J'aime C. Moehlman's Week 6

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HIV Research Project

Continued from Week 5

  • We ran two multiple sequence alignment (one for each grouping).
  • The first group included subjects 10,11 and 15.
  • The second group included subjects 6,12 and 13.
  • Each of the subjects clones were chosen from visit 4 in order to keep the amount of time passed a constant in our experiment.
  • When running the multiple sequence alignments we discovered that the two groups were similar.
  • We then tried a clustalW(distance matrix) to see if the differences were significant between the two groups; again the amount difference was not significant enough to prove our hypothesis.
  • We decided to approach our hypothesis and question with two experiments: comparing the similarities of each group, and the second was to compare the differences from each group(the minimum and maximums).

Env Gene Article

Adaptation in the env Gene of HIV-1 and Evolutionary Theories of Disease Progression - S. Williamson


  • HIV symptoms- after initial infection, long period of no symptoms follows during which CD4 T-cells decline.
  • After the immune system can't contain viral replication, HIV progresses to AIDS.
  • Many hypotheses suggest adaptation leads to pathogenicity.
  • Characterizing rate and pattern of adaptation, removing misleading neutral mutations.
  • "Env" gene codes for envelope glycoprotein gp160, which is precursor for gp41 and gp120.
  • Focuses on region of "env" that gives rise to gp120--embedded in lipid membrane, responsible for host cell receptor binding site; divided into 5 regions (V1-V5).
  • Contains sites for antibodies, and two T lymphocytes.


  • V1-V2 region has highest adaptation rates- once every 2.5 months- but are only from perinatally infected children.
  • V3 region- one adaptive event per 5.9 months.
  • V4-V5- every 12.2 months.
  • Adaptive event occurs every 45 days in whole gene.
  • Generation time of HIV-1: 1.2-2.6 days.
  • Therefore, 1 adaptive event every 25 generations-- fastest rate in single protein-coding gene.
  • Slow progressors= progression time to AIDS over 7 years; Moderate progressors= between 5-7 years
  • Adaptive events in slow progressors significantly higher than moderate.
  • Viral adaptation in C2-V5 region is related to disease duration.

HIV Research Presentation

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User: J'aime C. Moehlman


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J'aime C. Moehlman's Week 13