Matthew R Allegretti Week 4

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Week 4 Assignment


  • To determine if HIV in 15 injection drug subjects derives from a common source.

Methods and Results

  • Activity 2 Part 1 and 2 from Exploring HIV evolution: An opportunity for research.

Activity 2

Part 1

Matthew R Allegretti Sequence table 9-20.png

  • Table 1: Individuals chosen to create unrooted tree.
  1. Sketch your distance tree on paper so that you can make notes on it.
  2. Do the clones from each subject cluster together?
  3. Do some subjects' clones show more diversity than others?
  4. Do some of the subjects cluster together?
  5. Write a brief description of your tree and how you interpret the clustering pattern with respect to the similarities and potential evolutionary relationships between subjects' HIV sequences.
  6. Copy and paste your tree from the Biology Workbench to share.
  • Matthew R Allegretti Activity 2 Part 1 Tree.gif
  • Figure 1: Unrooted tree created using sequences of individuals in table 1.
Part 2

Data and Files


Research Project

  1. What is your question?
    • Primary-Do immunodeficiency diseases in other species show similar trends to the Markham et al. (1998) subjects. Backup-Were any clones sequenced at one point, then missed while in a quiescent state, re-emerging at a later time?
  2. Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
    • Immune deficiency viruses will act on other species in similar fashions. This is due to similar immune responses and viral selection to counter these responses among mammals.
  3. Which subjects, visits, and clones will you use to answer your question?
    • You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
    • We will select 50 subjects, with roughly a fourth from the Markham et al. (1998) study, HIV-2, Simian Immunodeficiency, and Bovine or feline immunodeficiency.
  4. Justify why you chose the subjects, visits, and clones you did.
    • We wanted to analyze HIV-2 sequences to compare to HIV-1 in humans, SIV to compare a similar virus in a closely related organism, and either feline or bovine immunodeficiency to observe the effects of an immunodeficiency disease in a less closely related mammal. We will use sequences from Markham et al. (1998) for HIV-1 data, drawing from the latest visits from the rapid progressor category.


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

Matthew R Allegretti 23:27, 26 September 2016 (EDT)

  • I worked with my homework partner Isai Lopez in class. We worked on the "Defining Your Research Project" portion of the assignment together. We agreed upon our research question for the HIV Evolution project.

Matthew R Allegretti 23:34, 26 September 2016 (EDT)


  • Week 3 Instructions
  • Donovan, S., & Weisstein, A. E. (2003). Exploring HIV evolution: An opportunity for research. Stanley (Eds.), Microbes Count, 137-148.
  • Biology Workbench
  • Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., ... & 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, 95(21), 12568-12573. Retrieved from

Useful links

Course Home Page