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.