poorgradstudent, What is amazing to me is that you were hypercritical when the issue of fraud in science came up, but it appears you aren't being critical enough now. You were accurately complaining about truncating Westerns, and they did that. They only used one primer pair to look at mRNA, which sure isn't very rigorous. I am trying to get at is the precision and accuracy of the analysis of the TOV-112 cell line, but you seem to not be as concerned about rigor as I am. What gives? Is it because you are close to this research area?
{{2. If you're talking about mutations that change the length of the protein, cause re-arrangements between other genes and c-Met (a la bcr-abl) then they may or may not be captured by the methods used in the paper.}}
That is exactly my point about the TOV-112 cell line and the papers you and Iwfal referenced. I am talking about how rigorous they were in their analyses, and it doesn't look like the were rigorous enough.
{{Which is why I replied as I did. To my knowledge the majority of c-Met mutations are missense, and these often impact amino acids at the tyrosine kinase domain. All of these will be captured. I'm not aware of a mutation that truncates the protein in a manner imagined by Vinmantoo, so my position is that the data in the paper are reliable unless someone finds an example that conforms to Vinmantoo's imaginary protein.}}
First of all, the example I cited doesn't represent an imaginary protein. It is a hypothetical one, and one that anyone with an open mind could see how it could be generated via deletion of the most terminal part of the mRNA, either by genomic deletion or splicing error. Just because you aren't aware of something, doesn't mean it can't happen, and it sure as hell doesn't mean that one isn't present in the TOV-112 cell line. That is the issue here, what is happening in the TOV-112 cell line, not a broad measure of all tumors. All I am asking for some rigorous methodology to be used to remove any doubt.
{{Final point, the new paper I linked in the previous post makes it rather clear that this cell line does not express the protein. They generated another antibody that also came up blank in the TOV-112D*.}}
All I am asking is for rigorous proof to rule out a situation where the terminal part of the protein beyond the kinase domain (or at most only the very terminal part of it) is deleted, whatever the mechanism. I downloaded the C-MET mRNA and looked for where the SINGLE primer pair the authors used in both manuscripts was located. The anti-sense primer is located at the c-terminal in 330bp of the 4172 bp mRNA, meaning it would miss a truncated c-MET that was missing only about the last 110 aa of the ORF. Now this is after most of the listed kinase domain. I don't know enough about how much of the kinase domain is sufficient for unregulated activity, but is certainly raises the possibility of such an event. As far as antibodies, I looked but didn't see where it stated which epitope they used for the second antibody. Now would you be so kind as to tell me EXACTLY what part of the protein was used, point me to where it can be found or post the relevant section here. Repeatedly saying supplemental data isn't sufficient nor is it very informative. Thank you
AI
