Retraction Watch

Tracking retractions as a window into the scientific process

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

with 133 comments

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

Written by Ivan Oransky

January 25th, 2014 at 9:54 am

Comments
  • Jaime A. Teixeira da Silva 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

    • O Baptista 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

      • O Baptista 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.

  • Jeanette Garwood 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)

  • Nurse Dina 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.

    • Qui? 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

      • Qui? 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.

        • Qui? 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)

          • Qui? 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.

          • Qui? 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.

          • ABV Prasad 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

          • T-bone steak 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.

          • Bhavin July 24, 2014 at 10:09 am

            Dear Qyi?,
            Excellent detection, many of Murthy publications are from predatory journals

      • Qui? November 19, 2014 at 1:42 am
  • Nasraoui, Bouzid 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).

  • Science Society 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).”

  • Tehran 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.”

  • Hyderabad 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.”

  • Strelitzia Watch 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?

  • Vivek Kumar query 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

  • Dendrobium concerns 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

    • Meera C. Das 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

  • Dendrobium concerns 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?

  • Qui? 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”

  • Anthurium query 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

  • Ceropegia query 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/

  • Das Eckey query 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

  • Wheat query 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?

  • Wheat query 2 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

  • Plant tissue culture query 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 

  • Balanites query 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.

    • Balanites query 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.”

  • Ceropegia query 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

  • Cotton concerns 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.

  • Moringa concerns 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.

  • Anthurium retraction report 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

  • Rare earth elements + plants report 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

  • Dendrobium query 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

  • Ipomoea query 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 

  • Prof. Deepak Pental 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

  • Vitex negundo concerns 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

    • Vitex negundo concerns December 1, 2014 at 1:51 pm

      Erratum: Concern 3 should read 100-fold instead of 10-fold.

      • Vitex negundo concerns 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.”

  • Of mice and maize 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.

    • herr doktor bimler December 3, 2014 at 6:07 pm

      Obviously a misspelling. Someone confused a rat with a maze.

  • Parthenium hysterophorus queries 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

  • Kailash C. Bansal query 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

  • Cymbidium CryoLetters concern 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?

  • Welbaum and Tay query 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

  • ISHS query 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

  • Cymbidium stealth retraction 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

  • Anthurium query 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

  • Clerodendrum indicum query 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

  • Jaime A. Teixeira da Silva 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.”

  • Avraham Albert Levy queries 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/

  • Anthurium concerns 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

  • Barnyard-grass + rice query 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

  • Pakistan Journal of Agricultural Sciences 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

  • Green manure query 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.

  • Plant Pathogen Pseudomonas syringae query 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

  • Voinnet and Baulcombe queries 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

  • Lutts + Walker query 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)

  • Vitex trifolia queries 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)

  • Potato virus 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.”

  • Annamalai University queries 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

  • Seyed Alireza Salami queries 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)

    • Seyed Alireza Salami queries 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

    • Seyed Alireza Salami queries 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.”

    • Seyed Alireza Salami queries 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)

  • Cauliflower Synthetic Seeds stealth retraction 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)

  • Agrobacterium tumefaciens query 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 

  • Circular RNA query 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

  • Potato stats query 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

  • Carbon nanotubes query 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

  • Chrysanthemum cut flowers query 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

  • Pear shoot regeneration query 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: ma.yousefiara@stu.mail.um.ac.ir
    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

  • Justicia gendarussa queries 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)

  • PPPR or MPMI 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.

    • PPPR of MPMI 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.

    • PPPR of MPMI 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?

    • PPPR of MPMI 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.

  • Albizia lebbeck queries 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)

  • Acacia sinuata queries 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.

  • Artemisia annua query 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

  • Artemisia annua query 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

  • Sandalwood queries 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

    • Sandalwood queries 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/).

    • Sandalwood queries 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

    • Sandalwood queries 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

    • Sandalwood queries 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

    • Sandalwood queries 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

    • Sandalwood queries 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

    • Sandalwood queries 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.

    • Sandalwood queries 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

    • Sandalwood queries 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

    • Sandalwood queries 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.

      This case has a PubPeer entry:
      https://pubpeer.com/publications/12E25C0BEEAC9954BC59CF5945DFC6#fb23035

    • Sandalwood queries 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.

      This case has a PubPeer entry:
      https://pubpeer.com/publications/5361D84E566D3B0E179C09A132C102#fb23074

    • Sandalwood queries 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.”

      This case has a PubPeer entry:
      https://pubpeer.com/publications/709D8119A5C417B84F3C2C0567DF17#fb23095

    • Sandalwood queries 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

  • JXB PPPR 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

    • JXB PPPR 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 geraint.parry@Liverpool.ac.uk

      Cheers,
      geraint”

    • JXB PPPR 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 eliza@ibt.unam.mx
      Best regards, Elizabeth Cordoba”

  • Phytophthora infestans query 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

  • KaPPA-View4 and KaPPA-Loader Jatropha queries 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

  • Darjeeling tea query 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

  • Arabidopsis root microtubule queries 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

  • Arabidopsis cadmium 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.

  • Plants with ears? 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

  • Science Society November 17, 2014 at 12:51 pm

    Till date Professor Pramod Tandon has published 21 Research Papers on Dendrobium according to Google scholar data base.
    Are there problems in any of those papers?
    http://scholar.google.co.in/scholar?as_q=Dendrobium&as_epq=&as_oq=&as_eq=&as_occt=title&as_sauthors=%22Pramod+Tandon%22&as_publication=&as_ylo=&as_yhi=&btnG=&hl=en&as_sdt=0%2C5

    Professor Pramod Tandon is a Big Name in the Field of Plant Tissue Culture
    He received Padma Shri award in 2009 in the field of Science and Engineering. He has been nominated as member of the high-profile National Advisory Council (NAC) in June 2010
    http://en.wikipedia.org/wiki/Pramod_Tandon

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