Retraction Watch

Tracking retractions as a window into the scientific process

NSF investigation of high-profile plant retractions ends in two debarments

with 24 comments

Jorge Vivanco

Jorge Vivanco

A nearly ten-year-long series of investigations into a pair of plant physiologists who received millions in funding from the U.S. National Science Foundation has resulted in debarments of less than two years for each of the researchers.

The NSF Office of Inspector General recently posted its close-out report on its decision and a review of the University’s investigation, which had recommended a total of eight retractions or corrections. Although the investigator’s names have been redacted, the text of retractions and corrections quoted in the report corresponds to papers by Jorge Vivanco and his then-postdoc Harsh Bais at Colorado State University.

Bais has since joined the faculty of the University of Delaware, where he is now an associate professor, and obtained $2.5 million worth of grants from the NSF and over $500,000 from the National Institutes of Health. Vivanco has been promoted to a full professor, and received more than $3 million in NSF funding along with awards from the U.S. Department of Agriculture.

We first wrote about the researchers in 2011 when they retracted their 2005 Nature paper after “a key reference” (also co-authored by the pair) was retracted after they were “unable to find experimental data.” This note, plus the appearance of some other retractions, made us wonder if there was more to the story. The OIG’s answer: Most definitely.

This story, like many others, begins with a finding that was too good to be true. In the April 2002 issue of Plant Physiology, Bais and Vivanco promised to “unravel part of the mystery” of why spotted knapweed is such a nasty invasive plant. According to the authors, the plant’s roots secreted a noxious compound called (-)catechin that caused plants around it to wilt and die. A 2003 New York Times article about their follow-up paper in Science was headlined Forensic botanists find the lethal weapon of a killer weed.” In a report to their USDA funders, the team summarized the impact of their findings:

Our studies have been highlighted in popular newspapers, magazines, and TV news shows, including The New York Times, Scientific American Magazine, National Geographic, CNN News, and the Discovery Channel. As a result of our studies a company has licensed one of the allelochemical compounds as an ecologically-benign herbicide.

But by October 2004, the duo’s collaborators within CSU, and at the USDA research center, began to have their doubts about research on this root compound and others, according to the OIG report. The batches that Bais was preparing were “inconsistent in color and smell” and contained “extraneous compounds.” Although the University terminated a commercial licensing award, Vivanco “continued to request and to obtain federal funding from NSF and other agencies . . . while suspecting or knowing [the research] to be irreproducible.”

CSU faculty members raised allegations of misconduct to the Dean of the College of Agricultural Sciences, and the Dean asked Vivanco’s department chair to conduct “several interviews and report back to him.” As the NSF report puts it,

An informal, undocumented evaluation of the allegations at the College level appeared to evolve into an informal inquiry outside of University 1 ‘s prescribed policy, including analyses of the batches of the Mixture and blind tests of the extraction methodologies reported in Article 1.

During that preliminary investigation, the department chair (Witness 13) recommended to Vivanco that the issue “be worked out in the literature,” according to the report. (The department chair has not yet responded to an email and phone call requesting comment.) In the spring of 2006, the report says Vivanco got much the same answer when he initiated a meeting with the College Research Integrity Officer to discuss the lingering problems with Bais’s data. The College RIO’s “general recommendation to [Vivanco] was that nothing could be proven.”

Ultimately, rather than retracting the papers with the suspect data, the OIG says Vivanco tried to “save-face” and downplay the earlier results in subsequent publications even as he tried to advance the story in grant proposals and publications. In 2007, he coauthored a paper that failed to replicate Bais’s findings in the field:

Although previous consistent reports of high soil catechin concentrations provided circumstantial evidence for a role of catechin in C. maculosa invasion (Bais et al. 2002, 2003; Perry et al. 2005b; Thelen et al. 2005; Weir et al. 2006), this more extensive study, together with those of Blair et al. (2005, 2006), suggests that high catechin concentrations rarely occur in C. maculosa soil. More confidence can be placed in the current results. Thus, the infrequency of soil catechin weakens the hypothesis that it plays a role in C. maculosa invasions.

The paper pointed that Bais’s work had not used controls and suggested that could be the source of the discrepancy. All of this was enough, evidently, to pique the interest of the NSF investigators, who began interviewing current and former CSU faculty and staff and learned about the preliminary investigation. The OIG requested that CSU look into the misconduct allegations once again, and, it’s at this point that CSU appointed an investigation committee, as required under its research misconduct policy.

This formal investigation concluded that Bais had intentionally falsified and fabricated data, while Vivanco had been complicit in research misconduct by capitalizing on the results after learning they were false. The CSU committee recommended that Vivanco be “considered for demotion by one academic rank” because he knew that the science used in his promotion was “highly suspect.” CSU, however, declined to demote him after a review. In 2014, NSF debarred Vivanco for three years and Bais for five, but, following an appeal, it has since set their terms to expire in May and June 2016, respectively, according to records in the System for Award Management.

All told, we’ve identified a total of five six retractions, along with a string of corrections. Excerpts from notices in the OIG report match language present in the pair’s notices in Science (correction), Phytochemistry (retraction), and the Journal of Agricultural and Food Chemistry (withdrawal). In addition to the Nature paper, the duo have also retracted a second paper in Phytochemistry, along with a paper in Plant Physiology, and they published corrections to papers in Journal of Chemical Ecology, the Proceedings of the XII International Symposium on the Biological Control of Weeds and the Journal of Agricultural and Food Chemistry.

Bais could not be reached by telephone and failed to respond to an email from Retraction Watch, but in his response to the investigation, which is included in the OIG report, he criticized it for relying on “circumstantial evidence.” Over the telephone, Vivanco said he was unaware that the report had been posted online, but declined to comment other than saying that the retractions are “a matter of fact.” He later provided a statement to Retraction Watch over email:

I cannot comment on the specifics of this as it involves personnel matters for researchers who may or may not still be at CSU.  Personally, I cooperated fully in a process that I think worked to correct the scientific literature and am confident that all publications for which I am the corresponding author are accurate and reflect the highest standards of research integrity.  While there are aspects of the outcome that I may not necessarily like or agree with, I have learned some important lessons which have made me a better PI going forward.

In a statement to Retraction Watch, Alan Rudolph, the Vice President for Research at Colorado State University had this to add:

It is CSU’s stated policy that we cannot speak to specifics with respect to allegations of research misconduct.  I can say that everyone involved in the adjudication of any allegation of misconduct takes their role very seriously and we have a strong commitment to research integrity.  This includes proactive training and mentoring of our students, post docs and junior faculty.  Our faculty are committed to maintaining the integrity of scientific inquiry and the scientific record.

Independently, Vivanco also retracted a 2012 paper in Frontiers in Plant Science, which he attributed to “mislabeling and duplication of images.” That paper did not include Bais as a coauthor.

Update  9/3/15 7:56 a.m. eastern: Bais sent us a document that he claims provides support for his research, which you can view in full here. He also sent us a statement, in which he says he’s appealing the NSF’s decision:

While I strongly disagree with many portions of the NSF’s Final Determination, it is important to note that it unequivocally states that my conduct was unintentional: “ . . . your misconduct was not intentional and you did not have primary authority or the CSU laboratory where the events occurred”.

My attorney, Barry Nelson Covert, Esq., and I have filed a request for reconsideration with the NSF and our legal team has filed an appeal of the NSF’s Final Determination with the United States District Court for the Eastern District of Virginia. We content that absent a finding of intent or willfulness, the NSF simply cannot find that there was research misconduct and can not impose the debarment. As such, the one-year debarment should be overturned.

Furthermore, I have categorically denied all the allegations. The allegations simply are not factual. We would be happy to provide you with our responses against the University and NSF’s Final determination.

Regarding the reproducibility of my work as a postdoc at CSU is concerned, as related to compounds 1-4 (from the report), the work has been reproduced by independent groups and also by researchers in Vivanco lab (where I am not a co-author) (at least 20 odd papers showed that catechin is toxic and is secreted by C. stoebe plants; see annex I).

Regarding your question related to the retraction of plant physiology paper, I strongly disagreed with the basis of retraction (which I specified in my email to Dr. Don Ort (Then, Chief Editor of Plant Physiology). The main area of disagreement with the retraction was the basis of the retraction cited by the corresponding author – which was completely irrational and non-scientific. Corresponding author claimed that Figure 1C-D and 2A-B is erroneous or non- reproducible. Figure 1C-D shows the chemical structure, whereas Figure 2A-B shows phytotoxic activity of catechin against Arabidopsis. There are at least 20 or so independent publications which established that both of these claims stand and independent labs have reported that catechin is not only secreted but is also phytotoxic against a range of plants.

The catechin work initiated by me during my postdoctoral term opened a new area wherein the phytotoxins involved in plant-plant interactions that could be further investigated for potential mode of action and genetic targets. My work showed that catechin phytotoxicity on the susceptible plants involve a specific signaling cascade to trigger the cell death and the North American plants are more susceptible to catechin toxicity compared to European counterparts. There were two different groups at CSU (Vivanco & Hufbauer) testing the hypothesis at both the lab and field scale that biological invasion in Centaurea is facilitated by secretion of phytotoxins. Dr. Hufbauer’ group has published that the concentrations reported for catechin secretion is towards the lower range then the original reports. Interestingly, Hufbauer’s group showed that catechin is secreted. The other claims of catechin secretion and phytotoxicity are all listed in annexure I. As per the retraction note, the data pertaining to Fig. 1C-D and 2A-B are erroneous or non-reproducible, contrastingly, both of these claims are shown independently in at least 20 other publications (see annexure I).

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Comments
  • Anonymous September 2, 2015 at 12:49 pm

    Given the wide-ranging problems, the remaining literature by Vivanco and Bais needs to be thoroughly examined.

  • Neil Dunn September 2, 2015 at 4:02 pm

    ” As a result of our studies a company has licensed one of the allelochemical compounds as an ecologically-benign herbicide.”
    It would be interesting to know the financial arrangements relative to the above quote i.e. per cent ownership of all individuals and the University that stood to profit.

  • LadyProf September 2, 2015 at 4:44 pm

    10 years of investigation and 2 years of punishment. That sounds (not) right.

  • Request September 3, 2015 at 6:51 am

    Is there any way to find a detailed description of how that funding was used, e.g., equipment, travel grants, chemicals, etc? An independent detailed examination of such massive funding is required. For example, how much funding was used for symposia in which problematic data was presented?

  • Ruth Hufbauer September 3, 2015 at 12:18 pm

    In response to Bais letter, actually the University and NSF OIG both determined that his actions were knowing and intentional.
    see: http://www.nsf.gov/oig/case-closeout/A07100053.pdf
    “The University concluded: Subject 1 intentionally (purposefully) fabricated data
    in all three areas of research”
    OIG’s assessment includes: “Intent: Subject 1 ‘s actions were knowing and intentional (purposeful).”

  • Ruth Hufbauer September 3, 2015 at 1:01 pm

    I do also see this however, on the second to last page.
    “..determination for fabrication and falsification by you is
    sustained and is finaL However, considering that your misconduct was not intentional…”

    I do not personally understand how fabrication can be unintentional.

  • scotus September 3, 2015 at 5:10 pm

    The Bais response makes the frequent but illogical argument that fabricated results are ok because they were “replicated” by others.

  • Debarment query September 3, 2015 at 10:16 pm

    From what I understand of this story, Vivanco and Bais cannot apply for and receive NSF grants for 2 years. Yet they retain their positions, except for Vivanco, who gets demoted one notch, but still retain their jobs, with a salary and presumably all other perks and incentives. Is my interpretation/assumption correct? If so, I also assume that they can easily still apply for other US and/or international funding. Given the serious nature of the report and the claims made therein (confirmed by Ruth Hufbauer), how is this debarment considered to be any form of “punishment”, or is it meant to simply be a softer “warning shot”?

  • One more erratum September 4, 2015 at 1:30 am

    An erratum not yet reported has been discovered, involving Vivanco (not Bais), and related to figure errors.

    Original:
    Root Secretion of Phytochemicals in Arabidopsis Is Predominantly Not Influenced by Diurnal Rhythms
    Molecular Plant, Volume 3, Issue 3, May 2010, Pages 491-498
    Dayakar V. Badri, Victor M. Loyola-Vargas, Corey D. Broeckling, Jorge M. Vivanco
    a Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, USA
    b Unidad de Bioquimica y Biologia Molecular de Plantas, Centro de Investigacion Cientifica de Yucatan, Calle 43 No. 130, Col. Chuburna de Hidalgo, Merida, Yucatan, Mexico
    http://www.sciencedirect.com/science/article/pii/S1674205214607279
    doi:10.1093/mp/ssq004

    Erratum:
    Root Secretion of Phytochemicals in Arabidopsis is Predominantly Not Influenced by Diurnal Rhythms
    Molecular Plant, Volume 8, Issue 2, 2 February 2015, Pages 343-344
    Dayakar V. Badri, Victor M. Loyola-Vargas, Corey D. Broeckling, Jorge M. Vivanco
    Excerpts from the erratum notice:
    “In Figure 5, the gel images corresponding to the genes Atpgp1, Atpgp4, Atpdr2, Atpdr6, Atpdr7, Atpdr8, Atmrp2, Atmrp5, Attap2, Atnap5, Atath6, Atath10 and Atgcn3 were misrepresented.” “In Figure 6, the gel images corresponding to the genes 4CL-1, 4CL-2, F3H, CYP79B3 and CYP79B15 were misrepresented.” “Therefore, the genes that followed distinct diurnal expression patterns were flavonol synthases (FS1, FS2), flavonone-3’-hydroxylase (F3H) and CYP79B15 (involved in camalexin biosynthesis), which showed decreased their expression under light conditions. The authors apologize for these errors.”

  • Three more corrigenda September 4, 2015 at 1:44 pm

    Three more corrigenda have been found for Vivanco.

    Original:
    Badri, D. V., Loyola-Vargas, V. M., Du, J., Stermitz, F. R., Broeckling, C. D., Iglesias-Andreu, L. and Vivanco, J. M. (2008) Transcriptome analysis of Arabidopsis roots treated with signaling compounds: a focus on signal transduction, metabolic regulation and secretion. New Phytologist Vol. 179, Issue 1, 209–223
    doi: 10.1111/j.1469-8137.2008.02458.x
    http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02458.x/abstract

    Corrigendum:
    Article first published online: 6 JAN 2014
    DOI: 10.1111/nph.12660
    New Phytologist Volume 201, Issue 4, page 1508, March 2014
    http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/abstract
    http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/epdf
    “Since its publication, the authors of Badri et al. (2008) have brought to our attention errors in Fig. 7(a) of their article (page 218), where the gel images of PDR6, PDR7 and actin were improperly represented. The correct Fig. 7 is printed below. The corrections of this figure do not alter the findings or conclusions in the article. We apologize to our readers for these mistakes.”

    Original:
    Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions
    Jacqueline M. Chaparro, Dayakar V. Badri, Matthew G. Bakker, Akifumi Sugiyama, Daniel K. Manter, Jorge M. Vivanco
    Research Article | published 01 Feb 2013 | PLOS ONE
    10.1371/journal.pone.0055731

    Corrigendum:
    Correction: Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions
    Jacqueline M. Chaparro, Dayakar V. Badri, Matthew G. Bakker, Akifumi Sugiyama, Daniel K. Manter, Jorge M. Vivanco
    Correction | published 28 Aug 2013 | PLOS ONE
    10.1371/annotation/51142aed-2d94-4195-8a8a-9cb24b3c733b
    http://journals.plos.org/plosone/article?id=10.1371/annotation/51142aed-2d94-4195-8a8a-9cb24b3c733b
    “Due to a copy and paste error, the expression profile of AtPDR9 in Figure 3B and the Actin panel in Figure 3C were duplicated. We provide the corrected Figure 3 along with the raw data for the corrected bands of AtPDR9 in Figure 3B and Actin in Figure 3C as reference for the readers. Further, we verified the gene expression data for AtPDR9 and Actin by repeating the RT-PCR using the same cDNA used to generate the previous RT-PCR data. There were errors in the Supporting Information file Table S3. The corrected version of the file are available here:”

    There is an error with the PDF file, which cannot be downloaded from the PLoS ONE web-site.

    Original:
    10.1074/jbc.M112.433300
    The Journal of Biological Chemistry, 288, 4502-4512
    http://www.jbc.org/content/288/7/4502.short

    Erratum:
    http://www.jbc.org/content/288/42/30503.short
    Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome.
    Dayakar V. Badri, Jacqueline M. Chaparro, Ruifu Zhang, Qirong Shen and Jorge M. Vivanco
    The Journal of Biological Chemistry, VOLUME 288 (2013) PAGES 4502–4512
    PAGE 4508:
    A sentence in “Discussion” contained an error.
    The following sentence, “We collected root exudates from plants that were 18–21 days old because it has been previously shown that at this time point (that corresponds to bolting) Arabidopsis plants secrete the largest number of phytochemicals” was incorrect. It should read as follows. “We collected root exudates from plants that were 18–21 days old because it has been previously shown that at this time point (that corresponds to vegetative) Arabidopsis plants secrete the largest number of phytochemicals.”

  • anonymousII September 4, 2015 at 2:28 pm

    The behavior described by the NSF OIG report is truly impressive in its extent. The long delay in finalizing the investigation allowed the perpetrators to use bogus publications to obtain millions of dollars of grant funds and professional advancement in their respective places of employment. The surprisingly weak response to the outrageous behavior described in the OIG report could suggest to students and young scientists that such behavior does pay off in science. I am deeply saddened.

    • Anonymous I September 4, 2015 at 6:46 pm

      Agreed. The research institutes also play an integral part in the leniency shown towards Vivanco and Bais. What message does this send to others who wish to cheat or manipulate data? What positive message, if any, is given to young and upcoming students? The response must go beyond sadness.

  • A note September 5, 2015 at 1:09 pm

    Readers should note that Harsh Pal Bais also uses an abbreviated form of his name in some of his the latest literature, namely Harsh Bais. As one example:

    Carla Spence, Harsh Bais. Role of plant growth regulators as chemical signals in plant–microbe interactions: a double edged sword. Current Opinion in Plant Biology, Volume 27, October 2015, Pages 52-58
    http://www.sciencedirect.com/science/article/pii/S1369526615000795

    • anonymous September 29, 2015 at 8:09 pm

      I’m wondering if you have ever authored a paper. The author guidelines for a journal often will specify that middle names should either be included, omitted, or just the first initial of the middle name should appear. Your post has the connotation that he is trying to hide something by omitting his middle name when actually he was probably just following formatting guidelines.

      • Not anonymous September 29, 2015 at 9:56 pm

        I can confirm that I have authored XYZ scientific papers. I can also confirm that I have a middle name. I can also confirm that in 100% of those papers, I have always determined what my name should be, and not what the publisher establishes that it should be. Because it is my name. My scientific name and my professional publishing name. My name never varies, and neither should the name of any scientist, unless of their own choice. Why then, if there is the risk of confusion with other scientists, would Dr. Bais choose to publish with two names? Or are you suggesting that a publisher forced Dr. Bais to publish by another name? Given my own experience, I struggle to believe that that the forced-by-the-publisher option is plausible. However, if true, as you suggest, please provide the evidence that a publisher has forced Bais to publish by another name. In that case, there must be serious consequences for that publisher.

        • anonymous September 30, 2015 at 6:18 pm

          You are talking about name changes and I am talking about differences in formatting. I am glad to hear that you are so consistent, but others (myself included) choose to follow formatting guidelines that can vary from journal to journal. I’m not saying you’re wrong, I’m just saying that I don’t necessarily think that Dr. Bais was trying to hide anything by including his middle name on some papers and not others.

          • Not anonymous September 30, 2015 at 8:36 pm

            Once again, I disagree with your assessment. I have only had one publisher force name formatting upon me. Even then, I was not forced to change my name, or drop my middle name. Of course, you and I may discuss hypothetical issues, but the best person to explain this strange use of “two” names in the literature, would be Bais himself.

  • Summary September 5, 2015 at 10:36 pm

    A summary, with PubPeer entries created in the past 48 hours.

    Retraction 1
    http://www.nature.com/nature/journal/v471/n7336/full/nature09809.html
    https://pubpeer.com/publications/2EC222F0D26DF17646E57F398372F7
    Mediation of pathogen resistance by exudation of antimicrobials from roots
    Harsh P. Bais, Balakrishnan Prithiviraj, Ajay K. Jha, Frederick M. Ausubel, Jorge M. Vivanco
    Nature 471, 124
    (03 March 2011)
    doi:10.1038/nature09809
    Published online
    02 March 2011
    Nature 434, 217–221 (2005)
    The authors wish to retract this Letter after a key reference by Walker et al.1 (ref. 9 in this Letter) was retracted from the scientific literature. The withdrawn paper1 reported ten compounds exuded by Arabidopsis thaliana roots, which were used in this Letter to monitor the defence response in Arabidopsis seedlings. In this Letter, these ten compounds were shown to have antimicrobial activity against specific pathovars of the bacterial phytopathogen Pseudomonas syringae but not against the pathovar Pseudomonas syringae pv. tomato strain DC3000 that is a highly virulent pathogen of Arabidopsis. Moreover, wild-type P. syringae DC3000 suppressed the exudation of the ten compounds whereas a DC3000 hrcC mutant did not, leading to the conclusion that DC3000 type III effectors block the exudation or synthesis of the ten compounds. As a consequence of the retraction of the Walker et al.1 paper, the validity of the use of the ten compounds as markers of the Arabidopsis defence response is now in doubt. Thus, the data in Fig. 3, Table 1, Supplementary Figs 5–8 and Supplementary Table 1 cannot be used to support the conclusions that P. syringae DC3000 is generally resistant to antimicrobial compounds exuded by Arabidopsis or that P. syringae DC3000 type III effectors block the exudation or synthesis of antimicrobial compounds.
    References
    Walker, T. S., Bais, H. P., Halligan, K. M., Stermitz, F. R. & Vivanco, J. M. Metabolic profiling of root exudates of Arabidopsis thaliana. J. Agric. Food Chem. 51, 2548–2554 (2003)

    Retraction 2 (withdrawal)
    https://pubpeer.com/publications/BFCB689C056C3B5851BAF4F84665B1
    Walker, T. S., Bais, H. P., Halligan, K. M., Stermitz, F. R. & Vivanco, J. M. Metabolic profiling of root exudates of Arabidopsis thaliana. J. Agric. Food Chem. 51, 2548–2554 (2003)
    http://pubs.acs.org/doi/abs/10.1021/jf021166h
    DOI: 10.1021/jf021166h
    This paper was withdrawn on October 7, 2009 (J. Agric. Food Chem. 2009, 57, 9346).
    “In addition to accumulating biologically active chemicals, plant roots continuously produce and secrete compounds into their immediate rhizosphere. However, the mechanisms that drive and regulate root secretion of secondary metabolites are not fully understood. To enlighten two neglected areas of root biology, root secretion and secondary metabolism, an in vitro system implementing root-specific elicitation over a 48-day time course was developed. After roots of Arabidopsis thaliana had been elicited with salicylic acid, jasmonic acid, chitosan, and two fungal cell wall elicitors, the secondary metabolites subsequently secreted were profiled. High-performance liquid chromatography was used to metabolically profile compounds in the root exudates, and 289 possible secondary metabolites were quantified. The chemical structures of 10 compounds were further characterized by 1H and 13C NMR:  butanoic acid, trans-cinnamic acid, o-coumaric acid, p-coumaric acid, ferulic acid, p-hydroxybenzamide, methyl p-hydroxybenzoate, 3-indolepropanoic acid, syringic acid, and vanillic acid. Several of these compounds exhibited a wide range of antimicrobial activity against both soil-borne bacteria and fungi at the concentration detected in the root exudates.”

    Retraction 3
    https://pubpeer.com/publications/A20FEAB38473A51B2430F916078C6C
    The original
    DOI: 10.1016/S00319422(02)002352 (cannot link to PubPeer)
    Phytochemistry 61 (2002) 539–543
    Exudation of fluorescent b-carbolines from Oxalis tuberosa L. roots
    Harsh Pal Bais a, Sang-Wook Park a, Frank R. Stermitz b, Kathleen M. Halligan b, Jorge M. Vivanco a,*
    a Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523-1173, USA
    b Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1173, USA
    http://ac.els-cdn.com/S0031942202002352/1-s2.0-S0031942202002352-main.pdf?_tid=71687d5c-52bd-11e5-ba5e-00000aacb360&acdnat=1441341111_dac5184b3b185933ce2f3575a1b0bd18

    RETRACTED: Exudation of fluorescent β-carbolines from Oxalis tuberosa L. roots
    Phytochemistry, Volume 61, Issue 5, November 2002, Pages 539-543
    Harsh Pal Bais, Sang-Wook Park, Frank R. Stermitz, Kathleen M. Halligan, Jorge M. Vivanco

    “Retraction notice to: Exudation of fluorescent beta-carbolines from Oxalis tuberosa L. roots” [Phytochemistry 61(5) (2002) 539–543]
    Phytochemistry, Volume 71, Issue 1, January 2010, Page 123
    Harsh Pal Bais, Sang-Wook Park, Frank R. Stermitz, Kathleen M. Halligan, Jorge M. Vivanco
    DOI: 10.1016/j.phytochem.2009.09.013
    “The authors have been unable to find written experimental data which documented the actual isolation of the purported β-carbolines (harmine and harmaline) from root exudates. The source of the compound in question as originally reported is unclear. While Oxalis tuberosa roots do release fluorescent exudates, the identity of the fluorescent compound(s) awaits actual purification and structural determination. The authors therefore wish to retract the original publication and deeply regret any inconvenience to the scientific readership.”

    Retraction 4
    Retraction notice to 7,8-benzoflavone: a phytotoxin from root exudates of invasive Russian knapweed [Phytochemistry 64 (2003) 493–497]
    Phytochemistry, Volume 70, Issue 1, January 2009, Page 156
    Frank R. Stermitz, Harsh P. Bais, Tommaso A. Foderaro, Jorge M. Vivanco
    DOI: 10.1016/j.phytochem.2008.11.009
    “A detailed study of extracts of the Russian knapweed Acroptilon [Centaurea] repens roots has failed to establish the presence of 7,8-benzoflavone, which therefore remains unknown as a plant natural product. The above authors therefore wish to retract the original publication which previously reported its existence, and deeply regret any inconvenience to the scientific readership.”
    https://pubpeer.com/publications/9A05915612D5601F80C46BA08CBB37

    Retraction 5
    Harsh Pal Bais, Travis S. Walker, Frank R. Stermitz, Ruth A. Hufbauer, Jorge M. Vivanco
    Enantiomeric-Dependent Phytotoxic and Antimicrobial Activity of (±)-Catechin. A Rhizosecreted Racemic Mixture from Spotted Knapweed
    Plant Physiol. 2002 128: 1173-1179.
    doi: 10.1104/pp.011019
    https://pubpeer.com/publications/BBC7D1FD9BE3733F6EC8B823DF612A

    Retraction notice:
    doi: http://dx.doi.org/10.1104/pp.109.900302
    doi: 10.1104/pp.109.900302
    Plant Physiology October 2009 vol. 151 no. 2 967
    http://www.plantphysiol.org/content/151/2/967
    Vol. 128: 1173–1179, 2002
    Stermitz F.R., Hufbauer R.A., and Vivanco J.M. Enantiomeric-Dependent Phytotoxic and Antimicrobial Activity of (±)-Catechin. A Rhizosecreted Racemic Mixture from Spotted Knapweed.
    “Several aspects of this study were recently found erroneous or nonreproducible (Figs. 1, C and D, and 2, A and B), and therefore it is our responsibility to report that the premise of this study is not correct and therefore this report is formally retracted. For instance, in a recent reinvestigation, the Vivanco laboratory was unable to detect catechin in any form secreted by the roots of Centaurea maculosa plants under in vitro conditions. Whether catechin found in other studies originated from roots, microbes, or other sources is not known. The chirality of this catechin has not been determined. The authors truly regret the inconvenience and difficulties that this action causes Plant Physiology and its readership.
    Editor’s note: H.P. Bais, the first author of the original study, strongly disagrees with the basis for the retraction.”
    http://www.plantphysiol.org/content/128/4/1173.full.pdf+html?sid=1154a846-6371-4e7c-8e4d-20af67eb4934

    Correction 1
    Science 12 February 2010: Vol. 327 no. 5967 pp. 781
    DOI:10.1126/science.327.5967.781-b

    Original
    Allelopathy and Exotic Plant Invasion: From Molecules and Genes to Species Interactions
    Harsh P. Bais, Ramarao Vepachedu, Simon Gilroy, Ragan M. Callaway, Jorge M. Vivanco
    Science 5 September 2003: 1377-1380. DOI: 10.1126/science.1083245
    http://www.sciencemag.org/content/301/5638/1377.abstract?sid=1e24892e-6bca-4937-a1ed-9ad767e620e3
    https://pubpeer.com/publications/0735AE47A28AEFE9F42D288AB7A22D

    Correction 2 (erratum)
    Journal of Chemical Ecology
    December 2004, Volume 30, Issue 12, pp 2575-2576
    ERRATUM: INTRASPECIFIC AND INTERSPECIFIC INTERACTIONS MEDIATED BY A PHYTOTOXIN, (—)-CATECHIN, SECRETED BY THE ROOTS OF Centaurea maculosa (SPOTTED KNAPWEED)
    TIFFANY L. WEIR, HARSH PAL BAIS, JORGE M. VIVANCO
    http://link.springer.com/article/10.1007/s10886-004-0204-5
    DOI: 10.1007/s10886-004-0204-5
    This paper forms part of a wider investigation into Harsh Bal Bais and Jorge M. Vivanco:
    http://retractionwatch.com/2015/09/02/nsf-investigation-of-high-profile-plant-retractions-ends-in-two-debarments/
    https://pubpeer.com/publications/5D8265DC06C39A1E0F80C844FFB70E

    Correction 3 (proceedings)
    No PubPeer entry.

    Correction 4
    Phytotoxic and Antimicrobial Activities of Catechin Derivatives
    Ravikanth Veluri , Tiffany L. Weir , Harsh Pal Bais , Frank R. Stermitz , and Jorge M. Vivanco *
    J. Agric. Food Chem., 2004, 52 (25), pp 7746–7746
    DOI: 10.1021/jf040453d
    Publication Date (Web): November 19, 2004
    http://pubs.acs.org/doi/abs/10.1021/jf040453d
    https://pubpeer.com/publications/41D09AEAA6FCCC372048119AF6A7A4

    Correction 5 (erratum)
    Original:
    Root Secretion of Phytochemicals in Arabidopsis Is Predominantly Not Influenced by Diurnal Rhythms
    Molecular Plant, Volume 3, Issue 3, May 2010, Pages 491-498
    Dayakar V. Badri, Victor M. Loyola-Vargas, Corey D. Broeckling, Jorge M. Vivanco
    a Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523, USA
    b Unidad de Bioquimica y Biologia Molecular de Plantas, Centro de Investigacion Cientifica de Yucatan, Calle 43 No. 130, Col. Chuburna de Hidalgo, Merida, Yucatan, Mexico
    http://www.sciencedirect.com/science/article/pii/S1674205214607279
    doi:10.1093/mp/ssq004

    Erratum:
    Root Secretion of Phytochemicals in Arabidopsis is Predominantly Not Influenced by Diurnal Rhythms
    Molecular Plant, Volume 8, Issue 2, 2 February 2015, Pages 343-344
    Dayakar V. Badri, Victor M. Loyola-Vargas, Corey D. Broeckling, Jorge M. Vivanco
    Excerpts from the erratum notice:
    “In Figure 5, the gel images corresponding to the genes Atpgp1, Atpgp4, Atpdr2, Atpdr6, Atpdr7, Atpdr8, Atmrp2, Atmrp5, Attap2, Atnap5, Atath6, Atath10 and Atgcn3 were misrepresented.” “In Figure 6, the gel images corresponding to the genes 4CL-1, 4CL-2, F3H, CYP79B3 and CYP79B15 were misrepresented.” “Therefore, the genes that followed distinct diurnal expression patterns were flavonol synthases (FS1, FS2), flavonone-3’-hydroxylase (F3H) and CYP79B15 (involved in camalexin biosynthesis), which showed decreased their expression under light conditions. The authors apologize for these errors.”

    https://pubpeer.com/publications/8F2D4C7B344FE663EC23B4B473C71D

    Correction 6 (erratum)
    https://pubpeer.com/publications/6DAA7E645BE3CA335780DACA289D10
    Original:
    10.1074/jbc.M112.433300
    The Journal of Biological Chemistry, 288, 4502-4512
    http://www.jbc.org/content/288/7/4502.short

    Erratum:
    http://www.jbc.org/content/288/42/30503.short
    Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome.
    Dayakar V. Badri, Jacqueline M. Chaparro, Ruifu Zhang, Qirong Shen and Jorge M. Vivanco
    The Journal of Biological Chemistry, VOLUME 288 (2013) PAGES 4502–4512
    PAGE 4508:
    A sentence in “Discussion” contained an error.
    The following sentence, “We collected root exudates from plants that were 18–21 days old because it has been previously shown that at this time point (that corresponds to bolting) Arabidopsis plants secrete the largest number of phytochemicals” was incorrect. It should read as follows. “We collected root exudates from plants that were 18–21 days old because it has been previously shown that at this time point (that corresponds to vegetative) Arabidopsis plants secrete the largest number of phytochemicals.”

    Correction 7 (corrigendum)
    https://pubpeer.com/publications/5EE2978D3ED7F15CF32BCC7A506CBE
    Original:
    Badri, D. V., Loyola-Vargas, V. M., Du, J., Stermitz, F. R., Broeckling, C. D., Iglesias-Andreu, L. and Vivanco, J. M. (2008) Transcriptome analysis of Arabidopsis roots treated with signaling compounds: a focus on signal transduction, metabolic regulation and secretion. New Phytologist Vol. 179, Issue 1, 209–223
    doi: 10.1111/j.1469-8137.2008.02458.x
    http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02458.x/abstract

    Corrigendum:
    Article first published online: 6 JAN 2014
    DOI: 10.1111/nph.12660
    New Phytologist Volume 201, Issue 4, page 1508, March 2014
    http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/abstract
    http://onlinelibrary.wiley.com/doi/10.1111/nph.12660/epdf
    “Since its publication, the authors of Badri et al. (2008) have brought to our attention errors in Fig. 7(a) of their article (page 218), where the gel images of PDR6, PDR7 and actin were improperly represented. The correct Fig. 7 is printed below. The corrections of this figure do not alter the findings or conclusions in the article. We apologize to our readers for these mistakes.”

    Correction 8 (corrigendum)
    https://pubpeer.com/publications/18779EFBD902A25CEB39D4AD1EF186
    Original:
    Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions
    Jacqueline M. Chaparro, Dayakar V. Badri, Matthew G. Bakker, Akifumi Sugiyama, Daniel K. Manter, Jorge M. Vivanco
    Research Article | published 01 Feb 2013 | PLOS ONE
    10.1371/journal.pone.0055731

    Corrigendum:
    Correction: Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions
    Jacqueline M. Chaparro, Dayakar V. Badri, Matthew G. Bakker, Akifumi Sugiyama, Daniel K. Manter, Jorge M. Vivanco
    Correction | published 28 Aug 2013 | PLOS ONE
    10.1371/annotation/51142aed-2d94-4195-8a8a-9cb24b3c733b
    http://journals.plos.org/plosone/article?id=10.1371/annotation/51142aed-2d94-4195-8a8a-9cb24b3c733b
    “Due to a copy and paste error, the expression profile of AtPDR9 in Figure 3B and the Actin panel in Figure 3C were duplicated. We provide the corrected Figure 3 along with the raw data for the corrected bands of AtPDR9 in Figure 3B and Actin in Figure 3C as reference for the readers. Further, we verified the gene expression data for AtPDR9 and Actin by repeating the RT-PCR using the same cDNA used to generate the previous RT-PCR data. There were errors in the Supporting Information file Table S3. The corrected version of the file are available here:”

    There is an error with the PDF file, which cannot be downloaded from the PLoS ONE web-site.

  • anonymousII September 6, 2015 at 4:03 pm

    There are apparently more than the five retractions listed above. See the July, 2009 issue of J. Chemical Ecol. (Vol. 35, no. 7, p. 860):

    Intraspecific and Interspecific Interactions Mediated by a Phytotoxin, (-)-Catechin, Secreted by the Roots of Centaurea maculosa (Spotted Knapweed)
    Tiffany L. Weir
    Harsh Pal Bais
    Jorge M. Vivanco
    Published online: 16 July 2009
    Erratum to: J Chem Ecol (2003) 29:2397–2412
    DOI 10.1023/A:1026313031091
    This article has been retracted by Tiffany L. Weir and Jorge M. Vivanco.
    Reason: After a reevaluation of this work, we no longer have confidence in several key observations and therefore, retract this paper. Specifically, the reported finding in Perry et al. (J of Chemical Ecology 33:2337–2344, 2007) of catechin in experimental blanks, suggest an exogenous source of catechin in our laboratory. The absence of experimental blanks in the current study
    along with the unreproducibly high levels of catechin reported from
    in vitro grown C. maculosa plants have led us to believe that the reported catechin may have originated from non-plant sources. In addition, a finding
    that some of our commercially purchased catechin was contaminated with 2,4-D along with our observation that catechin caused callus formation in some seedlings suggests that at least some of these experiments may have been conducted using a contaminated source. Because we cannot be sure that contaminated catechin was not used, the results of the phytotoxicity and germination inhibition experiments are meaningless.

    • Alison McCook September 18, 2015 at 11:07 am

      You’re right — we just miscounted. There are actually six retractions we’ve found so far. It’s fixed above. Thanks!

  • Concern September 15, 2015 at 3:33 pm

    Given this serious academic background, should Jorge M. Vivanco be on the steering committee of the society that publishes Plant Signaling & Behavior (Taylor & Francis)?
    http://www.plantbehavior.org/who.html

    And should Harsh P. Bais be on the editor board of the same journal:
    http://www.tandfonline.com/action/journalInformation?show=editorialBoard&journalCode=kpsb20#.VfhvvHIVjIU

  • Alan R. Price November 29, 2015 at 12:35 am

    In response to Debarmentquery, it is not correct to assume that the debarments proposed by the National Science Foundation (NS) would prevent applications for NSF grants. As stated in the NSF decision letter to the respondent attached to the NSF OIG report (linked above)::

    “In light of your misconduct, this letter serves as formal notice that NSF is proposing to debar you from directly or indirectly obtaining the benefits of Federal grants for three years. During your period of debarment, you will be precluded from receiving Federal financial and non-financial assistance and benefits under non-procurement Federal programs and activities. In addition, you will be prohibited from receiving any Federal contracts or approved sub-contracts under the Federal Acquisition Regulations (“FAR”).”
    (see FAR at https://www.acquisition.gov/?q=browsefar)

    A debarment by any Federal agencies (NSF, ORI for HHS, etc) then prohibits the person for the stated period from applying for or receiving any Federal funds (grants, fellowships, cooperative agreements, contracts, etc.) from any Federal agency.

  • A scientist November 29, 2015 at 11:27 am

    Harsh P. Bais:
    “I have categorically denied all the allegations. The allegations simply are not factual.”

    Facts:
    1) 6 retractions.
    2) Multiple corrections.
    3) No longer on editor board of Taylor & Francis’ Communicative & Integrative Biology:
    https://imgur.com/AyZC4HJ
    4) No longer on editor board of Taylor & Francis’ Plant Signaling & Behavior:
    https://imgur.com/I97MraX

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