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.

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