Retraction Watch

Tracking retractions as a window into the scientific process

Corrections (and one EoC) propagate for distinguished plant biologist, Olivier Voinnet

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Olivier Voinnet

Olivier Voinnet

There may be some deeply rooted issues in the work of high-profile plant biologist Olivier Voinnet, biology department research director at ETH in Zurich. Corrections have continued to pile up months after his work was hit with a barrage of criticism on PubPeer. We’ve tracked a total of seven corrections over the past five months (not including the April retraction of a 2004 paper in The Plant Cell). One of the corrected papers also received an Expression of Concern this week.

Collectively, the corrected papers have accumulated more than 1200 citations.

In January, Voinnet said he planned to correct multiple papers, after receiving “an anonymous email.”

One of the recent corrections we found is for a 2003 article in The Plant Journal, “An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus,” which details using proteins from a tomato virus to help alter gene expression. The study has been cited 862 times, according to Thomson Scientific’s Web of Knowledge. Here’s the correction notice, posted June 8:

In the article by Voinnet et al. (2003), it has recently been noted that the original Figure 3b in this paper was assembled incorrectly and included image duplications. As the original data are no longer available for assembly of a corrected figure, the experiment was repeated, in agreement with the editors, by co-author S. Rivas. The data from the repeated experiment, presented below together with the original figure legend, lead to the same interpretation and conclusions as in the original paper.

Earlier this week, Nature Genetics published a notice in for “Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections.”  The 2006 paper has been cited 75 times and described the role of siRNAs in viral infections, this time for the tumor-causing Agrobacterium tumefaciens:

In the version of this article initially published, in Figure 5c (miR162) and Figure 5e (miR171), the rRNA images were duplicated without explanation. The figure legend should have stated that these two panels show the fluorescence image of the common rRNA loading control and autoradiographs of the same blot stripped and rehybridized with the two miRNAs, respectively. The authors state that all the display items in this publication and its Supplementary Information are previously unpublished work and accurate representations of the experiments described. The legend of Figure 5 should read:

Figure 5. RNA blot analysis of endogenous small RNAs in leaves, stems and tumors of A. thaliana. Cis-acting (a) and trans-acting (b) siRNAs. (c) Evolutionarily conserved miRNAs. Note that a 24-nt species18 for miR156 and miR162 is eliminated in tumors. (d) A. thaliana–specific miR163. (e) Schematic of the GFP-based sensor construct reporting cleavage by the evolutionarily conserved miR171 (upper panel). RNA blot analysis of miR171 and of the GFP sensor mRNA (middle and lower panels, respectively). The middle panel of e and bottom panel of c show the rRNA and stripped and reprobed RNA blot for the same gel. (f) Accumulation of two evolutionarily conserved miRNAs targeting important positive regulators of the plant auxin response. L, leaf; S, stem; T, tumor; rRNA, ethidium bromide staining of ribosomal RNA.

Genes & Development published a correction in February for an incorrect loading control panel in a 2004 paper on plant miRNA. Here’s the note for “In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA”, which has been cited 231 times:

In the above-mentioned article, due to an error in the figure preparation, the ribosomal RNA loading control shown in Figure 3C was incorrect. This error has no bearing on the conclusions of the article; however, the panel with the correct loading control is shown below.

The authors apologize for any concern this may have caused.

PLOS Genetics issued a notice in March for a 2009 study about embryonic stem cell differentiation, “Highly Dynamic and Sex-Specific Expression of microRNAs During Early ES Cell Differentiation.” The study has been cited 13 times:

Fig. 3 is incorrect. A mistake was made by the authors during the assembly of panel 3B. The loading control U6 is duplicated for the XY D0 and D2 samples. The authors apologize for this error and have provided a corrected version here.

The same journal published a correction in May for another stem cell study, “RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells,” cited 13 times:

Panel A in and panels A and F in S4 Fig are not presented correctly. The lanes in the corrected figures are separated by tracks for other mutants that are not relevant for the current work and can be seen in the original blots, provided here as S7 and S8 Figs. The authors apologise for the mistake and have provided corrected versions, along with the original blots that were used to create the figures. These errors do not affect the conclusions of this article.

The paper has just also received an Expression of Concern, published June 29:

Concerns have been raised regarding some of the data in the PLOS Genetics article “RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells”, notably in panel A in Fig 4, in panels A and F in S4 Fig, and with the statistical analyses used to produce Fig 2. The authors have responded to these concerns, acknowledging that some errors were made in figure preparation and with some statistical tests, however a final resolution has not yet been reached, and the matter is being evaluated by the authors’ institution.

This Expression of Concern should not be considered as a statement regarding validity of the work but rather as a notification to readers, and an intent to provide additional information as it becomes available.

PLOS Pathogens posted a correction in April for a 2014 paper on genetic resistance to disease in plants. The study — “The Arabidopsis miR472-RDR6 Silencing Pathway Modulates PAMP- and Effector-Triggered Immunity through the Post-transcriptional Control of Disease Resistance Genes” — has been cited 12 times:

S7 Figure in the article is a duplicate of S14 Figure. There was an error in the deposition of the S7 Fig. file, please see the correct version of S7 Figure here. The Supporting Information legends for these figures are unchanged.

The Plant Journal also issued another notice in the beginning of June for a 2002 article co-authored by Voinnet on how peanut clump pecluvirus overcomes plants’ genetic defenses. “Identification, subcellular localization and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus” has been cited 102 times:

In the article by Dunoyer et al. (2002), Figures 2, 3 and 6 contain northern or western blot images comprising spliced lanes that were not indicated in the original Figures, and in agreement with the editors, we have decided to replace these figures with updated versions in which the spliced lanes are now clearly indicated by white vertical bars. While correcting these figures, it was found that one panel of Figure 2c was also incorrect and this has been replaced with the correct panel. The corresponding figure legends have also been modified to acknowledge these changes.

Voinnet received the EMBO Gold Medal in 2009 and the Rössler Prize in 2013.

We’ve reached out to Voinnet for a comment on these corrections and we’ll update if he replies.

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