Rough description of chapters 12-3-12

2015-01-13

azim58 - Rough description of chapters 12-3-12

Ch 1. Random sequence mimotopes capture immune-specific antibodies and
predict epitope motifs

Comment: this would be about the work for the paper we are writing with

Shen

Ch 2. High throughput screening of tumor cDNA libraries

Comment: this chapter and chapter 1 would make up the majority of the

disseration. Some of the main topics in this chapter could be as follows.

tumor cDNA libraries (lysates, nitrocellulose arrays, etc.)
phage antibody libraries
random peptide array

Ch 3 Age Associated Stem Cell Autoimmunity

Comment: this would be about the T cell assays and the Gemini project

Ch 4 Entropy and Immunosignature

Comment: this would be about my preliminary discovery about how older

mice did have a higher entropy on the array than younger mice

Ch 5 Motif Peptide Analysis

Comment: this would be about some programming I did to try to discover

the original antigen from the motifs in the best binding random peptides.
I have not shown this analysis to anyone in our lab because I wanted to
wait until it was completed and it was successful. However, I see that
this may never happen. I ran into some issues with computational power,
computational time, and my own personal time for working on this.
Nevertheless, some level of progress was made, and I do have thoughts on
the issue.

Ch 6 Automatic Array Alignment

Comment: I successfully wrote a program to automatically align one block

of the array in a manner that was 94% identical to a human alignment.
Then we turned the program over to a computer guy working with Valentin
Dinu, and after working on it for some time, he was not able to make a
program to align the whole array rather than just one block.
Nevertheless, this is still something I have results on.