Matthew R Allegretti Week 4
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Week 4 Assignment
Purpose
- 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
- Table 1: Caption
- Sketch your distance tree on paper so that you can make notes on it.
- Do the clones from each subject cluster together?
- Do some subjects' clones show more diversity than others?
- Do some of the subjects cluster together?
- 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.
- Copy and paste your tree from the Biology Workbench to share.
Part 2
Data and Files
- Media:Visit_1_Subjects_1_thru_9_HIV.txt
- Media:Visit_1_Subjects_10_thru_15_HIV.txt
- Media:Matthew R Allegretti Activity 2 Part 1 Tree.gif
- Media:Matthew R Allegretti Sequence_table_9-20.png
Conclusion
Research Project
- What is your question?
- A-Do immunodeficiency diseases in other species show similar trends to the Markham et al. (1998) subjects. B-Were any of the subjects affected by other viruses? HIV-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.
- 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.
- 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.
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.
- My partner and I agreed on our research topic.
References
- 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 http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf
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