Feedback after and around fall 2012 committee meeting

2015-01-13

azim58 - 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.

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