Feedback+after+and+around+fall+2012+committee+meeting

Feedback after and around fall 2012 committee meeting

Stephen wanted me to look at the SMC1fs blast hits in more detail to make sure that none of them actually matched the SMC1fs sequence since we did not previously think that this was in the database. see SMC hit investigation 12-15-12

slide 1 In my final dissertation I may need to have a different title since Stephen thinks a lot of the other work should go in the appendix slide 2 Stephen thinks the motif peptide analysis should just be taken out completely. He thinks that the automatic array alignment, age associated stem cell autoimmunity, and entropy immunosignature work should go in the appendix Slide 3 It would have been better to represent the target in the well as the peptide that it was. The blob in the well currently looks like a protein Slide 4 Phil was interested in making this heatmap be some type of bar graph, but the rest of the committee seemed to think that it was fine the way that it was. Slide 5 no major comments Slide 6 The committee seems to think that Table 2 should be taken out of the paper completely since the original antigen is not in the database, and in a list of 20,000 proteins that match with a short sequence the sequence of interest is bound to be present. Slide 7 The committee (particularly Stephen) thinks that the potential antigen discovery program work should not be included in the dissertation. The program would not work for the smc1fs antigen. It may work for other proteins that are in the databases such as insulin in the diabetes diseases. However, the committee thought that the method is not very novel. It is interesting to note that despite how common the committee thinks the method is that we do not have a method in our lab of determining the antigen that corresponds to certain immunosignatures. This method could potentially reveal these antigens. Nevertheless, the fact that I never did complete this program due to some technical issues is certainly a reason not to include the work in my dissertation. slide 8 no major comments slide 9 The committee was okay with me putting the automatic array alignment stuff into my dissertation. They also thought it would be good for me to put my future SVM idea into the dissertation as well. slide 10 no major comments slide 11 nmc slide 12 nmc slide 13 nmc slide 14 nmc slide 15 nmc slide 16 nmc slide 17 Comments about most of the spots decreasing. It could be good to know what proportion were decreasing and what proportion were increasing. slide 18 No major comments Slide 19 nmc Slide 20 nmc slide 21 The committee did have several comments on the whole process about screening the library. They thought it would have been good to take the SMC1fs spot through at every step. They are also very interested in finding out the full sequences of the spots that may bind well in the library. Bert Jacobs was also interested in seeing whether the tumor sera bound to the SMC1fs spot. I looked at whether the SMC1fs sera bound to the SMC1fs spot, but not at whether the tumor sera bound to this spot.

As of right now there are basically 2 ways I can try to determine whether my genes are truly truncated products are not. One way would be to perform a PCR that amplifies from exon 1 to the last exon. Unfortunately, the wild type transcript could be in the cell in addition to a mis-spliced transcript and this would not be detected. I could also use the 3' poly T primer along with the 5' primer with the primestar polymerase which seems to amplify long transcripts very well.

slide 22-30 no major comment

slide 31-40 I did not have time to talk about and had to skip

slide 41-42 no major comments

slide 43 For some reason Phil, Stephen, and Kathy had an opinion about the "LsA" label. They were sure that Bart's dogs had lymphomas not lymphosarcomas. I talked to Bart after the presentation, and he said that the dogs did have lymphosarcoma.