Cell Press is looking into anonymous allegations that a pair of influential papers on gene activation in yeast may contain more than two dozen instances of image manipulation, according to a spokesperson for the journal.
The concerns raised on PubPeer have even sparked an investigation by an institution in Spain, which found no evidence to support the allegations. But not everyone agrees with that verdict.
The images are of Western blots and chromatin immunoprecipitation (ChIP) assays, and appear in two reports published by Cell Press — one in Cell from 1999, the other in Molecular Cell from 2001 — and in a 1998 report in the American Society for Microbiology’s Molecular and Cellular Biology.
According to the comments on PubPeer, a number of figures in the papers contain duplications — and even triplications — of individual bands and lanes.
A spokesman from Cell Press said the publisher is looking into the allegations, but would not share details of the investigation.
The first author of all three papers is Maria Pia Cosma, now with the Centre for Genomic Regulation (CGR) in Barcelona, who earned her PhD in 2000 from the University of Naples Federico II in Italy.
In a comment on PubPeer from April 9, Cosma noted that the only data available today from the studies are low-resolution images in PDF files.
The figures were made after scanning pictures of multiplex PCR amplifications ran in agarose gels. The final pictures were submitted as print out documents and finally re-scanned. This is a 14 year-old paper, at that time, journals had no clear guidelines on how to present gel data.
Cosma did not respond to emails or phone calls from Retraction Watch, despite asserting in the comment that she was “open to a constructive discussion about the matter with anybody willing to contact me.”
One outside expert agreed the images look suspicious.
“After looking at all the images in these three papers, my personal opinion is that the similarities are too many to have arisen by chance, or to have resulted from accidentally incorporating parts of the same original images twice when composing the figures,” said David Vaux, a cell biologist at the Walter + Eliza Hall Institute of Medical Research in Melbourne (and a member of the board of directors of the not-for-profit Center for Scientific Integrity, our parent organization).
Vaux, who emailed us while attending the 4th World Conference on Research Integrity in Rio de Janeiro, said he had formed his “opinion based on examining results of many such experiments as a researcher, as laboratory head, journal peer reviewer, journal editor, and journal reader.” But he issued this caution:
However, because I do not have access to the original images, and cannot interview all of the authors, I cannot be certain that the images were falsified, or, if so, which of the authors were responsible.
The Cell paper from 1999, “Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter”, has been cited 536 times, according to Thomson Scientific’s Web of Knowledge.
This was a very influential paper, said Craig L. Peterson from the University of Massachusetts Medical School in Worcester, who has done similar research. “It was one of the first papers to use ChIP to monitor sequential recruitment of transcriptional regulators to a eukaryotic gene, yeast HO.”
Peterson noted that he understands “why people might think that the bands in question were duplicated,” but doesn’t believe the “possible issues” would “refute the actual conclusions made from the experiment.” Even his work upholds their findings, he added:
Our data are mostly consistent with the Cosma paper, though the exact experiments in the same genetic background (i.e. ash1 mutants) have not been performed as far as I am aware. In general, the results from Cosma et al. ARE NOT considered controversial. I think this is a non-issue that does not warrant further discussion.
The other papers, “Mutations in the extracellular domain cause RET loss of function by a dominant negative mechanism” (Molecular and Cellular Biology), and “Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF” (Molecular Cell), have been cited 44 and 109 times, respectively.
Kim Nasmyth of the University of Oxford, the senior author on two of the papers, said he has “No idea how to explain the similarities” in the images:
If someone comes to me with clear evidence for wrongdoing then I will be more than happy to respond. However, I am not aware that this has happened. For all I know, the allegations are part of a personal vendetta against Pia.
Nasmyth added that an independent investigation had not substantiated the claims.
That investigation was done by Jose M. Rodriguez Sanchez, a senior engineer in computer science from the Universitat Politecnica de Catalunya in Barcelona.
“The conclusion of the expert’s analyses, available upon request, is that none of the allegations on [sic] data manipulation are valid, i.e. the assessment unequivocally disproved the posted claims,” say CRG’s director, Luis Serrano, Juan Valcarcel, also of CRG, and Jaume Bertranpetit of the Institucio Catalana de Recerca i Estudis Avançats in a joint comment on PubPeer.
The analyses were done as pixel-by-pixel comparisons of images that, according to the PubPeer comment by Cosma, had been scanned, printed out, and then re-scanned. As described in his three reports, Rodriguez magnified the images and scrutinized them using various tools in Photoshop. Whenever he found a difference, no matter how tiny, he took it as evidence against duplication.
Of the 30 allegations from PubPeer that he examined, Rodriguez concluded that every single one was false.
But this method doesn’t pass muster with everyone, including Vaux:
I do not dispute his analysis, but I disagree with his conclusions, because he was not provided with the original images (just the published ones), and he did not consider the possibility that images could be altered after they were digitally duplicated.
An anonymous PubPeer commenter offered this view:
There are such an amazing number of similarities in several of these cases, but the “analysis” does not seem to evaluate the extent of similarities and instead seems to be looking for the faintest speck of non-identity. As if two identical pictures of the night sky were juxtaposed, and one star was slightly smudged in one, the “expert” would conclude “they are different”. Not only is this expert analysis unconvincing, it almost seems amateurish.
Update 5:08 p.m. eastern 6/4/15: Valcarcel has provided more details about how the report was commissioned:
A committee was set up at CRG to examine the allegations in Pubpeer. The committee urged Dr. Cosma to address the allegations and seek an independent assessment. The standard procedure to obtain the most authoritative, independent and legally-binding professional assessments of this kind in our legal system is to request them from the relevant Official College, in this case the Official College of Computer Engineers of Catalonia. Dr. Cosma contacted the College and the College assigned an expert with competence for the specific tasks requested. The expert acted independently to carry out this task, was not contacted by anyone at CRG during the course of the assessment and legally declared that he had no conflict of interest to carry out his job on behalf of the CRG.
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