Matthew R Allegretti Week 6

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Week 6 Assignment

Purpose

To examine if there is a relationship between baseline median intravisit nucleotide differences among clones and average change in intravisit nucleotide differences per clone per year.

Methods and Results

  1. We selected sequences based on their baseline median intravisit nucleotide differences among clone, selecting the six subjects, with the three highest and three lowest values.
    • Subjects 1, 4, 9, 13, 14, and 15 were chosen.
  2. We then generated a tree for each of the initial sequences of each subject using the CLUSTALW tool.
    • S1 unrooted
    • S4 Rooted
    • S9 unrooted
    • S13 Rooted
    • S14 Rooted
    • S15 unrooted
  3. We inserted aligned sequences into Biology Workbench and perfomed ClustalDIST to find minimum and maximum distances between clones within each visit.
    • Assembled our information into a table.
  4. Plotted for correlation between:
    • Baseline median intravisit nucleotide differences among clones vs. slope of change in intravisit nucleotide differences per clone per year
    • Initial clone number vs. slope of change in intravisit nucleotide differences per clone per year.
    • Base pair difference range vs. slope of change in intravisit nucleotide differences per clone per year.
  5. Run T-tests to examine significance of each correlation.
    • All P values exceeded .05
    • Graph 1
    • Graph 2
    • Graph 3

Data and Files

Conclusion

The purpose of this project was to examine if there is a relationship initial viral conditions and average change in intravisit nucleotide differences per clone per year. Our results showed that there was not a reasonable correlation between the initial factors we examined and the change over time in base pair diversity of the env gene. While this likely means that none of the factors we examined truly influenced the adaptation that occurred within the various strains of HIV, it may be inconclusive because of the vastly different initial conditions each strain began with. Another study suggested that one of the largest influence over the selective pressures on HIV may come from the drug habits (frequency, sterile state of needles) during infection. Additional introduction of other viruses from continued injection drug use may further cripple the immune system of an infected individual to the point that HIV is not heavily pressured to evolve within its host's system.

Acknowledgments

  • Isai Lopez
  • While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Isai provided me with the syntax to resize images.

Matthew R Allegretti 18:05, 4 October 2016 (EDT)

  • I worked with my homework partner Isai Lopez. We communicated electronically and met in person once to create and practice our presentation.

Matthew R Allegretti 23:02, 10 October 2016 (EDT)

References

  • Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A. Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., Yu, X. F. (1998) Patterns of HIV-1 Evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences USA, 95(21), 12568-12573. DOI: 10.1073/pnas.95.21.12568
  • Tully, D. C., Ogilvie, C. B., Batorsky, R. E., Bean, D. J., Power, K. A., Ghebremichael, M., et al. (2016) Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathog 12(5): e1005619. doi:10.1371/journal.ppat.1005619
  • Mehandru, S., Deren, S., Kang, S. Y., Banfield, A., Garg, A., Garmon, D., et al. (2015) Behavioural, Mucosal and Systemic Immune Parameters in HIV-infected and Uninfected Injection Drug Users. Journal of addiction research & therapy, 6(4), 1. doi:10.4172/2155-6105.1000257

Useful links

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