retracted, and not a trace can be found either on the publisher’s web-site, the journal web-site or on any Google or other internet search engines. In other words, a stealth retraction.

*Incidentally, the duplicated paper was published by Academic Journals, a publisher listed on Beall’s list of predatory open access journals:
http://scholarlyoa.com/publishers/

This case has a PubPeer entry:
https://pubpeer.com/publications/8F0B31D4CDD2BF8EFB531CB41536B7#fb18279

The authors have another paper with concerns listed at PubPeer:
https://pubpeer.com/publications/44D816438CDBCF351D11B405B824BE#fb17832

Reply
Anthurium query says:

December 11, 2014 at 12:33 am

Beyramizade and Azadi (2008) vs Beyramizade et al. (2008) (Iran and Japan).
1) Duplicate figure (Fig. 1A of the latter paper the same as top right figure on page 184 of the former paper) and methodology (i.e., response of leaves to 2,4-D and BA, and callus and shoot regeneration potential). There is no statement that indicates that the same figure was used, or due attribution.
2) Strangely, different results are presented despite the exact same cultivar and methodology. What does this suggest: an irreproducible protocol, or worse?
3) In the latter study, authors claim somatic embryogenesis but show absolutely no proof of somatic embryos through scanning electron microscopy, cross sections showing leaf and root tissue connectivity, only some embryo-like structures, at best (Fig. 2B).
4) “Leaf plate explants” used. What are these?
5) No financial assistance was acknowledged in either paper.

Beyramizade E, Azadi P. Effect of growth regulators on shoot formation of Anthurium andraeanum Lind. Pajouhesh & Sazandegi 2008;76:179-184. (in Farsi with English abstract)
Department of Biotechnology, National Research Center of Ornamental Plants, Mahallat, Iran
http://en.journals.sid.ir/ViewPaper.aspx?ID=119133

Beyramizade E, Azadi P, Mii M. Optimization of factors affecting organogenesis and somatic embryogenesis of Anthurium andraeanum Lind. Tera. Propag Ornament Plant 2008;8:198-203.
Masahiro Mii: Laboratory of Plant Cell Technology, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo City, Chiba 271-8510, Japan
http://www.journal-pop.org/2008_8_4_198-203.html
http://journal-pop.org/References/Vol_8_4(198-203).pdf

About Mii:
http://www.researchgate.net/profile/Masahiro_Mii
http://academic.research.microsoft.com/Author/27549444/masahiro-mii
A legend of sorts: http://ajw.asahi.com/article/behind_news/social_affairs/AJ201203220005

About Azadi:
Azadi is the Director General of National Institute of Ornamental Plants (NIOP), Mahallat, Iran, and also the President of Iranian society for ornamental plants (ISOP) (www.isop.ir):
http://www.isopcongress.ir/Files/CurriculumVitaeAzadi2014.pdf

Azadi and Mii have been the topic of potential figure duplication at PubPeer (without any public responses, or correction of the literature):
https://pubpeer.com/publications/B3161A9A5157B83F1A08506CD22966#fb16666
https://pubpeer.com/publications/5740E043753A1CEC14D4494FD2EAA8#fb16667

Listed at PubPeer, together with another query about the same authors:
https://pubpeer.com/publications/5740E043753A1CEC14D4494FD2EAA8#fb18313

Reply
Clerodendrum indicum query says:

December 11, 2014 at 12:40 am

Anindita Mukherjee (a), Abhijit Bandyopadhyay (a), Sikha Dutta (a), Sukalyan Basu (b) (2013) Phytoaccumulation of iron by callus tissue of Clerodendrum indicum (L), Chemistry and Ecology, 29:6, 564-571.
DOI: 10.1080/02757540.2013.779681
a) Department of Botany, The University of Burdwan, Burdwan 713104, India
b) Department of Chemistry, The University of Burdwan, Burdwan 713104, India
Received 9 April 2012; final version received 21 February 2013
http://www.tandfonline.com/doi/full/10.1080/02757540.2013.779681#.VIkozJVxnIU
http://www.tandfonline.com/doi/pdf/10.1080/02757540.2013.779681 (open access)

The authors, in their 2013 paper published in Chemistry and Ecology (Taylor and Francis), report on a methodology in sections 2-1 through to 2.3, on the callus induction of Clerodendrum indicum. However, that methodology is not original, and was already published, by the same group of authors, in 2012, as follows.

Anindita Mukherjee, Sikha Dutta, Abhijit Bandyopadhyay (2012) Micropropagation of Clerodendrum indicum (L.)Kuntze: An Unexplored Medicinal Plant. International Journal of Pharma and Bio Sciences Oct; 3(4): (B) 659-668 (paper No. 74, open access)
http://www.ijpbs.net/archive-issue.php?issueid=20 (click on Biological Science)
No DOI.

The authors fail to reference those important results and source of methodology from manuscript published in 2012. The text and the reference also fail to indicate the existence of this prior publication. This is a very important, and serious, omission.

Could the authors, editors, and publisher kindly take the necessary steps to correct the literature so that this very important information is indicated (e.g., an erratum).

Incidentally, the 2012 journal is listed as a “predatory” stand-alone journal by Jeffrey Beall:
http://scholarlyoa.com/individual-journals/

There is a PubPeer entry for this case:
https://pubpeer.com/publications/9260619E6F61AA7D51ED7D0231C2BE#fb18324

Reply
Jaime A. Teixeira da Silva says:

December 11, 2014 at 2:04 pm

Given the clear extent of wide-ranging problems in the plant science literature, I wish to make a public call for ALL editors-in-chief (representing therefore the communal voice of ALL editors on that board) of all plant science journals, particularly those that carry an impact factor (and even those that do not carry one), especially from the main STM publishers, including Elsevier, Springer Science + Business Media (including BioMed Central), Wiley, Taylor and Francis (including the Routledge group), McMillan Publishers (including the Nature Publishing Group), Oxford University Press, and all publishers listed here (http://journalseek.net/publishers.htm), as well as all COPE-paying publishers, and ICMJE-enforcing publishers, to make a voluntary public commitment to editorial quality and editor ethics, as defined by the UNCC, and to post such a declaration publically on their web-pages.

This will go a very long way to ensure editor accountability, openness in manuscript processing, transparency when there are publisher- and editor-related issues. It will ensure, ultimately, that editors are held up to the exact same standards that authors are held up to, in a fair, equal, unbiased and equally scrutinous way.

https://editorethics.uncc.edu/editor-ethics-2-0-code/ (Dec 2014) (verbatim quotation)

“Ethical Practices of Journal Editors: Voluntary Code of Conduct
I __________as an Editor or Associate Editor of____________, already bound by the ethical standards of my respective journal(s), professional association(s), and discipline, affirm [as an individual and not on behalf of my journal(s) or sponsoring association] the importance of the following practices:
Article I. Refraining from coercive citation practices, inappropriate citation inflation practices, and citation cartels (whereby editors link together and encourage authors to cite work published in the journals with whom they have partnered).
In both public submission guidelines, and well as within the peer review process, authors will be encouraged to omit citations that are irrelevant to a paper’s main thesis. Specifically, I will refrain from encouraging authors to cite my journal, or those of my colleagues, unless the papers suggested are pertinent to specific issues raised within the context of the review. In other words, it should never be a requirement to cite papers from a particular journal unless the work is directly relevant and germane to the scientific conversation of the paper itself. I acknowledge that any blanket request to cite a particular journal, as well as the suggestion of citations without a clear explanation of how the additions address a specific gap in the paper, is coercive and unethical.
I will monitor for, refrain from, and discourage the practice of citation cartels, reviewer/action editor self-serving citation advisement, and editorial regimes and partnerships. As for the latter, this could include serving as a guest editor (or having one of my associate editors serve in this capacity) of another journal with the intent of using it as a mechanism to cite articles from one’s principal journal.
As an editor, I recognize that metrics such as impact factors are one of many imperfect methods of measuring the impact of published papers, and will not engage in efforts to game or influence these calculations (such as those listed above). I also recognize that, although all journals are entitled to aspire to certain acceptance rate levels and determine their own threshold for what is acceptable work to be published, journals should not artificially reduce the number of papers accepted so as to increase the probability of creating a more favorable impact factor.
I will also consider the ethical implications of how editorial material is presented, and ensure that the use of editorials or the citations therein are in no way used to game citation counts or impact factor computations.
Article II. Promotion of ethical research practices.
In recognizing the global dialog regarding data fraud, research integrity, and implicit pressures on authors to manipulate findings, hide results, etc., I will, whenever possible and appropriate given the scope of my journal, encourage:
1. data transparency including identifying potential conflicts of interest
2. the citing of archival data sources properly, and for one-off data collections, revealing to action editors the full set of variables (if reasonable) and other papers emerging from the data sample under review (or for larger-scale investigations, involving publicly available, representative datasets, providing adequate context with which to assess the unique contribution of the reported study).
3. the reporting (and publishing) of theoretically/methodologically relevant null results
4. substantive and important replication efforts and the use of both (quality) inductive and deductive research.
5. the refraining from opportunistic post-hoc hypothesizing under the guise of deductive research.
6. compliance to journal policy, and discipline-specific ethical standards surrounding data sharing, data retention (to permit colleagues to verify results), and the reporting of results.
7. careful monitoring for plagiarism, self-plagiarism, and the re-submission of papers rejected by previous editorial teams.
Article III. Fairness to authors.
I will encourage:
1. the providing of clear feedback to authors about what is required to make a paper publishable.
2. the keeping of commitments made in decision letters.
3. the keeping of the revision process timely and/or not overly cumbersome or unduly prolonged.
4. the holding of action editors and reviewers accountable to a high level of due diligence. I recognize that reviewers are expected to prepare high quality reviews that may require additional work beyond reading the manuscript, and that they should not review papers for which they are unqualified. I will monitor review quality and consider returning poor quality reviews, providing such reviewers feedback and/or flagging poor reviewers in the reviewer database. I also recognize that editors and reviewers have an obligation to justify, with relevant citations as appropriate, any recommendations for substantial change in the substantive focus or analytic methods of a paper.
5. the timely dissemination of published work. I recognize the need to make authors’ published work publicly available as quickly as possible (e.g., through the immediate production of papers and posting on early view, online first, and other web-based listings of in press papers. These papers should be fully formatted and contain a permanent doi code.
Article IV. The handling of investigations into potential errors and/or potential unethical research practices.
I recognize that an investigation into alleged errors and/or unethical research practices is a very sensitive matter which involves the protection of the rights of multiple stakeholder groups, including but not limited to authors, accusers, reviewers, action editors, journals, and publishers. In instances where appeals or accusations require an investigation, I commit to handle such situations in a way that maximizes procedural justice and professionalism toward all involved. In many cases this may involve following a standard procedure for handling such issues, such as those put out by the Committee on Publication Ethics (COPE; who provides flowcharts for handling ethical problems and guidelines on retractions) or other governing bodies (American Psychological Association, Academy of Management, etc.). In other instances, it may involve following practices established by the journal publisher which are designed to uphold professional ethical standards.
Article V. Communicating ethical standards.
I commit to communicate these and other relevant ethical standards to associate editors, board members, and authors; and to convey these principles within appropriate public forums (e.g., editors’ panels at professional conferences). I will encourage reviewers and action editors to report to the Editor (or to the Editor Ethics Advisory Board) when they feel
the articles herein have been violated. I will encourage action editors to similarly report occasions when reviewers are seen as engaging in unethical practices.
Article VI. Dissemination of this code.
I approve of this Code and its signatories being posted on a public Internet site.
Affirming names are in ABC order by date of the affirmation.”

Reply
Avraham Albert Levy queries says:

December 14, 2014 at 1:57 pm

Concerns have been raised about some of the images in some of Prof. Levy’s manuscripts.
Wheat, Nature Genetics:
https://pubpeer.com/publications/021DF5B37988FD51AA82DF7EE91435#fb18719
Arabidopsis, The Plant Journal:
https://pubpeer.com/publications/34E373A96F6D20C3F21574831F8302#fb18713
Tomato, Journal of Experimental Botany:
https://pubpeer.com/publications/31CB6054868D8AAA6F60522F9EB61B#fb18711
Prof. Levy is at the Weizmann Institute of Science in Israel:
http://www.weizmann.ac.il/plants/levy/

Reply
1. Wheat says:
  
  April 2, 2015 at 12:23 pm
  
  An update: https://pubpeer.com/publications/021DF5B37988FD51AA82DF7EE91435#fb27862
  April 2nd, 2015 11:27am UTC
  “Hello, I am Prof. Levy, the corresponding author of this article. This is a follow up posting to my posting of December 17th. Following the PubPeer Scrutiny, Nature Genetics has agreed to publish a correction of Figure2 based on the original blots scans as I had sent to them in 2007. The correction will appear in the June issue of Nat Genet. As mentioned in my earlier posting the conclusions or the article remain completely unchanged and valid. The figure manipulation that had been done is of course not the proper way to present data, but was not aimed in any way at manipulating results or conclusions, but rather to make weak bands more visible. I believe all sides involved have learned their lesson.”
  
  Reply
  1. Wheat corrected says:
    
    August 29, 2015 at 12:25 am
    
    A correction has appeared for this paper:
    http://www.nature.com/ng/journal/v47/n9/full/ng0915-1099b.html
    
    Reply
Anthurium concerns says:

December 14, 2014 at 5:38 pm

There are at least another two dozen papers in the anthurium tissue culture literature with problems, errors and/or concerns. Analyses are made at PubPeer.

Farsi M (1), Taghavizadeh Yazdi ME (2), Qasemiomran V (3). Micropropagation of Anthurium andraeanum cv. Terra. African Journal of Biotechnology 2012;11(68):13162-13166.
1Ferdowsi University of Mashhad, Mashhad, I. R. Iran.
2Department of Plant Sciences, Eram Biotechnology Research Center, Technical and Vocational Training Organization, Mashad, I. R. Iran
3Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources University, Sari, Iran.
http://www.ms.academicjournals.org/journal/AJB/article-abstract/F030B9532224
http://www.ms.academicjournals.org/article/article1380816254_Farsi%20et%20al.pdf
Total views: 227; PDF downloads: 146
DOI: 10.5897/AJB12.893
Publisher and copyright holder: Academic Journals (Nigeria), listed as “predatory” by Jeffrey Beall:
http://scholarlyoa.com/publishers/
PubPeer analysis:
https://pubpeer.com/publications/5356319CAAB66A911B78574FF2711C#fb18264

Islam SA, Dewan MMR, Mukul MHR, Hossen MA, Khatun F. In vitro regeneration of Anthurium andraeanum cv. Nitta. Bangladesh Journal of Agricultural Research 2010;35(2):217-226.
1Scientific Officer, Bangladesh Rice Research Institute (BRRI), Gazipur-1701, Bangladesh (all except Khatun).
2Department of Agricultural Extention Education, Bangladesh Agricultural University (BAU), Mymensingh-2202, Bangladesh (Khatun).
http://www.banglajol.info/index.php/BJAR/issue/view/356
http://www.banglajol.info/index.php/BJAR/article/view/5884
http://www.banglajol.info/index.php/BJAR/article/viewFile/5884/4618
DOI: 10.3329/bjar.v35i2.5884
PubPeer analysis:
https://pubpeer.com/publications/40F0D7CDEE1BE9C43B9008E7819877#fb18267

Anindita Mukherjee (a), Abhijit Bandyopadhyay (a), Sikha Dutta (a), Sukalyan Basu (b) (2013) Phytoaccumulation of iron by callus tissue of Clerodendrum indicum (L), Chemistry and Ecology, 29:6, 564-571.
DOI: 10.1080/02757540.2013.779681
a) Department of Botany, The University of Burdwan, Burdwan 713104, India
b) Department of Chemistry, The University of Burdwan, Burdwan 713104, India
Received 9 April 2012; final version received 21 February 2013
http://www.tandfonline.com/doi/full/10.1080/02757540.2013.779681#.VIkozJVxnIU
http://www.tandfonline.com/doi/pdf/10.1080/02757540.2013.779681 (open access)
PubPeer analysis:
https://pubpeer.com/publications/9260619E6F61AA7D51ED7D0231C2BE#fb18324

Jahan MT, Islam MR, Khan R, Mamun ANK, Ahmed G, Hakim L. In vitro clonal propagation of anthurium (Anthurium andraeanum L.) using callus culture. Plant Tissue Culture and Biotechnology 2009;19(1):61-69.
DOI: 10.3329/ptcb.v19i1.4961
Plant Biotechnology and Genetic Engineering Division, Institute of Food and Radiation Biology (IFRB), Atomic Energy Research Establishment (AERE), Post‐DEPZ, Savar, Dhaka, Bangladesh
No received, revised, accepted or published dates.
http://www.banglajol.info/index.php/PTCB/article/view/4961+ruseli%20porno (open access)
PubPeer analysis:
https://pubpeer.com/publications/40B0C68EA97A393602B9255C7C651D#fb18548

Peiris SE (1), De Silva EDUD (2), Edussuriya M (3), Attanayake AMURK (1), Peiris BCN (1). CSUP technique: a low cost sterilization method using sodium hypochlorite to replace the use of expensive equipment in micropropagation. Journal of the National Science Foundation of Sri Lanka 2012;40(1):49-54.
DOI: 10.4038/jnsfsr.v40i1.4168
1 Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
2 Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihinthale, Sri Lanka.
3 Department of Chemistry, Faculty of Science, University of Ruhuna, Matara, Sri Lanka.
Revised: 22 July 2011 ; Accepted: 16 September 2011
http://www.sljol.info/index.php/JNSFSL/article/view/4168 (open access)
PubPeer analysis:
https://pubpeer.com/publications/FE35CECA0454A5577B9693F5C4B009　

Atak Ç, Çelik Ö. Micropropagation of Anthurium spp. In: Nabin Kumar Dhal, N.K., Sahu, S.C. (Eds.), Plant Science, Intech, Croatia 2012; pp 241-254.
http://www.intechopen.com/books/plant-science/micropropagation-of-anthurium-spp- (open access)
DOI: 10.5772/51426
Atak Ç, Çelik Ö. Micropropagation of Anthurium andraeanum from leaf explants. Pakistan Journal of Botany 2009;41(3):1155-1161.
Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Kultur University, Ataköy, Istanbul, Turkey
http://pakbs.org/pjbot/PDFs/41(3)/PJB41(3)1155.pdf (open access)
PubPeer analysis:
https://pubpeer.com/publications/D3F78C630ED61FAAD1083C8925D90D#fb18201

Bejoy M, Sumitha VR, Anish NP. Foliar regeneration in Anthurium andraeanum Hort. cv. Agnihothri. Biotechnology (Pakistan) 2008;7(1):134-138.
Commercial Tissue Culture Unit, Tropical Botanic Garden and Research Institute, Palode 695 562, Trivandrum, Kerala, India
DOI: 10.3923/biotech.2008.134.138
http://scialert.net/archivedetails.php?issn=1682-296x&issueno=26
http://scialert.net/qredirect.php?doi=biotech.2008.134.138&linkid=pdf (open access)
PubPeer analysis:
https://pubpeer.com/publications/62C91250EC6834E221A129EFE40F88#fb18205

Farsi M (1), Taghavizadeh Yazdi ME (2), Qasemiomran V (3). Micropropagation of Anthurium andraeanum cv. Terra. African Journal of Biotechnology 2012;11(68):13162-13166.
1Ferdowsi University of Mashhad, Mashhad, I. R. Iran.
2Department of Plant Sciences, Eram Biotechnology Research Center, Technical and Vocational Training Organization, Mashad, I. R. Iran
3Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources University, Sari, Iran.
http://www.ms.academicjournals.org/journal/AJB/article-abstract/F030B9532224
http://www.ms.academicjournals.org/article/article1380816254_Farsi%20et%20al.pdf
Total views: 227; PDF downloads: 146
DOI: 10.5897/AJB12.893
Publisher and copyright holder: Academic Journals (Nigeria), listed as “predatory” by Jeffrey Beall:
http://scholarlyoa.com/publishers/
PubPeer analysis:
https://pubpeer.com/publications/5356319CAAB66A911B78574FF2711C#fb18264

Islam SA, Dewan MMR, Mukul MHR, Hossen MA, Khatun F. In vitro regeneration of Anthurium andraeanum cv. Nitta. Bangladesh Journal of Agricultural Research 2010;35(2):217-226.
1Scientific Officer, Bangladesh Rice Research Institute (BRRI), Gazipur-1701, Bangladesh (all except Khatun).
2Department of Agricultural Extention Education, Bangladesh Agricultural University (BAU), Mymensingh-2202, Bangladesh (Khatun).
http://www.banglajol.info/index.php/BJAR/issue/view/356
http://www.banglajol.info/index.php/BJAR/article/view/5884
http://www.banglajol.info/index.php/BJAR/article/viewFile/5884/4618
DOI: 10.3329/bjar.v35i2.5884
PubPeer analysis:
https://pubpeer.com/publications/40F0D7CDEE1BE9C43B9008E7819877#fb18267

Jahan MT, Islam MR, Khan R, Mamun ANK, Ahmed G, Hakim L. In vitro clonal propagation of anthurium (Anthurium andraeanum L.) using callus culture. Plant Tissue Culture and Biotechnology 2009;19(1):61-69.
DOI: 10.3329/ptcb.v19i1.4961
Plant Biotechnology and Genetic Engineering Division, Institute of Food and Radiation Biology (IFRB), Atomic Energy Research Establishment (AERE), Post‐DEPZ, Savar, Dhaka, Bangladesh
No received, revised, accepted or published dates.
http://www.banglajol.info/index.php/PTCB/article/view/4961+ruseli%20porno (open access)
PubPeer analysis:
https://pubpeer.com/publications/40B0C68EA97A393602B9255C7C651D#fb18548

Peiris SE (1), De Silva EDUD (2), Edussuriya M (3), Attanayake AMURK (1), Peiris BCN (1). CSUP technique: a low cost sterilization method using sodium hypochlorite to replace the use of expensive equipment in micropropagation. Journal of the National Science Foundation of Sri Lanka 2012;40(1):49-54.
DOI: 10.4038/jnsfsr.v40i1.4168
1 Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
2 Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihinthale, Sri Lanka.
3 Department of Chemistry, Faculty of Science, University of Ruhuna, Matara, Sri Lanka.
Revised: 22 July 2011 ; Accepted: 16 September 2011
http://www.sljol.info/index.php/JNSFSL/article/view/4168 (open access)
PubPeer analysis:
https://pubpeer.com/publications/FE35CECA0454A5577B9693F5C4B009

Reply
Barnyard-grass + rice query says:

December 15, 2014 at 2:38 am

Hisashi Kato-Noguchi (2011) The chemical cross talk between rice and barnyardgrass. Plant Signaling & Behavior 6:3, 1207-1209
Copyright: 2011 Landes Bioscience (now Taylor and Francis)
Department of Applied Biological Science; Faculty of Agriculture; Kagawa University; Miki, Kagawa Japan
DOI: 10.4161/psb.6.8.15869
Submitted: 15 April 2011; Accepted: 15 April 2011
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260724/pdf/psb0608_1207.pdf (open access)

It states:
Addendum to: Kato-Noguchi H. Barnyard grass-induced rice allelopathy and momilactone B. Journal of Plant Physiology 2011; 168:1016-20; PMID: 21392842 (Elsevier)
http://www.sciencedirect.com/science/article/pii/S0176161711000836
DOI: 10.1016/j.jplph.2010.12.021

Queries/concerns at PubPeer:
PSB: https://pubpeer.com/publications/4DE0D4122B6A6A7217D911E531D61E#fb18749
JPP: https://pubpeer.com/publications/9B92B05C287761C01069E76B078B99#fb18741

Reply
Pakistan Journal of Agricultural Sciences says:

December 15, 2014 at 11:32 am

There is one journal that is of concern to me: Pakistan Journal of Agricultural Sciences. It has an impact factor of 1.054, although the web-site advertises an incorrect (outdated) IF of 1.240. What is of concern is that in over 50 years of publishing history, and 51 volumes, not a single retraction appears, and only one single erratum (spelt incorrectly as “erratrum”), in the latest September, 2014 issue:
http://www.pakjas.com.pk/papers/2339.pdf
(and no small erratum, either)

Translated: a near-perfect publishing track record. However, a broad glance and random picks will reveal several problems, making this journal an ideal pick for journal-based PPPR. Such an analysis would allow for scientists to better understand how journals obtain their IF, and if there is any correlation with paper qality.

Site: http://www.pakjas.com.pk

Reply
Green manure query says:

December 17, 2014 at 2:46 pm

Armin Hababi 1, Abdollah Javanmard 1, Seyed Bahman Mosavi 2, Mohammad Rezaei 3, Naser Sabaghnia 1 (2013) Effect of green manure on some soil physicochemical characteristics. International Journal of Agronomy and Plant Production 4 (11), 3089-3095
1- Department of Agronomy and Plant Breeding Faculty of Agriculture, Maragheh University, Maragheh, Iran.
2- Department of Soil Science, Faculty of Agriculture, Maragheh University, Maragheh, Iran.
3- West Azerbaijan Agriculture Research Centre, Iran.
*Corresponding author: Armin Hababi
Available online at http:// http://www.ijappjournal.com
http://www.ijappjournal.com/2013-4-11/
http://ijappjournal.com/wp-content/uploads/2013/07/3089-3095.pdf (open access)
ISSN 2051-1914 ©2013 VictorQuest Publications

Abdollah Javanmard 1, Seyed Bahman Mousavi 2, Naser Sabaghnia 1 (2014) Organic carbon, calcium carbonate equivalent, bulk density, moisture percentage by green manure. International Journal of Advances in Science and Technology (IJAST) JITSI special issue, 160-164
1- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Maragheh University, Maragheh, Iran
2- Department of Soil Science, Faculty of Agriculture, Maragheh University, Maragheh, Iran
http://www.sciencepublication.org/ijast/
http://sciencepublication.org/index.php?page=jitsi
http://www.sciencepublication.org/documents/jitsi/28.pdf (open access)
ISSN 2348-5426 (Publisher: Science Publications)

Issues:
1) Neither reference acknowledges the existence of the other, nor do either paper indicate that the data was duplicated elsewhere.
2) Why is authorship so different when the data sets are almost identical?
3) Figures 1, 2, 3 and 4 (and thus data) IDENTICAL.
4) IJAPP paper abstracted at CABI: http://www.cabdirect.org/abstracts/20133395503.html;jsessionid=94039485CC2A17CB3581C87FE9A17996

VictorQuest Publications, listed by Jeffrey Beall as a predatory OA publisher (http://scholarlyoa.com/publishers/) were recently featured on his blog:
http://scholarlyoa.com/2014/09/30/oa-publisher-disappears-from-internet-goes-out-of-business/

Science Publications (http://www.sciencepublication.org/index.php) is also listed as a predatory OA publisher on Beall’s blog.

Incidentally, the senior author, Dr. Naser Sabaghnia, serves on the editor board of the Australian Journal of Crop Science, published by Southern Cross Publshers, also listed on Beall’s list of predatory OA publishers:

Dr. Sabaghnia is the publisher of Current Opinion in Agriculture, which carries a controversial “Universal Impact Factor”:
http://www.uifactor.org/JournalDetails.aspx?jid=532
http://cuopag.com/index.php/journal
http://scholarlyoa.com/2014/03/20/misleading-metrics-a-new-list-on-this-blog/

Curiously, Dr. Sabaghnia received a UIF for “extraordinary achievement” in 2012:
http://uifactor.org/Certificate.aspx?jid=532&&Year=2012

Regrettably, neither paper carries a DOI, so it cannot be linked to PubPeer.

Reply
Plant Pathogen Pseudomonas syringae query says:

December 18, 2014 at 10:08 pm

Queries have been raised at PubPeer about gels in this manuscript:
https://pubpeer.com/publications/052181C04E63B1FF75C24995BF104E#fb19057
Molecular Plant-Microbe Interactions®
Vol. 18, No. 8, 2005, pp. 877–888. DOI: 10.1094/MPMI -18-0877. © 2005 The American Phytopathological Society
Bioinformatics Correctly Identifies Many Type III Secretion Substrates in the Plant Pathogen Pseudomonas syringae and the Biocontrol Isolate P. fluorescens SBW25
Boris A. Vinatzer, Joanna Jelenska, Jean T. Greenberg
Department of Molecular Genetics and Cell Biology, The University of Chicago, 1103 East 57th Street, EBC410, Chicago, IL 60637, U.S.A.
Submitted 27 December 2004. Accepted 23 March 2005.
http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-18-0877
http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-18-0877

Reply
Voinnet and Baulcombe queries says:

December 18, 2014 at 11:48 pm

This case focuses on two very high-level plant scientists, Olivier Voinnet, and David C Baulcombe. Even though their career paths appear to have diverged somewhere between 2003 and 2006 (estimated from the dates of communal papers discussed next), it may be important to cluster them together at this pint while examining the literature. The following papers have issues, primarily with figures and gels, being questioned at PubPeer.

https://pubpeer.com/publications/0E1C65AA039023FBBFBFE822585950
Cell Volume 95, Issue 2, p 177–187, 16 October 1998
Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA
Olivier Voinnet, Philippe Vain, Susan Angell, David C Baulcombe
The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, United Kingdom
Received: June 15, 1998; Received in revised form: August 24, 1998;
© 1998 Cell Press. Published by Elsevier Inc.
DOI: http://dx.doi.org/10.1016/S0092-8674(00)81749-3
http://ac.els-cdn.com/S0092867400817493/1-s2.0-S0092867400817493-main.pdf?_tid=77ce4fd0-8646-11e4-9aca-00000aacb35f&acdnat=1418859974_43c56780970ff1b1e8d6eed2b60d3177
http://www.ncbi.nlm.nih.gov/pubmed/9790525

https://pubpeer.com/publications/789232CA5153F6C4121B7482A117F8
The Plant Cell, Vol. 10, 937–946, June 1998, http://www.plantcell.org © 1998 American Society of Plant Physiologists
Initiation and Maintenance of Virus-Induced Gene Silencing
M. Teresa Ruiz, Olivier Voinnet, David C. Baulcombe
Sainsbury Laboratory, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
Received February 9, 1998; accepted April 13, 1998.
doi: http://dx.doi.org/10.1105/tpc.10.6.937
http://www.plantcell.org/content/10/6/937.long
http://www.plantcell.org/content/10/6/937.full.pdf+html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC144041/pdf/100937.pdf
http://www.ncbi.nlm.nih.gov/pubmed/9634582

https://pubpeer.com/publications/E9D8C3258451C9255C03C027044EA4#fb18962
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14147-52.
Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants.
Olivier Voinnet, Yvonne M. Pinto, David C. Baulcombe
The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, United Kingdom
DOI: 10.1073/pnas.96.24.14147
PubMed ID10570213
Publication History: Published on November 23, 1999
Edited by George Bruening, UC Davis
http://www.pnas.org/content/96/24/14147.full.pdf+html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24205/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24205/pdf/pq014147.pdf

https://pubpeer.com/publications/903A14BA0CD6BBDE4A823AD931D16D
Cell Volume 103, Issue 1, p157–167, 29 September 2000
A Viral Movement Protein Prevents Spread of the Gene Silencing Signal in Nicotiana benthamiana
Olivier Voinnet, Carsten Lederer†, David C Baulcombe
The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, United Kingdom
Received: February 8, 2000; Received in revised form: August 2, 2000;
DOI: http://dx.doi.org/10.1016/S0092-8674(00)00095-7
http://www.cell.com/cell/abstract/S0092-8674(00)00095-7
http://ac.els-cdn.com/S0092867400000957/1-s2.0-S0092867400000957-main.pdf?_tid=b7662e4e-872f-11e4-8a98-00000aacb361&acdnat=1418960153_40ffb2a08f171d7cf9c1c2b5c047c8f4
http://www.ncbi.nlm.nih.gov/pubmed/11051555

https://pubpeer.com/publications/A090AEA18BF0DDC626CEB413174345
The Plant Journal, 33: 949–956 (2003).
An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus.
Olivier Voinnet†, Susana Rivas, Pere Mestre, David Baulcombe
The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
† Current address: Institut de Biologie Moleculaire des Plantes du CNRS, 12, rue du General Zimmer, 67084 Strasbourg Cedex, France.
doi: 10.1046/j.1365-313X.2003.01676.x
Issue published online: 28 FEB 2003
Article first published online: 28 FEB 2003
Received 9 September 2002; revised 16 December 2002; accepted 20 December 2002.
http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313X.2003.01676.x/abstract
http://www.ncbi.nlm.nih.gov/pubmed/12609035

https://pubpeer.com/publications/80DD1F3E653159C8F89739FF7C7129
PNAS December 19, 2006 vol. 103 no. 51 19593-19598
RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer-like proteins
Guillaume Moissiard, Olivier Voinnet
Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France
Author contributions: O.V. designed research; G.M. performed research; G.M. and O.V. analyzed data; and O.V. wrote the paper.
DOI: 10.1073/pnas.0604627103
PubMed ID: 17164336
Publication History: Published online before print on December 12, 2006
http://www.pnas.org/content/103/51/19593
http://www.pnas.org/content/103/51/19593.full.pdf+html

https://pubpeer.com/publications/358DABD0BE713B03950C76D7652140
Nature Cell Biology 11 (2009) 1143 – 1149
Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity
Derrick J Gibbings, Constance Ciaudo, Mathieu Erhardt, Olivier Voinnet
doi: 10.1038/ncb1929
Published online: 16 August 2009
Corrected online: 8 September 2009: link not working
Erratum: http://www.nature.com/ncb/journal/v11/n10/pdf/ncb1009-1272b.pdf
http://www.nature.com/ncb/journal/v11/n9/full/ncb1929.html

https://pubpeer.com/publications/C9E1F1DE1F0367633BCD9F0D21588D
PLoS Genet 5(8): e1000620. doi:10.1371/journal.pgen.1000620 (2009)
Highly Dynamic and Sex-Specific Expression of microRNAs During Early ES Cell Differentiation
Constance Ciaudo1,2, Nicolas Servant 3,4, Vale´ rie Cognat 1, Alexis Sarazin 5, Emmanuelle Kieffer 6, Ste´phane Viville 6, Vincent Colot 5, Emmanuel Barillot 3,4, Edith Heard 2*, Olivier Voinnet 1*
1 CNRS UPR2357—Institut de Biologie Mole´culaire des Plantes, Universite´ de Strasbourg, Strasbourg, France, 2 CNRS UMR3215—INSERM U934, Institut Curie, Paris, France,
3 INSERM U900, Institut Curie, Paris, France, 4 Ecole des Mines de Paris, ParisTech, Fontainebleau, France, 5 CNRS UMR 8186—De´partement de Biologie, Ecole Normale
Supe´ rieure, Paris, France, 6 CNRS UMR7104—INSERM U964, Institut de Ge´ne´tique et de Biologie Mole´culaire et Cellulaire, Department of Developmental Biology,
Universite´ de Strasbourg, Faculte´ de Me´decine, Centre Hospitalier Universitaire de Strasbourg, Illkirch, France
Editor: Michael T. McManus, University of California San Francisco, United States of America
Received April 21, 2009; Accepted July 29, 2009; Published August 28, 2009
“Conceived and designed the experiments: CC EH OV. Performed the experiments: CC. Analyzed the data: CC NS VC AS EH OV. Contributed reagents/materials/analysis tools: CC NS VC AS EK SV VC EB EH OV. Wrote the paper: CC EH OV.”
http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1000620&representation=PDF
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000620

https://pubpeer.com/publications/FD08039FB188E781A80C1C469FFFAB
PNAS vol. 109 no. 5, 1778–1783 (2012)
Isoprenoid biosynthesis is required for miRNA function and affects membrane association of ARGONAUTE 1 in Arabidopsis
Peter Brodersena,1, Lali Sakvarelidze-Acharda, Hubert Schallera, Mehdi Khafifb,2, Grégory Schottc, Abdelhafid Bendahmaneb, and Olivier Voinneta,c,3
a Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, 67084 Strasbourg Cedex, France;
b Unité de Recherche en Génomique Végétale, CP 57008 Evry Cedex, France; and
c Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zürich 8092, Switzerland
1 Present address: Copenhagen University, Department of Biology, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
2 Present address: Institut National de la Recherche Agronomique, Laboratoires des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441, 31326 Castanet-Tolosan, France.
Author contributions: P.B. and O.V. designed research; P.B., L.S.-A., H.S., M.K., and G.S. performed research; H.S. contributed new reagents/analytic tools; P.B., H.S., A.B., and O.V. analyzed data; and P.B. and O.V. wrote the paper.
*This Direct Submission article had a prearranged editor.
The authors declare no conflict of interest.
doi: 10.1073/pnas.1112500109
Edited by James C. Carrington, Donald Danforth Plant Science Center, St. Louis, MO, and approved December 16, 2011 (received for review July 30, 2011)
http://www.pnas.org/content/109/5/1778

Some additional facts:
Voinnet: https://pubpeer.com/search?q=voinnet
Olivier Voinnet (about 42 yo) is a winner of the EMBO Gold Medal and has already won a prize worth 200000 CHF.
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_05_29/caredit.a0900071
http://www.ethlife.ethz.ch/archive_articles/130613_roesslerpreis_voinnet_per/index_EN
“On June 13, 2013, Dr. Olivier Voinnet was awarded CHF 200,000 Rössler Research Prize for his groundbreaking discovery in the field of RNAi molecular and cell biology.”
http://www.lifome.com/blog/118/famous-scientific-awards-the-achievements-rna-interference.html

The four Voinnet papers commented on PubPeer (for similar issues) have amassed some 2000 citations (according to Google Scholar).
http://scholar.google.co.uk/citations?user=a1D7YVUAAAAJ&hl=en
Now PI at the Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zürich 8092, Switzerland

Sir David C. Baulcombe: https://pubpeer.com/search?q=baulcombe
University of Cambridge
http://en.wikipedia.org/wiki/David_Baulcombe

In 2013, a LabTimes article lists Voinnet and Baulcombe as ranked 7th and 20th in terms of top 30 most-cited authors of plant sciences in Europe:
http://www.labtimes.org/labtimes/ranking/2013_04/index.lasso

Reply
1. Voinnet and Baulcombe queries says:
  
  January 4, 2015 at 4:07 pm
  
  One more query emerges at PubPeer:
  https://pubpeer.com/publications/C212754B71B23CD2137797D265935D#fb20363
  The EMBO Journal Volume 17, Issue 22, 6739 – 6746; 16 November 1998
  Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana
  Gianinna Brigneti, Olivier Voinnet, Wan‐Xiang Li, Liang‐Hui Ji, Shou‐Wei Ding, David C. Baulcombe
  1 The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
  2 Molecular Virology Laboratory, Institute of Molecular Agrobiology, National University of Singapore, 1 Research Link, Singapore, 117604 (Li, JI and Ding)
  3 G.Brigneti and O.Voinnet contributed equally to this work
  http://emboj.embopress.org/content/17/22/6739
  http://emboj.embopress.org/content/embojnl/17/22/6739.full.pdf
  DOI: http://dx.doi.org/10.1093/emboj/17.22.6739
  PubMed: 9822616
  
  Reply
2. Voinnet and Baulcombe queries says:
  
  January 6, 2015 at 2:43 am
  
  One more query emerges at PubPeer:
  https://pubpeer.com/publications/F5BA8FE3EF8860205332839D02BBDD#fb20469
  The Plant Cell, Vol. 16, 1235–1250, May 2004
  Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing W
  Patrice Dunoyer, Charles-Henri Lecellier, Eneida Abreu Parizotto, Christophe Himber, and Olivier Voinnet
  Institut de Biologie Mole´ culaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France
  doi: 10.1105/tpc.020719
  Received January 6, 2004; accepted February 24, 2004.
  http://www.plantcell.org/content/16/5/1235
  http://www.plantcell.org/content/16/5/1235.full.pdf+html?with-ds=yes
  
  Reply
3. Baulcombe response 1 says:
  
  January 9, 2015 at 8:35 am
  
  Sir David Baulcombe has provided his first public response:
  https://pubpeer.com/publications/789232CA5153F6C4121B7482A117F8#fb20860
  stating: “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and have now notified the editor. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  Reply
4. Voinnet and Baulcombe queries says:
  
  January 9, 2015 at 9:23 am
  
  Public responses (verbatim quotes):
  
  Voinnet: https://pubpeer.com/search?q=voinnet (12 papers; one is a redundant statement)
  Baulcombe: https://pubpeer.com/search?q=baulcombe (7 papers; one is a compliment)
  
  https://pubpeer.com/publications/0E1C65AA039023FBBFBFE822585950
  “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and have now notified the editor. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  https://pubpeer.com/publications/789232CA5153F6C4121B7482A117F8
  “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and have now notified the editor. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  https://pubpeer.com/publications/C212754B71B23CD2137797D265935D
  “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem when I was informed about the pubpeer entry a few days ago. Since then I have been investigating the problem and I will notify the editor shortly. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  https://pubpeer.com/publications/E9D8C3258451C9255C03C027044EA4
  “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and have now notified the editor. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  https://pubpeer.com/publications/903A14BA0CD6BBDE4A823AD931D16D
  “This response is from David Baulcombe – corresponding author on this paper and Olivier Voinnet who carried out the experiment and drafted the figure. We accept that the figure legends were incomplete because they did not point out that Figure 3 (panel D, right hand panel lane 4) and Figure 5 (panel D lane 1) are the same image. This duplication is not an error because the Northern experiments for these figures were carried out at the same time, exposed on the same autoradiograph and both used the same negative control sample (Mock: M). Neither of these images was spliced but the two figures show parts of the same autoradiograph, with the overlap across the negative control track (M). We have the original autoradiograph. We apologise for the lack of clarity and have asked the journal editor for the opportunity to publish a clarification statement.”
  
  https://pubpeer.com/publications/A090AEA18BF0DDC626CEB413174345
  “This response is from David Baulcombe – corresponding author on this paper. I first became aware of the problem with this paper just before Christmas when I received an anonymous email. Since then I have been investigating the problem and I will notify the editor shortly. I recognize that I should have detected the error before the article was submitted and I apologise for the error.”
  
  No responses yet from Voinnet on the following:
  
  https://pubpeer.com/publications/F5BA8FE3EF8860205332839D02BBDD
  
  https://pubpeer.com/publications/80DD1F3E653159C8F89739FF7C7129
  
  https://pubpeer.com/publications/358DABD0BE713B03950C76D7652140
  
  https://pubpeer.com/publications/C9E1F1DE1F0367633BCD9F0D21588D
  
  https://pubpeer.com/publications/FD08039FB188E781A80C1C469FFFAB
  
  Reply
Lutts + Walker query says:

December 19, 2014 at 5:56 am

Journal of Arid Environments 100-101 (2014): 111-121
Atriplex halimus L.: Its biology and uses
David J. Walker a,*, Stanley Lutts b, Maria Sánchez-García c, Enrique Correal a
a Instituto Murciano de Investigación y Desarrollo Agricola y Alimentario, Calle Mayor s/n, La Alberca, 30150 Murcia, Spain
b Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute e Agronomy (ELIA), Université catholique de Louvain, Croix du sud 4-5 bte L7.07.13 à, 1348 Louvain-la-Neuve, Belgium
c CEBAS-CSIC, Campus Universitario de Espinardo, Apartado de Correos 164, 30100 Espinardo, Murcia, Spain
Received 17 June 2013; Received in revised form 20 September 2013; Accepted 26 September 2013; Available online 11 October 2013
http://www.sciencedirect.com/science/article/pii/S0140196313001547
DOI: 10.1016/j.jaridenv.2013.09.004

Emirates Journal of Food and Agriculture 2014. 26 (12): 1081-1090
doi: 10.9755/ejfa.v26i12.19116
http://www.ejfa.info/
The tolerance of Atriplex halimus L. to environmental stresses
David J. Walker 1* and Stanley Lutts 2
1 Instituto Murciano de Investigación y Desarrollo Agricola y Alimentario, Calle Mayor s/n, La Alberca, 30150 Murcia, Spain
2 Groupe de Recherche en Physiologie végétale (GRPV), Earth and Life Institute – Agronomy, ELIA – Université catholique de Louvain, Croix du sud 4-5 bte L7.07.13 à 1348 Louvain-la-Neuve, Belgium
http://ejfa.info/index.php/ejfa/article/view/19116
http://ejfa.info/index.php/ejfa/article/view/19116/9607 (open access)

Issues:
1) Neither paper acknowledges the existence of the other.
2) Fig 1A (JAE) is identical to Fig 1 (EJFA).
3) The topics, even sections discussed, are the same (not identical): pp. 114-116 (JAE) vs pp. 1082-1086 (EJFA).
4) Identical text in parts (select examples next; plagiarism software not used, only a manual visual scan).

JAE (p. 112): “It grows in areas of low annual rainfall (R) and high potential evapotranspiration (PET), many of which can be classified as arid (R=100-400 mm, R:PET=0.06-0.28) or semi-arid (R=400-600 mm and R:PET=0.28-0.45)”
EJFA (p. 1081): “It grows in zones of low annual rainfall (R) and high potential evapotranspiration (PET): many of these can be classified as arid (R = 100-400 mm, R:PET = 0.06-0.28) or semi-arid (R = 400-600 mm, R:PET = 0.28-0.45).”

JAE (p. 114, 4.1): “A. halimus is a species adapted to sites having summers with very-high light intensity and temperature. Since it possesses the C4 carboxylation pathway, the optimum temperature for photosynthesis is relatively high, around 35 C (Le Houérou, 1992; Shomer-Ilan et al., 1981; Zervoudakis et al., 1998). Streb et al. (1997) concluded that A. halimus is able to withstand high light intensity (photosynthetically active radiation > 2000 mmol m-2 s-1)”
EJFA (p. 1085, Extreme temperatures and light): “Atriplex halimus is adapted to climate zones having summers with very-high light intensity and temperature. Since it possesses the C4 carboxylation pathway, the optimum temperature for photosynthesis is relatively high, around 35ºC (Shomer-Ilan et al., 1981; Le Houérou, 1992; Zervoudakis et al., 1998). Streb et al. (1997), studying leaves of A. halimus plants exposed to photosynthetically active radiation in the field as high as 2200 μmol m-2 s-1”

JAE (p. 114, 4.2): “Le Houérou (1992) classified A. halimus as a “euhalophyte”, able to withstand soil salinity levels equivalent to saturated paste EC values of 25-30 dS m-1. Debez et al. (2001) demonstrated that the seed germination of a coastal population of A. halimus was more salt-tolerant than that of a population from a non-saline site; complete inhibition occurred at 700 and 350 mM NaCl, respectively,”
EJFA (p. 1082, right column): “Le Houérou (1992) stated that A. halimus can withstand soil salinity equivalent to ECs values of 25-30 dS m-1” and “Debez et al. (2001) found the germination of a coastal population of A. halimus to be more tolerant to salinity than that of an inland population from a non-saline site (total inhibition at 350 and 700 mM NaCl, respectively)”

JAE (p. 114, 4.2): “This active intracellular accumulation of osmolytes or “osmotic adjustment” generates low values of tissue water potential (Ψw); simultaneous decreases in osmotic potential (Ψs) (e.g., -7.5 MPa; Bajji et al., 1998) maintain tissue turgor. Hence, the plants can maintain water uptake and transport from extremely saline external media.”
EJFA (p. 1083, left bottom to right top column): “This osmotic adjustment (OA, the active intracellular accumulation of osmolytes) generates low values of tissue Ψw; even-lower coincident values of osmotic potential (Ψs) (e.g., -7.5 MPa; Bajji et al., 1998) maintain tissue turgor. Hence, the plants can maintain water uptake from extremely saline external media.”

JAE (p. 114, 4.2): “Together with the accumulation of ionic osmolytes in the vacuole, there is cytoplasmic accumulation of “compatible” organic osmolytes (notably proline and glycinebetaine) which do not interfere with metabolic processes. These maintain the osmotic balance across the tonoplast and protect membranes, organelles and proteins; proline also regulates carbon and nitrogen metabolism, acts as an anti-oxidant and promotes recovery once the stress has eased (Szabados and Savouré, 2009).”
EJFA (p. 1083, right column): “Simultaneous to the accumulation of ionic osmolytes in the vacuole, there is cytosolic and organellar accumulation of “compatible” organic osmolytes, which do not affect metabolic processes even at very-high concentrations, in order to maintain the osmotic balance across the tonoplast, protect membranes, organelles and proteins and (in the case of proline) to regulate metabolism, act as anti-oxidants and promote recovery once the stress has eased (Szabados and Savouré, 2009).”

JAE (p. 115, 4.2): “At very-high external salt concentrations (>300 mM NaCl), damage appears, regarding stomatal conductance (Nemat Alla et al., 2011), the root plasma membrane permeability, root hydraulic conductivity and chlorophyll content (Nedjimi and Daoud, 2009), photosynthesis (Boughalleb et al., 2009; Khedr et al., 2011) and intracellular organelles (Blumenthal-Goldschmidt and Poljakoff-Mayber, 1968; Wong and Jäger, 1978). The tissue levels of mineral nutrients such as Ca2t, Mg2t and inorganic phosphorus also decline (Bajji et al., 1998).”
EJFA (p. 1084, left column): “At elevated external salt concentrations (≥ 300 mM NaCl), the protective mechanisms of A. halimus are not sufficient to maintain stomatal conductance (Nemat Alla et al., 2011), the root plasma membrane permeability, root hydraulic conductivity and chlorophyll content (Nedjimi and Daoud, 2009) or the photosynthetic machinery (Schwarz and Gale, 1981; Boughalleb et al., 2009; Khedr et al., 2011), or to protect the integrity of intracellular organelles (Blumenthal-Goldschmidt and Poljakoff-Mayber, 1968; Kelley, 1974; Wong and Jäger, 1978). Very-high external salinity also diminishes tissue levels of mineral nutrients such as inorganic phosphorus, Mg2+ and Ca2+ (Bajji et al., 1998).”

JAE (p. 115, 4.3): “water-deprived plants of A. halimus can generate extremely-low values of Ψw and Ψs (e.g., -4.20 and -6.57 MPa, respectively; Bajji et al., 1998). Differences between populations of A. halimus, related to the pedo-climatic conditions at their native sites, exist with respect to their adaptation to external water shortage and their tolerance, in terms of growth.”
EJFA (p. 1084, right column): “Water-deprived plants of A. halimus generate very-low values of Ψw and Ψs (as low as –4.20 and -6.57 MPa, respectively; Bajji et al., 1998). Differences between populations of A. halimus, related to the pedo-climatic conditions at their native sites, have been found with respect to their mechanism of adaptation to external water shortage and their tolerance (maintenance of growth).”

JAE (p. 115, 4.3): “Ben Hassine and co-workers (Ben Hassine and Lutts, 2010; Ben Hassine et al., 2009, 2008) compared two Tunisian populations of A. halimus, one from an inland, arid site and one from a coastal, saline site: the former was more tolerant of water deprivation (in terms of growth) and accumulated more proline, had more-negative values of Ψw and Ψs (and higher turgor), higher CO2 assimilation rate and lower stomatal conductivity (and hence higher water use efficiency). There seems to be a specific accumulation of Nat as the cationic osmolyte under drought (Ben Hassine et al., 2010; Martínez et al., 2005; Nedjimi, 2012).”
EJFA (p. 1084, right column bottom to 1085 left column, top): “Ben Hassine and co-workers (Ben Hassine et al., 2008, 2009; Ben Hassine and Lutts, 2010) studied the effects of water deprivation on two Tunisian populations of A. halimus, one from an arid site and one from a saline site. The former was more tolerant and accumulated more proline, had more-negative values of Ψw and Ψs (and higher turgor), a higher CO2 assimilation rate and lower stomatal conductivity (and hence higher water use efficiency). A role of Na+ in drought tolerance was indicated by the results of Ben Hassine et al. (2010) and Nedjimi (2012).”

JAE (p. 115, 4.4): “These authors also proposed that the role of abscisic acid (ABA) differs between the two stresses: under osmotic stress, it enhances stomatal regulation and water use efficiency whereas under external salinity it promotes excretion of Nat and Cl- into the vesiculated hairs.” And “Ben Hassine and co-workers suggested that the slower (chloroplastic) accumulation of glycinebetaine protects the photosynthetic apparatus against permanent soil salinity, while proline (which accumulates more quickly) may protect against oxidative damage and also regulate carbon and nitrogen metabolism when the plants are faced with short-term drought.”
EJFA (p. 1085 left column): “These authors proposed that the role of ABA differs between the two stresses: under osmotic stress, it enhances stomatal regulation and water use efficiency whereas under external salinity it promotes excretion of Na+ and Cl- into the vesiculated hairs.” And “Ben Hassine and co-workers (Ben Hassine et al., 2008, 2009; Ben Hassine and Lutts, 2010) suggested that the slower (chloroplastic) accumulation of GB protects the photosynthetic apparatus against permanent soil salinity, whilst proline (which accumulates more quickly) may protect against oxidative damage and also regulate carbon and nitrogen metabolism when the plants are faced with short-term drought.”

JAE (p. 115, 4.4): “Khedr et al. (2012) studied the Dehydration Responsive Element Binding (DREB) transcription factor in A. halimus, which regulates the expression of many stress-inducible genes, and showed that it was up-regulated greatly by both water deprivation and salinity; in the latter case, it was the osmotic component of the stress that was responsible. Nemat Alla et al. (2012) published a metabolomics-based analysis of the changes in A. halimus caused by exposure to salt (NaCl) or water deprivation (polyethylene glycol). They found common responses to these two stresses (e.g., up-regulation of the tricarboxylic acid cycle and synthesis of β-alanine) and others that were specific to salinity (e.g., up-regulation of ABA transport and alkaloid synthesis) or polyethylene glycol (e.g., up-regulation of tryptophane metabolism).”
EJFA (p. 1085, left column bottom to right column, top): “Khedr et al. (2012) studied the Dehydration Responsive Element Binding (DREB) transcription factor in A. halimus, which regulates the expression of many stress-inducible genes, and showed that it was up-regulated greatly by both water deprivation and salinity; in the latter case, it was the osmotic component of the stress that was responsible. Nemat Alla et al. (2012) published a metabolomics-based analysis of the changes in A. halimus caused by exposure to salt (NaCl) or water deprivation (PEG). They found common responses to these two stresses (e.g., up-regulation of the tricarboxylic acid cycle and synthesis of β-alanine) and others that were specific to salinity (e.g., up-regulation of ABA transport and alkaloid synthesis) or PEG (e.g., up-regulation of tryptophane metabolism).”

JAE (p. 115, 4.5): “Le Houérou (1992) placed A. halimus in a group of species exhibiting moderate cold tolerance (able to withstand temperatures as low as -10 to -12 C). Walker et al. (2008) showed that the tolerance of A. halimus to sub-zero temperatures in the field (as low as -18 C) correlated positively with leaf accumulation of Na+, K+, amino acids, quaternary ammonium compounds and soluble sugars. In behaviour analogous to that in salinity and drought adaptation, the leaf sap Ψw and Ψs values of cold-acclimated plants (as low as -2.69 and -6.32 MPa, respectively) were lower than in the following spring. This reflects the importance of osmotic adjustment with regard to minimizing cellular dehydration through water loss to extracellular ice (Xin and Browse, 2000).”
EJFA (p. 1085, right column, bottom): “Le Houérou (1992) placed A. halimus in a group of Atriplex species exhibiting moderate cold tolerance (able to withstand temperatures as low as -12ºC). Walker et al. (2008) found that the cold tolerance of A. halimus leaves was greater in early winter (acclimation) than in spring (following deacclimation). In this study, plant tolerance of temperatures in the field as low as -18ºC correlated positively with leaf accumulation of Na+, K+, amino acids, QACs and soluble sugars, the leaf sap Ψw and the % dry matter (DM) of the tissue. Mirroring the behaviour shown in drought and salinity adaptation, the leaf Ψw and Ψs values of cold-acclimated plants in winter (as low as -2.69 and -6.32 MPa, respectively) were lower than in the following spring. This underlines the role of OA with regard to minimising cellular dehydration through water loss to extracellular ice, the main cause of freezing damage (Xin and Browse, 2000)”

JAE (p. 115, 4.5): “of Walker et al. (2008), diploid populations (subsp. halimus) resulted more tolerant than tetraploid ones (subsp. schweinfurthii), probably due to the less negative Ψs values of the latter.” And “Salahas et al. (2002) found that high concentrations of glycinebetaine and proline protected both this enzyme and pyruvate orthophosphate dikinase against cold inactivation.”
EJFA (p. 1085, right column bottom to 1086 left column, top): “Walker et al. (2008) found diploid populations (sub-species halimus) to be more cold-tolerant than tetraploid ones (schweinfurthii), probably due to the less-negative Ψs values of the latter.” And “Salahas et al. (2002) found that high concentrations of GB and proline protected PEP carboxylase and pyruvate orthophosphate dikinase (EC 2.7.9.1) against cold inactivation.”

JAE (p. 115-116, 4.6): “The term “trace elements” refers to elements such as arsenic (As), cadmium (Cd), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb) and zinc (Zn), which are important contaminants of soil due to anthropogenic activities such as agriculture, industry and mining. Since A. halimus has colonised trace element-contaminated sites, for example, in southern Spain (Lutts et al., 2004; Márquez-García et al., 2013) and Algeria (Lotmani et al., 2011), its tolerance mechanisms have been researched. The germination of A. halimus seems resistant to elevated levels of trace elements in soil (Lotmani et al., 2011; Martínez-Fernández and Walker, 2012). Studies of A. halimus grown in pots of contaminated soil (Manousaki and Kalogerakis, 2009; Martínez-Fernández and Walker, 2012), in hydroponic culture (Lefèvre et al., 2009; Lutts et al., 2004) or in Petri dishes (Márquez-García et al., 2013) show that, in terms of growth, it is tolerant of high concentrations of Cd, Cu, Mn, Ni, Pb and Zn in the growth medium.”
EJFA (p. 1086, left column, Trace elements): “Trace elements such as arsenic (As), copper (Cu), cadmium (Cd), manganese (Mn), nickel (Ni), lead (Pb) and zinc (Zn) are important contaminants of soil due to previous and/or ongoing anthropogenic activities such as agriculture, industry and mining. Since A. halimus has colonised TEs-contaminated sites, for example in southern Spain (Lutts et al., 2004; Márquez-García et al., 2013) and Algeria (Lotmani et al., 2011), the processes which may contribute to this have been investigated. The germination of A. halimus was found to be high in TEs-contaminated soils (Lotmani et al., 2011; Martínez-Fernández and Walker, 2012), … Experiments performed with A. halimus in pots of contaminated soil (Manousaki and Kalogerakis, 2009; Martínez-Fernández and Walker, 2012; Pérez-Esteban et al., 2013), in hydroponic culture (Lefèvre et al., 2009; Lutts et al., 2004) or in Petri dishes (Márquez-García et al., 2013) show that its growth is tolerant of high concentrations of Cd, Cu, Mn, Ni, Pb or Zn in the medium.”

JAE (p. 116, 4.6): “The Cd tolerance mechanisms may include precipitation with oxalate, in the stem (Lutts et al., 2004), and excretion into vesiculated hairs (Lefèvre et al., 2009). Lefèvre et al. (2009) also found that Cd exposure increased the accumulation of glycinebetaine, proline and spermine and spermidine, as under salinity (Ben Hassine et al., 2009)…. A. halimus has a high tolerance of elevated tissue Zn concentrations, which may result from co-precipitation with oxalate (Lutts et al., 2004)”
EJFA (p. 1086, left bottom to right top column, Trace elements): “The Cd tolerance mechanisms may include precipitation with oxalate in the stems (Lutts et al., 2004) and excretion into vesiculated hairs (Lefèvre et al., 2009). …Lefèvre et al. (2009) found no effect of Cd on soluble sugars accumulation, but did find accumulation of GB, proline, spermine and spermidine, as with salt exposure (Ben Hassine et al., 2009)…. Atriplex halimus has a high tolerance of elevated external and internal Zn concentrations, which may result from co-precipitation with oxalate (Lutts et al., 2004).”

It is also curious to note that a spelling mistake exists with Prof. Stanley Lutts name in this 2009 paper:
Acta Physiologiae Plantarum March 2010, Volume 32, Issue 2, pp 325-331 Date: 10 Nov 2009
Does habitat of Atriplex halimus L. affect plant strategy for osmotic adjustment?
Abir Ben Hassine, Sadok Bouzid, Staneley Lutts
http://link.springer.com/article/10.1007%2Fs11738-009-0410-4
One would think that an author would like their names published correctly, for posterity’s sake, and for having a correct literature (those who reference this paper are thus attributing a citation to someone who in fact does not exist, by a mere technicality).

Stanley Lutts:
http://www.uclouvain.be/stanley.lutts
http://www.researchgate.net/profile/Stanley_Lutts
http://scholar.google.com/citations?user=1_yYtMwAAAAJ&hl=fr

David J. Walker (listed as David Walker James):
http://www.imida.es/equipos/eq_cultivos_alter_comp.html
http://www.imida.es/equipos/eq_cultivos_alter_pub.html (oddly incomplete publications list)
http://ejfa.info/index.php/ejfa/pages/view/editorial_board (Editor board of EJFA)

There are two PubPeer entries for this case:
https://pubpeer.com/publications/0379550F6348AC6D7C32950CC7AA1C#fb19061 (JAE)
https://pubpeer.com/publications/82CB37CFD9A717E100C98014E73A54#fb19062 (EJFA)

Reply
Vitex trifolia queries says:

December 19, 2014 at 7:57 pm

Paper 1:
Ahmed M. R., M. Anis. 2012. Role of TDZ in the quick regeneration of multiple shoots from nodal explant of Vitex trifolia L. – an important medicinal plant. Applied Biochemistry and Biotechnology 168, 957–966.
Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, UP, India
http://link.springer.com/article/10.1007%2Fs10457-007-9078-1
http://www.ncbi.nlm.nih.gov/pubmed/23065400
DOI: 10.1007/s12010-012-9799-0
Publisher: Springer Netherlands
27 citations

Paper 2:
Ahmed M. R., M. Anis. 2014a. In vitro regeneration and the antioxidant enzymatic system on acclimatization of micropropagated Vitex trifolia L. Agroforestry Systems 88, 437–447.
Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, UP, India
http://link.springer.com/article/10.1007%2Fs10457-007-9078-1
DOI: 10.1007/s10457-014-9703-8
Publisher: Springer Netherlands
27 citations

Concern 1: figure duplication

Fig 1E (paper 1) = Fig 1F (paper 2) (side view vs top view)
Paper 1 plants derived from nodal segments BUT Paper 2 plants derived from shoot tips. It is evident that the exact same acclimatized flowering plants cannot be derived from completely different explant sources.

Concern 2:
“The disinfected shoots apex were trimmed further into small segments (0.5–0.8 cm) aseptically and implanted on sterile shoot induction medium.” (Paper 2, p. 439). The protocol is about regeneration using shoot tips. However, if this statement is true, then this implies that not only shoot tips were used, suggesting an overlap with plant material (explants) from Paper 1.

These concerns would immediately cause doubt about the veracity of plant material in other papers:
Paper 3
Ahmed R., M. Anis. 2014b. Rapid in vitro propagation system through shoot tip cultures of Vitex trifolia L. – an important multipurpose plant of the Pacific traditional Medicine. Physiology and Molecular Biology of Plants 20, 385–392.
DOI: 10.1007/s12298-014-0233-7

Paper 4
Ahmad N., S. Bin Javed, M. I. Khan, M. Anis. 2013. Rapid plant regeneration and analysis of genetic fidelity in micropropagated plants of Vitex trifolia: an important medicinal plant. Acta Physiologiae Plantarum 35, 2493–2500.
DOI: 10.1007/s11738-013-1285-y

Concern 3:
There is an uncanny resemblance in the methodology and data trends between Paper 4 and a 2013 paper on Vitex negundo (Paper 5). So much so, that the table headers of Table 2 (p. 2497) and Table 3 (p. 2498) incorrectly state that the data represents data of Vitex negundo and not actually Vitex trifolia, the topic of study of Paper 4. Table 4 (p. 2499) states “Banding pattern in Vitex species”, but does not specifically state that the banding refers to Vitex trifolia.

Paper 5:
Ahmad N., M. I. Khan, S. Ahmed, S. Bin Javed, M. Faisal, M. Anis, S. Rehman, S.M. Umair. 2013. Change in total phenolic content and antibacterial activity in regenerants of Vitex negundo L. Acta Physiologiae Plantarum 35, 791–800.

Small error (Paper 3, p. 389, right column, top): “highest response of 92 % cultures with a mean number (7.2±0.1) of shoots per explant (Table 3)” should read (Table 2). An erratum is required because the reference to Table 2, of similar parameters, is confusing.

Funding
Paper 1: “Md. Rafique Ahmed is thankful to the University Grants Commission (UGC), Govt. of India, New Delhi for its award of Junior Research Fellow (F1-17.1/2011/MANF-MUS-MAN-581) (SA-III/manfugc). Research support provided by the Department of Science and Technology (DST) in the form of DST-FIST (2011-16) and UGC in the form of UGC-SAP; DRS-I Programme is duly acknowledged.”
Paper 2: “Md. Rafique Ahmed thanks the University Grants Commission (UGC), Government of India, New Delhi for the award of a Senior Research Fellowship under MANF. Research support was provided by the Department of Science and Technology DST-FIST (2011–16) and the University Grants Commission, through the UGC-DRS-I Programme (2009–2014).”
Paper 3: “Md. Rafique Ahmed is thankful to the University Grants Commission (UGC), Goverment of India, New Delhi for the award of a Junior Research Fellowship (F1-17.1/2011/MANF-MUSMAN-581 (SA-III/manfugc). Research support provided by the Department of Science and Technology and University Grants Commission under DST-FIST (2011-16) and UGC-SAP, DRS-I (2009-2014) Programme respectively is duly acknowledged.”
Paper 4: “The award of DST, Young Scientist (SR/FT/LS-014/2009) scheme to Naseem Ahmad by the Department of Science and Technology (DST), Government of India, New Delhi, is greatly acknowledged. Research support from the Department of Science and Technology (Govt. of India), New Delhi under the DST-FIST(2011) and UGC-SAP (2009) Programme, is also acknowledged.”

Incidentally, Prof. Mohammad Anis and co-authors have been the subject of another large query regarding Egyptian Myrobalan Tree (Balanites aegyptiaca Del.) with 4 PubPeer entries:
https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878　
https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879　
https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880　

And concerns with another Vitex species, Vitex negundo, registered as 3 PubPeer entries:
https://pubpeer.com/publications/DD4131C0A025F3536F8D1825FAB38D#fb19073
https://pubpeer.com/publications/228844D355BBACF479209E2D15459E#fb17547
https://pubpeer.com/publications/806685230E231DFBD444AF5E964742#fb19059

It is curious what the authors state in their 2013 paper (Paper 4): “Some very good reports on in vitro propagation of the Vitex species like Vitex negundo are available…Ahmad and Anis 2007a; … Ahmad et al. 2008; Ahmad and Anis 2011; Ahmad et al. 2013).” (p. 2494) The next sentence makes a false claim: “However, no report on the successful in vitro mass multiplication of V. trifolia is available except a single preliminary report (Hiregoudar et al. 2006) with limited insight about the process.”, failing to recognize – and bring to the attention of the reader – their own paper in 2012 (Paper 1), as well as another excellent study (Arulanandam J. P., S. Ghanthikumar. 2011. Indirect organogenesis of Vitex trifolia Linn. – an important medicinal plant. Indian J. Nat. Prod. Resour. 2 (June), 261–264). Incidentally, Paper 1 is not referenced in the 2013 paper (Paper 4).

Finally, in all the Vitex papers, there is a query regarding relative humidity in your growth chamber, which tends to differ among publications, but most frequently 60–65% relative humidity. Could you please indicate the equipment (model, maker) that you have used to assess relative humidity.

The authors, who have been contacted, are kindly requested to address these issues publically and to correct the literature.

This case has 4 PubPeer entries:
https://pubpeer.com/publications/A6882B9CDFABE0E6BB8F785C56DD73#fb19080 (paper 1)
https://pubpeer.com/publications/35233FCE60069A90AB2EEF823F6F66#fb19082 (paper 2)
https://pubpeer.com/publications/E808598705E04B19E6818A514BE5D2#fb19083 (paper 3)
https://pubpeer.com/publications/B82DC5E43C2F12595413064EA6447F#fb19085 (paper 4)

Reply
Potato virus says:

December 22, 2014 at 2:19 pm

How does one accidentally leave out the name of two authors? That is precisely what happened in this Tunisian potato virus paper published by Springer’s Potato Research:
The original:
Potato Research September 2010, Volume 53, Issue 3, pp 151-166
Incidence and Characterization of Potato virus Y in Seed Potatoes in Tunisia
Sonia Boukhris-Bouhachem, Fattouma Djilani-Khouadja, Hatem Fakhfakh, Laurent Glais, Michel Tribodet, Camille Kerlan
http://link.springer.com/article/10.1007/s11540-010-9159-9

The erratum:
http://link.springer.com/article/10.1007/s11540-011-9191-4
which states: “In the original version of this article (Potato Research 53 (3): 151–166) the names of two contributing authors were not included. The full list of authors should read:
Boukhris-Bouhachem S., Rouze-Jouan J., Khamassi N., Djilani-Khouadja F., Fakhfakh H., Glais L, Tribodet M, Kerlan C.”

Reply
Annamalai University queries says:

December 27, 2014 at 11:02 pm

A storm is brewing at PubPeer surrounding several articles by a group from India. It relates to claims about the methodology related to the production of silver or gold nanoparticles in plants.

The authors are all from the Physics and Engineering Physics departments of Annamalai University. The authors have not yet responded to anonymous calls to respond to these public criticisms.
Physics: http://annamalaiuniversity.ac.in/deptprofile_0128.php?deptcode=0128
Engineering Physics:
http://www.annamalaiuniversity.ac.in/faculty_dept.php?factcode=51
http://www.annamalaiuniversity.ac.in/faculty_dept.php?factcode=53

All concerns/doubts are about 5 papers published in Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy.

https://pubpeer.com/publications/1A9D4450FF6594B7A71B5A182B228F#fb19167
http://www.sciencedirect.com/science/article/pii/S1386142514008671

https://pubpeer.com/publications/9A63831088B58E071F70A69D834612#fb19166
http://www.sciencedirect.com/science/article/pii/S1386142514005307

https://pubpeer.com/publications/50BE46B628DE5079A849CF6221504D#fb19342　
http://www.sciencedirect.com/science/article/pii/S1386142514014875

https://pubpeer.com/publications/0FCA4DB408DEBB3C0950EF1E748D3D#fb19296
http://www.sciencedirect.com/science/article/pii/S1386142513012304

https://pubpeer.com/publications/3A9AA913F9F0AB41936FBC0A11E410#fb19283
http://www.sciencedirect.com/science/article/pii/S1386142514017934

It is also curious to notice a high abundance of papers published by members of the Physics Department in predatory open access publishers:
http://www.scholarlyoa.com

Reply
1. Annamalai University queries says:
  
  January 4, 2015 at 4:04 am
  
  One more paper claiming similar methodology, but in a Hindawi journal, is also raising eye-brows:
  https://pubpeer.com/publications/0960FCB873A17ABBCD3F6A1556261E
  Journal of Nanoscience
  Volume 2014 (2014), Article ID 905404, 8 pages
  http://dx.doi.org/10.1155/2014/905404
  Research Article
  Biosynthesis and Characterization of Gold and Silver Nanoparticles Using Milk Thistle (Silybum marianum) Seed Extract
  R. Gopalakrishnan and K. Raghu
  Department of Physics, Annamalai University, Annamalainagar, Tamil Nadu 608 002, India
  Received 26 November 2013; Accepted 18 January 2014; Published 12 March 2014
  Academic Editor: Liqiang Jing
  http://www.hindawi.com/journals/jns/2014/905404/
  
  Reply
  1. Annamalai University queries says:
    
    January 8, 2015 at 2:51 am
    
    A 7th paper by this group is now being questioned:
    Synthesis of silver nanoparticles using Solanum trilobatum fruits extract and its antibacterial, cytotoxic activity against human breast cancer cell line MCF 7
    Manikandan Ramar, Beulaja Manikandan, Prabhu Narayanan Marimuthu, Thiagarajan Raman, Anjugam Mahalingam, Palanisamy Subramanian, Saravanan Karthick, Arumugam Munusamy, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2014)
    https://pubpeer.com/publications/BB7E0AECB98505F6A460C6D0EE07EF#fb20700
    http://www.sciencedirect.com/science/article/pii/S138614251401840X
    
    Reply
Seyed Alireza Salami queries says:

January 2, 2015 at 2:02 pm

This involves two separate cases, but a common author: Seyed Alireza Salami

Both cases discussed at PubPeer:
https://pubpeer.com/publications/4C4A8720A74D3ECDD6B8171EA30513#fb20089

Case 1
Factors Affecting Callus Induction and Organogenesis in Saffron (Crocus sativus L.)
Maryam Vahedi, Siamak Kalantari, Seyed Alireza Salami
Department of Horticultural Science, Faculty of Agricultural Sciences and Engineering, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
Plant Tissue Culture and Biotechnology 24(1): 1-9, 2014 (June)
DOI: http://dx.doi.org/10.3329/ptcb.v24i1.19184 (10.3329/ptcb.v24i1.19184)
http://www.banglajol.info/index.php/PTCB/article/view/19184

Issues: numerous scientific flaws.

Case 2 (partial apparent duplication)

Paper 1:
Salami, S.A., Ebadi, A., Zamani, Z. and Koohi Habibi , M. 2009. DISTRIBUTION OF GFLV IN IRANIAN VINEYARDS AND IMPROVEMENTS TO SANITATION PROTOCOLS FOR PRODUCTION OF VIRUS-FREE GRAPEVINES. Acta Horticulturae (ISHS) 829:389-393
DISTRIBUTION OF GFLV IN IRANIAN VINEYARDS AND IMPROVEMENTS TO SANITATION PROTOCOLS FOR PRODUCTION OF VIRUS-FREE GRAPEVINES
http://www.ishs.org/ishs-article/829_62

Paper 2:
S. A. Salami ; A. Ebadi ; Z. Zamani ; M. Koohi Habibi
Incidence of Grapevine Fanleaf Virus in Iran: A Survey Study and Production of Virus-Free Material Using Meristem Culture and Thermothe¬rapy
European Journal of Horticultural Science (EJHS) 74 (1). S. 42–46, 2009, ISSN 1611-4426.
http://www.ejhs.de/artikel.dll/ejhs-19-08_MTE2Mzc0Mg.PDF?UID=C3C8F430F2CE34601CA5428D4B3B2F1DA6114A8EA77A755ED1
http://www.ejhs.de/Incidence-of-IGrapevine-Fanleaf-VirusI-in-Iran-A-Survey-Study-and-Production-of-Virus-Free-Material-Using-Meri,QUlEPTExNjM3NDAmTUlEPTE0MjkmQVJPT1Q9NzUxODMmVEVNUF9NQUlOPVNjaWVudGlmaWNzX1BvcnRyYWl0Lmh0bQ.html?UID=C3C8F430F2CE34601CA5428D4B3B2F1DA6114A8EA77A755ED0

Both copyrighted papers can be accessed on the author’s ResearchGate web-page for comparison:
http://www.researchgate.net/profile/Seyed_Alireza_Salami2/publications

Issues/concerns:
a) Most of the study is almost identical, with wording different, most likely due to different peer review by both journals. Paper 2 includes additional data.
b) Some self-plagiarism (see sample below from Introduction).
c) Duplicated data and figure: Figure 2 of Table 1 is identical to Figure 2 of Paper 2; Table 1 of paper 1 is identical to Table 3 of Paper 2.
d) Neither paper acknowledges the existence of the other; paper 1 contains no data bout submission, revision or acceptance dates but paper 2 indicates: “Received September 11, 2007 / Accepted October 09, 2008”

From paper 1: “Fanleaf degeneration, a disease caused by Grapevine fanleaf virus (GFLV), reducing the yield by up to 80% by itself. GFLV is thought to have originated from ancient Persia and spread to the west through infected propagation material (Vuittenz, 1970; Zaki-Aghl and Izadpanah, 2003). The presence of GFLV has also been reported in different regions of Iran (Ghorbani, 1988; Zaki-aghl and Izadpanah, 2003). Considerable progress has been made regarding the implementation of certification schemes in several countries, most focused on using certified propagation material obtained from in vitro meristem-tip culture and heat therapy (Gifford and Hewitt, 1961; Lehoczky et al., 1992; Szegedi, 1995; Leonhardt et al., 1998). Wide distribution of GFLV and other viral diseases in Iran, and the need for an intensive sanitation program, prompted us to carry out appropriate experiments in order to evaluate the effect of meristem-tip culture and thermotherapy for GFLV eradication and also to set up systems for selecting material free of viruses. Information on the present geographical distribution and the incidence of GFLV were also studied.”

From paper 2: “Fanleaf degeneration, a disease caused by Grapevine fanleaf virus (GFLV), is the most destructive viral disease worldwide reducing the yield by up to 80 %. GFLV is though to have originated from ancient Persia and then spread to the west through infected propagation material (VUITTENZ 1970; ZAKI-AGHL and IZADPANAH 2003). The first report of GFLV in Iran was based on visual symptoms (VUITTENZ 1970). The presence of GFLV in Urmia, North-west of Iran, was later reported by GHORBANI 1988. Recently, reports concerned the incidence and prevalent of GFLV in Iranian vineyards (RAKHSHANDEHROO et al. 2005; BASHIR and HAJIZADEH 2007). … Considerable progresses were made regarding the implementation of certification schemes in several countries, most, focused on using certified propagation material obtained from in vitro meristem culture and heat therapy (GIFFORD and HEWITT 1961; LEHOCZKY et al. 1992; SZEGEDI 1995; LEONHARDT et al. 1998). Due to the severity and wide distribution of GFLV and other viral diseases in Iran (HABILI et al. 2003; RAKHSHANDEHROO et al. 2005), the increasing demand for sustainable and environmentally safe viticulture practices and intensive sanitation program, there is a great need to develop appropriate experiments in order to evaluate the effect of the meristem culture and thermotherapy for GFLV eradication and also to set up systems for selecting material free of viruses. The goal of the current study was to determine the incidence and distribution of GFLV in Iran as well as the ability of meristem culture and thermotherapy in virus-free plant material production.”

Should data be duplicated, even if partially? Is this compatible with the publishing ethics codes of both journals and publishers? If this practice is acceptable, then what message does that send to all other authors of both journals?

This is important to know the policy of EJHS, especially since EJHS will be published, from January 1, 2015, by The International Society for Horticultural Science (ISHS), which currently publishes Acta Horticulturae. (see EJHS top page for details)

Reply
1. Seyed Alireza Salami queries says:
  
  January 3, 2015 at 7:45 am
  
  The papers below are linked to these other papers by Dr. Salami because paper 2 has no DOI and paper 1 DOI does not link to PubPeer.
  
  Paper 1
  Full Length Research Paper
  S.A. Salami 1*, A. Ebadi 1, M.R. Naghavi 2 and I.B. Dry 3
  Cloning and functional characterization of a class III chitinase gene from grapevine: Inhibition of fungal growth by recombinant VvChiF III
  1 Department of Horticulture, Faculty of Horticultural Sciences and Plant Protection, University of Tehran, Karaj, Iran.
  2 Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tehran, Karaj 31587, Iran.
  3 CSIRO Plant Industry, PO Box 350, Glen Osmond SA 5064, Australia.
  African Journal of Biotechnology 7 (24), 4400-4405, 17 December, 2008
  http://www.ms.academicjournals.org/journal/AJB/article-stat/06C93A78730
  http://www.ajol.info/index.php/ajb/article/viewFile/59597/47887 (open access)
  DOI: 10.5897/AJB08.842
  ISSN 1684–5315 © 2008 Academic Journals
  
  Paper 2
  A. Ebadi, S.A. Salami, M.R. Naghavi, I.B. Dry
  Cloning and Characterization of VvChiF III Gene from Vitis vinifera cv. ‘Flame seedless’
  Acta Horticulturae (ISHS) 839:659-664
  http://www.actahort.org/books/839/839_90.htm
  © International Society for Horticultural Science
  Editors: Magda-Viola Hanke, Frank Dunemann, Henryk Flachowsky
  http://www.actahort.org/books/839/index.htm
  
  Both copyrighted papers can be accessed on the author’s ResearchGate web-page for comparison:
  http://www.researchgate.net/profile/Seyed_Alireza_Salami2/publications
  
  Issues/concerns:
  a) Many parts of the study are almost identical (DNA extraction, PCR amplification, cloning and sequencing), with wording different, most likely due to different peer review by both journals. Paper 1 includes additional data. In essence, the exact same gene is characterized in both papers.
  b) Some self-plagiarism (see sample below from Introduction).
  c) Duplicated data and figures: Figure 1 of paper 1 is identical to Figure 1 of paper 2 (lanes 2 and 3 removed in paper 2); Figure 2 of paper 1 is identical to Figure 2 of Paper 2 (i.e., the exact same amino acid sequence is represented and compared to three other sequences, but the visual representation is different).
  d) Neither paper acknowledges the existence of the other; paper 2 contains no data about submission, revision or acceptance dates but paper 1 indicates: “Accepted 20 October, 2008”
  
  … indicates text split by other text.
  
  Paper 1
  “plants have evolved a range of mechanisms to resist pathogen invasion (Allen et al., 2004). The first line of defense to pathogen attack are the cuticle and the cell wall which represent physical barriers to penetration. Secondly plant cells contain both preformed and inducible antimicrobial compounds such as phenols, sulphur compounds, phenolic glycosides, unsaturated lactones, saponins, cyangenic glycosides, glucosinolates, phytoalexins together with pathogenesis related (PR) proteins (Osbourn 1996; Dixon, 2001; Van Loon et al., 2006). In recent years, several molecular approaches have been used to investigate resistance against fungal diseases in grapevine that have provided some insight into these defence mechanisms. Two groups of PR proteins that have a significant role in the defence against invading fungal pathogens are the -1,3-glucanase (PR group 2) and chitinases (PR group 3) and plant chitinases are thought have an important role in the plant defence system against fungal pathogens due to its ability to hydrolyze chitin which is abundant in the cell walls of many fungi. Chitinase induction during fungal attack as well as in vitro inhibition of fungal growth has been demonstrated (Schlumbaum et al., 1986; Linthorst, 1991; Arlorio et al., 1992; Collinge et al., 1993; Herrera-Estrella and Chet, 1999; Ano et al., 2003)…. Enhanced resistance to fungal pathogens has also been demonstrated in transgenic plants over-expressing chitinase or b-1,3-glucanase, with a synergistic benefit where both genes are present (Broglie et al., 1991; Jach et al., 1995; Jongedijk et al., 1995; Grison et al., 1996; Asao et al., 1997; Yamamoto et al., 2000)…Consequently, plant chitinases are the subject of intensive research that may ultimately lead to disease resistant crops and decreased use of ecologically harmful pesticides. This area of research is also of particular interest in grapes because of their widespread production for winemaking, dried fruit, and table grapes and their susceptibility to a wide range of fungal pathogens such as powdery mildew, downy mildew and botrytis.”
  
  Paper 2
  “Generally plants have evolved a range of different defense mechanisms against pathogen invasion, leading to co-evolution of pathogen attack and plant defence mechanisms (Allen et al., 2004). The first line of defense to pathogen attack are the cuticle and the cell wall which represent physical barriers. Secondly, plant cells contain preformed and inducible antimicrobial compounds such as phenols, sulphur compounds, phenolic glycosides, unsaturated lactones, saponins, cyangenic glycosides, and glucosinolates, phytoalexins together with pathogenesis-related (PR) proteins (Osbourn, 1996; Dixon, 2001; Van Loon et al., 2006). In recent years, several molecular approaches have been used to investigate resistance against fungal diseases in grapevine that have provided some insight into these defense mechanisms. Two groups of PR proteins that have a significant role in the defence against invading fungal pathogens are chitinase and β-1,3-glucanases. Plant chitinases are thought to be closely related to plants’ defense system against pathogens due to its ability to hydrolyze chitin, a biopolymer of Nacetyl-D-glucosamine which is abundant in the cell walls of many fungi. … chitinase induction during fungal attack as well as in vitro inhibition of fungal has been demonstrated (Schlumbaum et al., 1986; Linthorst, 1991; Arlorio et al., 1992; Collinge et al., 1993; Herrera-Strella and Chet, 1999; Ano et al., 2003),…enhanced resistance to fungal pathogens has also been demonstrated in transgenic plants over-expressing chitinase or β-1,3-glucanase, with a synergistic benefit where both genes are present (Broglie et al., 1991; Jach et al., 1995; Jongedijk et al., 1995; Grison et al., 1996; Asao et al., 1997; Yamamoto et al., 2000)…Consequently, plant chitinases are the subject of intensive research that may ultimately lead to disease resistant crops and decreased use of ecologically harmful fungicides. This area of research is also of particular interest in grapes because of their widespread production for winemaking, dried fruit, and table grapes and their susceptibility to a wide range of fungal pathogens such as powdery mildew, downy mildew and botrytis.”
  
  Seyed Alireza Salami
  http://utcan.ut.ac.ir/member/asalami.aspx
  Mohammad Reza Naghavi
  http://utcan.ut.ac.ir/member/naghavi.aspx
  Ian B. Dry
  http://www.csiro.au/Organisation-Structure/Divisions/Plant-Industry/Dr-Ian-Dry-fighting-grapevine-disease.aspx
  
  Reply
2. Seyed Alireza Salami queries says:
  
  January 3, 2015 at 8:52 am
  
  The papers below are linked to these other papers by Dr. Salami because both papers have no DOI.
  
  Paper 1:
  Alireza Salami, Ali Ebadi, Zabihalah Zamani, Maryam Ghasemi. 2005. Improvement in Apex Culture in an Iranian Grapevine (Vitis vinifera L. ‘Bidaneh Sefid’) through Fragmented Shoot Apices. International Journal of Agriculture & Biology 7(3): 333-336
  http://www.fspublishers.org/Issue.php?categoryID=29
  http://www.fspublishers.org/published_papers/97146_..pdf
  Publisher: Friends Science Publishers*
  * Listed as a predatory open access publisher:
  http://scholarlyoa.com/publishers/
  
  Paper 2:
  S.A. Salami, A. Ebadi and Z. Zamani
  Commercial Mass Clonal Propagation of Grapevine cv. ‘Bidaneh Sefid’: In Vitro Fragmented Shoot Apex Culture of an Elite Germplasm. Acta Horticulturae 829:383-388
  http://www.ishs.org/ishs-article/829_61
  http://www.actahort.org/books/829/829_61.htm
  
  Both copyrighted papers can be accessed on the author’s ResearchGate web-page for comparison:
  http://www.researchgate.net/profile/Seyed_Alireza_Salami2/publications
  
  Issues/concerns:
  a) Many parts of the study are almost identical. In essence, the exact same protocol for plant regeneration through fragmented shoot apices is described in both papers.
  b) Some self-plagiarism (see sample below from Introduction).
  c) Duplicated data and figures: Figure 1-6 of paper 1 is identical to Figure 3a-f of paper 2.
  d) Neither paper acknowledges the existence of the other; paper 2 contains no data about submission, revision or acceptance dates but paper 1 indicates: “Received 05 January 2005; Accepted 15 April 2005”
  e) Curiously, paper 2 states “Shoot apex of virus-free grapevine cv. ‘Bidaneh Sefid’ containing two to three leaf primordia (5-10 mm in length) were excised and sterilized according to Salami et al. (2009).” The 2009 paper refers to the European Journal of Horticultural Science paper, which suggests that reference to the 2005 was intentionally omitted.
  f) Only paper 1 acknowledges financial assistance: “This project was supported by Agriculture Faculty, Department of Horticulture of Tehran University. Tehran. Iran.”
  
  Paper 1
  “Every year, a variety of virus diseases occur on vines that effect on production and quality. Avoidance the viruses is the best way to protect the vineyards from virus diseases. Using certified materials ensure that the materials have been tasted for known strains of viruses and viruses have been eliminated. So vine plantation must be from certified virusfree sources. Since only a few plants are usually certified virus-free, it takes several years to propagate enough vines by conventional methods (Harris & Stevenson, 1979)…there is a need for the rapid buildup of unique techniques so that vines may be available in sufficient quantities for commercial production (Raymond et al., 1984)…Tissue culture results in rapid clonal multiplication and uniformity in obtained clones, vigorous growth, normal yield and healthy plants (Blazina et al., 1991)…Many in vitro techniques can be used for mass clonal propagation of vitis species. Some reports concerning mass propagation of vitis species by shoot apices (Barlass & Skene, 1978; Chee & Pool, 1982; Fanizza et al., 1984; Goussard, 1981; Harris & Stevenson, 1979; Li & Eaton, 1984; Monette, 1983; Morini, et al., 1985), axillary buds (Jona & Webb, 1978; Lee & Wetzstein, 1990; Novak & Juvova, 1982; Pool & Powell, 1975), and some reports demonstrate the feasibility of producing vines via somatic embryogenesis (Krul & Worley, 1977; Krul & Myerson, 1980; Mullins & Srinivasan, 1976; Srinivasan & Mullins, 1980)…From the economic point of view, after producing healthy plants, it needs a method that can potentially produce large number of healthy vines in a short period. To achieve this, in this study we described a simple and rapid method by which large scale of adventitious buds were proliferated from singe fragmented shoot apex of an Iranian grapevine cultivar Bidaneh Sefid. Apart from brief references (Barlass & Skene, 1978, 1980) formation of adventitious buds from single fragmented shoot apex of grapevine are still rare and has not been reported with Iranian cultivars yet. This cultivar is same as Thompson seedless cultivar and is used extensively for producing raisins. Raisins produce from this cultivar is considered unique in the world in kind and quality.”
  
  Paper 2
  “However, every year a wide variety of virus diseases occur on vines that effect both production and quality. Using certified materials ensures that planting materials have been tested for known strains of viruses and they have been eliminated. It is important therefore to ensure that all planting material comes from certified virus-free sources. However, since only a few plants are usually certified as virus-free stocks, it takes several years to propagate enough vines by conventional methods (Harris and Stevenson, 1979)… there is a need for the rapid buildup of unique specimens so that sufficient quantities of vines are available for commercial production (Chee et al., 1984)… Tissue culture results in rapid clonal multiplication and uniformity in the clones obtained, vigorous growth, normal yield and healthy plants (Blazina et al., 1991)… Many in vitro techniques can be used for rapidly propagate Vitis species including the use of shoot apices (Barlass and Skene, 1978; Chee and Pool, 1982; Fanizza et al., 1984; Goussard, 1981; Harris and Stevenson, 1979; Li and Eaton, 1984; Monette, 1983; Morini et al., 1985) and axillary buds (Jona and Webb, 1978; Lee and Wetzstein, 1990; Novak and Juvona, 1982; Pool and Powell, 1975). Some reports also demonstrate the feasibility of producing vines via somatic embryogenesis (Krul and Worley, 1977; Krul and Myerson, 1980; Mullins and Srinivasan, 1976; Srinivasan and Mullins, 1980)…From the economic point of view, once healthy plants are produced, a method with high potential of producing large numbers of healthy vines in a short period of time is required. To achieve this, we describe a simple and rapid method by which large numbers of adventitious buds were proliferated from a single fragmented shoot apex of an Iranian grapevine cultivar ‘Bidaneh Sefid’. Apart from a brief reference (Barlass and Skene, 1978), reports on the formation of adventitious buds via single fragmented shoot apex of Vitis vinifera are still rare and have not yet been reported for Iranian cultivars yet. ‘Bidaneh Sefid’ is a native Iranian grapevine cultivar which looks like ‘Thompson Seedless’ cultivar in many aspects and may have originally been transferred from Iran to other regions of the world and renamed as ‘Thompson Seedless’. This cultivar is used extensively for producing raisins and is considered unique in the world in terms of quality and popularity.”
  
  Reply
3. Seyed Alireza Salami queries says:
  
  January 5, 2015 at 2:24 am
  
  The papers below are linked to these other papers by Dr. Salami because neither paper has a DOI.
  
  Paper 1:
  Salami, S.A., Ebadi, A., Zamani, Z. and Koohi Habibi , M. 2009. DISTRIBUTION OF GFLV IN IRANIAN VINEYARDS AND IMPROVEMENTS TO SANITATION PROTOCOLS FOR PRODUCTION OF VIRUS-FREE GRAPEVINES. Acta Horticulturae (ISHS) 829:389-393
  DISTRIBUTION OF GFLV IN IRANIAN VINEYARDS AND IMPROVEMENTS TO SANITATION PROTOCOLS FOR PRODUCTION OF VIRUS-FREE GRAPEVINES
  http://www.ishs.org/ishs-article/829_62
  
  Paper 2:
  S. A. Salami ; A. Ebadi ; Z. Zamani ; M. Koohi Habibi
  Incidence of Grapevine Fanleaf Virus in Iran: A Survey Study and Production of Virus-Free Material Using Meristem Culture and Thermothe¬rapy
  European Journal of Horticultural Science (EJHS) 74 (1). S. 42–46, 2009, ISSN 1611-4426.
  http://www.ejhs.de/artikel.dll/ejhs-19-08_MTE2Mzc0Mg.PDF?UID=C3C8F430F2CE34601CA5428D4B3B2F1DA6114A8EA77A755ED1
  http://www.ejhs.de/Incidence-of-IGrapevine-Fanleaf-VirusI-in-Iran-A-Survey-Study-and-Production-of-Virus-Free-Material-Using-Meri,QUlEPTExNjM3NDAmTUlEPTE0MjkmQVJPT1Q9NzUxODMmVEVNUF9NQUlOPVNjaWVudGlmaWNzX1BvcnRyYWl0Lmh0bQ.html?UID=C3C8F430F2CE34601CA5428D4B3B2F1DA6114A8EA77A755ED0
  
  Both copyrighted papers can be accessed on the author’s ResearchGate web-page for comparison:
  http://www.researchgate.net/profile/Seyed_Alireza_Salami2/publications
  
  Issues/concerns:
  a) Most of the study is almost identical, with wording different, most likely due to different peer review by both journals. Paper 2 includes additional data.
  b) Some apparent self-plagiarism (see sample below from Introduction).
  c) Apparent duplicated data and figure: Figure 2 of Paper 1 is identical to Figure 2 of Paper 2; Table 1 of paper 1 is identical to Table 3 of Paper 2.
  d) Neither paper acknowledges the existence of the other; paper 1 contains no data bout submission, revision or acceptance dates but paper 2 indicates: “Received September 11, 2007 / Accepted October 09, 2008”
  
  From paper 1: “Fanleaf degeneration, a disease caused by Grapevine fanleaf virus (GFLV), reducing the yield by up to 80% by itself. GFLV is thought to have originated from ancient Persia and spread to the west through infected propagation material (Vuittenz, 1970; Zaki-Aghl and Izadpanah, 2003). The presence of GFLV has also been reported in different regions of Iran (Ghorbani, 1988; Zaki-aghl and Izadpanah, 2003). Considerable progress has been made regarding the implementation of certification schemes in several countries, most focused on using certified propagation material obtained from in vitro meristem-tip culture and heat therapy (Gifford and Hewitt, 1961; Lehoczky et al., 1992; Szegedi, 1995; Leonhardt et al., 1998). Wide distribution of GFLV and other viral diseases in Iran, and the need for an intensive sanitation program, prompted us to carry out appropriate experiments in order to evaluate the effect of meristem-tip culture and thermotherapy for GFLV eradication and also to set up systems for selecting material free of viruses. Information on the present geographical distribution and the incidence of GFLV were also studied.”
  
  From paper 2: “Fanleaf degeneration, a disease caused by Grapevine fanleaf virus (GFLV), is the most destructive viral disease worldwide reducing the yield by up to 80 %. GFLV is though to have originated from ancient Persia and then spread to the west through infected propagation material (VUITTENZ 1970; ZAKI-AGHL and IZADPANAH 2003). The first report of GFLV in Iran was based on visual symptoms (VUITTENZ 1970). The presence of GFLV in Urmia, North-west of Iran, was later reported by GHORBANI 1988. Recently, reports concerned the incidence and prevalent of GFLV in Iranian vineyards (RAKHSHANDEHROO et al. 2005; BASHIR and HAJIZADEH 2007). … Considerable progresses were made regarding the implementation of certification schemes in several countries, most, focused on using certified propagation material obtained from in vitro meristem culture and heat therapy (GIFFORD and HEWITT 1961; LEHOCZKY et al. 1992; SZEGEDI 1995; LEONHARDT et al. 1998). Due to the severity and wide distribution of GFLV and other viral diseases in Iran (HABILI et al. 2003; RAKHSHANDEHROO et al. 2005), the increasing demand for sustainable and environmentally safe viticulture practices and intensive sanitation program, there is a great need to develop appropriate experiments in order to evaluate the effect of the meristem culture and thermotherapy for GFLV eradication and also to set up systems for selecting material free of viruses. The goal of the current study was to determine the incidence and distribution of GFLV in Iran as well as the ability of meristem culture and thermotherapy in virus-free plant material production.”
  
  This is an important case because the EJHS is now being published, from January 1, 2015, by The International Society for Horticultural Science (ISHS), which currently publishes Acta Horticulturae. (see EJHS top page for details)
  
  Reply
Cauliflower Synthetic Seeds stealth retraction says:

January 5, 2015 at 2:31 am

Abbreviations: F, figure; M&M, materials and methods; R&D, results and discussion; T, table; =, identical to

P-1
In vitro Development of Cauliflower Synthetic Seeds and Development of Plantlets In vivo
Zahida Qamar, Md. Belal Hossain *, Idrees A. Nasir, Bushra Tabassum, Tayyab Husnain
National Centre of Excellence in Molecular Biology, University of the Punjab, 87‐West Canal Bank Road Thokar Niaz Baig, Lahore‐53700, Pakistan
* Present address: Department of Plant Pathology, Sher‐e‐Bangla Agricultural University, Dhaka‐1207, Bangladesh
Plant Tissue Culture and Biotechnology 24(1): 27-36, 2014 (June)
DOI: http://dx.doi.org/10.3329/ptcb.v24i1.19193 (10.3329/ptcb.v24i1.19193)
http://www.banglajol.info/index.php/PTCB/article/view/19193
No publishing-related dates.

P-2
In-vitro development of cauliflower synthetic seeds and conversion to plantlets.
Advancements in Life Sciences 1(2), 104-111, February 2014
Zahida Qamar1*, Idrees Ahmed Nasir1, Tayyab Husnain1
1- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore -Pakistan
Date Received: 09/19/2013; Date Revised: 01/29/2014; Date Published Online: 02/25/2014
http://www.als-journal.com/manuscript5-11-1-sm/
http://www.als-journal.com/articles/vol1issue2/Invitro_Cauliflower_Synthetic_Seeds.pdf
No DOI.

Problems:
1) Apparent duplications, including to the text, tables and figures (see 5 below).
2) Many factual comments in introduction made without support from the literature.
3) M&M: almost identical wording of methodology.
4) R&D: unsubstantiated claims of somatic embryogenesis.
5) Apparent figure duplications: F1, 1a, 2 (P-1) = F1A, 1B, 2 (P-2); F3 (P-1) = F2 (second) (P-2); F5 (P-1) = F3 (P-2); F6 (P-1) = Graph 1 (P-2); F7 (P-1) = F4 (P-2);
6) P-2: there are 2X figure 2.
7) References in P-2 has several errors.

This case was posted anonymously to PubPeer on January 2, 2015:
https://pubpeer.com/publications/792C45783C123EB199C5D9E5D874A6#fb20107

All authors, related institutional members and publishers were contacted. Within 48 hours (by January 4, 2015), Paper 2 had been retracted, but without any evidence of the original paper, or the reason for retraction, raising concern not only about the authors, but also about the publisher of paper 2, published in Advancements in Life Sciences.

What is particularly curious is that Idrees Ahmed Nasir, co-author of both papers, is also the Editor-in-Chief of Advancements in Life Sciences:
http://www.als-journal.com/editorial-board/
http://pu.edu.pk/images/cv/1310371197504.pdf (no papers listed on that CV)

The senior author of both papers, Prof. Tayyab Husnain, is the Director of the Centre for Excellence in Molecular Biology:
http://pu.edu.pk/home/department/54/
http://pu.edu.pk/images/cv/1349342945CV%20Prof.%20Dr.Tayyab%20Husnain.pdf (outdated CV)

Reply
Agrobacterium tumefaciens query says:

January 5, 2015 at 2:51 am

Viral and chloroplastic signals essential for initiation and efficiency of translation in Agrobacterium tumefaciens
Tauqeer Ahmad, Srividhya Venkataraman, Kathleen Hefferon, Mounir G. AbouHaidar
Biochemical and Biophysical Research Communications Volume 452, Issue 1, 12 September 2014, Pages 14–20
Department of Cell and Systems Biology, University of Toronto, St. George Campus, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
DOI: 10.1016/j.bbrc.2014.07.135
http://www.sciencedirect.com/science/article/pii/S0006291X14013989

Queries about possible gel band splicing.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/77D69F484C641B3F8B7F4A1B581E9C#fb20315　

Reply
Circular RNA query says:

January 5, 2015 at 2:51 am

Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt
Mounir Georges AbouHaidara,1, Srividhya Venkataramana, Ashkan Golshanib, Bolin Liua, Tauqeer Ahmada
PNAS 111 (40), 14542–14547
a Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3B2;
b Biology Department, Carleton University, Ottawa, ON, Canada K1S 5B6
DOI: 10.1073/pnas.1402814111
http://www.pnas.org/content/111/40/14542
Author contributions: M.G.A. designed research; S.V., A.G., B.L., and T.A. performed research; M.G.A., S.V., and A.G. analyzed data; and M.G.A. and S.V. wrote the paper.

Queries about possible gel band splicing.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/C3BF114C14D6F897D1C9895B84ED3C#fb20316

Reply
Potato stats query says:

January 5, 2015 at 2:52 am

Research Article
BioMed Research International Volume 2014 (2014), Article ID 439259, 7 pages
http://dx.doi.org/10.1155/2014/439259
Combination of the Auxins NAA, IBA, and IAA with GA3 Improves the Commercial Seed-Tuber Production of Potato (Solanum tuberosum L.) under In Vitro Conditions
Ahmet Metin Kumlay
Department of Field Crops, Faculty of Agriculture, Igdir University, 76000 Igdir, Turkey
Received 18 April 2014; Accepted 19 May 2014; Published 17 June 2014
Academic Editor: Khalid Mahmood Khawar
DOI: 10.1155/2014/439259
http://www.hindawi.com/journals/bmri/2014/439259/

Queries about statistical analyses and interpretation.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/07FD4F1BACA695E8C5E5717FBD70DC#fb20318

Reply
Carbon nanotubes query says:

January 5, 2015 at 2:53 am

Potential Impact of Multi-Walled Carbon Nanotubes Exposure to the Seedling Stage of Selected Plant Species.
Nanomaterials 2014, 4, 203-221.
Parvin Begum, Refi Ikhtiari, Bunshi Fugetsu
Laboratory of Environmental Medical Chemistry, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
DOI: 10.3390/nano4020203
http://www.mdpi.com/2079-4991/4/2/203

Queries about what constitutes originality in an original research paper when 4 out of 6 of the figures have already been published.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/A24FAF0D5D2B0DDE8E811876ECC93A#fb20319

Reply
1. Carbon nanotubes query says:
  
  March 2, 2015 at 2:57 pm
  
  This paper was retracted on March 2, 2015.
  http://www.mdpi.com/2079-4991/5/1/268
  “We have become aware that a substantial part of the main text of [1] is copied from multiple other publications. In total, 46% of the main text was taken from publications by the same authors [2,3] and 10% from other papers [4,5]. Because of the extent of text taken verbatim from previously published articles, we have made the decision to retract the article. All the authors of [1] have agreed to this decision. This paper is thus declared retracted and shall be marked accordingly for the scientific record. MDPI is a member of the Committee on Publication Ethics (COPE) and takes the responsibility to enforce strict ethical policies and standards very seriously. We aim to ensure the publication only of
  truly original scientific works. MDPI would like to apologize to the readers of Nanomaterials that this case remained undetected until now. We sincerely appreciate the efforts of anyone who brings matters of plagiarism to our attention in an effort to maintain scientific integrity.”
  
  Reply
Chrysanthemum cut flowers query says:

January 5, 2015 at 9:02 am

Journal of Stored Products and Postharvest Research Vol. 4(4), pp. 51-54, December, 2013
Effect of low temperature storage on conservation varieties of Chrysanthemum cutting
Marcos Ribeiro da Silva Vieira 1, Adriano do Nascimento Simões 1, Glauber Henrique Sousa Nunes 2, Pahlevi Augusto de Souza 3
1 Universidade Federal Rural de Pernambuco, Unidade Acadêmica de Serra Talhada, CEP: 59909-460, Serra Talhada, PE, Brasil.
2 Departamento de Ciências Vegetais/UFERSA, Caixa Postal 137, CEP: 59625-900, Mossoró, RN, Brasil.
3 Instituto Federal de Educação, Ciência e Tecnologia do Ceará, CEP: 62930-000, Limoeiro do Norte, CE, Brasil.
DOI: 10.5897/JSPPR2013.0155
Publisher: Academic Journals, listed as predatory on http://scholarlyoa.com/publishers/
http://www.academicjournals.org/journal/JSPPR/article-stat/18E189242282
http://www3.iupui.academicjournals.org/article/article1387278218_Vieira%20et%20al.pdf (open access)
Total views: 858
Total downloaded: 460

Queries about interpretation of statistical analyses caused by poor English grammar.

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/C625318CE6EAD77AEA233DA2B70FE9#fb20409

Reply
Pear shoot regeneration query says:

January 5, 2015 at 10:20 am

Paper 1
Plant Tissue Culture and Biotechnology 24(1): 87-92, 2014 (June)
Induction of Direct Adventitious Shoot Regeneration in Pear (Pyrus communis L.)
Mahdieh Yousefiara *, Maryam Jafarkhani Kermani, Abdolreza Bagheri 1, Ali Akbar Habashi, Hamid Abdollahi 2
Department of Tissue Culture and Gene Transformation, Agricultural Biotechnology Research Institute of Iran (ABRII), Mahdasht Road, P.O. Box 31535‐1897, Karaj, Iran
*Author for correspondence: . 1 Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, P. O. Box 91775‐1163, Mashhad, Iran. 2 Department of Horticultural Research, Seed and Plant Improvement Institute, P.O. Box 4119, Karaj, Iran.
DOI: http://dx.doi.org/10.3329/ptcb.v24i1.19215
http://www.banglajol.info/index.php/PTCB/issue/view/1143
http://www.banglajol.info/index.php/PTCB/article/view/19215
http://baptcb.org/ptc/Full_article/ptc24_1_09.pdf (open access)

Paper 2
Journal of Plant Molecular Breeding (JPMB) Vol. 2/No. 1/June 2014/ 21-28 (volume number is incorrect on the PDF: it should be volume 3)
Study of factors affecting direct shoot regeneration of pear (Pyrus communis L.)
M. Yousefiara 1, M. Jafarkhani Kermani 2, A. Bagheri 1, A.A. Habashi 2, H. Abdollahi 3
1. Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad.
2. Department of Tissue Culture and Gene Transformation, Agricultural Biotechnology Research Institute of Iran (ABRII).
3. Department of Horticultural Research, Seed and Plant Improvement Institute, Karaj, Iran.
Corresponding Author, Email: [email protected]
Received: April 2014; Accepted: June 2014
http://www.jpmb-gabit.ir/
Publisher: Genetics & Agricultural Biotechnology Institute of Tabarestan (GABIT)
http://www.jpmb-gabit.ir/issue_1505_1506_Volume+3%2C+Issue+1%2C+Spring+2014%2C+Page+1-89.html (open access)
http://www.jpmb-gabit.ir/article_8426_1505.html
Article views: 264; PDF downloads: 218

a) Discrepancies in institutional addresses for the exact same authors.
b) Apparent self-plagiarism.
c) Acknowledgements: “This work was funded by Agricultural Biotechnology Research Institute of Iran (Project number: 12-05-05-8602-87002).”
d) Apparent duplicated data and figures: Figure 1 of paper 1 is identical to Figure 2 of paper 2; Figure 2 of paper 1 is identical to Figure 3 of Paper 2; Figure 3 of paper 1 is identical to Figure 4 of paper 2; Figure 4 of paper 1 is identical to Figure 5 of paper 2;.
e) Neither paper acknowledges the existence of the other.

Mahdieh Yousefiara
http://ma.yousefiara.student.um.ac.ir/
Abdolreza Bagheri
http://profsite.um.ac.ir/~abagheri/
Maryam Jafarkhani Kermani and Ali Akbar Habashi
http://www.abrii.ac.ir/en/AboutABRII/HumanResources/tabid/266/agentType/ViewType/PropertyTypeID/45/Default.aspx
Hamid Abdollahi
http://www.researchgate.net/profile/Hamid_Abdollahi3

There is a PubPeer entry for this case:
https://pubpeer.com/publications/3E98D19D10F5ACC255D36690BD6DAE#fb20416

Reply
Justicia gendarussa queries says:

January 7, 2015 at 1:07 am

Abbreviations: F = figure; P = paper; T = table

Paper 1 (P1)
K.L. Krishna, K. Mruthunjaya and J.A. Patel, 2009. Antioxidant and Hepatoprotective Activity of Leaf Extract of Justicia gendarussa Burm. International Journal of Biological Chemistry, 3: 99-110.
DOI: 10.3923/ijbc.2009.99.110
URL: http://scialert.net/abstract/?doi=ijbc.2009.99.110
http://www.scialert.net/qredirect.php?doi=ijbc.2009.99.110&linkid=pdf (open access)
Publisher: Academic Journals Inc. (listed at http://scholarlyoa.com/publishers/)
No information about submission, acceptance or publication dates.

Paper 2 (P2)
KL Krishna 1, Tejal A Mehta 2, Jagruti A Patel 2. 2010a. In-vitro hepatoprotective activity of Justicia gendarussa stem on isolated rat hepatocytes. Pharmacologyonline 2: 9-13
1 JSS College of Pharmacy, JSS University, Sri Shivarathreeswara Nagara, Mysore, Karnataka, India
2 Institute of Pharmacy, Nirma University of Science and Technology, Ahmedabad, Gujarat, India
No DOI.
http://pharmacologyonline.silae.it/files/archives/2010/vol2/002.Patel.pdf
http://pharmacologyonline.silae.it/front/archives_2010_2
Publisher: SILAE – Società Italo-Latinoamericana di Etnomedicina (http://www.silae.it/eng/front)
No information about submission, acceptance or publication dates.

Paper 3 (P3)
K.L. Krishna, K. Mruthunjaya and Jagruti A. Patel, 2010b. Antioxidant and Hepatoprotective Potential of Stem Methanolic Extract of Justicia gendarussa Burm. International Journal of Pharmacology, 6: 72-80.
DOI: 10.3923/ijp.2010.72.80
Publisher: ANSInet (listed at http://scholarlyoa.com/publishers/)
http://www.scialert.net/abstract/?doi=ijp.2010.72.80
http://scialert.net/fulltext/?doi=ijp.2010.72.80
http://scialert.net/qredirect.php?doi=ijp.2010.72.80&linkid=pdf (open access)
http://www.medwelljournals.com/ref.php?doi=ijp.2010.72.80
Cited by 26 (Google Scholar) http://scholar.google.com.pk/scholar?cites=264560318958090756&as_sdt=2005&sciodt=0,5&hl=en
http://www.medwelljournals.com/citation.php?doi=ijp.2010.72.80 (10 citations)
No information about submission, acceptance or publication dates.

Issues:
k) Comparing P1 and P3. T2 of both papers (Ascorbic acid, Gallic acid and BHT values identical; 18 data points the same). Ironically the IC50 value for BHT is different.
l) Comparing P1 and P3. T3 of both papers (Ascorbic acid and Gallic acid values identical; 12 data points the same).
m) Comparing P1 and P3. T5 of both papers (SGOT, SGPT, total bilirubin, direct bilirubin, ALP and total protein values of normal, CCL4 and Silymarin identical; 18 data points the same).
n) Comparing P1 and P3. In both papers, T5 GOT = F1, T5 SGPT = F2, T5 total bilirubin = F3, T5 direct bilirubin = F4, T5 total protein = F5, T5 SALP = F6 (36 data points the same).
o) In P1: T6 = F7 (wet liver weight) (6 data points the same).
p) In P2: T1 = F1 (% cell viability) (6 data points the same).
q) In P2: T1 = F2 (GOT) (6 data points the same).
r) In P2: T1 = F3 (GPT) (6 data points the same).
s) Comparing P1 and P3, considering points a-d above. How can extracts from completely different plant organs (leaves vs stems) give absolutely identical values for so many parameters, to two decimal places?
t) Comparing P1 and P2. How can a leaf vs stem extract give a 10-fold difference value for GOT, GPT and total proteins when P1 vs P3 give identical values?

The authors, editors and publishers are requested to correct the literature. The authors are requested to address these queries and concerns publically.

KL Krishna
http://www.jsspharma.org/dr-kl-krishna
Tejal A Mehta (Head of Department)
http://www.nirmauni.ac.in/ipnu/Faculty/Prof-Tejal-Amit-Mehta
Why are the three papers not listed on the list of publications? This is of concern.

There are two PubPeer entries for this case:
https://pubpeer.com/publications/EE5938271679169AE3875983A1F35F#fb20525 (P1)
https://pubpeer.com/publications/1E6D96150A6191A2DBA23F8CFF6D54#fb20534 (P3)

Reply
PPPR or MPMI says:

January 7, 2015 at 2:14 am

PPPR of MPMI, Molecular Plant-Microbe Interactions, published by The American Phytopathological Society. This is for 2013 papers:
http://apsjournals.apsnet.org/loi/mpmi

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-12-12-0283-R
MPMI Vol. 26, No. 6, 2013, pp. 676–685. http://dx.doi.org/10.1094/MPMI-12-12-0283-R
A Rhamnose-Rich O-Antigen Mediates Adhesion, Virulence, and Host Colonization for the Xylem-Limited Phytopathogen Xylella fastidiosa
Jennifer C. Clifford, Jeannette N. Rapicavoli, and M. Caroline Roper
Department of Plant Pathology and Microbiology, University of California, Riverside 92512, U.S.A.
Submitted 4 December 2012. Accepted 8 February 2013.
https://pubpeer.com/publications/FCBD4AC078D8BBD20445A4901F396C#fb20530

Fig. 2. Vertical line between lanes 2 and 3.
Stats in Fig 3A inconsistent with representation in 3B (“a” is lowest value in A but highest value in B)

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-08-12-0190-R
MPMI Vol. 26, No. 4, 2013, pp. 387–397. http://dx.doi.org/10.1094/MPMI-08-12-0190-R
Nonhost Resistance of Tomato to the Bean Pathogen Pseudomonas syringae pv. syringae B728a Is Due to a Defective E3 Ubiquitin Ligase Domain in AvrPtoBB728a
Ching-Fang Chien,1 Johannes Mathieu,2 Chun-Hua Hsu,1 Patrick Boyle,2 Gregory B. Martin,2,3 and Nai-Chun Lin1
1 Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan, R.O.C.;
2 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.;
3Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A. and Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia
Submitted 2 August 2012. Accepted 12 December 2012.
https://pubpeer.com/publications/F688350B3AB8E5541CBC9B16CD9233#fb20531

Fig. 3C. Vertical line between TRV2 lane 45 and TRV2:Prf lane 35 (for both ERF and EF-1α).

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-06-12-0142-R
MPMI Vol. 26, No. 2, 2013, pp. 168–181. http://dx.doi.org/10.1094/MPMI-06-12-0142-R
The Benyvirus RNA Silencing Suppressor Is Essential for Long-Distance Movement, Requires Both Zinc-Finger and NoLS Basic Residues but Not a Nucleolar Localization for Its Silencing-Suppression Activity
Sotaro Chiba,1,2 Kamal Hleibieh,1 Alice Delbianco,1,3 Elodie Klein,1 Claudio Ratti,3 Véronique Ziegler-Graff,1 Salah Bouzoubaa,1 and David Gilmer1
1Institut de Biologie Moléculaire des Plantes, Laboratoire Propre du CNRS (UPR 2357) Conventionné avec l’Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France;
2Institute of Plant Science and Resources, Okayama University, 2-20-1 Kurashiki, Japan;
3Università di Bologna, Dipartimento di Scienze e Tecnologie Agroambientali Area Patologia Vegetale, Viale G. Fanin, 40, II piano 40127, Bologna, Italy
Submitted 1 June 2012. Accepted 20 September 2012.
https://pubpeer.com/publications/6FE390E2E6887DBB23CAEC8736204E#fb20532

Fig. 4G. Vertical line between lane 3 and 4 for GF.
Fig. 6A. Vertical line between lane 1 and 2 (top gel).

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-04-13-0094-R
MPMI Vol. 26, No. 9, 2013, pp. 1106–1112. http://dx.doi.org/10.1094/MPMI-04-13-0094-R
A Replicase of Potato virus X Acts as the Resistance-Breaking Determinant for JAX1-Mediated Resistance
Kyoko Sugawara, Takuya Shiraishi, Tetsuya Yoshida, Naoko Fujita, Osamu Netsu, Yasuyuki Yamaji, and Shigetou Namba
Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
Submitted 3 April 2013. Accepted 26 April 2013.
https://pubpeer.com/publications/00E2E91BEEA3C200638E13A63E0AB7#fb20540

Fig. 1C For PVX, compare NX and lane 1

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-01-13-0017-R
MPMI Vol. 26, No. 8, 2013, pp. 946–957. http://dx.doi.org/10.1094/MPMI-01-13-0017-R
Infection of Brachypodium distachyon with Selected Grass Rust Pathogens
Michael Ayliffe,1 Davinder Singh,2 Robert Park,2 Matthew Moscou,3 and Tony Pryor1
1CSIRO Plant Industry, Box 1600, Clunies Ross Street, Acton, Canberra, 2601, Australia;
2The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 11, Camden, NSW, 2570, Australia;
3The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
Submitted 15 January 2013. Accepted 8 April 2013.
https://pubpeer.com/publications/9D39E1946BF75AB8CB84A8B38553A8#fb20535

Fig 6, divided gel lanes, acceptable quality?

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-12-12-0280-R
MPMI Vol. 26, No. 5, 2013, pp. 503–514. http://dx.doi.org/10.1094/MPMI-12-12-0280-R
Modification of Tobacco rattle virus RNA1 to Serve as a VIGS Vector Reveals That the 29K Movement Protein Is an RNA Silencing Suppressor of the Virus
Xianbao Deng, Jani Kelloniemi, Tuuli Haikonen, Anssi L. Vuorinen, Paula Elomaa, Teemu H. Teeri, and Jari P. T. Valkonen
Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Finland
Submitted 2 December 2012. Accepted 19 January 2013.
https://pubpeer.com/publications/28521D56CD8496FE3A7DD4F97A8AE5#fb20537

Fig. 4 28S rRNA (separate gel for lane 4 OK?)

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-08-12-0200-R
MPMI Vol. 26, No. 5, 2013, pp. 528–536. http://dx.doi.org/10.1094/MPMI-08-12-0200-R
In Vitro Translocation Experiments with RxLR-Reporter Fusion Proteins of Avr1b from Phytophthora sojae and AVR3a from Phytophthora infestans Fail to Demonstrate Specific Autonomous Uptake in Plant and Animal Cells
Stephan Wawra,1 Armin Djamei,2 Isabell Albert,3 Thorsten Nürnberger,3 Regine Kahmann,2 and Pieter van West1
1Aberdeen Oomycete Laboratory, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, U.K.;
2Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, Marburg, 35043, Germany;
3Department of Plant Biochemistry, Center for Plant Molecular Biology, Eberhard Karls University, Auf der Morgenstelle 5, Tübingen, 72076, Germany
Submitted 11 August 2012. Accepted 23 January 2013.
https://pubpeer.com/publications/91E319D3FCCDB480FB9E980D769DF3#fb20538

Fig. 1 and 2, so many important data points/figures n.d. (not determined). How can a complete picture of the results be formed? How can the interpretation of the results be accurate with so many gaps?

http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-10-12-0235-R
MPMI Vol. 26, No. 4, 2013, pp. 442–450. http://dx.doi.org/10.1094/MPMI-10-12-0235-R
Identification of Functional Genic Components of Major Fusarium Head Blight Resistance Quantitative Trait Loci in Wheat Cultivar Sumai 3
Yongbin Zhuang, Aravind Gala, and Yang Yen
Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, U.S.A.
Submitted 1 October 2012. Accepted 3 December 2012.
https://pubpeer.com/publications/A14E5EA45A2DA6E8D311D192A63406#fb20539

Fig. 2: 6BL graph for B appears to be identical to that for C.

Reply
1. PPPR of MPMI says:
  
  January 7, 2015 at 8:16 am
  
  Part 2: stats-related issues of 2013 papers in MPMI
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-02-13-0055-R
  MPMI Vol. 26, No. 12, 2013, pp. 1473–1485. http://dx.doi.org/10.1094/MPMI-02-13-0055-R
  Iron, Oxidative Stress, and Virulence: Roles of Iron-Sensitive Transcription Factor Sre1 and the Redox Sensor ChAp1 in the Maize Pathogen Cochliobolus heterostrophus
  Ning Zhang,1,2 Mohd Zainudin NurAinIzzati,1,3 Keren Scher,4 Bradford J. Condon,1 Benjamin A. Horwitz,4 and B. Gillian Turgeon1
  1Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.;
  2Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ 08901, U.S.A.;
  3Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang Selangor, Malaysia; 4Department of Biology, Technion, Haifa 32000, Israel
  Submitted 23 February 2013. Accepted 17 August 2013.
  https://pubpeer.com/publications/30C513940BB9ACE8D59E799B8C2F54#fb20599　
  
  “double Chap1sre1 mutant progeny were slightly but significantly less sensitive (Fig. 5)” (p. 1476)
  Problem is there are no statistical analyses in Fig 5 (p. 1482), and no significant differences between any treatments are shown, so is this statement incorrect / misleading?
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-04-13-0112-R
  MPMI Vol. 26, No. 10, 2013, pp. 1239–1248. http://dx.doi.org/10.1094/MPMI-04-13-0112-R
  The Rice Bacterial Pathogen Xanthomonas oryzae pv. oryzae Produces 3-Hydroxybenzoic Acid and 4-Hydroxybenzoic Acid via XanB2 for Use in Xanthomonadin, Ubiquinone, and Exopolysaccharide Biosynthesis
  Lian Zhou,1 Tin-Wei Huang,1 Jia-Yuan Wang,1 Shuang Sun,1 Gongyou Chen,2 Alan Poplawsky,3 and Ya-Wen He1
  1State Key Laboratory of Microbial Metabolism and National Center for Molecular Characterization of GMOs, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
  2School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
  3Department of Plant, Soil & Entomological Sciences, University of Idaho, Moscow 83844-2339, U.S.A.
  Submitted 22 April 2013. Accepted 22 May 2013.
  https://pubpeer.com/publications/9E6FB627F5A2D23F4A257C484E2DBF#fb20600　
  
  Fig 8B and C. Why are values intermediate to a and b listed as c? Surely b would be intermediate to a and b? Stats representation incorrect / inaccurate.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-07-12-0178-R
  MPMI Vol. 26, No. 9, 2013, pp. 1068–1078. http://dx.doi.org/10.1094/MPMI-07-12-0178-R
  Expression Analysis of Aquaporins from Desert Truffle Mycorrhizal Symbiosis Reveals a Fine-Tuned Regulation Under Drought
  Alfonso Navarro-Ródenas,1 Gloria Bárzana,2 Emilio Nicolás,3 Andrea Carra,4 Andrea Schubert,5 and Asunción Morte1
  1Departamento Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain;
  2Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (CSIC), Profesor Albareda, no. 1, Granada 18008, Spain;
  3Departamento de Riego, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), 30100 Murcia, Spain;
  4Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Turin, Italy;
  5Department of Agricultural, Forest and Food Sciences, University of Turin, Via Leonardo da Vinci 44, Grugliasco, 10095 Turin, Italy
  Submitted 17 July 2012. Accepted 26 April 2013.
  https://pubpeer.com/publications/AF1F116E66EFF0BF3B5EFD2D70916D#fb20601　
  
  Stats representation in Tables 1 and 2 inverse in some data sets (“a” sometimes represent highest values, sometimes lowest values), so inconsistent stats representation.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-04-13-0096-R
  MPMI Vol. 26, No. 9, 2013, pp. 1079–1088. http://dx.doi.org/10.1094/MPMI-04-13-0096-R
  Arabidopsis thaliana FLOWERING LOCUS D Is Required for Systemic Acquired Resistance
  Vijayata Singh,1 Shweta Roy,1 Mrunmay Kumar Giri,1 Ratnesh Chaturvedi,2 Zulkarnain Chowdhury,2 Jyoti Shah,2 and Ashis Kumar Nandi1
  1School of Life Sciences, Jawaharlal Nehru University, New Delhi -110067, India;
  2Department of Biological Sciences and Signaling Mechanisms in Plants Cluster, University of North Texas, Denton 76203, U.S.A.
  Submitted 6 April 2013. Accepted 23 May 2013.
  https://pubpeer.com/publications/71C0F3DF2D3C25926742CE8BA5F2F7#fb20602　
  
  Stats representation is inverse in some data sets (“a” sometimes represent highest values, sometimes lowest values), so inconsistent stats representation.
  This is true for graphs in Fig 1A vs Fig 2; 3AB vs 3C; 4 vs 5; 6A vs CD
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-01-13-0014-R
  MPMI Vol. 26, No. 8, 2013, pp. 903–917. http://dx.doi.org/10.1094/MPMI-01-13-0014-R
  Characterization of the LOV1-Mediated, Victorin-Induced, Cell-Death Response with Virus-Induced Gene Silencing
  Brian M. Gilbert and Thomas J. Wolpert
  Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331, U.S.A.
  Submitted 14 January 2013. Accepted 11 April 2013.
  https://pubpeer.com/publications/E220AD8D0870AA823EB7DAF57442E5#fb20603　
  
  Fig 8A, why is c between a and b (as opposed to higher than b)?
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-10-12-0241-R
  MPMI Vol. 26, No. 5, 2013, pp. 546–553. http://dx.doi.org/10.1094/MPMI-10-12-0241-R
  Quorum Sensing and Indole-3-Acetic Acid Degradation Play a Role in Colonization and Plant Growth Promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN
  Ana Zúñiga,1,2 María Josefina Poupin,1,2 Raúl Donoso,1,2 Thomas Ledger,1,2 Nicolás Guiliani,3 Rodrigo A. Gutiérrez,2 and Bernardo González1,2
  1Facultad de Ingeniería y Ciencias. Universidad Adolfo Ibáñez. Santiago, Chile;
  2Millennium Nucleus-PFG. FONDAP Center for Genome Regulation. Pontificia Universidad Católica de Chile. Santiago, Chile;
  3Departamento de Biología, Facultad de Ciencias, Universidad de Chile. Santiago, Chile
  Submitted 8 October 2012. Accepted 28 December 2012.
  https://pubpeer.com/publications/17783094D84E54EE9900D3CE4B6A8E#fb20604　
  
  Fig 1B and 2A stats errors? For example, in Fig. 1B, looking at the error bars between select treatments in primary root length, fresh weight, total chl and # of lateral roots, some values look to be significantly different to others, but no statistical differences indicated. In Fig. 2A, why is c between a and b (as opposed to higher than b)?
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-12-12-0297-R
  MPMI Vol. 26, No. 5, 2013, pp. 575–584. http://dx.doi.org/10.1094/MPMI-12-12-0297-R
  Trans-Specific Gene Silencing of Acetyl-CoA Carboxylase in a Root-Parasitic Plant
  Pradeepa C. G. Bandaranayake1 and John I. Yoder2
  1Department of Crop Science, Faculty of Agriculture University of Peradeniya, Sri Lanka 20400;
  2Department of Plant Sciences University of California–Davis, Davis 96516, U.S.A.
  Submitted 26 December 2012. Accepted 25 January 2013.
  https://pubpeer.com/publications/3786852C3214FF70D7BF3A0256A87D#fb20605　
  
  Fig 5. Why does d represent a lower value than b when a is the lowest and e is the highest?
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-07-12-0177-R
  MPMI Vol. 26, No. 4, 2013, pp. 431–441. http://dx.doi.org/10.1094/MPMI-07-12-0177-R
  Random T-DNA Mutagenesis Identifies a Cu/Zn Superoxide Dismutase Gene as a Virulence Factor of Sclerotinia sclerotiorum
  Liangsheng Xu and Weidong Chen
  Department of Plant Pathology, Washington State University, and United States Department of Agriculture–Agricultural Research Service, Washington State University, Pullman 99164, U.S.A.
  Submitted 14 July 2012. Accepted 8 December 2012.
  https://pubpeer.com/publications/021390EF973D1FE3541DC1A9E75126#fb20606　
  
  Page 435 states: “Transcription levels of SsSOD1 of the wild type significantly increased over time upon inoculation onto pea leaves (Fig. 6).” However, there are no statistical analyses in Fig. 6, only error bars. The M&M section also does not indicate that significant differences between means were assessed using any stats analyses.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-09-12-0222-R
  MPMI Vol. 26, No. 3, 2013, pp. 278–286. http://dx.doi.org/10.1094/MPMI-09-12-0222-R
  Evidence for Functional Diversification Within a Fungal NEP1-Like Protein Family
  Parthasarathy Santhanam,1 H. Peter van Esse,1 Isabell Albert,2 Luigi Faino,1 Thorsten Nürnberger,2 and Bart P. H. J. Thomma1,3
  1Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
  2Center for Plant Molecular Biology-Plant Biochemistry, University of Tübingen, D-72076 Tübingen, Germany;
  3Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
  Submitted 13 September 2012. Accepted 5 October 2012.
  https://pubpeer.com/publications/091167383C0B1CE858655D993939CD#fb20607　
  
  Fig 6A and 8A, why is c between a and b (as opposed to higher than b)?
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-06-12-0152-R
  MPMI Vol. 26, No. 3, 2013, pp. 287–296. http://dx.doi.org/10.1094/MPMI-06-12-0152-R
  Cytokinins Act Synergistically with Salicylic Acid to Activate Defense Gene Expression in Rice
  Chang-Jie Jiang,1 Masaki Shimono,1 Shoji Sugano,1 Mikiko Kojima,2 Xinqiong Liu,1 Haruhiko Inoue,1 Hitoshi Sakakibara,2 and Hiroshi Takatsuji1
  1Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, 305-8602 Japan;
  2Plant Productivity Systems Research Group, RIKEN Plant Science Center, Suehiro 1-7-22, Tsurumi, Yokohama 230-0045, Japan
  Submitted 13 June 2012. Accepted 4 October 2012.
  https://pubpeer.com/publications/F800DEEADDB2A9C9F17E51E3F17C3C#fb20608　
  
  Page 290 states: “In these lines, the CK inducibility of OsRR6 was decreased significantly (Fig. 5C)”, “Compared with nontransgenic controls, GVG::CKX2 plants with blast infection revealed no significant difference in disease incidence (Fig. 5D).” and also “No significant differences in blast resistance were observed across the treatments (Fig.5F).”
  Page 293 states: “In support of this notion, neither transgenic expression of rice CKX2 nor CK treatment of wild-type rice seedlings significantly altered blast resistance (Fig. 5D and F).” and also “Pretreatment with CK at concentrations of 1 to 100 μM had no significant effect on blast resistance (Fig. 5F).”
  However, there are no statistical analyses in Fig. 5, only error bars. The M&M section also does not indicate that significant differences between means were assessed using any stats analyses.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-07-12-0170-R
  MPMI Vol. 26, No. 3, 2013, pp. 345–355. http://dx.doi.org/10.1094/MPMI-07-12-0170-R
  Differential Activation of Ammonium Transporters During the Accumulation of Ammonia by Colletotrichum gloeosporioides and Its Effect on Appressoria Formation and Pathogenicity
  Chen Shnaiderman,1,2 Itay Miyara,1 Ilana Kobiler,1 Amir Sherman,3 and Dov Prusky1
  1Department of Postharvest Science of Fresh Produce, ARO, Bet Dagan, Israel;
  2The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel;
  3Genomic Unit, Plant Sciences Institute, ARO, Bet Dagan, Israel
  Submitted 9 July 2012. Accepted 30 October 2012.
  https://pubpeer.com/publications/7BEC381CB25C0A0C78A8BABDE011A2#fb20609　
  
  Fig. 2 legend states: “Values within averages marked with different letters at each sampling time differ significantly according to Tukey-Kramer honestly significant difference test at P ≤ 0.05.”
  However, there are no statistical analyses in Fig. 2, only error bars. Even so, some means appear, by a rough comparison, to be significantly different (e.g., pH or ammonia levels of Δamet3 and Ectopic17). The M&M section also does not indicate that significant differences between means were assessed using any stats analyses, even though some graphs/figures contain stats analyses (e.g., Fig. 3 or 6B).
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-12-0117-R
  MPMI Vol. 26, No. 2, 2013, pp. 191–202. http://dx.doi.org/10.1094/MPMI-05-12-0117-R
  Identification and Characterization of In planta–Expressed Secreted Effector Proteins from Magnaporthe oryzae That Induce Cell Death in Rice
  Songbiao Chen,1,2,3 Pattavipha Songkumarn,2 R. C. Venu,2 Malali Gowda,2 Maria Bellizzi,2 Jinnan Hu,2 Wende Liu,1 Daniel Ebbole,4 Blake Meyers,5 Thomas Mitchell,2 and Guo-Liang Wang1,2
  1State Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
  2Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A.; 3Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, China;
  4Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 79016, U.S.A.;
  5Delaware Biotechnology Institute, University of Delaware, Newark, DE, U.S.A.
  Submitted 16 May 2012. Accepted 24 September 2012.
  https://pubpeer.com/publications/5DA0553A1FF41A9AD8D5F07638AF52#fb20610　
  
  Page 195 states: “transient expression of the five FLMoCDIP but not the NS-MoCDIP induced a significant reduction in cell viability in maize protoplasts (Fig. 5A)”
  However, there are no statistical analyses in Fig. 5 (p. 196), only error bars. The M&M section also does not indicate that significant differences between means were assessed using any stats analyses.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-12-0138-R
  MPMI Vol. 26, No. 2, 2013, pp. 227–239. http://dx.doi.org/10.1094/MPMI-05-12-0138-R
  Gibberellin 20-Oxidase Gene OsGA20ox3 Regulates Plant Stature and Disease Development in Rice
  Xue Qin,1,2 Jun Hua Liu,1,2 Wen Sheng Zhao,1,2 Xu Jun Chen,2 Ze Jian Guo,2 and You Liang Peng1,2
  1State Key Laboratory of Agrobiotechnology and 2Department of Plant Pathology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
  Submitted 29 May 2012. Accepted 12 September 2012.
  https://pubpeer.com/publications/0B18408A7A1BB8E2DF914225CB6010#fb20611　
  
  Fig 5B: why is the “a” not the highest or lowest level?
  Fig. 6B: should c be higher than d?
  “a” sometimes represents the lowest values (e.g., Fig. 6F) but sometimes the highest value (e.g., all graphs in Fig. 7). Statistical representation is thus inconsistent.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-12-0107-R
  MPMI Vol. 26, No. 1, 2013, pp. 75–86. http://dx.doi.org/10.1094/MPMI-05-12-0107-R
  Ethylene Signaling Pathway Modulates Attractiveness of Host Roots to the Root-Knot Nematode Meloidogyne hapla
  Sylwia L. Fudali, Congli Wang, and Valerie M. Williamson
  Department of Nematology, University of California, Davis 95616, U.S.A.
  Submitted 7 May 2012. Accepted 14 June 2012.
  https://pubpeer.com/publications/A25B2AA36E49A1DCB4ED1EC631E8D7#fb20613　
  
  “a” represents the lowest value in Fig. 8 but the highest value in Fig. 2. Statistical representation is thus inconsistent.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-12-0108-FI
  MPMI Vol. 26, No. 1, 2013, pp. 106–115. http://dx.doi.org/10.1094/MPMI-05-12-0108-FI
  Brassinosteroids Suppress Rice Defense Against Root-Knot Nematodes Through Antagonism With the Jasmonate Pathway
  Kamrun Nahar,1 Tina Kyndt,1 Bettina Hause,2 Monica Höfte,3 and Godelieve Gheysen1
  1Department of Molecular Biotechnology, Ghent University, Coupure links 653, B–9000 Ghent, Belgium;
  2Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany;
  3Department of Crop Protection, Ghent University, Coupure links 653, B–9000 Ghent, Belgium
  Submitted 8 May 2012. Accepted 3 September 2012.
  https://pubpeer.com/publications/8E19191FD1227E3F0B1FEF7AA10CA9#fb20614　
  
  Fig 1B, 1C, 2C: why is the “a” not the highest or lowest level?
  Table 1, OPDA column: why does c represent the highest and the lowest values?
  Statistical representation is thus inconsistent.
  
  http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-05-12-0114-FI
  MPMI Vol. 26, No. 1, 2013, pp. 55–66. http://dx.doi.org/10.1094/MPMI-05-12-0114-FI
  A Novel Effector Protein, MJ-NULG1a, Targeted to Giant Cell Nuclei Plays a Role in Meloidogyne javanica Parasitism
  Borong Lin,1 Kan Zhuo,1 Ping Wu,1 Ruqiang Cui,1,2 Lian-Hui Zhang,3 and Jinling Liao1
  1Laboratory of Plant Nematology, South China Agricultural University, Guangzhou, China;
  2College of Agronomy, JiangXi Agricultural University, Nanchang 330045, China;
  3Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
  Submitted 16 May 2012. Accepted 22 June 2012.
  https://pubpeer.com/publications/6618849DAAFC44C7F37E7411415E8F#fb20615　
  
  “a” represents the lowest value in Fig. 8B,C but the highest value in Fig. 7. Statistical representation is thus inconsistent.
  
  Reply
2. PPPR of MPMI says:
  
  January 13, 2015 at 12:33 pm
  
  Public response 1 has arrived, confirming gel manipulation:
  https://pubpeer.com/publications/6FE390E2E6887DBB23CAEC8736204E#fb21312
  “Hello this is David Gilmer, corresponding author and supervisor of the paper cited. There is indeed a vertical line between lanes 3 and 4 for GF and also for P and RNA (Fig4G). This figure was assembled from 2 gels and 2 blots. Fig 6A, the figure was cutted to remove the sample present on the left of 1+2 (lane 2) RNA loading corresponds to a parallel loading on a dedicated gel. Regards David Gilmer”
  
  So, what will be done by the authors and the journal?
  
  Reply
3. PPPR of MPMI says:
  
  January 28, 2015 at 2:11 pm
  
  Activation of the Arabidopsis thaliana Mitogen-Activated Protein Kinase MPK11 by the Flagellin-Derived Elicitor Peptide, flg22
  April 2012, Volume 25, Number 4, Pages 471 – 480
  Gerit Bethke,1,2 Pascal Pecher,1 Lennart Eschen-Lippold,1 Kenichi Tsuda,2 Fumiaki Katagiri,2 Jane Glazebrook,2 Dierk Scheel,1 and Justin Lee1
  1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, D-06120 Halle, Germany;
  2Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Avenue, St. Paul 55108, U.S.A.
  http://dx.doi.org/10.1094/MPMI-11-11-0281
  http://www.apsnet.org/publications/mpmi/2012/April/Pages/25_4_471.aspx
  http://www.ncbi.nlm.nih.gov/pubmed/22204645
  PubPeer: https://pubpeer.com/publications/B239A41839EB9A760B56564F2561AB#fb23251
  
  Apparent lane duplication.
  
  Reply
4. PPPR of MPMI says:
  
  February 5, 2015 at 4:33 pm
  
  The first author of one of the MPMI papers examined has come forward to PubPeer to acknowledge the possible error and to reaffirm that the error is being examined:
  https://pubpeer.com/publications/B239A41839EB9A760B56564F2561AB#fb24126
  
  Reply
5. PPPR of MPMI says:
  
  February 10, 2015 at 2:32 pm
  
  REF: http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-11-11-0281
  The corresponding author of the paper reported here on January 28, 2015, Professor Justin Lee, at the Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Germany, has come forward, stating:
  “I am the corresponding author of this paper.
  The western blot panel for the Landsberg-erecta (Ler) genotype was indeed erroneously duplicated and depicted additionally as the mpk11 mutant. On behalf of all authors, an Erratum has been submitted to the journal.
  I append here the scans from 2 experiments where the original western blot data are shown; the blots used (or will be used for the Erratum) are marked with #.
  http://dx.doi.org/10.6084/m9.figshare.1304956
  I hope this clarifies the situation and would like to emphasize that the data in our paper is not compromised and has in fact been recently confirmed by another laboratory (Nitta et al. 2014, Plant Signal Behav 9: e976155 (doi: 10.4161/15592324.2014.976155).
  We thank the anonymous PubPeer colleague(s) for pointing out this error in our figure and apologize for any confusion caused.”
  
  It is of great importance to note that anonymous PPPR and reporting led to the detection of this error, which has now given the authors to correct the literature. They are commended for taking that initiative, and for assuming that responsibility publicly.
  
  Reply
6. PPPR or MPMI says:
  
  February 11, 2015 at 2:42 pm
  
  A significant development that involves a paper of the EIC, being questioned at PubPeer, with a confirmed duplicated figure.
  
  “I am Jane Glazebrook, a middle author on this paper and Editor-in-Chief of MPMI. I welcome the scrutiny of published papers by PubPeer, but I think that authors should be notified when someone posts a complaint about a paper on PubPeer. We did not receive any notification in this case. The first author chanced upon the post on February 5, while running a search for a different reason. Authors cannot respond if they are unaware of the criticism.”
  
  “@ Jane.
  The PubPeer site indicates that authors are automatically notified.
  https://pubpeer.com/about
  https://pubpeer.com/faq
  That said, I’m not sure what addresses are available to them (presumably at least that of the corresponding author). The paper is recent enough that any addresses should at least have been current. Are you sure that no alerts were received by any of your coauthors and they hadn’t quite gotten around to notifying you? (The first post is not that old.)”
  
  “I am Dierk Scheel, another co-author and certainly apologize for this mistake. However, none of us has received an alert on this.”
  
  Peer 0: “We have several checks in place to ensure that authors are notified of comments but unfortunately they all failed for this paper. The corresponding author was not sent an email alert until earlier today. We have learned from this bug and will make sure it doesn’t repeat. We apologize to the authors.”
  
  Reply
Albizia lebbeck queries says:

January 8, 2015 at 11:36 pm

The scientific soundness of another four papers, this time on Albizia lebbeck, by the same group of authors, is being questioned.

P1 (2011)
Journal of Forestry Research March 2011, Volume 22, Issue 1, pp 47-52
Influence of cytokinins, basal media and pH on adventitious shoot regeneration from excised root cultures of Albizia lebbeck
Shahnaz Perveen 1, Ankita Varshney 1, Mohammad Anis 1,2, Ibrahim M. Aref 2
1 Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh-202002, India;
2 Department of Plant Production, College of Food & Agricultural Sciences, King Saud University, P.O Box 2460, Riyadh 11451, Saudi Arabia
http://link.springer.com/article/10.1007%2Fs11676-011-0124-5
http://jfr.nefu.edu.cn/EN/abstract/abstract211.shtml
DOI: 10.1007/s11676-011-0124-5
Received: 2010-02-26; Accepted: 2010-06-08

P2 (2012)
European Journal of Forest Research May 2012, Volume 131, Issue 3, pp 669-681
Date: 01 Jul 2011
In vitro morphogenic response and metal accumulation in Albizia lebbeck (L.) cultures grown under metal stress
Shahnaz Perveen, Mohammad Anis, I. M. Aref
S. Perveen; M. Anis; I. M. Aref
Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202 002, India
M. Anis; I. M. Aref
Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
http://link.springer.com/article/10.1007/s10342-011-0540-2
DOI: 10.1007/s10342-011-0540-2
Received: 29 October 2010 / Revised: 2 June 2011 / Accepted: 17 June 2011 / Published online: 1 July 2011

P3 (2013)
Forest Systems 2013 22(2), 241-248
In vitro plant regeneration of Albizia lebbeck (L.) Benth. from seed explants
S. Perveen1, M. Anis1,2* and I. M. Aref2
1 Plant Biotechnology Laboratory. Department of Botany. Aligarh Muslim University. Aligarh 202 002, India
2 Department of Plant Production. College of Food and Agricultural Sciences. King Saud University. P.O. Box 2460. Riyadh, 11451, Saudi Arabia
http://revistas.inia.es/index.php/fs/article/view/3261
DOI: 10.5424/fs/2013222-03261

P4 (2014)
Acta Physiologiae Plantarum August 2014, Volume 36, Issue 8, pp 2067-2077
Date: 14 Jul 2014
Encapsulation of internode regenerated adventitious shoot buds of Indian Siris in alginate beads for temporary storage and twofold clonal plant production
S. Perveen 1, M. Anis 1,2
1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
2. Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
http://link.springer.com/article/10.1007/s11738-014-1584-y
DOI: 10.1007/s11738-014-1584-y
Communicated by Johann Van Huylenbroeck (curiously, linked to a retraction: http://www.actahort.org/books/961/961_15.htm) although serving on the editor board of this journal:
http://www.springer.com/life+sciences/plant+sciences/journal/11738?detailsPage=editorialBoard
Received: 27 September 2013 / Revised: 4 May 2014 / Accepted: 9 May 2014

The corresponding PubPeer entries are:
P1: https://pubpeer.com/publications/232DE11B6BD650222F40B5CD8D6CF3#fb20790
P2: https://pubpeer.com/publications/2F9A823A2CE0A55A24BE9672796AED#fb20791
P3: https://pubpeer.com/publications/ADC7B2E58385AAFBBBD6DD334B0D57#fb20792
P4: https://pubpeer.com/publications/C280E692EB5721CA9FC89DFC7BE99E#fb20793

Incidentally, Prof. Mohammad Anis and co-authors have been the subject of another large query regarding Egyptian Myrobalan Tree (Balanites aegyptiaca Del.) with 4 PubPeer entries:
https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878　
https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879　
https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880　

And concerns with another Vitex species, Vitex negundo, registered as 3 PubPeer entries:
https://pubpeer.com/publications/DD4131C0A025F3536F8D1825FAB38D#fb19073
https://pubpeer.com/publications/228844D355BBACF479209E2D15459E#fb17547
https://pubpeer.com/publications/806685230E231DFBD444AF5E964742#fb19059

And concerns with another Vitex species, Vitex trifolia , registered as 4 PubPeer entries:
https://pubpeer.com/publications/A6882B9CDFABE0E6BB8F785C56DD73#fb19080 (paper 1)
https://pubpeer.com/publications/35233FCE60069A90AB2EEF823F6F66#fb19082 (paper 2)
https://pubpeer.com/publications/E808598705E04B19E6818A514BE5D2#fb19083 (paper 3)
https://pubpeer.com/publications/B82DC5E43C2F12595413064EA6447F#fb19085 (paper 4)

Reply
Acacia sinuata queries says:

January 9, 2015 at 8:31 am

Two of these papers have no DOI while the third DOI of the Springer book chapter does not link to PubPeer.

An Improved method of organogenesis from cotyledon callus of Acacia sinuata (Lour.) Merr. using thidiazuron
Anwar Shahzad, Naseem Ahmad, Mohammad Anis
Journal of Plant Biotechnology 01/2006; 8(1):15-19.
http://www.researchgate.net/publication/233882930_An_Improved_method_of_organogenesisfrom_cotyledon_callusof_Acacia_sinuata_(Lour.)_Merr._using_thidiazuron
No DOI.

Anis M, Husain MK, Faisal M, Shahzad A, Ahmad N, Siddique I and Khan H (2009). In vitro approaches for plant regeneration and conservation of some potential medicinal plants. In: Recent Advances in Plant Biotechnology & Its Applications (Eds) Kumar A & Sopory SK, I.K. International Pvt. Ltd., New Delhi. 14: 397-410.
No DOI.

Recent Trends in Biotechnology and Therapeutic Applications of Medicinal Plants In: In Vitro Conservation Protocols for Some Commercially Important Medicinal Plants, 2013, pp 323-347
Date: 15 Apr 2013
Anwar Shahzad, Shahina Parveen
http://link.springer.com/chapter/10.1007%2F978-94-007-6603-7_15
DOI: 10.1007/978-94-007-6603-7_15 (DOI does not link to PubPeer)

Queries/concerns:
1) 2006 Fig 1F is apparently the same as 2009 book chapter Fig 2D (p. 403). The book chapter does not acknowledge the source or previous publication of the 2006 paper figure.
2) Although the 2013 book chapter discusses this medicinal plant, it fails to reference the 2009 book.
3) In the 2013 book chapter, on page 325 and 327-328, there is a detailed protocol discussing plant material, explant sterilization from seedlings (15.2.1.), medium (15.2.2.), rooting (15.2.3.) and hardening (15.2.4.) but there is just one problem: for what plant? The actual plant for which this protocol applies is not defined, thus making it redundant text.
4) About the 2006 paper: A) what is the commercial source and grade of the plant growth regulators used? B) Table lists one parameter as “number of green spots”. What are these and what are they botanically-speaking? C) Is the 50-60% relative humidity in the M&M related to inside the culture flasks or the culture chamber, and how exactly was RH measured? D) What was the temperature and light intensity of the acclimatization conditions? E) The microshoots used for the rooting experiment were derived exactly from which previous treatment? This is not defined but could be an extremely important influencing factor since the previously used growth regulators can still serve as pulses affecting later growth. F) The plantlets that were acclimatized were derived from which treatment(s) exactly? Were plantlets derived from different treatments compared individually, were they plantlets from a single treatment or were plantlets pooled from various treatments?

The authors are kindly requested to address these issues.

Reply
Artemisia annua query says:

January 11, 2015 at 3:42 am

ORIGINAL ARTICLE
Pharmacognosy Magazine
Publisher: MedKnow
Year : 2014 | Volume : 10 | Issue : 37 | Page : 176-180
Optimization of genetic transformation of Artemisia annua L. Using Agrobacterium for Artemisinin production
Elfahmi 1, Sony Suhandono 2, Agus Chahyadi 1
1 Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, West Java, Indonesia
2 Plant Molecular Biology, School of Life Sciences and Technology, Institut Teknologi Bandung, West Java, Indonesia
Date of Submission: 01-Oct-2012; Date of Decision: 11-Nov-2012; Date of Web Publication: 21-Feb-2014
DOI: 10.4103/0973-1296.127372
PMID: 24914301
http://www.phcog.com/article.asp?issn=0973-1296;year=2014;volume=10;issue=37;spage=176;epage=180;aulast=Elfahmi,
http://www.phcog.com/viewimage.asp?img=PhcogMag_2014_10_37_176_127372_f4.jpg
http://europepmc.org/articles/PMC4047588

Fig 2 vertical line between lanes A and M

Curious to note how the authors’ presentation at an Omics* congress mentions, in small print, a 2001 and a 2003 Voinnet paper related to RNAi and VIGS. Voinnet’s work is also being questioned at PubPeer** and Retraction Watch***:
http://omicsgroup.com/conferences/ACS/conference/pdfs/11060-Speaker-Pdf-T.pdf

* http://scholarlyoa.com/2013/01/25/omics-predatory-meetings/
** https://pubpeer.com/search? q=voinnet&sessionid=DBEA6455D1A88F0EFF18&commit=Search+Publications
*** http://retractionwatch.com/2015/01/09/award-winning-plant-researcher-correcting-several-papers-critiqued-pubpeer/

There is a PubPeer entry for this paper:
https://pubpeer.com/publications/91430DCFCA90064307B161BCF535F3#fb21065

Reply
Artemisia annua query says:

January 11, 2015 at 4:04 pm

Importance of Artemisia annua
http://www.nature.com/scitable/blog/bio2.0/artemisia_annua_a_vital_partner

P1
Plant Biotechnology Reports January 2011, Volume 5, Issue 1, pp 53-60
Date: 27 Nov 2010
Enhancement of artemisinin content by constitutive expression of the HMG-CoA reductase gene in high-yielding strain of Artemisia annua L.
Tazyeen Nafis, Mohd. Akmal, Mauji Ram, Pravej Alam, Seema Ahlawat, Anis Mohd, Malik Zainul Abdin
Centre for Transgenic Plant Development, Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India
DOI: 10.1007/s11816-010-0156-x
http://link.springer.com/article/10.1007/s11816-010-0156-x

P2
Indian Journal of Biotechnology (Jan, 2014) 13: 26-33
Anis Mohammad, Pravej Alam, Malik M. Ahmad, Athar Ali, Javed Ahmad, Malik Zainul Abdin
Impact of plant growth regulators (PGRs) on callogenesis and artemisinin content in Artemisia annua L. plants
http://nopr.niscair.res.in/handle/123456789/28697 (issue)
http://nopr.niscair.res.in/handle/123456789/28710 (paper)
http://nopr.niscair.res.in/bitstream/123456789/28710/1/IJBT%2013%281%29%2026-33.pdf (open access)
No DOI.

P3
Journal of Plant Interactions (2014) 9:1, 655-665
Pravej Alam, Kamaluddin, Mather Ali Khan, Anis Mohammad, Riyazudeen Khan, Malik Zainul Abdin (2014) Enhanced artemisinin accumulation and metabolic profiling of transgenic Artemisia annua L. plants over-expressing by rate-limiting enzymes from isoprenoid pathway
a Department of Biotechnology, Faculty of Science, Centre for Transgenic Plant Development, Jamia Hamdard, New Delhi 110062, India
b Department of Plant Breeding and Genetics, Faculty of Agriculture, Regional Research Station, Sher-e-Kashmir University of Agriculture and Technology, Wadura, Jammu and Kashmir, India
Received: 7 Nov 2013; Accepted: 6 Feb 2014; Accepted author version posted online: 11 Feb 2014; Published online: 10 Mar 2014.
http://www.tandfonline.com/doi/abs/10.1080/17429145.2014.893030#.VLGo-cv9nIU (open access)
http://www.tandfonline.com/doi/pdf/10.1080/17429145.2014.893030
DOI: 10.1080/17429145.2014.893030

Queries:
1) P1: notice vertical line between lanes T10 and T11 (Fig. 2A, right gel).
2) P1: (Abstract) “while the high-performance liquid chromatography analysis showed that artemisinin content was significantly increased in a number of the transgenic lines.” (p. 58) “In our study, transgenic lines T2 and T9 failed to show any significant increase in artemisinin content,” There are no statistical analyses in the results, nor any indication in the materials section, that statistical analyses were conducted. The authors are requested to please release this data set that proves their claims.
3) P1: In Fig. 2B, please explain no banding (i.e., no transgene copies) in lanes in T3 and T8, even though your are claiming these to be transgenic lines.
4) P1: In Fig. 3, there are faint non-specific bands in T4 and T5 lanes. What do these represent? What else is being transcribed if these primers are supposedly very specific to the hmgr gene?
5) P1: Can you explain the negative value of HMGR activity in T9 in Fig. 4, especially when T9 displays three bands in Fig. 2B and no bands in Fig. 3. Also please explain the apparent discrepancies between Fig 2B and Fig. 3 for T9, when T2 shows similar trends for Fig. 2B and 3 (relative to T9), but a positive value of HMGR activity in T9 in Fig. 4.
6) P2: Fig 1a dark phase photo (1 mg/l BAP + 0.5 mg/l 2,4-D) is identical to Fig 2a dark phase photo (1 mg/l BAP + 1 mg/l 2,4-D). However, Fig 1 = transgenic callus while Fig. 2 = non-transgenic callus. How can the exact same callus form on two different media?
7) P2: (p. 29) “The biomass yield of transgenic calli was significantly higher… (Figs. 3a-c).” (p. 30) “…no significant differences in the artemisinin content were observed…(Figs. 6-c).” Presumably, that should be Figs. 6a-c. These statements are problematic for two reasons: a) there are no statistical analyses in the figures to merit such a claim of significance or non-significance between treatment means; b) observation of the differences in means and the error bars suggests quite the contrary, i.e., that there may be significant differences. The authors are requested to release the data sets and statistical analyses for scrutiny.
8) P2: This paper purports to report the differences in artemisinin production between control (untransformed) and transformed lines of Artemisia annua. In the Methods section, it states “For transgenic callus, the in vitro-raised A. annua plants (0.059% artemisinin) overexpressing hmgr gene from Catharanthus roseus (L.) G. Don. was used as the source of explants.” This is extremely problematic because absolutely nowhere in this paper does it indicate how such transgenic plants were produced, if indeed they were transgenic (i.e., there are no molecular analyses to support their claims: see arguments below about the invalid nature of Fig 6), nor, if in fact these transgenic plants were produced based on previously published protocols, what those protocols might have been. Their own protocols? Others’ protocols? The latter may be unlikely since their previous publication (P1) and concurrent publication (P3) used two transgenes and not one. The methodology related to the production of transgenic callus is NOT reproducible and thus all claims, results and comparisons are invalid. The authors are requested to clarify the entire methodology as errata or supplementary files, and to PROVE the transgenic nature of the callus they produced and used as the basis for this comparative experiment. It is very odd that the authors also did not reference their own work published in P1. For example, if this callus was from any of the 9 transgenic lines (T1-T9) of the P1 paper, then which line exactly did they use?
9) P3: Fig 6a. Magnify the PDF file to about 600%: you will see different pixelation between the TR4 and TR5 lanes (vertical line observed?). Also compare TR5 and TR7. Can the authors present the images of the original gels in high resolution, please?
10) P3: (p. 656) “Among the transgenic lines developed in our laboratory, the high artemisinin-yielding lines [TR4 (1.73 mg/g DW), TR5 (1.72 mg/g), and TR7 (1.59 mg/g)]” Are these three transgenic lines equivalent to T4, T5 or T7 in P1? It seems not because the level of artemisinin production claimed in P3 by these 3 lines does not correspond to the artemisinin levels produced by T4, T5 or T7 in P1. What then are these three high-artemisinin-producing lines, where is the evidence that they produce this level of artemisinin, and what is the reference for those results? Please provide a public release of the data and evidence/proof for these production levels, or the appropriate reference(s). The entire basic protocol for the production of these transgenic lines is missing, making this entire protocol unreproducible: what is the protocol for introducing the hmgr and ads genes?
11) P3: Why are the forward and reverse primers for the hmgr gene different between P1 and P3? What is the original source for the primers of all of these genes? Did you design these primers yourselves or did you use the sequences from a previously reported study? Same applies for the ads gene in P3 (yours or primers designed by someone else and published elsewhere?).
12) P3: Fig. 1B is unclear. Please provide a high resolution figure so that the peaks and retention times can be seen perfectly clearly.
13) P3: Fig. 2: Are these pooled percentages across the three “transgenic” lines? If so, why does no information about this appear in the figure legend, or the link between that data and the data in Table 1?
14) P3: Again, the data in figures 3, 4 and 5 are meaningless until the authors provide concrete proof that the three lines they are truly transgenic.
15) P3: Fig 6 is the apparent proof of the transgenic nature of the thee lines. But these gels are invalid or incomplete because there are no control lanes, no marker lane, and no indication /confirmation of the actual size of the bands corresponding to the correct fragment size. In essence, just having 4 bands could be bands of almost anything created by RT-PCR. In particular, a positive lane of the sample of pure hmgr and ads genes is lacking.
16) P3: Fig 6 legend is inaccurate: “TR4 – TR7” implies that there is also T6, which is not true.

The authors are requested to address these queries and to also make available the final version of the following paper with all figures on their ResearchGate profile for comparison with P1:
P4
Recent Patents on Biotechnology, Volume 8 – Number 1 (Bentham Science)
Efficient Method for Agrobacterium Mediated Transformation of Artemisia annua L.; Pp: 102 – 107
Pravej Alam, Anis Mohammad, M.M. Ahmad, Mather Ali Khan, Mohd. Nadeem, Riyazuddeen Khan, Mohd. Akmal, Seema Ahlawat, M.Z. Abdin
DOI: 10.2174/18722083113079990001
http://benthamscience.com/journal/contents.php?journalID=rpbiot&issueID=121400
http://eurekaselect.com/110173

P1: Acknowledgments “Tazyeen N. is highly grateful to the Council of Scientific and Industrial Research, India, for the award of JRF and SRF fellowship for her Doctoral research.”
P2: Acknowledgment “AM is thankful to the University Grant Commission, New Delhi, India for providing RFSMS Scholarship.”
P3: Acknowledgements “We are thankful to Dr. M. A. A. Khan Scientist NISCAIR, New Delhi, India for editing the manuscript. The financial support from DST, Government of India and M/s Ipca Pvt. Ltd., Mumbai, India is gratefully acknowledged. P.A. is thankful to Jamia Hamdard, New Delhi, India for providing Junior Research fellowship. We are also thankful to Dr. Ajay Kumar from AIRF, Jawaharlal Nehru University, New Delhi for providing GC–MS facility.”

Kamaluddin, of P3, is not listed on the indicated SKUAST web-page:
http://www.skuast.org/site/Templates%20HTML/foa/pbg.html

There are the PubPeer entries for this case:
P1: https://pubpeer.com/publications/3E09E054F463B7DEA9BB205F6C8786#fb21066
P3: https://pubpeer.com/publications/C510F15863E1F9536EBBFC4474EAA1#fb21067
P4: https://pubpeer.com/publications/7E95C83EC1A3A1CAE1159346B42140#fb21068

Reply
1. Artemisia annua query says:
  
  June 7, 2015 at 2:56 am
  
  A response from Prof. Malik Zainul Abdin* is posted at PubPeer, in which he states: “We have gone through these queries and find that they are not based on the fact.”
  
  Please observe three figures from the 4 questioned papers:
  Fig 1 (P1) vs Fig 1 (P2)
  http://imgur.com/cQeqRxK
  Fig 1a (P3) vs Fig 1A (P4)
  http://imgur.com/SOETSvx
  Fig 1d (P3) vs Fig 1D (P4)
  http://imgur.com/6oWDyq9
  
  * Head, Faculty of Science, Jamia Hamdard University
  http://www.jamiahamdard.ac.in/academic/faculty_of_science.htm
  http://jamiahamdard.edu/faculty-of-science/
  Head, Biotechnology Faculty
  http://jamiahamdard.edu/faculty-dept-of-biotechnology/
  
  Reply
Sandalwood queries says:

January 13, 2015 at 2:42 pm

Gels of two sandalwood papers are being queried at PubPeer.

Calcium-Mediated Signaling during Sandalwood Somatic Embryogenesis. Role for Exogenous Calcium as Second Messenger
Veena S. Anil, K. Sankara Rao
Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
doi: http://dx.doi.org/10.1104/pp.123.4.1301
Plant Physiology August 2000 vol. 123 no. 4, pp 1301-1312
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC59089/
http://www.plantphysiol.org/content/123/4/1301.full

Figure 8: vertical line between EGTA and A23187 lanes.
Authors are requested to release high resolution images of the original gel(s).

https://pubpeer.com/publications/D8938C53FAACFC9A1E086D4E41562F

Anil, V.S. and Sankara Rao, K. (2001) Purification and characterization of a Ca2+-dependent protein kinase from sandalwood (Santalum album L.): Evidence for Ca2+-induced conformational changes. Phytochemistry 58: 203–212.
http://www.sciencedirect.com/science/article/pii/S003194220100231X
DOI: 10.1016/S0031-9422(01)00231-X

Fig 1A: odd vertical streaks between lanes 1 and 2, and 4 and 5.
Authors are requested to release high resolution images of the original gel(s).

https://pubpeer.com/publications/386B59D4FE74AF6BB5A0F60D6E6D92

Reply
1. Sandalwood queries says:
  
  January 18, 2015 at 10:58 pm
  
  Universal Journal of Plant Science 2(4): 86-91, 2014
  DOI: 10.13189/ujps.2014.020402 (but cannot link to PubPeer), so linked to another sandalwood query at PubPeer:
  https://pubpeer.com/publications/D8938C53FAACFC9A1E086D4E41562F
  Antibacterial Potentiality of Red Sandalwood Callus Against Pathogenic Isolates of Aeromonas and Pseudomonas.
  Tamzida Shamim Ashrafee 1, MM Rahman 2, Anindita Chakraborty 1, Shamsul H. Prodhan 1
  1 Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
  2 Dept. of Biotechnology, Bangabandhu Sheikh Muzibur Rahman Agricultural University, Salna, Gazipur-1706 Bangladesh
  
  Concerns and issues:
  
  1) Rinses at the end of the sterilization procedure for leaves and internodes not described.
  2) Exact amount of callus used in each subculture not described.
  3) No indication of the issue of callus browning, its implications, or how to avoid it, even though callus browning is evident in Fig. 1A, B, E and F.
  4) The commercial source or grade of none of the reagents is provided.
  5) The equipment used for photography, or the model, maker or manufacturer of all of the equipment used in the antifungal assays not described.
  6) No culture conditions for callus induction provided, including light, agar conc., pH of medium, or gelling agent.
  7) Crude results presented, no treatment analyses, or comparisons. No statistical analyses.
  8) The protocol is not reproducible and has serious gaps in information.
  9) Poor scientific English, for example: “the foggy upper portion of preparation was taken to sterilized eppendroff tube” (p. 87-88)
  10) In explant preparation, a reference for the methodology is provided (“(Prakash et. al.2006)”). This reference does not appear in the reference list.
  11) Acknowledgements: “The Present study was conducted in Plant genetixc Engineering and USDA microbiology laboratories of department of Genetic Engineering and Biotechnology. We are thankful to these two laboratories and also to all teachers.”
  12) The publisher Horizon Research Publishing Corp.,USA (HRPUB) (http://www.hrpub.org/) is on Beall’s list of predatory OA journals (http://scholarlyoa.com/publishers/).
  
  Reply
2. Sandalwood queries says:
  
  January 19, 2015 at 1:08 am
  
  No DOI, so linked to another sandalwood query at PubPeer:
  https://pubpeer.com/publications/D8938C53FAACFC9A1E086D4E41562F
  
  International Journal of Agricultural Technology 2012 Vol. 8(2): 571-583
  Publisher: Association of Agricultural Technology in Southeast Asia (AATSEA), Thailand
  Available online http://www.ijat-aatsea.com
  Microcloning of sandalwood (Santalum album Linn.) from cultured leaf discs.
  D. Bele 1, M.K. Tripathi 1*, G. Tiwari 2, B.S. Baghel 3, S. Tiwari 4
  1 Horticultural Biotechnology Laboratory, KNK-College of Horticulture, Mandsaur, India
  2 Department of Medicinal and Aromatic Plants, KNK-College of Horticulture, Mandsaur, India
  3Office of Dean, KNK-College of Horticulture, Mandsaur Rajmata Vijayraje Scindia Agricultural University, Gwalior M.P., India
  4Division of Transgenic and Tissue Culture, Biotechnology Centre JN Agricultural University, Jabalpur M.P. India
  http://www.ijat-aatsea.com/Past_v8_n2.html
  http://www.ijat-aatsea.com/pdf/v8_n2_12_March/15_IJAT%202012_8_2__D.pdf (open access)
  
  Concerns and issues:
  
  1) The first four sentences of the introduction, full of factual claims, are not supported by any references.
  2) A disc is a circular or ring-shaped object. The authors claim to use leaf discs, but then state in the M&M section “small square pieces (5-8 mm)” (p. 573). A circle cannot be a square. Is that 5-8 mm2 (i.e., the area)? Thus, size and shape of explant used unclear. The confusion is confounded by statements like “leaves measuring 0.5-1.5 cm in length” (p. 574) or “7-8 pieces of leaf discs.”: does the latter mean that the square discs were cut into even smaller pieces?
  3) Maker and volume of Petri dishes not specified. In fact, the commercial source and grade of none of the reagents and chemicals is specified.
  4) Non-standard terms used: “somatic embryoids”, most likely because the exact structures were unclear (see explanation next).
  5) “transferred to Green House” (p. 574). Why are capitals used?
  6) The authors claim somatic embryogenesis throughout the manuscript but provide absolutely no evidence of this organogenic process, neither cytological, histological, genetic or otherwise. The several stages of somatic embryogenesis are not shown, or specified. This vague mix between shoot organogenesis and “somatic embryogenesis” may explain why such a strange dichotomy in the results. Most likely all structures observed were shoot initials or shoot buds and that all organogenesis observed was shoot formation, simply because not root initials formed simultaneously with the shoots.
  7) “all the media were supplemented with 30 g.l-1 sucrose, 7.5 g.l-1 agar and pH was adjusted to 5.8±0.1.” (p. 173) Yet, on page 574, the authors claim to use at least two different sucrose concentrations: 20 g.l-1 for somatic embryoids and calli, and 15 g.l-1 for rooting and plantlet development.
  8) “For regeneration and rooting, reduced level of sucrose was used on the basis of work conducted by various scientists” (p. 173) Yet, none of those scientists’ are listed, or their references.
  9) The age and size of plantlets used for acclimatization not defined. The treatments from which plantlets were derived for acclimatization, and the number of plantlets derived from each treatment, or in total, not defined. Survival of acclimatized plantlets not quantified.
  10) The abbreviations lists the following: 2, 4, 5-T – 2, 4, 5- trichlorophenoxyacetic acid. It is used once in the text: “Howerver [sic], other auxins NAA and 2,4,5-T was not found as effective as 2,4-D for inducing somatic embryogenesis in sandal.” (p. 577) Where is the data for NAA and 2,4,5-T? Also, there is absolutely no methodology related to these plant hormones.
  11) “163.63% plant regeneration via somatic embryogenesis” reported in the abstract. The only similar value reported in the data is in Table 2, at 163.61, although the units in Table 2 are not specified. If indeed these are percentage values, then 163% is mathematically impossible. If not percentages, then what are these values?
  12) Roots could not be induced on any medium (Table 3), but this is likely because the authors did not transfer shoots, or cultures to fresh medium containing auxins. Had they tested a range of auxins, and also read more of the published sandalwood literature that claimed successful root induction in vitro, they might have obtained positive results.
  13) There are no acknowledgements or publishing dates, except for: “Published in March 2012” (p. 583)
  14) How to cite the paper on the first page (p. 571) lists the journal’s name incorrectly as Journal of Agricultural Technology.
  
  Incidentally, the link to the above Ashrafee et al. 2014 paper is:
  http://www.hrpub.org/download/20140525/UJPS2-10302228.pdf
  
  Reply
3. Sandalwood queries says:
  
  January 19, 2015 at 3:40 am
  
  Julien Crovadore, Michel Schalk & François Lefort (2012) Selection and Mass Production of Santalum Album L. Calli for Induction of Sesquiterpenes. Biotechnology & Biotechnological Equipment, 26:2, 2870-2874
  DOI: 10.5504/BBEQ.2012.0028
  http://www.tandfonline.com/doi/abs/10.5504/BBEQ.2012.0028#.VLy6E8v9nIU
  http://www.tandfonline.com/doi/pdf/10.5504/BBEQ.2012.0028 (open access)
  http://www.diagnosisnet.com/bbeq/article/0a0572b2-21a6-4e4a-afb8-6affd1168f5d
  Biotechnology & Biotechnological Equipment: 2013 JCR Impact Factor: 0.379
  
  Queries / issues / concerns:
  
  1) “Sandalwood seedlings were planted in 5 L pots (Klassmann2 substrate) with previously established two-year-old grafted Citrus plants. These trials were all successful and sandalwood plants established a root hemiparasitic relation with the Citrus vascular system.” (p. 2871-2872) However, the exact cultivar grafted and the exact rootstock not defined (Citrus is a very large genus with many cultivars and root stocks so details are essential to establish an effective semi-parasitic relationship). No histological evidence is provided to support the claim of a relation with the Citrus vascular system. “The implementation of this acclimatization protocol could be very useful in sandalwood planting programs.” Only if precise information is provided, which it is not.
  2) “The samples were extracted with pentane” (p. 2871) This methodology is incomplete. Using what apparatus? Extraction for how long? What was the mass to volume ratio of callus to extractant?
  3) “The identification of the products was based on the matching of the mass spectra and coincidence of the retention indices with data from Firmenich internal databases.” The second author is from this company. How accurate are these data-bases relative to, for example, more common data-bases like Adams?
  4) “Genetic identity of plant material (leaves from grown plant and calli) was checked by PCR amplification and subsequent sequencing of the ITS region.” (p. 2871). The entire protocol for PCR, including primers used, and sequencing is missing. Moreover, only one short sentence “PCR amplification from DNA extracted from leaves and calli yielded a unique sequence for the ITS region which was registered in GenBank under the accession number HM235968.” in the results claims a result, without any other evidence, or gel images. The authors should make available publicly PCR gels showing the comparison between callus-derived banding and mother plants, and explain, in detail, the similarities or differences. Incidentally, the GenBank URL was not indicated in the paper, but is https://www.ncbi.nlm.nih.gov/nuccore/HM235968
  5) Polyembryony is claimed (“polyembryony was observed for a number of plants (ca. 2%)”, p. 2871) but not proved.
  6) “Regarding explants responsiveness, the hypocotyl tissue proved to be the most reactive followed by the shoot tips. These two explants did not produce the same callus types.” (p. 2874) Absolutely no data is provided to support these claims, even though the authors also claim to have used the following explants (“Explants from different parts of plants obtained by in vitro germination were sampled: hypocotyls and crown sections (3-10 mm in length), cotyledon and leaf pieces (10-16 mm2 of surface area) and root segments (3-5 mm in length). Explants were taken from sterile seedlings of different stages.”) (p. 2871).
  7) There is no discussion of the GC-MS results relative to the other literature on sandalwood essential oil. Moreover, exact RI values and concentrations obtained for all of the sesquiterpenes and other secondary metabolites, is not provided (for example in tabulated form). Why have the authors not discussed the absolute or relative yield from the 200 callus lines they claim to have obtained? (“yielding a bank of over 200 calli from a single selected lineage”) (p. 2874)
  8) Acknowledgements: We are grateful to the Swiss Federal Commission for Technological and Innovation (CTI/KTI) and Firmenich S.A. for funding these works in the frame of the CTI Project No 9083.1 PFLS-LS. There is no conflict of interest statement.
  9) There are no publishing dates, except for: “Published online: 16 Apr 2014”. When was submission, revisions, acceptance?
  10) Who holds the copyright for this paper, the authors, Taylor & Francis or Diagnosis Press?
  
  There is a PubPeer entry for this paper:
  https://pubpeer.com/publications/DB09D4AE74D1302FA5FCDBBC7F267F#fb22058
  
  Reply
4. Sandalwood queries says:
  
  January 19, 2015 at 11:17 am
  
  Janarthanam B, Dhamotharan R, Sumathi E (2012) Thidiazuron (TDZ) – induced plant regeneration from internodal explants of Santalum album L. Journal of Bioscience Research 3(3):145-153
  Publisher: JSBR.org (seems impossible to find the content of papers through a menu)
  http://jbsr.org/pdf2/october%202012/Sumathi.pdf
  
  Janarthanam B, Sumathi E (2011) High frequency shoot regeneration from internodal explants of Santalum album L. International Journal of Botany, 7: 249-254.
  DOI: 10.3923/ijb.2011.249.254
  URL: http://scialert.net/abstract/?doi=ijb.2011.249.254
  http://scialert.net/fulltext/?doi=ijb.2011.249.254
  
  Received: September 12, 2011; Accepted: November 16, 2011; Published: December 07, 2011
  
  F = figure; T = table
  
  1) 2011 T1 = 2012 T1
  
  2) 2011 T3 2iP shoot length = 2012 T3 TDZ shoot length (4 identical values for the control, 5%, 10%, 15% coconutmilk). Two completely different plant growth regulators cannot, of course, give identical values.
  
  3) 2011 T4 IBA = 2012 T4 IAA (for % rooting and #roots/shoot for 0.1 and 0.25 mg/l), although 2012 values have been rounded up. How can there be identical values for two growth parameters for two completely different cytokinins?
  
  4) 2011 T4 NAA (0.25 and 0.5 mg/l) = 2012 T4 IAA (1 and 2 mg/l) (for % rooting and #roots/shoot), although 2012 values have been rounded up. How can there be identical values for two growth parameters for two completely different cytokinins at two completely different concentrations?
  
  5) 2011 F1 abd = 2012 F1 ABD
  
  6) 2012 paper title indicates internodes. Table 2 title indicates nodes. Which explant is correct for this manuscript?
  
  There is a PubPeer entry for this paper:
  https://pubpeer.com/publications/D58F168229A9981C70A70919AE5F41#fb22079
  
  Reply
5. Sandalwood queries says:
  
  January 19, 2015 at 3:32 pm
  
  Das S., Ray S., Dey S., Dasgupta S. (2001) Optimisation of sucrose, inorganic nitrogen and abscisic acid levels for Santalum album L. somatic embryo production in suspension culture. Process Biochemistry 37, 51–56.
  http://www.sciencedirect.com/science/article/pii/S0032959201001686
  doi:10.1016/S0032-9592(01)00168-6
  
  1) The following important experimental conditions not reported: age of mother plant; density and culture vessel NR for embryogenic callus production; surface sterilization procedure for seeds used to establish in vitro seedlings.
  2) Commercial source and grade of chemical reagents and growth hormones not indicated.
  3) Somatic embryogenesis claimed in the paper, but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos).
  4) pH and light, two basic and essential factors of liquid cultures, not reported.
  5) Wrong reference provided for the Woody Plant Medium. It is not, as the authors reported, the 1981 abstract by McCown in HortScience; rather, it is: Lloyd G, McCown B. 1980. Commercially feasible micropropagation of mountain laurel, Kalmia latifolia, by use of shoot tip culture. Proceedings of the International Plant Propagators’ Society 30: 67–76. This error needs to be corrected.
  6) Das et al. 1998 book chapter in ACIAR proceedings dealing with medium pH and carbon source not mentioned, or referenced. Why not?
  
  Das S., Pal S., Mujib A., Sahoo S.S., Dey S., Ponde N.R., Dasgupta S.A. (1999) A novel process for mass propagation of Santalum album L. in liquid media and bioreactor. Acta Horticulturae 502, 281-288.
  Departments of Biotechnology and Chemical Engineering, Indian Institute of Technology-Kharagpur, Pin, Kharagpur, 721 -302, India
  http://www.actahort.org/books/502/502_45.htm
  
  1) The following important experimental conditions not reported: age of mother plant; density and culture vessel NR for embryogenic callus production; surface sterilization procedure for seeds used to establish in vitro seedlings.
  2) Commercial source and grade of chemical reagents and growth hormones not indicated.
  3) Somatic embryogenesis claimed in the paper, but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos).
  4) Abnormalities in regenerants claimed, but not explained, defined clearly, or shown.
  
  There is a PubPeer entry for both these papers:
  https://pubpeer.com/publications/8E02A105443B3DABBF6E891A1F6663#fb22181
  
  Reply
6. Sandalwood queries says:
  
  January 20, 2015 at 4:28 am
  
  Two papers by the same authors are clustered together in this report.
  
  Lakshmi Sita, G., Raghava Ram, N.V., Vaidyanathan, C.S., 1979.
  Differentiation of embryoids and plantlets from shoot callus of sandalwood.
  Plant Sci. Lett. 15, 265–270.
  doi:10.1016/0304-4211(79)90118-4
  Microbiology and Cell Biology Laboratory, Indian Institute of Science, Bangalore 560 012 (India)
  http://www.sciencedirect.com/science/article/pii/0304421179901184
  
  1) The following conditions not specified, or reported: culture vessels used, gelling agent, explant density.
  2) Commercial source and grade of chemical reagents and growth hormones not indicated.
  3) Somatic embryogenesis claimed in the paper, but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos).
  
  There is a PubPeer entry for this paper:
  https://pubpeer.com/publications/E1E15FBCA7D219CC346382C0CC19EE
  
  Lakshmi Sita, G.; Raghava Ram, N. V.; Vaidy Anathan, C. S.
  Triploid plants from endosperm cultures of sandalwood by experimental embryogenesis.
  Plant Sci. Lett. 20:63-69; 1980a.
  doi:10.1016/0304-4211(80)90070-X
  Microbiology and Cell Biology Laboratory, Indian Institute of Science, Bangalore 560 012 (India)
  http://www.sciencedirect.com/science/article/pii/030442118090070X
  1) This protocol relies heavily on the previous protocol (1979) developed for shoot tips and shoot segments. However, as indicated elsewhere on PubPeer (https://pubpeer.com/publications/E1E15FBCA7D219CC346382C0CC19EE), there are some flaws with that methodology and results, thus making the methodology of this 1980a paper automatically flawed. To reiterate, the errors (same as 1979 paper and new) are listed next.
  2) The following conditions not specified, or reported: culture vessels used, gelling agent, explant density.
  3) Commercial source and grade of chemical reagents and growth hormones not indicated.
  4) Somatic embryogenesis claimed in the paper, but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos).
  5) “Experiments conducted with diploid shoot callus were repeated [7].” (p. 66) referring to the 1979 paper. However, in the 1979 paper, absolutely no cytological or ploidy analyses were conducted proving that any tissue used (or any tissues that resulted) were diploid. This the assumption is false.
  6) “Differentiating callus was transferred to a liquid medium onto a shaker to separate various stages of embryoids.” (p. 66) The exact basal medium used in liquid culture is not specified. Shaking conditions not specified (e.g., rpm).
  7) Fig 5 and Fig 6 show rooted plantlets forming on what appears to be membrane rafts overlaying (possibly) liquid medium. None of this important information is explained in the M&M section.
  8) Fig. 5 legend: “A diploid plant obtained from shoot callus via embryogenesis, in liquid medium.” However, this is not part of the experiment of this study, and appears to be a result from the 1979 study. No clarification about this discrepancy is provided by the authors.
  9) Fig. 6 legend: “Triploid plant in liquid medium.” Howver, there are no cytological or ploidy analyses anywhere to confirm the ploidy. The basal assumption used by the authors is that the endosperm is triploid while shoot tip tissue is diploid.
  10) “We have produced successfully hundreds of triploid plants which look almost like the diploids” (p. 67) No proof or exact quantification of production by both methods, just a broad statement. No other organogenesis quantified.
  11) “Root tip squashes showed the triploid number of chromosome 3n = 30.” (p. 67) No proof to support this, and such methodology (root tip squashes) not defined or mentioned in the M&M section.
  12) Highly speculative discussion, but this aspect perhaps not surprising (and is forgivable) given the historically early stage of plant tissue culture.
  
  There is a PubPeer entry for this paper:
  https://pubpeer.com/publications/CBEB7D43FCE9E23E7DE5528AD83ED9#fb22248
  
  Who will correct the errors of the 1979 and 1980a papers? Considering that this journal does not exist, will the publisher (Elsevier Science) be responsible for issuing an erratum for each paper?
  1979
  http://www.sciencedirect.com/science/article/pii/0304421179901184
  1980a
  http://www.sciencedirect.com/science/article/pii/030442118090070X
  
  Reply
7. Sandalwood queries says:
  
  January 21, 2015 at 6:41 am
  
  Four studies related to a PPPR on sandalwood, a tree from which the second most expensive wood on the planet is derived, are clstered here. They have been linked on the same PubPeer page as none have DOIs:
  https://pubpeer.com/publications/D58F168229A9981C70A70919AE5F41#fb22327
  
  Ilah A., Abdin M. Z., Mujib A. (2002) Somatic embryo irregularities in in vitro cloning of sandal (Santalum album L.). Sandalwood Research Newsletter 15: 2–3.
  http://www.sandalwoodfoundation.org/newsletter/
  http://www.sandalwoodfoundation.org/wp-content/uploads/2013/08/SRN-015.pdf
  
  1) “Locally collected seeds were germinated in vitro.” It is impossible to just germinate seeds in vitro as they are always infected by fungi and bacteria. A sterilization procedure is always required. None if however provided by the authors.
  2) The following conditions not specified, or reported: medium pH, carbon source, gelling agent required for solid medium, culture vessels used, explant sizes, age or geographic origin of the mother plant from which seeds were derived.
  3) Commercial source and grade of chemical reagents and growth hormones not indicated.
  4) Somatic embryogenesis claimed in the paper, but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos).
  5) No abbreviations defined in full at first mention. One plant growth regulator, in particular, unclear what it is: CPA.
  6) Error in author’s name of a key reference Murashige and Skoog, misspelt twice as Skoong.
  7) The basal medium required for callus induction and somatic embryo induction, the two most basic processes and the basis of this entire paper, undefined.
  8) Photoperiod and light source: undefined.
  9) Authors claimed liquid medium to be superior to solid medium, citing Table 1 data. However, Table 1 data contains no statistical analyses that show significant differences between means. Moreover, globular, heart and cotyledonary stages show the exact opposite trend, i.e., solid medium is superior to liquid medium.
  10) A medium is stated as being McCown. No reference is provided for it. In fact, this is completely incorrect. The medium name is Woody plant medium and the authors are Lloyd G, McCown B. 1980. Commercially feasible micropropagation of mountain laurel, Kalmia latifolia, by use of shoot tip culture. Proceedings of the International Plant Propagators’ Society 30: 67–76.
  11) 53-68% of cultures showed abnormalities. But no plausible explanation provided.
  12) Table 2 provides root induction data using two auxins, yet no explanation about the methodology in the M&M section.
  13) Use of odd neologisms that will confuse the reader, e.g., somatic seedling.
  
  These errors need to be corrected / clarified.
  
  Mujib, A., 2005. In vitro regeneration of sandal (Santalum album L.) from leaves. Turkish Journal of Botany 29, 63–67.
  http://dergipark.ulakbim.gov.tr/tbtkbotany/article/view/5000019126 (open access)
  
  1) Why was the Ilah et al. 2002 paper not referenced?
  2) The abbreviations of all plant growth regulators, WPM not defined. The abbreviation for the cytokinin 2iP (i.e., 6-(γ,γ-dimethylallylamino)purine) incorrect (2,i-p).
  3) Many adjectives used in the results section: “effective”, “ineffective”, “high”, “better”, etc. but without any statistical analyses to prove these claims.
  4) Photosynthetic photon flux intensity of the light not reported.
  5) Root induction medium defined only at the end of the results section and not in the M&M section.
  6) Sample sizes used to evaluate data in Tables 1 and 2 not indicated.
  
  Rai R, McComb J (1997) Direct somatic embryogenesis from mature embryos of sandalwood. Sandalwood Research Newsletter 6, 2-3.
  http://www.sandalwoodfoundation.org/wp-content/uploads/2013/08/SRN-006.pdf
  
  vs
  
  Rai, V.R.V., McComb, J., 2002. Direct somatic embryogenesis from mature embryos of sandalwood. Plant Cell, Tissue and Organ Culture 69(1), 65–70.
  doi: 10.1023/A:1015037920529
  http://link.springer.com/article/10.1023/A%3A1015037920529
  
  1) Somatic embryogenesis claimed in the paper (and is the basal premise, as evidenced by the title), but not proved by any analyses (cytological, histological, genetic). Weak evidence (only photos, the most convincing being Fig. 1F).
  2) Last line of the abstract: “This is the first report on in vitro regeneration via direct somatic embryogenesis of sandalwood.” This is a false claim. The exact same authors had reported this result 5 years earlier in Rai R, McComb J (1997) Direct somatic embryogenesis from mature embryos of sandalwood. Sandalwood Research Newsletter 6, 2-3 (http://www.sandalwoodfoundation.org/wp-content/uploads/2013/08/SRN-006.pdf), in which the authors state “This report is the first on in vitro regeneration via direct, rather than indirect somatic embryogenesis of sandalwood.” The 2002 paper fails to reference the 1997 report. Two fundamental differences between both reports: 1) MS + 2 mg/l BA (1997) or 4.5 µM TDZ (2002) (somatic embryo induction medium); 2) ½MS + 0.5 mg/l IAA (1997) or 2.8 µM GA3 (2002) (conversion/germination of somatic embryos).
  3) Apart from these issues, the 2002 paper is a simple but solid study.
  
  Reply
8. Sandalwood queries says:
  
  January 22, 2015 at 12:57 am
  
  Revathy, E. 1, Arumugam, S. 2 (2011) Somatic embryogenesis and plantlets regeneration from seedling explants of Santalum album L. (Santalaceae). International Journal of Current Research 33(6), 237-241
  1 PG Department of Biochemistry, Valliammal College for Women, Chennai – 600 102, India
  2 Department of Zoology, Presidency College, Chennai – 600 005, India
  http://www.journalcra.com/?q=node/618
  http://www.journalcra.com/sites/default/files/Download%20810.pdf
  Received: 18th March, 2011; Received in revised form: 2nd April, 2011; Accepted: 5th May, 2011; Published online: 6th June 2011
  Listed on Jeffrey Beall’s: http://scholarlyoa.com/individual-journals/ (copyright on PDF indicates Academic Journals)
  No DOI.
  
  1) Commercial source and grade of chemical reagents (except for agar) and growth hormones not indicated.
  2) Somatic embryogenesis claimed in the paper (and is the basal premise, as evidenced by the title), but not proved by any analyses (cytological, histological, genetic). Zero evidence provided.
  3) “The maximum rooting response achieved on medium supplemented only with 2.46 μM IBA was 70 per cent, with an average of 5.3 ±0.25 roots per shoot (Table 5).” (p. 240) However, Table 5 (p. 239) shows a maximum value of 60%.
  4) No statistical analyses.
  5) Nodes, internodes, juvenile leaves and shoot tips prepared, but only data on internodes provided.
  
  This case is linked to this PPPR on sandalwood at PubPeer:
  https://pubpeer.com/publications/D58F168229A9981C70A70919AE5F41#fb22154
  
  Reply
9. Sandalwood queries says:
  
  January 26, 2015 at 2:35 pm
  
  Rugkhla, A., Jones, M.G.K., 1998. Somatic embryogenesis and plantlet formation in Santalum album and S. spicatum. Journal of Experimental Botany 49 (320), 563–571.
  1 School of Biological and Environmental Sciences, Murdoch University, Perth, WA 6150, Australia
  2 Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
  Received 24 October 1997; Accepted 28 October 1997
  doi: 10.1093/jxb/49.320.563
  http://jxb.oxfordjournals.org/content/49/320/563.abstract
  http://jxb.oxfordjournals.org/content/49/320/563.full.pdf (open access)
  
  This study provides some support that previous studies in the literature claiming somatic embryogenesis, as documented at PubPeer*, are not reproducible: “Preliminary results on somatic embryogenesis of Santalum album obtained following the published methods, were unreliable, particularly for the two steps of inducing embryogenic callus using 2,4-D and subculturing into GA3 (Lakshmi Sita et al., 1979) or IAA and BAP (Rao and Bapat, 1992).”
  * https://pubpeer.com/publications/D58F168229A9981C70A70919AE5F41#fb22154
  
  Queries / issues / concerns:
  1) Paper submitted and accepted in 4 days.
  2) Exact size of explants and age of mother plants, explant density and culture vessels, and light source not reported.
  3) Commercial source and grade of chemical reagents (except for gelrite) and growth hormones not indicated.
  4) The methods indicates (p. 564): “Nodal segments were taken from new sprouting branches of mature trees of S. album and S. spicatum.” Two lines later, it states: “The pericarp of S. album seeds were removed under”. In other words, from this point onwards, for the next approx.. 6 paragraphs of methodology, it appears as if the methodology applies only to S. album (Indian sandalwood) but not to S. spicatum (Western Australian sandalwood). There is absolutely no way of knowing precisely what steps were true and applicable for which species, or if all steps were valid for both.
  5) Tables 1, 2, 3 and 6 define clearly the species studied, but Tables 4 and 5 do not. Unfortunately, the text also does not clarify this important issue.
  6) Histological segments in Fig. 2 as proof of somatic embryogenesis not very convincing, but (sadly) still much more proof that any other paper to date claiming somatic embryogenesis.
  7) Acclimatization not performed so the efficiency of the plantlets regenerated in vitro could not be assessed.
  
  This case has a PubPeer entry:
  https://pubpeer.com/publications/40F1330E3A965DDDEFFA4187629788#fb23031
  
  Reply
10. Sandalwood queries says:
  
  January 26, 2015 at 2:36 pm
  
  Shekhawat, U.K.S., Ganapathi, T.R., Srinivas, L., Bapat, V.A., Rathore, T.S., 2008. Agrobacterium-mediated genetic transformation of embryogenic cell suspension cultures of Santalum album L. Plant Cell, Tissue and Organ Culture 92(3), 261–271.
  Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
  Tree Improvement and Propagation Division, Institute of Wood Science and Technology, 18th Cross, Malleswaram, Bangalore 560 003, India
  Received: 9 August 2007 / Accepted: 6 December 2007 / Published online: 15 December 2007
  doi: 10.1007/s11240-007-9330-4
  http://link.springer.com/article/10.1007%2Fs11240-007-9330-4
  
  1) Stem segments used, but were these nodes or internodes?
  2) What was the age of the mother tree and what was the exact location of the tree that was sampled?
  3) Commercial source and grade of chemical reagents (except for the binary vector and PCR, RT-PCR reactions) and growth hormones, acetosyringone, GUS assay, antibiotics (cefotaxime, carbenicillin, hygromycin) not indicated.
  4) How were the primers for RT-PCR designed (in-house or based on the literature)?
  5) No histological proof that cultures were “embryogenic”.
  6) Lane numbering of Fig 4 (Southern blot) odd: there are clearly 6 lanes, but only 5 are labelled and explained in the figure legend. Fig 3B also has the same odd lane numbering problem: there are clearly 8 lanes, but only 7 are labelled and explained.
  7) Number of copies of transgene that were inserted not indicated, or estimated.
  8) (p. 268) “The selected transformed colonies when transferred to medium supplemented with BAP and IAA combination showed the development of somatic embryos in almost 100% of the cultures (Fig. 1c). These embryos displayed intense GUS staining (Fig. 1d). The transformed somatic embryos showed the development of shoots in 10–15% of the cultures and all of these developed into complete plantlets on White’s medium (Fig. 1e, f).” Fig. 1c does show some fluffy callus-like structures, but to claim that they are somatic embryos requires at least histological proof. No such proof is provided, so the claim is doubtful. This doubt is further accentuated by the claims of Fig. 1d, which shows what appear to be shoot initials rather than somatic embryos. Finally, Fig. 1 e shows a soot with no root system, clearly indicating that this is not a structure that was derived from a somatic embryo, which would have both a shoot and a root. This fortifies the concerns of widely unsubstantiated claims of somatic embryogenesis in sandalwood: https://pubpeer.com/publications/D58F168229A9981C70A70919AE5F41#fb22154
  9) RT-PCR results in Fig. 3 only for suspension cultures but Southern analyses in Fig. 4 for putatively transformed plants. There is no link between the material analyzed with both techniques, making the effectiveness difficult to interpret.
  
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  https://pubpeer.com/publications/12E25C0BEEAC9954BC59CF5945DFC6#fb23035
  
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11. Sandalwood queries says:
  
  January 27, 2015 at 2:34 am
  
  Singh, C.K., Raj, S.R., Patil, V.R., Jaiswal, P.S., Subhash, N., 2013. Plant regeneration from leaf explants of mature sandalwood (Santalum album L.) trees under in vitro conditions. In Vitro Cell. Dev. Biol. Plant 49, 216–222.
  Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, Gujarat, India
  doi: 10.1007/s11627-013-9495-y
  Received: 21 August 2012 / Accepted: 4 February 2013 / Published online: 23 February 2013 / Editor: John Forster
  http://link.springer.com/article/10.1007/s11627-013-9495-y
  
  1) In the very first line of the abstract, the authors state: “Sandalwood (Santalum album L.) is a small evergreen, hemi-parasitic tree having more than 18 woody species that are mostly distributed in South Asia, Australia, and Hawaii.” The number 18 is rather odd, considering that two different numbers appear reported elsewhere in the sandalwood literature. Fox, in 2000, states that the Santalaceae consists of 29 genera with approximately 400 species, 25 species specific to the Santalum genus. Harbaugh and Baldwin (2007) place those numbers as “15 extant species, approximately 14 varieties, and one recently extinct species, distributed throughout India, Australia, and the Pacific Islands.” Where do the authors get the number 18 from, and why has this fact not been supported by any reference within the main body of text?
  2) In the third sentence of the abstract, the authors state: “The percentage of seed germination is poor and germination time exceeds 12 mo.” This is a misrepresentation of the facts, and of the literature. For example, Hirano (1990) showed that simple removal of the testa, and a dip of naked seed in a fungicide for 5 min, could result in 67% germination for Indonesian S. album, and 26 days to germination.
  3) I question the originality of this manuscript. Allow me to explain. In the abstract, the authors state: “In this study, efficient plant regeneration was achieved via indirect organogenesis from callus cultures derived from leaf tissues of S. album.” In the title, they state “Plant regeneration from leaf explants of mature sandalwood”. At the end of the introduction, they state: “The first incidence of plant regeneration from callus using leaf explants from mature sandalwood trees is reported here.” Indeed, if there were no other studies that reported on regeneration from leaves in sandalwood, these three claims would be true. But this is not the case. There are at least five studies in the sandalwood in vitro literature that report regeneration from leaf tissues and leaves: Rugkhla and Jones 1998, Mujib 2005, Revathy and Arumugam 2011, Bele et al. 2012, Crovadore et al. 2012. Not one of these studies is referenced by the authors. This can only reflect three options: a) the authors did a very poor scouting of the literature; b) the authors purposefully omitted the reference to previous studies from leaves in a bid to enhance the “originality” of their paper; c) the editors and peers did an equally poor job of checking the literature, not seeing that in fact the originality of this paper was not that high. The authors are requested to indicate why none of these 5 studies were referenced. The editors are requested to indicate how such an important issue was mised, or how such oversight could have taken place.
  4) Related to the above, the concerns are even greater when we examine specific aspects of those studies that were omitted. The Rugkhla and Jones 1998 paper examined the use of TDZ, as did Bele et al. 2012. Mujib used WPM and BA (woody plant medium). Revathy and Arumugam 2011 studied the effectiveness of BA+NAA. Revathy and Arumugam 2011, and Bele et al. 2012 examined the use of 2,4-D. All of the aspects that the authors of this paper are claiming to be studied for the first time in sandalwood for leaf tissue have, in fact, already been studied, for leaf tissue. This may reflect very serious editorial oversight.
  5) Introduction. The plant is introduced as: “Sandalwood (Santalum album)” In fact, this is not accurate. There are many types of sandalwood, including Australian sandalwood (S. spicatum), Hawaiian sandalwood (S. ellipticum, S. freycinetianum, and S. paniculatum), red sandalwood (Pterocarpus santalinus), etc. The sandalwood that the authors studied was Indian sandalwood, Santalum album L.
  6) Introduction: “The tree is medium sized, about 12–15 m tall, and reaches its full maturity in 60 to 80 yr. At maturity, the center of the trunk (the heartwood) achieves its greatest oil content. The oil is highly valued for its fragrance and is used in perfumes, cosmetics, and medical industries, among others. It is also a major constituent in agarbathi (incense sticks) manufacturing. S. album has the highest oil content (about 6%) among all the species of the genus Santalum.” Not a single one of these facts is supported by a reference.
  7) Introduction: “The best hosts for sandalwood are nitrogen-fixing trees because growth depends on the amino acid availability such that the host plant does not compete with the sandalwood for nutrients (Brand 2005).” Something odd: “Brand J (2005) stated that the best hosts for sandalwood are nitrogen fixing trees because growth depends on the amino acid availability and the host plant should not compete with the sandalwood for nutrients.” from http://www.spc.int/lrd/research/sandalwood-micropropagation
  8) Introduction: “There has been at least 20% loss over the last 10 yr or three generations, based on actual or potential levels of exploitation. The existing populations are devoid of trees of a commercial girth not only due to illicit felling, but also grazing, recurrent fires, and the lethal phytoplasmic spike epidemics. Natural regeneration of S. album is low because of low percentage of seed germination (10–20%), scavenging of germinated seeds by squirrels and rodents, as well as browsing and trampling of young seedlings by wildlife and cattle.” Not a single one of these facts is supported by a reference.
  9) Introduction: “For large-scale production of sandalwood, different in vitro techniques can be used to clone superior lines, which is a major prerequisite for Agrobacterium-mediated transformation and protoplast fusion gene transfer techniques.” How do the authors know this is true for sandalwood? There are no references, but there should at least be two: Shiri and Rao 1998; Shekhawat et al. 2008.
  10) Introduction: “In vitro regeneration of S. album has been reported from hypocotyl, nodal, and endosperm explants (Bapat and Rao 1979; Lakshmi Sita et al. 1979; Rao and Bapat 1992).” Another total misrepresentation of the literature. There are, in my best estimate, at least 40 studies (including journals and book chapters) with different explants, 5 of which used leaf tissue. Why did the editors/peers not see this gap?
  11) Introduction: “Leaves from mature trees provide a useful source of explants, which are easily available and elicit a good response.” That’s a premature comment to make, unless they were reflecting on the results from the 5 reported studies that they failed to declare in their paper.
  12) Introduction: “The objective of this study was to develop a more efficient and reliable protocol for in vitro regeneration of sandalwood from leaf explants of mature sandalwood trees using different combinations of plant growth regulators.” Again, serious objections are raised about these claims and statements. More efficient and reliable relative to what? If the literature was so poorly explored in the introduction, and so misrepresented, then what are the authors actually comparing their protocol to? The authors in fact only tested TDZ and 2,4-D for callus induction, and BA and NAA for shoot induction from callus, all four PGRs had already been tested for leaf and other explants in the sandalwood literature, emphasizing again the clear lack of originality of this paper’s methodology.
  13) M&M: mature trees used, but the age is not indicated.
  14) M&M: a false claim and an equally false supporting reference is made regarding the sterilization protocol. The authors state: “Single leaf samples were cut to ∼4 cm2 and dipped in 0.1% (v/v) liquid detergent (Tween-20) for 5 min. After this, explants were washed four or five times with distilled water. Explants were subsequently treated with 1,000 ppm Bavistin, 200 ppm cefotaxime, and 200 ppm kanamycin for 10 min and washed three times with sterile distilled water in a laminar flow hood. Subsequently, the explants were surface sterilized with 0.1% (w/v) mercuric chloride for 3–4 min and thoroughly washed six to eight times with sterile distilled water (Maina et al. 2010).” The Maina et al. (2010) reference states: “Surface sterilization entailed rinsing seeds in 70% ethanol (1 min) followed by treatment with various combinations of different durations (5, 10, 15, 30 min and overnight) and concentrations of NaOCl (3.5% (w/v) in commercial bleach) ranging from 0.018, 0.35, 0.53, 0.70 to 1.05% (w/v) NaOCl. This was compared to sterilization with 0.1% (w/v) aqueous mercuric chloride (HgCl2) for 8 min (Sharma and Anjaiah, 2000). All treatments included a few drops of Tween 20. Sterilization was followed by thorough washes with sterile water and subsequent soaking for 2 h before use.” IT is evident that the wrong reference has been quoted and that the protocol used does not correspond, unlike what the authors state, to the Maina et al. 2010 reference.
  15) M&M: conflicting information: “The remaining segment (~1–1.5 cm) was inoculated horizontally on the culture medium.” Versus, a few lines later “Surface-sterilized leaf explants (1–2 cm)” Is it 1.5 or is it 2? Is it an area, or what exactly does this unit represent? Length, diameter?
  16) M&M: The authors claim to have used 40-60% relative humidity. Is this in the culture chamber or in the culture flask?
  17) M&M: When describing the light and temperature conditions of culture, “except for cases where specific physiological conditions were required.” What does this even mean? What other “physiological conditions” are the authors referring to since no physiological measurements were made in the paper?
  18) There is a serious problem with the callus-related steps used for shoot induction. The hint begins in the abstract that states “24.6 shoot buds/callus”. What is a callus in this context? A callus clump? The M&M describes a method in which, “For shoot bud induction, the regenerated calli were transferred to the WPM medium.” However, the authors do not indicate the exact size, volume or mass of callus that served as the initial explant for shoot induction. It is evident that, at least in theory, a callus clump that has a wider surface area with the medium, or that has greater volume, might also form more shoot buds. This is a serious methodological oversight. The same error is then repeated in a second callus/shoot-related step: “After shoot bud induction, calli were transferred to media supplemented with different concentrations of BA (1.0, 2.0, 3.0, 4.0, and 5.0 mgl−1) and Kn (1.0, 1.5, 2.0, 2.5, and 3.0 mgl−1) for the passage of shoot proliferation.”
  19) M&M: “For root induction, regenerated shoots (4–5 cm) were excised from the parent culture and transferred onto WPM medium” This is the first time that the term “parent culture” is mentioned. What is it? What medium exactly is it grown on? From what medium exactly were the shoots derived, considering that you had 11 BAxNAA combinations (incl. contols)? Or were shoots pooled from all treatments? The same problem/ambiguity repeats itself in the acclimatization step: “The in vitro-regenerated plantlets with well-developed shoots (3–4 cm)” There are 6 IBA treatments (incl. control). So, shoots were derived from which treatment? Or were shoots pooled from all IBA treatments?
  20) M&M: what light source and relative humidity levels were used during acclimatization? How exactly was the soil sterilized, and why, if the coco-peat was not sterilized? These important details are not mentioned.
  21) Results: “After 4–5 wk, more than 90%of plants were able to survive on the substrate made of coco-peat and soil (1:1; Fig. 1i).” The “plantlet” in Fig. 1i looks like it was plucked straight from in vitro and added to the potting mixture simply as photographic evidence of an “acclimatized plant”. A 5 week old acclimatized plantlet does not have that “skimpy” appearance.
  22) Contradiction or confusion of results related to optimal shoot production. The abstract states: “The WPM medium supplemented with 2.5 mgl−1 BA+0.4 mgl−1 NAA was the most effective, producing the highest number of shoot buds (24.6) per callus. The highest number of shoots per explant (20.67) and shoot length (5.17 cm) were observed in media supplemented with 5.0 mgl−1 BA and 3.0 mg1−1 Kn, respectively.” In fact, this statement is partially correct, but misleading because data in table 4 indicates that statistically, 4 media were equivalent in terms of shoot production: 4 mg/l BA, 5 mg/l BA, 2.5 mg/l Kn and 3.0 mg/l Kn.
  23) Fig 1 legend for b: the plant growth regulator is missing.
  24) Fig 1 legend for c: is the medium the same as that for b?
  25) What is the exact medium of photos in Fig 1d to 1h?
  26) Results: “concentrations of TDZ (0.4 and 0.6mgl−1) showed the highest frequency of callus induction (Table 1).” But the percentages are 100% and 91.6%, respectively. Why has the second concentration been listed as “highest”? The same idea is repeated in the next section: “Lower concentrations of TDZ at 0.4 and 0.6 mgl−1 showed excellent callus growth from leaf explants in comparison to higher concentrations of growth regulators (Fig. 1a–c; Table 1).”
  27) Results repeated for 2,4-D: “Low concentrations of 2,4-D, i.e., 1.5 and 2.0 mgl−1 also showed a better response in comparison to higher concentrations.” and “Lower concentrations of 2,4-D, 1.5 and 2.0 mgl−1, also showed good callus growth.”.
  28) Results: “TDZ exhibits the unique property of mimicking both auxin and cytokinin effects on growth and differentiation of cultured explants, although structurally it is different from either auxins or purine-based cytokinins.” That’s a serious piece of factual information. However it is not supported by any literature. There are a few reviews on TDZ that could have easily been referenced to support these claims, but which were not.
  29) Results: “TDZ and 2,4-D were reported to induce callus formation in a variety of plant culture systems with a rate of cell proliferation and intrinsic activity higher than that obtained with other growth regulators (Capelle et al. 1983; Murthy et al. 1998), which are also in agreement with the present study.” The all-encompassing “is in agreement with this study” rationale, which is frequently used by the authors to try and find similarities with other, sometimes, totally unrelated studies, such as: “This is in agreement with the observations of Sahai et al. (2010)”, comparing the response of a hardwood tree, sandalwood, with a herbaceous medicinal plant, Tylophora indica. Other instances of incomparable comparisons include “Similar observations were also made by Wang et al. (2011),”, “The above outcomes are in accordance with the findings of Janarthana and Seshadri (2008) and Mungole et al. (2011)”, “Azad et al. (2005) and Chandra and Bhanja (2002) also noted”, “The results of the present study agree with Vyas et al. (2005),”, “The findings on percentage of rooting are in agreement with the results of Ali et al. (2009)…and with Metivier et al. (2007)”
  30) Actually, what would have been appropriate, and what should have taken place, should have been a comparison with the 40+ sandalwood in vitro studies, and the responses of those explants to different PGRs, including the response of leaves in the 5 leaf-related sandalwood references that the authors forgot to mention.
  31) Last paragraph of R&D: “These results demonstrate that leaf explants of S. album have significant morphogenetic potential for callus formation and indirect organogenesis;” This was already proved at least 5 times in the sandalwood literature, had the authors taken the time to examine it carefully and had the peers and editors made the task of examining the literature a top priority.
  32) Last paragraph of R&D: “A reliable in vitro regeneration technique is an essential component for most methods of genetic transformation (Schwarz and Beaty 2000) and protoplast fusion.” Tough to assess that reference from 12-13 years ago in a difficult-to-access source. Surely, the authors could have referenced the two sandalwood genetic transformation studies (Shiri and Rao 1998; Shekhawat et al. 2008)?
  33) Conclusions: “In the present investigation, the protocol for the in vitro regeneration from leaf explants has been developed.” There is nothing new here that hasn’t already been explored for sandalwood before.
  34) Conclusions: “Regeneration via callus has been a potent source of producing parental clones as well as somaclonal variants in plants.” Not only is this a total contradiction, it reflects the authors basic misunderstanding of tissue culture principles. Callus is not a desired outcome for clonal production because of the inherent risks of somaclonal variation. This statement is thus a non-statement.
  35) Conclusions: “Moreover, regeneration involving a callus phase would be suitable for combining transformation events to recover transgenic plants. Hence, the above procedure may be employed in relation to the aforesaid facts for genetic improvement and also could be used as a tool to introduce new variants of S. album in a somaclonal variant selection program.” Had there been a brush-up of the grammar, this idea could have been stated in a much more succinct way, no doubt.
  36) The Acknowledgments are really bizarre: “The authors gratefully acknowledge the Plant Tissue Culture Laboratory, Department of Agricultural Biotechnology, Anand Agricultural University, Anand, Gujarat, India, for providing laboratory facilities.” Why are the authors thanking their own laboratory for laboratory facilities?
  37) A small but important point for the Maina et al. 2010 reference. The abbreviation for African is written as “Aff”. It should be Afr. In fact, the term “Aff” is actually extremely derogatory about Africans, making this most likely an unintentional, but really serious editorial gaffe.
  38) Why can the authors add Springer and/or Society for In Vitro Biology copyrighted material as open access on Research Gate? http://www.researchgate.net/publication/242012281_Plant_regeneration_from_leaf_explants_of_mature_sandalwood_(Santalum_album_L.)_trees_under_in_vitro_conditions
  
  The following needs to take place:
  a) The authors need to explain clearly, point by point, why there are so many oddities and errors. In particular, the issue of originality needs to be explained in detail.
  b) The editors need to explain why there appears to have been what appears to be some serious editorial oversight, at least related to the literature. Can the peer reports be released, even anonymously? Can there be accountability as to which editors were responsible for approving a paper which, in fact, was not as original as it was being made to appear?
  
  Many scientists are vying for a place to have their research published in this journal, one of the few specialty journals in plant science related to plant tissue culture. It is thus incomprehensible how this piece of literature passed peer review and was accepted as an “original research paper”.
  
  References cited:
  Bele D., Tripathi M.K., Tiwari G., Baghel B.S., Tiwari S. (2012) Microcloning of sandalwood (Santalum album Linn.) from cultured leaf discs. International Journal of Agricultural Technology 8(2): 571-583.
  Crovadore J, Schalk M, Lefort F (2012) Selection and mass production of Santalum album L. calli for induction of sesquiterpenes. Biotechnology & Biotechnological Equipment 26:2, 2870-2874
  Fox JE. Sandalwood: the royal tree. Biologist (London), 2000; 47: 31–34
  Harbaugh DT, Baldwin BG. 2007. Phylogeny and biogeography of the sandalwoods (Santalum, Santalaceae): repeated dispersals throughout the Pacific. American Journal of Botany 94(6): 1028–1040.
  Hirano RT. 1990. Propagation of Santalum, sandalwood tree. USDA Forest Service Gen. Tech. Rep. PSW-122, pp. 43-45
  Maina SM, Emongor Q, Sharma K, Gichuki ST, Gathaara M, De Villiers SM (2010) Surface sterilant effect on the regeneration efficiency from cotyledon explants of groundnut (Arachis hypogea L.) varieties adapted to eastern and Southern Africa. Aff J Biotechnol 9:2866–2871
  http://www.academicjournals.org/article/article1380702686_Maina%20et%20al.pdf
  Mujib, A., 2005. In vitro regeneration of sandal (Santalum album L.) from leaves. Turkish Journal of Botany 29, 63–67.
  Revathy, E., Arumugam, S. (2011) Somatic embryogenesis and plantlets regeneration from seedling explants of Santalum album L. (Santalaceae). International Journal of Current Research 33(6), 237-241
  Rugkhla, A., Jones, M.G.K., 1998. Somatic embryogenesis and plantlet formation in Santalum album and S. spicatum. Journal of Experimental Botany 49, 563–571.
  Shiri, V., Rao, K.S., 1998. Introduction and expression of marker genes in sandalwood (Santalum album L.) following Agrobacterium-mediated transformation. Plant Sci. 131, 53–63.
  Shekhawat, U.K.S., Ganapathi, T.R., Srinivas, L., Bapat, V.A., Rathore, T.S., 2008. Agrobacterium-mediated genetic transformation of embryogenic cell suspension cultures of Santalum album L. Plant Cell. Tissue Organ Cult. 92, 261–271.
  
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  https://pubpeer.com/publications/5361D84E566D3B0E179C09A132C102#fb23074
  
  Reply
12. Sandalwood queries says:
  
  January 27, 2015 at 4:32 am
  
  Sankara Rao, K., Chrungoo, N.K., Sinha, A., 1996. Characterization of somatic embryogenesis in sandalwood (Santalum album L.). In Vitro Cellular & Developmental Biology – Plant 32, 123–128.
  Department of Biochemistry, Indian Institute of Science, Bangalore 560 012 India
  doi: 10.1007/BF02822754
  Received 9 November 1994; accepted 26 February 1996; editor G. C. Phillips
  http://link.springer.com/article/10.1007%2FBF02822754
  
  1) Somatic embryogenesis claimed in the paper (and is the basal premise, as evidenced by the title), but not proved by any analyses (cytological, histological, genetic). The most convincing evidence is a macroscopic view, with a dissecting microscope, of what appears to be bipolar structures.
  2) M&M: “Callus initiation and somatic embryo induction were standardized earlier (Sankara Rao, unpublished).” This is not very useful. As of January, 2015, this protocol still seems to remain unpublished, thus the scientific community will never know what failed and what worked. Did the authors at least send the raw data to the editors/journal when the paper was submitted to verify that this claim was true? If so, can IVCDB – Plant release that document publicly?
  3) M&M: “Cultures of sandalwood (Santalum album L.)” The correct name is Indian sandalwood. See discussion on this issue at another sandalwood paper report: https://pubpeer.com/publications/5361D84E566D3B0E179C09A132C102#fb23074
  4) M&M: The following important aspects of the protocol were not reported: Age of mother plant, exact size of explants, explant density and culture vessels used.
  5) M&M: Commercial source and grade of chemical reagents and growth hormones not indicated.
  6) “…concentration of 1 mg/l each (MS1a) or 2,4-D at a concentration of 2 mg/l and kinetin at 0.5 mg/l (MS1b) for callus formation. Both the media were equally effective in inducing callus formation. The freshly formed callus was subcultured on MS medium containing 3% sucrose and 1 mg/l of 2,4-D (MS2) for proliferation/embryogenic induction. A hormone-free MS medium containing 2% mannitol (MS3) was used for synchronous embryo differentiation. Half strength hormone-free medium with or without mannitol (MS4) was used for maturation of bipolar embryos.” It is unclear what is “synchronous embryo differentiation” and how MS3 differs from MS4, both functionally and in terms of differentiation. Absolutely no explanation exists as to what age or size of explants are transferred from MS1 to MS2 to MS3 and finally on to MS4.
  7) Light intensity, light source, photoperiod (or darkness?), temperature and any other culture room conditions not reported. It is, in essence, impossible to reproduce this experimental protocol.
  8) Lane splicing in Figure 2 (between lanes 1 and 2) and in Figure 3 (between lanes 1, 2 and 3?).
  9) The authors claim 4 stages to “somatic embryogenesis”, but only show macro-images of stage 1 and stage 4. Why no images of the other two stages? The fact that no verifiable proof has been provided for the existence and developmental and/or structural difference between these 4 stages immediately calls into question the validity of all of the biochemical analyses conducted in Figures 2-6, because there is absolutely no guarantee that in fact there is no overlap in tissue, similarity of tissue/organs or even the same developmental stage.
  10) Very unfortunately, this flawed protocol is then used as the basis for a subsequent protocol on the genetic transformation of sandalwood: Shiri, V., Rao, K.S., 1998. Introduction and expression of marker genes in sandalwood (Santalum album L.) following Agrobacterium-mediated transformation. Plant Sci. 131, 53–63. doi:10.1016/S0168-9452(97)00232-X (which will be critiqued separately at PubPeer).
  11) ACKNOWLEDGMENTS: “We thank Dr. A. Harmon, University of Florida at Gainesville, for probing our blots with anti-CDPK mAb. This research work was supported by Department of Science and Technology, New Delhi, in the form of a grant to K.S.R. One of us (N.K.C.) acknowledges the award of a visiting associateship by DST.”
  
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  https://pubpeer.com/publications/709D8119A5C417B84F3C2C0567DF17#fb23095
  
  Reply
13. Sandalwood queries says:
  
  January 27, 2015 at 6:22 am
  
  Shiri, V., Rao, K.S., 1998. Introduction and expression of marker genes in sandalwood (Santalum album L.) following Agrobacterium-mediated transformation. Plant Science 131, 53–63.
  Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
  Received 20 June 1997; received in revised form 13 October 1997; accepted 14 October 1997
  doi: 10.1016/S0168-9452(97)00232-X
  http://www.sciencedirect.com/science/article/pii/S016894529700232X
  
  1) Somatic embryogenesis claimed in the paper (and is the basal premise, as evidenced by the title), but not proved by any analyses (cytological, histological, genetic). The most convincing evidence is a macroscopic view, with a dissecting microscope, of what appears to be bipolar structures in Fig 1c.
  2) Abstract and introduction: “sandalwood (Santalum album L.)” The correct name is Indian sandalwood. See discussion on this issue at another sandalwood paper report: https://pubpeer.com/publications/5361D84E566D3B0E179C09A132C102#fb23074
  3) M&M: “The torpedo–cotyledonary stage somatic embryos (0.75–1.2 cm) examined for transformation were obtained from an embryogenic sandalwood culture line established in our laboratory [23].” Reference [23] refers to Sankara Rao, K., Chrungoo, N.K., Sinha, A., 1996. Characterization of somatic embryogenesis in sandalwood (Santalum album L.). In Vitro Cellular & Developmental Biology – Plant 32, 123–128, a paper with its own fair share of issues, also discussed at PubPeer: https://pubpeer.com/publications/709D8119A5C417B84F3C2C0567DF17#fb23095. This indicates that whatever flaws existed in the 1996 paper have potentially automatically carried through into this paper, as well.
  4) M&M: The exact size of explants, timing of transfer or developmental stage of explants transferred between different media is not clear, nor is it explained. This leaves room for ample interpretations and error.
  5) M&M: “agar-solidified media” and “Murashige and Skoog [25] agar-solidified medium and White’s [26] agar-solidified medium”. However, the concentration of gar used not indicated.
  6) M&M: Commercial source and grade of chemical reagents and growth hormones, GUS assay, PAGE, antibiotics (kanamycin), soilrite, PCR (except for Taq Pol), Southern hybridization, radioactive ATP, restriction enzymes, and dot blot not indicated.
  7) M&M: For PAGE, “About 500 mg of somatic embryos” However, the exact stage of development, size or timing of sampling is not indicated. So, what tissue should be used exactly?
  8) The success of regeneration and genetic transformation not quantified, including transformation efficiency, or number of putative transformants generated.
  9) References [4] and [20] Chinese authors’ names not abbreviated. Reference [5], accents missing from Spanish authors’ names (http://www.sciencedirect.com/science/article/pii/0168945294040218). Reference [11] Taiwanese authors’ names not abbreviated. References [13] and [14] spelling mistake with Agrobacterium. Reference [18], accents missing from Spanish authors’ names (http://link.springer.com/article/10.1007%2FBF00232724); last author’s name misspelt (should be Navarro). Reference [20], royal gala should be Royal Gala. How does one check the veracity of reference [24]? Reference [26] is missing the date; it should be 1963.
  10) Is it possible that the flaws in the methodology of the two related papers may explain why no more transformation studies have emerged between 1998 and 2015?
  
  This case has a PubPeer entry:
  https://pubpeer.com/publications/F89430D4B1AFA543CA215B6A63911E#fb23104
  
  Reply
14. Sandalwood queries says:
  
  March 25, 2015 at 12:35 pm
  
  P = papers; BC = book chapter.
  
  Several concerns have been raised about these related papers and book chapters.
  
  P1
  Bapat, V.A. and P.S. Rao, 1979. Somatic embryogenesis and plantlet formation in tissue culture of sandalwood (Santalum album L.). Annals of Botany 44(5): 629-630.
  No DOI.
  http://aob.oxfordjournals.org/content/44/5.toc
  
  P2
  Bapat, V. A.; Rao, P. S. 1984. Regulatory factors for in vitro multiplication of sandalwood tree (Santalum album Linn.). I. Shoot bud regeneration and somatic embryogenesis in hypocotyl cultures. Proceedings of the Indian Academy of Sciences Plant Science Section B 93(1): 19-27.
  No DOI.
  https://archive.org/stream/proceedingsofthe020242mbp#page/n23/mode/2up
  Now published by Springer? http://link.springer.com/journal/volumesAndIssues/40011
  
  P3
  Bapat, V.A. and P.S. Rao, 1988. Sandalwood plantlets from synthetic seeds. Plant Cell Reports 7(6): 434-436.
  DOI: 10.1007/BF00269531 (DOI cannot link to PubPeer)
  http://link.springer.com/article/10.1007/BF00269531
  
  P4
  Bapat, V. A.; Gill, R.; Rao, P. S. 1985. Regeneration of somatic embryos and plantlets from stem callus protoplasts of sandalwood tree (Santalum album L.). Current Science 54(19): 978-982.
  No DOI. Open access.
  http://www.currentscience.ac.in/php/toc.php?vol=054&issue=19
  http://www.currentscience.ac.in/Downloads/article_id_054_19_0978_0982_0.pdf
  
  BC1
  Bapat, V.A., Rao, P.S., 1993. Micropropagation of sandalwood (Santalum album L.) and mulberry (Morus indica L.). In: Ahuja, M.R. (Ed.), Micropropagation of Woody Plants. Kluwer Academic Publishers (now Springer), pp. 317–345.
  DOI: 10.1007/978-94-015-8116-5_19
  http://link.springer.com/chapter/10.1007/978-94-015-8116-5_19
  
  P5
  Rao, P.S., Bapat, V.A., 1978. Vegetative propagation of sandalwood plants through tissue culture. Canadian Journal of Botany 56: 1153–1156.
  DOI: 10.1139/b78-129
  http://www.nrcresearchpress.com/doi/abs/10.1139/b78-129#.VM9RX8v9nIU
  
  BC2
  Rao, P.S., Bapat, V.A., 1992. Micropropagation of sandalwood (Santalum album L.). In: Bajaj, Y.P.S. (Ed.), High-Tech and Micropropagation II. Biotechnology in Agriculture and Forestry. Springer, Berlin, pp. 193–210.
  DOI: 10.1007/978-3-642-76422-6_10
  http://link.springer.com/chapter/10.1007/978-3-642-76422-6_10
  
  P6
  Rao, P.S., Bapat, V.A., Mhatre, M., 1984. Regulatory factors for in vitro multiplication of sandalwood tree (Santalum album Linn.). II. Plant regeneration in nodal and internodal stem explants and occurrence of somaclonal variation in tissue culture raised plants. Proceedings of the Indian National Academy of Science: B 50(2): 196–202.
  No DOI.
  Web-site cannot be traced clearly.
  
  P7
  Rao, P.S., Ozias-Akins, P., 1985. Plant regeneration through somatic embryogenesis in protoplast cultures of sandalwood (Santalum album L.). Protoplasma 124(1-2): 80–86.
  DOI: 10.1007/BF01279726
  http://link.springer.com/article/10.1007%2FBF01279726
  
  There are 4 PubPeer entries for this case:
  https://pubpeer.com/publications/225988CDB994AA3E79C90FFA1D4EE0#fb23714 (BC1)
  https://pubpeer.com/publications/4D2CB9A98D4CAD786B65F63F07F80F#fb23716 (BC2)
  https://pubpeer.com/publications/967ABAFECEB9F4C2BCB4659082B8AA#fb23715 (P5)
  https://pubpeer.com/publications/8A5FF81216E3DB38507655CD0E51AC#fb23717 (P7)
  
  Reply
15. Sandalwood queries says:
  
  March 31, 2015 at 9:14 pm
  
  This is a duplicate publication in the same volume, but different issue. The only difference is the page header and the quality/style of font used throughout. The remainder of the text is 100% identical, including tables, figures, acknowledgements and all other sections.
  
  Jean-Fran ois Butaud , Phila Raharivelomanana , Jean-Pierre Bianchini & Vincent Baron (2003a) A New Chemotype of Sandalwood (Santalum insulare Bertero ex A. DC.) from Marquesas Islands. Journal of Essential Oil Research, 15:4, 238-241
  DOI: 10.1080/10412905.2003.9712129
  http://www.tandfonline.com/toc/tjeo20/15/4#.VRtFucuJjIU
  http://www.tandfonline.com/doi/abs/10.1080/10412905.2003.9712129#.VRtF28uJjIU
  
  Jean-François Butaud 1, Phila Raharivelomanana 2, Jean-Pierre Bianchini 2, Vincent Baron 3 (2003b) A New Chemotype of Sandalwood (Santalum insulare Bertero ex A. DC.) from Marquesas Islands, Journal of Essential Oil Research, 15:5, 323-326
  DOI: 10.1080/10412905.2003.9698600
  1 Département Forêt et Gestion de l’Espace Rural , Service de Développement Rural , BP 100, 98713, Papeete, Tahiti, French Polynesia
  2 Laboratoire de Chimie Analytique Appliquée , Université de la Polynésie française , BP 6570, 98702, Faaa, Tahiti, French Polynesia
  3 Centre de Coopération Internationale en Recherche Agronomique pour le Développement , BP 467, 98713, Papeete, Tahiti, French Polynesia
  http://www.tandfonline.com/toc/tjeo20/15/5#.VRtF-suJjIU
  http://www.tandfonline.com/doi/abs/10.1080/10412905.2003.9698600#.VRtGGcuJjIU
  
  Journal of Essential Oil Research (Taylor and Francis)
  2013 IF = 0.815
  http://www.tandfonline.com/loi/tjeo20#.VRli0cuJjIU
  
  PubPeer:
  https://pubpeer.com/publications/EEA3271B280632E36A367F47C005D2 (2003a and 2003b) Only the 2003a DOI links to PubPeer.
  
  Reply
  1. Sandalwood retraction says:
    
    May 4, 2016 at 2:42 pm
    
    Retracted.
    
    http://www.tandfonline.com/doi/pdf/10.1080/10412905.2016.1182340
    
    Jean-François Butaud 1, Phila Raharivelomanana 2, Jean-Pierre Bianchini 2, Vincent Baron 3 (2003b) A New Chemotype of Sandalwood (Santalum insulare Bertero ex A. DC.) from Marquesas Islands, Journal of Essential Oil Research, 15:5, 323-326
    DOI: 10.1080/10412905.2003.9698600
    1 Département Forêt et Gestion de l’Espace Rural , Service de Développement Rural , BP 100, 98713, Papeete, Tahiti, French Polynesia
    2 Laboratoire de Chimie Analytique Appliquée , Université de la Polynésie française , BP 6570, 98702, Faaa, Tahiti, French Polynesia
    3 Centre de Coopération Internationale en Recherche Agronomique pour le Développement , BP 467, 98713, Papeete, Tahiti, French Polynesia
    http://www.tandfonline.com/toc/tjeo20/15/5#.VRtF-suJjIU
    http://www.tandfonline.com/doi/abs/10.1080/10412905.2003.9698600#.VRtGGcuJjIU
    
    Reply
16. Sandalwood queries says:
  
  July 27, 2015 at 1:37 am
  
  Please compare the following two papers.
  
  Dani K.G.S, Ravikumar P., Kumar P.R., A. Kush (2009) Genetic diversity estimates in three geographically isolated populations of Santalum album in India. Sandalwood Research Newsletter 24: 1-6
  
  K. G. Srikanta Dani, P. Ravikumar, R. Pravin Kumar, A. Kush (2011) Genetic variation within and among small isolated populations of Santalum album. Biologia Plantarum June 2011, Volume 55, Issue 2, pp 323-326
  Vittal Mallya Scientific Research Foundation, Bangalore-560076, India
  http://link.springer.com/article/10.1007/s10535-011-0046-2
  DOI: 10.1007/s10535-011-0046-2
  
  https://imgur.com/4jWr71I
  https://imgur.com/pV4HWnJ
  
  PubPeer:
  https://pubpeer.com/publications/C8DF14CAAC7A4C805F1EA85EBCC061
  
  Reply
17. Sandalwood queries says:
  
  November 24, 2015 at 7:30 pm
  
  Please compare Fig. 5 of the 2014 paper with Plate 2 of the 2015 paper.
  https://imgur.com/SVkSsku
  
  Rocha D, Ashokan PK, Santhoshkumar AV, Anoop EV, Sureshkumar P (2014) Influence of host plant on the physiological attributes of field-grown sandal tree (Santalum album). Journal of Tropical Forest Science 26(2):166–172.
  Kerala Agricultural University, India
  http://www.frim.gov.my/v1/JTFSOnline/jtfs/v26n2/166-172.pdf
  http://www.myjurnal.my/public/article-view.php?id=78852
  
  Rocha D, Ashokan PK, Santhoshkumar AV, Anoop EV, Sureshkumar P (2015) Anatomy and functional status of haustoria in field grown sandalwood tree (Santalum album L.). Forest Research 04:148. doi: 10.4172/2168-9776.1000148
  http://www.omicsgroup.org/journals/anatomy-and-functional-status-of-haustoria-in-field-grown-sandalwood-tree-santalum-album-l-2168-9776-1000148.pdf
  
  https://pubpeer.com/publications/91AE6850623DDBEBDB25F779A095EB
  
  Reply
JXB PPPR says:

January 15, 2015 at 2:26 pm

As part of a first phase of post-publication peer review of the plant science literature, the 2014 and 2015 papers published in Journal of Experimental Botany (JXB), published by Oxford University Press, carrying an impact factor of 5.794, and ranked highly (top 10?) in the plant science category (Thomson Reuter’s JCR ranking), and that are open access, have been crudely assessed for evident errors in statistics, or “issues” with images. This first report collects 5 papers for which an “issue” has been identified, each with a PubPeer entry / ID number, as detailed next.
http://jxb.oxfordjournals.org/
JXB is a member of COPE:
http://publicationethics.org/members/journals/Journal%2520of%2520Experimental%2520Botany?

1

https://pubpeer.com/publications/29131D0F3C0B9F1C39427AC662CCB8#fb21482

Fig. 5A. Vertical lines between several lanes in Mi-1.2 and G2-LTF.
Fig. 5B. Vertical lines between several lanes in G2-LTF.
How to interpret this?

http://jxb.oxfordjournals.org/content/66/2/549.short
http://jxb.oxfordjournals.org/content/66/2/549.full.pdf+html
Godshen R. Pallipparambil, Ronald J. Sayler, Jeffrey P. Shapiro, Jean M. G. Thomas, Timothy J. Kring, Fiona L. Goggin
Mi-1.2, an R gene for aphid resistance in tomato, has direct negative effects on a zoophytophagous biocontrol agent, Orius insidiosus
Journal of Experimental Botany (2015) 66 (2): 549-557 first published online September 4, 2014
doi: 10.1093/jxb/eru361
1 319 Agricultural Building, Department of Entomology, University of Arkansas, Fayetteville, AR 72701, USA
2 Plant Science Building, Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
3 USDA, ARS, CMAVE, 1700 SW 23rd Dr., Gainesville, FL 32608-1069, USA

2

https://pubpeer.com/publications/91C030779D3F79AFD9D7B205EAC82B#fb21483

Fig. 1D Is that a vertical line dividing Mtl and T0 lanes in the STP1 sample?
Fig 4A, 4B and C, a lot of vertical separations and lines between lanes?
Is this an acceptable way of representing such gels?

http://jxb.oxfordjournals.org/content/66/1/147.short
http://jxb.oxfordjournals.org/content/66/1/147.full.pdf+html
Elizabeth Cordoba, Denise Lizeth Aceves-Zamudio, Alma Fabiola Hernández-Bernal, Maricela Ramos-Vega, Patricia León
Sugar regulation of SUGAR TRANSPORTER PROTEIN 1 (STP1) expression in Arabidopsis thaliana
Journal of Experimental Botany (2015) 66 (1): 147-159 first published online October 3, 2014
doi: 10.1093/jxb/eru394
Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos. Mexico. C.P. 62210, Mexico

3

https://pubpeer.com/publications/EC2BC303ABCE64E94D3C0DB0DBE72A#fb21527

Fig S1 3rd row from top, 3rd gel across WT
Please compare with
Fig S1 4th row from top, 4th gel across WT
A beginner learning the ropes. The 4 bands seem very similar in terms of shapes, distances between bands, relative positions and distinctive markings. How can one be sure about similarity or difference?

http://jxb.oxfordjournals.org/content/65/20/5877.short
http://jxb.oxfordjournals.org/content/suppl/2014/07/17/eru338.DC1/jexbot125666_file001.pdf
P. J. M. van Kleeff, N. Jaspert, K. W. Li, S. Rauch, C. Oecking, A. H. de Boer
Higher order Arabidopsis 14-3-3 mutants show 14-3-3 involvement in primary root growth both under control and abiotic stress conditions
Journal of Experimental Botany (2014) 65 (20): 5877-5888 first published online September 4, 2014
doi: 10.1093/jxb/eru338
1 Faculty of Earth and Life Sciences, Department of Structural Biology, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
2 Centre for Plant Molecular Biology—Plant Physiology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
3 Faculty of Earth and Life Sciences, Department of Molecular and Cellular Neurobiology, Centre for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands

4

https://pubpeer.com/publications/B7F7EFBE979EC6A2DFB644D9AC1AA0#fb21525

Suppl. Fig. 1B ACTIN and Fig. 1E ACTIN have vertical lines between 2nd and 3rd lanes.

http://jxb.oxfordjournals.org/content/65/20/6057.abstract
http://jxb.oxfordjournals.org/content/suppl/2014/07/28/eru346.DC1/jexbot130393_file001.pdf
Geraint Parry
Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth
Journal of Experimental Botany (2014) 65 (20): 6057-6067 first published online August 27, 2014
doi: 10.1093/jxb/eru346
Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK

5

https://pubpeer.com/publications/EF154530F5243946D4ABF9125D773A#fb21529

Fig 1D. Apparent vertical line between lanes 3 and 4.
Suppl. Fig. S2. Compare A, B, C, D, E, F, G, H UBQ lanes (same control for all gels?). Figure legend only states “ubiquitin (UBQ) amplification was used as a loading control”
Suppl. Fig. S3F. Apparent vertical line between lane 3 (1.0) and lane 4 (1.4).

http://jxb.oxfordjournals.org/content/65/20/6123.short
http://jxb.oxfordjournals.org/content/65/20/6123.full.pdf+html
http://jxb.oxfordjournals.org/content/suppl/2014/08/02/eru353.DC1/jexbot126110_file001.pdf
Katarzyna Kruszka, Andrzej Pacak, Aleksandra Swida-Barteczka, Przemyslaw Nuc, Sylwia Alaba, Zuzanna Wroblewska, Wojciech Karlowski, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley
Journal of Experimental Botany (2014) 65 (20): 6123-6135 first published online September 2, 2014
doi: 10.1093/jxb/eru353
1 Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
2 Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland

Reply
1. JXB PPPR says:
  
  January 16, 2015 at 7:27 am
  
  The first resonse to the JXB PPPR arrived at PubPeer within 24 hours after the queries were made. This is a case of responsible behaviour and commendable transparency.
  “Dear Sir/ Madam,
  
  Thanks for highlighting this issue. I hope you’ll be convinced the explanation is simple as to the presence of the lines.
  
  The purpose of these bands is to show presence/absence of Actin expression in the RT+ vs RT- samples in either wildtype or the mutant (nup58 s1B, nup160 s1E) and doesn’t involve any quantification.
  
  The RT+/- bands for Col or nup58/nup160 were run at different places on the gel so these lanes were cropped to make the figure as it is. Perhaps there should have been a gap placed between these portions instead of pushing them together as in the present form. However as I am not making any claims aside from +/- in lanes adjacent to each other I don’t think this is a major issue. If there had been a line between RT+ and RT – samples from the same genotype then there would have been cause for concern but that is not the case. The RT+ and RT- lanes from the same genotype have been kept together and moved around as appropriate.
  
  I hope this explanation is sufficient. If required I can send the original gels to whomever is interested. Please contact me on [email protected]
  
  Cheers,
  geraint”
  
  Reply
2. JXB PPPR says:
  
  January 18, 2015 at 1:13 pm
  
  A second response to one of 5 papers being queried has arrived at PubPeer:
  “To whom correspond, I appreciate the interest in to clarify some aspects in this paper.
  For Fig 1D, the original gel was run with other samples between the different treatments, we cropped and put together the showed lanes, but the cropped lanes were with their correspondent controls, T0 and –C. For Fig 4A, the samples were run in the same gel, Col -0 and kin10 side by side and kin11 below those samples, and then the lanes were cropped and put together as showed in the figure. For 4B, the samples were run with another samples in the same gel, and then cropped and put together with their correspondent controls. For 4D, the samples Col-0 and rgs1 were run in the same gel but rgs1 below the Col-0 samples, and the rgs1-2 in another gel with its correspondent Col-0 control. For purpose to be not repetitive, only one of the Col-0 was used for the panel, because they showed the same pattern. I hope this simple explanation satisfies the exposed concerns. If you are interested, I can show you the original gels and hybridizations. Don’t hesitate to contact me at [email protected]
  Best regards, Elizabeth Cordoba”
  
  Reply
Phytophthora infestans query says:

January 18, 2015 at 2:16 pm

Apparent figure duplication in a potato phytopathology-related paper.

The Irish Potato Famine Pathogen Phytophthora infestans Translocates the CRN8 Kinase into Host Plant Cells
Mireille van Damme 1,2, Tolga O. Bozkurt 1, Cahid Cakir 3, Sebastian Schornack 1, Jan Sklenar 1, Alexandra M. E. Jones 1, Sophien Kamoun 1*
1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
2 Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
3 United States Department of Agriculture-Agricultural Research Service, The Plant Stress and Germplasm Development Unit, Lubbock, Texas, United States of America

http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002875
http://www.plospathogens.org/article/fetchObject.action? uri=info:doi/10.1371/journal.ppat.1002875&representation=PDF

There is a PubPeer entry for this case:
https://pubpeer.com/publications/D3DF6B4B19C383804BB3748B60604D#fb21978

Reply
1. Phytophthora infestans query says:
  
  January 18, 2015 at 2:46 pm
  
  The senior author has responded, identified the errors, and assured a solution, all within a few hours after the issue was published at PubPeer, stating:
  “This is an awful and unjustifiable mistake. I sincerely apologize for not noticing this error previously. I will now dig deeper in the lab archives to identify if additional data can be retrieved etc. and will take the necessary actions to correct the error. I appreciate the scrutiny and the post-publication review. Although it is unpleasant to be targeted, I personally feel that this is a healthy process for science and I will do my best to respond to any queries. There is indeed a duplication and we apologize for this error. The coauthors and I feel terrible that this mistake has happened. This is an awful and unjustifiable mistake. We will next prepare a correction and contact the journal. Please do let me know if you have more queries.”
  
  Reply
2. Phytophthora infestans query says:
  
  January 19, 2015 at 1:29 pm
  
  Incidentally, the senior author is Sophien Kamoun, Director, The John Innes Centre, UK, and co-author of a letter critical of the famous Seralini retraction:
  http://www.sciencedirect.com/science/article/pii/S0278691512007946
  
  Reply
3. Phytophthora infestans query says:
  
  January 22, 2015 at 12:08 pm
  
  Of relevance to this discussion, and case:
  https://blushgreengrassatafridayafternoon.wordpress.com/2015/01/22/be-positive-from-witch-hunts-to-the-new-reward-culture/
  https://blushgreengrassatafridayafternoon.wordpress.com/2015/01/22/dont-judge-too-fast/
  A very clear link to the Voinnet case, and heated debate among plant molecular biologists:
  https://pubpeer.com/topics/1/1A0BDA96C3E7BD263364577E50E08F#fb22500
  
  Reply
KaPPA-View4 and KaPPA-Loader Jatropha queries says:

January 20, 2015 at 9:35 am

Queries have emerged about why software that received now almost 10 years’ funding in Japan has still not yet resulted in a functional program:
https://pubpeer.com/publications/DBDE5251F404436030CFAFBE212B76#fb22265

Development of KaPPA-View4 for omics studies on Jatropha and a database system KaPPA-Loader for construction of local omics databases
Nozomu Sakurai, Yoshiyuki Ogata, Takeshi Ara, Ryosuke Sano, Nayumi Akimoto, Atsushi Hiruta, Hideyuki Suzuki, Masataka Kajikawa, Utut Widyastuti, Sony Suharsono, Akiho Yokota, Kinya Akashi, Jun Kikuchi, Daisuke Shibata
Plant Biotechnology 29 (2012), 131–135
DOI: 10.5511/plantbiotechnology.12.0508a
http://www.bunken.org/jspcmb/journal/pb29_2/29_131.pdf

Reply
Darjeeling tea query says:

January 29, 2015 at 3:40 pm

Physiology and Molecular Biology of Plants July 2013, Volume 19, Issue 3, pp 421-433
Date: 28 Jun 2013
Antioxidants and ROS scavenging ability in ten Darjeeling tea clones may serve as markers for selection of potentially adapted clones against abiotic stress
Nirjhar Dasgupta 1, Prosenjit Biswas 2, Rakesh Kumar 2, Narendra Kumar 2, Biswajit Bera 3, Sauren Das 1
http://link.springer.com/article/10.1007%2Fs12298-013-0187-1
DOI: 10.1007/s12298-013-0187-1
1. Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B.T. Road, Kolkata, 700108, India
2. Darjeeling Tea Research and Development Centre, A.K. Mukherjee Road, Kurseong, Darjeeling, 734203, India
3. Tea Board of India, Ministry of Commerce and Industry, Government of India, 14, B.T.M Sarani, Kolkata, 700001, India

Two gels are being queried at PubPeer:
https://pubpeer.com/publications/9543DEAD0C5A57B5EFA7A7D1B26B88#fb23344

Reply
1. Darjeeling tea and mangrove query says:
  
  October 5, 2015 at 1:11 pm
  
  The Editor-in-Chief has promised to retract this article.
  
  In the meantime, queries related to images/gels in two more Sauren Das-leadered articles appear at PubPeer.
  
  Springer
  RAPD and ISSR marker mediated genetic polymorphism of two mangroves Bruguiera gymnorrhiza and Heritiera fomes from Indian Sundarbans in relation to their sustainability.
  Nirjhar Dasgupta, Paramita Nandy, Chandan Sengupta, Sauren Das
  Physiology and Molecular Biology of Plants
  July 2015, Volume 21, Issue 3, pp 375-384
  https://pubpeer.com/publications/4CD16CB744AA08F7AD29D79CEB1B1E#fb37725
  http://link.springer.com/article/10.1007%2Fs12298-015-0308-0
  
  Taylor and Francis
  Salinity-imposed changes of some isozymes and total leaf protein expression in five mangroves from two different habitats
  Nirjhar Dasgupta, Paramita Nandy (Datta), Chandrakant Tiwari, Sauren Das, Journal of Plant Interactions (2010)
  https://pubpeer.com/publications/44F5A1AAB6464648557DDB9979CD60#fb37726
  http://www.tandfonline.com/doi/abs/10.1080/17429140903438076#.VhKuMnKhfIU
  
  Reply
2. Darjeeling tea query says:
  
  March 22, 2016 at 12:14 pm
  
  Retracted:
  
  “This article has been retracted by the editor on account of falsification/fabrication of data in Figure 3 of the above paper, as the corresponding author failed to defend the charge levelled initially at Pubpeer and validated subsequently through an editorial enquiry at PMBP, and also failed to reproduce fresh results sought by the editor. The employer of the author has been intimated.”
  
  http://link.springer.com/article/10.1007%2Fs12298-013-0187-1
  
  Reply
Arabidopsis root microtubule queries says:

January 29, 2015 at 3:58 pm

http://www.nature.com/nature/journal/v516/n7529/full/nature13889.html
Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules
Nature 516, 90–93 (04 December 2014)
doi:10.1038/nature13889
Received 12 November 2013; Accepted 23 September 2014; Published online 17 November 2014
Xu Chen,1, 2, 3, Laurie Grandont,4, Hongjiang Li,1, 2, 3, Robert Hauschild,1, Sébastien Paque,4, Anas Abuzeineh,2, 3, Hana Rakusová,1, 2, 3, Eva Benkova,1, 2, 3, Catherine Perrot-Rechenmann4, & Jiří Friml1, 2, 3,
Affiliations
1. Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
2. Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent University, B-9052 Gent, Belgium
3. Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Gent, Belgium
4. Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences LabEx, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, Cedex, France

A discussion and challenge of the validity of the findings has started at PubPeer:
https://pubpeer.com/publications/E00843D756AEC3E5EF6B7F0C68878B#fb23336

Reply
1. Arabidopsis root microtubule queries says:
  
  February 3, 2015 at 3:46 pm
  
  Several calls for papers related to ABP1 to be re-evaluated, based on new evidence from a 2015 PNAS paper, are being made at PubPeer.
  
  Cell surface ABP1-TMK auxin-sensing complex activates ROP GTPase signaling
  Tongda Xu, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, Xu Chen, Riet De Rycke, Hana Rakusová, Wuyi Wang, Alan M Jones, Jirí Friml, Sara E Patterson, Anthony B Bleecker, Zhenbiao Yang, Science, 343 (2014)
  https://pubpeer.com/publications/01AA515880332485C9D41C5DCCC3E9#fb23851
  
  ABP1 Mediates Auxin Inhibition of Clathrin-Dependent Endocytosis in Arabidopsis
  Stéphanie Robert, Jürgen Kleine-Vehn, Elke Barbez, Michael Sauer, Tomasz Paciorek, Pawel Baster, Steffen Vanneste, Jing Zhang, Sibu Simon, Milada Čovanová, Kenichiro Hayashi, Pankaj Dhonukshe, Zhenbiao Yang, Sebastian Y. Bednarek, Alan M. Jones, Christian Luschnig, Fernando Aniento, Eva Zažímalová, Jiří Friml, Cell (2010)
  https://pubpeer.com/publications/CF164E4BEEECF4F3A11E929F393B57#fb23852
  
  Cell surface- and rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis
  Tongda Xu, Mingzhang Wen, Shingo Nagawa, Ying Fu, Jin-Gui Chen, Ming-Jing Wu, Catherine Perrot-Rechenmann, Jiří Friml, Alan M Jones, Zhenbiao Yang, Cell, 143 (2010)
  https://pubpeer.com/publications/610B18CEB0D504801D01A326644FD3#fb23853
  
  Reply
2. Arabidopsis root microtubule queries says:
  
  February 5, 2015 at 2:32 pm
  
  Incidentally, queries about the role of auxin biosynthesis in embryonic patterning in another of Friml’s papers remain unanswered for over a year now.
  https://pubpeer.com/publications/B5B747042EF3AA0864621F6033F6F1
  Local Auxin Sources Orient the Apical-Basal Axis in Arabidopsis Embryos
  Hélène S. Robert, Peter Grones, Anna N. Stepanova, Linda M. Robles, Annemarie S. Lokerse, Jose M. Alonso, Dolf Weijers, Jiří Friml,
  Current Biology (2013)
  http://www.cell.com/current-biology/abstract/S0960-9822(13)01186-X
  
  RW readers may recall the link between Jiří Friml and Pankaj Dhonukshe and Ben Scheres, whose 2011 Nature paper was retracted:
  Retraction: Generation of cell polarity in plants links endocytosis, auxin distribution and cell fate decisions
  Pankaj Dhonukshe, Hirokazu Tanaka, Tatsuaki Goh, Kazuo Ebine, Ari Pekka Mähönen, Kalika Prasad, Ikram Blilou, Niko Geldner, Jian Xu, Tomohiro Uemura, Joanne Chory, Takashi Ueda, Akihiko Nakano, Ben Scheres & Jiří Friml
  Nature 511, 370 (17 July 2014) doi:10.1038/nature13549
  http://www.nature.com/nature/journal/v511/n7509/nature13549/metrics/blogs
  https://retractionwatch.files.wordpress.com/2014/02/reply-dhonukshe-to-uu.pdf
  http://retractionwatch.com/category/pankaj-dhonukshe/
  
  Reply
3. Arabidopsis root microtubule queries says:
  
  February 13, 2015 at 5:12 am
  
  Prof. Jiri Friml has come forward to address the community, stating:
  
  “I am very much in favor of open and constructive scientific discussion; however, I do not feel that anonymous forums are the best place to conduct it. Despite many of the participants are truly discussing the scientific aspects and trying to understand the underlying nature, the anonymity gives also opportunity to use such venues for other purposes. I have seen participants of these discussions whether intentionally or unintentionally bring sleepless nights and kill scientific confidence of good colleagues that often did not deserve it. I have also seen anonymous requests being sent to the head of the institutes and heads of the PR offices. In some cases it was obviously not to best outcome for the people and for the science. Therefore, I am already unsubscribed for quite some time from these forums and do not receive alerts if there is a discussion related to my work. I kindly ask for understanding and I apologize to people that comes to these forums primarily to get scientific insights and clarifications. I however reserve the right not to participate in the anonymous discussions and present my findings or opinions by other channels. I will try my best (as I do for years) to respond to non-anonymous queries addressed to me directly.
  
  For this specific case, despite having reservations about the form and the venue for presenting his case, I find the non-anonymous comment of my colleague Tobias Baskin scientifically intriguing. Therefore, I make an exception and, please, find below our response”
  
  Please refer to PubPeer for the complete response and discussion.
  
  Reply
4. Arabidopsis root microtubule queries says:
  
  June 2, 2015 at 9:40 pm
  
  The challenge to the Friml paper by Tobias Baskin has been published in Trends in Plant Science:
  http://www.sciencedirect.com/science/article/pii/S1360138515001375
  Auxin inhibits expansion rate independently of cortical microtubules
  
  Reply
5. Arabidopsis root microtubule queries says:
  
  November 7, 2015 at 4:20 am
  
  Peter Schopfer and Klaus Palme offer a critical post-pub critique of this paper:
  http://www.plantphysiol.org/content/early/2015/11/04/pp.15.01403?papetoc
  
  Reply
Arabidopsis cadmium says:

January 30, 2015 at 6:20 am

A query was made about a gel in a paper at PubPeer:
https://pubpeer.com/publications/3DB2D593B869295D1193136549AB53#fb23245

Molecular Plant (2014) 7 (9): 1455-1469.
OPT3 is a component of the iron-signaling network between leaves and roots and misregulation of OPT3 leads to an over-accumulation of cadmium in seeds
David G. Mendoza-Cózatl1,2,7⇑, Qingqing Xie1,3,7, Garo Z. Akmakjian1,7, Timothy O. Jobe1, Ami Patel2,6, Minviluz G. Stacey2, Lihui Song5, Dustin Wayne Demoin5, Silvia S. Jurisson5, Gary Stacey2,4 and Julian I. Schroeder1
1Division of Biological Sciences, Cell and Developmental Biology Section and Center for Food and Fuel for the 21st Century, University of California, San Diego, La Jolla, California 92093, USA.
2Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA.
3Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China.
4Department of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA.
5Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA.
6Current address – Laboratory for Infectious Disease Research, University of Missouri, Columbia Missouri 65211, USA.
DOI: 10.1093/mp/ssu067
http://mplant.oxfordjournals.org/content/early/2014/07/10/mp.ssu067.full.pdf
http://mplant.oxfordjournals.org/content/7/9/1455
http://mplant.oxfordjournals.org/content/early/2014/05/30/mp.ssu067
http://mplant.oxfordjournals.org/content/7/9/1455.full.pdf+html

The query:
Fig. 6: ACT2 gel appears to be the same in B and C.
The figure legend simply indicates, in the explanation in B, and in C, that “ACT2 was used a loading control”

The authors responded as follows:
“Thank you for your comment. It is correct that the ACT2 images in Figure 6 panels B and C for these root expression experiments are the same. We have checked our records and verified that the loading control is shown for two genes (OPT3 in panel B-Roots and IRT1 in panel C-Roots) as described in the caption of figure 6. These data in figure 6 B and C are from the same cDNA pool (i.e. the indicated “Roots” cDNA). This duplication is not a mistake, these PCR reactions (for ACT2, IRT1 and OPT3) were run in parallel, stopped at the indicated cycles, and were run in the same agarose gel. Therefore, the loading controls are needed as reference for the amount of cDNA that was used in both panels 6B and 6C. In hindsight, we could have described this better in the legend to Figure 6B,C to point out that the same control is shown twice, as a reference for each panel. We have contacted the journal to request that an update to the caption to figure 6B,C is published. We apologize for not having thought of clarifying this point earlier.”

The authors are applauded for seeking to correct the literature.

Reply
1. Arabidopsis cadmium says:
  
  April 13, 2015 at 7:24 am
  
  The promised erratum will not be forthcoming: “As mentioned in our original post, we contacted the editorial team of the journal to inquire about publishing a clarification, as described above. After reviewing our request, the editorial team concluded that the clarification would be relatively minor to formally publish a clarification. The journal would publish if there is an error in a paper. The journal encourages us to communicate directly with colleagues who contact us with any questions and we are happy to address any questions sent to us by colleagues. We have also communicated this reply to the journal prior to posting it here. Thank you again.”
  
  This implies that for clarity, readers would have to contact the authors every time. This seems like a waste of human resources and time and effort. An erratum linked to the original web-page of the paper would surely serve the public and broader readership more than having to accidentally discover that information is missing through PubPeer?
  
  Reply
Plants with ears? says:

February 1, 2015 at 11:01 am

A blog on science-based gardeing is questioning the premise of a paper published in BMC Ecology.

The blog:
http://blogs.extension.org/gardenprofessors/2015/01/23/nanomechanical-oscillations/

The paper being questioned:
Love thy neighbour: facilitation through an alternative signalling modality in plants
Monica Gagliano 1* and Michael Renton 2
* Corresponding author:
Author Affiliations
1 Centre for Evolutionary Biology, School of Animal Biology, University of Western Australia, Crawley, WA 6009, Australia
2 School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia

The PubPeer entry:
https://pubpeer.com/publications/FF697CF8CD514E7A437EBC24D245AD#fb23537

Reply
Jaime A. Teixeira da Silva says:

February 2, 2015 at 4:29 pm

I have reported a duplicate publication to Springer’s In Vitro Cellular & Developmental Biology – Plant on February 3, 2015.
Chand, S., Singh, A.K., 2004. In vitro shoot regeneration from cotyledonary node explants of a multipurpose leguminous tree Pterocarpus marsupium Roxb. In Vitro Cell. Dev. Biol. Plant 40(2), 167–170 and 40(5), 464-466.
https://pubpeer.com/publications/3F2AAD44E05FE1D200EAC7E718089C#fb23767
http://link.springer.com/article/10.1079/IVP2003488
DOI: 10.1079/IVP2003488
https://pubpeer.com/publications/D112CA83735753D1EFE2B6BFF664B2#fb23766
http://link.springer.com/article/10.1079/IVP2004548
DOI: 10.1079/IVP2004548

Reply
1. Jaime A. Teixeira da Silva says:
  
  June 2, 2015 at 9:37 pm
  
  An erratum has been published, but the duplicate paper remains:
  http://link.springer.com/journal/11627/51/2/page/1
  http://link.springer.com/article/10.1007/s11627-015-9689-6
  The notice reads as follows: “This article, published in In Vitro Cellular & Developmental
  Biology – Plant 40, issue 5, 464–466 (DOI 10.1079/IVP2004548), is a duplicate version of another article entitled ‘In vitro shoot regeneration from cotyledonary node explants of a multipurpose leguminous tree, Pterocarpus marsupium roxb’ written by the same authors and which was accidently published in the same journal. We apologize to the readers of the journal for not detecting this omission which regrettably occurred during the publishing process and was not associated with the authors of the original manuscript. When citing this article, the initial publication should be used: In Vitro Cellular & Developmental Biology – Plant 40, issue 2, 167–170 (DOI 10.1079/IVP2003488).”
  
  A key question remains: why did the authors and other scientists who cited the duplicate paper, and were thus aware of its existence, not report this to the publisher in the 10-year period?
  
  Reply
Red sanders queries says:

February 3, 2015 at 1:52 am

Balaraju, K., Agastian, P., Ignacimuthu, S., Park, K-S., 2011. A rapid in vitro propagation of red sanders (Pterocarpus santalinus L.) using shoot tip explants. Acta Physiologiae Plantarum 33, 2501–2510.
P. Agastian: Department of Plant Biology and Biotechnology, School of Life Sciences, Loyola College, Chennai 600 034, Tamil Nadu, India
K. Balaraju; S. Ignacimuthu: Plant Biotechnology Division, Entomology Research Institute, Loyola College, Chennai 600 034, Tamil Nadu, India
K. Balaraju; K. Park: National Academy of Agricultural Science (NAAS), RDA, Suwon 441-707, South Korea
doi: 10.1007/s11738-011-0795-8
Received: 16 November 2010; Revised: 26 April 2011; Accepted: 30 May 2011; Published online: 12 June 2011
Copyright: Franciszek Gorski Institute of Plant Physiology, Polish Academy of Sciences, Krakow 2011
Communicated by: E. Lojkowska
http://link.springer.com/article/10.1007%2Fs11738-011-0795-8

Concerns and issues:

1) Scientific / botanical name slightly incorrect: Should be L.f. or Linn.f., but not only L.
2) Title: “A” not required. In fact, English grammar consistently poor throughout the manuscript. For example, in the abstract: “An efficient protocol has been developed for the in vitro propagation of Pterocarpus santalinus L. using shoot tip explants which is a valuable woody medicinal plant.” A shoot tip explant is not a medicinal plant, Pterocarpus is. Thus the sentence should be written correctly as: “An efficient protocol has been developed for the in vitro propagation of Pterocarpus santalinus L., a valuable woody medicinal plant, using shoot tips.” The term “explant” in the original sentence is redundant. Reading this paper is thus a painful experience. Why was there no text editing by the journal editors?
3) “Pterocarpus santalinus L. … is a rare and threatened forest legume tree” Yet no reference is provided to support this claim. The IUCN web-site indicates that this status has been official since at least 1997: http://www.iucnredlist.org/details/full/32104/0
4) Given the endangered status, the authors claim, in the M&M: “Healthy seeds were collected from the wild habitats”. Firstly, why has the exact geographic location not been indicated? Secondly, was permission provided to collect endangered plant material from the wild?
5) “It is priced in the vicinity of US$ 2000 per ton in the international market and is most notably exported from India to Japan and other countries (Raju and Nagaraju 1999; Sanjappa 2001).” What is the relevance of prices in at least a decade old literature for a 2011 paper?
6) When referring to seed disinfection, the authors state: “the upper layers were peeled off”. Botanically speaking, what is an upper layer of a seed? Do they mean, perhaps, the outer layer, namely the testa?
7) “Then, the seeds were washed with water, soaked for 24 h in various concentrations (50–300 ppm) of GA3 to break the dormancy” The abstract simply indicates that GA3 was important and nowhere in the manuscript does it indicate the optimal GA3 concentration for seed germination. If there were trials using different concentrations, then the results of those trials are also not shown anywhere in the paper.
8) Inconsistent use of units: ppm, mg/l.
9) M&M: “Apical meristem explants were collected from in vivo grown seedlings” Age not specified. One has to read the abstract to learn that the age of seedlings is 20 days old.
10) M&M: “Apical meristem explants” Apical meristems and shoot tips are completely different things. The shoot tip contains an apical meristem, but the size of both is very different. While the former may be several mm in size, the latter is several dozen or a few hundred micrometers. The exact size of explants is not indicated, casting doubt on what the exact explant was.
11) M&M: “In vivo grown seedlings were used as explants (1–2 explants per test tube).” This is confusing, and contradictory. In vivo refers to plants outside of test tubes, while the authors also refer to explants within test tubes within the same sentence.
12) M&M: In the main body of text, in particular in the M&M, none of the plant growth regulators’ names are defined in full, including BAP, KN, TDZ, NAA, GA3, and IAA. One has to go to the first page abbreviations list to learn of the exact definition.
13) M&M, Multiple shoot induction and elongation medium: vague references or imprecise information about the plant tissue that one should use. So, “Shoot tips excised from surface sterilized in vivo grown seedlings”: what size of shoot tips? “explants were transferred to the medium”: here, what is the explant exactly? “the shoots were subcultured”: shoots of what size, with how many nodes, and including leaves, or not? Of what age exactly should any of this plant material be?
14) M&M and R&D: there is a disparity between the methodology reported and the results reported. In the M&M, it states: “plantlets … transferred to paper cups containing autoclaved organic manure and garden soil in combination with sand in different ratios (1:1, 1:2, and 1:3).” However, the R&D reports on data in Table 5 for three combinations (organic manure + sand; vermi-compost + sand; garden soil + sand), all in a 1:1 ratio. The methodology and the results are incompatible. Incidentally, what earthworm species was used to generate the vermicompost and using what substrate?
15) M&M, RAPD analysis: “Genomic DNA was isolated from the leaves of donor plants from 45 to 60 days old seedlings and also from randomly selected regenerants (65 days old) obtained from shoot tip explants of P. santalinus.” This suggests that the authors were simply comparing the DNA from ex vitro (mother plants) and in vitro seedling tissue. Is this assumption correct? The comparison is flawed for two reasons: a) the authors were comparing leaf tissue with shoot tips, so it is surprising that they reported zero variability; even different tissues from different organs would likely have different RAPD banding patterns; b) there are a few dozen permutations of treatments related to different PGRs, yet the authors fail to analyze the DNA of plantlets from any of these treatments? Would this be an accurate characterization of the flawed RAPD protocol?
16) M&M, RAPD: 10 decamer primers is very little. Based on what rationale did the authors select these 10 primers? Were there initial trials using a wider pool of 10-mer primers?
17) M&M: Why is Table 6 mentioned first in the text, and not Table 1 (p. 2504)?
18) M&M: “100 bp and 1 kb DNA ladders were used as DNA markers” What is the commercial manufacturer of these markers?
19) M&M: “DNA fingerprinting profiles were compared to evaluate clonal fidelity and genetic stability of in vitro regenerated plants.” It is unclear exactly from the dozens of treatments, which in vitro plants were tested? Why do the authors sometimes refer to them as plants and sometimes as plantlets? What, in the authors’ view, is the difference between these?
20) M&M: very simple statistics used (means and SD). No significance tests applied.
21) Results: “There were no significant differences on the average number of roots produced per shoot in the treatment containing IAA and NAA.” Presumably the authors are referring to the data in Table 4. There are no statistical analyses so this is a misleading statement.
22) Results: Fig. 1f legend: “Fully grown elongated shootlet with leaves in MS basal medium” There is no such term as shootlet. Moreover, the “shootlet” also has roots, making it a plantlet. Thus, incorrect terminology and characterization. If this plantlet formed on medium without auxins, then why did the authors use auxins to induce roots, or did they perhaps mischaracterize the medium in the photo?
23) Results: Fig 3b. The 1 kb arrow is indicating a marker band of the same size on the left and right hand sides of the gel. If so, then why are the bands so misaligned? A comparison of sample bands would reveal different sizes, depending on the marker used for comparison.
24) Results: Most of the photos in Fig 1 and 2 are fuzzy and out of focus.
25) Results: What is the precise origin (i.e., from what treatment exactly) of the “shoot tip explants” used in Table 1 and Table 2? Similarly, what is the precise origin (i.e., from what treatment exactly) of the “shoots” used in Table 3 and Table 4? Finally, what is the precise origin (i.e., from what treatment exactly) of the plantlets used in Table 5 (acclimatization) and of the plants used in Table 6 (RAPD)? None of the table headers or footers provides this absolutely essential information while the text does not explain these details.
26) Results: The banding of the RAPDs shown in Figures 3a and 3b is extremely fuzzy and impossible to clearly see distinct bands. Can the authors please provide the high-resolution images, as well as the high-res images of the RAPDs for the other 8 RAPD primers as proof of this “homogeneity” that they claim?
27) Discussion: Excessively broad, clustered comments and meaningless comparisons characterize this discussion. A typical case, for example: “results corroborate with the earlier findings of several workers, where the addition of low-level of auxin with cytokinin promoted shoot proliferation in Acacia catechu (Kaur et al. 1998), Eucalyptus grandis (Luis et al. 1999) and Lagerstromia parviflora (Tiwari et al. 2002).” In most cases, details of the studies being compared is not provided, so this “corroboration” is in fact not proved. Not to mention that it is almost insulting to refer to other scientists as “workers”.
28) References: Kameswara Rao et al. (2001) should be “Effect of oral administration” and not “Effect pf pra; administration”. Luis et al. (1999): all authors names are completely incorrect). Currently listed as Luis PBC, Adraine CMGM, Silvica BRCC, Anna Christina MB; actual names are Luis Pedro Barrueto Cid, Adriane C.M.G. Machado, Sílvia B.R.C. Carvalheira, Ana Cristina M. Brasileiro. The correct abbreviations should be: Cid LPB, Machado ACMG, Carvalheira SBRC, Brasileiro ACM. The reference lust should be duly corrected, and reference to Luis et al. (1999) in the text must be corrected to Cid et al. (1999). http://link.springer.com/article/10.1023%2FA%3A1006283816625 . Romano et al. (2002). There is a spelling error with the last author’s name as well as with the name of the plant: it should be Martins-Loução and Ceratonia, respectively. http://link.springer.com/article/10.1023/A%3A1012912504288 . Italics missing from the Latin names of plants in Luis et al. (E. urophylla), Perinet and Lalonde (1983) (Alnus glutinosa), Purohit et al. (2002b) (glauca).

Was this paper really peer reviewed and text edited by Acta Physiologiae Plantarum and Springer Science + Business Medium?

There is a PubPeer entry for this case:
https://pubpeer.com/publications/6CDF7987DCF9626443188B153EDEE3#fb23827

Reply
1. Red sanders queries says:
  
  February 6, 2015 at 7:18 am
  
  P1
  Anis M, Husain MK, Shahzad A (2005) In vitro plantlet regeneration of Pterocarpus marsupium Roxb. an endangered leguminous tree. Current Science 88:861–863
  http://www.iisc.ernet.in/~currsci/mar252005/861.pdf (open access)
  
  Queries / concerns / issues:
  
  1) Authors claim to have prepared four explants (cotyledonary nodes, cotyledons, nodal segments, shoot tips). Yet, data is only provided for cotyledonary nodes. What was the response for the other explants and where is the data for them?
  2) No plant growth regulators defined anywhere in the text, i.e., only abbreviations used.
  3) The commercial source or grade of plant growth regulators not provided.
  4) Which phenolic acid and at what concentration was added to the pulse during the root induction step?
  5) No details about substrates or any greenhouse conditions necessary for acclimatization described.
  6) Success of seed germination and infection levels not reported.
  
  P2
  Husain, M.K., Anis, M., Shahzad, A., 2007. In vitro propagation of Indian Kino (Pterocarpus marsupium Roxb.) using thidiazuron. In Vitro Cellular and Developmental Biology – Plant 43(1), 59–64.
  Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202 002, India
  http://link.springer.com/article/10.1007/s11627-006-9011-8
  doi: 10.1007/s11627-006-9011-8
  Received: 7 November 2006 / Accepted: 15 November 2006 / Published online: 14 February 2007 / Editor: Schuyler S. Korban
  
  Queries:
  
  1) Why was the order of sterilization procedures for seeds quite different to the Anis et al. 2005 protocol?
  2) Success of seed germination and infection levels not reported.
  3) Why was IAA essential for shoot elongation (together with BA) in the Anis et al. 2005 protocol, but not in this study?
  
  P3
  Mohd Kashif Husain, Mohammad Anis, Anwar Shahzad. 2008. In vitro propagation of a multipurpose leguminous tree (Pterocarpus marsupium Roxb.) using nodal explants. Acta Physiologiae Plantarum 30(3), 353–359.
  Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh 202 002, India
  http://link.springer.com/article/10.1007%2Fs11738-007-0130-6
  doi: 10.1007/s11738-007-0130-6
  Received: 22 August 2007 / Revised: 11 December 2007 / Accepted: 15 December 2007 / Published online: 9 January 2008
  Communicated by E. Lojkowska
  
  Queries / concerns / issues:
  
  1) Abstract: “after a pulse (dip) treatment for 7 days” How can a dip be 7 days long?
  2) Almost identically worded text in 2007, 2008 and 2010 papers (P2, P3 and P4): see examples below*. In the case of the methodology (seed germination, sterilization, seedling preparation, culture conditions and media), why did the authors at least not indicate that the exact same method in the 2008 paper was already published in the 2007 paper?** Since there is no overlap in submission or publishing dates between both papers, the authors should have referenced the methodology of the 2007 paper as being identical.
  3) Why does the relative humidity in all of the Mohammad Anis-related papers (see other entries at PubPeer) seem to fluctuate considerably between experiments? 55-60% in P1, 50-60% in P2, 55-65% in P3, 50-60% in P4. Is there a problem with the tissue culture facilities or equipment? If there is such great variation (15%) in relative humidity, then how can the reader be confident that other aspects of the tissue culture rom are properly functional, such as temperature, light, etc.?
  4) Inconsistent terminology between papers. In P2, explants are referred to as cotyledonary nodes, while in P3, the exact same explants are referred to as nodal explants. What message does this send to students who wish to learn from such protocols, and what term exactly should they use?
  5) Why are completely different concentrations of IBA and phloroglucinol required for rooting in the 2007 and 2008 papers when the exact same explants are used? Does that imply that the conditions were not properly tested in the 2007 paper?
  6) Why was potting medium different between the 2007 and 2008 papers? If not idea in the 2007 paper, then why was this not indicated in either paper?
  7) Why DMRT for data analysis in the 2007 paper but Tukey’s in the 2008/2010 papers?
  8) “Nodal explants taken from 18-day-old axenic seedling showed better response for shoot induction as compared to 6-, 12-, and 24-day-old seedlings (data not shown).” Please compare with the statement in the 2007 paper: “The induction of multiple shoots varied with the age of CNs; a significantly greater percentage response was recorded from 18-d-old explant compared to 6-, 12-, and 24-d-old explants (data not shown).” CN = cotyledonary node. So, when do the authors plan to show this “unpublished data”? Why should one paper refer to the process simply as shoot induction while the other is multiple shoot induction? What is the difference?
  9) How did the authors make the choice between the one Chand and Singh (2004) paper and its duplicate? https://pubpeer.com/publications/3F2AAD44E05FE1D200EAC7E718089C#fb23861
  10) This error highlights the potential risks between papers being carried through in the literature. In the references, Luis et al. (1999): all authors names are completely incorrect). Currently listed as Luis PBC, Adraine CMGM, Silvica BRCC, Anna Christina MB; actual names are Luis Pedro Barrueto Cid, Adriane C.M.G. Machado, Sílvia B.R.C. Carvalheira, Ana Cristina M. Brasileiro. The correct abbreviations should be: Cid LPB, Machado ACMG, Carvalheira SBRC, Brasileiro ACM. The reference list should be duly corrected, and reference to Luis et al. (1999) in the text must be corrected to Cid et al. (1999). http://link.springer.com/article/10.1023%2FA%3A1006283816625 . There is a strong possibility that other scientists may have copied this error into their own paper: https://pubpeer.com/publications/6CDF7987DCF9626443188B153EDEE3#fb23827
  
  P4
  Mohd Kashif Husain 1, Mohammad Anis 2,3, Anwar Shahzad 2. 2010. Somatic embryogenesis and plant regeneration in Pterocarpus marsupium Roxb. Trees 24(4), 781–787.
  1. Biotechnology Division, Indian Institute of Integrative Medicine (IIIM), Council of Scientific and Industrial Research (CSIR), Canal-Road, Jammu-Tawi, 180001, India
  2. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
  3. Department of Plant Production, College of Food and Agricultural Science, King Saud University, Riyadh, 11451, Saudi Arabia
  http://link.springer.com/article/10.1007%2Fs00468-010-0448-3
  doi: 10.1007/s00468-010-0448-3
  Received: 14 August 2009 / Revised: 29 April 2010 / Accepted: 11 May 2010 / Published online: 25 May 2010
  Communicated by K. Klimaszewska
  
  Queries / concerns / issues:
  
  1) The basal premise of this paper (somatic embryogenesis) is highly suspect (i.e., insufficiently supported by cytological, histological and genetic evidence).
  2) Introduction: “characterized for its quick growth, quality of timber and disease resistance. The tree possesses gum-kino, which is a powerful astringent and used to cure various diseases.” What are the exact literature sources to support these factual claims?
  3) Same query as in P3 regarding the wording of methodology and not indicating that the protocol was already employed in the 2007 and 2008 papers**. Only one tiny aspect of the protocol is different in this paper. Use of HgCl2 for 6 min, and not 5 as for P2 and P3. Slip of the finger on the key-board perhaps?
  4) The authors claim that “globular and heart-shaped somatic embryos formed” on 10 different media supplemented with BA and 2-iP (Table 1). Which somatic embryos, and from which developmental stage exactly, and from which treatment in Table 1 exactly were used to test the parameters in Table 2?
  5) The same problem applies to the transition between Table 2 and Table 3. Which somatic embryos, and from which developmental stage exactly, and from which treatment in Table 2 exactly were used to test the parameters in Table 3?
  6) Fig. 3a, b. Which structures exactly are the heart and which are the torpedo stage somatic embryos? Some arrows or labels seem to be missing.
  7) So you are claiming that the structure in Fig. 3c is a cotyledonary stage somatic embryo?
  8) Table 3 header indicates that 2% sucrose is required in the germination medium, but this information is not included in the M&M section. Is 2% sucrose needed, or not?
  
  * Examples of very similarly worded text in Introduction of three papers (P2, P3 and P4).
  2007
  “An aqueous infusion of the wood is said to be of use in diabetes, and water stored in the vessel made of the wood is reputed to have antidiabetic properties (Anonymous, 2003). Two important phenolic constituents, marsupsin and pterostilbene, isolated from the heartwood of P. marsupium are reported to possess antihyperglycemic activity (Manickam et al., 1997). The indiscriminate exploitation of the species, together with low percentage of germination, has resulted in a decrease in the size of its natural stand, which ultimately has led to its inclusion in the list of depleted plant species (Chaudhuri and Sarkar, 2002). In view of its inherent qualities and restricted distribution, its propagation and multiplication through tissue culture is urgently required (Anis et al., 2005). Many woody plant species (McCown, 2000) and particularly tree legumes are known for their recalcitrant nature of regeneration (Jha et al., 2004. ”
  vs
  2008
  “It is reported that an aqueous infusion of the wood is said to be of use in diabetes and water stored in vessels made of the wood is reputed to have antidiabetic properties (Anonymous 2003). Two important phenolic constituents: marsupsin and pterostilbene, isolated from the heartwood of P. marsupium are reported to possess antihyperglycemic activity (Manickam et al. 1997). Over exploitation of the tree for its various useful applications coupled with low-germinability, Pterocarpus marsupium has been included in the list of depleted plant species (Chaudhuri and Sarkar 2002). Inevitably, therefore, its propagation and multiplication through tissue-culture technique is urgently needed (Anis et al. 2005). Many woody plant species (McCown 2000) and particularly tree legumes are known for their recalcitrant nature (Jha et al. 2004).”
  vs
  2010
  “Traditionally in India, an aqueous infusion of the wood is used to treat diabetes and water stored in vessels made of the wood is reputed to have anti-diabetic properties (Anonymous 2003). Phenolic constituents (marsupsin and pterostilbene) isolated from the heartwood and aqueous extract of stem bark of P. marsupium have shown to possess antihyperglycemic activity (Manickam et al. 1997. The exploitation of this medicinally as well as economically important tree from the natural habitat and inadequate efforts for its cultivation resulted in marked decline in the population of the species and has, therefore, been included on the list of depleted plant species (Chaudhuri and Sarkar 2002).”
  
  **
  2007
  “The mature winged fruits of P. marsupium were obtained from the Tropical Forest Research Institute, Jabalpur, India. The healthy seeds were excised from the fruits and washed thoroughly in running tap water for 30 min, rinsed with 5% (v/v) Teepol (a liquid detergent; Glaxo, India) for 10 min and kept in 1% (w/v) Bavistin (carnbandazim powder, BASF, India), a broad spectrum fungicide, for 15 min. The treated seeds were agitated in distilled water for 24 h to remove the chemical inhibitors to germination. The leachates were replaced with sterile distilled water. The seeds were surface disinfected with 70% (v/v) ethanol for 30 s, followed by with an aqueous solution of 0.1% (w/v) freshly prepared HgCl2 for 5 min, and finally rinsed five times with sterile distilled water.”
  vs
  2008
  “The mature winged fruits of P. marsupium were procured through the courtesy of Tropical Forest Research Institute (TFRI), Jabalpur, India. The healthy seeds were isolated mechanically from the fruits with the help of a cutter and washed in running tap water for 30 min to remove any adherent particles. Thoroughly washed seeds were then immersed in 5% (v/v) Teepol, a liquid detergent, for 10 min and kept in 1% (w/v) Bavistin (Carnbandazim Powder), a broad-spectrum fungicide, for 15 min. The treated seeds were agitated in distilled water for 24 h to remove the chemical inhibitors to germination. The leachates were replaced with sterile distilled water. The seeds were surface sterilized with 70% (v/v) ethanol for 30 s, followed by an aqueous solution of 0.1% (w/v) freshly prepared HgCl2 under the sterile condition for 5 min.”
  vs
  2010
  “The mature winged fruits of P. marsupium were obtained from the Tropical Forest Research Institute, Jabalpur, India. The healthy seeds were excised from the fruits and washed thoroughly in running tap water for 30 min followed by rinsing with 5% (v/v) Teepol (a liquid detergent, Glaxo, India) for 10 min. The treated seeds were agitated in distilled water (10 seeds/100 ml) for 24 h to remove the chemical inhibitors of germination. The leachates were replaced with sterile distilled water. Seeds were surface disinfested with 70% (v/v) ethanol for 30 s, followed by 0.1% (w/v) HgCl2 solution for 6 min and finally rinsed six times with sterile distilled water.”
  
  P3: Acknowledgments: “The award of a Senior Research Fellowship to MK Husain by the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi is greatly acknowledged. We also acknowledge the Department of Biotechnology (DBT), Government of India, New Delhi for financial assistance and The Director, Tropical Forest Research Institute (TFRI), Jabalpur, India in the procurement of seed material.”
  P4: Acknowledgments: “The award of Research Associateship to M. K. Husain by the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, is greatly acknowledged. We also acknowledge the Department of Biotechnology (DBT), Government of India, New Delhi, for financial assistance and Dr. Shamim A. Ansari, Scientist, Tropical Forest Research Institute (TFRI), Jabalpur, for his helpful discussion. The authors are also thankful to Dr. K. Klimaszewska, Communicating Editor, for critical evaluation and valuable comments on the manuscript.”
  
  There are three PubPeer entries:
  P2: https://pubpeer.com/publications/09A1EEB8D7F210D7F8AEA052D1323A#fb24131
  P3: https://pubpeer.com/publications/8D88FE9E7EBD7D43942558B2777E51#fb24133
  P4: https://pubpeer.com/publications/9AC8618F6376905D80D0A6DFA98D45#fb24134
  
  Reply
2. Red sanders queries says:
  
  February 28, 2015 at 10:15 am
  
  P1
  Radhika Tippani, Rajesh Yarra, Mallesham Bulle, Mahendar Porika, Sadanandam Abbagani, Christopher Thammidala. 2013b. In vitro plantlet regeneration and Agrobacterium tumefaciens-mediated genetic transformation of Indian Kino tree (Pterocarpus marsupium Roxb.). Acta Physiologiae Plantarum 35(12), 3437–3446.
  http://link.springer.com/article/10.1007/s11738-013-1378-7
  doi: 10.1007/s11738-013-1378-7
  Received: 26 March 2013 / Revised: 15 August 2013 / Accepted: 30 August 2013 / Published online: 1 October 2013
  Communicated by M. Prasad.
  
  P2
  Tippani, R., Vemunoori, A.K., Yarra, R., Nanna, R.S., Abbagani, S., Thammidala, C., 2013a. Adventitious shoot regeneration from immature zygotic embryos of Indian Kino tree (Pterocarpus marsupium Roxb.) and genetic integrity analysis of in vitro derived plants using ISSR markers. Horticulture, Environment, and Biotechnology 54(6), 531–537.
  http://link.springer.com/article/10.1007/s13580-013-0161-4
  doi: 10.1007/s13580-013-0161-4
  Received November 6, 2012 / Revised August 4, 2013 / Accepted September 5, 2013
  
  Queries / concerns / issues:
  
  1) Few queries related to P2, only why were so few ISSR markers tested? Most queries below pertain to P1, in some cases relative to P2.
  2) For immature zygotic embryo (IZE) germination, three concentrations of BA are tested: 0.2, 0.4 and 0.9 µM. But the results and manuscript do not indicate which of these three concentrations was ideal. No data is provided for this experimental part.
  3) Culture vessels and explant density of in vitro culture not reported.
  4) Callus was induced from IZEs and shoots then formed from callus. In general, due to possible somaclonal variation, shoots derived from callus are generally avoided. However, in this protocol, callus + shoots were jointly cultured while callus was used for genetic transformation. Undoubtedly, for practical purposes (easier explant handling?) callus was used for the latter. However, the genetic stability of regenerants is questioned.
  5) The light intensity is reported as microEinsteins in P1 and as micromole in the P2 paper. Why the inconsistency? The former is generally not an accepted SI unit.
  6) Similar inconsistency, or disparity, in acclimatization potting mixtures and MS medium used to irrigate acclimatized plants. Why did the two studies use different mixtures when the exact same plantlets formed? Which one is in fact more effective?
  7) Why was relative humidity of the culture reported for P2, but not in P1?
  8) Why was IBA required with 1/2 MS in P1, but not in P2?
  9) The authors report data in number of shoots/callus. But this unit “callus” is unclear. Is this a callus cluster? If so, what was the initial weight, or volume? These important details are not indicated, so it is unclear if the starting material used for the trials indicated in Table 2 are uniform, or not. The same vagueness applies for the term callus/calli, which is used as a unit in Table 4, and in the stats section.
  10) Table 1 indicates that multiple shoots or shoot elongation occurred on 8 treatments. Which shoots, i.e., exactly from which treatment, were used for the rooting experiments in Table 3. No information appears in the methodology or in the table header or footer.
  11) Why are there no control treatments (PGR-free) in Tables 1 and 2? Is the data analysis correct without comparison to control treatments?
  12) The authors have used the wrong symbol to represent the Greek word beta, or β. They have represented beta as ß (the German letter “eszett”).
  13) The source of Agrobacterium tumefaciens strain LBA4404 with pCAMBIA1301 (http://www.cambia.org/daisy/cambia/2046/version/1/part/4/data/pCAMBIA1301.pdf?branch=main&language=default) is indicated in the Acknowledgements only, but such important information should also have appeared in the M&M section, given the central importance of this plasmid and Agrobacterium strain. Does this particular plasmid not have to be used under license from Cambia Labs (http://www.cambia.org/daisy/cambialabs/home.html) rather than from a third party?
  14) What is the commercial source of all of the antibiotics used (hygromycin, rifampicin, chloramphenicol, cefotaxime) and acetosyringone?
  15) What is YEB medium, what are its constituents and a reference for it?
  16) The authors indicate a set of primers for detecting the uidA and hpt genes, but do not indicate if they devised these primers, of if these sequences were based on already reported primers in the literature. The authors should clarify this.
  17) The same doubt applies for the PCR conditions for both genes. Are these optimized in-house, or based on the reported literature?
  18) EcoRI, actin and agarose were used. What is the commercial source of this restriction enzyme and actin and agarose?
  19) Why was RT-PCR of the uidA gene done, and not of the hpt gene?
  20) “All the data were statistically analyzed using analysis of variance (ANOVA) and the means were compared using Duncans Multiple Range Test (DMRT).” Why are there no statistical analyses for percentage data? An apostrophe is missing in Duncan’s.
  21) A transformation efficiency of 20.92% was claimed in the abstract, and claimed as being the highest level. Firstly, this information is incorrect. Tables 4 and 5 reveal that the highest transformation efficiency was 22.2% for shoots and 22.7% for plants was the highest level. In the text, the authors refer to the same % as “average”, but based on what, a mean of all treatments described in Table 4 + Table 5? The “average” best % they report is confusing. Secondly, the authors used growth on hygromycin-supplemented medium to assess transformation efficiency. Most plant transformation studies use molecular methods, at minimum using PCR, to quantify this efficiency, and it is frequent to observe percentages in the range of fractions of one percent to 2-3%. So, by reporting values in excess of 20% is over-inflating the reality. Can the authors please indicate the transformation efficiencies based on the molecular detection methods.
  22) “were transferred to green house for acclimatization” Are the authors sure of the colour of the house, or are they perhaps referring to a greenhouse?
  23) “Optimal callus induction was observed on MS + 1.07µM NAA (Data not shown).” It seems very odd that the most important (i.e., “optimal”) data should not be shown?
  24) Is the explant in Fig 1a a cotyledon (it looks too fat and round, possibly the seed, or excised zygotic embryo)? What is the explant in Fig 1b (a cotyledon)? Why are there no size bars on any of the photos in Fig 1 or 2?
  25) Fig 2f, g and h. What is the source (i.e., exact medium) of these putatively transgenic shoots?
  26) Are the putative transgenic lines 1-3 reported in Fig. 3a, b, c and d the same? Similarly, is W the same?
  27) In all of the molecular analyses, the authors refer to “non-transformed plantlets” as the control. However, they never indicate the exact plantlets from which exact treatment makes up this elusive control. Can the authors please clarify this, including the actual source tissue used for the molecular analyses and also the exact age and stage of development (i.e., from which medium) of the plantlets.
  28) In the introduction, the authors remark: “Genetic transformation of woody species using A. tumefaciens has been limited because of secretion of phenolics by excised explants”. Can the authors provide some information about the presence of phenolics in the tissue culture of this plant, the frequency and also preventive measures to avoid explant and medium browning? Given the apparently wide-spread phenomenon claimed by authors, it is surprising to see absolutely zero discussion of this important issue in the discussion.
  29) Discussion: “For successful genetic transformation experiments, development of callus-based plantlet regeneration system is prerequisite (Gorpenchenko et al. 2006).” This is an extremely misleading claim. It is preferable to have regeneration directly than indirectly through callus, although when using callus, the chances of obtaining transformants is likely to be higher. This and claiming that it is a prerequisite are very different things.
  30) Discussion: “Nevertheless, low transformation frequencies were reported and, like for other perennial crops, the availability of callus cultures suitable for genetic transformation remains one of the main bottlenecks for developing genetic transformation strategies.” Remarkably similar to text on page 7 of Ribas et al. “Nevertheless low transformation frequencies were reported and, like for other perennial crops, the availability of embryogenic tissues suitable for genetic transformation remains one of the main bottlenecks for developing genetic transformation strategies.” http://www.biomedcentral.com/1471-2229/11/92 The giveaway was “perennial crops”.
  31) Who was the Acta Physiologiae Plantarum editor overseeing and approving this manuscript for publication and were the peers truly peers?
  
  Author contribution SA, CT conceived, designed the experiments and contributed reagents; RT, RY and MB performed the experiments; RT, MP analyzed the data; RT and CT wrote the paper. All the authors have read and approved the final manuscript.
  
  Acknowledgments: “RT is thankful to Jawaharlal Nehru Memorial Fund, New Delhi, India for financial support. The authors gratefully acknowledge Prof. Peng Zhang, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, China for providing pCAMBIA1301‘construct.”
  
  There are two PubPeer entries:
  P1: https://pubpeer.com/publications/E1CA0337226AB3A9135D3B812B78D5
  P2: https://pubpeer.com/publications/F2D1EF3C32EF79A26325A9CD0152EC
  
  Reply
3. Red sanders queries says:
  
  February 28, 2015 at 12:53 pm
  
  Anuradah, M., Pullaiah, T., 1999. Propagation studies of red sanders (Pterocarpus santalinus L.f.) in vitro- an endangered taxon of Andhra Pradesh, India. Taiwania 44, 311–324.
  Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, India
  http://tai2.ntu.edu.tw/taiwania/pdf/tai.1999.44.3.311.pdf (open access)
  No DOI
  
  Queries / concerns / issues:
  1) Although the authors studied 8 explant types, the exact explant size is not defined.
  2) The reliability of the in vitro seed germination protocol is highly questionable, at least in terms of the lack of infection. Pods were surface disinfected and then seeds were excised from these pods and sown directly in vitro without any further surface disinfection. It is highly unlikely that infection was not a factor, but this issue is not discussed anywhere.
  3) 40-70% germination frequency is reported, but it is unclear why this massive range: one would expect a single % value given the fact that only a single treatment was used.
  4) The carbon source, if any, is not explained for the seed germination medium, or shoot induction media.
  5) The commercial source or grade of all chemicals and reagents, including the plant growth regulators, not provided. The gelling agent, or its concentration used to gel the medium, not indicated.
  6) Contradictory information in two consecutive paragraphs indicated in the rhizogenesis methodology: “Half and full strength MS medium and White’s medium…were employed” vs “The basal medium used was that of MS…, White’s medium” (p. 312).
  7) On page 318 of the R&D, the authors describe trials for rooting over 12, 24, 48 and 72 h. None of these details about the methodology are however provided in the M&M.
  8) No details about the light source used, photoperiod, light intensity or culture temperature.
  9) Acclimatization claimed in sand + soil, but not quantified, nor are any other details about the methodology provided.
  
  No acknowledgements.
  
  There is a PubPeer entry (linked to other papers because this paper has no DOI):
  https://pubpeer.com/publications/6CDF7987DCF9626443188B153EDEE3
  
  Reply
4. Red sanders queries says:
  
  March 1, 2015 at 4:56 pm
  
  Chisha-Kasumu, E., Price, A.H., Woodward, S., 2006. In vitro shoot multiplication and rooting from seedling explants of Pterocarpus angolensis in Zambia. South African Forestry Journal 208, 31–37
  http://www.tandfonline.com/doi/abs/10.2989/10295920609505259?journalCode=tsfs18#.VPMO48v9nIU
  DOI: 10.2989/10295920609505259
  
  Errors in reference list:
  1) Crouch et al. 1998, page numbers missing: pp. 11-22: http://www.ejbiotechnology.info/content/vol1/issue1/full/2/2.pdf
  2) Farooq and Farooq 2003: plant name missing: Tamarindus indica http://scialert.net/abstract/?doi=pjbs.2003.1591.1592
  3) Kumar et al. 2001: Palni LMS should be AMS http://www.jhortscib.org/Vol76/76_1/index.htm
  4) Magingo and McP. Dick 2001. Journal name incorrect (Agroforestry Systems Journal): should be Agroforestry Systems http://link.springer.com/article/10.1023/A%3A1006425509228
  5) Van der Riet et al 1998. Errors with three authors’ family names. Van der Reit should be Van der Riet; de Sousa Corriea should be de Sousa Correia; Kruger should be Krüger. http://www.tandfonline.com/doi/pdf/10.1080/02571862.1998.10635132
  6) Yanping et al. 2000. All Chinese authors’ names are incorrect. These are the first, given names and should be represented, instead, as follows: Yin YP, Gao RQ, Sun QQ, Li SF. Consequently, on page 32 (methods), Yanping should be substituted for Yin. The original ISTA journal page and Ingenta do not list this volume, but the original can be understood in another paper: http://link.springer.com/article/10.1007%2Fs11738-006-0010-5 (see ref #36).
  
  Pubpeer entry:
  https://pubpeer.com/publications/4CFA54AA623268FE67EC9406575A94#fb25964
  
  Ekambaranellore Prakash (1, 2), Patan Shaik Sha Valli Khan (3, 4), Thoguru Jonh Vivek Sreenivasa Rao (1, 5), Elu Singh Meru (1). 2006. Micropropagation of red sanders (Pterocarpus santalinus L.) using mature nodal explants. Journal of Forestry Research 11(5), 329–335.
  1. Biotechnology Research Centre, Tirupati, India
  2. Division of Biotechnology and Pharmaceuticals Research, National Health Research Institutes, Miaoli County, Taiwan, ROC
  3. Medicinal Plants and Horticultural Resources Division, Institute of Bioresources and Sustainable Development, Takeylpat Institutional Area, Imphal, India
  4. BIOFAR-EVA, CRP-Gabriel Lippmann, 41 Rue du Brill, Belvaux, L-44 22, GD, Luxembourg
  5. Department of Agronomy, University of Kentucky, Lexington, KY, USA
  http://link.springer.com/article/10.1007%2Fs10310-006-0230-y
  DOI: 10.1007/s10310-006-0230-y
  
  Queries / concerns / issues:
  1) Abstract and M&M conflicting information. Abstract: “About 70% of the micropropagated plantlets were established successfully in 20-cm pots containing a mixture of soil and farmyard manure (4 :1 ratio) and formed new leaflets.” M&M (p. 331): “Primary hardened plantlets were then repotted in larger earthen pots (20cm diameter) containing soil:farmyard manure (3: 1)”. 4:1 or 3:1? R&D states (p. 335) “containing a mixture of soil and farmyard manure (4:1 ratio).”
  2) Introduction: “The red color of the wood is used as a natural dye in pharmaceutical, paper, pulp, textile, tannery, and food industries. The wood is also considered in indigenous medicine as an astringent, tonic, and diaphoretic, and is useful to cure bilious infections and skin diseases.” Not a single reference is provided, however, to support any of these claims or facts.
  3) “The experimental tree was growing in the Mamunder Reserve Forest of Cuddapah District, Andhra Pradesh, India.” Was permission obtained from the Indian Forestry Department to sample from this forest reserve?
  4) The commercial source or grade of all chemicals and reagents, including the plant growth regulators and antioxidants, not provided. Explant density not explicitly indicated, only estimated by the reader from photos. “25 × 150 m culture tubes”: m is most likely ml.
  5) R&D text states “Plantlets acclimatized in the plant growth chamber benefited from the high humidity and other incubation conditions during the 2 weeks and showed 70% survival (Fig. 7).” Fig. 7 legend states: “Five-month-old plants after acclimatization”. Information between text and legend is incompatible. The actual photo appears to be a freshly potted in vitro plantlet.
  6) References. Anuradha and Pullaih (1999): second author’s name misspelt (should be Pullaiah). Same error on page 330, introduction. Journal name also incorrect: Phyotomorphology (should be Phytomorphology). Raju and Nagaraju (1999): Pardesh should be Pradesh. Romano et al. (2002): last author’s name misspelt as Martinus-Lucao but should be Martins-Loução (http://link.springer.com/article/10.1023/A%3A1012912504288); Ceratomia should be Ceratonia.
  7) It is curious that the authors cite the partially (estimated about 80%) duplicated papers, Chand et al. (2004a, 2004b)* without having considered reporting this to the original journal.
  
  * At PubPeer:
  https://pubpeer.com/publications/3F2AAD44E05FE1D200EAC7E718089C#fb23767
  https://pubpeer.com/publications/D112CA83735753D1EFE2B6BFF664B2#fb23766
  
  PubPeer entry:
  https://pubpeer.com/publications/A86976D3DC00380640F55CDF20ED8C#fb25970
  
  The two following studies have no DOI and no PubPeer entry, and only minor errors, but worth registering nonethelesss.
  
  Arockiasamy, S., Ignacimuthu, S., Melchias, G., 2000. Influence of growth regulators and explant type on in vitro shoot propagation and rooting of red sandal wood (Pterocarpus santalinus L.). Indian J. Exp. Biol. 38, 1270–1273.
  Entomology Research Institute, Loyola College, Chennai, India
  Department of Botany, St. Joseph’s College, Tiruchirapalli, India
  No DOI
  
  Queries / concerns / issues:
  1) Introduction: Leguminoceae misspelt (should be Leguminosae/Fabaceae).
  2) The commercial source or grade of almost all chemicals and reagents, except for agar, including the plant growth regulators, not provided. The gelling agent, or its concentration or pH used to gel the medium, not indicated for the shoot and root induction media.
  3) Table 1 statistical description incorrect: “Values in the column and rows…” The analyses were apparently made within rows. Even so, letters of comparison are very confusing. The same confusion applies to the Table 2 data.
  
  Rajeswari, V., Paliwal, K., 2008. In vitro plant regeneration of red sanders (Pterocarpus santalinus L.f.) from cotyledonary nodes. Indian J. Biotechnol. 7, 541–546.
  http://nopr.niscair.res.in/bitstream/123456789/2349/1/IJBT%207%284%29%20541-546.pdf?origin=publication_detail (open access)
  No DOI.
  
  Queries / concerns / issues:
  1) Age and geographic source of mother plant not described.
  2) One of the explants used are “leaf nodes”. Botanically, this does not exist: only stems have nodes. Are these leaves used from leaves forming from axillary buds, or are these axillary buds forming at the junction of leaves and stems? This ambiguity makes this explant difficult to differentiate from the second explant used “cotyledonary nodes”, since both explant types were derived from 30-day-old seedlings.
  3) The commercial source or grade of almost all chemicals and reagents, including the plant growth regulators, not provided.
  4) “Seeds were sown on seedbed for germination.” The first and most important step of the entire experiment, seed germination, is unclear and incompletely explained. What is the substrate used, and what are the environmental conditions to induce germination?
  5) The abstract claims optimal rooting using 5 µM IAA. However, Table 4 indicates 5 µM IAA + 1 µM IBA.
  6) Some minor errors in the reference list.
  
  Reply
Chlorophytum borivilianum queries says:

February 9, 2015 at 1:41 pm

P1
Physiology and Molecular Biology of Plants July 2012, Volume 18, Issue 3, pp 253-263
Date: 29 Apr 2012
Plant regeneration in Chlorophytum borivilianum Sant. et Fernand. from embryogenic callus and cell suspension culture and assessment of genetic fidelity of plants derived through somatic embryogenesis
Mohd. Zahid Rizvi 1,3, Arun Kumar Kukreja 1, Narendra Singh Bisht 2
1. Plant Tissue Culture Division, Central Institute of Medicinal and Aromatic Plants (CIMAP), Lucknow, P.O. CIMAP-226015, Uttar Pradesh, India
2. Department of Botany, Hemwati Nandan Bahuguna Garhwal University (Pauri Campus), Garhwal-246174, India
3. Department of Botany, Shia Post Graduate College, Sitapur Road, Lucknow-226020, India
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3550513/
http://link.springer.com/article/10.1007/s12298-012-0113-y
DOI: 10.1007/s12298-012-0113-y

P2
Physiology and Molecular Biology of Plants July 2010, Volume 16, Issue 3, pp 249-257
Date: 30 Nov 2010
In vitro propagation of an endangered medicinal herb Chlorophytum borivilianum Sant. et Fernand. through somatic embryogenesis
Mohd Zahid Rizvi, Arun Kumar Kukreja, Narendra Singh Bisht
http://link.springer.com/article/10.1007/s12298-010-0026-6
DOI: 10.1007/s12298-010-0026-6

P3
Rizvi MZ, Kukreja AK and Khanuja SPS (2007) In vitro culture of C. borivilianum Sant. et Fernanad. in liquid culture medium as a cost‐effective measure. Current Science 92(1): 87-90.
http://www.currentscience.ac.in/Downloads/article_id_092_01_0087_0090_0.pdf (open access)
http://www.iisc.ernet.in/currsci/jan102007/87.pdf
No DOI.

P4
African Journal of Biotechnology Vol.13(17), pp. 1772-1778, April 2014
Mohammed Zahid Rizvi *, Arun Kumar Kukreja
Plant Tissue Culture Division, Central Institute of Medicinal and Aromatic Plants (CIMAP) near Kukrail Picnic Spot Road, P.O. CIMAP-226015, Lucknow, Uttar Pradesh, India.
*Present Address: Department of Botany, Shia Post Graduate College, Sitapur Road, Lucknow-226020, Uttar Pradesh, India.
Micropropagation of an endangered medicinal herb Chlorophytum borivilianum Sant. et Fernand. in bioreactor.
http://www.academicjournals.org/journal/AJB/article-abstract/8EB7BE644267
http://www.academicjournals.org/article/article1398760058_Rizvi%20and%20Kukreja.pdf
DOI: 10.5897/AJB2013.12904
The publisher, Academic Journals, is listed at http://scholarlyoa.com/publishers/

There are 3 PubPeer entries for this case:
P1: https://pubpeer.com/publications/54A5AA3709C3D71CFA697E572FD180#fb24034
P2: https://pubpeer.com/publications/4B50870045F2D908C0AADB10ACB680#fb24035
P4: https://pubpeer.com/publications/AF376BA33D395F7919AFDED3935F5E#fb24036

Reply
1. Chlorophytum borivilianum retracted says:
  
  November 4, 2015 at 9:12 am
  
  The 2012 PMBP paper was retracted today.
  
  http://link.springer.com/article/10.1007/s12298-015-0312-4
  DOI: 10.1007/s12298-015-0312-4
  “This article has been retracted by the authors due to inappropriate republication of two photographs (results) that have already been published in their following article published
  earlier in PMBP: Mohd Zahid Rizvi, Arun Kumar Kukreja, Narendra Singh Bisht “In vitro propagation of an endangered medicinal herb Chlorophytum borivilianum Sant. et Fernand.
  through somatic embryogenesis”, Physiology and Molecular Biology of Plants July 2010, Volume 16, Issue 3, pp 249–257. The authors and editors regret the error due to oversight.”
  
  Reply
Saffron queries says:

February 9, 2015 at 1:43 pm

Saffron is the world’s most expensive spice, and is derived from the stigmas of the medicinal plant, Crocus sativus. Concers have been raised in a paper meploying saffron to treat colorectal cancer:
https://pubpeer.com/publications/C1DF18F5DBE44542EF4FBEEA87BDC0#fb24598

Reply
Author contributorship says:

February 9, 2015 at 3:50 pm

One paper in Plant Cell Reports that does not define authors’ contributions, even though the journal’s instructions for authors requires it, and even though other papers in the exact same volume contain it, is being questioned at PubPeer:
https://pubpeer.com/publications/CCA4284AD13FE38868AD159273497D#fb24624

Plant Cell Reports February 2015, Volume 34, Issue 2, pp 223-231
Date: 25 Oct 2014
Arabidopsis AtERF71/HRE2 functions as transcriptional activator via cis-acting GCC box or DRE/CRT element and is involved in root development through regulation of root cell expansion
Sun-Young Lee, Eun Young Hwang, Hye-Yeon Seok, Vaishali N. Tarte, Mi Suk Jeong, Se Bok Jang, Yong-Hwan Moon
http://link.springer.com/article/10.1007%2Fs00299-014-1701-9

Reply
1. Author contributorship says:
  
  February 10, 2015 at 2:22 am
  
  Within a few hours, the senior author responsibly responded publicly, and provided a solution, stating:
  “To whom it may concern,
  
  Thank you so much for pointing this out. We did not pay attention that the contribution statement was missing in the final version of paper. We checked all the versions of the manuscript that we submitted to Plant Cell Reports and found that the contribution statement was originally included in the submitted manuscript and the pdf file for a review. However, the statement was missed in a proof-read. We will let the publisher correct this mistake.
  
  The contribution statement in the submitted manuscript is as following:
  Contributions
  Most experiments and data analyses were performed by both S.-Y. Lee and E.Y. Hwang. H.-Y. Seok assisted in the construction of plasmids and transcriptional activation analysis. V.N. Tarte assisted in the root development experiment. M.S. Jeong contributed to biochemical analysis. S.B. Jang and Y.-H. Moon were responsible for overall conceptualization and supervision of the experiments and worked on data processing and manuscript preparation.
  
  Thank you again.
  Regards,
  Yong-Hwan Moon”
  
  The authors are commended for expressing their desire to correct this small, but important, error. This case will be updated once the erratum or corrigendum appears at Plant Cell Reports.
  
  Reply
2. Author contributorship says:
  
  February 10, 2015 at 3:42 am
  
  Key questions:
  a) How does the contributor statement just “disappear” between first submission and accepted version unless “someone” actively removed it?
  b) Did the authors accidentally “forget” the statement, or did the publisher or editor accidentally “remove” it?
  c) Did the proof department in India accidentally remove it during the proof developmental stage, or forget to include it?
  d) How many other papers in this journal suffer from such quality control “lapses”?
  e) From when exactly did it become obligatory to include this authorship statement in this journal? No dates appear on the PCR web-site.
  
  We need an answer to these questions to understand who was actually responsible, so we hope that the erratum (author error) or corrigendum (editor/publisher error) clarifies this. In some ways, the type of note published (erratum vs corrigendum) will already provide some insght into this oversight.
  
  This accentuates the fact that quality control may be lax, even in such high ranking* plant science journals, even for such simple things as authorship statements which requires no “peers”. PPPR is not an option, it is an absolute necessity.
  
  * IF = 2.936
  
  Reply
Thai medicinal plants and cancer lines says:

February 14, 2015 at 1:27 pm

A selection of Thai medicinal plants have been used to treat oral (KB) and human cervical (HeLa) cancers:
http://informahealthcare.com/doi/abs/10.3109/13880209.2014.959613
Problem is, according to Amanda Capes-Davis, who has documented these issues nicely in some papers in the literature, that “KB is not an oral cancer cell line.”

If indeed, true, then the following queries arise:

a) what are the KB lines that these authors are referring to?

b) Where did they obtain these KB lines (friend or commercial source)?

c) What are the actual differences between KB lines and HeLa cells?

d) Did these authors provide authentication to the journal during submission to prove that KB lines are KB lines?

e) How many other papers have used non-existent KB lines?

f) As a sub-set of e), how many plant scientists have claimed to use plant extracts from medicinal plants to treat a cancer using a non-existent KB (or other) line?

Some literature by Dr. Capes-Davis on such issues:
http://onlinelibrary.wiley.com/doi/10.1002/ijc.27931/abstract
http://www.atcc.org/~/media/PDFs/CapesDavies.ash
http://standards.atcc.org/kwspub/home/the_international_cell_line_authentication_committee-iclac_/Database_of_Cross_Contaminated_or_Misidentified_Cell_Lines.pdf

Reply
Female ginseng says:

February 15, 2015 at 5:42 am

Angelica gigas Nakai is commonly termed female ginseng. Errors in gels in some figures had been detected in a paper on the neuroprotective property of decursin, and an erratum was published. One small problem, the erratum still contains some of the originally erroneous figures. Authors’ fault, or publisher’s (Hindawi) fault?
Evidence-Based Complementary and Alternative Medicine
Original: http://www.hindawi.com/journals/ecam/2013/467245/
Erratum: http://www.hindawi.com/journals/ecam/2014/473967/
Is there a special term for the erratum of an erratum (erratum squared)?

Reply
Stomatal development query says:

February 22, 2015 at 12:39 pm

An important part of a Nature paper’s methodology related to stomatal development in model plant Arabidopsis thaliana appears to be missing.
https://pubpeer.com/publications/51FF2043DA908ABD9D8AB9CF5B7EF5#fb25540
http://www.nature.com/nature/journal/v513/n7517/full/nature13452.html#affil-auth
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274335/

Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development
Cawas B. Engineer, Majid Ghassemian, Jeffrey C. Anderson, Scott C. Peck, Honghong Hu & Julian I. Schroeder
Nature 513, 246–250 (11 September 2014)
doi:10.1038/nature13452
Received 23 June 2012 Accepted 06 May 2014 Published online 06 July 2014
Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
Cawas B. Engineer, Honghong Hu & Julian I. Schroeder
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
Majid Ghassemian
Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
Jeffrey C. Anderson & Scott C. Peck
Present address: College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Honghong Hu

Reply
1. Stomatal development query says:
  
  February 25, 2015 at 11:23 pm
  
  The authors have responded, acknowledging that a part of the methodology had mistakenly been omitted, while also addressing other fine-scale details about queries that were made at PubPeer. They indicate that they have contacted Nature to seek a correction: “We thank the PubPeer author for their comments and provide responses below to their questions. We apologize for the oversight of inadvertently not including the analysis methods used for our publically available RNA-Seq datasets. We have also contacted the journal to request that updates are provided, including on these methods and to clarify information which may have caused misunderstanding here.” It is unclear exactly which of the authors provided this response, which was posted as an anonymous unregistered submission.
  
  Reply
2. Stomatal development query says:
  
  March 24, 2015 at 1:47 am
  
  The authors have recognized more errors in their paper, extending beyond those that they stated that they would correct on February 25, 2015: “Thank you for your comments. We have found an error in the RNA-Seq-derived insets. We regret not having identified this problem previously. We have sent corrections as well as the clarifications mentioned above to Nature. In reference to the potential off-targets of primers used for EPF2 qPCR experiments, we re-analyzed the sequences carefully. We note that it is correct that partial matches of the primer sequences occur in the genome. However, these imperfect putative binding sites are not identical to the full-length primer sequence, in contrast to the EPF2 target. Furthermore, analysis of the primer pair used in our paper, using the Primer Blast tool available at NCBI as well as the MFEprimer tool available online predict only the expected EPF2 PCR product indicating that putative alternative binding sites do not lead to other PCR products. Furthermore, Primer Blast (NCBI) does not predict a product when the single primer is used as forward and reverse primers. Thus we conclude that our primers were designed properly. As mentioned above, we have notified Nature and seek to publish a correction as soon as possible.”
  
  Reply
Silver and gold nanoparticles from plants queries says:

February 22, 2015 at 1:00 pm

In addition to the 7 papers documented above between December 27 2014 and January 8 2015, there are now three more papers at PubPeer being questioned about the validity of the methodology related to the production of silver and gold nanoparticles in plants (and one in a marine fungus). In some cases, patterns are beginning to form. For example, case 10 comes from the same institute as the 7 previously questioned papers, i.e., Annamalai University (India).

Case 8
https://pubpeer.com/publications/BA09D565229B83A3431E5DD416DFEB#fb25452
http://link.springer.com/article/10.1007%2Fs00436-014-3895-8
Parasitology Research June 2014, Volume 113, Issue 6, pp 2363-2373
Mosquito larvicidal properties of silver nanoparticles synthesized using Heliotropium indicum (Boraginaceae) against Aedes aegypti, Anopheles stephensi, and Culex quinquefasciatus (Diptera: Culicidae)
Kaliyan Veerakumar, Marimuthu Govindarajan, Mohan Rajeswary, Udaiyan Muthukumaran
Unit of Vector Biology and Phytochemistry, Department of Zoology, Annamalai University, Annamalainagar, 608002, Tamilnadu, India
DOI: 10.1007/s00436-014-3895-8

Case 9
https://pubpeer.com/publications/7242F95D6608C179A4026F2FCDA795#fb25451
http://link.springer.com/article/10.1007%2Fs11356-015-4148-9
Environmental Science and Pollution Research January 2015
Date: 31 Jan 2015
Biosynthesized silver nanoparticles using floral extract of Chrysanthemum indicum L.—potential for malaria vector control
Selvaraj Arokiyaraj, Vannam Dinesh Kumar, Vijay Elakya, Tamilselvan Kamala, Sung Kwon Park, Muthiah Ragam, Muthupandian Saravanan, Mohomad Bououdina, Mariadhas Valan Arasu, Kalimuthu Kovendan, Savariar Vincent
1. Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea
3. Department of Biotechnology, Vel Tech High Tech Dr. RR Dr. SR Engineering College, Avadi, Chennai, 600 062, Tamil Nadu, India
2. P.G. Research and Department of Advanced Zoology and Biotechnology, Centre for Environmental Research and Development, Loyola College, Nungambakkam, Chennai, 600 034, Tamil Nadu, India
4. Deparment of Biotechnology, Rajalakshmi Engineering College, Chennai, 602 105, Tamil Nadu, India
5. Department of Animal Nutrition and Physiology, National Institute of Animal Science, RDA, Suwon, 441-706, Republic of Korea
6. Department of Physics, Fatima College, Madurai, 625 018, Tamil Nadu, India
7. Department of Medical Microbiology and Immunology, Institute of Biomedical Sciences, College of Health Science, Mekelle University, PO Box 231, Mekelle, Ethiopia
8. Nanotechnology Centre, University of Bahrain, PO Box 32038, Sakhir, Kingdom of Bahrain
9. Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
10. Division of Entomology, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
DOI: 10.1007/s11356-015-4148-9

Case 10
https://pubpeer.com/publications/03B096D3A5DDAEFAA49F0EC6D337F9#fb25444
http://www.sciencedirect.com/science/article/pii/S0927776509000381
Colloids and Surfaces B: Biointerfaces
Volume 71, Issue 1, 1 June 2009, Pages 133–137
Studies on silver nanoparticles synthesized by a marine fungus, Penicillium fellutanum isolated from coastal mangrove sediment
K. Kathiresan, S. Manivannan, M.A. Nabeel, B. Dhivya
Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai 608502, Tamil Nadu, India

Reply
1. Silver and gold nanoparticles from plants queries says:
  
  April 14, 2015 at 12:45 pm
  
  More concerns about papers that claim the production of silver nanoparticles from plant and algal extracts.
  
  http://www.sciencedirect.com/science/article/pii/S1386142515002474
  https://pubpeer.com/publications/82FD4B6B9FA35478FE0030B85FD075#fb28423
  Size controlled biogenic silver nanoparticles as antibacterial agent against isolates from HIV infected patients
  K.S. Uma Suganya, K. Govindaraju, V. Ganesh Kumar, T. Stalin Dhas, V. Karthick, G. Singaravelu, M. Elanchezhiyan, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2015)
  Nanoscience Division, Centre for Ocean Research, Sathyabama University, Chennai 600 119, India
  Nanoscience Division, Department of Zoology, Thiruvalluvar University, Vellore 632 115, India
  Department of Microbiology, Dr ALM Post Graduate Institute of Basic Medical Sciences (IBMS), Chennai 600 113, India
  
  http://www.sciencedirect.com/science/article/pii/S2215017X14000319
  https://pubpeer.com/publications/76081F033D50F831FC183588FDE0E2#fb28422
  Acalypha indica Linn: Biogenic synthesis of silver and gold nanoparticles and their cytotoxic effects against MDA-MB-231, human breast cancer cells
  C. Krishnaraj, P. Muthukumaran, R. Ramachandran, M.D. Balakumaran, P.T. Kalaichelvan, Biotechnology Reports (2014)
  Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
  
  Reply
Cannabis sativa = marijuana says:

February 28, 2015 at 6:04 am

Greater attention is going to have to be paid to marijuana research, especially as more and more states legalize recreational “Marijuana” throughout the USA (e.g., [1]). One argument that is being discussed at PubPeer is the link between marijuana and cannabidiol (CBD):
https://pubpeer.com/publications/E8097D2179245BB71987C86D786D81#fb25893
The literature in favor of legalization and against it must be analyzed extremely carefully, especially from the plant’s perspective, because this is not only a new political tool, it is a sensitive social issue. Thus, trials that employ CBD or marijuana extracts or other Cannabis-derived extracts had better be carefully analyzed post-publication to ensure that what is being used in trials to test for positive or damaging effects is in fact what the researchers think it is. Raw plant extracts without chemical analyses used in medical trials need to be assessed with great caution. Before the marijuana literature goes to pot.

[1] http://www.washingtonpost.com/local/with-marijuana-legalization-green-rush-is-on-in-dc/2015/02/25/23c3f1de-bc78-11e4-b274-e5209a3bc9a9_story.html

Reply
Withania queries says:

March 4, 2015 at 6:58 pm

Rohit Jain 1, Arunima Sinha 1, Sumita Kachhwaha 1, 2, S L Kothari 1, 2 (2009) Micropropagation of Withania coagulans (Stocks) Dunal: a critically endangered medicinal herb. Journal of Plant Biochemistry and Biotechnology 18:249–252.
1 Department of Botany, University of Rajasthan, Jaipur 302 004, India
2 Centre for Converging Technologies (CCT), University of Rajasthan, Jaipur 302 004, India
http://link.springer.com/article/10.1007/BF03263330
DOI: 10.1007/BF03263330
Publisher: Springer India

Queries / concerns / issues:
1) The title states “A Critically Endangered Medicinal Herb”. The abstract states “a highly endangered medicinal herb”. The introduction states “Overexploitation and the reproductive failure have rendered the species highly vulnerable to complete extinction.” Yet, the IUCN does not list this plant as having any of these statuses (http://www.iucnredlist.org/search). It is highly emotive language like this, without suitable support from any source, that is problematic, because it may be bloating a situation of a plant that may perfectly well be growing in every nook and cranny. Think about it, would a reviewer or editor be more prone to accepting a protocol for a “highly or critically endangered medicinal plant faced with extinction”, or for a “medicinal herb”? This phenomenon seems to be symptomatic of many studies originating from India, and deserves greater examination. Consequently, this aspect has been pointed out here to stimulate further examination of the literature and discussion. If the authors have concrete proof and literature to prove and support their claims, then they should present it publicly, even if not in English.
2) Agar concentration of medium not reported.
3) The commercial source and grade of all reagents is not defined, except for phloroglucinol and choline chloride. None of the reagents, or their commercial source, used for RAPD, are defined, nor is the model and maker of the thermocycler employed.
4) “Twelve RAPD primers were taken” The source of the primers and the identity of the 12 primers used is not indicated anywhere. Only one primer is specified in Fig. 1F (OPA-19).
5) There are concerns about the statistical analyses (Fischer’s LSD) in Tables 1 and 2. The comparisons are odd, or oddly represented (ordering/ranking).
6) The number of buds that developed from shoots and shoot tips from in vitro shoots was assessed in Table 2. However, nowhere in the methodology is there any explanation of this protocol or comparison.

“Acknowledgements: We thank Council of Scientific and Industrial Research (CSIR), New Delhi for the financial support in the form of a R&D project: CSIR-38(1178)/EMR-II/07. Rohit Jain and Arunima Sinha also thank CSIR for the award of Senior Research Fellowships.”

PubPeer:
https://pubpeer.com/publications/AADA9B0647004DBA5CA0EAFFD7243F#fb26119

Reply
1. Withania queries says:
  
  March 5, 2015 at 5:59 pm
  
  P1
  Jafar Valizadeh, Moharm Valizadeh (2009) In vitro callus induction and plant regeneration from Withania coagulans: a valuable medicinal plant. Pakistan Journal of Biological Science 12(21):1415–1419.
  This publisher (Asian Network for Scientific Information) is listed at: http://scholarlyoa.com/publishers/
  http://www.ncbi.nlm.nih.gov/pubmed/20128512
  http://www.scialert.net/fulltext/?doi=pjbs.2009.1415.1419
  http://scialert.net/abstract/?doi=pjbs.2009.1415.1419
  http://scialert.net/qredirect.php?doi=pjbs.2009.1415.1419&linkid=pdf (open access)
  DOI: 10.3923/pjbs.2009.1415.1419
  
  P2
  Jafar Valizadeh, Moharm Valizadeh (2011) Development of efficient micropropagation protocol for Withania coagulans (Stocks) Dunal. African Journal of Biotechnology 10(39):7611–7616.
  1 Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran.
  2 Research Center of Medicinal and Aromatic Plants, University of Sistan and Baluchestan, Zahedan, Iran.
  http://www.ajol.info/index.php/ajb/article/view/94819
  http://www.isabb.academicjournals.org/journal/AJB/article-abstract/A4AB8EC35370
  http://www.academicjournals.org/article/article1380883438_Valizadeh%20and%20Valizadeh.pdf (open access)
  doi: 10.5897/AJB11.075 (has DOI, but cannot be linked to PubPeer)
  This publisher (Academic Journals) is listed at: http://scholarlyoa.com/publishers/
  
  Queries / concerns / issues:
  1) In P1, abstract claims 75% survival of acclimatized plants while the text claims 90%.
  2) Fig. 1D of P1 is apparently the same as Fig. 1B of P2. Also, Fig. 1F of P1 is apparently the same as Fig. 1D of P2. Apart from apparent figure duplication, the most serious part, if indeed the figures are the same, is that this is impossible. P1 represents in vitro plants that are derived from a callus-mediated route while P2 represents plants derived from a direct route (not through callus). In other words, it is impossible to derive the exact same plants from two completely independent processes.
  3) P2 does not reference P1 (i.e., does not acknowledge its existence despite being the exact same authors).
  
  ACKNOWLEDGEMENTS
  “This research work was conducted at the Research Center of Medicinal and Aromatic Plants, University of Sistan and Baluchestan, Zahedan, Iran. The authors sincerely acknowledge the deputy of research of Sistan and Baluchestan University, Zahedan, Iran, for financial assistance under project number 86016-87/4/13. Thanks are also due to Majid Jafari, Department of Plant Pathology, College of Agriculture and Natural Resources of Saravan, Iran, for his help and kind co-operation.”
  
  PubPeer:
  https://pubpeer.com/publications/40E403FA640A8089FC158AF975772C#fb26184
  
  Reply
2. Withania queries says:
  
  March 5, 2015 at 11:38 pm
  
  The following papers have been added here since they all refer to the same plant. Most of these papers have no DOI, and those that do have a DOI cannot be linked to PubPeer. Thus, this seems the most logical place to add them to further the discussion about the problems in the literature related to this medicinal plant.
  
  Abouzid SF 1, El-Bassuony AA 2, Nasib A 3, Khan S 3, Qureshi J 3, Choudhary MI 3 (2010) Withaferin a production by root cultures of Withania coagulans. International Journal of Applied Research in Natural Products 3:23–27.
  1 Department of Pharmacognosy, Faculty of Pharmacy, University of Beni-Sueif, Beni-Sueif, Egypt.
  2 Basic Science Department, Industrial Education College, Beni-Sueif University, Beni-Sueif, Egypt.
  3 H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
  http://www.ijarnp.org/index.php/ijarnp/article/view/32
  http://www.ijarnp.org/index.php/ijarnp/article/viewFile/32/32 (open access)
  Publisher: Healthy Synergies Publications
  No DOI.
  
  Queries / concerns / issues:
  1) The commercial source and grade of all reagents (except for the grade of HPLC) is not defined. Light intensity, medium pH of liquid cultures, agar concentration of solid medium for seed germination, rinses after seed surface sterilization, all important aspects, are not described.
  2) Dry weights were used to determine a growth index. However, it is unclear for how long roots were dried and at what temperature, or if until constant weight.
  
  Leila Edalatifard 1, Seyed Ali Mohammad Modares Sanavy 1, Hossain Askari 2 (2014) The optimum condition under light and media for seed germination of Withania coagulans. International Journal of Farming and Allied Sciences 3:722–728.
  Journal listed at http://scholarlyoa.com/individual-journals/
  1. Department of Agronomy, Tarbiat Modares University, Tehran, Iran
  2. Department of Biotechnology, Faculty of New Technologies Engineering, Shahid Beheshti University, Tehran, Iran
  http://ijfas.com/2014-3-7/
  http://ijfas.com/wp-content/uploads/2014/08/722-728.pdf (open access)
  No DOI.
  
  Queries / concerns / issues:
  1) The commercial source and grade of all reagents is not defined. Light source, medium pH, carbon source not described.
  2) “Seeds of Withania coagulans were purchased from the local market.” But the authors are from Egypt and Pakistan, so local is from which country?
  3) The reference for B5 medium, or Gamborg medium, nor indicated (Gamborg et al. 1968). It is: Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension culture of soybean root cells. Exp Cell Res 50(1): 151-158.
  4) The authors claim to have sampled seeds of 12 ecovars from wild populations in Sistan and Baluchestan Province. Wikipedia (http://en.wikipedia.org/wiki/Sistan_and_Baluchestan_Province) indicates that “The province is the largest in Iran, with an area of 181,785 km²”. However, the map that the authors show in Fig 1 is useless, namely a rough sketch of the province within Iran. Given the massive area of this province, it would have been important to provide a map of the province only, with very specific locations, with geographical coordinates, of the exact sampling sites, so that the reader can judge if these are sufficiently separated populations. Without knowing this geographic distance between sampled populations, there is no way of knowing if this is one factor influencing the differences in seed germination.
  5) The acknowledgements state “The authors are thankful Dr. Craker and Dr. Imanoe.” Thank them for what? The full identities are not known, nor is their institution. Is the first person acknowledged Lyle Craker, an expert medicinal plant researcher? That could be odd, given the errors/misses in this paper.
  6) Reference list is problematic. For example, Afolayan et al. (2002), not referenced in the text. In the text “Kanna and (2013)” (p. 722) listed, but none such reference can be found in the reference list. There is a Khan (2004) in the reference list, but this is not cited in the text. There are several other similar cases, i.e., unreliable and inconsistently used citations.
  
  Syed Abdullah Gilani 1,2, Akira Kikuchi 1, Kazuo N. Watanabe 1 (2009) Genetic variation within and among fragmented populations of endangered medicinal plant, Withania coagulans (Solanaceae) from Pakistan and its implications for conservation. African Journal of Biotechnology 8(13):2948–2958.
  1 Gene Research Center, Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba Ibaraki, 305-8572, Japan.
  2 Department of Botany, Kohat University of Science and Technology (KUST), Kohat, Pakistan.
  DOI: 10.5897/AJB09.525 (but DOI cannot link to PubPeer)
  http://www3.iupui.academicjournals.org/journal/AJB/article-abstract/6D6E7377782
  http://www3.iupui.academicjournals.org/article/article1379923642_Gilani%20et%20al.pdf (open access)
  Journal listed at http://scholarlyoa.com/individual-journals/
  
  Queries / concerns / issues:
  1) Plants were sampled in Pakistan. DNA analyses were conducted in Japan. There is no information about how plant material was effectively transported between countries without tissue oxidation.
  2) “15 PBA primers sets were used for the current study (Tables 2 and 3)” (p. 2949). But, Table 3 states “Details of 13 PBA primer-sets”. This discrepancy is very important because surely polymorphism could be influenced by the number of primers used?
  3) The commercial source and grade of all reagents is not defined for DNA extraction, EtBr or for the agarose used. The model and maker of the spectrophotometer and thermal cycler is not defined.
  4) Several minor scientific writing errors, e.g., micro written as u, ethydium should be ethidium, etc.
  5) Last sentence of Discussion: “However, for sustainable harvesting of W. coagulans, it is necessary to provide complete guidelines to the local communities in a published form for proper plant collection, harvesting of fruits and drying and storage methods to protect the habitat from the over-exploitation of natural resources (Gilani et al., 2007).” However, this reference does not refer to W. coagulans (Gilani SA, Kikuchi A, Shinwari ZK, Khattak ZI, Watanabe KN (2007). Phytochemical, Pharmacological and Ethnobotanical Studies of Rhazya stricta Decne. Phytother. Res. 21: 301-307.).
  
  Bhanwar Lal Jat 1, Girraj Prasad Meena 2, CR Choudhary 3, Raaz K Maheshwari 4, Garima Jeswani 5 (2014) In vitro propagation of Withania coagulance [sic] through seedling segment (epicotyledonary node). International Journal of Chemistry and Pharmaceutical Sciences 2:979–989.
  1 Department of Botany, SBRM Govt PG College, Nagaur, Rajasthan
  2 PhD Scholar, Mewar University, Gangrar, Chittorgarh, Rajasthan
  3 Pro-President of Mewar University, Gangrar, Chittorgarh, Rajasthan
  4 Department of Chemistry, SBRM Govt PG College, Nagaur, Rajasthan
  5 Department of Physiology, SN Medical College, Jodhpur, Rajasthan, India
  Received: 10 May 2014, Accepted: 18 June 2014, Published Online: 27 July 2014
  http://www.pharmaresearchlibrary.com/in-vitro-propagation-of-withania-coagulance-through-seedling-segment-epicotyledonary-node/
  http://www.pharmaresearchlibrary.com/wp-content/uploads/2014/08/IJCPS2116.pdf (open access)
  This publisher (Pharma Research Library) is listed at: http://scholarlyoa.com/publishers/
  Curiously, the publisher (different journal) was featured here:
  http://scholarlyoa.com/2015/03/03/shortest-ever-review-article-published/
  No DOI.
  
  Queries / concerns / issues:
  1) The Latin name of the plant is incorrectly spelt (species) throughout the manuscript. It should be coagulans but is written as coagulance (error throughout the whole paper). In the first line of the introduction, it is written with a double error: coaguulance. Did the authors not read the literature carefully? The most concerning part of this error is that the authors also exchanged the correct species names in the entire literature for the wrong name, resulting in at least 5 incorrect references (see reference list).
  2) The scientific writing is indescribable. One can ascertain this from the very first sentence of the abstract, which states “The seeds of Withania coaguulance . were germinated which elongated after 4-5 weeks.” The list is far too long (almost every sentence has an error or problems); readers are encouraged to read the paper in detail to observe an unlimited list of scientific writing errors. This is a serious didactic problem: students who may be looking for information about this medicinal plant and who access papers like this, full of errors, are likely to believe what they read and then propagate the errors in their own papers or reports. For example, what are “seedling expants”?
  3) The entire first paragraph (243 words) of the introduction is full of facts yet not a single supporting reference to support these multiple claims.
  4) Introduction: “We now describe the isolation and structure elucidation of two new withanolides, coagulin 111 and with as omidienone 121.” This paper does not describe any new withanolides. Was this text perhaps “borrowed” from another study?
  5) The first ever study on the use of nodal explants to micropropagate this plant was by Jain et al. (2009) (Jain R, Sinha A, Kachhwaha S, Kothari SL (2009) Micropropagation of Withania coagulans (Stocks) Dunal: a critically endangered medicinal herb. J Plant Biochem Biotechnol 18:249–252. DOI: 10.1007/BF03263330). This is a widely accessible paper in a well-known Springer journal. Why has it not been discussed, or acknowledged?
  6) “The germplasm (seeds) was collected from various sites.” India is not a small country. Where exactly were the sampling sites, how many in total and how many samples were taken from how many independent mother plants?
  7) The authors claim seed sterilization with Tween-20 and then a few rinses in distilled water. This is highly unlikely and would most likely result in heavy contamination in vitro. Would the authors care to revise their indicated protocol?
  8) “Pure or analytical grade chemicals of E. / C. Merck, British Drug Houses (BDH), Sigma chemical company, USA, Koch-light Laboratories, England, C.H. Boerhringer Sohn Ingelheim Am Rhien, Germany, Reachim, U.S.S.R., Himedia Laboratories, India, Qualigens Fine chemicals, India, and Loba chemical company, India were used throughout the period of study.” But which chemicals and reagents exactly from each supplier were used?
  9) “The amount of Agar-Agar varied from 0.5 – 0.8% and that of sucrose 3 to 4% which was used as a source of carbohydrates” How can anybody who wishes to repeat this protocol do so? Which concentration exactly was used?
  10) “under 1500-2000 lux intensity of yellow and white light” The lighting source is very unclear. Are they yellow because the lamps are old? At least the type of lamps used and the manufacturer should have been indicated. Furthermore, “The temperature, light and humidity were varied according to the experiments.”, but these details are not provided, so it is unclear what stage of the experiment this statement is referring to.
  11) Under rooting: “When the aseptic shoots were raised in sufficient numbers, these were transferred to root inducing media like White’s MS basal, MS 1/2 salt strength 3/4 and 1/4 strength of MS Salts. In vitro produced shoots were also transferred to the other media like B5 basal medium, WP medium and WS medium supplemented with vitamin, amino acids, and various root inducing hormones like NAA, IAA, and IBA. The physical conditions, concentrations and combination of growth regulators, vitamins, amino acids and inorganic salts of media were changed according to the need of culture.” Are the authors trying to describe two distinct organogenic pathways here, indirect (i.e., through callus) and direct (i.e., direct shoot induction)? Why did the authors select different basal media for each process? The reference for MS medium was provided on page 980, but what are the references for White’s, B5, WP and WS? In fact, what are WP and WS media? What does the last sentence even mean, given that the exact conditions under which these parameters change has not been described anywhere?
  12) “Before the establishment of in vitro raised plantlets these were kept in the culture vessel until the nutrients of the medium completely exhausted. This was done to strengthen the plants.” How could the authors tell when the medium was “exhausted”? Could the authors provide supporting evidence for the last sentence’s claim?
  13) “The strengthened plants before transfer to the earthen pots were washed thoroughly with tap water” When transferring plantlets to ex vitro conditions, why did the authors have to wash the whole plant? Were plantlets dirty? Usually only agar is washed gently off roots, but I have never seen entire plantlets being washed. Please explain the logic.
  14) “These plantlets were transferred to pots containing a mixture of vermiculite + sand + gravelli soil in the ratio (1:1:1) or to the pot containing only sand dune soil for hardening and acclimatizing.” Is gravelli a new sort of pasta, or perhaps gravel? How can international readers obtain sand dune soil? Please explain the source of this exquisite soil.
  15) On page 981, there is a massive paragraph (328 words) that explains, in very poor details, the importance of hardening. Firstly, such theoretical details should be restricted to the introduction, but in studies like these, these are basic background facts that do not require an explanation, so the entire text should have been left out of the study altogether, or reduced to one symbolic sentence.
  16) “During acclimatization initially the plantlets were kept covered with glass cover and watered with Hoagland nutrient solution.” No reference provided for Hoagland’s medium.
  17) Since only means and SD’s were provided, it is unclear which results in Tables 1-4 are significantly different from which other results.
  18) The R&D section is extremely painful to read, let alone decipher what the authors wrote. Consequently, the main findings, or only the most important ones, simply cannot be distinguished.
  19) Where is the data that describes the difference in growth resulting from the use of the multiple (at least 6-8) basal media?
  20) It is not clear which shoots (i.e., from which shoot induction treatment(s)) were used for rooting experiments.
  21) The figure legends are extremely broad and do not define exact media or PGR concentrations being observed. For example: “Figure 2: Effect of Cytokinins and auxins on shoot multiplication”
  22) The pots used for acclimatization are pretty shabby (see Fig. 5). The pots and plants in both left and right photos look remarkably similar, although the location of the photo and a few extra/fewer props appear visible.
  23) The paper was published in 2014. Yet, the only references that the authors could produce were from 1965-1987. Not a single other reference of the other about 10 tissue culture studies of this plant were referenced. Despite this, the authors conclude: “As suggested in the published literature, very less significant micropropagation work has been done on this plant species.” An extremely poorly written discussion and gross mischaracterization and representation of the literature.
  24) The reference list is full of errors.
  25) A lot of very highly ranked individuals were thanked in the acknowledgements. Could the authors please explain exactly what sort of encouragement or scientific advice was provided by each?
  
  “Acknowledgement: The authors express deep sense of gratitude & heartfelt thanks to Dr Ramesh Joshi Lecturer in Dept of Botany, Govt PG College Ajmer, for providing lab facility. Sincere thanks is extended to Prof Ashok Gadiya, Chairman of Mewar University, Chittorgarh, Prof. C.B. Gena, Former Vice-chancellor of Maharaja Ganga Singh University Bikaner and Prof. Bhagirath Singh , Former Vice-chancellor of MDS University, Ajmer, Rajasthan, whose continuous encouragement and constant help to carry out this research work.”
  
  Vandana Gupta 1, Bipin Bihari Keshari 2 (2013) Withania coagulans Dunal (Paneer Doda): a review. International Journal of Ayurvedic and Herbal Medicine 3(5):1136–1144.
  1 Ph. D., Scholar, Department of Kayachikitsa, Faculty of Ayurveda, I. M. S., Banaras Hindu university, Varanasi (India)
  2 Ph. D., Scholar, Department of Samhita & Sanskrit, Faculty of Ayurveda, I. M. S., Banaras Hindu university, Varanasi (India)
  http://www.interscience.org.uk/index.php/archive/24-volume-3-issue-5-september-october-2013
  http://interscience.org.uk/v3-i5/3%20ijahm.pdf (open access)
  No DOI.
  The publisher (http://www.interscience.org.uk/) is listed at http://scholarlyoa.com/publishers/
  
  This is a review on a medicinal plant written by two PhD scholars. And it shows. Poorly written, ample grammatical and scientific writing errors, information unsupported by literature and general errors and comments that underscore the value and credibility of what has been written.
  
  Prakash Chandra Gupta (2012) Withania coagulans Dunal – an overview. International Journal of Pharmaceutical Science: Reviews and Research 12:68–71.
  Department of Zoology, K. N. Government P. G. College, Gyanpur, S. R. N., Bhadohi, India
  http://globalresearchonline.net/journalcontents/v12-2/013.pdf (open access)
  No DOI.
  The publisher (http://globalresearchonline.net/) is listed on Jeffrey Beall’s http://scholarlyoa.com/publishers/
  
  Photos on page 68 of the flowers and fruits appear to have been used from the internet, without due attribution to the source (e.g., http://www.flickr.com; http://www.zimbio.com; naturalherbs.tradeindia.com). Readers may verify this by adding the term “Withania coagulans” to Yahoo or Google and clicking in image results. It is difficult to verify the original source and whether the sources indicated on Yahoo and Google represent the original sources, or not. Independent of the actual source, the fact that the original source might not have been that of the authors deserves to be queried. Can the authors please provide the original files as proof that these are their images?
  
  Rohit Jain, Sumita Kachhwaha, S. L. Kothari (2012) Phytochemistry, pharmacology, and biotechnology of Withania somnifera and Withania coagulans: a review. Journal of Medicinal Plants Research 6: 5388–5399.
  Department of Botany, University of Rajasthan, Jaipur, India–302004.
  doi: 10.5897/JMPR12.704 (but cannot link to PubPeer)
  http://wwmw.academicjournals.org/journal/JMPR/article-abstract/7E1E1F121678
  http://www.academicjournals.org/article/article1380706253_Jain%20et%20al.pdf
  The publisher, Academic Journals (Nigeria), is listed on Jeffrey Beall’s http://scholarlyoa.com/publishers/
  
  Photos on page 5390 of the plant and fruits of Withania somnifera appear to have been lifted straight from the internet, without due attribution to the source (withfriendship.com; http://www.feenkraut.de; http://www.ashwagandhahealthbenefits.com). Readers may verify this by adding the term “Withania somnifera” to Yahoo or Google and clicking in image results. It is in fact difficult to verify the original source and whether the sources indicated on Yahoo and Google represent the original sources, or not. One possible explanation is that these authors are the original copyright holders of these images, but then a public declaration of this, with proof, would be required, to set aside all doubt. For example, even the photo on Google images under http://www.ashwagandhahealthbenefits.com shows that the copyright of one of the photos belongs to Henriette Kress at http://www.henriettesherbal.com . Independent of the actual source, the fact that the original source might not have been that of the authors deserves to be queried. Can the authors please provide the original files as proof that these are their images?
  
  One has to also question the sources of Figures 2 and 3, the chemical structures of the withanolide skeleton, withaferin A and withanolide A since the images are not only very fuzzy (suggesting that they were not designed in ChemDraw or a similar organic chemistry software), but their structural representations are different (Fig 2 vs Fig 3). Nowhere do the authors indicate that these figures of these structures are from another source(s). The authors should thus present the original files as proof of originality, or correct the paper by indicating the actual source of the figures (e.g., web-site). Can the authors please provide the original files as proof that these are their images?
  
  Reply
3. Withania queries says:
  
  March 6, 2015 at 2:05 pm
  
  Mirjalili MH, Moyano E, Bonfill M, Cusido RM, Palazón J (2011) Overexpression of the Arabidopsis thaliana squalene synthase gene in Withania coagulans hairy root cultures. Biologia Plantarum 55: 357–360.
  1 Department of Agriculture, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, 1983963113, Tehran, Iran
  2 Departament de Ciencies Experimentals i de la Salut. Universitat Pompeu Fabra, E-08003, Barcelona, Spain
  3 Laboratori de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, E-08028, Barcelona, Spain
  http://link.springer.com/article/10.1007/s10535-011-0054-2
  DOI: 10.1007/s10535-011-0054-2
  
  There is an apparent splice (vertical line) between lanes 3 and 4 of the virD1 gene gel in Figure 1. The fact that two gels may have been spliced together has not been indicated in the figure legend. Could the authors provide the two original gels or explain if in fact this gel consists of two spliced gels?
  
  PubPeer:
  https://pubpeer.com/publications/88D835F612ACFF158F57536ACD7C1E#fb26247
  
  Reply
4. Withania queries says:
  
  May 13, 2015 at 1:05 pm
  
  Claims made in the following Withania paper are being questioned at PubPeer.
  
  Hossein M. Mirjalili 1, Seyyed M. Fakhr-Tabatabaei 1, Mercedes Bonfill 2, Houshang Alizadeh 3, Rosa M. Cusido 2, Alireza Ghassempour 4, Javier Palazon 2 (2009a) Morphology and withanolide production of Withania coagulans hairy root cultures. Engineering in Life Sciences 9: 197-204
  1. Department of Horticultural Sciences, Faculty of Agriculture, University of Tehran, Karaj, Iran
  2. Laboratori de Fisiologia Vegetal, Facultat de Farmacia, Universitat de Barcelona, Avda. Diagonal 6, 08028 Barcelona, Spain
  3. Department of Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
  4. Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, Tehran, Iran
  http://onlinelibrary.wiley.com/doi/10.1002/elsc.200800081/abstract
  DOI: 10.1002/elsc.200800081
  
  PubPeer:
  https://pubpeer.com/publications/A9A71D3D71E34300533A57CB45429F
  
  Reply
5. Withania queries says:
  
  May 13, 2015 at 1:07 pm
  
  Queries about a Withania paper have been raised at PubPeer.
  
  Rohit Jain 1, Arunima Sinha 1, Devendra Jain 1, Sumita Kachhwaha 1,2, S. L. Kothari 1,2 (2011) Adventitious shoot regeneration and in vitro biosynthesis of steroidal lactones in Withania coagulans (Stocks) Dunal. Plant Cell, Tissue and Organ Culture 105:135–140.
  1 Department of Botany, University of Rajasthan, Jaipur 302004, India
  2 Centre for Converging Technologies (CCT), University of Rajasthan, Jaipur 302 004, India
  http://link.springer.com/article/10.1007%2Fs11240-010-9840-3
  DOI: 10.1007/s11240-010-9840-3
  
  PubPeer:
  https://pubpeer.com/publications/C7ADF2936A19A48A309A1497F90E1D
  
  Reply
Breast cancer and plant lectins query says:

March 6, 2015 at 2:02 pm

Expression of antigen tf and galectin-3 in fibroadenoma
Itandehui Belem Gallegos 1, Eduardo Pérez-Campos 2, Margarito Martinez 2, Miguel Ángel Mayoral 1, Laura Pérez 1, Sergio Aguilar 1, Edgar Zenteno 3, Maria del Socorro Pina 1, Pedro Hernández 1
1 Centro de Investigaciones en Ciencias Medicas y Biológicas Facultad de Medicina, Universidad Autónoma Benito Juárez de Oaxaca, 68020, Oaxaca, Mexico.
2 Unidad de Investigación en Bioquímica, Instituto Tecnológico de Oaxaca, Oaxaca, Mexico.
3 Laboratorio de Inmunología, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico 04510, Mexico.
Received: 30 August 2012; Accepted: 18 December 2012; Published: 24 December 2012
DOI: 10.1186/1756-0500-5-694
http://www.biomedcentral.com/content/pdf/1756-0500-5-694.pdf
http://download.springer.com/static/pdf/361/art%253A10.1186%252F1756-0500-5-694.pdf?auth66=1425590149_46f627868cebb9707efd95361e8ca202&ext=.pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532378/

Concern:
The photos used in Fig. B2 and Fig. C2 appear to be identical, simply inverted 180 degrees (upside down) and slight difference in contrast. The figure legend states that they are very different things, however:
“Artocarpus integrifolia lectin recognizes ducts in healthy (B1) and fibroadenoma samples (B2). Arachis hypogaea recognizes ducts in healthy (C1) and in fibroadenoma samples (C2).”

PubPeer:
https://pubpeer.com/publications/23265237

Reply
Hippophae rhamnoides query says:

March 7, 2015 at 2:09 pm

Claim: Apparently duplicated figures/tables.

In the first PubPeer entry listed below, the first author, Song Lou, responds as follows: “I am the first author, please give me a little time to prepare the explanation, I will give the reply asap, including all the questions: citations, figure, discussions.”

PubPeer
https://pubpeer.com/publications/7CD18F66577E6DEB568A84FCCE09CB#fb26249
https://pubpeer.com/publications/D7E0A209E0955B39361BBBC6DE3292#fb26250

http://pubs.acs.org/doi/abs/10.1021/ie201494k
Synthesis of Functional Adsorption Resin and Its Adsorption Properties in Purification of Flavonoids from Hippophae rhamnoides L. Leaves
Song Lou †‡, Zhenbin Chen †§, Yongfeng Liu †‡, Helin Ye †‡, and Duolong Di *†
† Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
‡ Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
§ State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials, Lanzhou University of Technology, Lanzhou, 730050, PR China
Ind. Eng. Chem. Res., 2012, 51 (6), pp 2682–2696
DOI: 10.1021/ie201494k
Publication Date (Web): January 10, 2012
Copyright © 2012 American Chemical Society
*Phone: +86-931-496-8248. Fax: +86-931-827-7088. E-mail:[redacted].

http://pubs.acs.org/doi/abs/10.1021/jf300633g
http://www.ncbi.nlm.nih.gov/pubmed/22655534
Synthesis of Resins with Ionic Liquids for Purification of Flavonoids from Hippophae rhamnoides L. Leaves
Song Lou †‡ and Duolong Di *†#
† Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People’s Republic of China
‡ Graduate University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
# Centre of Resource Chemical and New Material, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Qingdao 266100, People’s Republic of China
J. Agric. Food Chem., 2012, 60 (26), pp 6546–6558
DOI: 10.1021/jf300633g
Publication Date (Web): June 1, 2012
Copyright © 2012 American Chemical Society
*Phone: +86-931-496-8248. Fax: +86-931-827-7088. E-mail: [redacted].

Reply
1. Hippophae rhamnoides query says:
  
  March 7, 2015 at 4:45 pm
  
  François-Xavier Coudert has laid claim to those requests, providing a useful and detailed summary, as follows:
  https://pubpeer.com/publications/F47D8A92175EF42AEBE9D2CA4B4940#fb26219
  “For the record, and to recap: here is the email I sent to the editors of the three journals. Now let’s wait and hear the authors’ point of view.
  
  ——————
  
  Dear Editors,
  
  I write to you report some issues raised on the PubPeer post-publication peer-review website about similarities and replication of figures and tables between three published papers:
  
  – Ind. Eng. Chem. Res. 2012, 51, 2682−2696, DOI: 10.1021/ie201494k
  – J. Agric. Food Chem. 2012, 60, 6546−6558, DOI: 10.1021/jf300633g
  – Chem. Phys. Chem. 2015, in press, DOI: 10.1002/cphc.201402614
  
  The similarities that were noted include:
  
  – Figure 2 of IECR paper is identical to Figure 2 of JAFC, with no attribution in either legend. Same for Figure 3 of JAFC, which is identical to panels (a) and (c) of IECR Figure 3. If the systems are indeed identical (which is not entirely clear for the text, but would explain why the figures are identical), the earlier source (IECR) should have been referenced in the JAFC figures.
  
  – The SEM image of “original MARs” in CPC Figure 3 is the same as IECR Figure 4 left (SEM image of “DDM-0”).
  
  – Tables 2, 4 and 5 of JAFC and CPC papers show the exact same values (6 significant digits) even though they were measured/fitted on chemically different systems (the JAFCS paper is about Mim/MARs = N-methylimidazole/MARs; the CPC paper is about Dim/MAR = n-decylimidazolium/MAR).
  
  – Table 3 in JAFC (Mim/MARs) is identical to columns 1, 2 and 4 of Table 3 from CPC (on DIm/MARs).
  
  – Figure 4 in JAFC and CPC are nearly identical, but not exactly identical data, again on Mim/MAR vs. DIm/MAR respectively.
  
  – Figure 8 from CPC (on DIm/MAR) is identical to Figure 7 from JAFC (on Mim/MARs). One can note that in the Figure 7 from JAFC, the caption says “Mim/MARs”, but the graph itself says “Dim/MARs” (although Dim/MARs are not discussed anywhere in the text).”
  
  Reply
2. Hippophae rhamnoides query says:
  
  May 18, 2015 at 1:28 pm
  
  Two papers related to these claims have now been retracted:
  http://retractionwatch.com/2015/05/18/improper-citation-pubpeer-comment-snowballs-into-double-retraction-in-phys-chem-journal/
  
  Reply
African violet query says:

March 18, 2015 at 10:26 pm

Zahra Ghorbanzade, Mohammad Ahmadabadi (2014) An improved system for rapid in vitro regeneration of Saintpaulia ionantha. Plant Tissue Culture and Biotechnology 24(1): 37-45.
Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, 35 km Tabriz-Maraqeh Road, Tabriz, Iran
Doi: 10.3329/ptcb.v24i1.19194
http://www.baptcb.org/ptc/Full_article/ptc24_1_04.pdf
http://www.banglajol.info/index.php/PTCB/article/view/19194

Queries / concerns / errors:
1) Abstract: what is an “adaptation system” for leaf explants? The term “adaptation” appears to be used incorrectly to describe “acclimatization”.
2) Abstract: “we developed a highly efficient and time-saving in vitro regeneration protocol” There is absolutely no evidence from the manuscript that this protocol is faster than any other previously reported protocol for African violet.
3) Botanical name for plant used is incorrect. Listed as Saintpaulia ionantha Wendl. but should be Saintpaulia ionantha H. Wendl.
4) Introduction. “most of the methods are largely time-consuming”. Is any tissue culture protocol not time consuming? “Also, in most of the protocols for in vitro propagation of African violets, shoot regeneration has been considered as the most important step, however, successful root induction and uninterrupted robust growth are critical for rapid and efficient plant hardening and adaptation. It is, therefore, necessary to optimize in vitro regeneration systems for rapid and efficient shoot and root induction with no significant effects on the plant phenotype. Several factors are involved in optimizing a tissue culture system; therefore, that the combination of appropriate concentrations of plant growth regulators is considered as the most important one. In this study, we aimed at developing a rapid shoot regeneration and subsequent root formation system for efficient multiplication of African violets from leaf and petiole segments.” Despite these claims of apparently creating a more efficient protocol, the authors provide absolutely no evidence from the literature what the problems with previous successful protocols were, and why an “improvement” was required.
5) “The plant segments were then washed with sterile water under aseptic conditions and cultured on MS.” MS supposedly refers to Murashige and Skoog (1962) medium. Despite this, MS s never defined and the appropriate reference is never provided. Furthermore, the authors refer incorrectly to Linsmeier and Skoog (1965) medium as RM medium, or revised MS medium, to give a tone of originality, but this is completely incorrect. Linsmeier and Skoog medium is always abbreviated as LS.
6) “For leaf culture, leaves of young sterile plants were cut in” Young = how old? Sterile = in vitro established? If yes, then absolutely no information is provided about these mother plants.
7) Inconsistent use of terms: refers interchangeably between hormones, growth regulators, and plant growth regulators to refer to the exact same substance.
8) Commercial source and grade of all chemicals and reagents not indicated.
9) “Three mm long root sections of sterile plants were cultured on the optimized medium.” The abstract and other parts of the methodology do not indicate that roots were also an explant, even though the results section provides data.
10) “In addition, MS supplemented with different plant growth regulators has been evaluated for shoot elongation as well for root formation and growth from in vitro regenerated shoots.” Absolutely no details provided about what the PGRs for root induction were, what the exact explants used for root induction experiments were, or what the age of plant material used for rooting trials was.
11) “thidiazuron (TDZ) and GA3 were filter-sterilized (0.2 μm, Whatman, UK) and added to the medium after autoclaving.” There is absolutely no explanation why these two PGRs were added, to induce what, or the concentrations tested.
12) R&D: Claims of somatic embryogenesis without any histological or cytological proof, not showing samples from all the representative stages.
13) R&D, 2nd line: “protocol for African violets (Saintpaulia ionantha Wendl.) was developed” not only is the common name incorrect, so too is there no need to define the full botanical name every time. Lax scientific writing.
14) R&D: “Our initial studies using two basic media including MS and Revised‐MS (RM) (Linsmaier and Skoog 1965), fortified with 1 mg/l BAP and 1 mg/l NAA indicated that the RM basic medium is more suitable for African violet regeneration (data not shown).” Although this statement refers to data of trials not reported (but which should have been included in this paper), an observation of Fig. 1, left photo, would appear to contradict this claim, where the same concentrations of these PGRs leads to darkened callus, and no green shoot development.
15) “It should be mentioned that on BAP containing media, regeneration occurred mainly through direct organogenesis, while the addition of TDZ promoted somatic embryogenesis (Fig. 1).” This conclusion makes no sense and is not supported either by the visual evidence presented in Fig. 1, or even by the data in Table 1, which shows massive amounts of shoots and callus forming in the presence of TDZ.
16) “We have tested this medium for shoot regeneration from petiole, internode and root explants. High efficiency rapid regeneration was obtained from petiole and internode explants. The results were comparable to those obtained from leaf explants (Fig. 2B and data not shown). However, for root explants, plant regeneration occurred through callus induction with lower efficiency (50%) (Data not shown). Also, the same protocol has been successfully used for shoot regeneration from at least five varieties of African violets. Similar high shoot regeneration rates were observed for all varieties, indicating genotype-independency of the developed protocol (Data not shown).” It is estimated that about 2/3 of the actual experimental protocol is supported by claims based on “data not shown”. How can so much data not be show for conclusions to be considered valid and for this paper to be considered an “original research paper”?
17) “The results showed that GA3 has positive effects on shoot multiplication of African violet cultures; however, shoot elongation as well as root formation have not been affected significantly (Fig. 2C).” How did the authors derive a statistically valid conclusion from a photo?
18) “Rapid root induction and elongation is one of the most important steps toward fast and successful production of in vitro regenerated shoots. However, this issue has not been considered in most of the protocols developed for in vitro propagation of African violets.” This is a totally false statement. Several previous studies on African violet have shown excellent rooting responses in vitro. Did the authors even bother to examine the literature carefully? As one random example, see Khan et al. (2007).
19) Absolutely no details about how plantlets derived form in vitro should be acclimatized were provided in the M&M section, and no indication from what treatments exactly the potted plants shown in Fig. 3B and 3C are derived.
20) “Acknowledgments: This research was supported by the Azarbaijan Shahid Madani University and the Biotechnology Development Council of the I. R. of Iran.”

It is honestly difficult to understand how a plant tissue culture specialist journal could have approved the publication of this manuscript with this many errors.

References:
Khan S, Naseeb S, Ali K (2007) Callus induction, plant regeneration and acclimatization of African violet (Saintpaulia ionantha) using leaves as explants Pak. J. Bot. 39: 1263-1268
Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassay with tobacco tissue culture. Physiol Plant 15: 473-495.

Pubpeer:
https://pubpeer.com/publications/5849257D78F0544E0F7FF11CB7C229

Reply
1. African violet query says:
  
  March 19, 2015 at 10:29 pm
  
  Mithila J 1, Hall JC 1, Victor J.M.R. 2, Saxena PK 3 (2003) Thidiazuron induces shoot organogenesis at low concentrations and somatic embryogenesis at high concentrations on leaf and petiole explants of African violet (Saintpaulia ionantha Wendl.). Plant Cell Reports 21: 408–414.
  1 Department of Environmental Biology, University of Guelph, Ontario, Canada N1G 2W1
  2 International Paper Corp, Bainbridge, Georgia, USA
  3 Department of Plant Agriculture, University of Guelph, Ontario, Canada N1G 2W1
  Doi: 10.1007/s00299-002-0544-y
  http://link.springer.com/article/10.1007%2Fs00299-002-0544-y
  
  Queries / concerns / errors:
  1) This is one of the pioneering studies of African violet of the 21st C. and thus any errors in this paper are quite significant as subsequent studies that relied on information from this paper may have been incorrectly influenced.
  2) The first error begins with the botanical name, which is incorrect. Listed as Saintpaulia ionantha Wendl. but should be Saintpaulia ionantha H. Wendl. Could this explain, perhaps, why Ghorbanzade and Ahmadabadi (2014) erred? https://pubpeer.com/publications/5849257D78F0544E0F7FF11CB7C229
  3) The commercial source of the plant growth regulators used is not indicated.
  4) The basal assumption of the manuscript may be incorrect. The authors claim that < 2.5 µM TDZ (thidiazuron) that shoots formed while at concentrations from 5-10 µM, somatic embryos formed. At least, that’s what the abstract states. But the result contradicts this claim by stating “Somatic embryos were observed in explants after 18-20 days of culture on medium containing 2.5-5 µM TDZ” (p. 411). Yet, Fig 5e and Fig 6, which apparently show somatic embryos and shoots, respectively, show that in both cases, there is vascular continuity with the explant tissue, indicating that they are one and the same structure, i.e., shoots. The same error is mirrored in Fig 1. Leaf hairs or trichomes do not form on somatic embryos (see, for example, Fig. 4B of Boutilier et al. 2002), making the classification of Fig 1b structures as somatic embryos incorrect. Finally, the authors do not show the sequential development of somatic embryos into different stages (globular, heart-shaped, torpedo-shaped, cotyledonary) and they also do not show somatic embryos with a bipolar structure germinating, thus calling into serious question the entire premise for classifying these structures as somatic embryos. The loose characterization to differentiate the two structures is further confirmed in the M&M section: “The regenerants that emerged with true leaves from the cut surface of the explant were recorded as shoots, whereas the structures that appeared globular and loosely attached on the surface of the explant were scored as somatic embryos.” Finally, the epidermis of Fig 5e structure is continuous with that of the mother explant tissue, indicating that this is a shoot, and not a somatic embryo, which would have its own independent epidermis.
  5) I am of the opinion that the entire basal premise for this manuscript is incorrect, and thus all claims made herein are also incorrect. The analyses made in the several figures and tables are impressive, but the entre basal presumption that the authors were dealing with distinct organs appears to be incorrect. If incorrect, then the analyses would be meaningless in their entirety, except perhaps for Fig. 4 data, which clumps (for some unknown reason) shoot and somatic embryo data together, as “regenerants”. Thus, the grand claims made in the Discussion, thus would appear to be invalid: “The most interesting aspects of our study on the regeneration of African violet are: (1) TDZ induced regeneration via both organogenesis and somatic embryogenesis in the same tissue; (2) the number of shoots and somatic embryos induced by TDZ was concentration-dependent.” (p. 413, right column)
  6) Results: “Leaf and petiole explants, which were cultured in medium containing either 2,4-D alone or in combination with TDZ, formed callus (data not shown). A combination of plant growth regulator treatments containing CPPU, NAA, and BA induced prolific shoot organogenesis (data not shown).” So much important, and informative, negative data was not shown. And, a thorough search of the literature does not apparently reveal any further publications by these authors on this plant, thus the scientific community will never know the details about these trials or experiments. This emphasizes the risks of adding (data not shown) to results sections.
  7) “and the embryos further developed into complete plants when cultured on MS basal medium.” (p. 409-410) There is absolutely zero evidence of this anywhere in the manuscript. The different pathways to plantlet development between the apparently two different developmental pathways would have been important (vital?) to show, but absolutely no evidence was provided.
  8) “Acknowledgements: This research was supported by the Natural Science and Engineering Research Council of Canada. The post graduate scholarship to JM from Natural Science and Engineering Council of Canada is gratefully acknowledged. We thank Dr. R.A. Fletcher for helpful discussions and comments.”
  
  Reference
  Kim Boutilier, Remko Offringa, Vijay K. Sharma, Henk Kieft, Thérèse Ouellet, Lemin Zhang, Jiro Hattori, Chun-Ming Liu, André A. M. van Lammeren, Brian L. A. Miki, Jan B. M. Custers, Michiel M. van Lookeren Campagne (2002) Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth. The Plant Cell, Vol. 14, 1737–1749. http://www.plantcell.org/content/14/8/1737.full
  
  PubPeer:
  https://pubpeer.com/publications/5849257D78F0544E0F7FF11CB7C229
  
  Reply
Arabidopsis queries says:

March 23, 2015 at 7:03 am

Banding in Fig. 2D of the following paper is being questioned at PubPeer:
https://pubpeer.com/publications/8177FC45E736E8CE858D38A2F6ACB2#fb27411
Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis
Javier Gallego-Bartolomé a, Eugenio G. Minguet a, Federico Grau-Enguix a, Mohamad Abbas a, Antonella Locascio a, Stephen G. Thomas b, David Alabadí a, Miguel A. Blázquez a
Author Affiliations
a Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain;
b Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
PNAS 109(33): 13446–13451
doi: 10.1073/pnas.1119992109
http://www.pnas.org/content/109/33/13446
http://www.pnas.org/content/109/33/13446.full.pdf?with-ds=yes
Edited by Mark Estelle, University of California at San Diego, La Jolla, CA, and approved July 10, 2012 (received for review December 5, 2011)

Reply
1. Arabidopsis queries says:
  
  March 23, 2015 at 5:05 pm
  
  The authors respond on the same day: “Here are the original full-scan images as saved from the LAS-3000 imager (http://imgur.com/02vQP8K). The first image corresponds to the anti-GFP blot, and the second one is the anti-HA blot. As you can check yourself, image in Fig. 2D has not been fabricated. Signed: Javier Gallego-Bartolomé (e-mail redacted), David Alabadí (e-mail redacted), Miguel Blázquez (e-mail redacted).”
  
  Reply
Barley seed stress queries says:

March 29, 2015 at 9:40 pm

Journal of Plant Physiology Volume 166, Issue 1, 1 January 2009, Pages 72–79
Investigation into the mechanism of stimulation by low-concentration stressors in barley seedlings
Erika Kovács a, b, , , Péter Nyitrai a, Pálma Czövek a, Mihály Óvári c, Áron Keresztes b
a Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, H-1117 Budapest, Pázmány P. sétány 1/C, Hungary
b Department of Plant Anatomy, Eötvös Loránd University, H-1117 Budapest, Pázmány P. sétány 1/C, Hungary
c Department of Organic Chemistry, Eötvös Loránd University, H-1117 Budapest, Pázmány P. sétány 1/A, Hungary
Received 20 November 2007, Revised 20 February 2008, Accepted 22 February 2008, Available online 21 April 2008
http://www.sciencedirect.com/science/article/pii/S0176161708000679

Acta Biologica Szegediensis Volume 52(1):179-180, 2008
On the mechanism of stimulation by low-concentration stressors in barley seedlings
Erika Kovács 1,2, Péter Nyitrai 1*, Áron Keresztes 2
1 Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, Budapest, Hungary
2 Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
No information about publication dates.
http://www2.sci.u-szeged.hu/ABS/2008/Acta%20HP/52179.pdf

Fig 1 of 2009 paper appears to be identical to Fig 2 of 2008 paper.
Fig 3 of 2009 paper appears to be identical to Fig 1 of 2008 paper.

2009 paper does not indicate the existence of the 2008 paper.

Pubpeer:
https://pubpeer.com/publications/BDEF10E1D044510CEEC9A2FBF6C0AA

Reply
Arabidopsis query says:

April 6, 2015 at 7:44 pm

Apparently missing error bars in a figure of an Arabidopsis paper were queried at PubPeer. An interesting discussion about other possible issues related to the size of the existent error bars and qRT-PCR ensued. Within 4 days, the authors recognized a problem, and are seeking to issue an erratum.

https://pubpeer.com/publications/3C81ABE9A2710ECDC9DA3FE53695E6#fb28024
Javier Gallego-Bartolomé, David Alabadí, Miguel A. Blázquez
Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
DELLA-Induced Early Transcriptional Changes during Etiolated Development in Arabidopsis thaliana
DOI: 10.1371/journal.pone.0023918
PLoS ONE 6(8): e23918.
Editor: Mohammed Bendahmane, Ecole Normale Superieure, France
Received: June 16, 2011; Accepted: August 1, 2011; Published: August 31, 2011
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023918

Gels of another 2012 PNAS paper by the Blázquez group, also on Arabidopsis, had been questioned at PubPeer, but the authors provided the original blots to counter the criticisms and concerns:
https://pubpeer.com/publications/8177FC45E736E8CE858D38A2F6ACB2

Reply
Tomato wilt query says:

April 8, 2015 at 12:47 am

International Journal of Current Microbiology and Applied Sciences
ISSN: 2319-7706 Volume 3 Number 9 (2014) pp. 839-846
Exopolysaccharides (EPS) mediated Induction of systemic resistance (ISR) in Bacillus – Fusarium oxysporum f.sp. lycopersici pathosystem in tomato (var. PKM-1)
P. Thenmozhi, S. Dinakar
Department of Microbiology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India
http://www.ijcmas.com/vol-3-9/P.Thenmozhi%20and%20S.%20Dinakar.pdf

Science Park Research Journal, Vol-2, Issue-52, 17 July 2014
Positive role of Bacillus exopolysaccharides (EPS) on the enhancement of induced systemic resistance (ISR) against Fusarium oxysporum f.sp. lycopersici in tomato
P. Thenmozhi, S. Dinakar
Department of Microbiology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India
http://www.scienceparks.in/ArticlePDF/94.pdf

Vast tracts of text appear to be similar in the introduction of both papers. No contact email for either of the authors.

Science Park Journals is listed here: http://scholarlyoa.com/publishers/
IJCMAS is listed here: http://scholarlyoa.com/individual-journals/

Reply
Nanoparticles from potato water says:

April 8, 2015 at 6:05 am

The creation of silver nanoparticles from water derived from boiled potatoes is being questioned:
https://pubpeer.com/publications/5CFC15B55C7D120F51491BCE699568#fb28137
http://www.sciencedirect.com/science/article/pii/S138614251500222X
Photocatalytic activity of biogenic silver nanoparticles synthesized using potato (Solanum tuberosum) infusion
Kaushik Roy, C.K. Sarkar, C.K. Ghosh, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2015)

Reply
Arabidopsis stomata query says:

April 8, 2015 at 4:23 pm

The Plant Cell August 2014 vol. 26 no. 8 3358-3371
http://www.plantcell.org/content/26/8/3358.full.pdf+html
http://www.plantcell.org/content/26/8/3358# (open access)
Manipulation of Mitogen-Activated Protein Kinase Kinase Signaling in the Arabidopsis Stomatal Lineage Reveals Motifs That Contribute to Protein Localization and Signaling Specificity
Gregory R. Lampard 1, Diego L. Wengier 1, Dominique C. Bergmann 1,2
1 Howard Hughes Medical Institute, Stanford University, Stanford, California 94305-5020 USA
2 Department of Biology, Stanford University, Stanford, California 94305-5020 USA
DOI: 10.1105/tpc.114.127415

Fig 6 D and E appear to be the same image, even though they are noted as Fama in ext and SPCH in int, respectively.

24 hours after the issue was posted at PubPeer, the authors responded:
“Dear Unreg Sub,

I reread our manuscript and you are absolutely correct. There is an error in Figure 6 and the same image has been placed in D and E. It is likely the image was introduced sometime in the multiple rounds of reorganization of these multipanel figures. To ensure the correct images for the respective genotypes are put in, we are currently looking through our archived image data and will alert the journal when we have identified the correct images.

In the meantime, the experimental data for which these panels serve as visual representations is quantified in Table 2.
MKK5DNext 0/28 had clusters at the FAMA stage (ie, the typical phenotype is WT)
MKK5DNint 3/62 had inhibition at the SPCH stage (ie, the typical phenotype is WT)
Because these data were derived from multiple independent transformations, we are confident that the phenotypes for these two variants at the two stages are correct.

Thank you for catching this error and alerting us so that it may be corrected in the public sphere.

Dominique Bergmann”

https://pubpeer.com/publications/B1E91FB1C91B8F6D91AA5DBE32798B#fb28149

Reply
Madagascar periwinkle query says:

April 26, 2015 at 8:40 am

Notulae Scientia Biologicae 6(2):167-172
Print ISSN 2067-3205; Electronic 2067-3264
Somatic Embryos in Catharanthus roseus: A Scanning Electron Microscopic Study
Junaid ASLAM, Abdul MUJIB, Mahendra Prasad SHARMA
Department of Botany, Jamia Hamdard (Hamdard University), New Delhi-110062, India
http://notulaebiologicae.ro/index.php/nsb/issue/view/239
http://notulaebiologicae.ro/index.php/nsb/article/view/9337
Open access; No DOI

Saudi Journal of Biological Sciences Volume 21, Issue 5, November 2014, Pages 442–449
Somatic embryo mediated mass production of Catharanthus roseus in culture vessel (bioreactor) – A comparative study
A. Mujib, Muzamil Ali, Tasiu Isah, Dipti
Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110062, India
Received 20 March 2014, Revised 20 May 2014, Accepted 22 May 2014, Available online 1 June 2014
doi:10.1016/j.sjbs.2014.05.007
http://www.sciencedirect.com/science/article/pii/S1319562X14000461
Open access.

There are concerns about the similarity of two figures in both papers.

PubPeer:
https://pubpeer.com/publications/593680294EA1DB9357802F6D18C1B8

Reply
1. Madagascar periwinkle query says:
  
  May 13, 2015 at 12:56 pm
  
  Figures in several papers by the same group on Madagascar periwinkle are being queried at PubPeer.
  
  2006a
  Somatic Embryogenesis Plant Cell Monographs Volume 2, 2006, pp 259-270
  Embryogenesis in Catharanthus roseus: Roles of Some External Factors in Proliferation, Maturation and Germination of Embryos
  A. Junaid, A. Mujib, M. A. Bhat, A. Ilah, M. P. Sharma
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, 110062 New Delhi, India
  http://link.springer.com/chapter/10.1007%2F7089_030
  DOI: 10.1007/7089_030 (cannot link to PubPeer)
  
  2006b
  Plant Cell, Tissue and Organ Culture March 2006, Volume 84, Issue 3, pp 325-332
  Somatic embryo proliferation, maturation and germination in Catharanthus roseus
  A. Junaid, A. Mujib, M.A. Bhat, M.P. Sharma
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Faculty of Science, Hamdard University, New Delhi, India
  http://link.springer.com/article/10.1007/s11240-005-9041-7
  DOI: 10.1007/s11240-005-9041-7
  
  2007a
  Biologia Plantarum December 2007, Volume 51, Issue 4, pp 641-646
  Somatic embryogenesis and plant regeneration in Catharanthus roseus
  A. Junaid, A. Mujib, M. A. Bhat, M. P. Sharma, J. Šamaj
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Faculty of Science, Hamdard University, New Delhi-110062, India
  J. Šamaj: Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
  http://link.springer.com/article/10.1007/s10535-007-0136-3
  DOI: 10.1007/s10535-007-0136-3
  
  2007b
  Plant Growth Regulation March 2007, Volume 51, Issue 3, pp 271-281
  Growth regulators affect primary and secondary somatic embryogenesis in Madagaskar periwinkle (Catharanthus roseus (L.) G. Don) at morphological and biochemical levels
  A. Junaid, A. Mujib, M. P. Sharma, Wei Tang
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110 062, India
  Wei Tang: Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
  http://link.springer.com/article/10.1007/s10725-007-9171-5
  DOI: 10.1007/s10725-007-9171-5
  
  2008
  Plant Biotechnology Reports August 2008, Volume 2, Issue 3, pp 179-189
  Cultural conditions affect somatic embryogenesis in Catharanthus roseus L. (G.) Don
  Junaid Aslam, A. Mujib, Samar Fatima, M. P. Sharma
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110 062, India
  http://link.springer.com/article/10.1007/s11816-008-0060-9
  DOI: 10.1007/s11816-008-0060-9
  
  2010
  In Vitro Cellular & Developmental Biology – Plant August 2010, Volume 46, Issue 4, pp 348-353
  Variations in vinblastine production at different stages of somatic embryogenesis, embryo, and field-grown plantlets of Catharanthus roseus L. (G) Don, as revealed by HPLC
  Junaid Aslam, Abdul Mujib, Zohra Fatima, Maheshwar Prasad Sharma
  Department of Botany, Cellular Differentiation and Molecular Genetics Section, Hamdard University, New Delhi 110 062, India
  http://link.springer.com/article/10.1007/s11627-010-9290-y
  DOI: 10.1007/s11627-010-9290-y
  
  2011
  Acta Physiologiae Plantarum March 2011, Volume 33, Issue 2, pp 473-480
  Influence of freezing and non-freezing temperature on somatic embryogenesis and vinblastine production in Catharanthus roseus (L.) G. Don.
  Junaid Aslam, A. Mujib, M. P. Sharma
  Cellular Differentiation and Molecular Genetic Section, Department of Botany, Hamdard University, New Delhi 110062, India
  http://link.springer.com/article/10.1007/s11738-010-0569-8
  DOI: 10.1007/s11738-010-0569-8
  
  2014
  Saudi Journal of Biological Sciences Volume 21, Issue 5, November 2014, Pages 442–449
  Somatic embryo mediated mass production of Catharanthus roseus in culture vessel (bioreactor) – A comparative study
  A. Mujib, Muzamil Ali, Tasiu Isah, Dipti
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110062, India
  Received 20 March 2014, Revised 20 May 2014, Accepted 22 May 2014, Available online 1 June 2014
  http://www.sciencedirect.com/science/article/pii/S1319562X14000461
  DOI: 10.1016/j.sjbs.2014.05.007
  
  PubPeer:
  2006b: https://pubpeer.com/publications/F2ABAE4C7D40B7DBE9227006F87891
  2007a: https://pubpeer.com/publications/C1BE7ACF42DECF80BDE3A8F645235D
  2007b: https://pubpeer.com/publications/50EF29FF8054D75CFC4F6C5FF27A93
  2008: https://pubpeer.com/publications/9A243AAA295D6587FFC1FF0C7EA952
  2010: https://pubpeer.com/publications/49970AA9FDBB6AC36E436BE67F8901
  2011: https://pubpeer.com/publications/7AD1F236632FCD39FA14BC4617F78D
  
  Reply
2. Madagascar periwinkle (and onion) query says:
  
  May 16, 2015 at 10:26 am
  
  Three more Madagascar periwinkle papers by the same group of authors are being questioned at PubPeer.
  
  2012a
  Current Biotechnology, 2012, 1, 217-226
  Protoplast Isolation, Culture and Plant Regeneration in Catharanthus roseus (L.) G. Don via Somatic Embryogenesis
  Mehpara Maqsood 1, A. Mujib 1, Dipti Tonk 1, M.Z. Abdin 2
  1 Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110062, India
  2 Department of Biotechnology, Hamdard University, New Delhi-110062, India
  http://www.researchgate.net/publication/263930454_Current_Biotechnology_Mehpara_2012
  http://benthamscience.com/journal/abstracts.php?journalID=cbiot&articleID=100803
  DOI: 10.2174/2211550111201030217
  
  2012b
  Biotechnology 11: 37-43 (2012)
  Synthetic Seed Development and Conversion to Plantlet in Catharanthus roseus (L.) G. Don.
  Mehpara Maqsood, A. Mujib, Zahid H. Siddiqui
  http://www.scialert.net/fulltext/?doi=biotech.2012.37.43
  http://ascidatabase.com/ascidetail.php?doi=biotech.2012.37.43&kw=
  DOI: 10.3923/biotech.2012.37.43
  
  2012c
  Plant Growth Regulation November 2012, Volume 68, Issue 2, pp 111-127
  Catharanthus roseus alkaloids: application of biotechnology for improving yield
  Abdul Mujib, Abdul Ilah, Junaid Aslam, Samar Fatima, Zahid Hameed Siddiqui, Mehpara Maqsood
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110062, India
  http://link.springer.com/article/10.1007/s10725-012-9704-4
  DOI: 10.1007/s10725-012-9704-4
  
  2012a: https://pubpeer.com/publications/A22AB5B1ABEE4DC732B27506072E14
  2012b: https://pubpeer.com/publications/E42C342A5B8A57331F508CC3C29DA2
  2012c: https://pubpeer.com/publications/EB54ECED7BD320C141E8F60AABB4C3
  
  In addition, queries about figures in two onion papers, also by the same group, are being queried.
  
  Anales de Biologia 32: 1-9
  Somatic embryogenesis in Allium sativum L. (cv. Yamuna Safed 3): Improving embryo maturation and germination with PGRs and carbohydrates.
  Sekh Abdul Nasim, Abdul Mujib, Rashmi Kapoor, Samar Fatima, Junaid Aslam & Mahmooduzzafar
  Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi 110062, India
  http://www.researchgate.net/publication/228509604_Somatic_embryogenesis_in_Allium_sativum_L.(cv._Yamuna_Safed_3)_Improving_embryo_maturation_and_germination_with_PGRs_and_carbohydrates
  http://www.um.es/analesdebiologia/numeros/32/
  http://revistas.um.es/analesbio/article/view/139401/0
  http://www.um.es/analesdebiologia/numeros/32/PDF/32_2010_01.pdf
  No DOI.
  
  versus
  
  The Open Horticulture Journal, 2013, 6, 9-18
  Somatic Embryogenesis of Some Member Ornamental Genera of Amaryllidaceae and Allied Families: the Similarities and Differences
  A. Mujib 1, S. Banerjee 2, M. Maqsood 1, P. D. Ghosh 3
  1 Cellular Differentiation and Molecular Genetics Section, Department of Botany, Hamdard University, New Delhi – 110062, India
  2 CSIRO Publishing, Melbourne, Victoria 3066, Australia
  3 Department of Genetics, University of Kalyani, Kalyani, West Bengal-741 235, India
  http://www.researchgate.net/publication/271835422_Somatic_Embryogenesis_of_Some_Member_Ornamental_Genera_of_Amaryl-lidaceae_and_Allied_Families_the_Similarities_and_Differences
  http://benthamopen.com/contents/pdf/TOHORTJ/TOHORTJ-6-9.pdf
  No DOI.
  
  Reply
3. Madagascar periwinkle query says:
  
  May 26, 2015 at 6:59 pm
  
  The authors have apparently responded stating, among other things, the following:
  
  “Even without these figures, the publication could have been made quite easily. We will be happy to remove or replace of those if it is absolutely necessary; it does not anyway impact at all the articles.”
  
  “We expect constructive suggestion, people may have different interest of analysis. Anyway, we still apologise for this unnecessary, avoidable, unintentional errors. Lesson is learnt, now onwards utmost care will be taken and far more professional attitude will be shown in selection of photographs in our future publication endeavour. We the first author and corresponding author regret to all co-authors, associated staff, administrator to whom inconvenience is caused. Life should move on by closing the past. Finally, we are extremely sorry and apologize for this unintentional incidence.”
  
  The key question: how and when will the authors correct the literature?
  https://pubpeer.com/publications/593680294EA1DB9357802F6D18C1B8#fb30712
  
  Reply
Berry question says:

April 26, 2015 at 10:29 pm

Paper 1
Adventitious shoot regeneration in a bioreactor system and EST-PCR based clonal fidelity in lowbush blueberry (Vaccinium angustifolium Ait.)
Samir C. Debnath
Atlantic Cool Climate Crop Research Centre, Agriculture and Agri-Food Canada, P.O. Box 39088, 308 Brookfield Road, St. John’s, Newfoundland and Labrador A1E 5Y7, Canada
Scientia Horticulturae 128(2) (2011) 124-130
doi: 10.1016/j.scienta.2011.01.012
Received 5 November 2010, Revised 13 January 2011, Accepted 13 January 2011, Available online 5 February 2011
http://www.sciencedirect.com/science/article/pii/S0304423811000173

Paper 2
Bioreactors and molecular analysis in berry crop micropropagation – A review
Samir C. Debnath
Atlantic Cool Climate Crop Research Centre, Agriculture and Agri-Food Canada, P.O. Box 39088, 308 Brookfield Road, St. John’s, Newfoundland and Labrador, Canada A1E 5Y7
Canadian Journal of Plant Science (2011) 91: 147-157
doi: 10.4141/CJPS10131
Received 10 June 2010, accepted 23 August 2010
http://pubs.aic.ca/toc/cjps/91/1
http://pubs.aic.ca/doi/pdf/10.4141/cjps10131 (open access)

There are concerns that the same image are representing two completely different plants.

Dr. Debnath is an Editor-in-Chief of paper 1 journal.

Pubpeer:
https://pubpeer.com/publications/975920570A46D93A15F253D6AB7E0A (paper 1)
https://pubpeer.com/publications/FC84EB091248845E2F7749A918BB1A (paper 2)

Reply
Cassia query says:

April 28, 2015 at 3:59 pm

Concerns have been raised about possible figure duplications across four Cassia manuscripts.
It should be noted that Prof. Mohammed Anis’ (AMU) papers are being heavily critiqued at PubPeer:
https://pubpeer.com/search?q=anis&sessionid=019B2F8AAFC3E5A5BB6F (some entries are not related)

2007a paper
Acta Physiologiae Plantarum June 2007, Volume 29, Issue 3, pp 233-238
In vitro shoot multiplication and plantlet regeneration from nodal explants of Cassia angustifolia (Vahl.): a medicinal plant
Iram Siddique, M. Anis
Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
DOI: 10.1007/s11738-007-0029-2
http://link.springer.com/article/10.1007%2Fs11738-007-0029-2

2010 paper
Applied Biochemistry and Biotechnology November 2010, Volume 162, Issue 7, pp 2067-2074
In Vitro Adventitious Shoot Regeneration via Indirect Organogenesis from Petiole Explants of Cassia angustifolia Vahl.—a Potential Medicinal Plant
Iram Siddique 1, M. Anis 1/2, I. M. Aref 2
1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
2. Department of Plant Production, College of Food & Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
DOI: 10.1007/s12010-010-8982-4
http://link.springer.com/article/10.1007%2Fs12010-010-8982-4

2012 paper
Advances in Micropropagation of a Highly Important Cassia species- A Review. Chapter 9, 191-206
M. Anis 1,2, Iram Siddique 3, Ruphi Naz 1, M. Rafique Ahmed 1, Ibrahim M. Aref 2
1 Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, India
2 Department of Plant Production, College of Food & Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
3 Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
Intech: http://cdn.intechopen.com/pdfs-wm/35412.pdf (open access)
In: New Perspectives in Plant Protection, Edited by Prof. Ali R. Bandani

2013 paper
Agroforestry Systems June 2013, Volume 87, Issue 3, pp 583-590
Stimulation of in vitro organogenesis from epicotyl explants and successive micropropagation round in Cassia angustifolia Vahl.: an important source of sennosides
Iram Siddique 1, Saad Bin Javed 2, Muneera R. Al-Othman 1, M. Anis 2
1. Department of Botany and Microbiology, College of Science, Female Centre for Scientific and Medical Colleges, King Saud University, P.O. Box 22452, Riyadh, 11495, Saudi Arabia
2. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
DOI: 10.1007/s10457-012-9578-5
http://link.springer.com/article/10.1007%2Fs10457-012-9578-5

PubPeer:
2007a paper: https://pubpeer.com/publications/9A4E9C53A90591E6DE54A9F9832251
2010 paper: https://pubpeer.com/publications/3055D20E1353B44E66CD23D0CEDA5D
2013 paper: https://pubpeer.com/publications/B077757B53536DA815692AC141D93E

Reply
Butterfly pea query says:

April 28, 2015 at 6:05 pm

There are concerns about possible figure and data duplications in the following two papers.

Seemab Mukhtar 1, Mohammad Anis 1/2, Naseem Ahmad 1 (2010)
In Vitro Optimization of Phytohormones on Micropropagation in Butterfly Pea (Clitoria ternatea L.)
Journal of Herbs, Spices & Medicinal Plants, 16:2, 98-105
1 Plant Biotechnology Laboratory, Department of Botany , Aligarth Muslim University , Aligarh, India
2 Department of Plant Production, College of Food and Agriculture , King Saud University , Riyadh, Saudi Arabia
Taylor and Francis
DOI: 10.1080/10496475.2010.499310
http://www.tandfonline.com/doi/abs/10.1080/10496475.2010.499310#

Physiology and Molecular Biology of Plants October 2012, Volume 18, Issue 4, pp 381-386
Influencing micropropagation in Clitoria ternatea L. through the manipulation of TDZ levels and use of different explant types
Seemab Mukhtar 1, Naseem Ahmad 1, Md Imran Khan 1, Mohammad Anis 1/2, Ibrahim M. Aref 2
1. Plant Biotechnology laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
2. Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, PO Box 2460, Riyadh, 11451, Saudi Arabia
DOI: 10.1007/s12298-012-0136-4
http://link.springer.com/article/10.1007/s12298-012-0136-4
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3550560/

Acknowledgements
2010: “The authors appreciate the assistance provided by the Department of Science and Technology, Government of India, under the DST-FIST Program (2005) to the Department of Botany, Aligarh Muslim University.”
2012: “Authors appreciate the financial assistance provided by the University Grants Commission, Govt. of India, under UGC-SAP (DRS-I) program (2009) and Department of Science and Technology (DST) Govt. of India, in the form of DST-FIST program (2011) to the Department of Botany, Aligarh Muslim University.”

PubPeer:
2010: https://pubpeer.com/publications/0B4435E6B9F5A1202B0BA66756E50B
2012: https://pubpeer.com/publications/DD7586286AE40608BB1C4C7BA59497

Reply
1. Butterfly pea (Clitoria) query says:
  
  September 21, 2015 at 5:19 pm
  
  An anonymous commentator, presumably an author, indicates on September 21 2015 that the PMBP paper has been retracted. “The paper published in PMBP 2012, Volume 18, Issue 4, pp 381-386 has been retracted from the journal. Regarding other papers we are in touch with editor of the journal and queries will be addressed shortly.”
  https://pubpeer.com/publications/DD7586286AE40608BB1C4C7BA59497#fb36818
  
  However, no retraction notice can be traced at SpringerLink.
  
  Reply
T says:

April 28, 2015 at 8:47 pm

Please don’t copy-paste pubpeer to this website.

Reply
Sugarcane query says:

April 28, 2015 at 11:52 pm

Concerns about possible figure duplication in two sugarcane papers.

Paper 1
In Vitro Cellular & Developmental Biology – Plant December 2014, Volume 50, Issue 6, pp 766-776
Gamma radiation, in vitro selection for salt (NaCl) tolerance, and characterization of mutants in sugarcane (Saccharum officinarum L.)
Ashok A. Nikam 1/3, Rachayya M. Devarumath 2/3, Mahadeo G. Shitole 4, Vikram S. Ghole 5, Prahlad N. Tawar 1, Penna Suprasanna 6
1. Tissue culture section, Vasantdada Sugar Institute, Manjari (Bk), Pune, 412307, India
2. Molecular Biology and Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk), Pune, 412307, India
3. Department of Biotechnology, University of Pune, Ganeshkhind, Pune, 411007, India
4. Department of Botany, University of Pune, Ganeshkhind, Pune, 411007, India
5. National Institute of Virology, Pashan, Pune, 411021, India
6. Functional Plant Biology, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
http://link.springer.com/article/10.1007/s11627-014-9630-4
DOI: 10.1007/s11627-014-9630-4

Paper 2 (open access)
The Crop Journal 3, 46-56 (2015)
Radiation-induced in vitro mutagenesis system for salt tolerance and other agronomic characters in sugarcane (Saccharum officinarum L.)
Ashok A. Nikam a, Rachayya M. Devarumath b, Akash Ahuja b, Harinath Babu b, Mahadeo G. Shitole c, Penna Suprasanna d⁎
a Tissue Culture Section, Vasantdada Sugar Institute, Manjari (Bk), Pune 412307, India
b Molecular Biology and Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk), Pune 412307, India
c Department of Botany, Pune University, Pune 411007, India
d Plant Stress Physiology & Biotechnology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
DOI: 10.1016/j.cj.2014.09.002
http://www.sciencedirect.com/science/article/pii/S2214514114000828

Pubpeer:
https://pubpeer.com/publications/FEDF8B546B7F4EF887135E600C3987 (paper 1)
https://pubpeer.com/publications/7344E002F91F6673895F3DE6259D14 (paper 2)

Reply
A good example: Arabidopsis says:

April 29, 2015 at 5:19 am

A good example set forth by Cyril Zipfel at TSL (UK)* and Laurent Zimmerli at NTU (Taiwan) in retracting this paper:
doi: http://dx.doi.org/10.1105/tpc.114.125682
The Plant Cell July 2014 vol. 26 no. 7 3201-3219
The Arabidopsis Malectin-Like Leucine-Rich Repeat Receptor-Like Kinase IOS1 Associates with the Pattern Recognition Receptors FLS2 and EFR and Is Critical for Priming of Pattern-Triggered Immunity
Ching-Wei Chen a,1, Dario Panzeri a,1, Yu-Hung Yeh a,2, Yasuhiro Kadot ab,2,3, Pin-Yao Huang a, Chia-Nan Tao a, Milena Roux b,4, Shiao-Chiao Chien a, Tzu-Chuan Chin a, Po-Wei Chu a, Cyril Zipfel b and Laurent Zimmerli a,5
a) Department of Life Science and Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
b) Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom

http://www.plantcell.org/content/26/7/3201
Received April 29, 2014.
Revised June 25, 2014.
Accepted July 13, 2014.
Published July 28, 2014.

https://pubpeer.com/publications/BE9E3ED702A790BA0A0D6D890AE69C#fb29122
“Shortly after publication, we identified irregularities in Figure 6 in Chen et al. (http://www.plantcell.org/content/26/7/3201.long) that was published in 2014 in The Plant Cell. The same blot image is shown twice in Figure 6, once in Figure 6A corresponding to the IP: α-GFP blot for FLS2-GFP and again in Figure 6C as IP: α-GFP for CERK1-GFP. Data for Figure 6 were produced by the first author Ching-Wei Chen from the Zimmerli laboratory. The blot image from Figure 6C is a copy from the IP: α-GFP blot for FLS2-GFP from Figure 6A. When repeating experiments presented in Figure 6C, we realized that we could not reproduce the original results. Instead, the new results suggested possible interaction of IOS1 with CERK1 in Nicotania benthamiana, raising questions about some of the conclusions of the article. This is also questioning the veracity of the work produced by the author Ching-Wei Chen. My coauthors and I feel that retraction of the article is necessary. A retraction statement will be published soon. We are currently repeating all experiments performed by the author Chin-Wei Chen to further clarify the role of IOS1 in Arabidopsis innate immunity. We hope to resubmit a new version of the IOS1 manuscript that can be fully trusted.

All authors are very sorry and embarrassed to have discovered data irregularities. We strongly apologize for publication of manipulated data.”

* Head of The Sainsbury Laboratory:
http://www.tsl.ac.uk/staff/cyril-zipfel/

Reply
1. T says:
  
  April 29, 2015 at 11:06 am
  
  Seriously, whoever you are….stop copy-pasting pubpeer to this website! Your posts have no context and make no sense.
  
  Reply
Tobacco query says:

May 1, 2015 at 9:41 pm

Possible duplicate banding is being questioned about this Plant Cell paper at PubPeer:
https://pubpeer.com/publications/C9707985CC5196B3B464FD27EFDA77#fb29236

Mahdi Khozaei 1, Stuart Fisk 1, Tracy Lawson 1, Yves Gibon 2, Ronan Sulpice 2, Mark Stitt 2, Stephane C. Lefebvre 1, Christine A. Raines 1
1. School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
2. Max-Planck-Institut für Molekulare Pflanzenphysiologie, 114476 Potsdam-Golm, Germany
Overexpression of Plastid Transketolase in Tobacco Results in a Thiamine Auxotrophic Phenotype
http://www.plantcell.org/content/27/2/432
http://www.plantcell.org/content/27/2/432.full.pdf+html
DOI: 10.1105/tpc.114.131011

Prof. Christine A. Raines is the Editor-in-Chief of Journal of Experimental Botany:
http://www.oxfordjournals.org/our_journals/exbotj/editorial_board.html

Reply
1. Tobacco query says:
  
  May 2, 2015 at 3:43 am
  
  The authors respond within 1 day: “I would like to thank our colleagues for drawing our attention to this figure. I have informed our co-authors and the researcher who generated this figure. We are investigating this further and will post our response when we complete this review.”
  
  Reply
Pea aphid says:

May 3, 2015 at 4:37 pm

After oddities in banding in figures of a a pea aphid paper were questioned in March, the authors responded today:
https://pubpeer.com/publications/EC7BBF573009B642F39B3BDAB5FD5B#fb29277

Reply
Tomato vermicomposting says:

May 3, 2015 at 4:45 pm

There are concerns about possible data/text duplication across two tomato vermicomposting papers published in the same year:
https://pubpeer.com/publications/7330346B68423D7E94A247C617BB52 (Scientia Horticulturae)
https://pubpeer.com/publications/EB73B99A3D3FA1EA0A5B0FFF9F6F16 (European Journal of Soil Biology)

Reply
Thrips-borne virus query says:

May 4, 2015 at 8:46 pm

Concerns of possible partial data duplication in two publications.

ASJES, C. J. and BLOM-BARNHOORN, G. J. (2001) Control of aphid-vectored and thrips-borne virus spread in lily, tulip, iris and dahlia by sprays of mineral oil, polydimethylsiloxane and pyrethroid insecticide in the field. Annals of Applied Biology, 139: 11–19.
Bulb Research Centre, P O Box 85, 2160 AB Lisse, The Netherlands
doi: 10.1111/j.1744-7348.2001.tb00125.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7348.2001.tb00125.x/abstract

C.J. Asjes and G.J. Blom-Barnhoorn (2002) Control of aphid vector spread of lily symptomless virus and lily mottle virus by mineral oil/insecticide sprays in Lilium. Acta Horticulturae 570, 277-281
http://www.actahort.org/books/570/570_35.htm

The 2002 paper does not reference the 2001 paper.

PubPeer:
https://pubpeer.com/publications/6EDCBD9624702CA97A072FBEFFCDEC

Reply
Sandersonia flower queries says:

May 4, 2015 at 9:17 pm

Concerns of possible data duplication across three publications:
https://pubpeer.com/publications/0FC58797E3FA0B01AD3870AC830FC0 (2002a)
https://pubpeer.com/publications/DAF5E5776FE29639B714D770F5C663 (2002b)

Scientia Horticulturae Volume 93, Issues 3–4, 19 April 2002a, Pages 321-332
Effects of constant temperature and irradiance on the flower stem quality of Sandersonia aurantiaca
L.J. Davies, I.R. Brooking, J.L. Catley, E.A. Halligan
http://www.sciencedirect.com/science/article/pii/S0304423801003442
DOI: 10.1016/S0304-4238(01)00344-2

Scientia Horticulturae Volume 95, Issues 1–2, 2 August 2002b, Pages 85-98
Effects of day/night temperature differential and irradiance on the flower stem quality of Sandersonia aurantiaca
L.J Davies, I.R Brooking, J.L Catley, E.A Halligan
http://www.sciencedirect.com/science/article/pii/S0304423802000262
DOI: 10.1016/S0304-4238(02)00026-2

Temperature and light requirements for Sandersonia aurantiaca flowering
Jocelyn L. Catley, Ian R. Brooking, Lindsay J. Davies and Elizabeth A. Halligan
The Horticulture and Food Research Institute of New Zealand Ltd., Private Bag 11030, Palmerston North, New Zealand
Acta Horticulturae 570, 105-112
http://www.actahort.org/books/570/570_10.htm

Reply
1. Sandersonia flower query says:
  
  May 13, 2015 at 12:50 pm
  
  The figures/data in a fourth paper are being queried at PubPeer.
  
  Scientia Horticulturae Volume 93, Issue 2, 15 March 2002d, Pages 157–166
  Jocelyn L. Catley, Ian R. Brooking, Lindsay J. Davies and Elizabeth A. Halligan
  Temperature and irradiance effects on Sandersonia aurantiaca flower shape and pedicel length
  http://www.sciencedirect.com/science/article/pii/S0304423801003247
  DOI: 10.1016/S0304-4238(01)00324-7
  
  PubPeer:
  https://pubpeer.com/publications/621310D468C7D3D7E558691E86FE55
  
  Reply
Barley DNA queries says:

May 4, 2015 at 9:38 pm

Concerns of possible figure duplication.

https://pubpeer.com/publications/497B342F95BF66A2BD31403ABB2B15#fb29343

http://www.sciencedirect.com/science/article/pii/S0305440312002142 (open access)
Journal of Archaeological Science Volume 39, Issue 10, October 2012, Pages 3230–3238
Phylogeographic analysis of barley DNA as evidence for the spread of Neolithic agriculture through Europe
Glynis Jones a, , , Huw Jones b, Michael P. Charles a, Martin K. Jones c, Sue Colledge d, Fiona J. Leigh b, Diane A. Lister c, Lydia M.J. Smith b, Wayne Powell e, Terrence A. Brown f
a Department of Archaeology, University of Sheffield, Northgate House, West Street, Sheffield S1 4ET, UK
b NIAB, Huntingdon Road, Cambridge CB 0LE, UK
c McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
d Institute of Archaeology, University College London, 31–34 Gordon Square, London WC1H 0PY, UK
e Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, UK
f Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
Received 24 January 2012, Revised 14 May 2012, Accepted 15 May 2012, Available online 7 June 2012

http://www.biomedcentral.com/1471-2148/11/320/abstract
http://www.biomedcentral.com/content/pdf/1471-2148-11-320.pdf
BMC Evolutionary Biology 2011, 11:320
Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces
Huw Jones 1, Peter Civáň 2,3, James Cockram 1, Fiona J Leigh 1, Lydia MJ Smith 1, Martin K Jones 4, Michael P Charles 5, José-Luis Molina-Cano 6, Wayne Powell 7, Glynis Jones 5 and Terence A Brown 2*
1 NIAB, Huntingdon Road, Cambridge CB3 0LE, UK.
2 Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK.
3 Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B1, 842 15 Bratislava, Slovakia.
4 McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK.
5 Department of Archaeology, University of Sheffield, Northgate House, West Street, Sheffield S1 4ET, UK.
6 IRTA, Av. Alcalde Rovira Roure 191, 25198 Lleida, Spain.
7 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, UK.

Reply
Citrus query says:

May 5, 2015 at 6:41 am

There is no DOI for either paper, so no PubPeer entry.

Omidbaigi, R., Faghih Nasiri, M., Bashiri Sadr, Z. 2002. Hesperidin in Citrus species, quantitative distribution during fruit maturation and optimal harvesting time. Acta Horticulturae (ISHS) 576:91-97
http://www.actahort.org/books/576/576_16.htm

Omidbaigi, R., Faghih Nasiri, M., Bashiri Sadr, Z. 2004.Quantitative distribution of hesperidin in Citrus species, during fruit maturation and optimal harvest time. Natural Product Radiance 3(1; Jan-Feb):12-15
http://nopr.niscair.res.in/bitstream/123456789/9379/1/NPR%203%281%29%2012-15.pdf

The experimental design, methodology, and data of Tables 1 and 2 in both papers appear to be identical. Figures of the 2002 paper were not included in the 2004 paper, but the same results in the text were reported. The 2004 paper does not reference the 2002 paper.

Prof. Omidbaigi has passed away (http://www.omidbaigi.com/sn/staticPages/page/biography).

Reply
Microspore query says:

May 5, 2015 at 4:37 pm

Concerns about possible figure duplication.

Plant Physiology October 2000 vol. 124 no. 2, 523-530
Insights into a key developmental switch and its importance for efficient plant breeding
Mei Wang, Sandra van Bergen, Bert Van Duijn
Department of Applied Plant Sciences, Center for Phytotechnology, Leiden University, The Netherlands
Organisation for Applied Scientific Research, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
Received May 10, 2000; accepted June 6, 2000.
DOI: 10.1104/pp.124.2.523
http://www.plantphysiology.org/content/124/2/523.full
http://www.plantphysiol.org/content/124/2/523.full.pdf+html

Acta Horticulturae (ISHS) 572, 51-57 (2002)
S. van Bergen, M. Wang
Microspore regeneration as a tool for plant breeding: barley microspore regeneration as a model system
http://www.actahort.org/books/572/572_5.htm

PubPeer:
https://pubpeer.com/publications/50120EB4C21C9B84894537D8C75714

Reply
1. Microspore query says:
  
  May 13, 2015 at 12:48 pm
  
  At the same PubPeer address, a comparison is made between figures in the 2000 Plant Physiology paper and a 2008 Springer book chapter listed next:
  
  Plant Embryogenesis Methods In Molecular Biology™ Volume 427, 2008, pp 77-89
  Culture and Time-Lapse Tracking of Barley Microspore-Derived Embryos
  Simone de F. Maraschin, Sandra van Bergen, Marco Vennik, Mei Wang
  http://link.springer.com/protocol/10.1007/978-1-59745-273-1_6
  DOI: 10.1007/978-1-59745-273-1_6
  
  Reply
2. Microspore query says:
  
  May 16, 2015 at 10:32 am
  
  More barley microspore papers being questioned at PubPeer.
  
  1993
  Plant Cell Rep. 12: 661-665 (1993)
  Microspore culture of Hordeum vulgare L.: the influence of density and osmolarity.
  Hoekstra S., van Zijderveld M.H., Heidekamp F., and van der Mark F., 1993.
  DOI: 10.1007/BF00233415
  http://link.springer.com/article/10.1007/BF00233415
  
  1996
  Journal of Plant Physiology Volume 148, Issue 6, 1996, Pages 696–700
  The Interaction of 2,4-D Application and Mannitol Pretreatment in Anther and Microspore Culture of Hordeum vulgare L. cv. Igri
  S. Hoekstra1, 3, , S. Hoekstra1, I.R. Hoekstra1, 4, R.A. Hoekstra2, E. Hoekstra1, 4
  DOI: 10.1016/S0176-1617(96)80370-1
  http://www.sciencedirect.com/science/article/pii/S0176161796803701
  
  1999a
  Anther and Pollen 1999, pp 191-200
  Effects of ABA during the pretreatment of barley anthers on androgenesis of Hordeum vulgare L. cultivars Igri and Digger
  S. van Bergen, M. J. Kottenhagen, R. M. van der Meulen, M. Wang
  DOI: 10.1007/978-3-642-59985-9_18 (DOI cannot link to PubPeer)
  http://link.springer.com/chapter/10.1007/978-3-642-59985-9_18
  
  1999b
  Anther and Pollen 1999, pp 201-210
  Programmed cell death during androgenesis in Hordeum vulgare L.
  M. Wang, S. van Bergen, Gem Lamers, B. J. Oppedijk, R. A. Schilperoort
  DOI: 10.1007/978-3-642-59985-9_19 (DOI cannot link to PubPeer)
  http://link.springer.com/chapter/10.1007%2F978-3-642-59985-9_19
  
  1999c
  Journal of Plant Growth Regulation 18:135–143 (1999)
  The role of abscisic acid in induction of androgenesis: a comparative study between Hordeum vulgare L cvs. Igri and Digger.
  Van Bergen S, Kottenhagen MJ, Van der Meulen RM, Wang M
  DOI: 10.1007/PL00007061
  http://link.springer.com/article/10.1007%2FPL00007061
  
  1999d
  Plant Molecular Biology 39:489–501 (1999)
  Apoptosis in developing anthers and the role of ABA in this process during androgenesis in Hordeum vulgare L.
  Mei Wang 1, Sietske Hoekstra 1;4, Sandra van Bergen 1, Gerda E.M. Lamers 2, Berry J. Oppedijk 1, Maurice W. van der Heijden 1, Wessel de Priester 2, Rob A. Schilperoort 3
  1 Center for Phytotechnology RUL/TNO, TNO Department of Plant Biotechnology, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands
  2 Center for Phytotechnology RUL/TNO, EMCA Unit, Institute of Molecular Plant Sciences, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
  3 Faculty of Mathematics and Natural Sciences, Leiden University, Van Steenisgebouw, Einsteinweg 2, 2333 CC
  Leiden, The Netherlands
  4 Present address: Mogen International N.V., Einsteinweg 97, 2333 CB Leiden, The Netherlands
  DOI: 10.1023/A:1006198431596 (DOI cannot link to PubPeer)
  http://link.springer.com/article/10.1023/A%3A1006198431596
  Received 15 September 1998; accepted in revised form 15 September 1998
  
  1993: https://pubpeer.com/publications/C6D018EAF495DFD4E16845C2822FDA
  1996: https://pubpeer.com/publications/94596C921D13DC692C3655CF86A1CD
  1999c: https://pubpeer.com/publications/27A08A52215482D3508AECA0A7AE3C
  
  In addition, there is a discrepancy in the authorship listed in the actual 1996 paper (PDF) and on Elsevier’s ScienceDirect.
  PDF = S. HOEKSTRA l,3*, S. VAN BERGEN l , I. R. VAN BROUWERSHAVEN l ,4, R. A. SCHILPEROORT 2, and F. HEIDEKAM l,4
  ScienceDirect = S. Hoekstra 1, 3, , S. Hoekstra 1, I.R. Hoekstra 1, 4, R.A. Hoekstra 2, E. Hoekstra 1, 4
  
  Reply
Ginseng query says:

May 5, 2015 at 4:39 pm

Concerns about possible data/table duplication.

In Vitro Cellular & Developmental Biology – Plant September–October 2000, Volume 36, Issue 5, pp 424-428
Improvement of ginsenoside production by jasmonic acid and some other elicitors in hairy root culture of ginseng (Panax ginseng C. A. Meyer)
Kee-Won Yu, Wen-Yuan Gao, Sung-Ho Son, Kee-Yoeup Paek
http://link.springer.com/article/10.1007%2Fs11627-000-0077-4
DOI: 10.1007/s11627-000-0077-4

Acta Horticulturae (ISHS) 597, 237-243 (2003)
Ginsenoside production by hairy root cultures of Panax ginseng C.A. Meyer in bioreactors
K.W. Yu, E.J. Hahn, K.Y. Paek
Research Center for the Development of Advanced Horticultural Technology, Chungbuk National University, Cheongju, Chungbuk 361-763, Korea

PubPeer:
https://pubpeer.com/publications/59C89E1E8EF2887C8E3E4C79F115D0

Reply
Polianthes query says:

May 5, 2015 at 4:41 pm

Concerns about possible data/table duplication.

Scientia Horticulturae Volume 88, Issue 3, 4 May 2001, Pages 235-241
Flower colours and pigments in hybrid tuberose (Polianthes).
Kuang-Liang Huang, Ikuo Miyajima, Hiroshi Okubo, Tsai-Mu Shen, Ta-Shiung Huang
1 Laboratory of Horticultural Science, Faculty of Agriculture, Kyushu University 46-01, Fukuoka 8128581, Japan
2 Department of Horticulture, National Chiayi University, Taiwan, PR China
Accepted 10 August 2000, Available online 14 March 2001
DOI: 10.1016/S0304-4238(00)00213-2
http://www.sciencedirect.com/science/article/pii/S0304423800002132

Acta Horticulturae (ISHS) 570, 367-371 (2002)
Breeding of Colored Tuberose (Polianthes) and Cultural Experiments in Taiwan
Kuang-Liang Huang, Ikuo Miyajima, Hiroshi Okubo, Tsai-Mu Shen, Ta-Shiung Huang
http://www.actahort.org/books/570/570_51.htm

Reply
1. Polianthes query says:
  
  May 5, 2015 at 4:42 pm
  
  PubPeer:
  2001 paper: https://pubpeer.com/publications/884684DE3053873BD6CFD06BDEE456
  
  Reply
Lily query says:

May 5, 2015 at 4:44 pm

Concerns about possible data/table duplication.

Miller, W.B., Chang, A., Legnani, G., Patel, N., Ranwala, A.P., Reitmeier, M., Scholl, S.S. and Stewart, B.B. 2002. Pre-plant bulb dips for height control in LA and Oriental hybrid lilies. Acta Horticulturae (ISHS) 570:351-357
http://www.actahort.org/books/570/570_49.htm

Garry Legnani, Christopher B Watkins, William B Miller. 2004. Low oxygen affects the quality of Asiatic hybrid lily bulbs during dry sale storage and subsequent forcing. Postharvest Biology and Technology 32, 223-233
Department of Horticulture, Cornell University, Ithaca NY 14853, USA
Received 14 April 2003, Accepted 26 October 2003, Available online 9 April 2004
DOI: 10.1016/j.postharvbio.2003.10.008
http://www.sciencedirect.com/science/article/pii/S0925521403002266

PubPeer:
https://pubpeer.com/publications/D25D6178BA7191EBE90D231B7713F0

Reply
1. Lily query says:
  
  May 12, 2015 at 10:07 pm
  
  Additional concerns of possible table/data/figure duplication in two more studies by the Miller group at Cornell University, reported at the same PubPeer address.
  
  Miller, W.B., Chang, A., Legnani, G., Patel, N., Ranwala, A.P., Reitmeier, M., Scholl, S.S. and Stewart, B.B. 2002. Pre-plant bulb dips for height control in LA and Oriental hybrid lilies. Acta Horticulturae (ISHS) 570:351-357
  http://www.actahort.org/books/570/570_49.htm
  
  Anil P. Ranwala, Garry Legnani, Mary Reitmeier, Barbara B. Stewart and William B. Miller. 2002. Efficacy of plant growth retardants as preplant bulb dips for height control in LA and Oriental hybrid lilies. HortTechnology 12(3):426-431.
  http://horttech.ashspublications.org/content/12/3/426.full.pdf+html
  
  Reply
Bromeliaceae fertilization queries says:

May 9, 2015 at 7:17 am

Concerns about possible figure / data / table duplication across 9 papers by the same Belgian team.

https://pubpeer.com/publications/1CEB976A759217ADB6FB6D0B10A4DB
https://pubpeer.com/publications/2B2E4F892F747C8C36C05A719B18D3

Specifically, the following papers are affected.

2002a
Acta Horticulturae (ISHS) 572, 21-28
I. Vervaeke, E. Parton, R. Deroose and M.P. De Proft
Controlling prefertilization barriers by in vitro pollination and fertilization of Bromeliaceae.
http://www.actahort.org/books/572/572_1.htm

2002b
Euphytica 03-2002, Volume 124, Issue 1, pp 75-83
Pollen tube growth and fertilization after different in vitro pollination techniques of Aechmea fasciata.
I. Vervaeke, E. Parton, L. Maene, R. Deroose, M.P. De Proft
http://link.springer.com/article/10.1023/A%3A1015650120583
DOI: 10.1023/A:1015650120583 (DOI cannot link to PubPeer)

2003a
Acta Horticulturae (ISHS) 612, 23-26.
Vervaeke, I., Londers, E., Deroose, R. and De Proft, M.P. 2003.
In vitro pollination and fertilization in Bromeliaceae.
http://www.actahort.org/books/612/612_2.htm

2003b
Acta Horticulturae (ISHS) 624:77-83
Vervaeke, I., Deroose, R. and De Proft, M.P. 2003.
Interspecific and intergeneric hybridization in Bromeliaceae.
http://www.actahort.org/books/624/624_10.htm

2003c
Euphytica 10-2003, Volume 134, Issue 1, pp 47-49
Inheritance of spineless leaves in Aechmea (Bromeliaceae)
I. Vervaeke, J. Wouters, L. Stichelbout, E. Londers, R. Deroose, M.P. De Proft
http://link.springer.com/article/10.1023%2FA%3A1026170602524
DOI: 10.1023/A:1026170602524

2004a
Plant Cell, Tissue and Organ Culture January 2004, Volume 76, Issue 1, pp 67-73
Semi in vivo pollen tube growth of Aechmea fasciata.
I. Vervaeke, R. Delen, J. Wouters, R. Deroose, M.P. De Proft
http://link.springer.com/article/10.1023/A%3A1025836915087
DOI: 10.1023/A:1025836915087 (DOI cannot link to PubPeer)

2004b
Plant Cell, Tissue and Organ Culture January 2004, Volume 76, Issue 1, pp 17-28
Division of the generative nucleus in cultured pollen tubes of the Bromeliaceae.
I. Vervaeke, R. Delen, J. Wouters, R. Deroose, M.P. De Proft
http://link.springer.com/article/10.1023%2FA%3A1025816722684
DOI: 10.1023/A:1025816722684 (DOI cannot link to PubPeer)

2004c
Annales Botanici Fennici 41: 201–208
Morphology of artificial hybrids of Vriesea splendens x Tillandsia cyanea and V. splendens x Guzmania lingulata (Bromeliaceae).
Vervaeke, I., Wouters, J., Londers, E., Deroose, R. & De Proft, M. P.
http://www.sekj.org/AnnBot.html
http://www.sekj.org/PDF/anbf41/anbf41-201.pdf (open access, no DOI)

2005a
Sexual Plant Reproduction June 2005, Volume 18, Issue 1, pp 9-19
The division of the generative nucleus and the formation of callose plugs in pollen tubes of Aechmea fasciata (Bromeliaceae) cultured in vitro.
I. Vervaeke, E. Londers, G. Piot, R. Deroose, M. P. De Proft
http://link.springer.com/article/10.1007%2Fs00497-005-0243-2
DOI: 10.1007/s00497-005-0243-2

Affiliations:
Ine Vervaeke, E. Parton, R. Delen, Reginal Deroose, L. Maene, Jan Wouters, Maurice P. De Proft:
Laboratory of Plant Culture, Catholic University of Leuven, W. De Croylaan 42, B-3001 Heverlee, Belgium
Reginal Deroose:
Deroose Plants NV, Droogte 139, Evergem, Belgium

Also note: ISHS (International Society for Horticultural Science) hosted by KU Leuven.

Other references:
2001a
Acta Horticulturae (ISHS) 552, 43-53
E. Parton, I. Vervaeke, R. Deroose and M.P. De Proft
Interspecific and intergeneric fertilization barriers in Bromeliaceae.
http://www.actahort.org/books/552/552_4.htm

2001b
Euphytica 03-2001, Volume 118, Issue 1, pp 91-97
Prefertilization barriers between different Bromeliaceae
I. Vervaeke, E. Parton, L. Maene, R. Deroose, M.P. De Proft
http://link.springer.com/article/10.1023/A%3A1004016709231
DOI: 10.1023/A:1004016709231

2005b
Plant Cell, Tissue and Organ Culture April 2005, Volume 81, Issue 1, pp 77-82
Influence of arginine, ornithine, DFMO and polyamines on division of the generative nucleus in cultured pollen tubes of Aechmea fasciata (Bromeliaceae)
I. Vervaeke, L. Stichelbout, E. Londers, R. Deroose, M. P. De. Proft
http://link.springer.com/article/10.1007%2Fs11240-004-2726-5
DOI: 10.1007/s11240-004-2726-5

Reply
Ruta graveolens query says:

May 13, 2015 at 12:44 pm

Questions have been raised at PubPeer regarding data in two rue papers.

Mohd Faisal, Naseem Ahmad, Mohammad Anis (2005) In vitro regeneration and mass propagation of Ruta graveolens L.—a multipurpose shrub. HortScience 40(5): 1478-1480.
Plant Tissue Culture Laboratory, Department of Botany, Aligarh Muslim University, Aligarh-202 002, India
http://hortsci.ashspublications.org/content/40/5/1478.abstract
http://hortsci.ashspublications.org/content/40/5/1478.full.pdf+html (open access)
No DOI.

Naseem Ahmad, Mohd Faisal, Mohammad Anis, Ibrahim M. Aref (2010) In vitro callus induction and plant regeneration from leaf explants of Ruta graveolens L. South African Journal of Botany 76:597-600.
http://www.sciencedirect.com/science/article/pii/S0254629910001328
http://fac.ksu.edu.sa/mofaisal/publication/29103
DOI: 10.1016/j.sajb.2010.03.008
Received 23 October 2009, Revised 22 March 2010, Accepted 24 March 2010, Available online 1 May 2010
Edited by Patricia Berjak

PubPeer:
https://pubpeer.com/publications/57F34E3B856AB5E10798749F03E106

Reply
Turkish genetic conservation query says:

May 13, 2015 at 12:45 pm

This case is reported here since there is no DOI so the study cannot be reported at PubPeer.

Acta Horticulturae (ISHS) 598, 17-25 (2003)
Plant Genetic Resources Conservation in Turkey
A. Karagöz
Central Research Institute for Field Crops, PO Box 226, 06042, Ankara, Turkey
http://www.metu.edu.tr/~kayaz/
http://www.agrivivo.net/organization/central-field-crops-research-institute

Kaya, Z., Kun, E. and Guner, A.1997. National plan for in situ conservation of plant genetic diversity in Turkey. Milli Egitim Basimevi, Istanbul, 125 p
Coordinator: Ministry of Environment
Collaborators: Ministry of Agriculture and Rural Affairs ; Ministry of Forestry
Prof. Dr. Zeki KAYA: Dept. of Biological Sciences Faculty of Art and Sciences Middle East Tech.Univ.-Ankara
Prof. Dr. Ekrem KÜN: Dept. of Field Crops Faculty of Agriculture Ankara University-Ankara
Prof. Dr. Adil GÜNER: Dept. of Biology Abant Ýzzet Baysal University-Bolu Ankara

Kindly compare the tables in both publications, as follows:
Table 3 (1997) vs Table 3 AH 2003
Table 4 (1997) vs Table 2 AH 2003
Table 5, bottom (1997) vs Table 4 AH 2003
Table 6 (1997) vs Table 5 AH 2003
Table 13 (1997) vs Table 6 AH 2003

The author does not reference the 1997 report.

Reply
Sandalwood queries says:

May 13, 2015 at 1:11 pm

Queries have arisen at PubPeer about the figures in several sandalwood papers.

P = papers; BC = book chapter.

P1
Bapat, V.A. and P.S. Rao, 1979. Somatic embryogenesis and plantlet formation in tissue culture of sandalwood (Santalum album L.). Annals of Botany 44(5): 629-630.
No DOI.
http://aob.oxfordjournals.org/content/44/5.toc

P2
Bapat, V. A.; Rao, P. S. 1984. Regulatory factors for in vitro multiplication of sandalwood tree (Santalum album Linn.). I. Shoot bud regeneration and somatic embryogenesis in hypocotyl cultures. Proceedings of the Indian Academy of Sciences Plant Science Section B 93(1): 19-27.
No DOI.
https://archive.org/stream/proceedingsofthe020242mbp#page/n23/mode/2up
Now published by Springer? http://link.springer.com/journal/volumesAndIssues/40011

P3
Bapat, V.A. and P.S. Rao, 1988. Sandalwood plantlets from synthetic seeds. Plant Cell Reports 7(6): 434-436.
DOI: 10.1007/BF00269531 (DOI cannot link to PubPeer)
http://link.springer.com/article/10.1007/BF00269531

P4
Bapat, V. A.; Gill, R.; Rao, P. S. 1985. Regeneration of somatic embryos and plantlets from stem callus protoplasts of sandalwood tree (Santalum album L.). Current Science 54(19): 978-982.
No DOI. Open access.
http://www.currentscience.ac.in/php/toc.php?vol=054&issue=19
http://www.currentscience.ac.in/Downloads/article_id_054_19_0978_0982_0.pdf

BC1
Bapat, V.A., Rao, P.S., 1993. Micropropagation of sandalwood (Santalum album L.) and mulberry (Morus indica L.). In: Ahuja, M.R. (Ed.), Micropropagation of Woody Plants. Kluwer Academic Publishers (now Springer), pp. 317–345.
DOI: 10.1007/978-94-015-8116-5_19
http://link.springer.com/chapter/10.1007/978-94-015-8116-5_19

P5
Rao, P.S., Bapat, V.A., 1978. Vegetative propagation of sandalwood plants through tissue culture. Canadian Journal of Botany 56: 1153–1156.
DOI: 10.1139/b78-129
http://www.nrcresearchpress.com/doi/abs/10.1139/b78-129#.VM9RX8v9nIU

BC2
Rao, P.S., Bapat, V.A., 1992. Micropropagation of sandalwood (Santalum album L.). In: Bajaj, Y.P.S. (Ed.), High-Tech and Micropropagation II. Biotechnology in Agriculture and Forestry. Springer, Berlin, pp. 193–210.
DOI: 10.1007/978-3-642-76422-6_10
http://link.springer.com/chapter/10.1007/978-3-642-76422-6_10

P6
Rao, P.S., Bapat, V.A., Mhatre, M., 1984. Regulatory factors for in vitro multiplication of sandalwood tree (Santalum album Linn.). II. Plant regeneration in nodal and internodal stem explants and occurrence of somaclonal variation in tissue culture raised plants. Proceedings of the Indian National Academy of Science: B 50(2): 196–202.
No DOI.
Web-site cannot be traced clearly.

P7
Rao, P.S., Ozias-Akins, P., 1985. Plant regeneration through somatic embryogenesis in protoplast cultures of sandalwood (Santalum album L.). Protoplasma 124(1-2): 80–86.
DOI: 10.1007/BF01279726
http://link.springer.com/article/10.1007%2FBF01279726

There are 4 PubPeer entries:
https://pubpeer.com/publications/225988CDB994AA3E79C90FFA1D4EE0#fb23714 (BC1)
https://pubpeer.com/publications/4D2CB9A98D4CAD786B65F63F07F80F#fb23716 (BC2)
https://pubpeer.com/publications/967ABAFECEB9F4C2BCB4659082B8AA#fb23715 (P5)
https://pubpeer.com/publications/8A5FF81216E3DB38507655CD0E51AC#fb23717 (P7)

Reply
Azalea query says:

May 14, 2015 at 3:54 pm

Concerns about a figure in two azalea papers.

Theoretical and Applied Genetics November 1999, Volume 99, Issue 7-8, pp 1155-1165
Validation of criteria for the selection of AFLP markers to assess the genetic variation of a breeders’ collection of evergreen azaleas
J. De Riek, J. Dendauw, M. Mertens, M. De Loose, J. Heursel, E. Van Bockstaele
DOI: 10.1007/s001220051320
http://link.springer.com/article/10.1007/s001220051320

Acta Horticulturae (ISHS) 521: 203-210 (2000)
De Riek, J., Mertens, M., Dendauw, J., Van Bockstaele, E., De Loose, M. and Heursel, J.
AZALEA (RHODODENDRON SIMSII HYBRIDS) GERMPLASM FROM CHINA ASSESSED BY MEANS OF FLUORESCENT AFLP.
http://www.actahort.org/books/521/521_22.htm

PubPeer:
https://pubpeer.com/publications/B649E8C7678E08BF6C80E6928C1C52

Reply
Wheat mega correction says:

May 14, 2015 at 5:18 pm

A substantially large corrigendum for a 2012 wheat paper.
Original:
Ral, J.-P., Bowerman, A. F., Li, Z., Sirault, X., Furbank, R., Pritchard, J. R., Bloemsma, M., Cavanagh, C. R., Howitt, C. A. and Morell, M. K. (2012), Down-regulation of Glucan, Water-Dikinase activity in wheat endosperm increases vegetative biomass and yield. Plant Biotechnology Journal, 10: 871–882.
1 CSIRO Food Futures National Research Flagship, Canberra, ACT, Australia
2 CSIRO Plant Industry, Canberra, ACT, Australia
3 Research School of Biology, The Australian National University, Canberra, ACT, Australia
doi: 10.1111/j.1467-7652.2012.00711.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00711.x/abstract

Corrigendum:
http://onlinelibrary.wiley.com/doi/10.1111/pbi.12046/abstract
http://onlinelibrary.wiley.com/doi/10.1111/pbi.12046/epdf

Reply
Radish query says:

May 18, 2015 at 5:44 pm

A query at PubPeer regarding a set of radish papers.
https://pubpeer.com/publications/9D16FEE4C42ED3378951F6097DAF8C

Effect of Brassinosteroids on Germination and Seedling Growth of Radish (Raphanus sativus L.) under PEG-6000 Induced Water Stress
Kommavarapu Mahesh, Parshavaneni Balaraju, Bellamkonda Ramakrishna, Sadhu Seeta Ram Rao
Osmania University, Hyderabad, India.
Received September 10th, 2013; revised October 16th, 2013; accepted November 3rd, 2013 2015
American Journal of Plant Sciences, 2013, 4, 2305-2313 Published Online December 2013 (http://www.scirp.org/journal/ajps) http://dx.doi.org/10.4236/ajps.2013.412285

http://www.journalajst.com/past-issue/201501
http://www.journalajst.com/sites/default/files/1928.pdf
Asian Journal of Science and Technology Vol. 6, Issue 01, pp. 951-955, January, 2015
Influence of peg imposed water stress and exogenous application of brassinosteroids on metabolites in radish
1Balaraju, P., 2Ayodhya Ramulu, Ch., 3Venkateshwarlu, M. and *4Ugandhar, T.
1Department of Botany, Govt. Degree and PG College Peddapally-505 172
2Regional Institute of Education, Unit IX, Sachiwalaya Marg, Bhubaneswar-751 022
3Department of Botany, University College Kakatiya University Warangal-506 009
4Department of Botany, SRR Govt. Arts and Science College Karimnagar-505 001

Reply
Pyricularia oryzae query says:

May 18, 2015 at 11:14 pm

A query about possible mirror images in a Pyricularia oryzae paper to represent different treatments was made at PubPeer on May 17:
https://pubpeer.com/publications/D2549ACBF89B0A7BBF12E9C755CBCD#fb30189

The corresponding author responded on May 19, as follows: “I am Y. Tosa, the corresponding author of this article. When I first received these comments, I was very much surprised. However, a scrutiny of the pictures led me to a conclusion that they are actually very similar and mirror images. The right one seems to have been produced by turning the left one over on a computer. I am going to contact the editor of MPMI and follow his advice. I think that we should retract this article.”

This is the paper in question:
Molecular Plant-Microbe Interactions
June 2010, Volume 23, Number 6
Pages 771-783
http://dx.doi.org/10.1094/MPMI-23-6-0771
Evolution of the Eleusine Subgroup of Pyricularia oryzae Inferred from Rearrangement at the Pwl1 Locus
Masaki Tanaka, Gang-Su Hyon, Toshiki Murata, Hitoshi Nakayashiki, and Yukio Tosa
Laboratory of Plant Pathology, Graduate School of Agricultural Sciences, Kobe University, Nada, Kobe 657-8501, Japan
http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-23-6-0771

Reply
Tobacco query says:

May 19, 2015 at 9:16 am

A query about possible figure duplication in a tobacco paper to represent different treatments was made at PubPeer on May 17:
https://pubpeer.com/publications/6C3F758FED8BA622AD952F09B5437B
http://imgur.com/Ufoza3p

The corresponding author, Greg Martin of Cornell UNiversity, responded on May 19, as follows, among other statements: “This is an inexcusable mistake due to negligence in assembling the figure. I apologize and personally accept complete responsibility for the problem. I am in touch with my co-authors and we will submit a corrected figure to the journal within the next few weeks.”

This is the paper in question:
Molecular Plant-Microbe Interactions
Vol. 23, No. 6, 2010, pp. 715–726. doi:10.1094/MPMI-23-6-0715.
Identification of Nicotiana benthamiana Genes Involved in Pathogen-Associated Molecular Pattern–Triggered Immunity
Suma Chakravarthy,1 André C. Velásquez,1,2 Sophia K. Ekengren,3 Alan Collmer,2 and Gregory B. Martin1
1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801, U.S.A.;
2 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.;
3 Department of Botany, Stockholm University, S-106 91 Stockholm, Sweden
Submitted 4 September 2009. Accepted 1 February 2010.
http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-23-6-0715

Reply
Arabidopsis query says:

June 3, 2015 at 11:04 am

A New Phytologist Arabidopsis paper is being questioned at PubPeer:
https://pubpeer.com/publications/62C12F3E3E297C2579D2BF989CE762#fb31098
Three BUB1 and BUBR1/MAD3-related spindle assembly checkpoint proteins are required for accurate mitosis in Arabidopsis
Laetitia Paganelli, Marie-Cécile Caillaud, Michaël Quentin, Isabelle Damiani, Benjamin Govetto, Philippe Lecomte, Pavel A. Karpov, Pierre Abad, Marie-Edith Chabouté, Bruno Favery, New Phytologist (2014) Volume 205, Issue 1, pages 202–215, January 2015
DOI: 10.1111/nph.13073
http://onlinelibrary.wiley.com/doi/10.1111/nph.13073/epdf

The senior author, Bruno Favery states: “Dear reader, I’m currently investigating these issues posted in PubPeer. I will give you, and New Phytologist, a response as soon as possible. Yours, B Favery”

Reply
Muscari query says:

June 11, 2015 at 8:29 pm

Azad MAK, Amin MN (2012) Effects of hormonal and basal nutrient medium on in vitro regeneration of an ornamental plant – Muscari armeniacum Leichtlin. ex Baker. Plant Tissue Culture & Biotechnology 22(2): 113-126
http://www.baptcb.org/ptc/abstracts.asp?YEAR=488
http://www.banglajol.info/index.php/PTCB/article/view/14200
DOI: 10.3329/ptcb.v22i2.14200

Queries at PubPeer:
https://pubpeer.com/publications/4735BE2F10FB823359CF7DE1384C98

Reply
Saffron query says:

June 22, 2015 at 9:44 pm

Kindly compare the PDF files of these two papers.

Sheibani, M., Nemati, S.H., Davarinejad, G.H., Azghandi, A.V. and Habashi, A.A. 2007. Induction of somatic embryogenesis in saffron using thidiazuron (TDZ). Acta Horticulturae (International Society for Horticultural Science) 739:259-267
Horticulture Department. College of Agriculture, Ferdowsi University of Mashhad, P.O. Box 9177948978, Mashhad, Iran
Culture and Gene Transformation Department, Agricultural Biotechnology Research Institute of Iran (ABRII), P.O. Box 31535-1897, Karaj, Iran
http://www.actahort.org/books/739/739_32.htm
http://www.ishs.org/ishs-article/739_32
http://confbank.um.ac.ir/modules/conf_display/conferences/saffron/pdf/p32.pdf
http://www.researchgate.net/publication/23674456_Induction_of_somatic_embryogenesis_in_saffron_using_thidiazuron_(TDZ)

M. Sheibani, A.V. Azghandi and S.H. Nemati , 2007. Induction of somatic embryogenesis in saffron using thidiazuron (TDZ). Pakistan Journal of Biological Sciences*, 10: 3564-3570.
DOI: 10.3923/pjbs.2007.3564.3570
http://scialert.net/abstract/?doi=pjbs.2007.3564.3570
http://scialert.net/fulltext/?doi=pjbs.2007.3564.3570
http://scialert.net/qredirect.php?doi=pjbs.2007.3564.3570&linkid=pdf
http://www.scimagojr.com/journalsearch.php?q=3900148614&tip=sid
* The publisher, Science Alert or ANSInet, is listed at http://scholarlyoa.com/publishers/

PubPeer:
https://pubpeer.com/publications/280039F32ADFC40FE9147C7A568CFA

Reply
Maize query says:

June 24, 2015 at 4:48 pm

Journal of Experimental Botany, Vol. 65, No. 17, pp. 4919–4930, 2014
doi: 10.1093/jxb/eru249
The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots
Yanxiang Zhang 1, Anja Paschold 1, Caroline Marcon 1, Sanzhen Liu 2, Huanhuan Tai 1, Josefine Nestler 1, Cheng-Ting Yeh 3, Nina Opitz 1, Christa Lanz 4, Patrick S. Schnable 2,3 and Frank Hochholdinger 1,*
1 INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, Friedrich-Ebert-Allee 144, 53113 Bonn, Germany
2 Department of Agronomy, Iowa State University, Ames 50011-3650, Iowa, USA
3 Center for Plant Genomics, Iowa State University, Ames 50011-3650, Iowa, USA
4 Department of Molecular Biology, Max-Planck-Institute for Developmental Biology, 72076 Tuebingen, Germany
http://jxb.oxfordjournals.org/content/65/17/4919.full.pdf+html
doi: 10.1093/jxb/eru249

A query about two apparently similar photos:
https://pubpeer.com/publications/24928984

The authors recognize the error, and respond (June 24, 2015), as follows: “Yes there was indeed a wrong cross section displayed in Figure 3F. We have fixed that error and sent an erratum to J Exp Bot.”

Reply
Plant defense correction says:

July 3, 2015 at 9:22 pm

Microbial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant Defense Responses
Junqi Song, Andrew F. Bent, PLoS Pathogens (2014) 10(6): e1004226
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004030
DOI: 10.1371/journal.ppat.1004030
Correction:
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004226
“Figure 1 in the original article contains two duplicate panels that were inserted during a manuscript revision. Two of the six images in Figure 1C were inadvertently deleted and replaced with duplicates of the adjacent photographic panels. The six correct Figure 1C photographic panels were used during peer review, and are now restored in the corrected version of Figure 1.”
https://pubpeer.com/publications/DE4B3B342EEF23E43AB0B01F47A15C#fb32724

Reply
Rice leaf streak correction says:

July 3, 2015 at 9:28 pm

PLoS Pathog 10(4): e1004126. doi: 10.1371/journal.ppat.1004126
Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene
Raul A. Cernadas, Erin L. Doyle, David O. Niño-Liu, Katherine E. Wilkins, Timothy Bancroft, Li Wang, Clarice L. Schmidt, Rico Caldo, Bing Yang, Frank F. White, Dan Nettleton, Roger P. Wise, Adam J. Bogdanove
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003972
Correction:
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004126
“There are data and labeling errors in Figure 3. In the original Figure 3, the gel image for Os07g06970 is incorrect. It is a duplicate of the image for Os01g40290. The new Figure 3 contains the correct image. Also, the original Figure 3 was generated using Locus IDs from Release 5.0 of the Rice Genome Annotation Project. Relative to Release 7.0, used for all other reporting in the article, one of these Locus IDs, Os10g38495, is obsolete. It has been updated in the new Figure 3 to the corresponding Release 7.0 Locus ID, Os10g38489. The remaining Locus IDs are the same in Release 5.0 and Release 7.0 and unchanged in the new Figure 3.”
https://pubpeer.com/publications/294B796502B0BC0788C23FAFD1CF06#fb32726

Reply
Apple bioreactor query says:

July 22, 2015 at 9:57 am

Please compare these two manuscripts.

Journal of Horticultural Science & Biotechnology (2003) 78 (5) 605-609
Micropropagation of apple rootstock M.9 EMLA using bioreactor
DEBASIS CHAKRABARTY 1, E. J. HAHN, Y. J. YOON, K. Y. PAEK*
Research Center for The Development of Advanced Horticultural Technology, Chungbuk National University, Cheong-ju 361-763, Korea
http://www.jhortscib.org/Vol78/78_5/3.htm

Production of Biomass and Bioactive Compounds Using Bioreactor Technology 2014, pp 693-709
Date: 16 Aug 2014
Biochemical and Physiological Aspects of Hyperhydricity in Liquid Culture System
Yaser Hassan Dewir 1, Yuvraj Indoliya 2, Debasis Chakrabarty 2, Kee-Yoeup Paek 3
1. Department of Horticulture, Faculty of Agriculture, Kafrelsheikh University, 33516, Kafr El-Sheikh, Egypt
2. Genetics and Molecular Biology, National Botanical Research Institute, Lucknow, India
3. Research Center for the Development of Advanced Horticultural Technology, Chungbuk National University, 361-763, Cheongju, Republic of Korea
http://link.springer.com/chapter/10.1007/978-94-017-9223-3_26
DOI: 10.1007/978-94-017-9223-3_26

http://imgur.com/bcwCqSU

PubPeer:
https://pubpeer.com/publications/D0E8F7DBA035C4FE742D6AFA63549A#fb33883

Reply
Arabidopsis corrected says:

July 23, 2015 at 9:38 pm

An Arabidopsis paper in PLOS Biology has been recently corrected, but new queries have emerged at PubPeer about satistical analyses.

Original:
PLoS Biol 11(12): e1001732. doi:10.1371/journal.pbio.1001732
A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex
Marie-Cécile Caillaud, Shuta Asai, Ghanasyam Rallapalli, Sophie Piquerez, Georgina Fabro, Jonathan D. G. Jones
The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom
Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
School of Life Sciences, University of Warwick, Coventry, United Kingdom
CIQUIBIC-CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001732

Correction:
The PLOS Biology Staff (2014) Correction: A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex. PLoS Biol 12(6): e1001909. doi: 10.1371/journal.pbio.1001909
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001909

Reply
1. Arabidopsis corrected says:
  
  July 23, 2015 at 9:38 pm
  
  PubPeer:
  https://pubpeer.com/publications/0D9514EB9544E56F630929A3D73CD3#fb33952
  
  Reply
4 The Plant Cell corrections says:

August 29, 2015 at 12:58 am

4 corrections in the latest issue of The Plant Cell have appeared:
http://www.plantcell.org/content/27/7.toc

The Plant Cell August 2014 vol. 26 no. 8 3358-3371
http://www.plantcell.org/content/26/8/3358.full.pdf+html
http://www.plantcell.org/content/26/8/3358# (open access)
Manipulation of Mitogen-Activated Protein Kinase Kinase Signaling in the Arabidopsis Stomatal Lineage Reveals Motifs That Contribute to Protein Localization and Signaling Specificity
Gregory R. Lampard 1, Diego L. Wengier 1, Dominique C. Bergmann 1,2
1 Howard Hughes Medical Institute, Stanford University, Stanford, California 94305-5020 USA
2 Department of Biology, Stanford University, Stanford, California 94305-5020 USA
DOI: 10.1105/tpc.114.127415

https://pubpeer.com/publications/B1E91FB1C91B8F6D91AA5DBE32798B#fb28149
Correction:
http://www.plantcell.org/content/27/7/2073.full.pdf+html

Possart, A., and Hiltbrunner, A. (2013). An evolutionarily conserved signaling mechanism mediates far-red light responses in land plants. Plant Cell 25: 102–114.
http://www.plantcell.org/content/27/7/2075.full.pdf+html

Sato, H., Mizoi, J., Tanaka, H., Maruyama, K., Qin, F., Osakabe, Y., Morimoto, K., Ohori, T., Kusakabe, K., Nagata, M.,
Shinozaki, K., and Yamaguchi-Shinozaki, K. (2014). Arabidopsis DPB3-1, a DREB2A interactor, specifically enhances heat stressinduced gene expression by forming a heat stress-specific transcriptional complex with NF-Y subunits. Plant Cell 26: 4954–4973.
http://www.plantcell.org/content/27/7/2076.full.pdf+html

Ruiz, M.T., Voinnet, O., and Baulcombe, D.C. (1998). Initiation and maintenance of virus-induced gene silencing. Plant Cell 10: 937–946.
http://www.plantcell.org/content/27/7/2078.full.pdf+html

The latter paper follows a retraction by the same author in the previous TPC issue:
Patrice Dunoyer, Charles-Henri Lecellier, Eneida Abreu Parizotto, Christophe Himber, and Olivier Voinnet (2004). Probing the MicroRNA and Small Interfering RNA Pathways with Virus-Encoded Suppressors of RNA Silencing. Plant Cell 16: 1235–1250.
http://www.plantcell.org/content/27/6/1815.full.pdf+html

Reply
ROP GTPases concerns says:

September 5, 2015 at 10:27 pm

Concerns about figures in four publications by Nadav Sorek (previously Tel Aviv University; now at UC Berkeley).

https://pubpeer.com/publications/FA9C72219E23013E12C18FB1CD1F30#fb35960
Activation Status-Coupled Transient S Acylation Determines Membrane Partitioning of a Plant Rho-Related GTPase
Molecular and Cellular Biology March 2007 vol. 27 no. 6 2144-2154
Nadav Sorek 1, Limor Poraty 1, Hasana Sternberg 1, Enat Bar 2, Efraim Lewinsohn 2, Shaul Yalovsky 1
1 Department of Plant Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
2 Department of Field and Vegetable Crops, Agricultural Research Organization, Newe Ya’ar Reseach Center, P.O. Box 1021, Ramat Yishay 30095, Israel
doi: 10.1128/MCB.02347-06
http://mcb.asm.org/content/27/6/2144

https://pubpeer.com/publications/565C3F0ED84C22A76BFC45B8BF8656
An S-Acylation Switch of Conserved G Domain Cysteines Is Required for Polarity Signaling by ROP GTPases
Current Biology Volume 20, Issue 10, p 914–920, 25 May 2010 (open access)
Nadav Sorek,1 Oshik Segev,2 Orit Gutman,3 Einat Bar,4 Sandra Richter,5 Limor Poraty,1 Joel A. Hirsch,2 Yoav I. Henis,3 Efraim Lewinsohn,4 Gerd Jürgens,5 Shaul Yalovsky,1
1 Department of Molecular Biology and Ecology of Plants
2 Department of Biochemistry
3 Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
4 Department of Field and Vegetable Crops, Agricultural Research Organization, Neve Ya’ar Reseach Center, P.O. Box 1021, Ramat Yishay 30095, Israel
5 Center for Plant Molecular Biology, University of Tübingen, D-72076 Tübingen, Germany
Erratum: Current Biology (2010) Vol. 20, Issue 14, p1326
DOI: http://dx.doi.org/10.1016/j.cub.2010.03.057

https://pubpeer.com/publications/09890676701890565C32F05A7F3E99
Differential Effects of Prenylation and S-Acylation on Type I and II ROPS Membrane Interaction and Function
Plant Physiology February 2011 vol. 155 no. 2706-2720
Nadav Sorek, Orit Gutman, Einat Bar, Mohamad Abu-Abied, Xuehui Feng, Mark P. Running, Efraim Lewinsohn, Naomi Ori, Einat Sadot, Yoav I. Henis, Shaul Yalovsky
Department of Molecular Biology and Ecology of Plants (N.S., S.Y.) and Department of Neurobiology (O.G., Y.I.H.), George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (X.F., M.P.R.); Department of Field and Vegetable Crops, Agricultural Research Organization, Neve Ya’ar Research Center, Ramat Yishay 30095, Israel (E.B., E.L.); Robert Smith Institute of Plant Sciences and Genetics of Agriculture, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel (N.O.); Department of Ornamental Horticulture, Agricultural Research Organization, Volcani Center, Bet-Dagan 50250, Israel (M.A.-A., E.S.)
http://www.plantphysiol.org/content/155/2/706

https://pubpeer.com/publications/0B9A78BC5C100434DA06CE7A6DCBCF#fb35042
https://pubpeer.com/publications/25331944
The Arabidopsis COBRA protein facilitates cellulose crystallization at the plasma membrane
Nadav Sorek ‡,§1, Hagit Sorek ‡, Aleksandra Kijac ¶, Heidi J. Szemenyei ‡,§, Stefan Bauer ‡, Kian Hématy ‖,**, David E. Wemmer ‡,¶ and Chris R. Somerville ‡,§,‡‡
1. From the ‡Energy Biosciences Institute,
2. the §Plant and Microbial Biology Department, and
3. the ¶Department of Chemistry, University of California, Berkeley, California 94720,
4. the ‖INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France,
5. **AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France, and
6. ‡‡Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
1. ↵1 Recipient of Postdoctoral Award FI-434-2010 from the Binational Agricultural Research and Development Fund. To whom correspondence should be addressed: Energy Biosciences Institute, University of California Berkeley, 1521 Berkeley Way, Berkeley, CA 94704. Tel.: 510-643-6265;
http://www.jbc.org/content/289/50/34911
First Published on October 20, 2014,
doi: 10.1074/jbc.M114.607192
December 12, 2014
The Journal of Biological Chemistry, 289, 34911-34920.

Reply
Arabidopsis query says:

September 25, 2015 at 9:49 pm

Queries about figures made in August at PubPeer* have led to the following response by the senior author on September 25: “The only image that was available for Figure 3 was the published figure. Therefore, we withdrew the paper from JBC. To resolve the issue of reproducibility beyond doubt, I will ask someone from outside the lab to redo the experiment represented by Figure 3. Chris Somerville”

* https://pubpeer.com/publications/0B9A78BC5C100434DA06CE7A6DCBCF#fb37041

The paper in question:
http://www.jbc.org/content/289/50/34911
The Arabidopsis COBRA Protein Facilitates Cellulose Crystallization at the Plasma Membrane*
doi: 10.1074/jbc.M114.607192
The Journal of Biological Chemistry, 289, 34911-34920.
Nadav Sorek‡,§1, Hagit Sorek‡, Aleksandra Kijac¶, Heidi J. Szemenyei‡,§, Stefan Bauer‡,
Kian Hématy‖,**, David E. Wemmer‡,¶ and Chris R. Somerville‡,§,‡‡
–
Author Affiliations
From the ‡Energy Biosciences Institute,
the §Plant and Microbial Biology Department, and
the ¶Department of Chemistry, University of California, Berkeley, California 94720,
the ‖INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France,
**AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France, and
‡‡Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
↵1 Recipient of Postdoctoral Award FI-434-2010 from the Binational Agricultural Research and Development Fund. To whom correspondence should be addressed: Energy Biosciences Institute, University of California Berkeley, 1521 Berkeley Way, Berkeley, CA 94704

Reply
1. Arabidopsis retracted says:
  
  November 5, 2015 at 11:28 am
  
  Retraction
  http://www.jbc.org/content/290/42/25274.short
  https://pubpeer.com/publications/0B9A78BC5C100434DA06CE7A6DCBCF#fb39829
  “The only image that was available for Figure 3 was the published figure. Therefore, we withdrew the paper from JBC. To resolve the issue of reproducibility beyond doubt, I will ask someone from outside the lab to redo the experiment represented by Figure 3. Chris Somerville”
  
  doi: 10.1074/jbc.A114.607192
  October 16, 2015, The Journal of Biological Chemistry, 290, 25274.
  http://www.jbc.org/content/290/42/25274.full.pdf+html
  “This article has been withdrawn by the authors.”
  
  Reply
Watermelon miRNA sequence query says:

September 26, 2015 at 8:22 pm

Queries regarding the authenticity of claimed miRNA sequences from plants in ingested food have been raised at PubPeer.
https://pubpeer.com/publications/E6B69635528A2382AFBDB1516BB041#fb37033

Effective detection and quantification of dietetically absorbed plant microRNAs in human plasma
Hongwei Liang, Suyang Zhang, Zheng Fu, Yanbo Wang, Nan Wang, Yanqing Liu, Chihao Zhao, Jinhui Wu, Yiqiao Hu, Junfeng Zhang, Xi Chen, Ke Zen, Chen-Yu Zhang
Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu 210093, China
The Journal of Nutritional Biochemistry May 2015 Volume 26, Issue 5, Pages 505–512
DOI: http://dx.doi.org/10.1016/j.jnutbio.2014.12.002
http://www.jnutbio.com/article/S0955-2863(15)00016-9/abstract

Reply
El Vigilante says:

September 29, 2015 at 5:10 pm

Prof. Blatt, the editor-in-chief of Plant Physiology, argues against anonymous comments at PubPeer, referring to the phenomenon as vigilantism. His editorial is important because it is one of the first main-stream plant science journals to address post-publication peer review and the role of the anonymous voice. So there is broadly merit in this editorial to raise and expand awareness. However, some aspects of Blatt’s editorial are critiqued at PubPeer:
https://pubpeer.com/publications/209CA2DF493322A5B5470F3B8EEDA0#fb37282

Reply
1. Arabidopsis query says:
  
  September 29, 2015 at 5:45 pm
  
  A Blatt paper is questioned at PubPeer:
  https://pubpeer.com/publications/CBE5FF3720F04311141D8254433C9B#fb37274
  The Plant Cell, Vol. 27: 1697–1717, June 2015
  The Arabidopsis R-SNARE VAMP721 Interacts with KAT1 and KC1 K+ Channels to Moderate K+ Current at the Plasma Membrane
  Ben Zhang,a Rucha Karnik,a Yizhou Wang,a NiklasWallmeroth,b Michael R. Blatt,a,1,2 and Christopher Grefenb,2
  a Laboratory of Plant Physiology and Biophysics, University of Glasgow, Glasgow G12 8QQ, United Kingdom
  b ZMBP Developmental Genetics, D-72076 Tuebingen, Germany
  
  Reply
2. Critic says:
  
  September 30, 2015 at 8:01 am
  
  A very critical assessment of the Blatt editorial by Paul S. Brookes, who describes the piece as “literary detritus”:
  http://www.psblab.org/?p=445
  
  Reply
3. Anon says:
  
  October 1, 2015 at 10:28 pm
  
  More comments and internet chatter about the Blatt editorial:
  http://www.ncbi.nlm.nih.gov/pubmed/26417050
  http://drugmonkey.scientopia.org/2015/09/30/throwing-punches-about-pubpeer/
  http://neurodojo.blogspot.jp/2015/09/journals-tired-of-complaining-about.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+Neurodojo+(NeuroDojo)
  
  Reply
Plant immunity query says:

September 29, 2015 at 5:59 pm

Posttranslational Modifications of the Master Transcriptional Regulator NPR1 Enable Dynamic but Tight Control of Plant Immune Responses
Abdelaty Saleh, John Withers, Rajinikanth Mohan, Jorge Marqués, Yangnan Gu, Shunping Yan, Raul Zavaliev, Mika Nomoto, Yasuomi Tada, Xinnian Dong, Cell Host & Microbe (2015) Volume 18, Issue 2, 12 August 2015, Pages 169–182
http://www.sciencedirect.com/science/article/pii/S1931312815002978

Fig1A and 1C queried at PubPeer:
http://imgur.com/Bkdo2ec
https://pubpeer.com/publications/DC3C42A4A9AE404C4290965617AE14#fb37098

Authors respond within 48 hours as follows: “Thank you for bringing this concern to our attention. We are trying to get in touch with the author who did this experiment. This author has recently left the lab and we found out today that he is traveling abroad with limited phone or email contact. In the mean time, we are repeating this experiment to further verify the result. Xinnian Dong”

Reply
1. Plant immunity query says:
  
  November 4, 2015 at 1:30 am
  
  Two additional figures beng queried in this paper.
  
  Fig. S5
  http://imgur.com/49ywbgf
  
  Fig. 3G
  http://imgur.com/CBK4ZP6
  http://imgur.com/rfnWLN2
  
  Reply
2. Plant immunity query says:
  
  March 8, 2016 at 10:28 am
  
  A corrigendum has been published:
  http://www.sciencedirect.com/science/article/pii/S1931312815005004
  http://www.cell.com/cell-host-microbe/pdf/S1931-3128%2815%2900500-4.pdf
  
  Reply
CO2 and plant nutrients paper says:

October 8, 2015 at 3:20 pm

Queries first emerged at PubPeer about a 2012 Plant Ecology paper in June, 2014. One year later, in July 2015, the authors responded to the anonymous comments. Subsequent to that, further errors were detected.

Today, October 8, 2015, the authors have decided to retract the study, stating: “In response to issues raised on this forum and our review of the original data, we have requested that the journal retract our paper. All inquiries should be addressed to the lead author, Benjamin Duval”.

CO2 effects on plant nutrient concentration depend on plant functional group and available nitrogen: a meta-analysis
Benjamin D. Duval (1,3,4), Joseph C. Blankinship (2), Paul Dijkstra (1,3), Bruce A. Hungate (1,3)
Plant Ecology (2012) March 2012, Volume 213, Issue 3, pp 505-521
1. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
3. Merriam Powell Center for Environmental Research, Flagstaff, AZ, 86011, USA
4. Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
2. School of Natural Sciences, University of California at Merced, Merced, CA, 95343, USA
https://pubpeer.com/publications/A01632233DC4B68C65A8B770E3908E#fb38093

Reply
1. CO2 and plant nutrients paper: retracted says:
  
  December 4, 2015 at 8:23 pm
  
  The manuscript was retracted on November 18, 2015:
  http://link.springer.com/article/10.1007/s11258-015-0541-1
  “This article has been retracted at the request of the authors because of multiple and unintentional data entry errors.”
  
  Reply
Nepalese sandalwood query says:

October 21, 2015 at 10:30 am

An apparent duplication.

Shyaula, S.L., Choudhary, M.I., Manandhar, M.D., 2013a. Megastigmane, iridoid, benzyl alcohol and phenyl propanoid glycosides from the Nepalese sandalwood Osyris wightiana Wall. ex. Wight. Moscow University Biological Sciences Bulletin (ВЕСТН. МОСК. УН-ТА) 54, 346–351.

Shyaula, S.L., Choudhary, M.I., Manandhar, M.D., 2013b. Megastigmane, iridoid, benzyl alcohol and phenyl propanoid glycosides from the Nepalese sandalwood Osyris wightiana Wall. ex Wight. Moscow University Chemistry Bulletin 68, 293–297. doi:10.3103/S0027131413060047

For 2013b:
https://pubpeer.com/publications/86ECCACB8CBECBBD4625D86CADA46B#fb38957

Reply
Electric fields in corn and oregano query says:

November 5, 2015 at 11:52 am

A figure common to two papers is queried.

Pulsed electromagnetic field: an organic compatible method to promote plant growth and yield in two corn types
Dimitrios J. Bilalis 1, Nikolaos Katsenios 1, Aspasia Efthimiadou 2, Anestis Karkanis 3
1 Agricultural University of Athens, Crop Science, Athens, Greece
2 Open University of Cyprus, Nicosia, Cyprus
3 University of Thessaly, Volos, Greece
Electromagnetic Biology and Medicine, 31(4): 333–343, 2012
DOI: 10.3109/15368378.2012.661699

Dimitrios Bilalis, Nikolaos Katsenios, Aspasia Efthimiadou, Panagiotis Efthimiadis, Anestis Karkanis (2012) Pulsed electromagnetic fields effect in oregano rooting and vegetative propagation: A potential new organic method. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 62:1, 94-99
DOI: 10.1080/09064710.2011.570374

https://imgur.com/7CMPIjP

https://pubpeer.com/publications/B62B4328A47FC04C932C2FE030005E
https://pubpeer.com/publications/4A6592E00413C5F25878C8C997FA00

Reply
1. Electric fields in crops query says:
  
  March 22, 2016 at 12:25 pm
  
  Influence of Pulsed Electromagnetic Field on Plant Growth, Nutrient Absorption and Yield of Durum Wheat
  Nikolaos KATSENIOS, Victor KAVVADIAS, Sideris THEOCHAROPOULOS, Dimitrios BILALIS, Zaharias IOANNOU, Antonios PAPADOPOULOS, Nektaria LIAKOPOULOU
  Notulae Scientia Biologicae (2015) 7(4): 505-509
  DOI: 10.15835/nsb.7.4.9691
  http://notulaebiologicae.ro/index.php/nsb/article/view/9691/8063
  https://pubpeer.com/publications/0A6D7658BCEBF5810A91861BB66722
  
  Effects of Presowing Pulsed Electromagnetic Treatment of Tomato Seed on Growth, Yield, and Lycopene Content
  Aspasia Efthimiadou, Nikolaos Katsenios, Anestis Karkanis, Panayiota Papastylianou, Vassilios Triantafyllidis, Ilias Travlos, Dimitrios J. Bilalis
  The Scientific World Journal
  Volume 2014 (2014), Article ID 369745, 6 pages
  DOI: 10.1155/2014/369745
  http://www.hindawi.com/journals/tswj/2014/369745/ref/
  https://pubpeer.com/publications/ACCBF9C8660B71B5DFC5CD203ACD5D
  
  Today a corrigendum was published for the Notulae Scientia Biologicae paper:
  http://www.notulaebiologicae.ro/index.php/nsb/article/view/9795
  
  Reply
Bacillus on plant biomass retraction says:

November 5, 2015 at 3:11 pm

Timothy D. Anderson (abc), J. Izaak Miller (abc), Henri-Pierre Fierobe (d), Robert T. Clubb (abc). 2015. Retraction for Anderson et al., Recombinant Bacillus subtilis that grows on untreated plant biomass. Applied and Environmental Microbiology 81:7957. doi:10.1128/AEM.02768-15.

a UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA
b Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
c Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
d Laboratoire de Chimie Bactérienne, IFR88-CNRS, Marseille, France

“Volume 79, no. 3, p. 867–876, 2013. With the concurrence of all of the authors, we retract this paper. The reason for the retraction is that we have been unable to reproduce the central finding of this paper (growth on biomass) after making repeated attempts during the past year. As such, we believe that the article needs to be retracted in order to set the record straight.”

http://aem.asm.org/content/81/22/7957.long

Reply
Magnetic fields and garden pea query says:

November 5, 2015 at 5:10 pm

Please compare Figures 1 and 2 of 2012a and Figure 6 of 2012b:
https://imgur.com/lgoh4A2

Iqbal M 1, Haq ZU 2, Jamil Y 2, Ahmad MR 2 (2012a) Effect of presowing magnetic treatment on properties of pea. International Agrophysics 26(1):25–31
doi: 10.2478/v10247-012-0004-z
1 Department of Chemistry and Biochemistry, 2 Department of Physics, University of Agriculture, Faisalabad-38040, Pakistan
http://www.degruyter.com/view/j/intag.2012.26.issue-1/v10247-012-0004-z/v10247-012-0004-z.xml
Received December 7, 2010; accepted January 19, 2011

Munawar Iqbal 1*, Dil Muhammad 2, Zia-Ul-Haq 2, Yasir Jamil 2, M. Raza Ahmad 2 (2012b) Effect of pre-sowing magnetic field treatment to garden pea (Pisum sativum L.) seed on germination and seedling growth. Pakistan Journal of Botany 44(6): 1851-1856.
1 Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad-38040, Pakistan
2 Department of Physics, University of Agriculture, Faisalabad-38040, Pakistan
http://www.pakbs.org/pjbot/tcontents/tcontent44(6)01-10.html
http://www.pakbs.org/pjbot/abstracts/44(6)/05.html
http://www.pakbs.org/pjbot/PDFs/44(6)/05.pdf
http://www.researchgate.net/publication/247404838_Effect_of_pre-sowing_magnetic_field_treatment_to_garden_pea_(Pisum_sativum_L.)_Seed_on_germination_and_seedling_growth
Received for publication 5 May 2010

https://pubpeer.com/publications/393ADEA80037D462BAE03BC0BCDF50

Reply
Arabidopsis FLC and AP1 query says:

November 10, 2015 at 6:08 pm

A figure is being queried.
Dynamic and stable histone H3 methylation patterns at the Arabidopsis FLC and AP1 loci
Abdelaty Saleh, Raul Alvarez-Venegas, Zoya Avramova, Gene, 423 (2008)
https://pubpeer.com/publications/5B64011B2D7E5D926A3A30061D9D99#fb40129

Reply
1. Arabidopsis FLC and AP1 query says:
  
  November 17, 2015 at 6:36 pm
  
  In fact, figures in a total of four studies by the Saleh and/or Avramova group are being questioned:
  https://pubpeer.com/publications/8E7779081E083FDB375D0223440D25
  https://pubpeer.com/publications/9E5164E8DF4D1BF0E8D834AC1FCF0D
  https://pubpeer.com/publications/5B64011B2D7E5D926A3A30061D9D99
  https://pubpeer.com/publications/DC3C42A4A9AE404C4290965617AE14
  
  Dr. Avramova responded on November 17, as follows:
  https://pubpeer.com/publications/8E7779081E083FDB375D0223440D25#fb40453
  “Dr. Saleh was a postdoc in my lab for about a year and a half and as a first author generated most of the results. However, I wrote the papers and as a corresponding author bear the responsibility for all problems. Going back through the problems, I am inclined to think that the deficiencies pointed out could be explained by lack of sufficient attention when assembling the composite panels. It is possible to mix up images with very similar patterns, and often with the same annotations, when arranging a composite image. I do not imply intention, other than providing a pretty illustration, because I have been following the experiments and scrutinizing the results very closely. Moreover, they have been validated throughout the years by quantitative methods and also by other groups. However, I did already initiate the process of adding formal corrections, currently with GENE, pending with the others.”
  
  Reply
Arabidopsis AGAMOUS query says:

November 15, 2015 at 6:24 am

Please observe the figures of this manuscript.
https://imgur.com/k5ozmye

The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF) establish ‘bivalent chromatin marks’ at the silent AGAMOUS locus
Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova, Nucleic Acids Res. (2007) 35 (18): 6290-6296.
doi: 10.1093/nar/gkm464

Reply
1. Arabidopsis AGAMOUS query says:
  
  November 15, 2015 at 7:27 am
  
  https://pubpeer.com/publications/17881378
  http://dx.doi.org/10.1093/nar/gkm464
  
  Reply
2. Arabidopsis AGAMOUS query says:
  
  March 8, 2016 at 4:48 am
  
  A correction has been published.
  http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1489
  Nucl. Acids Res. (2015)
  doi: 10.1093/nar/gkv1489
  
  Reply
Plant sterol guggulsterone query says:

November 16, 2015 at 2:57 am

Please observe three figures of this manuscript.

Prevention of Endotoxin-Induced Uveitis in Rats by Plant Sterol Guggulsterone
Nilesh M. Kalariya, Mohammad Shoeb, Aramati B. M. Reddy, Min Zhang, Frederik J. G. M. van Kuijk, Kota V. Ramana, Investigative Ophthalmology & Visual Science October 2010, Vol.51, 5105-5113.
doi:10.1167/iovs.09-4873
http://iovs.arvojournals.org/article.aspx?articleid=2126571
http://i.imgur.com/u0kHn73.jpg

https://pubpeer.com/publications/594E633850CA97479C951980AD117E

Reply
1. Plant sterol guggulsterone query says:
  
  November 16, 2015 at 3:00 pm
  
  Other queries by the same group of scientists:
  https://pubpeer.com/publications/38FE8AAE5F0F6AFD5A2E55FFD3722C
  https://pubpeer.com/publications/CE44E1F0BEC06FF25BF509F0A9567D
  https://pubpeer.com/publications/3B724104BEB0E3FAF68053336CFD87
  https://pubpeer.com/publications/12E454B7C904F7F16C12DB16E46C9D
  https://pubpeer.com/publications/A8F2CC20A969D94C251DC2D6679929
  https://pubpeer.com/publications/556DC5719A7B91A5284B128AC25584
  https://pubpeer.com/publications/77B8F56F91471E987F0E3DF9F0EC82
  https://pubpeer.com/publications/6534E2A0A222E70B247530BB87E3A7
  https://pubpeer.com/publications/5950AC2B5205BD42984DCC73868459
  
  Reply
Maize ZmpTAC12 query says:

November 18, 2015 at 12:20 am

http://onlinelibrary.wiley.com/doi/10.1111/nph.13248/abstract
http://onlinelibrary.wiley.com/doi/10.1111/nph.13248/epdf
ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize
Jeannette Pfalz, Ute Holtzegel, Alice Barkan, Wolfram Weisheit, Maria Mittag, Thomas Pfannschmidt
New Phytologist Volume 206, Issue 3, May 2015, Pages 1024–1037
DOI: 10.1111/nph.13248
https://pubpeer.com/publications/71C0C8E06877FED2CA710A1B9F3487

Query made on May 22, 2015.
Author response on June 3, 2015, with a promise to correct the error: “Thanks for pointing out that mistake. It is indeed a copy error. We have contacted the editorial office in order to solve this problem. Perhaps we can correct the figure and add original files as an erratum.”

5 months later, still no correction.

Reply
Plant immunity query says:

November 23, 2015 at 4:03 am

Receptor-like kinase SOBIR1/EVR interacts with receptor-like proteins in plant immunity against fungal infection
Thomas W H Liebrand, Grardy C M van den Berg, Zhao Zhang, Patrick Smit, Jan H G Cordewener, Antoine H P America, Antione H P America, Jan Sklenar, Alexandra M E Jones, Wladimir I L Tameling, Silke Robatzek, Bart P H J Thomma, Matthieu H A J Joosten, Proc. Natl. Acad. Sci. U.S.A., 110 (2013)
http://www.pnas.org/content/110/24/10010
https://pubpeer.com/publications/F289FC1960BCFB741F2F16F873925D#fb40769

Western blots in a PNAS paper questioned. Authors respond in August and on November 22, 2015, stating: “I do note that the FLS2 band is not identical as in the manuscript, I may have used a shorter exposure or placed the wrong band there. If so, I am sorry for that.”

The paper already has one correction:
http://www.pnas.org/content/110/32/13228.1.short

Reply
GM soybeans for goats query says:

December 7, 2015 at 10:48 am

Please compare figure 1 of these two papers:
http://imgur.com/CCEJROQ

Genetically modified soybean in a goat diet: Influence on kid performance
R. Tudisco, S. Calabrò, M.I. Cutrignelli, G. Moniello, M. Grossi, V. Mastellone, P. Lombardi, M.E. Pero, F. Infascelli
Small Ruminant Research (2015) Volume 126, Supplement 1, Pages 67–74
http://www.sciencedirect.com/science/article/pii/S0921448815000528

Animal / Volume 4 / Issue 10 / October 2010, pp 1662-1671
Copyright © The Animal Consortium 2010
DOI: http://dx.doi.org/10.1017/S1751731110000728 (About DOI), Published online: 05 May 2010
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=7875679&fileId=S1751731110000728

Reply
1. GM soybeans for goats query and retraction says:
  
  December 15, 2015 at 10:54 pm
  
  Figures in two more transgenic soybean papers by the same group of authors are being questioned at PubPeer.
  
  Fate of transgenic DNA and evaluation of metabolic effects in goats fed genetically modified soybean and in their offsprings
  R. Tudisco, V. Mastellone, M. I. Cutrignelli, P. Lombardi, F. Bovera, N. Mirabella, G. Piccolo, S. Calabrò, L. Avallone, F. Infascelli, Animal (2010)
  https://pubpeer.com/publications/8B2DD6BE9FBD8918D1EB64D22816E6
  http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=7875679&fileId=S1751731110000728
  (open access)
  
  Gamma-Glutamyl Transferase Activity in Kids Born from Goats Fed Genetically Modified Soybean
  Vincenzo Mastellone, Raffaella Tudisco, Giovanni Monastra, Maria Elena Pero, Serena Calabrò, Pietro Lombardi, Micaela Grossi, Monica Isabella Cutrignelli, Luigi Avallone, Federico Infascelli, FNS (2013)
  https://pubpeer.com/publications/903F7BF22D3C8C46EA499B0C299A23
  http://www.scirp.org/journal/PaperInformation.aspx?PaperID=33017
  Now retracted (15 December, 2015):
  “The article has been retracted due to the investigation of complaints received against it. The data of figure 1(b) came from the previous published paper by Tudisco R, Mastellone V, Cutrignelli MI, Lombardi P, Bovera F, Mirabella N, Piccolo G, Calabrò S, Avallone , Infascelli F. Animal.“Fate of transgenic DNA and evaluation of metabolic effects in goats fed genetically modified soybean and in their offsprings”4(10):1662-71, 2010. The scientific community takes a very strong view on this matter and we treat all unethical behavior such as plagiarism seriously. This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE’s Retraction Guidelines. Aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Professor Alessandra Bordoni (EiC of FNS) The full retraction notice in PDF is preceding the original paper, which is marked “RETRACTED”.”
  
  Please read page 1 of the retraction notice. Very fascinating, including the name of theindividual who reported the error, the nature of the error, the date of the report and the validity of the data, despite the retraction. SCIRP is listed on Jeffrey Beall’s list of predatory OA publishers.
  
  Reply
2. GM soybeans for goats query says:
  
  December 16, 2015 at 2:50 am
  
  Figure in another transgenic soybean paper by the same group of authors was questioned at PubPeer, then retracted on December 15, 2015.
  
  Gamma-Glutamyl Transferase Activity in Kids Born from Goats Fed Genetically Modified Soybean
  Vincenzo Mastellone, Raffaella Tudisco, Giovanni Monastra, Maria Elena Pero, Serena Calabrò, Pietro Lombardi, Micaela Grossi, Monica Isabella Cutrignelli, Luigi Avallone, Federico Infascelli, FNS (2013)
  https://pubpeer.com/publications/903F7BF22D3C8C46EA499B0C299A23
  http://www.scirp.org/journal/PaperInformation.aspx?PaperID=33017
  
  Additional information about the 2010 Animal paper listed above:
  Fate of transgenic DNA and evaluation of metabolic effects in goats fed genetically modified soybean and in their offsprings
  R. Tudisco, V. Mastellone, M. I. Cutrignelli, P. Lombardi, F. Bovera, N. Mirabella, G. Piccolo, S. Calabrò, L. Avallone, F. Infascelli, Animal (2010)
  https://pubpeer.com/publications/8B2DD6BE9FBD8918D1EB64D22816E6
  
  Reply
Phytopathogen and transgenic tobacco queries says:

December 9, 2015 at 2:57 am

Figures in two phytopathogen-related papers by an overlapping same set of authors are being queried at PubPeer.

The attack of the phytopathogens and the trumpet solo: Identification of a novel plant antifungal peptide with distinct fold and disulfide bond pattern
Santi M. Mandal, William F. Porto, Prabuddha Dey, Mrinal K. Maiti, Ananta K. Ghosh, Octavio L. Franco
Biochimie (2013) Volume 95, Issue 10, October 2013, Pages 1939–1948
doi: 10.1016/j.biochi.2013.06.027
http://www.sciencedirect.com/science/article/pii/S0300908413002083
https://pubpeer.com/publications/5E527DE675FC35C7FAB62C4F96EE8E
http://i.imgur.com/nKnqVf4.jpg

Transgenically expressed rice germin-like protein1 in tobacco causes hyper-accumulation of H2O2 and reinforcement of the cell wall components
Joydeep Banerjee, Natasha Das, Prabuddha Dey, Mrinal K. Maiti
Biochemical and Biophysical Research Communications (2010) Volume 402, Issue 4, 26 November 2010, Pages 637–643
doi:10.1016/j.bbrc.2010.10.073
http://www.sciencedirect.com/science/article/pii/S0006291X10019510
https://pubpeer.com/publications/E13E0C3F6FB6C6EB7FA1F4B9EA1144
http://i.imgur.com/Yr83pXE.jpg

Reply
1. Phytopathogen and transgenic tobacco queries says:
  
  December 9, 2015 at 11:55 am
  
  Figures in two more PLOS ONE papers by Prabuddha Dey and Mrinal K. Maiti being questioned at PubPeer.
  
  Functional Characterization of Two Structurally Novel Diacylglycerol Acyltransferase2 Isozymes Responsible for the Enhanced Production of Stearate-Rich Storage Lipid in Candida tropicalis SY005
  Prabuddha Dey, Monami Chakraborty, Maulik R. Kamdar, Mrinal K. Maiti, PLoS ONE (2014)
  DOI: 10.1371/journal.pone.0094472
  https://pubpeer.com/publications/BCF76B0C5B84994CE8B921485C11AE
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094472
  
  Enhancement of Lipid Productivity in Oleaginous Colletotrichum Fungus through Genetic Transformation Using the Yeast CtDGAT2b Gene under Model-Optimized Growth Condition
  Prabuddha Dey, Nikunj Mall, Atrayee Chattopadhyay, Monami Chakraborty, Mrinal K. Maiti, PLoS ONE (2014)
  DOI: 10.1371/journal.pone.0111253
  https://pubpeer.com/publications/D6C9FDF7E133DACFA23C6949225788
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111253
  
  Reply
2. Transgenic rice query says:
  
  April 19, 2016 at 12:21 am
  
  Another Mrinal K. Maiti PLOS ONE paper is being questioned at PubPeer.
  
  Dey A, Samanta MK, Gayen S, Sen SK, Maiti MK (2016) Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes. PLoS ONE 11(3): e0150763. doi: 10.1371/journal.pone.0150763
  http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0150763
  https://pubpeer.com/publications/6E0D32D9BB5248906632B47440DEA1
  
  Reply
Artemisia NSCs query says:

December 18, 2015 at 2:40 am

Aspects of the methodology of the following paper are being questioned at PubPeer.

Geographic pattern and effects of climate and taxonomy on nonstructural carbohydrates of Artemisia species and their close relatives across northern China
Xuejun Yang, Zhenying Huang, Keliang Zhang, J. Hans C. Cornelissen, Biogeochemistry September 2015, Volume 125, Issue 3, pp 337-348
http://link.springer.com/article/10.1007%2Fs10533-015-0128-x

https://pubpeer.com/publications/834191278324EB8469598EE2255D7C

Reply
Sinapis alba query says:

December 18, 2015 at 3:20 pm

Please compare data in Table 2 (2004) vs Table 1 (2006):
https://imgur.com/NuyLmqO

Toxicity comparison of some possible toxic metals (Cd, Cu, Pb, Se, Zn) on young seedlings of Sinapis alba L.
A. Fargašová
Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia
PLANT SOIL AND ENVIRONMENT 50, 2004 (1): 33–38
http://www.agriculturejournals.cz/publicFiles/51054.pdf
http://www.agriculturejournals.cz/web/pse.htm?volume=50&firstPage=33&type=publishedArticle

Effect of Se-metal pair combinations (Cd, Zn, Cu, Pb) on photosynthetic pigments production and metal accumulation in Sinapis alba L. seedlings
A. Fargašová 1, J. Pastierová 1, K. Svetková 2
1 Faculty of Natural Sciences, Comenius University in Bratislava, Slovak Republic
2 Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Slovak Republic
PLANT SOIL AND ENVIRONMENT 52, 2006 (1): 8-15
http://www.agriculturejournals.cz/publicFiles/50511.pdf
http://www.agriculturejournals.cz/web/pse.htm?volume=52&firstPage=8&type=publishedArticle

Both papers have no DOI, so not possible to link on PubPeer.

Reply
Saintpaulia ionantha query says:

December 20, 2015 at 7:28 pm

Please compare these two papers.

Enard, C., Franza, T., Neema, C., Gill, P.R., Persmark, M., Neilands, J.B., Expert, D., 1991. The requirement of chrysobactin dependent iron transport for virulence incited by Erwinia chrysanthemi on Saintpaulia ionantha, in: Chen, Y., Hadar, Y. (Eds.), Iron Nutrition and Interactions in Plants, Volume 43 of the Series Developments in Plant and Soil Sciences. Springer Netherlands, Dordrecht, pp. 303–311. doi:10.1007/978-94-011-3294-7_37
DOI: 10.1007/978-94-011-3294-7_37
(DOI cannot be resolved at PubPeer)

Enard, C., Franza, T., Neema, C., Gill, P.R., Persmark, M., Neilands, J.B., Expert, D., 1991. The requirement of chrysobactin dependent iron transport for virulence incited by Erwinia chrysanthemi on Saintpaulia ionantha. Plant Soil 130, 263–271.
http://link.springer.com/article/10.1007%2FBF00011882
DOI: 10.1007/BF00011882

PubPeer:
https://pubpeer.com/publications/4986DDE724E5487EB46074129F0991

Reply
Populus nigra query says:

December 21, 2015 at 3:31 am

Please compare these two studies.

Lucic A., A. Nikolic, S. Mladenovic Drinic, V. Isajev, V. Lavadinovic (2008) Genetic characterisation of genotypes of Austrian pine (Pinus nigra Arnold) populations using protein markers. Genetika 40(2): 157- 168.
http://www.doiserbia.nb.rs/img/doi/0534-0012/2008/0534-00120802157L.pdf
DOI: 10.2298/GENSR0802157L

Aleksandar Lučić, Vasilije Isajev, Ljubinko Rakonjac, Vladan Popović, Radovan Nevenić, Tatjana Ćirković-Mitrović, Ljiljana Brašanac-Bosanac (2012) Analysis of genetic variability of Austrian pine (Pinus nigra Arnold) in Serbia using protein markers. South-East European Forestry (SEEFOR) 3(1): 3-10
1 Institute of Forestry, Kneza Viseslava 3, 11000 Belgrade, Serbia
2 University of Belgrade, Faculty of Forestry, Kneza Viseslava 1, 11000 Belgrade, Serbia
(All authors 1, except for Isajev = 2)
http://www.seefor.eu/archive/2012/vol-3-no-1/82-vol3-no1-lucic-et-al-analysis-of-genetic-variability-of-austrian-pine-pinus-nigra-arnold-in-serbia-using-protein-markers.html
http://www.seefor.eu/images/arhiva/vol3_no1/lucic/lucic.pdf
DOI: 10.15177/seefor.12-01

https://pubpeer.com/publications/E5189059FA90C8073D32D9E62E2460
https://pubpeer.com/publications/231F3795999229B9F6D18B106AF67A

Reply
1. Populus nigra query says:
  
  December 23, 2015 at 1:24 pm
  
  Within 72 hours, the Editor-in-Chief promise to retract the paper:
  https://pubpeer.com/publications/E5189059FA90C8073D32D9E62E2460#fb42876
  
  Reply
Japanese plum postharvest query says:

December 30, 2015 at 2:18 am

Please compare these two papers

Sukhvinder Pal Singh, Zora Singh. 2012. Postharvest oxidative behaviour of 1-methylcyclopropene treated Japanese plums (prunus salicina Lindell) during storage under controlled and modified atmospheres. Postharvest Biology and Technology 74: 26-35.
DOI: 10.1016/j.postharvbio.2012.06.012
http://www.sciencedirect.com/science/article/pii/S0925521412001548

Sukhvinder Pal Singh, Zora Singh. 2013.Controlled and modified atmospheres influence chilling injury, fruit quality and antioxidative system of Japanese plums (Prunus salicina Lindell). International Journal of Food Science and Technology 48: 363-374.
DOI: 10.1111/j.1365-2621.2012.03196.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2621.2012.03196.x/abstract

2012
https://pubpeer.com/publications/75732845EB92337B7BDDEBF4A785C7

2013
https://pubpeer.com/publications/D358145735BA491911B930CF3ACD43

Reply
1. Japanese plum postharvest query says:
  
  January 8, 2016 at 8:53 pm
  
  Please compare these five papers.
  
  Ahmad S. Khan, Zora Singh (2005) Postharvest application of 1-MCP affects ethylene biosynthesis and firmness of ‘Tegan Blue’ plum. Acta Horticulturae (ISHS) 687:409-412
  DOI: 10.17660/ActaHortic.2005.687.62
  http://www.actahort.org/books/687/687_62.htm
  International Society for Horticultural Science (ISHS)
  
  Ahmad S. Khan, Zora Singh (2007) 1-MCP regulates ethylene biosynthesis and fruit softening during ripening of Tegan Blue plum. Postharvest Biology and Technology Volume 43, Issue 3, pp 298–306
  DOI: 10.1016/j.postharvbio.2006.10.005
  http://www.sciencedirect.com/science/article/pii/S0925521406002808
  Elsevier
  
  Khan, A. S., and Z. Singh. (2008a). 1-Methylcyclopropene application and modified atmosphere packaging affect ethylene biosynthesis, fruit softening, and quality of ‘Tegan Blue’ Japanese plum during cold storage. Journal of the American Society for Horticultural Science 133: 290-299.
  http://journal.ashspublications.org/content/133/2/290.full.pdf+html
  American Society for Horticultural Science (ASHS)
  
  Khan, A.S. and Singh, Z. (2008b). 1-MCP application affects ethylene production, storage life and quality of ‘Tegan Blue’ plum. Acta Horticulturae (ISHS) 774, 143-150
  DOI: 10.17660/ActaHortic.2008.774.17
  http://dx.doi.org/10.17660/ActaHortic.2008.774.17
  International Society for Horticultural Science (ISHS)
  
  Ahmad S. Khan *, Zora Singh, Ewald E. Swinny ** (2009) Postharvest application of 1-methylcyclopropene modulates fruit ripening, storage life and quality of ‘Tegan Blue’ Japanese plum kept in ambient and cold storage. International Journal of Food Science & Technology, 44: 1272–1280.
  *Current address: Institute of Horticultural Sciences, University of Agriculture, Faisalabad, 38040, Pakistan
  **Current address: Food and Biological Chemistry Laboratory, Chemistry Centre, Perth, Western Australia, Australia
  doi: 10.1111/j.1365-2621.2009.01957.x
  http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2621.2009.01957.x/abstract
  Wiley
  
  Ahmad S. Khan, Zora Singh (2009b) Plant Science Volume 176, Issue 4, April, Pages 539–544
  1-MCP application suppresses ethylene biosynthesis and retards fruit softening during cold storage of Tegan Blue Japanese plum
  DOI: 10.1016/j.plantsci.2009.01.012
  http://www.sciencedirect.com/science/article/pii/S0168945209000132
  Elsevier
  
  2005: https://www.pubpeer.com/publications/468279CF9449216FC754B905836D14
  2007: https://www.pubpeer.com/publications/728D92B1DCC379C0AAE03DE2893060
  2008a: No DOI.
  2008b: https://www.pubpeer.com/publications/5237F0EA3092E0058AEAFF39EAA999
  2009: https://www.pubpeer.com/publications/D9E4BE6A173A8F699A0915BC2EA1F0
  2009b: https://pubpeer.com/publications/F8D1D9B0BEAC451BA232FE6FA372F6
  
  Reply
Tylophora indica query says:

December 31, 2015 at 12:54 am

Please observe potted plants across three publications.
http://imgur.com/5KFPWMJ

Thomas, T.D., Philip, B., 2005. Thidiazuron-induced high-frequency shoot organogenesis from leaf-derived callus of a medicinal climber, Tylophora Indica (Burm. f.) Merrill. In Vitro Cellular & Developmental Biology – Plant 41, 124–128. doi:10.1079/IVP2004575
http://link.springer.com/article/10.1079%2FIVP2004575
Springer
https://pubpeer.com/publications/F9B11E6638582815B7FE18FF653A4C

Thomas, T.D., 2006. Effect of sugars, gibberellic acid and abscisic acid on somatic embryogenesis in Tylophora indica (Burm. f.) Merrill. Chinese Journal of Biotechnology 22, 465–471. doi:10.1016/S1872-2075(06)60039-3
http://www.sciencedirect.com/science/article/pii/S1872207506600393
Elsevier
https://pubpeer.com/publications/9D42C52129B5745B5000BE3C25DCFE

Thomas, T.D., 2009. Isolation, callus formation and plantlet regeneration from mesophyll protoplasts of Tylophora indica (Burm. f.) Merrill: an important medicinal plant. In Vitro Cellular & Developmental Biology – Plant 45, 591–598. doi:10.1007/s11627-008-9190-6
http://link.springer.com/article/10.1007/s11627-008-9190-6
Springer
https://pubpeer.com/publications/998300F86FEA6500E4E7D25258A8D4

Reply
1. Tylophora indica query says:
  
  April 3, 2016 at 10:46 pm
  
  Please observe a figure from a 2016 book chapter (see PubPeer entry for 2009 paper).
  
  T. Dennis Thomas, Yoichiro Hoshino (2016) In Vitro Strategies for the Conservation of Some Medicinal and Horticultural Climbers. In: Anwar Shahzad, Shiwali Sharma, Saeed A. Siddiqui (eds.) Biotechnological strategies for the conservation of medicinal and ornamental climbers, Springer International Publishing, Switzerland, pp 259-290
  DOI: 10.1007/978-3-319-19288-8_10 (does not link to PubPeer)
  http://link.springer.com/chapter/10.1007/978-3-319-19288-8_10
  
  http://imgur.com/ZuCp5xC
  
  Reply
Ornamental cryopreservation query says:

January 3, 2016 at 8:23 pm

Please compare the two following publications:

Cryopreservation as a tool used in long-term storage of ornamental species – A review
Scientia Horticulturae, Volume 168, 26 March 2014, Pages 88-107
Dariusz Kulus, Małgorzata Zalewska
doi: 10.1016/j.scienta.2014.01.014
http://www.sciencedirect.com/science/article/pii/S0304423814000181

Somatic Embryogenesis in Ornamentals and Its Applications pp 1-25
Date: 23 December 2015
Application of Cryogenic Technologies and Somatic Embryogenesis in the Storage and Protection of Valuable Genetic Resources of Ornamental Plants
Editor: Abdul Mujib (Department of Botany, Hamdard University)
Dariusz Kulus
Department of Ornamental Plants and Vegetable Crops – Laboratory of Biotechnology, UTP University of Technology and Life Sciences in Bydgoszcz, Bernardyńska 6, PL-85-029, Bydgoszcz, Poland
http://link.springer.com/chapter/10.1007/978-81-322-2683-3_1
DOI: 10.1007/978-81-322-2683-3_1

https://pubpeer.com/publications/E1479C9953B3276D3A5C060F4DE8B6

Reply
Arabidopsis query says:

January 5, 2016 at 11:44 pm

Kindly observe the concerns about this paper originally raised on March 3, 2014:
https://pubpeer.com/publications/0D9514EB9544E56F630929A3D73CD3

“A downy mildew effector attenuates salicylic Acid-triggered immunity in Arabidopsis by interacting with the host mediator complex”
Marie-Cécile Caillaud, Shuta Asai, Ghanasyam Rallapalli, Sophie Piquerez, Georgina Fabro, Jonathan D G Jones, PLoS Biol., 11 (2013)

April 1, 2014, Jonathan D G Jones stated: “The authors are right to point out that the same GFP expression positive control image was used in 4C and 5A. The embarrassing error occurred when these figures were reconfigured in response to reviewer’s comments, at a time when the first author was leaving Norwich for France and about to give birth. We are working on a corrected version of Figs 4 and 5, and are discussing with PLOS biology to publish a corrigendum, and we also supplied the missing legend for Fig 5D which the critics helpfully pointed out.”

An erratum was published at the end of June, 2014:
10.1371/journal.pbio.1001909

Further errors and concerns were identified.

July 30, 2015: “thanks to “unregistered submission” for pointing out some valid scepticism about the statistics that were not commented on by either first or second round of reviewers. We are re-running analyses now and plan to post an update on this together with the details of this analysis 1st week of September (holidays and other commitments mean we can’t respond fully beforehand) Jonathan Jones”

October 15, 2015: “We’ve sent a revised statistical analysis to PLOS (which we believe confirms original conclusions) and they are consulting other statisticians about this, and we’ve shown them the data used to assemble fig 3b. It’s now with the journal- I’d have responded at greater length this week but the person leading on this at PLOS is away this week, JJ”

Reply
Mango postharvest query says:

January 9, 2016 at 12:31 am

Please compare these two papers.

Singh, Z. and Zaharah, S.S. (2013). Controlled atmosphere storage of mango fruit – an overview. Acta Horticulturae (ISHS) 992, 481-492
DOI: 10.17660/ActaHortic.2013.992.59
http://dx.doi.org/10.17660/ActaHortic.2013.992.59
http://www.actahort.org/books/992/992_59.htm
International Society for Horticultural Science

Singh, Z. and Zaharah, S.S. (2015). Controlled atmosphere storage of mango fruit: challenges and thrusts and its implications in international mango trade. Acta Horticulturae (ISHS) 1066, 179-191
DOI: 10.17660/ActaHortic.2015.1066.21
http://dx.doi.org/10.17660/ActaHortic.2015.1066.21
http://www.actahort.org/books/1066/1066_21.htm
International Society for Horticultural Science

2013:
https://pubpeer.com/publications/EF853E47669C2EAC6FEBDE383DB70E
2015:
https://pubpeer.com/publications/52D7661BD94A6DDDBE13A5F3F8AC07

Reply
Saffron query says:

January 14, 2016 at 1:57 pm

Please compare these three papers.
Karaoğlu C, Çöcü S, İpek A, Parmaksız I, Uranbey S, Sarıhan E, Arslan N, Kaya, M D, Sancak C, Özcan S, Gürbüz B, Mirici S, Er C, Khawar KM, 2007. In vitro micropropagation of saffron. Acta Horticulturae (ISHS) 739, 223–228.
Doi: 10.17660/ActaHortic.2007.739.28
http://www.actahort.org/books/739/739_28.htm

Wani BA, Mohiddin FA, 2009. Micropropagation of genus Crocus – A review. African Journal of Agricultural Research 4, 1545–1548.
http://www.academicjournals.org/article/article1380816952_Wani%20and%20Mohiddin.pdf

Glendon D. Ascough, John E. Erwin, Johannes van Staden (2009) Micropropagation of iridaceae – a review. Plant Cell, Tissue and Organ Culture 97 (1): 1-19
http://link.springer.com/article/10.1007/s11240-009-9499-9
DOI: 10.1007/s11240-009-9499-9

2007: https://pubpeer.com/publications/7EB6D8783A8FC2BB58EB15EFC82AFE
Ascough et al. 2009: https://pubpeer.com/publications/153301F8427DB986F6328C6DF02EC5

Reply
1. Saffron query says:
  
  January 15, 2016 at 11:54 pm
  
  Please observe these two publications.
  
  Sharifi G, Ebrahimzadeh H (2010) Changes of antioxidant enzyme, activities and isoenzyme profiles during in vitro shoot formation in saffron (Crocus sativus L.). Acta Biologica Hungarica 61(1), 73-89.
  DOI: 10.1556/ABiol.61.2010.1.8
  http://www.akademiai.com/doi/abs/10.1556/ABiol.61.2010.1.8
  Publisher: Akadémiai Kiadó
  
  Golandam Sharifi (2012) Plant antioxidative enzymes – case study: in vitro organogenesis of saffron (Crocus sativus L.).In: (Ed.) Mohammed Amr El-Missiry, Antioxidant Enzyme, ISBN 978-953-51-0789-7
  DOI: 10.5772/48590
  Department of Basic Sciences, Iranian Encyclopedia Compiling Foundation, Tehran, Iran
  http://www.intechopen.com/books/antioxidant-enzyme/plant-antioxidative-enzymes-case-study-in-vitro-organogenesis-of-saffron-crocus-sativus-l-
  http://www.intechopen.com/books/antioxidant-enzyme
  Publisher: Intech
  
  2010: https://www.pubpeer.com/publications/2DE5DEA6B2E1B46548930C04A7CBDF
  2012: https://www.pubpeer.com/publications/870ABF7D35DF689EE91954877EDC83
  
  Reply
  1. Saffron query says:
    
    April 12, 2016 at 1:35 pm
    
    Case closed.
    
    From Intech, yesterday, three key statements:
    
    “The investigation ultimately determined that the author’s reuse of her previously published work was done in an ethical and responsible manner.”
    
    “The journal’s [Acta Biologica Hungarica] representative has confirmed that they hold the reuse to be acceptable, and provided the author with a retroactive permission for the reproduction of text and figures in the chapter.”
    
    “…a disclaimer will be added to the chapter webpage stressing that parts of the chapter are reproduced from the author’s previous publications.”
    
    Reply
2. Saffron query says:
  
  April 21, 2016 at 1:45 pm
  
  Wani BA, Mohiddin FA, 2009. Micropropagation of genus Crocus – A review. African Journal of Agricultural Research 4, 1545–1548
  
  Retracted:
  http://www.academicjournals.org/journal/AJAR/article-full-text-pdf/5656B9232309
  
  “The authors, Bilal Ahmad Wani and F. A. Mohiddin, have requested for the retraction of their article titled “Micropropagation of genus Crocus – A review”, which was published in Vol. 4 (13), pp. 1545-1548, December 2009, from the journal’s website and publisher’s database. The retraction is based on the complaint that the data contained in the article were a direct replica of another published previously. Based on this, I, Bilal Ahmad Wani, kindly request the journal to remove the paper at the earliest to avoid further inconvenience to the owners of the original article. Bilal Ahmad Wani is deeply sorry for any inconvenience this may have caused the editorial staff, readers, co-author and other researchers. To further stop any complication from the viewership and distribution of this article, the African Journal of Agricultural Research is retracting the article in its entirety with the consent of Bilal Ahmad Wani.”
  
  Reply
Urtica vs Nasturtium query says:

January 16, 2016 at 8:51 am

Please observe these two papers.

Didem Aksoy Körpe 1, Özlem Darcansoy Iseri 1, Feride Iffet Sahin 1,2, Evren Cabi 3, Mehmet Haberal 1,4
International Journal of Food Sciences and Nutrition May 2013; 64(3): 355–362
High-antibacterial activity of Urtica spp. seed extracts on food and plant pathogenic bacteria
DOI: 10.3109/09637486.2012.734290
http://www.ncbi.nlm.nih.gov/pubmed/23067263
http://www.tandfonline.com/doi/abs/10.3109/09637486.2012.734290?journalCode=iijf20#.VpoIMlJpXss
Informa Healthcare (Informa UK, Ltd)
Taylor & Francis

Özlem Darcansoy Iseri 1, Didem Aksoy Körpe 1, Feride Iffet Sahin 1,2, Mehmet Haberal 1,3 (2014)
Screening of Nasturtium officinale extracts for biological activities: implications for plant pathogens.
Journal of Biologically Active Products from Nature, 4:1, 19-28
DOI: 10.1080/22311866.2014.886962
http://dx.doi.org/10.1080/22311866.2014.886962
http://www.tandfonline.com/doi/abs/10.1080/22311866.2014.886962
Taylor & Francis

2013: https://pubpeer.com/publications/A10E165F7AC6CDE08CFDE7F1232665
2014: https://pubpeer.com/publications/7A32DBE802DBEDDAB8D54E44AE4EAE

Reply
Arabidopsis query says:

January 31, 2016 at 6:22 am

Kindly observe the figures of this paper.

Journal of Experimental Botany (2016) 67 (1): 175-194.
Overexpression of soybean miR172c confers tolerance to water deficit and salt stress, but increases ABA sensitivity in transgenic Arabidopsis thaliana
Wenbin Li, Tao Wang, Yuhang Zhang, Yongguang Li, EXBOTJ (2015)
doi: 10.1093/jxb/erv450
http://jxb.oxfordjournals.org/content/67/1/175

https://pubpeer.com/publications/E5B053CB26789D2743043FFC25393C

Reply
Cactus query says:

February 16, 2016 at 1:30 am

Kindly compare the following two Springer book chapters.

1990
Plant Cell and Tissue Culture
Volume 6 of the series Methods in Molecular Biology™ pp 219-225
Vegetative Propagation of Cacti and Other Succulents In Vitro
Jill Gratton, Michael F. Fay
Royal Botanic Gardens, Kew, Surrey, UK
http://link.springer.com/protocol/10.1385/0-89603-161-6%3A219
DOI: 10.1385/0-89603-161-6:219

1997
Plant Cell Culture Protocols
Volume 111 of the series Methods In Molecular Biology™ pp 135-140
In Vitro Propagation of Succulent Plants
Jill Gratton 1, Michael F. Fay 2
http://link.springer.com/protocol/10.1385/1-59259-583-9%3A135
1. Royal Botanic Gardens, Kew, Richmond, Surrey, UK
2. Department of Life Sciences, University of Nottingham, University Park, Nottingham, UK
DOI: 10.1385/1-59259-583-9:135

https://pubpeer.com/publications/C3FD0438340D73CE148AD34F3B3E50

Reply
1. Cactus query says:
  
  February 17, 2016 at 3:06 am
  
  Kindly compare some of the data in these two manuscripts.
  
  1999a
  Plant Cell, Tissue and Organ Culture 58: 1–9, 1999.
  Alterations in growth and crassulacean acid metabolism (CAM) activity of in vitro cultured cactus
  Guadalupe Malda, Ralph A. Backhaus, Chris Martin
  Received 10 February 1998; accepted in revised form 21 September 1999
  Springer
  http://link.springer.com/article/10.1023%2FA%3A1006377206855
  DOI: 10.1023/A:1006377206855 (DOI does not link to PubPeer)
  
  1999b
  Scientia Horticulturae 81 (1999) 71-87
  In vitro culture as a potential method for the conservation of endangered plants possessing crassulacean acid metabolism
  Guadalupe Malda, Humberto Suzan, Ralph Backhaus
  Accepted 22 October 1998, Available online 24 March 1999
  Elsevier
  http://www.sciencedirect.com/science/article/pii/S0304423898002507
  DOI: 10.1016/S0304-4238(98)00250-7
  
  1999b: https://pubpeer.com/publications/79FB47DF0B7ABD1CBE21B065B45F0A
  
  Reply
Ranunculus query says:

February 17, 2016 at 3:09 am

Please compare the figures of this 2007 original research paper and 2009 book chapter, both published by Springer.

Original Article
Plant Biotechnology Reports
April 2007, Volume 1, Issue 1, pp 57-60
Plant regeneration from zygotic embryo-derived embryogenic cell suspension cultures of Ranunculus kazusensis
Sung Ran Min, Jang Ryol Liu, Suk Weon Kim
http://link.springer.com/article/10.1007/s11816-006-0005-0
DOI: 10.1007/s11816-006-0005-0

Protocol
Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants
Volume 547 of the series Methods in Molecular Biology pp 107-115
Establishment of Plant Regeneration and Cryopreservation System from Zygotic Embryo-Derived Embryogenic Cell Suspension Cultures of Ranunculus kazusensis
Suk Weon Kim, Myung Jin Oh
Editors: Praveen K. Saxena, S. Mohan Jain
Springer
http://link.springer.com/protocol/10.1007%2F978-1-60327-287-2_9
http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-60327-287-2_9
http://www.ncbi.nlm.nih.gov/pubmed/19521839
DOI: 10.1007/978-1-60327-287-2_9

Author and editors contacted: 17 February, 2016.

2007: https://pubpeer.com/publications/3362D658151A92F175CE458B27C8D4
2009: https://pubpeer.com/publications/6DE49092C11F6A74621E8404C51BBB

Reply
Maize query says:

February 17, 2016 at 10:52 am

Kindly observe some of the figures of this paper.

Article: Stress Sensitivity Is Associated with Differential Accumulation of Reactive Oxygen and Nitrogen Species in Maize Genotypes with Contrasting Levels of Drought Tolerance
by Liming Yang, Jake C. Fountain, Hui Wang, Xinzhi Ni, Pingsheng Ji, Robert D. Lee, Robert C. Kemerait, Brian T. Scully and Baozhu Guo
International Journal of Molecular Science 2015, 16(10), 24791-24819;
doi: 10.3390/ijms161024791
Received: 12 July 2015 / Revised: 28 September 2015 / Accepted: 12 October 2015 / Published: 19 October 2015
http://www.mdpi.com/1422-0067/16/10/24791
http://www.mdpi.com/1422-0067/16/10/24791/htm

https://pubpeer.com/publications/4D809A0B478B67948A6E7D4630A71B

Reply
Maize query says:

February 17, 2016 at 10:15 pm

Please compare the figures of these 2006 and 2009 original research papers and a 2009 book chapter, all three published by Springer.

Article
Journal of Plant Biology
June 2006, 49:193
Optimization of culturing conditions for the production of biomass and phenolics from adventitious roots of Echinacea angustifolia
Chun-Hua Wu, Yaser Hassan Dewir, Eun-Joo Hahn, Kee-Yoeup Paek
http://link.springer.com/article/10.1007/BF03030532
DOI: 10.1007/BF03030532

Article
Biotechnology and Bioprocess Engineering
February 2009, Volume 14, Issue 1, pp 91-98
Application of an airlift bioreactor system for the production of adventitious root biomass and caffeic acid derivatives of Echinacea purpurea
Jin-A Jeong, Chun-Hua Wu, Hosakatte Niranjana Murthy, Eun-Joo Hahn, Kee-Yoeup Paek
http://link.springer.com/article/10.1007/s12257-007-0142-5
DOI: 10.1007/s12257-007-0142-5

Protocol
Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants
Volume 547 of the series Methods in Molecular Biology pp 3-16
Establishment of Adventitious Root Cultures of Echinacea purpurea for the Production of Caffeic Acid Derivatives
Kee-Yoeup Paek, Hosakatte Niranjana Murthy, Eun-Joo Hahn
http://link.springer.com/protocol/10.1007/978-1-60327-287-2_1
DOI: 10.1007/978-1-60327-287-2_1

2006: https://pubpeer.com/publications/E9D7CCA09466120FA20579F8FD1E97
2009 BBE: https://pubpeer.com/publications/3DA1D0600D57D14FB7D97F1DF3891C
2009 book: https://pubpeer.com/publications/6DE49092C11F6A74621E8404C51BBB

Reply
Echinacea query says:

February 17, 2016 at 10:16 pm

Please compare the figures of these 2006 and 2009 original research papers and a 2009 book chapter, all three published by Springer.

Article
Journal of Plant Biology
June 2006, 49:193
Optimization of culturing conditions for the production of biomass and phenolics from adventitious roots of Echinacea angustifolia
Chun-Hua Wu, Yaser Hassan Dewir, Eun-Joo Hahn, Kee-Yoeup Paek
http://link.springer.com/article/10.1007/BF03030532
DOI: 10.1007/BF03030532

Article
Biotechnology and Bioprocess Engineering
February 2009, Volume 14, Issue 1, pp 91-98
Application of an airlift bioreactor system for the production of adventitious root biomass and caffeic acid derivatives of Echinacea purpurea
Jin-A Jeong, Chun-Hua Wu, Hosakatte Niranjana Murthy, Eun-Joo Hahn, Kee-Yoeup Paek
http://link.springer.com/article/10.1007/s12257-007-0142-5
DOI: 10.1007/s12257-007-0142-5

Protocol
Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants
Volume 547 of the series Methods in Molecular Biology pp 3-16
Establishment of Adventitious Root Cultures of Echinacea purpurea for the Production of Caffeic Acid Derivatives
Kee-Yoeup Paek, Hosakatte Niranjana Murthy, Eun-Joo Hahn
http://link.springer.com/protocol/10.1007/978-1-60327-287-2_1
DOI: 10.1007/978-1-60327-287-2_1

2006: https://pubpeer.com/publications/E9D7CCA09466120FA20579F8FD1E97
2009 BBE: https://pubpeer.com/publications/3DA1D0600D57D14FB7D97F1DF3891C
2009 book: https://pubpeer.com/publications/6DE49092C11F6A74621E8404C51BBB

Reply
Senna query says:

February 22, 2016 at 1:41 pm

Please compare these two papers.

Clinical Phytoscience (2015) 1:6
DOI 10.1186/s40816-015-0007-y
Phytochemical screening, antioxidant and antimicrobial activities of Senna occidentalis (L.) leaves extract
Oluwakayode Odeja, Grace Obi, Christiana Ene Ogwuche, Elias Emeka Elemike, Yemi Oderinlo
http://link.springer.com/article/10.1186/s40816-015-0007-y
International Journal of Herbal Medicine 2014; 2 (4): 26-30
Phytochemical screening, antioxidant and antimicrobial activities of Senna occidentalis (L.) leaves
Odeja OO, Obi G, Ogwuche CE, Elemike EE, Oderinlo OO.
http://www.florajournal.com/vol2issue4/dec2014/2-3-24.1.pdf

https://pubpeer.com/publications/862A591F15D4D988FD7BC160D9A42A

Reply
1. Lantana camara retraction says:
  
  June 17, 2016 at 9:28 am
  
  RETRACTED ARTICLE: Phytochemical Screening, Antioxidant and Antimicrobial activities of Senna occidentalis (L.) leaves Extract
  Oluwakayode Odeja, Grace Obi, Christiana Ene Ogwuche, Elias Emeka ElemikeEmail author and Yemi Oderinlo
  Clinical PhytoscienceInternational Journal of Phytomedicine and Phytotherapy 2015 1:6
  DOI: 10.1186/s40816-015-0007-y
  http://clinphytoscience.springeropen.com/articles/10.1186/s40816-015-0007-y
  
  Retraction Note: Phytochemical Screening, Antioxidant and Antimicrobial activities of Senna occidentalis (L.) leaves Extract
  Oluwakayode Odeja, Grace Obi, Christiana Ene Ogwuche, Elias Emeka ElemikeEmail author and Yemi Oderinlo
  Clinical PhytoscienceInternational Journal of Phytomedicine and Phytotherapy 2016 2:13
  DOI: 10.1186/s40816-016-0028-1
  http://clinphytoscience.springeropen.com/articles/10.1186/s40816-016-0028-1
  
  Reply
Arabidopsis query says:

February 26, 2016 at 4:44 am

Please observe figure 3 of this paper.

New Phytologist (2014) 203(2): 592–606
The Arabidopsis thaliana mitogen-activated protein kinases MPK3 and MPK6 target a subclass of ‘VQ-motif’-containing proteins to regulate immune responses
Pascal Pecher, Lennart Eschen-Lippold, Siska Herklotz, Katja Kuhle, Kai Naumann, Gerit Bethke, Joachim Uhrig, Martin Weyhe, Dierk Scheel, Justin Lee
doi: 10.1111/nph.12817
http://onlinelibrary.wiley.com/doi/10.1111/nph.12817/abstract

https://pubpeer.com/publications/156E9291D3B8BA0F00058C51AE24CA

Reply
Gymnema sylvestre query says:

March 2, 2016 at 3:46 am

Kindly observe figure 2 of this paper.

Industrial Crops and Products
Volume 77, 23 December 2015, Pages 901–909
Assessment of diversity amongst natural populations of Gymnema sylvestre from India and development of a validated HPLC protocol for identification and quantification of gymnemagenin
Tushar Dhanani, Raghuraj Singh, Ajit Waman, Prakash Patel, Ponnuchamy Manivel, Satyanshu Kumar
http://www.sciencedirect.com/science/article/pii/S0926669015304362
doi: 10.1016/j.indcrop.2015.09.076

https://pubpeer.com/publications/68DE197E8B050C68E5B68341976B13

Reply
Arabidopsis query says:

March 10, 2016 at 10:20 am

A PLOS Biology paper has just received a second correction.

Caillaud M-C, Asai S, Rallapalli G, Piquerez S, Fabro G, Jones JDG (2013) A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex. PLoS Biol 11(12): e1001732. doi:10.1371/journal.pbio.1001732
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001732

Correction 1:
25 Jun 2014: The PLOS Biology Staff (2014) Correction: A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex. PLoS Biol 12(6): e1001909. doi: 10.1371/journal.pbio.1001909
10.1371/journal.pbio.1001909
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001909

Correction 2:
2 Mar 2016: Caillaud MC, Asai S, Rallapalli G, Piquerez S, Fabro G, et al. (2016) Correction: A Downy Mildew Effector Attenuates Salicylic Acid-Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex. PLoS Biol 14(3): e1002408. doi: 10.1371/journal.pbio.1002408
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002408

https://pubpeer.com/publications/0D9514EB9544E56F630929A3D73CD3

Reply
Salvia query says:

March 12, 2016 at 1:06 pm

Please observe the figure in this paper.

Applied Biochemistry and Biotechnology
March 2015, Volume 175, Issue 5, pp 2689-2702
First online: 06 January 2015
Calcium Mobilization in Salicylic Acid-Induced Salvia miltiorrhiza Cell Cultures and Its Effect on the Accumulation of Rosmarinic Acid
Hongbo Guo, Nan Zhu, Michael K. Deyholos, Jun Liu, Xiaoru Zhang, Juane Dong
http://link.springer.com/article/10.1007/s12010-014-1459-0
DOI: 10.1007/s12010-014-1459-0
https://pubpeer.com/publications/652E23E5270826434A05D05DE6E8A3

Reply
Cannabis query says:

March 13, 2016 at 11:08 am

Please observe the figure in this paper.

Applied Biochemistry and Biotechnology
March 2015, Volume 175, Issue 5, pp 2366-2375
First online: 10 December 2014
Effect of Induced Polyploidy on Some Biochemical Parameters in Cannabis sativa L.
Mahsa Bagheri, Hakimeh Mansouri
http://link.springer.com/article/10.1007/s12010-014-1435-8
DOI: 10.1007/s12010-014-1435-8
https://pubpeer.com/publications/127296A4E1194D41102331774F33EC

Reply
Tobacco (Nicotiana tabacum) query says:

March 13, 2016 at 11:43 am

Kindly observe several figures in this paper.

Applied Biochemistry and Biotechnology
April 2015, Volume 175, Issue 8, pp 3599-3616
Comparison and Evaluation of Two Diagnostic Methods for Detection of npt II and GUS Genes in Nicotiana tabacum
Mohammad Amin Almasi, Mehdi Aghapour-ojaghkandi, Khadijeh Bagheri, Mohammadreza Ghazvini, Seyed Mohammad Hosseyni-dehabadi
http://link.springer.com/article/10.1007/s12010-015-1529-y
DOI: 10.1007/s12010-015-1529-y
https://pubpeer.com/publications/E1DC2AB1ECCD0F788EDF8EA326161C

Reply
Tobacco query says:

March 17, 2016 at 4:04 pm

Please observe the figures in these two manuscripts.

Journal of Experimental Botany (2006) 57 (10): 2173-2182.
Effects of simultaneous expression of heterologous genes involved in phytochelatin biosynthesis on thiol content and cadmium accumulation in tobacco plants
Adam Wawrzyński, Edyta Kopera, Anna Wawrzyńska, Jolanta Kamińska, Wojciech Bal, Agnieszka Sirko
http://jxb.oxfordjournals.org/content/57/10/2173.long
http://www.ncbi.nlm.nih.gov/pubmed/16720610
DOI: 10.1093/jxb/erj176
PMID: 16720610

Acta Biochimica Polonica 48(3): 647-656 (2001)
Modification of non-protein thiols contents in transgenic tobacco plants producing bacterial enzymes of cysteine biosynthesis pathway
Frantz Liszewska, Anna Blaszczyk, Agnieszka Sirko
http://www.actabp.pl/#File?./html/3_2001/647.html

https://pubpeer.com/publications/92F9FF864C2F67D50CBF3A76EBEE5D

Reply
Spilanthes and Cassia query says:

March 17, 2016 at 5:16 pm

Kindly observe the figures in these two papers.

Physiology and Molecular Biology of Plants
April 2013, Volume 19, Issue 2, pp 251-260
In vitro clonal propagation and genetic fidelity of the regenerants of Spilanthes calva DC. using RAPD and ISSR marker
Mohd. Razaq, Monika Heikrujam, Siva K. Chetri, Veena Agrawal
http://www.ncbi.nlm.nih.gov/pubmed/24431493
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656186/
http://link.springer.com/article/10.1007%2Fs12298-012-0152-4
DOI: 10.1007/s12298-012-0152-4
PMID: 24431493
PMCID: PMC3656186

Physiology and Molecular Biology of Plants
October 2014, Volume 20, Issue 4, pp 517-526
Micropropagation and validation of genetic and biochemical fidelity amongst regenerants of Cassia angustifolia Vahl employing RAPD marker and HPLC
Siva K. Chetri, Pratima Rani Sardar, Veena Agrawal
http://www.ncbi.nlm.nih.gov/pubmed/25320475
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185055/
http://link.springer.com/article/10.1007%2Fs12298-014-0257-z
DOI: 10.1007/s12298-014-0257-z
PMID: 25320475
PMCID: PMC4185055

Spilanthes 2013:
https://pubpeer.com/publications/EDB5AB063FCEF7910C501B737D2CFF
https://pubpeer.com/publications/24431493

Cassia 2014:
https://pubpeer.com/publications/05729B4AAC5F81445C083DC4C3E8A2

Reply
Aegle marmelos withdrawn says:

March 19, 2016 at 3:14 pm

Evaluation of antioxidant activity, quantitative estimation of phenols and flavonoids in different parts of Aegle marmelos”
Nadeem A. Siddique, Mohd Mujeeb, Abul K. Najmi, H.N. Khan, Humaira Farooqi, Journal of Saudi Chemical Society (2010)
http://www.sciencedirect.com/science/article/pii/S1319610310001213
DOI: 10.1016/j.jscs.2010.10.005

This paper was withdrawn, but the precise reason is not indicated and the withdrawn paper is not shown.

Another paper with the same title and authorship was discovered, however:

African Journal of Plant Science Vol. 4 (1), pp. 001-005, January, 2010
Evaluation of antioxidant activity, quantitative estimation of phenols and flavonoids in different parts of Aegle marmelos
Nadeem Ahmad Siddique, Mohd Mujeeb, Abdul Kalam Najmi, Mohd Akram
http://www.academicjournals.org/journal/AJPS/article-full-text-pdf/8F7047F11260
http://www.academicjournals.org/journal/AJPS/article-abstract/8F7047F11260

https://pubpeer.com/publications/8DF19C3EF575DF9A556E6C3C22CE15

Reply
Primula veris query says:

March 27, 2016 at 1:54 pm

Please observe these two papers*

Physiology and Molecular Biology of Plants
January 2015, Volume 21, Issue 1, pp 117-122
Initial determination of DNA polymorphism of some Primula veris L. populations from Kosovo and Austria
Naim Berisha, Fadil Millaku, Bekim Gashi, Elez Krasniqi, Johannes Novak
http://link.springer.com/article/10.1007/s12298-014-0275-x
DOI: 10.1007/s12298-014-0275-x
http://www.ncbi.nlm.nih.gov/pubmed/25650329
PMID: 25650329
PMCID: PMC4312321

Journal of Applied Biological Sciences 8(3): 59-64 (2014)
Initial determination of DNA polymorphism of some Primula veris L. populations from Kosovo and Austria
Naim BERISHA, Fadil MILLAKU, Bekim GASHI, Elez KRASNIQI, Johannes NOVAK
http://www.nobel.gen.tr/MakaleDetay2.aspx?ID=3511&islem=pdf
http://www.nobel.gen.tr/Makaleler/JABS-Issue%203-6aa5d7af8e41428898b949b41d65a2ad.pdf
Publisher: Nobel International Journals

* copy available from the ResearchGate profile of the first author:
https://www.researchgate.net/profile/Naim_Berisha/publications

Reply
Eleusine coracana query says:

March 28, 2016 at 1:09 am

Please observe figure 3 of this paper.

Physiology and Molecular Biology of Plants
October 2015, Volume 21, Issue 4, pp 551-558
Oxidative stress induced expression of monodehydroascorbate reductase gene in Eleusine coracana
Jebi Sudan, Bhawana Negi, Sandeep Arora
http://link.springer.com/article/10.1007/s12298-015-0327-x
doi: 10.1007/s12298-015-0327-x
http://www.ncbi.nlm.nih.gov/pubmed/26600681

https://pubpeer.com/publications/3FD42C4A4F3C6D18586280BBC4ED3A

Reply
Psoralea corylifolia query says:

March 31, 2016 at 3:44 am

Please observe these three papers.

2011:
Plant Physiology and Biochemistry Volume 49, Issue 10, October 2011, Pages 1138–1146
In vitro isolation, elicitation of psoralen in callus cultures of Psoralea corylifolia and cloning of psoralen synthase gene
Behrooz M. Parast, Siva K. Chetri, Kuldeep Sharma, Veena Agrawal
http://www.sciencedirect.com/science/article/pii/S0981942811001124
doi: 10.1016/j.plaphy.2011.03.017
http://www.ncbi.nlm.nih.gov/pubmed/21524916
PMID: 21524916

2012:
Analytical Chemistry Letters, 2:4, 227-234 (2012)
Quantification of psoralen in plant parts of Psoralea corylifolia growing in vivo and in vitro and enhancement of psoralen by organic elicitors
Behrooz Mohammad Parast, Mousa Rasouli, Milad Manafi, Veena Agrawal
http://dx.doi.org/10.1080/22297928.2012.10648273
http://www.tandfonline.com/doi/abs/10.1080/22297928.2012.10648273
DOI: 10.1080/22297928.2012.10648273

2015:
Pharmaceutical Biology 2015; 53(5): 735–738
In vitro enhancement of psoralen as an important anticancer compound in Psoralea corylifolia through precursor feeding
Behrooz Mohammadparast, Ali Reza Rustaiee, Mousa Rasouli, Sannaz Zardari, Veena Agrawal
http://www.tandfonline.com/doi/abs/10.3109/13880209.2014.942786
http://www.ncbi.nlm.nih.gov/pubmed/25331001
PMID: 25331001
DOI: 10.3109/13880209.2014.942786

2011:
https://pubpeer.com/publications/5178100E66900C222717D3B3AB84ED

2012:
https://pubpeer.com/publications/B2BAE4F6C925E4A03BD8762098002C

2015:
https://pubpeer.com/publications/A297EAFD0DFB48981742DD9E7EF42D

Reply
Brassidium Shooting Star orchid query says:

April 1, 2016 at 2:32 pm

Please observe the figures in this manuscript.

Applied Biochemistry and Biotechnology (2014) 172:1131–1145
Cryopreservation of Brassidium Shooting Star Orchid Using the PVS3 Method Supported with Preliminary Histological Analysis
Safiah Ahmad Mubbarakh, Safrina Rahmah, Zuraida Abdul Rahman, Nazrin Nadirah Mohd Sah, Sreeramanan Subramaniam
DOI: 10.1007/s12010-013-0597-0
http://link.springer.com/article/10.1007/s12010-013-0597-0

https://pubpeer.com/publications/5F9BFACB594F4E7A5704FDBDAB0B63

Reply
1. Brassidium Shooting Star orchid query says:
  
  April 4, 2016 at 8:53 am
  
  Authors respond within 24 hours.
  
  “After reviewing the details of the comments issued previously, we have noted and accepted one error with modifications made for the rest of the points. Thank you for pointing this out to us. We have submitted the corrected figures to the publisher.
  
  The error noted in the placement and captioning of images 7h and 10e is noted with gratitude. Hence, Figure 10e has been replaced with a new image that represents a PLB that was subjected to the cryopreservation treatment.
  
  All other photographs listed as repetitions or reproductions of similar images throughout the article are those of tissue segments that belong to the same group of treatment in the study. For instance, Figures 7g, 9b, and 10c represent the image of a PLB that was subjected to preculture in 0.75 M sucrose, dehydration in PVS3 for 20 minutes, and unloading in 1.2 M sucrose for 20 minutes. The same case was noted for the following set of images: Figures 7c and 9d, 9c and 10d, and finally 7e and 10a.
  
  However, we have replaced the images to not overlap, if this is the main concern of the reviewer (to avoid confusion). Consequently, all photographs in Figure 7 have not been altered. All alterations were conducted in Figures 8, 9 and 10, and are listed as below:
  
  1. Figure 7h was retained, and Figure 10e was replaced with a new image.
  2. Figure 8f was retained, and Figure 8e was replaced with a new image.
  3. Figure 7g was retained, and Figures 9b and 10c were replaced with new images.
  4. Figure 7c was retained, and Figure 9d was replaced with a new image.
  5. Figure 9c was retained, and Figure 10d was replaced with a new image.
  6. Figure 7e was retained, and Figure 10a was replaced with a new image.
  
  Despite changing the mentioned images, all captions and labels for the new images have been retained as they represent similar sections of the original photographs (refer to the attachment in the word files [Fig. 7, 8, 9 and 10] and individual images [Figs. 7a-j ; Fig. 8a-8h ; Fig. 9a-3 ; Figs. 10 a-e]. All the images attached with scale bar.”
  
  Reply
Tylophora indica query says:

April 3, 2016 at 1:29 pm

Please observe one figure in each of these two papers.

Rao, P.S., Narayanaswami, S., Benjamin, B.D., 1970. Differentiation ex ovulo of embryos and plantlets stem tissue cultures of Tylophora indica. Physiologia Plantarum 23, 140–144.
doi: 10.1111/j.1399-3054.1970.tb06401.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.1970.tb06401.x/abstract

Rao, P.S., Narayanaswami, S., 1972. Morphogenetic investigations in callus cultures of Tylophora indica. Physiologia Plantarum 27, 271–276.
doi: 10.1111/j.1399-3054.1972.tb03613.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.1972.tb03613.x/abstract

1970: https://pubpeer.com/publications/A2526467F09E90EFC53B891B05AEE0
1972: https://pubpeer.com/publications/15D2204042A2A7EE16AB8D5D43D093

Reply
Rhinacanthus nasutus query says:

April 3, 2016 at 11:43 pm

Kindly observe the RAPD gel of this paper.

Applied Biochemistry and Biotechnology
February 2014, Volume 172, Issue 3, pp 1172-1182
Shoot organogenesis from root-derived callus of Rhinacanthus nasutus (L.) Kurz. and assessment of clonal fidelity of micropropagted plants using RAPD analysis
Meena K. Cheruvathur, T. Dennis Thomas
http://link.springer.com/article/10.1007/s12010-013-0598-z
DOI: 10.1007/s12010-013-0598-z

https://pubpeer.com/publications/CAA562128AE2FA4FFF978FA8FA2A16

Reply
Black gram (Vigna mungo L.) query says:

April 5, 2016 at 3:23 am

Kindly observe these 6 papers.

Physiology and Molecular Biology of Plants
pp 1-11
First online: 05 March 2016
Expression of a bacterial chitinase (ChiB) gene enhances resistance against E. polygoni induced powdery mildew disease in the transgenic Black gram (Vigna mungo L.) (cv. T9)
D. K. Das
Post Graduate Department of Biotechnology, T. M. Bhagalpur University, Bhagalpur, India
http://link.springer.com/article/10.1007/s12298-016-0344-4
DOI: 10.1007/s12298-016-0344-4

Agrobacterium Mediated Transformation of Vigna mungo (L.) Hepper with Cry1Ac Gene for Insect Resistance
American Journal of Plant Sciences Vol.7 No.2, Pub. Date: February 22, 2016
Dilip Kumar Das, Mrinalini Bhagat, Sangeeta Shree
http://www.scirp.org/journal/PaperInformation.aspx?PaperID=63629
DOI: 10.4236/ajps.2016.72031

Plant Science Volume 134, Issue 2, 5 June 1998, Pages 199–206
An efficient regeneration system of black gram (Vigna mungo L.) through organogenesis
Dilip K Das, N.Shiva Prakash, Neera Bhalla-Sarin
http://www.sciencedirect.com/science/article/pii/S0168945298000442
doi: 10.1016/S0168-9452(98)00044-2

In Vitro Cellular & Developmental Biology – Plant
September 2002, Volume 38, Issue 5, pp 456-459
Improved method of regeneration of black gram (Vigna mungo L.) through liquid culture.
Dilip K. Das, Prasanna Bhomkar, N. Shiva Prakash, Neera Bhalla-Sarin
http://link.springer.com/article/10.1079/IVP2002336
DOI: 10.1079/IVP2002336

Current Trends in Biotechnology and Pharmacy 4(3): 820-833 (July, 2010)
Expression of a bacterial chitinase (ChiB) gene enhances antifungal potential in transgenic Litchi chinensis Sonn. (cv. Bedana)
Das, D.K., Rahman, A.
http://abap.co.in/expression-bacterial-chitinase-chib-gene-enhances-antifungal-potential-transgenic-litchi-chinensis-s
http://www.abap.co.in/expression-bacterial-chitinase-chib-gene-enhances-antifungal-potential-transgenic-litchi-chinensis-s

Plant Cell, Tissue and Organ Culture (PCTOC)
May 2012, Volume 109, Issue 2, pp 315-325
First online: 15 March 2012
Expression of a rice chitinase gene enhances antifungal response in transgenic litchi (cv. Bedana)
D. K. Das, A. Rahman
http://link.springer.com/article/10.1007/s11240-011-0097-2
DOI: 10.1007/s11240-011-0097-2

2016 PMBP:
https://pubpeer.com/publications/13DCE80F38834887D2AC8D3B5616F3
2016 AJPS:
https://pubpeer.com/publications/E6FADB2C85219B0E8E779556798361
2012 PCTOC:
https://pubpeer.com/publications/78C0893198FFC429B2C08B9BBD3F1B
1998 PS:
https://pubpeer.com/publications/C31EC503888E9468CFA63B9DC3487C
2002 IVCDBP:
https://pubpeer.com/publications/06F2678890FAA22419D1266F1C7B1B

Reply
Silver and gold nanoparticles from plants queries says:

April 5, 2016 at 4:12 pm

Kindly observe the queries related to the production of nanoparticles in these 6 papers.

Environmental Science and Pollution Research
October 2014, Volume 21, Issue 19, pp 11439-11446
Rapid biological synthesis of silver nanoparticles using Leucas martinicensis leaf extract for catalytic and antibacterial activity
S. Ashokkumar, S. Ravi, V. Kathiravan, S. Velmurugan
http://link.springer.com/article/10.1007/s11356-014-3012-7
http://www.ncbi.nlm.nih.gov/pubmed/24906826
PMID: 24906826
DOI: 10.1007/s11356-014-3012-7
https://pubpeer.com/publications/C7A458A513D4E438E0FAA90D1C842B

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy Volume 121, 5 March 2014, Pages 88–93
Synthesis, characterization and catalytic activity of silver nanoparticles using Tribulus terrestris leaf extract
S. Ashokkumar, S. Ravi, V. Kathiravan, S. Velmurugan
http://www.sciencedirect.com/science/article/pii/S1386142513012304
http://www.ncbi.nlm.nih.gov/pubmed/24231743
PMID: 24231743
doi: 10.1016/j.saa.2013.10.073
https://pubpeer.com/publications/0FCA4DB408DEBB3C0950EF1E748D3D

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 136, Part B, 5 February 2015, Pages 1052-1057
Facile, eco-friendly and template free photosynthesis of cauliflower like ZnO nanoparticles using leaf extract of Tamarindus indica (L.) and its biological evolution of antibacterial and antifungal activities
K. Elumalai, S. Velmurugan, S. Ravi, V. Kathiravan, S. Ashokkumar
http://www.sciencedirect.com/science/article/pii/S1386142514014875
http://www.ncbi.nlm.nih.gov/pubmed/25459502
PMID: 25459502
DOI: 10.1016/j.saa.2014.09.129
https://pubpeer.com/publications/50BE46B628DE5079A849CF6221504D

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 143, 15 May 2015, Pages 158-164
Green synthesis of zinc oxide nanoparticles using Moringa oleifera leaf extract and evaluation of its antimicrobial activity
K. Elumalai, S. Velmurugan, S. Ravi, V. Kathiravan, S. Ashokkumar
http://www.sciencedirect.com/science/article/pii/S1386142515001638
DOI: 10.1016/j.saa.2015.02.011
http://www.ncbi.nlm.nih.gov/pubmed/25725211
PMID: 25725211
https://pubpeer.com/publications/3357523210A65BBACD98ED3773FEA6

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 134, 5 January 2015, Pages 34-39
Synthesis of silver nanoparticles using A. indicum leaf extract and their antibacterial activity
S. Ashokkumar, S. Ravi, V. Kathiravan, S. Velmurugan
http://www.sciencedirect.com/science/article/pii/S1386142514008671
doi:10.1016/j.saa.2014.05.076
http://www.ncbi.nlm.nih.gov/pubmed/24997264
PMID: 24997264
https://pubpeer.com/publications/1A9D4450FF6594B7A71B5A182B228F

Applied Surface Science
Volume 345, 1 August 2015, Pages 329–336
Green synthesis, characterization and antimicrobial activities of zinc oxide nanoparticles from the leaf extract of Azadirachta indica (L.)
K. Elumalai, S. Velmurugan
http://www.sciencedirect.com/science/article/pii/S0169433215007928
doi:10.1016/j.apsusc.2015.03.176
https://pubpeer.com/publications/A3B24EB94EF995620CB365CBF2FD5A

Reply
Tylophora indica query says:

April 7, 2016 at 2:56 am

Kindly observe these four publications.

Sahai, A., Shahzad, A., Anis, M., 2010a. High frequency plant production via shoot organogenesis and somatic embryogenesis from callus in Tylophora indica, an endangered plant species. Turkish Journal of Botany 34, 11–20.
doi: 10.3906/bot-0809-3 (does not link to PubPeer)
http://journals.tubitak.gov.tr/botany/issues/bot-10-34-1/bot-34-1-2-0809-3.pdf

Sahai, A., Shahzad, A., Sharma, S., 2010b. Histology of organogenesis and somatic embryogenesis in excised root cultures of an endangered species Tylophora indica (Asclepiadaceae). Australian Journal of Botany 58, 198–205.
doi: 10.1071/BT09220
http://www.publish.csiro.au/paper/BT09220
https://pubpeer.com/publications/F2CF9E24F8E64B1FD3A0585D496A10

Jahan, N., Khatoon, R., Shahzad, A., Shahid, M., Ahmad, S., 2013. Comparison of antibacterial activity of parent plant of Tylophora indica Merr. with its in vitro raised plant and leaf callus. African Journal of Biotechnology 12(31), 4891–4896.
doi: 10.5897/AJB2013.12488
http://www.academicjournals.org/journal/AJB/article-full-text-pdf/741499B30776
http://www.academicjournals.org/journal/AJB/article-stat/741499B30776
https://pubpeer.com/publications/29137ADA528E6ACB41CB9F52691B02

Khatoon, R., Jahan, N., Shahzad, A., Shahid, M., 2013. Comparison of antifungal activity of medicinal plant Tylophora indica Merr. with its in vitro raised plant and callus. Journal of Applied Pharmaceutical Science 3, 41–45.
doi: 10.7324/JAPS.2013.3808 (does not link to PubPeer)
http://japsonline.com/admin/php/uploads/994_pdf.pdf

Reply
Bacopa monnieri query says:

April 7, 2016 at 10:01 am

Please observe the gel in this publication.

Journal of Genetic Engineering and Biotechnology
Volume 12, Issue 2, December 2014, Pages 89–94
Strain specific Agrobacterium-mediated genetic transformation of Bacopa monnieri
Sheetal Yadav, Poojadevi Sharma, Anshu Srivastava, Priti Desai, Neeta Shrivastava
http://www.sciencedirect.com/science/article/pii/S1687157X14000365
doi: 10.1016/j.jgeb.2014.11.003

https://pubpeer.com/publications/E05EBCA691317E6673DB86DCEBBA41

Reply
Aegle Moringa query says:

April 10, 2016 at 7:25 pm

Kindly observe these two papers.

International Journal of Science and Research Volume 4, Issue 7, July 2015, 1767-1770
Identification, isolation and estimation of flavonoids and effect of growth regulators and salts on flavonoids in Aegle marmelos and Moringa oleifera in vitro
Kavita Soni, Asha Goswami
http://ijsr.net/archive/v4i7/v4i7.php#sthash.UIivNdbW.dpbs (page 2)
http://www.ijsr.net/archive/v4i7/SUB156871.pdf

Indian Journal of Scientific Research Volume 6, Issue 1, July 2015, 121-125
Identification, isolation and estimation of flavonoids and effect of growth regulators and salts on flavonoids in Aegle marmelos and Moringa oleifera in vitro
Kavita Soni, Asha Goswami
http://www.ijsr.in/1archive.php?id=55
http://www.ijsr.in/upload/1823585183CHAPTER_20.pdf

Reply
Tylophora indica query says:

April 11, 2016 at 8:14 am

Kindly observe these two papers.

Roop Narayan Verma, Shazia M. Jamal, Madan Mohan Sharma, D. V. Rao, Amla Batra, 2010. Regulation of organogenesis using leaf, internode and petiole explants in Tylophora indica (Burm. f.) Merr. International Journal of Pharmaceutical Sciences Review and Research 5, 35–40.
http://globalresearchonline.net/journalcontents/volume5issue1/Article-006.pdf

Madan Mohan Sharma, Roop Narayan Verma, Abhijeet Singh, Amla Batra, 2014. Assessment of clonal fidelity of Tylophora indica (Burm. f.) Merrill “in vitro” plantlets by ISSR molecular markers. Springer Plus 3, 400. DOI: 10.1186/2193-1801-3-400
http://springerplus.springeropen.com/articles/10.1186/2193-1801-3-400

https://pubpeer.com/publications/14A1CCD756F55F1AA941793EAD850A

Reply
1. Medicinal plant query says:
  
  April 13, 2016 at 4:07 am
  
  Please observe these three papers, with Amla Batra as the common author.
  
  Our Nature (2009) 7:110-115
  In Vitro Regeneration of Phyllanthus amarus Schum. And Thonn.: An Important Medicinal Plant
  A. Sen, M.M. Sharma, D. Grover and A. Batra
  http://nepjol.info/index.php/ON/article/viewFile/2557/2281
  
  International Journal of Pharmaceutical Sciences and Research, 2011; Vol. 2(8): 2146-2151
  Crucial role of nitrogen in in- vitro regeneration of Phyllanthus amarus Schum. and Thonn.
  Antara Sen, Amla Batra
  http://ijpsr.com/bft-article/crucial-role-of-nitrogen-in-in-vitro-regeneration-of-phyllanthus-amarus-schum-and-thonn/
  
  https://pubpeer.com/publications/14A1CCD756F55F1AA941793EAD850A
  
  Leukemia & Lymphoma 56(11): 3168-3182
  Anti-leukemic activities of alcoholic extracts of two traditional Indian Medicinal Plants
  Shipra Bhargava, Hemant Malhotra, Om Singh Rathore, Bharti Malhotra, Pratibha Sharma, Amla Batra, Asha Sharma, Shubhada V. Chiplunkar
  http://www.tandfonline.com/doi/abs/10.3109/10428194.2015.1026813
  DOI: 10.3109/10428194.2015.1026813
  
  https://pubpeer.com/publications/E1A8F24D2448ABAA919B3D0FA0836B
  
  Reply
RAP Arabidopsis query says:

April 12, 2016 at 6:45 am

The Plant Cell February 2014 vol. 26 no. 2, 777-787
RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation
Laura Kleinknecht, Fei Wang, Roland Stübe, Katrin Philippar, Jörg Nickelsen, Alexandra-Viola Bohne
http://dx.doi.org/10.1105/tpc.114.122853
http://www.plantcell.org/content/26/2/777.full.pdf+html

4 out of 8 figures corrected:
http://www.plantcell.org/content/early/2016/04/06/tpc.16.00094.full.pdf+html

Reply
Ramonda query says:

April 13, 2016 at 2:30 am

Kindly observe these four papers.

Paper 1: PMBP 2015
Physiology and Molecular Biology of Plants January 2015, Volume 21, Issue 1, pp 123-136
Micropropagation and in vitro conservation of the rare and threatened plants Ramonda serbica and Ramonda nathaliae
Bekim Gashi, Kasamedin Abdullai, Valbona Sota, Efigjeni Kongjika
http://link.springer.com/article/10.1007/s12298-014-0261-3
DOI: 10.1007/s12298-014-0261-3
http://www.ncbi.nlm.nih.gov/pubmed/25648356
https://pubpeer.com/publications/B3DFB45C0981DC022E459E41B0E2CC

Paper 2: Ekoloji 2013
Bekim Gashi, Fadil Millaku, Kasamedin Abdullai, Evelina Daskalova, Slaveya Dontcheva, Elez Krasniqi, Valbona Mata, Efigjeni Kongjika
Ecological and morphological characteristics and in vitro conservation of Ramonda serbica Panc. in Kosovo. Ekoloji, 89: 19-28. (2013)
doi: 10.5053/ekoloji.2013.893
http://www.ekoloji.com.tr/resimler/89-3.pdf
https://www.researchgate.net/publication/259398854
https://pubpeer.com/publications/822274ED7893F69F2F87C860D249F9

Paper 3: B&BE 2012
E. Daskalova, S. Dontcheva, Z. Zekaj, A. Bacu, V. Sota, K. Abdullai, B. Gashi, I. Minkov, V. Toneva & E. Kongjika (2012) Initial Determination of Polymorphism and In Vitro Conservation of Some Ramonda Serbica and Ramonda Nathaliae Populations from Albania, Macedonia and Bulgaria, Biotechnology & Biotechnological Equipment, 26:sup1, 16-25
http://dx.doi.org/10.5504/50YRTIMB.2011.0004
http://www.tandfonline.com/doi/abs/10.5504/50YRTIMB.2011.0004
DOI: 10.5504/50YRTIMB.2011.0004
https://pubpeer.com/publications/19F03B001A8DD6C49A6CDB917BD250

Paper 4: 2012 Proceedings
Bekim Gashi, Fadil Millaku, Kasamedin Abdullai, Elez Krasniqi, Efigjeni Kongjika
Ecological and morphological characteristics of rare and endangered plant Ramonda serbica from different localities of the republic of Kosovo
Proceedings of the 4th Congress of Ecologists of Macedonia with International Participation, Ohrid, 12-15 October 2012, Macedonian Ecological Society, pp. 33-39
https://www.researchgate.net/publication/284552098

Reply
Alfalfa query says:

April 15, 2016 at 9:35 am

Kindly observe these two papers.

Australian Journal of Basic and Applied Sciences, 5(9): 816-824, 2011
Use of Abiotic and Biotic Inducers in Controlling Fungal Diseases and Improving Growth in Alfalfa
Morsy, K.M., Abdel-Monaim, M.F. and Mazen, M. M.
http://ajbasweb.com/old/ajbas/2011/September-2011/816-824.pdf

World Journal of Agricultural Sciences 7 (5): 566-576, 2011
Use of Abiotic and Biotic Inducers for Controlling Fungal Diseases and Improving Growth of Alfalfa
Kadry Mohamed Morsy, Montaser Fawzy Abdel-Monaim, Mohamed Mahmoud Mazen
http://www.idosi.org/wjas/wjas7(5).htm
http://idosi.org/wjas/wjas7(5)/8.pdf

Reply
Tree seed Vitamin D query says:

April 15, 2016 at 10:41 am

Kindly observe these three papers.

Australian Journal of Basic and Applied Sciences, 5(9): 1-5, 2011
Some Aspect of Dormancy Studies and Vitamin D Content of Four Tree Seed Species
Ajiboye A.A, Agboola D.A, M.O Atayese, M. Kadiri
http://ajbasweb.com/old/ajbas/2011/September-2011/1-5.pdf

International Research Journal of Plant Science (ISSN: 2141-5447) Vol. 2(2) pp. 032-036,
Some aspect of dormancy studies and vitamin D content in four tree seed species
Ajiboye A.A, Agboola D.A
http://www.interesjournals.org/irjps/february-2011-vol-2-issue-2/some-aspect-of-dormancy-studies-and-vitamin-d-content-in-four-tree-seed-species
http://interesjournals.org/full-articles/some-aspect-of-dormancy-studies-and-vitamin-d-content-in-four-tree-seed-species.pdf?view=inline
http://www.interesjournals.org/full-articles/some-aspect-of-dormancy-studies-and-vitamin-d-content-in-four-tree-seed-species.pdf?view=inline

European Journal of Biological Sciences 1 (3): 23-27, 2009
Some Aspect of Dormancy Studies and Vitamin D Content of Four Tree Seed Species
A.A Ajiboye, D.A. Agboola, M.O Atayese, M. Kadiri
http://www.idosi.org/ejbs/ejbs1(3)09.htm
http://www.idosi.org/ejbs/1(3)09/1.pdf

Reply
Indian cauliflower query says:

April 18, 2016 at 2:08 am

Please observe gel bands (JHSB paper) and gels (inter-paper comparison).

The Journal of Horticultural Science and Biotechnology, 89:5, 480-486 (2014)
Race-specific genetics of resistance to black rot disease [Xanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson] and the development of three random amplified polymorphic DNA markers in cauliflower.
P. Saha, P. Kalia, P. Sharma, T. R. Sharma
DOI: 10.1080/14620316.2014.11513109
http://www.tandfonline.com/doi/abs/10.1080/14620316.2014.11513109
http://dx.doi.org/10.1080/14620316.2014.11513109
https://pubpeer.com/publications/3ADCD662540AADB95B90324030ABA6

Plant Breeding 133(2), 268–274 (2014)
Molecular mapping of black rot resistance locus Xca1bo on chromosome 3 in Indian cauliflower (Brassica oleracea var. botrytis L.)
Partha Saha 1, Pritam Kalia 1,3, Humira Sonah 2, Tilak R. Sharma 2
1 Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 11002, India
2 National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, 11002, India
doi: 10.1111/pbr.12152
http://onlinelibrary.wiley.com/doi/10.1111/pbr.12152/abstract
https://pubpeer.com/publications/778F5E9A313CFAE6FA3F7D8D943671

Reply
Rice blast query says:

April 18, 2016 at 11:05 am

Kindly observe a figure in these two papers.

Journal of Plant Biochemistry and Biotechnology (Jan–June 2011) 20(1):55–65
Functional complementation of rice blast resistance gene Pi-kh(Pi54) conferring resistance to diverse strains of Magnaporthe oryzae
Amit Kumar Rai, Satya Pal Kumar, Santosh Kumar Gupta, Naveen Gautam, Nagendera Kumar Singh, Tilak Raj Sharma
http://link.springer.com/article/10.1007/s13562-010-0026-1
DOI: 10.1007/s13562-010-0026-1
https://pubpeer.com/publications/7F09BD3CE4AC7968E59EB4DECE8563

Journal of Experimental Botany, Vol. 63, No. 2, pp. 757–772, 2012
The single functional blast resistance gene Pi54 activates a complex defence mechanism in rice
Santosh Kumar Gupta 1,2, Amit Kumar Rai 1,2, Shamsher Singh Kanwar 2, Duni Chand 2, Nagendera Kumar Singh 1, Tilak Raj Sharma 1
1 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
2 Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla-171005, India
http://jxb.oxfordjournals.org/content/63/2/757.full.pdf
DOI: 10.1093/jxb/err297
https://pubpeer.com/publications/3A18D96FC2BB85D6AB3C115BA830DB

Reply
Japonica and indica rice query says:

April 18, 2016 at 6:30 pm

Please observe Fig 1 + 10 of this paper.

Yuvraj Indoliya 1,2, Poonam Tiwari 1, Abhisekh Singh Chauhan 1, Ridhi Goel 1,2, Manju Shri 1, Sumit Kumar Bag 1,2, Debasis Chakrabarty 1,2
1 Council of Scientific and Industrial Research – National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India
2 Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India
Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies. Scientific Reports 6, 23050
doi: 10.1038/srep23050
http://www.nature.com/articles/srep23050
https://pubpeer.com/publications/DFFC91D92CCE6FA3C60DD19433A14F

Reply
Transgenic wheat query says:

April 19, 2016 at 12:23 am

Please observe Fig. 2 of this paper.

Shanshan Dong, Yan Liu, Cigang Yu, Zhenhua Zhang, Ming Chen, Changyong Wang (2016) Investigating Pollen and Gene Flow of WYMV-Resistant Transgenic Wheat N12-1 Using a Dwarf Male-Sterile Line as the Pollen Receptor. PLoS ONE 11(3): e0151373. doi:10.1371/journal.pone.0151373
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0151373
https://pubpeer.com/publications/A4008AFAC7C816C377C22FF95C9E40

Reply
Withania somnifera query says:

April 19, 2016 at 12:28 am

Kindly observe Fig. 6 of this paper.

Smrati Mishra, Shilpi Bansal, Bhawana Mishra, Rajender Singh Sangwan, Asha, Jyoti Singh Jadaun, Neelam S. Sangwan (2016) RNAi and Homologous Over-Expression Based Functional Approaches Reveal Triterpenoid Synthase Gene-Cycloartenol Synthase Is Involved in Downstream Withanolide Biosynthesis in Withania somnifera. PLoS ONE 11(2): e0149691.
doi: 10.1371/journal.pone.0149691
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0149691
https://pubpeer.com/publications/C388A7BB232DCF21BDA4C4D6243C39

Reply
Chrysanthemum query says:

April 19, 2016 at 12:58 am

Please observe figures in these two PLOS ONE papers by the same authors.

Qingqing Fan, Aiping Song, Jingjing Xin, Sumei Chen, Jiafu Jiang, Yinjie Wang, Xiran Li, Fadi Chen (2015) CmWRKY15 Facilitates Alternaria tenuissima Infection of Chrysanthemum. PLoS ONE 10(11): e0143349.
1 College of Horticulture, Nanjing Agricultural University, Nanjing, China
2 Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & Equipment, Nanjing, China
doi: 10.1371/journal.pone.0143349
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0143349
http://www.be-md.ncbi.nlm.nih.gov/pmc/articles/PMC4658048/
https://pubpeer.com/publications/C45C20B3A5966FC21B15D733B9F629

Qingqing Fan, Aiping Song, Jiafu Jiang, Ting Zhang, Hainan Sun, Yinjie Wang, Sumei Chen, Fadi Chen (2016) CmWRKY1 Enhances the Dehydration Tolerance of Chrysanthemum through the Regulation of ABA-Associated Genes. PLoS ONE 11(3): e0150572.
doi: 10.1371/journal.pone.0150572
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150572
http://www.be-md.ncbi.nlm.nih.gov/pmc/articles/PMC4777562/
https://pubpeer.com/publications/721A74392F038941D823813B08C638

Reply
Transgenic tobacco (cotton gene) query says:

April 19, 2016 at 2:08 am

Kindly observe some figures in this paper.

Xiaoqian Chu, Chen Wang, Xiaobo Chen, Wenjing Lu, Han Li, Xiuling Wang, Lili Hao, Xingqi Guo (2015) The Cotton WRKY Gene GhWRKY41 Positively Regulates Salt and Drought Stress Tolerance in Transgenic Nicotiana benthamiana. PLoS ONE 10(11): e0143022.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
doi:10.1371/journal.pone.0143022
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0143022
http://www.ncbi.nlm.nih.gov/pubmed/26562293
https://pubpeer.com/publications/77A11078CAC9E80C5A45CD9E01045F

Reply
1. Transgenic tobacco (cotton gene) corrigendum says:
  
  June 25, 2016 at 2:52 pm
  
  Corrigendum published on June 2, 1016:
  http://journals.plos.org/plosone/article?id=info:doi/10.1371/journal.pone.0157026
  
  “The authors would like to correct Figs 6 and 8, as errors were introduced in the preparation of these figures for publication. In Figs 4A and 6A, the same image was used to represent the MS control in both figures. The authors have provided a corrected Fig 6 here with a new MS image from another biological replicate. In Fig 8A, the same image was inadvertently used to represent both the WT Control and OE2 Control conditions. The authors have provided a corrected Fig 8 here with the correct OE2 Control image. The authors confirm that these changes do not alter their findings and have provided the underlying images for Fig 8 as Supporting Information.”
  
  Reply
2. Transgenic tobacco (cotton gene) query says:
  
  June 26, 2016 at 2:32 am
  
  Kindly observe this paper.
  
  Haihong Jia, Chen Wang, Fang Wang, Shuchang Liu, Guilin Li, Xingqi Guo (2015) GhWRKY68 Reduces Resistance to Salt and Drought in Transgenic Nicotiana benthamiana. PLoS ONE 10(3): e0120646.
  doi:10.1371/journal.pone.0120646
  http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0120646
  https://www.pubpeer.com/publications/6336A3743ADD03B68441208CD66561
  
  Reply
Sugarcane and mustard queries says:

April 19, 2016 at 3:51 am

Please observe these papers from the same research institute (Bhabha Atomic Research Centre, Mumbai, India).

Case a

In Vitro Cellular & Developmental Biology – Plant December 2014, Volume 50, Issue 6, pp 766-776
Gamma radiation, in vitro selection for salt (NaCl) tolerance, and characterization of mutants in sugarcane (Saccharum officinarum L.)
Ashok A. Nikam, Rachayya M. Devarumath, Mahadeo G. Shitole, Vikram S. Ghole, Prahlad N. Tawar, Penna Suprasanna
http://link.springer.com/article/10.1007/s11627-014-9630-4
DOI: 10.1007/s11627-014-9630-4
https://pubpeer.com/publications/FEDF8B546B7F4EF887135E600C3987

Versus

The Crop Journal 3, 46-56 (2015)
Radiation-induced in vitro mutagenesis system for salt tolerance and other agronomic characters in sugarcane (Saccharum officinarum L.)
Ashok A. Nikam, Rachayya M. Devarumath, Akash Ahuja, Harinath Babu, Mahadeo G. Shitole, Penna Suprasanna
DOI: 10.1016/j.cj.2014.09.002
http://www.sciencedirect.com/science/article/pii/S2214514114000828
https://pubpeer.com/publications/7344E002F91F6673895F3DE6259D14

Case b

Plant Molecular Biology March 2016, Volume 90, Issue 4, pp 375-387
Brassica RNA binding protein ERD4 is involved in conferring salt, drought tolerance and enhancing plant growth in Arabidopsis
Archana N. Rai, Srinath Tamirisa, K. V. Rao, Vinay Kumar, P. Suprasanna
DOI: 10.1007/s11103-015-0423-x
http://link.springer.com/article/10.1007/s11103-015-0423-x
https://pubpeer.com/publications/F2D03946483D4C86569CD34751C4C7

Reply
1. Sugarcane query says:
  
  April 19, 2016 at 10:39 am
  
  Kindly observe these two papers by the same senior author, Penna Suprasanna.
  
  Sugar Tech March 2006, Volume 8, Issue 1, pp 63-68
  Molecular profiling using RAPD technique of salt and drought tolerant regenerants of sugarcane
  Patade Vikas Yadav, Penna Suprasanna, Kulkarni Umakant Gopalrao, Bapat Vishwas Anant
  http://link.springer.com/article/10.1007/BF02943744
  DOI: 10.1007/BF02943744
  https://pubpeer.com/publications/A09A5FC461564190F250C4D2C2FBF2
  
  Agricultural Sciences in China, Volume 7, Issue 9, September 2008, Pages 1147-1152
  Gamma Irradiation of Embryogenic Callus Cultures and In vitro Selection for Salt Tolerance in Sugarcane (Saccharum officinarum L.)
  Vikas Y Patade, P Suprasanna, VA Bapat
  http://www.sciencedirect.com/science/article/pii/S1671292708601583
  DOI: 10.1016/S1671-2927(08)60158-3
  https://pubpeer.com/publications/360D1FF077F19D98D6855FB645EFA3
  
  Reply
2. Sesuvium portulacastrum query says:
  
  April 19, 2016 at 10:41 am
  
  Kindly observe Fig. 2 of this paper.
  
  Genetic Resources and Crop Evolution August 2009, Volume 56, Issue 5, pp 705-717
  Morphological and molecular diversity analysis among the Indian clones of Sesuvium portulacastrum L.
  Vinayak H. Lokhande, Tukaram D. Nikam, Vikas Y. Patade, Penna Suprasanna
  1. Department of Botany, University of Pune, Pune, 411007, India
  2. Functional Plant Biology Section, Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
  http://link.springer.com/article/10.1007%2Fs10722-008-9396-9
  DOI: 10.1007/s10722-008-9396-9
  https://pubpeer.com/publications/5E489F3AB2E885A71FE0BE6F197FE3
  
  Reply
3. Sesuvium portulacastrum query says:
  
  April 19, 2016 at 10:43 am
  
  Kindly observe these two papers.
  
  Agronomy and Sustainable Development (2013) 33:329-348
  Sesuvium portulacastrum, a plant for drought, salt stress, sand fixation, food and phytoremediation. A review
  Vinayak H. Lokhande, Bhoomi K. Gor, Neetin S. Desai, Tukaram D. Nikam, Penna Suprasanna
  DOI: 10.1007/s13593-012-0113-x
  http://link.springer.com/article/10.1007%2Fs13593-012-0113-x
  https://pubpeer.com/publications/3D6F655129F9108D8277C6780E2662
  
  Biotechnology Reports Volume 8, December 2015, Pages 56–63
  Hairy root induction and phytoremediation of textile dye, Reactive green 19A-HE4BD, in a halophyte, Sesuvium portulacastrum (L.) L.
  Vinayak H. Lokhande, Subhash Kudale, Ganesh Nikalje, Neetin Desai, Penna Suprasanna
  Shri Shiv Chhatrapati College of Arts, Commerce and Science, Bodkenagar, Junnar, Pune 410 502, India
  School of Biotechnology and Bioinformatics, Dr. D. Y. Patil University, C. B. D. Belapur, Navi Mumbai 400 614, India
  Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
  Department of Botany, Savitribai Phule Pune University, Pune 411 007, India
  http://www.sciencedirect.com/science/article/pii/S2215017X15000442
  DOI: 10.1016/j.btre.2015.08.002
  https://pubpeer.com/publications/5FBA6E7341256F2F520EE97490D56B
  
  Reply
Salvia miltiorrhiza query says:

April 19, 2016 at 10:49 am

Kindly observe Fig. 3 of this paper.

Yangyun Zhou 1, Wei Sun 2, Junfeng Chen 1, Hexin Tan 3, Ying Xiao 1, Qing Li 1, Qian Ji 3, Shouhong Gao 1, Li Chen 1, Shilin Chen 2, Lei Zhang 3, Wansheng Chen 1
1 Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
2 Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
3 Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza. Scientific Reports 6, 22852 (2016)
doi: 10.1038/srep22852
http://www.nature.com/articles/srep22852#f3

https://pubpeer.com/publications/D2301EBA839778867FCDE23BB8E2DB

Reply
Xanthomonas campestris (on Chinese radish) query says:

April 19, 2016 at 10:55 am

Kindly observe Fig. 3A of the following two papers.

An, S.-Q., Febrer, M., McCarthy, Y., Tang, D.-J., Clissold, L., Kaithakottil, G., Swarbreck, D., Tang, J.-L., Rogers, J., Dow, J. M. and Ryan, R. P. (2013a), High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis. Molecular Microbiology, 88: 1058–1069.
doi: 10.1111/mmi.12229
http://onlinelibrary.wiley.com/doi/10.1111/mmi.12229/epdf
http://onlinelibrary.wiley.com/doi/10.1111/mmi.12229/abstract

Shi‐Qi An, Ko‐Hsin Chin, Melanie Febrer, Yvonne McCarthy, Jauo‐Guey Yang, Chung‐Liang Liu, David Swarbreck, Jane Rogers, J Maxwell Dow, Shan‐Ho Chou, Robert P Ryan (2013b) A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis. The EMBO Journal 32(18), 2430-2438.
DOI: 10.1038/emboj.2013.165
http://emboj.embopress.org/content/32/18/2430
http://emboj.embopress.org/content/embojnl/32/18/2430.full.pdf

https://pubpeer.com/publications/50B2EB760523D9573A3E161E021091

Reply
1. Xanthomonas campestris (on Chinese radish) query says:
  
  April 19, 2016 at 11:04 am
  
  Kindly observe Fig. 1A of the following two papers.
  
  Ryan, R. P., Fouhy, Y., Lucey, J. F., Jiang, B.-L., He, Y.-Q., Feng, J.-X., Tang, J.-L. and Dow, J. M. (2007), Cyclic di-GMP signalling in the virulence and environmental adaptation of Xanthomonas campestris. Molecular Microbiology, 63: 429–442.
  doi: 10.1111/j.1365-2958.2006.05531.x
  http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05531.x/abstract
  http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05531.x/epdf
  
  MCCARTHY, Y., RYAN, R. P., O’DONOVAN, K., HE, Y.-Q., JIANG, B.-L., FENG, J.-X., TANG, J.-L. and DOW, J. M. (2008), The role of PilZ domain proteins in the virulence of Xanthomonas campestris pv. campestris. Molecular Plant Pathology, 9: 819–824.
  doi: 10.1111/j.1364-3703.2008.00495.x
  http://onlinelibrary.wiley.com/doi/10.1111/j.1364-3703.2008.00495.x/abstract
  http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1364-3703.2008.00495.x
  
  https://pubpeer.com/publications/B1BAB266DC2527F429653D32BC8BB6
  
  Reply
2. Xanthomonas campestris query says:
  
  April 19, 2016 at 11:12 am
  
  Please observe Fig. 3A/3B and Fig. 4A/4B of this paper.
  
  PNAS April 25, 2006 103(17): 6712–6717
  Cell–cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover
  Robert P. Ryan, Yvonne Fouhy, Jean F. Lucey, Lisa C. Crossman, Stephen Spiro, Ya-Wen He, Lian-Hui Zhang, Stephan Heeb, Miguel Camara, Paul Williams, J. Maxwell Dow
  DOI: 10.1073/pnas.0600345103
  http://www.pnas.org/content/103/17/6712
  http://www.pnas.org/content/103/17/6712.full.pdf
  
  https://pubpeer.com/publications/54D08BB40C04AB4CAEF659CD7A13C8
  
  Reply
3. Xanthomonas campestris query says:
  
  April 19, 2016 at 11:22 am
  
  Kindly observe Fig. 2B and 2C of this paper.
  
  PNAS March 30, 2010, 107(13): 5989–5994
  Cell–cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris
  Robert P. Ryan, Yvonne McCarthy, Maxuel Andrade, Chuck S. Farah, Judith P. Armitage, J. Maxwell Dow
  DOI: 10.1073/pnas.0912839107
  http://www.pnas.org/content/107/13/5989
  http://www.pnas.org/content/107/13/5989.full.pdf
  
  Reply
African violet query says:

April 21, 2016 at 1:19 am

Kindly observe these two publications.

Vazquez AM, Davey MR, Short KC (1977) Organogenesis in culture of Saintpaulia ionantha. Acta Horticulturae (ISHS) 78:249–258.
doi: 10.17660/ActaHortic.1977.78.32
http://www.actahort.org/books/78/78_32.htm
https://pubpeer.com/publications/ECE53F600C504A7960163C5433A173

Vazquez AM, Short KC (1978) Morphogenesis in cultured floral parts of African violet. Journal of Experimental Botany 29:1265–1271.
doi: 10.1093/jxb/29.5.1265
http://jxb.oxfordjournals.org/content/29/5/1265.full.pdf
https://pubpeer.com/publications/7E14F9D001F10408B2E59C5E379776

Reply
1. African violet query says:
  
  April 22, 2016 at 2:59 pm
  
  Kindly observe these two papers.
  
  Farjadi-Shakib M, Mousavi A, Naderi R (2012a) Optimization of chromosomal preparation and cytological analysis of in vitro cultured African violet (Saintpaulia ionantha Wendl.). Acta Horticulturae (ISHS) 937:917–922. doi: 10.17660/ActaHortic.2012.937.113
  http://www.actahort.org/books/937/937_113.htm
  https://pubpeer.com/publications/1D6108F0F8CD63765FB8FF97C74651
  
  Farjadi-Shakib M, Naderi R, Mousavi A (2012b) Effects of gamma-ray irradiation on African violet in vitro adventitious shoots. Acta Horticulturae (ISHS) 937:923–927. doi: 10.17660/ActaHortic.2012.937.114
  http://www.actahort.org/books/937/937_114.htm
  https://pubpeer.com/publications/FDFB279D79ACF24E4CAA1A76BA3A09
  
  Reply
2. African violet query says:
  
  April 28, 2016 at 3:55 am
  
  Kindly observe these two papers.
  
  Jain SM (1993) Somaclonal variation in Begonia × elatior and Saintpaulia ionantha L. Scientia Horticulturae 54:221–231.
  doi: 10.1016/0304-4238(93)90090-D
  http://www.sciencedirect.com/science/article/pii/030442389390090D
  https://www.pubpeer.com/publications/3751B782B80E94F801E22C5AFE2107
  
  Mohan Jain S, Oy K (1993) Studies on somaclonal variation in ornamental plants. Acta Horticulturae (ISHS) 336:365–372.
  doi: 10.17660/ActaHortic.1993.336.48
  http://www.actahort.org/books/336/336_48.htm
  https://www.pubpeer.com/publications/C519B6D54E45EC69FDAD65436F8404
  
  Reply
3. African violet query says:
  
  May 1, 2016 at 3:00 am
  
  Kindly observe these 6 papers.
  
  Daud N, Mat Taha R, Hasbullah NA (2008a) Studies on plant regeneration and somaclonal variation in Saintpaulia ionantha Wendl. (African violet). Pakistan Journal of Biological Science 11:1240–1245.
  doi: 10.3923/pjbs.2008.1240.1245
  http://www.scialert.net/abstract/?doi=pjbs.2008.1240.1245
  http://www.ncbi.nlm.nih.gov/pubmed/18819532
  PMID: 18819532
  https://www.pubpeer.com/publications/C2040146CA56F2CBF11EDEDEBC609C
  
  Daud N, Taha RM (2008) Plant regeneration and floral bud formation from intact floral parts of African violet (Saintpaulia ionantha H. Wendl.) cultured in vitro. Pakistan Journal of Biological Science 11:1055–1058.
  doi: 10.3923/pjbs.2008.1055.1058
  http://www.scialert.net/abstract/?doi=pjbs.2008.1055.1058
  http://www.ncbi.nlm.nih.gov/pubmed/18810979
  PMID: 18810979
  https://www.pubpeer.com/publications/6BE191A562B93C85C6B4CCDE62338D
  
  Daud N, Taha RM, Hasbullah NA (2008b) Artificial seed production from encapsulated micro shoots of Saintpaulia ionantha Wendl. (African violet). Journal of Applied Science 8:4662–4667.
  doi: 10.3923/jas.2008.4662.4667
  http://www.scialert.net/abstract/?doi=jas.2008.4662.4667
  https://www.pubpeer.com/publications/16DC5E03AA7AA5E993D9CC19895CB5
  
  Taha RM, Daud N, Hasbullah NA, Awal A (2009) Somatic embryogenesis and production of artificial seeds in Saintpaulia ionantha Wendl. Acta Horticulturae (ISHS) 829:331–336.
  doi: 10.17660/ActaHortic.2009.829.51
  http://www.actahort.org/books/829/829_51.htm
  https://www.pubpeer.com/publications/0AF4E2A1DF8007C92A52950B0FB6E6
  
  Taha RM, Daud N, Hasbullah NA (2010a) Establishment of efficient regeneration system, acclimatization and somaclonal variation in Saintpaulia ionantha H. Wendl. Acta Horticulturae (ISHS) 865:115–121.
  doi: 10.17660/ActaHortic.2010.865.14
  http://www.actahort.org/books/865/865_14.htm
  https://www.pubpeer.com/publications/7CD71EFC0A44D94D6B4CEFDE176A47
  
  Taha RM, Hasbullah NA, Awal A (2010b) In vitro plantlets from somatic embryos of selected ornamental plants – a new prospect for interior decorations and horticulture industry. Acta Horticulturae (ISHS) 881:745–747.
  doi: 10.17660/ActaHortic.2010.881.123
  http://www.actahort.org/books/881/881_123.htm
  https://www.pubpeer.com/publications/16759CFAA02FFEC8F445C2E40B2433
  
  Reply
Begonia query says:

May 4, 2016 at 2:05 pm

Kindly observe these 4 papers.

International Journal of Environmental Sciences – Catrina 2 (2): 189 – 192 (2007).
© 2007 BY THE EGYPTIAN SOCIETY FOR ENVIRONMENTAL SCIENCES
In vitro Formation of Synthetic Seed from Microshoots of Begonia x hiemalis Fotch.
Asmah Awal 1, Rosna M. Taha 2, Nor A. Hasbullah 2
1 MARA University of Technology, Negeri Sembilan Branch, 72000 Kuala Pilah, Negeri Sembilan, Malaysia.
2 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
http://eses-catrina.com/index.php?news=117

Journal of Biological Sciences 8: 920-924 (2008).
Induction of Somatic Embryogenesis and Plant Regeneration in Begonia x hiemalis Fotsch. in vitro.
Asmah Awal, Rosna Mat Taha and Nor Azlina Hasbullah.
DOI: 10.3923/jbs.2008.920.924
URL: http://scialert.net/abstract/?doi=jbs.2008.920.924
http://scialert.net/fulltext/?doi=jbs.2008.920.924
https://www.pubpeer.com/publications/D8DA1CD72BEB1CE4E39EBCDC275DED

Acta Horticulturae (ISHS) 829, 39-44 (2009).
SOMATIC EMBRYOGENESIS IN BEGONIA X HIEMALIS FOTSCH. IN VITRO.
Awal, A., Taha, R.M. and Hasbullah, N.A.
DOI: 10.17660/ActaHortic.2009.829.3
http://dx.doi.org/10.17660/ActaHortic.2009.829.3
http://www.actahort.org/books/829/829_3.htm
https://www.pubpeer.com/publications/D15AB07412AA98DEDE22CC97669FBD

Australian Journal of Crop Science 7(5; April): 691-698 (2013).
Effect of adenine, sucrose and plant growth regulators on the indirect organogenesis and on in vitro flowering in Begonia x hiemalis Fotsch.
Asmah Awal, Abdul Bakrudeen Ali Ahmed, Rosna Mat Taha, Jamilah Syafawati Yaacob, Sadegh Mohajer
http://www.cropj.com/april2013.html
http://www.cropj.com/abdul_7_5_2013_691_698.pdf

Reply
Celosia query says:

May 5, 2016 at 3:37 am

Kindly observe these two papers.

African Journal of Biotechnology Vol. 10(80), pp. 18349-18355, 14 December, 2011
Provision of low cost media options for in vitro culture of Celosia sp.
Norhayati Daud 1, Rosna Mat Taha 2, Nor Nafizah Mohd Noor 1, Hasimah Alimon 1
1 Department of Biology, Faculty of Science and Mathematics, Sultan Idris Education University, 35900 Tanjong Malim, Perak, Malaysia.
2 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
DOI: 10.5897/AJB11.2234
http://www.academicjournals.org/journal/AJB/article-abstract/37C230133202
http://www.academicjournals.org/journal/AJB/article-full-text-pdf/37C230133202
https://www.pubpeer.com/publications/69C94739BC11DCC027BC3CE30BE3C7

International Journal of Botany, 7: 183-188, 2011.
Potential of Alternative Gelling Agents in Media for the in vitro Micro-propagation of Celosia sp..
Norhayati Daud, Rosna Mat Taha, Nor Nafizah Mohd Noor and Hasimah Alimon.
DOI: 10.3923/ijb.2011.183.188
URL: http://scialert.net/abstract/?doi=ijb.2011.183.188
http://scialert.net/fulltext/?doi=ijb.2011.183.188&org=11
https://www.pubpeer.com/publications/A86BE269FDB1F399B17E8E281D9248

Reply
Gerbera query says:

May 6, 2016 at 3:43 pm

Kindly observe these 5 papers.

Pakistan Journal of Biological Sciences, 11: 1449-1454 (2008).
Nor Azlina Hasbullah, Rosna Mat Taha and Asmah Awal.
Growth Optimization and Organogenesis of Gerbera jamesonii Bolus ex. Hook f. in vitro.
DOI: 10.3923/pjbs.2008.1449.1454
http://scialert.net/abstract/?doi=pjbs.2008.1449.1454
https://www.pubpeer.com/publications/751D7C01D601CE5C135BB13161129F

Acta Horticulturae (ISHS) 829, 91-98 (2009).
Taha, R.M., Hasbullah, N.A. and Awal, A.
Production of synthetic seeds from micro shoots and somatic embryos of Gerbera jamesonii Bolus ex. Hook f.
DOI: 10.17660/ActaHortic.2009.829.12
http://dx.doi.org/10.17660/ActaHortic.2009.829.12
https://www.pubpeer.com/publications/B7D0C110790D43B05E111A08ADAA4D

Acta Horticulturae (ISHS) 865, 401-404 (2010).
Taha, R.M., Hasbullah, N.A., Abdul Aziz, A.H., Awal, A.
Establishment of in vitro plantlets and acclimatization of Gerbera jamesonii Bolus Ex. Hook F.
DOI: 10.17660/ActaHortic.2010.865.60
http://dx.doi.org/10.17660/ActaHortic.2010.865.60
http://www.actahort.org/books/865/865_60.htm
https://www.pubpeer.com/publications/70E95183818DB9DC55F4FF270B2980

African Journal of Biotechnology Vol. 10(63), pp. 13762-13768 (2011).
Establishment of somatic embryogenesis from Gerbera jamesonii Bolus EX. Hook F. through suspension culture
Nor Azlina Hasbullah 1, Azani Saleh 2, Rosna Mat Taha 1
1 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia.
2 International Education Centre (INTEC), MARA University of Technology, Section 17 Campus, 40200 Shah Alam, Selangor, Malaysia.
DOI: 10.5897/AJB11.1653 (cannot link to PubPeer)
http://www.ajol.info/index.php/ajb/article/view/96809
http://www.academicjournals.org/journal/AJB/article-abstract/34F97DC37624
http://www.academicjournals.org/journal/AJB/article-full-text-pdf/34F97DC37624

Horticultura Brasileira 30: 252-257 (2012).
Irradiation effect on in vitro organogenesis, callus growth and plantlet development of Gerbera jamesonii.
HASBULLAH NA; TAHA RM; SALEH A; MAHMAD N.
DOI: 10.1590/S0102-05362012000200012
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-05362012000200012
https://www.pubpeer.com/publications/6A2840E16516DEFC4D4D0CBAFBBCA6

Reply
Begonia and Justicia in vitro flowering queries says:

May 8, 2016 at 11:43 pm

KIndly observe these two papers.

Mat Taha, R., Hasbullah, N.A., Awal, A. (2010).
IN VITRO FLOWERING OF SELECTED ORNAMENTAL PLANTS.
Acta Horticulturae (ISHS) 881, 141-146
Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
DOI: 10.17660/ActaHortic.2010.881.15
http://dx.doi.org/10.17660/ActaHortic.2010.881.15
http://www.actahort.org/books/881/881_15.htm

Australian Journal of Crop Science 7(2): 281-288 (2013)
Callus induction, plant regeneration and somaclonal variation in in vivo and in vitro grown White shrimp plant (Justicia betonica Linn.).
Jamilah Syafawati Yaacob, Rosna Mat Taha, Norizam Jaafar, Zuliana Hasni, Hashimah Elias, Normadiha Mohamed
http://www.cropj.com/yaccob_7_2_2013_281_288.pdf

https://www.pubpeer.com/publications/FB303F8A18AB16FB37676E56C46DF1

Reply
Phyla and Gymnema queries says:

May 9, 2016 at 12:39 pm

Kindly observe the following 4 papers.

KMITL Science and Technology Journal Vol. 9 No. 1 Jan. – Jun. 2009, pp. 18-26
Somatic Embryogenesis and Plant Regeneration from Cell Suspension Culture of Gymnema sylvestre (Retz) R. Br. Ex Roemer & Schultes
Abdul Bakrudeen Ali Ahmed, Adhikarla Suryanarayana Rao, Mandali Venkateswara Rao
http://repository.um.edu.my/9370/1/2009%20%20kmitl.PDF
https://www.tci-thaijo.org/index.php/archkmitl

Spanish Journal of Agricultural Research 2011 9(4), 1262-1270
Optimized conditions for callus induction, plant regeneration and alkaloids accumulation in stem and shoot tip explants of Phyla nodiflora
A. B. A. Ahmed, R. Pallela, A. S. Rao, M. V. Rao, R. Mat Taha
DOI: 10.5424/sjar/20110904-453-10
http://revistas.inia.es/index.php/sjar/article/view/2451
https://www.pubpeer.com/publications/370A6B7C6794FA4B4233B4D558385E

Brazilian Archives of Biology and Technology Vol. 54, n. 1: pp.7-13, January-February 2011
Effect of picloram, additives and plant growth regulators on somatic embryogenesis of Phyla nodiflora (L.) Greene.
Abdul Bakrudeen Ali Ahmed, Adhikarla Suryanarayana Rao, Mandali Venkateswara Rao, Rosna Mat Taha
DOI: 10.1590/S1516-89132011000100002
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132011000100002
https://www.pubpeer.com/publications/DA7698775A798283FB52A92E615BFA

The ScientificWorld Journal Volume 2012, Article ID 897867, 11 pages
Production of Gymnemic Acid Depends on Medium, Explants, PGRs, Color Lights, Temperature, Photoperiod, and Sucrose Sources in Batch Culture of Gymnema sylvestre
A. Bakrudeen Ali Ahmed, A. S. Rao, M. V. Rao, Rosna Mat Taha
http://www.hindawi.com/journals/tswj/2012/897867/
doi: 10.1100/2012/897867
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353709/
PMCID: PMC3353709
https://www.pubpeer.com/publications/28C7E85109DAB71318928C7D2E1CE3

Reply
Sainfoin queries says:

May 9, 2016 at 9:41 pm

Kindly observe these three papers.

The Scientific World Journal Volume 2014, Article ID 854093, 9 pages
Stimulatory effects of gamma irradiation on phytochemical properties, mitotic behaviour, and nutritional composition of sainfoin (Onobrychis viciifolia Scop.)
Sadegh Mohajer, Rosna Mat Taha, Ma Ma Lay, Arash Khorasani Esmaeili, Mahsa Khalili
http://dx.doi.org/10.1155/2014/854093
DOI: 10.1155/2014/854093
http://www.hindawi.com/journals/tswj/2014/854093/
https://www.pubpeer.com/publications/7F4B44A6FB3DA47EB361A92CEC8639

Journal of Agricultural Science and Technology (2014) Vol. 16 (suppl. Issue): 1683-1698
Observations on the cytology and karyogram of an Onobrychis viciifolia Scop. new variety in callus, in vivo and in vitro cultures
S. Mohajer, R. M. Taha
http://jast.modares.ac.ir/article_11774_5044.html
http://jast.modares.ac.ir/article_11774_173a71fe2a56c271cd2f680f50b8c222.pdf

The Journal of Animal & Plant Sciences, 26(1): 2016, Page: 116-122
Effects of cryopreservation and relative humidity on viability and nutritional composition of sainfoin (Onobrychis viciifolia Scop.)
S. Mohajer, R. M. Taha, M. Mohajer
http://www.thejaps.org.pk/Volume/2016/26-01/index.php
http://www.thejaps.org.pk/docs/v-26-01/15.pdf

Reply
Gymnema sylvestre queries says:

May 12, 2016 at 8:56 am

Kindly observe these 7 papers.

Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants (2009)
Volume 547 of the series Methods in Molecular Biology pp 93-105
In Vitro Production of Gymnemic Acid from Gymnema sylvestre (Retz) R. Br. Ex Roemer and Schultes Through Callus Culture Under Abiotic Stress Conditions
Abdul Bakrudeen Ali Ahmed, Adhikarla Suryanarayana Rao, Mandali Venkateswara Rao
http://link.springer.com/protocol/10.1007/978-1-60327-287-2_8
http://www.ncbi.nlm.nih.gov/pubmed/19521838
PMID: 19521838; DOI: 10.1007/978-1-60327-287-2_8
https://www.pubpeer.com/publications/6DE49092C11F6A74621E8404C51BBB
https://www.pubpeer.com/publications/19521838

KMITL Science and Technology Journal Vol. 9 No. 1 Jan. – Jun. 2009, pp. 18-26
Somatic Embryogenesis and Plant Regeneration from Cell Suspension Culture of Gymnema sylvestre (Retz) R. Br. Ex Roemer & Schultes
Abdul Bakrudeen Ali Ahmed, Adhikarla Suryanarayana Rao, Mandali Venkateswara Rao
http://repository.um.edu.my/9370/1/2009%20%20kmitl.PDF
https://www.tci-thaijo.org/index.php/archkmitl

Phytomedicine 17 (2010) 1033–1039
In vitro callus and in vivo leaf extract of Gymnema sylvestre stimulate B-cells regeneration and anti-diabetic activity in Wistar rats
A. Bakrudeen Ali Ahmed, A.S. Rao, M.V. Rao
doi: 10.1016/j.phymed.2010.03.019
http://www.sciencedirect.com/science/article/pii/S094471131000111X
https://www.pubpeer.com/publications/1E85D6D1BAB7C123D9407F3C54CDB9

The ScientificWorld Journal Volume 2012, Article ID 897867, 11 pages
Production of gymnemic acid depends on medium, explants, PGRs, color lights, temperature, photoperiod, and sucrose sources in batch culture of Gymnema sylvestre
A. Bakrudeen Ali Ahmed, A. S. Rao, M. V. Rao, RosnaMat Taha
http://www.hindawi.com/journals/tswj/2012/897867/
doi: 10.1100/2012/897867; PMCID: PMC3353709
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353709/
https://www.pubpeer.com/publications/28C7E85109DAB71318928C7D2E1CE3

AgroFOOD industry hi-tech – May/June 2012 – vol 23 n 3, pp. 31-34
Different wavelengths light to induce physiological changes callus for the biosynthesis of gymnemic acid in Gymnema sylvestre
A. BAKRUDEEN ALI AHMED, A.S. RAO, M.V. RAO, R.M. TAHA
http://www.teknoscienze.com/articles/agro-food-industry-hi-tech-different-wavelengths-light-to-induce-physiological-changes-callus.aspx#.Vy-lX-RdIWM

Acta Chromatographica 25(2), 339–361 (2013)
HPTLC/HPLC and Gravimetric Methodology for the Identification and Quantification of Gymnemic Acid from Gymnema sylvestre Methanolic Extracts
A.B.A. AHMED, A.S. RAO, M.V. RAO, R.M. TAHA
DOI: 10.1556/AChrom.25.2013.2.10
http://www.akademiai.com/doi/abs/10.1556/AChrom.25.2013.2.10
https://www.pubpeer.com/publications/E88581490B0C45B08146C6DF17720B

2014 4th International Conference on Biotechnology and Environment Management
IPCBEE vol.75 (2014) © (2014) IACSIT Press, Singapore
Optimization of Gymnemic acid production with anti-diabetic studies and regeneration of Langerhans cells from Gymnema sylvestre
Bakrudeen Ali Ahmed Abdul, Rao, M.V., Rao, A.S., Rosna Mat Taha
DOI: 10.7763/IPCBEE.2014.V75.14
http://www.ipcbee.com/vol75/014-ICBEM2014-R1004.pdf

Reply
1. Anonymous says:
  
  June 26, 2016 at 1:02 am
  
  “On Sunday, June 26, 2016 1:38 PM, Ketua ISB [redacted] wrote:
  
  Dear Dr [redacted],
  
  Good Day,
  
  This is to inform to you that the University of Malaya had formed an investigation panel to investigate publishing practices by Prof. Rosna Mat Taha. The university will get in touch with you if more information are needed.
  
  Thank you very much,
  
  Head
  Institute of Biological Science
  University of Malaya
  50603 Kuala Lumpur
  MALAYSIA
  Tel: [redacted]
  Fax: [redacted]”
  
  Reply
Maize retraction says:

May 13, 2016 at 4:06 am

Original
Li C, Wang C, Meng L, Xing J, Wang T, Yang H, et al. (2014) Ectopic Expression of a Maize Hybrid Down-Regulated Gene ZmARF25 Decreases Organ Size by Affecting Cellular Proliferation in Arabidopsis. PLoS ONE 9(4): e94830. doi: 10.1371/journal.pone.0094830. pmid:24756087
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094830

Retraction
The PLOS ONE Editors (2016) Retraction: Ectopic Expression of a Maize Hybrid Down-Regulated Gene ZmARF25 Decreases Organ Size by Affecting Cellular Proliferation in Arabidopsis. PLoS ONE 11(5): e0155904. doi:10.1371/journal.pone.0155904
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0155904

«It has been brought to the attention of the PLOS ONE Editors that there is partial duplication of images in Figures 4B, 4C and 5A.
Upon our follow up with the authors of the article, it was established that images for sample 35S::ZmARF25 plant #4 panel 4B (siliques) and 4C (plants) were generated by Photoshop software manipulation of images from other plants. In Figure 5A, the same image was erroneously used for both samples.
In view of the intentional manipulation of photographic images related to sample 35S::ZmARF25 plant #4, the PLOS ONE Editors retract this article. The authors expressed deep regret for this circumstance and apologize to the community.»

«Funding: This work was financially supported by the National Natural Science Foundation of China (31230054 and 30925023)(http://www.nsfc.gov.cn/Portal0/default152.htm), the National Basic Research Program of China (973 Program) (2012CB910900) (http://www.973.gov.cn/Default_3.aspx) and 863 Project of China(2012AA10A305)(http://www.863.gov.cn/#). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.»

Reply
Maize query says:

May 13, 2016 at 3:16 pm

Kindly observe the following two papers.

Acta Agriculturae Slovenica 105(1), 1 March 2015, pp. 85-94
The effect of salt stress on the germination of maize (Zea mays L.) seeds and photosynthetic pigments
Sali ALIU 1, Imer RUSINOVCI 1, Shukri FETAHU 1, Bekim GASHI 2, Emilija SIMEONOVSKA 3, Ludvik ROZMAN 4
1 University of Prishtina, Faculty of Agriculture, Department of Crop Science, Prishtina, Kosovo
2 University of Prishtina, Faculty of Natural Science, Department of Biology, Prishtina, Kosovo
3 The Faculty of Agriculture Science and Food, Skopje, Macedonia
4 University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
Received February 12, 2015; accepted March 09, 2015.
DOI: 10.14720/aas.2015.105.1.09
http://aas.bf.uni-lj.si/marec2015/09Aliu.pdf

ORIGINAL SCIENTIFIC PAPER
Proceedings: 50th Croatian and 10th International Symposium on Agriculture, Opatija, Croatia, pp. 299-303
The effects of salt stress on seed germination of some maize (Zea mays L.) genotypes
Sali ALIU 1, Imer RUSINOVCI 1, Bekim GASHI 2, Vitore SHALA-MAYRHOFER 3, Shukri FETAHU 1, Fetah ELEZI 4, Marc LEMMENS 3
1 University of Prishtina, Faculty of Agriculture, Department of Crop Sciences, stret „Bill Clinton“ N.N., 10000 Prishtina, Kosovo,
2 University of Prishtina, Faculty of Natural Science, Department of Biology, 10000 Prishtina, Kosovo
3 University of Natural Resources and Life Science, Institute for Biotechnology, Vienna, Austria
4 Agricultural University, Faculty of Agriculture, Departament of Crop Sciences, Albania

https://www.pubpeer.com/publications/44C4E777A75D080C4FFA6D214AECE6

Reply
Withania query says:

May 14, 2016 at 1:03 am

Kindly observe these 5 papers.

Indian Journal of Biotechnology 9 (July 10): 325-328 (2010)
Intraspecific variation in the internal transcribed spacer (ITS) regions of rDNA in Withania somnifera (Linn.) Dunal
Bilal Ahmad Mir 1, Sushma Koul 1, Arun Kumar 1, Maharaj K. Kaul 1, Amarjit Singh Soodan 2, Soom Nath Raina 3
1 Biodiversity and Applied Botany Division, Indian Institute of Integrative Medicine (CSIR), Jammu 180001, India
2 Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
3. Amity Institute of Biotechnology, Amity University, Sector – 125, Noida, 201303, UP, India
http://nopr.niscair.res.in/bitstream/123456789/9894/1/IJBT%209%283%29%20325-328.pdf

Plant Systematics and Evolution February 2011, Volume 291, Issue 3, pp 141-151
Utility of a multidisciplinary approach for genome diagnostics of cultivated and wild germplasm resources of medicinal Withania somnifera, and the status of new species, W. ashwagandha, in the cultivated taxon
Arun Kumar 1, Bilal A. Mir 1, Deepmala Sehgal 2, Tanvir H. Dar 2, Sushma Koul 1, Maharaj K. Kaul 1, Soom N. Raina 3, Ghulam N. Qazi 1
1. Indian Institute of Integrative Medicine, Jammu, 180001, India
2. Department of Botany, University of Delhi, Delhi, 110007, India
3. Amity Institute of Biotechnology, Amity University, Sector – 125, Noida, 201303, UP, India
http://link.springer.com/article/10.1007%2Fs00606-010-0372-4
DOI: 10.1007/s00606-010-0372-4
https://www.pubpeer.com/publications/A9E56EC18C6FE8F656E9D73442D054

Journal of Medicinal Plants Research Vol. 6(5), pp. 754-762, 9 February, 2012
Reproductive behaviour and breeding system of wild and cultivated types of Withania somnifera (L.) Dunal
Bilal Ahmad Mir 1,2, Sushma Koul 1, Arun Kuar 1, Shushant Sharma 3, Maharaj K. Kaul 1, Amarjit S. Soodan 3
1 Biodiversity and Applied Botany Division, Indian Institute of Integrative Medicine (CSIR), Jammu 180001, India
2 Department of Botany, University of Kashmir, Hazratbal, Srinagar-160001, India
3 Botanical and Environmental sciences Department, Guru Nanak Dev University, Amritsar, India
DOI: 10.5897/JMPR11.1303
https://www.researchgate.net/publication/233529841
Linked to?
http://repository.up.ac.za/dspace/bitstream/handle/2263/21582/Mir_Reproductive%282013%29.pdf?sequence=1&isAllowed=y
https://www.pubpeer.com/publications/DB991B2B35D6FCF02B9325D9C24708

Industrial Crops and Products 45: 442-446 (2013)
Reproductive biology of Withania ashwagandha sp. novo (Solanaceae)
Bilal Ahmad Mir a,b, Sushma Koul b, Amarjit Singh Soodan c
a Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria 0002, South Africa
b Biodiversity and Applied Botany Division, Indian Institute of Integrative Medicine (CSIR), Jammu 180001, India
c Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
DOI: 10.1016/j.indcrop.2012.12.023
http://www.sciencedirect.com/science/article/pii/S0926669012006577
https://www.pubpeer.com/publications/8EF5BE83FC43E1C046B1B402559474

Physiology and Molecular Biology of Plants
July 2014, Volume 20, Issue 3, pp 357-364
In vitro propagation and withaferin A production in Withania ashwagandha, a rare medicinal plant of India
Bilal Ahmad Mir 1,2, Shabir Ahmad Mir 3, Sushma Koul 1
1. Biodiversity & Applied Botany Division, Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
2. Department of Genetics, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, 0028, South Africa
3. Department of Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
http://link.springer.com/article/10.1007/s12298-014-0243-5
DOI: 10.1007/s12298-014-0243-5
http://www.ncbi.nlm.nih.gov/pubmed/25049463
PMID: 25049463
PMCID: PMC4101142
https://pubpeer.com/publications/25049463

Reply
Wheat retraction says:

May 14, 2016 at 5:29 am

RETRACTION of: Overexpression of VP, a vacuolar H+-pyrophosphatase gene in wheat (Triticum aestivum L.), improves tobacco plant growth under Pi and N deprivation, high salinity, and drought
Xiaojuan Li 1, Chengjin Guo 1, Juntao Gu 2, Weiwei Duan 1, Miao Zhao 3, Chunying Ma 1, Xiaoming Du 2, Wenjing Lu 2, Kai Xiao 1
1 College of Agronomy, Agricultural University of Hebei, Baoding 071001, China
2 College of Life Sciences, Agricultural University of Hebei, Baoding 071001, China
3 Science and Technology College, North China Electric Power University, Baoding 071051, China
http://jxb.oxfordjournals.org/content/67/9/2913.full

Journal of Experimental Botany Vol 65 (2); 2014 pp. 683–696.

doi: 10.1093/jxb/ert442

“The Editor-in-Chief and Publisher have retracted this article due to concerns relating to the validity of several figures:

Figure 2A and B. The two bands used to represent TaVP expression in 0hr & 12hr high salinity and 0hr & 12hr drought treatments in root tissue appear to be duplicates, as are the three tubulin bands used as controls for root tissue and leaf tissue

Figure 3A. TaVP expression. The same control band has been used nine different times to represent all eight lines and the WT control.

Additionally both figures mentioned above have been individually constructed from different gels/blots. Journal policy requires this should have been made explicit in the construction of the figure (i.e. by using dividing lines or spaces) and in the figure legend.

The Journal applied forensic image analysis to verify the above irregularities, and also obtained advice from experts in the field. It is felt that the falsification of these images raises sufficient doubt over subsequent interpretations of data reported in the paper and as such the decision has been taken to retract.”

Reply
Pinus massoniana erratum says:

May 25, 2016 at 2:42 am

Trees June 2016, Volume 30, Issue 3, pp 1017-1017
Erratum to: Influence of climate warming and resin collection on the growth of Masson pine (Pinus massoniana) in a subtropical forest, southern China
Feng Chen , Yu-jiang Yuan, Shu-long Yu, Tong-wen Zhang
Original doi: 10.1007/s00468-015-1222-3.

“The original version of Fig. 8 was first published in ‘‘Papadopoulos AM (2013) Resin Tapping History of an Aleppo Pine Forest in Central Greece. The Open Forest Science Journal, 6 (Suppl 1: M5), pp 50–53’’ under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/legalcode).
The figure was copied and modified without including appropriate reference to the original author and article. The new figure labeling is erroneous and the legend is misleading. The figure shows a cross section of Pinus halepensis Mill, not Pinus massoniana, and the wound occurred before 1995. The authors regret this error and apologize for any confusion and inconvenience this may have caused.”

http://link.springer.com/article/10.1007/s00468-015-1313-1

Reply
Saffron query says:

May 29, 2016 at 10:19 pm

Please observe Fig. 3 of this review.

A review of the chemistry and uses of crocins and crocetin, the carotenoid natural dyes in saffron, with particular emphasis on applications as colorants including their use as biological stains
SZ Bathaie, A Farajzade, R Hoshyar
Biotechnic & Histochemistry 2014, 89(6): 401–411.
DOI: 10.3109/10520295.2014.890741
http://www.tandfonline.com/doi/full/10.3109/10520295.2014.890741
https://www.pubpeer.com/publications/66350EDD2321F9022E534E0C95EE49

Reply
Annatto (Bixa orellana) query says:

May 30, 2016 at 2:35 am

Kindly observe the figures and table data of these two papers.

Madhuri Sharon, Marie Claire D’Souza (2000) In vitro clonal propagation of annatto (Bixa orellana L.). Current Science 78:1532–1535
http://www.iisc.ernet.in/currsci/jun252000/RESEARCH%20COMMUNICATIONS.pdf

Marie-Claire D’Souza, Madhuri Sharon (2001) In vitro clonal propagation of annatto (Bixa orellana L.). In Vitro Cellular and Developmental Biology – Plant 37:168–172
doi: 10.1007/s11627-001-0029-7 (does not link to PubPeer)
http://link.springer.com/article/10.1007/s11627-001-0029-7

Reply
1. Annatto (Bixa orellana) query says:
  
  May 30, 2016 at 11:57 am
  
  Kindly observe the figures and tables of these two papers.
  
  Madhuri Sharon*, Manisha Sharan, Marie Claire Castello
  European Journal of Experimental Biology, 2012, 2 (1):142-150
  In Vitro Culture studies of Bixa orellana L: I – Differential requirements for plant regeneration from hypocotyl, leaf, cotyledonary leaf and root explants
  GUFIC Biosciences, Plant Tissue Culture Lab, 11th Road, MIDC, Marol, Mumbai, India
  http://pelagiaresearchlibrary.com/european-journal-of-experimental-biology/vol2-iss1/EJEB-2012-2-1-142-150.pdf
  
  Manisha Sharan, Marie Claire Castello, Madhuri Sharon*
  European Journal of Experimental Biology, 2012, 2 (1):156-162
  In Vitro Culture studies of Bixa orellana L: III Plant Regeneration from Roots through Direct and Indirect Somatic Embryogenesis
  GUFIC Biosciences, Plant Tissue Culture Lab, 11th Road, MIDC, Marol, Mumbai, India
  http://pelagiaresearchlibrary.com/european-journal-of-experimental-biology/vol2-iss1/EJEB-2012-2-1-156-162.pdf
  
  Reply
2. Annatto (Bixa orellana) query says:
  
  June 5, 2016 at 10:54 pm
  
  On Monday, June 6, 2016, William Erskine, Director of the Centre for Plant Genetics and Breeding (PGB), University of Western Australia, wrote:
  “Marie-Claire Castello is employed as a part-time technical general staff member at UWA (not as an academic). I was able to meet with her last week on the issue raised. I understand that three of the four papers from her PhD highlighted in your email were published without her input/ consent. I’ve seen that she has now contacted the editors requesting their retraction.”
  
  Reply
Grass pea (Lathyrus sativus) query says:

June 3, 2016 at 2:03 am

Kindly observe these three papers.

2016
Caryologia (in press)
Karyotype analysis and identification of extra chromosomes in primary aneuploid stocks of grass pea (Lathyrus sativus L.) by fluorescence chromosome banding
Dibyendu Talukdar (1), Tulika Talukdar (2)
(1) Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, West Bengal, India
(2) Department of Botany, A.P.C. Roy Govt. College, University of North Bengal, Siliguri, India
http://www.tandfonline.com/doi/full/10.1080/00087114.2016.1169091
DOI: 10.1080/00087114.2016.1169091
https://www.pubpeer.com/publications/87013C3650C36BDA450B2D55AD23A6

2014
Dibyendu TALUKDAR
Increasing nuclear ploidy enhances the capability of antioxidant defense and reduces chromotoxicity in Lathyrus sativus roots under cadmium stress
Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, West Bengal, India
Turkish Journal of Botany 38: 696-712
DOI: 10.3906/bot-1310-9
http://journals.tubitak.gov.tr/botany/issues/bot-14-38-4/bot-38-4-8-1310-9.pdf
https://www.pubpeer.com/publications/3AA848D99561DC867DEB6B30E1CB3F

2014
Dibyendu Talukdar 1, Tulika Talukdar 2
1 Department of Botany, R.P.M College, University of Calcutta, Uttarpara, Hooghly, West Bengal 712 258, India
2 Department of Botany, Acharya Prafulla Chandra Roy Government College, University of North Bengal, Darjeeling, West Bengal 734 010, India
Leaf Rolling and Stem Fasciation in Grass Pea (Lathyrus sativus L.) Mutant Are Mediated through Glutathione-Dependent Cellular and Metabolic Changes and Associated with a Metabolic Diversion through Cysteine during Phenotypic Reversal
BioMed Research International 2014, Article ID 479180, 21 pages
doi: 10.1155/2014/479180
http://www.hindawi.com/journals/bmri/2014/479180/
https://www.pubpeer.com/publications/2BC89A1339D0BEC8C25F018B7A20BB

Reply
1. Grass pea (Lathyrus sativus) query says:
  
  June 3, 2016 at 4:46 am
  
  Please compare these two papers.
  
  2013a
  ISRN Agronomy, vol. 2013, Article ID 284830, 15 pages, 2013.
  Dibyendu Talukdar
  Growth Responses and Leaf Antioxidant Metabolism of Grass Pea (Lathyrus sativus L.) Genotypes under Salinity Stress
  doi: 10.1155/2013/284830
  http://www.hindawi.com/journals/isrn/2013/284830/
  https://www.pubpeer.com/publications/F4C1CEC4F85DA6A889636EFDB66B33
  
  2013c
  Agricultural Research December 2013, Volume 2, Issue 4, pp 330-339
  Plant Growth and Leaf Antioxidant Metabolism of Four Elite Grass Pea (Lathyrus sativus) Genotypes, Differing in Arsenic Tolerance
  Dibyendu Talukdar
  DOI: 10.1007/s40003-013-0085-3
  http://link.springer.com/article/10.1007%2Fs40003-013-0085-3
  https://www.pubpeer.com/publications/2301D6B639356515DE3681DC9F6559
  
  Reply
  1. Grass pea (Lathyrus sativus) query says:
    
    June 3, 2016 at 8:40 am
    
    Please compare these two papers.
    
    2013c
    Agricultural Research December 2013, Volume 2, Issue 4, pp 330-339
    Plant Growth and Leaf Antioxidant Metabolism of Four Elite Grass Pea (Lathyrus sativus) Genotypes, Differing in Arsenic Tolerance
    Dibyendu Talukdar
    DOI: 10.1007/s40003-013-0085-3
    http://link.springer.com/article/10.1007%2Fs40003-013-0085-3
    https://www.pubpeer.com/publications/2301D6B639356515DE3681DC9F6559
    
    2014d
    Sciknow Publications Ltd. Biochemistry & Molecular Biology 2014, 2(1):7-16
    Differential morpho-agronomic and physiological responses of grass pea (Lathyrus sativus L.) and lentil (Lens culinaris Medik.) genotypes to arsenic
    Dibyendu Talukdar
    Department of Botany, R.P.M. College, Uttarpara, West Bengal, Hooghly 712 258, India
    DOI: 10.12966/bmb.03.02.2014
    http://www.sciknow.org/article/detail/id/862
    https://www.pubpeer.com/publications/A57E86E0100329E0434EC41F5FE5CA
    
    Reply
2. Grass pea (Lathyrus sativus) query says:
  
  June 3, 2016 at 9:14 am
  
  Kindly observe these two papers.
  
  BioMed Research International, vol. 2014, Article ID 479180, 21 pages, 2014.
  Dibyendu Talukdar 1, Tulika Talukdar 2
  Leaf Rolling and Stem Fasciation in Grass Pea (Lathyrus sativus L.) Mutant Are Mediated through Glutathione-Dependent Cellular and Metabolic Changes and Associated with a Metabolic Diversion through Cysteine during Phenotypic Reversal.
  1 Department of Botany, R.P.M College, University of Calcutta, Uttarpara, Hooghly, West Bengal 712 258, India
  2 Department of Botany, Acharya Prafulla Chandra Roy Government College, University of North Bengal, Darjeeling, West Bengal 734 010, India
  doi: 10.1155/2014/479180
  http://www.hindawi.com/journals/bmri/2014/479180/
  https://www.pubpeer.com/publications/2BC89A1339D0BEC8C25F018B7A20BB
  
  Journal of Plant Science & Molecular Breeding 2013 2(4), 12 pages
  Arsenic exposure modifies Fusarium wilt tolerance in grass pea (Lathyrus sativus L.) genotypes through modulation of antioxidant defense response
  Dibyendu Talukdar
  Plant Cell and Stress Biology Laboratory, Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, Hooghly 712258, West Bengal, India
  doi: 10.7243/2050-2389-2-4
  http://www.hoajonline.com/journals/pdf/2050-2389-2-4.pdf
  https://www.pubpeer.com/publications/F55297BFC8623057692FE77BF17B0D
  
  Reply
3. Grass pea (Lathyrus sativus) query says:
  
  June 5, 2016 at 2:13 am
  
  Kindly observe the following two papers.
  
  International Journal of Genetics and Molecular Biology Vol. 2(6), pp. 112-120, June 2010
  Allozyme variations in leaf esterase and root peroxidase isozymes and linkage with dwarfing genes in induced dwarf mutants of grass pea (Lathyrus sativus L.)
  Dibyendu Talukdar
  Department of Botany, University of Kalyani, Kalyani, 741 235, West Bengal, India
  
  The Scientific World Journal, vol. 2012, Article ID 345983, 11 pages, 2012
  Dibyendu Talukdar
  Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, West Bengal, Hooghly 712 258, India
  Flavonoid-Deficient Mutants in Grass Pea (Lathyrus sativus L.): Genetic Control, Linkage Relationships, and Mapping with Aconitase and S-Nitrosoglutathione Reductase Isozyme Loci
  doi: 10.1100/2012/345983
  Academic Editors: K. Chakravarty, E. Olmos, and K. Shoji
  http://www.hindawi.com/journals/tswj/2012/345983/
  https://www.pubpeer.com/publications/6FB48D0539772FC0C0BFECD9E14887
  
  Reply
Common bean (Phaseolus vulgaris) query says:

June 3, 2016 at 3:30 am

Please observe these two papers.

BioMed Research International, vol. 2013, Article ID 782450, 11 pages, 2013.
Dibyendu Talukdar 1, Tulika Talukdar 2
Superoxide-Dismutase Deficient Mutants in Common Beans (Phaseolus vulgaris L.): Genetic Control, Differential Expressions of Isozymes, and Sensitivity to Arsenic.
1 Department of Botany, R.P.M College, University of Calcutta, Uttarpara, Hooghly, West Bengal 712 258, India
2 Department of Botany, Acharya Prafulla Chandra Roy Government College, University of North Bengal, Darjeeling, West Bengal 734 010, India
doi: 10.1155/2013/782450
http://www.hindawi.com/journals/bmri/2013/782450/
https://www.pubpeer.com/publications/72B72D5FBB2FBE0327249F03FF92A5

Environmental and Experimental Biology (2014) 12: 73–81
A common bean (Phaseolus vulgaris) mutant with constitutively low cysteine desulfhydrase activity exhibits growth inhibition but uniquely shows tolerance to arsenate stress
Dibyendu Talukdar
Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, Hooghly 712258, West Bengal, India
http://eeb.lu.lv/EEB/201407/EEB_12_Talukdar.pdf

Reply
Invasive plant species query says:

June 3, 2016 at 6:17 am

Kindly observe these two papers.

Talukdar D & Talukdar T (2016) Inventory of invasive alien plants in Bethuadahari wildlife sanctuary in Nadia district, West Bengal, India. Tropical Plant Research 3(1): 120–130
http://www.tropicalplantresearch.com/archives/?year=2016&vol=3&issue=1
http://www.tropicalplantresearch.com/archives/?year=2016&vol=3&issue=1&ArticleId=94

Biswas S, Maity M, Srimany S, Chatterjee S, Karmakar T, Datta R, Patra J, Koley M and Talukdar D: Compositions, Distributions and Status of Economic Plants among Invasive Floras of Uttarpara, West Bengal, India. International Journal of Pharmacognosy 2014; 1(12) 800-809:
http://dx.doi.org/10.13040/IJPSR.0975-8232.IJP.1(12).800-809
http://ijpjournal.com/articles/?iyear=65&imonth=83
http://ijpjournal.com/bft-article/compositions-distributions-and-status-of-economic-plants-among-invasive-floras-of-uttarpara-west-bengal-india/

https://www.pubpeer.com/publications/87013C3650C36BDA450B2D55AD23A6#fb52283

Reply
Lentil, grass pea and fenugreek queries says:

June 5, 2016 at 1:24 am

Kindly observe these 5 papers.

Plant Gene & Trait 2014, Vol. 5, No.5, 33-39
Differential response of cysteine-deficient lentil (Lens culinaris Medik.) mutants impaired in foliar o-acetylserine(thiol)-lyase expression
Dibyendu Talukdar
Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, Hooghly 712258, West Bengal, India
doi: 10.5376/pgt.2014.05.0005
http://pgt.biopublisher.ca
http://biopublisher.ca/index.php/pgt/article/html/1320/
https://www.pubpeer.com/publications/D3D3D69E235F8130BDF311B2255A6E

Journal of Genetics 88(2): 165-175 (2009)
Dwarf mutations in grass pea (Lathyrus sativus L.): origin, morphology, inheritance and linkage studies
Dibyendu Talukdar
Department of Botany, University of Kalyani, Kalyani 741 235, India
DOI: 10.1007/s12041-009-0024-z
https://www.pubpeer.com/publications/893CFE54F623370316DB3BCE7AFD21

African Journal of Agricultural Research Vol. 4 (13), pp. 1549-1559, December, 2009 Special Review
Recent progress on genetic analysis of novel mutants and aneuploid research in grass pea (Lathyrus sativus L.)
Dibyendu Talukdar
Department of Botany, R. P. M. College, Uttarpara 712258, Hoogly, West Bengal, India
http://www.academicjournals.org/journal/AJAR/article-full-text-pdf/643F48532326

Dibyendu Talukdar (2013) Cytogenetics of a reciprocal translocation integrating distichous pedicel and tendril-less leaf mutations in Lathyrus sativus L., Caryologia 66:1, 21-30, DOI: 10.1080/00087114.2013.780437
http://dx.doi.org/10.1080/00087114.2013.780437
https://www.pubpeer.com/publications/934EB812C177567D7DF7AB55F0C085

Russian Journal of Plant Physiology, 2013, Vol. 60, No. 5, pp. 652-660. Pleiades Publishing, Ltd.
Arsenic-Induced Changes in Growth and Antioxidant Metabolism of Fenugreek
Dibyendu Talukdar
Plant Cell and Stress Biology Laboratory, Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, Hooghly 712258, West Bengal, India
DOI: 10.1134/S1021443713050130
http://link.springer.com/article/10.1134%2FS1021443713050130
https://www.pubpeer.com/publications/07E6D21EF08032FD31D895066EE98E

Reply
1. Lentil, grass pea and alien plants queries says:
  
  June 10, 2016 at 12:08 am
  
  Kindly observe these 9 papers.
  
  Caryologia Vol. 63, no. 1: 62-72, 2010
  Cytogenetic characterization of induced autotetraploids in grass pea (Lathyrus sativus L.)
  Talukdar Dibyendu
  Department of Botany, University of Kalyani, Kalyani, Nadia-741 235, West Bengal, India
  http://www.tandfonline.com/doi/abs/10.1080/00087114.2010.10589709
  DOI: 10.1080/00087114.2010.10589709
  https://www.pubpeer.com/publications/5C6CE3B6ECA61D270A2128FB18AEE2
  
  International Journal of Current Research Vol. 4, Issue, 04, pp.032-040, April, 2012
  ALIEN INVASIVE LEGUMES AND ALLELOPATHY: A CASE STUDY AT GANGETIC WEST BENGAL, INDIA
  1 Dibyendu Talukdar, 2 Tulika Talukdar
  1 Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, Hooghly. West Bengal, 712258, India
  2 Department of Botany, Krishnagar Govt. College, University of Kalyani, Krishnagar, Nadia, West Bengal, India
  http://www.journalcra.com/archive/201204
  http://www.journalcra.com/article/alien-invasive-legumes-and-allelopathy-case-study-gangetic-west-bengal-india
  http://www.journalcra.com/sites/default/files/1851.pdf
  
  Dibyendu Talukdar (2013) Cytogenetics of a reciprocal translocation integrating distichous pedicel and tendril-less leaf mutations in Lathyrus sativus L., Caryologia 66:1, 21-30, DOI: 10.1080/00087114.2013.780437
  http://dx.doi.org/10.1080/00087114.2013.780437
  https://www.pubpeer.com/publications/934EB812C177567D7DF7AB55F0C085
  
  International Journal of Agricultural Science and Research (IJASR) Vol. 3 Issue 2, Jun 2013, 217-232
  CATALASE-DEFICIENT MUTANTS IN LENTIL (Lens culinaris MEDIK.): PERTURBATIONS IN MORPHO-PHYSIOLOGY, ANTIOXIDANT REDOX AND CYTOGENETIC PARAMETERS
  DIBYENDU TALUKDAR 1, TULIKA TALUKDAR 2
  1 Department of Botany, R. P. M. College, Uttarpara, West Bengal, India
  2 Department of Botany, Krishnagar Government College, Krishnanagar, Nadia, West Bengal, India
  http://pakacademicsearch.com/journals/226/3/2
  http://pakacademicsearch.com/pdf-files/agr/226/217-232%20Vol.%203%20Issue%202,%20Jun%202013.pdf
  
  Annual Review & Research in Biology 3(3): 195-212, 2013
  Selenium Priming Selectively Ameliorates Weed – Induced Phytotoxicity by Modulating Antioxidant Defense Components in Lentil (Lens culinaris Medik.) and Grass Pea (Lathyrus sativus L.)
  Dibyendu Talukdar
  Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, Hooghly 712258, West Bengal, India.
  http://sciencedomain.org/issue/220
  http://sciencedomain.org/abstract/1259
  
  BioMed Research International 2014, Article ID 479180, 21 pages
  Dibyendu Talukdar 1, Tulika Talukdar 2
  1 Department of Botany, R.P.M College, University of Calcutta, Uttarpara, Hooghly, West Bengal 712 258, India
  2 Department of Botany, Acharya Prafulla Chandra Roy Government College, University of North Bengal, Darjeeling, West Bengal 734 010, India
  Leaf Rolling and Stem Fasciation in Grass Pea (Lathyrus sativus L.) Mutant Are Mediated through Glutathione-Dependent Cellular and Metabolic Changes and Associated with a Metabolic Diversion through Cysteine during Phenotypic Reversal
  http://www.hindawi.com/journals/bmri/2014/479180/
  https://www.pubpeer.com/publications/2BC89A1339D0BEC8C25F018B7A20BB
  doi: 10.1155/2014/479180
  
  Turkish Journal of Botany 38: 696-712 (2014)
  Dibyendu TALUKDAR
  Increasing nuclear ploidy enhances the capability of antioxidant defense and reduces chromotoxicity in Lathyrus sativus roots under cadmium stress
  Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, West Bengal, India
  http://journals.tubitak.gov.tr/botany/issues/bot-14-38-4/bot-38-4-8-1310-9.pdf
  https://www.pubpeer.com/publications/3AA848D99561DC867DEB6B30E1CB3F
  DOI: 10.3906/bot-1310-9
  
  Discovery Genetics, 2015, 1(1), 17-22
  Meiosis-driven cytogenetic consequences and transmission of double trisomics in grass pea (Lathyrus sativus L.)
  Dibyendu Talukdar
  Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, Hooghly 712258, West Bengal, India
  http://www.discovery.org.in/ (site not traceable; domain listed for sale)
  http://discoveryjournals.com/genetics/current_issue/v1/n1/index.htm
  http://discoveryjournals.com/genetics/current_issue/v1/n1/A4.pdf
  
  Caryologia (in press)
  Karyotype analysis and identification of extra chromosomes in primary aneuploid stocks of grass pea (Lathyrus sativus L.) by fluorescence chromosome banding
  Dibyendu Talukdara* & Tulika Talukdarb
  Received: 15 Dec 2015; Accepted: 10 Mar 2016; Published online: 14 Apr 2016
  http://www.tandfonline.com/doi/full/10.1080/00087114.2016.1169091
  DOI: 10.1080/00087114.2016.1169091
  
  Reply
Annatto (Bixa orellana) query says:

June 6, 2016 at 4:55 am

Kindly compare these two papers.

Mendes AMDS, de Figueiredo AF, da Silva JF (2005) Growth and maturation of urucum fruits and seeds. Revista Brasileira de Sementes 27(2): 25-34. Doi: 10.1590/S0101-31222005000200005 (in Portuguese with English abstract)
http://www.scielo.br/scielo.php?script=sci_abstract&pid=S0101-31222005000200005&lng=pt&nrm=iso&tlng=pt
http://www.scielo.br/pdf/rbs/v27n2/a05v27n2.pdf

Mendes AMDS, de Figueiredo AF, da Silva JF (2006) Growth and maturation of urucum fruits and seeds. Revista Brasileira de Sementes 28(1): 133-141. Doi: 10.1590/S0101-31222006000100019 (in Portuguese with English abstract)
http://www.scielo.br/scielo.php?script=sci_abstract&pid=S0101-31222006000100019&lng=pt&nrm=iso&tlng=pt
http://www.scielo.br/pdf/rbs/v28n1/a19v28n1.pdf

Reply
Annatto (Bixa orellana) query says:

June 8, 2016 at 2:58 am

Kindly compare these two papers.

Vespasiano Borges de Paiva Neto, Tiago Ribeiro da Mota, Wagner Campos Otoni. 2003A. Direct organogenesis from hypocotyl-derived explants of annatto (Bixa orellana). Plant Cell, Tissue and Organ Culture 75:159–167.
Doi: 10.1023/A:1025063906822
http://link.springer.com/article/10.1023/A%3A1025063906822

Paiva Neto VB, Carvalho CR, Otoni WC. 2003B. Mannose: a potential selection system for genetic transformation of annatto. Biologia Plantarum 47(3):441–444.
Doi: 10.1023/B:BIOP.0000023891.16785.fc
http://link.springer.com/article/10.1023%2FB%3ABIOP.0000023891.16785.fc

https://www.pubpeer.com/publications/82C950A2307F34B0249F1A7AB77874

Reply
Saffron query says:

June 12, 2016 at 3:00 am

Kindly observe this paper.

Scientific Reports 6:25139
Saffron with resistance exercise improves diabetic parameters through the GLUT4/AMPK pathway in-vitro and in-vivo
Firouzeh Dehghan 1, Fatemeh Hajiaghaalipour 2, Ashril Yusof 1, Sekaran Muniandy 2, Seyed Ali Hosseini 3, Sedigheh Heydari 3, Landa Zeenelabdin Ali Salim 4, Mohammad Ali Azarbayjani 5
1 Department of Exercise Science, Sports Centre, University of Malaya, 50603 Kuala lumpur, Malaysia.
2 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
3 Department of Physical Education and Sport Science, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran.
4 Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
5 Department of Exercise Physiology, Central Tehran Branch, Islamic Azad University, Tehran, Iran.
http://www.ncbi.nlm.nih.gov/pubmed/27122001
http://www.nature.com/articles/srep25139
https://www.pubpeer.com/publications/813EA0E5E714084734DC84141D24A4
DOI: 10.1038/srep25139

Reply
Tropical seedweeds query says:

June 12, 2016 at 3:33 am

Kindly observe this paper.

BMC Complementary and Alternative Medicine 2015, 15:339
Antioxidant and cytotoxic activities of three species of tropical seaweeds
Yin Yin Chia, M S Kanthimathi, Kong Soo Khoo, Jayakumar Rajarajeswaran, Hwee Ming Cheng, Wai Sum Yap
doi: 10.1186/s12906-015-0867-1
http://www.biomedcentral.com/1472-6882/15/339/prepub
http://bmccomplementalternmed.biomedcentral.com/articles/10.1186/s12906-015-0867-1
https://www.pubpeer.com/publications/33BDB1EFE4BCFA44268BDA1EB23530

Reply
1. Anonymous says:
  
  June 14, 2016 at 5:00 am
  
  The first author offers some insight into this gel at PubPeer, stating (2 excerpts):
  “The tiny dot as indicated (at around 8000 bp) was most likely due to the scratch/dent on the scanner. It appeared at the same position (around 8 kb) as I always place my gels at the corner of the scanner (same position) each time I scan the gels.”
  
  “As explained earlier, the dots and smudges are most likely due to the dents/scratches and marks on the gel doc. The gels are always placed on the same position when I did the scanning and hence, the same position of spots on the gel images. The gel doc in our department is old, heavily used. It’s not surprising at all to encounter all these here and there. I changed to use another gel doc in another facility after the one in our department had finally broken down, hence the other lanes (4 and 5) don’t show the marks.”
  
  Reply
Grass pea, bean and lentil queries says:

June 14, 2016 at 12:53 pm

Kindly observe these four papers.

Dibyendu Talukdar 1, Tulika Talukdar 2
1 Department of Botany, R.P.M College, University of Calcutta, Uttarpara, Hooghly, West Bengal 712 258, India
2 Department of Botany, Acharya Prafulla Chandra Roy Government College, University of North Bengal, Darjeeling, West Bengal 734 010, India
Leaf Rolling and Stem Fasciation in Grass Pea (Lathyrus sativus L.) Mutant Are Mediated through Glutathione-Dependent Cellular and Metabolic Changes and Associated with a Metabolic Diversion through Cysteine during Phenotypic Reversal
BioMed Research International 2014, Article ID 479180, 21 pages
doi: 10.1155/2014/479180
http://www.hindawi.com/journals/bmri/2014/479180/
https://www.pubpeer.com/publications/2BC89A1339D0BEC8C25F018B7A20BB

3 Biotech (2015) 5(5):819–829
Functional interplay between glutathione and hydrogen sulfide in regulation of thiol cascade during arsenate tolerance of common bean (Phaseolus vulgaris L.) genotypes
Dibyendu Talukdar
Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, West Bengal 712258, India
DOI: 10.1007/s13205-015-0285-6
http://link.springer.com/article/10.1007/s13205-015-0285-6
https://www.pubpeer.com/publications/8124B57359F781DD3FC9A4953BAFF9

Brazilian Journal of Botany (2016) 39(1): 55–66
Glutathione deficiency in a grass pea (Lathyrus sativus L.) mutant reveals major reshuffle in up-stream thiol cascade and downstream antioxidant defense under arsenate stress
Dibyendu Talukdar
Department of Botany, R.P.M. College (University of Calcutta), Uttarpara, West Bengal 712258, India
DOI: 10.1007/s40415-015-0213-3
http://link.springer.com/article/10.1007/s40415-015-0213-3
https://www.pubpeer.com/publications/E02A109BA990BC9E09BE24D9BF6675

Turkish Journal of Botany 40(4), (2016), 343-355
A metabolic diversion in the upstream thiol cascade of cysteine-deficient lentil (Lens culinaris Medik.) mutants induces arsenate tolerance by modulating downstream antioxidant defense
Dibyendu TALUKDAR
Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, West Bengal, India
doi: 10.3906/bot-1506-49
http://journals.tubitak.gov.tr/botany/abstract.htm;jsessionid=1C3A5BF91A2754B5277DB48D70485A31?id=18882
http://journals.tubitak.gov.tr/botany/issues/bot-16-40-4/bot-40-4-1-1506-49.pdf
https://www.pubpeer.com/publications/CBDF158175CB78D03BBB97C2A8B302

Reply
Common bean (Phaseolus vulgaris) query says:

June 14, 2016 at 3:57 pm

Kindly observe this paper.

Physiology and Molecular Biology of Plants January 2013, Volume 19, Issue 1, pp 69-79
Arsenic-induced oxidative stress in the common bean legume, Phaseolus vulgaris L. seedlings and its amelioration by exogenous nitric oxide
Dibyendu Talukdar
Plant Cell and Stress Biology Laboratory, Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, Hooghly, West Bengal, 712258, India
http://link.springer.com/article/10.1007%2Fs12298-012-0140-8
DOI: 10.1007/s12298-012-0140-8
https://www.pubpeer.com/publications/16D768E7C3D3AAC42A37B48846BE3B

Reply
Lantana camara query says:

June 14, 2016 at 5:03 pm

Kindly observe this paper.

Plant Science Today (2016) 3(2): 72-87
RAPD-based DNA fingerprinting in Lantana camara L. ecotypes and development of a digital database platform ‘LANRAD’
Tulika Talukdar 1, Dibyendu Talukdar 2
1 Department of Botany, A.P.C. Roy Govt. College, University of North Bengal, Siliguri, Darjeeling, West Bengal, India
2 Department of Botany, R.P.M. College, University of Calcutta, Uttarpara, Hooghly, West Bengal, India
http://horizonepublishing.com/journals/index.php/PST/article/view/177/127
http://dx.doi.org/10.14719/pst.2016.3.2.177
https://www.pubpeer.com/publications/AB4A4455C3D193F560C3396E259701

Reply
1. Lantana camara retraction says:
  
  June 24, 2016 at 11:22 am
  
  This paper was retracted today.
  http://horizonepublishing.com/journals/index.php/PST/article/view/245/149
  Plant Science Today (2016) 3(2): 248
  http://dx.doi.org/10.14719/pst.2016.3.2.245
  
  Reply
  1. Lantana camara retraction says:
    
    June 27, 2016 at 11:48 am
    
    An update: the wording of the original retraction notice has been modified.
    “Reason for retraction: RAPD gel images given in the paper seems manipulated. According to the authors, the images were provided by a service provider. The authors failed to provide the original/raw images to prove their innocence. Since the paper is centred around these gel images, the publisher has no other way than to retract the article. The corresponding author had agreed for the retraction.”
    
    The original PDF file can no longer be found on the web-site.
    
    http://horizonepublishing.com/journals/index.php/PST/article/view/245
    http://horizonepublishing.com/journals/index.php/PST/article/view/177
    
    Reply
Tomato retraction says:

June 16, 2016 at 3:06 am

African Journal of Biotechnology Vol. 5 (2), pp. 108-112, 16 January 2006
Reproducibility testing of RAPD and SSR markers in
Tomato
Rajput S.G. 1, Wable K.J. 2, Sharma K.M. 1, Kubde P.D. 2 and Mulay S.A. 2
1 Marathwada Agriculture University, Parbhani-431402, INDIA.
2 Bejo Sheetal Seeds Pvt. Ltd. Jalna INDIA.
http://www.academicjournals.org/article/article1379771757_Rajput%20et%20al.pdf

Retraction:
http://www.ajol.info/index.php/ajb/article/view/137758/127320
“The retraction is based on the fact that company has asked me to retract this paper
from journal’s website and publisher’s database since it is giving business inputs to
their competitors. Rajput S.G. is deeply sorry for any inconvenience this may have caused to the editorial staff, readers and co-author. In an effort to stop the distribution of this publication and the data contained therein, African Journal of Biotechnology is retracting the article in its entirety with the consent of Rajput S.G.”

Reply
Arabidopsis retraction says:

June 17, 2016 at 9:06 am

Frontiers in Plant Science, 04 February 2014 |
http://dx.doi.org/10.3389/fpls.2014.00016
The Carboxy-terminus of BAK1 regulates kinase activity and is required for normal growth of Arabidopsis
Man-Ho Oh 1,2, Xuejun Wang 1, Sang Yeol Kim 1, Xia Wu 1,3, Steven D. Clouse 4, Steven C. Huber 1,5*
1 Department of Plant Biology, University of Illinois, Urbana, IL, USA
2 Department of Biological Science, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
3 Department of Genome Sciences, University of Washington, Seattle, WA, USA
4 Department of Horticultural Science, NC State University, Raleigh, NC, USA
5 United States Department of Agriculture, Agricultural Research Service, Urbana, IL, USA
http://journal.frontiersin.org/article/10.3389/fpls.2014.00016/full

Retraction:
http://journal.frontiersin.org/article/10.3389/fpls.2016.00960/full
doi: 10.3389/fpls.2016.00960

Reply
Arabidopsis retraction says:

June 21, 2016 at 4:40 am

PNAS vol. 107 no. 41 : 17827–17832
Autophosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and basal defense gene expression
Man-Ho Oh a,b, Xiaofeng Wang c, Xia Wu d, Youfu Zhao e, Steven D. Clouse c, and Steven C. Huber a,b,1
a Agricultural Research Service, United States Department of Agriculture and
b Department of Plant Biology, University of Illinois, Urbana, IL 61801;
c Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695;
d Physiological and Molecular Plant Biology Program, Department of Plant Biology, University of Illinois, Urbana, IL 61801; and
e Department of Crop Sciences, University of Illinois, Urbana, IL 61801
doi: 10.1073/pnas.0915064107
http://www.pnas.org/content/107/41/17827.full.pdf
http://www.pnas.org/content/107/41/17827.short

Retraction:
http://www.pnas.org/content/early/2016/06/17/1608778113.full
doi: 10.1073/pnas.1608778113

https://www.pubpeer.com/publications/72AB146DD48340D087E1CE9B94B1AE

Reply
Hypericum perforatum query says:

June 22, 2016 at 4:32 am

Kindly observe the following paper.

Acta Physiologiae Plantarum February 2015, 37:37
Effect of sucrose on shoot regeneration in Agrobacterium transformed Hypericum perforatum L. roots
Branka Vinterhalter 1, Snežana Zdravković-Korać 1, Nevena Mitić 1, Borut Bohanec 2, Dragan Vinterhalter 1, Jelena Savić 1
1. Institute for Biological Research “Siniša Stanković”, University of Belgrade, Bulevar Despota Stefana 142, 11060, Belgrade, Serbia
2. Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
http://link.springer.com/article/10.1007/s11738-015-1785-z
DOI: 10.1007/s11738-015-1785-z
https://www.pubpeer.com/publications/AD8C384D27EA4D35636D8912A3D949

Reply
1. Hypericum perforatum query says:
  
  June 23, 2016 at 3:21 pm
  
  The corresponding author responds at PubPeer, as follows:
  “Willing to make amplicon bands more visible I have emphasized two existing bands on the gel picture. My intention was not to fix or at any other way change obtained results. It was purely esthetical, to make them more visible, especially since their intensity was not of interest and of no crucial importance for this work. The analysis of the presented genes expression was however done by qRT-PCR used also for result comparison and comments (Table 3). I am attaching the original PCR gel picture.
  Sincerely,
  Jelena Savic (corresponding author)”
  
  Reply
Dragon's blood (Calamus draco) retraction says:

June 25, 2016 at 7:28 am

Retraction of “Dragonbloodin A1 and A2: Flavan Trimers and Anti-inflammatory Principles from Sanguis Draconis”
Wen-Ke Du, Hsin-Yi Hung, Ping-Chung Kuo, Tsong-Long Hwang, Ler-Chun Shiu, Kom-Bei Shiu, E-Jian Lee, Shih-Huang Tai, and Tian-Shung Wu*
Org. Lett., 2016, 18 (12), pp 3042–3042
DOI: 10.1021/acs.orglett.6b00593
http://pubs.acs.org/doi/abs/10.1021/acs.orglett.6b00593

Reply
Jaime A. Teixeira da Silva says:

June 28, 2016 at 12:11 am

It is with great shock and sadness that I wish to report errors in my own literature. I was alerted to comments and observations made at PubPeer about work conducted almost 2 decades ago, and to be consistent with my message to other plant scientists about correcting their literature when errors are known, I have immediately taken the following steps, on the same day that I received these reports (i.e., today).

First of all, I have requested a retraction of a duplicate paper in NZJCHS, as follows:
Evaluation of carbon sources as positive selection agents for chrysanthemum (Dendranthema × grandiflorum) transformation
Jaime A. Teixeira da Silva
New Zealand Journal of Crop and Horticultural Science Volume 32, Issue 1, March 2004, pages 55-67
Which duplicates:
Teixeira da Silva, J.A. (2004) The effect of carbon source on the in vitro organogenesis of chrysanthemum thin cell layers. Bragantia 63(2): 165-177.

In this case, I sent an email to the EIC, Prof. Kevin Davies, offered an explanation, a sincere apology, and the request to immediately retract this paper.

In addition, most likely the same astute reader reported figure duplication in three papers, all published in 2003, one of which was a review. All were published at the same time and it would have been impossible to cross reference the figures since the papers themselves had not been published. Fortunately, I have been given this opportunity to correct the affected papers.

I have, also today, immediately contacted the Editors in Chief of Asian Journal of Plant Sciences (AnsiNet), Dr. Sayyada Khatoon and African Journal of Biotechnology (Academic Journals), Dr. Nyerhovwo Tonukari and Dr. George Ude. I should note that these journals and publishers are classified by Jeffrey Beall as predatory open access publishers (something that was not known in the nascent phase of these journals/publishers back in 2003), and were the only alternative places for publication of plant science outside of mainstream publishers. In retrospect, and given my science activism at present, I truly regret having made that choice.

The affected papers are:

Teixeira da Silva, J.A. (2003) Thin Cell Layer technology in ornamental plant micropropagation and biotechnology. African Journal of Biotechnology 2(12): 683-691. http://academicjournals.org/article/article1380108344_Teixeira%20da%20Silva.pdf DOI: 10.5897/AJB2003.000-1125

Teixeira da Silva, J.A., Fukai, S. (2003) Chrysanthemum organogenesis through thin cell layer technology and plant growth regulator control. Asian Journal of Plant Sciences 2(6): 505-514.

Teixeira da Silva, J.A. (2003) Thin cell layer technology for induced response and control of rhizogenesis in chrysanthemum. Plant Growth Regulation January 2003, Volume 39, Issue 1, pp 67-76

I wish to offer my apologies to any readers or chrysanthemum scientists who may be hurt by this fact. I have disappointed myself and this has been a very terrible and painful day, over and above the so many other conflicts that I am involved with, and that many of my critics at PubPeer and Retraction Watch are aware of.

No matter how disgraceful or painful, I hope that setting my own publishing record straight will spur other plant scientists, those listed above and others, to do the right thing, and to act immediately to correct the literature when errors are reported, or detected. Although this shocking experience for me will no doubt involve a phase of serious introspection, and most likely a reflection on what science means to me after a lifetime of painful struggles to do the right thing, it will not prevent me from continuing to highlight what I believe to be a field of science in crisis, namely plant science, especially horticulture.

I promise today that I will also be publishing a post-publication peer review of the chrysanthemum literature, in which I will be critical both of my own papers, and of other papers that have still not been corrected, even 2 or 3 years after alerting authors, editors and publishers to these issues.

Again, I offer my sincerest apologies to all concerned.

Reply
Arabidopsis query says:

June 28, 2016 at 3:01 am

Kindly observe these two papers.

PsbP-domain protein1, a nuclear-encoded thylakoid lumenal protein, is essential for photosystem I assembly in Arabidopsis
Jun Liu, Huixia Yang, Qingtao Lu, Xiaogang Wen, Fan Chen, Lianwei Peng, Lixin Zhang, Congming Lu
The Plant Cell December 2012 vol. 24 no. 12 4992-5006
http://www.plantcell.org/content/24/12/4992
https://pubpeer.com/publications/FBD2DDA8227ABAFEDC38A7C29CF77E
DOI: 10.1105/tpc.112.106542

Corrected by:
http://www.plantcell.org/content/28/3/823.full.pdf+html

LPA2 is required for efficient assembly of photosystem II in Arabidopsis thaliana
Jinfang Ma, Lianwei Peng, Jinkui Guo, Qingtao Lu, Congming Lu, Lixin Zhang
The Plant Cell June 2007 vol. 19 no. 6 1980-1993
https://pubpeer.com/publications/D91BA4C2BCACF7469204826404FE1F
http://www.plantcell.org/content/19/6/1980
DOI: 10.1105/tpc.107.050526

Reply
Plant defense correction says:

June 28, 2016 at 3:03 am

Microbial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant Defense Responses
Junqi Song, Andrew F. Bent, PLoS Pathogens (2014) 10(6): e1004226
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004030
DOI: 10.1371/journal.ppat.1004030
https://pubpeer.com/publications/DE4B3B342EEF23E43AB0B01F47A15C

Correction:
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004226
“Figure 1 in the original article contains two duplicate panels that were inserted during a manuscript revision. Two of the six images in Figure 1C were inadvertently deleted and replaced with duplicates of the adjacent photographic panels. The six correct Figure 1C photographic panels were used during peer review, and are now restored in the corrected version of Figure 1.”

Reply
Rice leaf streak correction says:

June 28, 2016 at 3:08 am

PLoS Pathog 10(4): e1004126. doi: 10.1371/journal.ppat.1004126
Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene
Raul A. Cernadas, Erin L. Doyle, David O. Niño-Liu, Katherine E. Wilkins, Timothy Bancroft, Li Wang, Clarice L. Schmidt, Rico Caldo, Bing Yang, Frank F. White, Dan Nettleton, Roger P. Wise, Adam J. Bogdanove
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003972
https://pubpeer.com/publications/294B796502B0BC0788C23FAFD1CF06

Correction:
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004126
“There are data and labeling errors in Figure 3. In the original Figure 3, the gel image for Os07g06970 is incorrect. It is a duplicate of the image for Os01g40290. The new Figure 3 contains the correct image. Also, the original Figure 3 was generated using Locus IDs from Release 5.0 of the Rice Genome Annotation Project. Relative to Release 7.0, used for all other reporting in the article, one of these Locus IDs, Os10g38495, is obsolete. It has been updated in the new Figure 3 to the corresponding Release 7.0 Locus ID, Os10g38489. The remaining Locus IDs are the same in Release 5.0 and Release 7.0 and unchanged in the new Figure 3.”

Reply
PMBP papers queries says:

July 13, 2016 at 9:17 pm

Several papers are being queried at Springer’s PMBP.

Physiology and Molecular Biology of Plants October 2015, Volume 21, Issue 4, pp 551-558
Oxidative stress induced expression of monodehydroascorbate reductase gene in Eleusine coracana
Jebi Sudan, Bhawana Negi, Sandeep Arora
http://link.springer.com/article/10.1007/s12298-015-0327-x
doi: 10.1007/s12298-015-0327-x
http://www.ncbi.nlm.nih.gov/pubmed/26600681
PMID: 26600681
PMCID: PMC4646862
Sandeep Arora
https://pubpeer.com/publications/3FD42C4A4F3C6D18586280BBC4ED3A

Physiology and Molecular Biology of Plants October 2014, Volume 20, Issue 4, pp 411-423
Screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers
Md. Nasim Ali, Lucina Yeasmin, Saikat Gantait, Rupak Goswami, Somsubhra Chakraborty
http://link.springer.com/article/10.1007/s12298-014-0250-6
DOI: 10.1007/s12298-014-0250-6
http://www.ncbi.nlm.nih.gov/pubmed/25320465
PMID: 25320465
PMCID: PMC4185050
https://pubpeer.com/publications/9F7583A990AA434BC0DE821CC8DA03

Physiology and Molecular Biology of Plants 2013 Apr; 19(2): 251–260.
Mohd. Razaq, Monika Heikrujam, Siva K. Chetri, Veena Agrawal
doi: 10.1007/s12298-012-0152-4
PMCID: PMC3656186
In vitro clonal propagation and genetic fidelity of the regenerants of Spilanthes calva DC. using RAPD and ISSR marker
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656186/
https://www.pubpeer.com/publications/EDB5AB063FCEF7910C501B737D2CFF

Physiology and Molecular Biology of Plants 2014 Oct; 20(4): 517–526.
Siva K. Chetri, Pratima Rani Sardar, Veena Agrawal
Micropropagation and validation of genetic and biochemical fidelity amongst regenerants of Cassia angustifolia Vahl employing RAPD marker and HPLC
PMCID: PMC4185055
doi: 10.1007/s12298-014-0257-z
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185055/
http://link.springer.com/article/10.1007/s12298-014-0257-z
https://www.pubpeer.com/publications/05729B4AAC5F81445C083DC4C3E8A2

Physiology and Molecular Biology of Plants April 2014, Volume 20, Issue 2, pp 235-240
Plant regeneration from leaf explants of Aloe barbadensis Mill. and genetic fidelity assessment through DNA markers
Souvagyalaxmi Sahoo, Gyana Ranjan Rout
http://link.springer.com/article/10.1007/s12298-014-0226-6
DOI: 10.1007/s12298-014-0226-6
http://www.ncbi.nlm.nih.gov/pubmed/24757327
PMID: 24757327
PMCID: PMC3988330
https://pubpeer.com/publications/3BBF3B92834C19CA3674A7A39557AC

Physiology and Molecular Biology of Plants April 2014, Volume 20, Issue 2, pp 241-247
Synergistic effect of BAP and GA3 on in vitro flowering of Guizotia abyssinica Cass.-A multipurpose oil crop
S. Baghel, Y. K. Bansal
http://link.springer.com/article/10.1007/s12298-014-0229-3
DOI: 10.1007/s12298-014-0229-3
https://pubpeer.com/publications/DAE01AAA4668240A02DABDE340FC56

Physiology and Molecular Biology of Plants pp 1-8
Effect of paclobutrazol on photosynthesis and expression of pyrroline-5-carboxylatesynthase in contrasting wheat genotypes under water deficit stress condition
Sharad Kumar Dwivedi, Santosh Kumar
http://link.springer.com/article/10.1007/s12298-016-0343-5
DOI: 10.1007/s12298-016-0343-5
https://pubpeer.com/publications/8537C9EBE42560E845C5DB01932AF9

Physiology and Molecular Biology of Plants pp 1-12
First online: 06 February 2016
In vitro propagation, micromorphological studies and ex vitro rooting of cannon ball tree (Couroupita guianensis aubl.): a multipurpose threatened species
Mahipal S. Shekhawat, M. Manokari
http://link.springer.com/article/10.1007/s12298-015-0335-x
DOI: 10.1007/s12298-015-0335-x
https://pubpeer.com/publications/B09FA0F662D60157C9056A2617C667

Physiology and Molecular Biology of Plants July 2014, Volume 20, Issue 3, pp 357-364
In vitro propagation and withaferin A production in Withania ashwagandha, a rare medicinal plant of India
Bilal Ahmad Mir, Shabir Ahmad Mir, Sushma Koul
http://link.springer.com/article/10.1007/s12298-014-0243-5
DOI: 10.1007/s12298-014-0243-5
http://www.ncbi.nlm.nih.gov/pubmed/25049463
PMID: 25049463
PMCID: PMC4101142
https://pubpeer.com/publications/25049463

Physiology and Molecular Biology of Plants pp 1-6
First online: 29 January 2016
Influence of Agrobacterium rhizogenes strains, acitosyringone, inoculum size and temperature on production of active ingredients from Picrorhiza kurrooa
Janhvi Mishra Rawat, Balwant Rawat, Susmita Mishra, Aakriti Bhandari, Rajneesh K Agnihotri, Anup Chandra
http://link.springer.com/article/10.1007/s12298-016-0341-7
DOI: 10.1007/s12298-016-0341-7
https://pubpeer.com/publications/6BFBCE80A000FFA9CAE853AAF1FAAA

Physiology and Molecular Biology of Plants July 2014, Volume 20, Issue 3, pp 279-285
Evaluation of plant-mediated Silver nanoparticles synthesis and its application in postharvest Physiology of cut Flowers
Mousa Solgi
http://link.springer.com/article/10.1007/s12298-014-0237-3
DOI: 10.1007/s12298-014-0237-3
http://www.ncbi.nlm.nih.gov/pubmed/25049454
PMID: 25049454
PMCID: PMC4101138
https://pubpeer.com/publications/CD6C9D57E931A7E6F88D7DB7FC8623

Physiology and Molecular Biology of Plants July 2015, Volume 21, Issue 3, pp 417-424
An efficient in vitro shoot regeneration from leaf petiolar explants and ex vitro rooting of Bixa orellana L.- A dye yielding plant
Arifullah Mohammed, Kishore K. Chiruvella, Nima D. Namsa, Rama Gopal Ghanta
http://link.springer.com/article/10.1007/s12298-015-0297-z
DOI: 10.1007/s12298-015-0297-z
http://www.ncbi.nlm.nih.gov/pubmed/26261406
PMID: 26261406
PMCID: PMC4524855
https://pubpeer.com/publications/FF50B8A188916EF52EDA421E8914CC

Physiology and Molecular Biology of Plants April 2015, Volume 21, Issue 2, pp 279-285
High frequency organogenesis in hypocotyl, cotyledon, leaf and petiole explants of broccoli (Brassica oleracea L. var. italica), an important vegetable crop
Pankaj Kumar, D. K. Srivastava
DOI: 10.1007/s12298-015-0282-6
http://link.springer.com/article/10.1007/s12298-015-0282-6
http://www.ncbi.nlm.nih.gov/pubmed/25964720
PMID: 25964720
PMCID: PMC4411387
https://pubpeer.com/publications/A433A442144C68E0C601C0A3CAAA00

Physiology and Molecular Biology of Plants April 2015, Volume 21, Issue 2, pp 243-247
Validation of SSR markers associated with rust (Uromyces fabae) resistance in pea (Pisum sativum L.)
Anil Kumar Singh, Rashmi Rai, Brahma Deo Singh, Ramesh Chand, Chandra Prakash Srivastava
http://link.springer.com/article/10.1007/s12298-015-0280-8
DOI: 10.1007/s12298-015-0280-8
http://www.ncbi.nlm.nih.gov/pubmed/25964717
PMID: 25964717
PMCID: PMC4411386
https://pubpeer.com/publications/A49EDFEE0C10DA567AF00E0FA20C1C

Physiology and Molecular Biology of Plants April 2015, Volume 21, Issue 2, pp 187-196
Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes
Minakshi Choudhary, Jayanand, Jasdeep Chatrath Padaria
http://link.springer.com/article/10.1007/s12298-015-0287-1
DOI: 10.1007/s12298-015-0287-1
http://www.ncbi.nlm.nih.gov/pubmed/25964713
PMID: 25964713
PMCID: PMC4411378
https://pubpeer.com/publications/B2C513C5EA35DE02EEEE60E2B86800

Physiology and Molecular Biology of Plants January 2015, Volume 21, Issue 1, pp 117-122
Initial determination of DNA polymorphism of some Primula veris L. populations from Kosovo and Austria
Naim Berisha, Fadil Millaku, Bekim Gashi, Elez Krasniqi, Johannes Novak
http://link.springer.com/article/10.1007/s12298-014-0275-x
DOI: 10.1007/s12298-014-0275-x
http://www.ncbi.nlm.nih.gov/pubmed/25650329
PMID: 25650329
PMCID: PMC4312321
https://pubpeer.com/publications/6027131E0A21281EC851A17E715F3D

Physiology and Molecular Biology of Plants pp 1-11
First online: 05 March 2016
Expression of a bacterial chitinase (ChiB) gene enhances resistance against E. polygoni induced powdery mildew disease in the transgenic Black gram (Vigna mungo L.) (cv. T9)
D. K. Das
http://link.springer.com/article/10.1007/s12298-016-0344-4
DOI: 10.1007/s12298-016-0344-4
https://pubpeer.com/publications/13DCE80F38834887D2AC8D3B5616F3

Physiology and Molecular Biology of Plants January 2015, Volume 21, Issue 1, pp 123-136
Micropropagation and in vitro conservation of the rare and threatened plants Ramonda serbica and Ramonda nathaliae
Bekim Gashi, Kasamedin Abdullai, Valbona Sota, Efigjeni Kongjika
http://link.springer.com/article/10.1007/s12298-014-0261-3
DOI: 10.1007/s12298-014-0261-3
http://www.ncbi.nlm.nih.gov/pubmed/25648356
PMID: 25648356
PMCID: PMC4312326
https://pubpeer.com/publications/B3DFB45C0981DC022E459E41B0E2CC

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Plant nanotubes retraction says:

July 13, 2016 at 9:42 pm

Potential Impact of Multi-Walled Carbon Nanotubes Exposure to the Seedling Stage of Selected Plant Species.
Nanomaterials 2014, 4, 203-221.
Parvin Begum, Refi Ikhtiari, Bunshi Fugetsu
DOI: 10.3390/nano4020203
https://pubpeer.com/publications/A24FAF0D5D2B0DDE8E811876ECC93A#fb20319
http://www.mdpi.com/2079-4991/4/2/203
https://pubpeer.com/publications/A24FAF0D5D2B0DDE8E811876ECC93A

Paper retracted:
http://www.mdpi.com/2079-4991/5/1/268
“We have become aware that a substantial part of the main text of [1] is copied from multiple other publications. In total, 46% of the main text was taken from publications by the same authors [2,3] and 10% from other papers [4,5]. Because of the extent of text taken verbatim from previously published articles, we have made the decision to retract the article. All the authors of [1] have agreed to this decision. This paper is thus declared retracted and shall be marked accordingly for the scientific record. MDPI is a member of the Committee on Publication Ethics (COPE) and takes the responsibility to enforce strict ethical policies and standards very seriously. We aim to ensure the publication only of truly original scientific works. MDPI would like to apologize to the readers of Nanomaterials that this case remained undetected until now. We sincerely appreciate the efforts of anyone who brings matters of plagiarism to our attention in an effort to maintain scientific integrity.”

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Transgenic Brassica retraction says:

July 13, 2016 at 9:51 pm

Plant Cell, Tissue and Organ Culture (PCTOC) August 2016, Volume 126, Issue 2, pp 371–371
RETRACTED ARTICLE: Overexpression of thaumatin gene confers enhanced resistance to Alternaria brassicae and tolerance to salinity and drought in transgenic Brassica juncea (L.) Czern
Alkesh Hada, Sandhya Rawat, Veda Krishnan, Monica Jolly, Theboral Jeevaraj, Markandan Manickavasagam, Andy Ganapathi, Archana Sachdev, Anita Grover
http://link.springer.com/article/10.1007/s11240-015-0846-8
DOI: 10.1007/s11240-015-0846-8
https://pubpeer.com/publications/E422304A29C66F0A5AD2A19A113D59

“This article has been retracted at the request of Dr. Grover, listed as corresponding author of this paper. It was found that the paper was handled by Dr. Hada instead, who submitted and approved for publication without the consent of all other authors.”

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