Alex A. Cardenas Week 5: Difference between revisions

Revision as of 15:42, 28 September 2011

3 main points
- Why did 6 of the 15 subjects develop AIDS and who has them? What did they have in common and what did they not have in common with subjects who did not develop AIDS?
- The dS/dN ratios are used in hoping to prove whether or not the subject will develop AIDS depending on the low and high ratios.
- Determine which subjects have AIDS and distinguish common factors for why each may have developed AIDS. From there we will compare them to subjects who do not have AIDS and see if they are on their way to develop AIDS.

15 injection drug users were observed in ALIVE study. Blood was taken and sampled every 6 months.
- After seroconversion, theses patients were followed and their CD4 T cell count is seen in this graph.
Subjects were placed into 3 groups:
- Have AIDS: 1, 3, 4, 20, 22, 25
- Leaning toward AIDS: 7, 8, 9, 14
  - These are 4 of the 6 moderate progressors that are leaning toward AIDS.
- Subjects who don't have AIDS: 2, 5, 6, 12, 13

This article was used to support some of the claims made last week regarding our research.
From the introduction there are 3 main stages
- In the first stage, there was a linear increase in both env divergence and diversity from the population.
- The next stage lasts 2 years on average and it was shown that there was a stabilization or decline in nucleotide diversity but the divergence continues.
- Divergence stabilizes in the last stage meaning that "env sequence evolution nearly comes to a halt" A statistical Characterization of Consistent Patterns of HIV Evolution Within infected patients September 28, 2011.
  - Usually beings one year before the onset of clinical AIDS and as stated, CD4+ T Cell counts are below 300 cells.
An indicator of disease progression was the CD4 T cell count and emergence of X4 viral genotype.
- Peak diversity = initial emergence of X4 virus
- Divergence stabilization = X4 reaching highest frequency.
Hypothesis #2 - evolutionary rates slow due to infection disrupting the immune system.
If max likelihood divergence stabilization model > (significantly) max likelihood of constant rate model = evolutionary slowdown.

@@ Line 24: / Line 24: @@
 **Peak diversity = initial emergence of X4 virus
 **Divergence stabilization = X4 reaching highest frequency.
+*Hypothesis #2 - evolutionary rates slow due to infection disrupting the immune system.
+*If max likelihood divergence stabilization model > (significantly) max likelihood of constant rate model = evolutionary slowdown.