Shivum Desai Journal Week 4

Exploring HIV Evolution: An Opportunity For Research- Week 4 Continuation

Purpose

The purpose of this study is to see if the HIV selected from four random subjects was originally from the same source of the virus.

Methods

1. First off the data files "visit_1_S1_S9.txt" and "visit_1_S10_S15.txt" were uploaded onto the Biology Workbench. In the nucleic acid section
2. The next step was to select 3 clones from 4 different subject, resulting in 12 total sequences.
3. These sequences then were analyzed using the CLUSTALw tool which allowed for multiple sequence alignment and the generation of a distance tree comparing all 12 sequences.
4. The main piece of data that resulted from this analysis was a distance tree that presented the relationship amongst the four subjects and their clones.
5. The tree was analyzed and recorded.

Results

Activity 2/Part 1

• The results from portion of the project yielded that clones from each subject do cluster together. However there are subjects like S12 and S15 that show an extremely large amount of diversity in comparison to S11 and S14. Additionally, none of the subjects cluster together except for S14 and S15, which is peculiar and yet it supports the idea that some of the subjects may have a virus that is from a common source. The tree overall shows that subjects 15, 14, and 12 are much closer related to each other than subject 11 is to any of the other subjects. At first it could be deduced that there could have been a relationship amougnst the sequences due to the order in which they were retrieved for mthe subject because they are all within five subjects of eahc other. However, that could not be true becuase S11 is very differne from S12. The only conclusion that can be drawn from the tree is that S12, S15, and S14 all have a mor eclosely related verison of HIV compared to S11.

Distance Tree

Activity 2/Part 2

Data Files

HIV Sequences

Useful Links

• Shivum Desai
• Week 4 Assignment Page
• Zachary T. Goldstein
• Week 4 Shared Journal Page

Acknowledgments

I would like to thank Dr. Dahlquist for her help on this assignment. As well as the help of Zachary T. Goldstein who was my partner in this experiment.