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Response to Paul Brookes

Posted by jholloszy on 17 Feb 2014 at 18:09 GMT

I am responding to Dr. Brookes’ comments “Correction does not address all issues raised”. My detailed response to Dr. Brookes’ comments on our study (posted on his blog) can be read on Pub Peer (https://pubpeer.com/publi...).

Comment 1: The “splicing issue” raised regarding Fig. 4A has not been addressed at all.

Response: The reason that the blots in the first lane of Fig. 4 are spliced is that, instead of our usual sequence of Control RSV Control RSV the original sequence in this blot was Control Control RSV RSV. So, the individual who made the Figure changed the sequence to conform with our other blots.

Comment 2: The phrase “inadvertently used the wrong blot is inadequate since … it was reuse of single bands within blots. How exactly does one use the wrong bank in a blot?

Response: The background of this comment is that in his initial post on his Blog criticizing our study, Dr. Brookes claimed that the last blot of the cytochrome c lane in Fig. 4C was the same as the last blot of the cytochrome c lane in Fig. 3A. This is a bogus invention of Dr. Brookes. These are not the same blots. This is a really crazy accusation. Why would we take a blot from one experiment and splice it to a lane of blots from a completely different experiment. If we had found a problem with the blot we would not have used it, but would obviously have used another set of blots from the same experiment. (The reason for replacing Fig. 4 is that the team at PLoS Biol., when checking the films of our blots, found that the blots in this lane were in the wrong sequence).

Comment 3: The correction images provided are askew – they appear to have been scanned in from paper copies and misaligned slightly during this process. There could be any number of reasons why files were not provided in a more direct manner (i.e. straight from the software they were generated in, without inserting a print-scan step). Regardless, the provision of apparent paper scans does nothing to enhance my confidence of these data.

Response: We have not been able to figure out what Dr. Brooks is talking about. Each lane of the blots in our Figures is a scan of a film of chemiluminescent blots of a single protein, i.e. one protein per gel. The films are scanned into TIF images and inserted into the Figures using SIGMA PLOT. It appears that Dr. Brookes is saying the blots in each lane should be perfectly aligned with each other. This is impossible, because it is not possible to pipette the homogenates onto the gels in a perfectly straight line, and because the proteins tend to migrate slightly on the gels.

No competing interests declared.