Robert W Arnold Week 4

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Electronic Journal Week 4

Robert W Arnold

Week 4 Assignment

  • Finished up Journal Club, had a good talk with the class about the research article. Really brought to light some questions I had when going through the research, specifically about CD4 T cells and how they work.
  • Started to come up with ideas for presentation, mainly thinking about researching the 6 of the 15 subjects which developed AIDS. I want to determine which ones specifically developed AIDS, their CD4 T call counts, dS/dN ratio, what they have in common with each other and what they don't have in common with the other subjects.

Presentation Points

  1. Which 6 of the 15 subjects developed AIDS? Why did these 6 develop AIDS? What do they have in common with each other? Specifically, CD4 T cell count, rapid, moderate or nonprogressor, dS/dN ratio, etc. What do they not have in common with the subjects who did not develop AIDS?
  2. We believe that the dS/dN ratios of the 6 subjects is the most telling factor in what determines if those subjects develop AIDS. We hope to prove that extremely low dS/dN ratios of 0.0, 0.2, and 0.3 will prove to be a determining factor in developing AIDS. Subjects 4, 9, 11, and 14 all have ratios of 0.0, subject 10 has a ratio on 0.2 and subject 1 has a ratio of 0.3. We do not believe the separation between rapid and moderate progressors has anything to do with AIDS development as subjects 1, 4, 10, and 11 are rapid and subjects 9 and 14 are moderate.
  3. All of the subjects will be viewed to determine which ones developed AIDS. From there we will determine their common factors and why each may have developed AIDS. Then we will compare them to the other subjects and determine if any other subject may be trending towards AIDS.

Basic Initial Research

  • We started off by drawing conclusions off of this figure and this table.
  • We originally believed that the dS/dN ratio was the determining factor in AIDS development.
  • Then we discovered that HIV progresses to AIDS at CD4 T cell counts lower than 200 cells/mm^3 or less than 14% total CD4 T cell count. Once below, AIDS diagnosis remains even if subject increases above 200 CD4 T cell count. [| Medline Plus HIV/AIDS]
  • Determined that by definition, all of the rapid progressors developed AIDS in the article.
  • Now that we have discoverd, we have begun to look at and classify all the subjects into 3 groups.
    • Those who have AIDS : 1, 3, 4, 10, 11, 15
    • Those trending towards AIDS: 7, 8, 9, 14
    • Those free of and trending away from AIDS: 2, 5, 6, 12, 13
  • 4 of the 6 moderate progressors seem to be trending towards AIDS
  • We are going to determine by using the ALIVE research to see if any of these subjects did in fact develop AIDS. Markham's research was an extremely limited group.
  • We see now that it is not just dS/dN ratio that causes AIDS but it can certainly contribute as both subjects 9 and 14 seem to be trending towards AIDS at an extremely fast rate.
  • Here is our basic idea for an outline with our research goals that we will base further research upon.
    • Evolution of HIV
      1. Development of AIDS from HIV
        • What causes an HIV patient to become diagnosed with AIDS
        • What factors are common between subjects with AIDS
        • What factors are different between subjects with AIDS
        • How do HIV subjects with and without AIDS differ
  • To answer these questions, we will be examining all of the different statistics from our subjects in the Markham research and check if they have any more checkups in the ALIVE research to determine if some of our at risk HIV subjects do in fact develop AIDS.
  • Zeb put the Table 1 figure into an excel sheet where we will be able to draw up graphs and organize the numbers to see if we can find any trends to help support our thoughts. Here is the table.
  • We plan on making phylogenetic trees and doing multiple sequence alignments with the subjects which will hopefully strengthen our research.


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