BIOL368/F14:Chloe Jones Week 5

HIV Evolution project

Introduction

• Question: Is the diversity of the clones for subject 1 & 2 greater when alone, or when together?
• Hypothesis: I think the clones will be genetically more diverse as time progresses because subject 1 is a rapid progressor which based on the Markam at el. leads me to believe that the clones will diverge with time.

Methods & Results

• Used GenBank, nucleic acid data assocaited with the Markam et al. paper to create a FASTA formatted sequence that could be analyzed using the tools in Biology Workbench
• Compare the all the clones from all the visits from Subject 1 and 2 separately using the ClustalW tool in the Biology Workbench . Sequence the clones from subject 1 and 2 based on the first visit using the ClustalW tool. Sequence the clones from subject 1 and 2 based on the last visit using the ClustalW tool.The ClustalW tools sets up multiple sequence alignments where the number of nucleotide difference can be counted, termed (s) . The tool also allows for the generation of phylogenetic trees. Next, I used the Clusdist to tool to generate a distance matrix where the minimum and maximum differences can be calculated amongst the groups.

Table 1. Clustadist analysis of the sequences from Subject 1 all visits .

Subject	Visits	S	Theta	Min Difference	Max Difference
Subject 1	3	93	0	0	35

Figure 1.Unrooted tree of HIV-1 viral strains for subjects 1, all visits.

Figure 2.Unrooted tree of HIV-1 viral strains for subjects 2, all visits.

Figure 3.Unrooted tree of HIV-1 viral strains for visit 1 of subject 1 & 2.

Figure 3.1Clustal Distance Matrix for Subjects 1 & 2 at Visit 1.

Figure 4.Unrooted tree of HIV-1 viral strains for the last visit of subject 1 & 2.

Figure 4.1Clustal Distance Matrix for Subjects 1 & 2 at last visit.

Table 2. Clustadist analysis of the sequences from Subject 2 all visits .

Subject	Visits	S	Theta	Min Difference	Max Difference
Subject 2	3	36	0	0	14

Table 3. Clustadist analysis of the sequences from Subject 1 and 2 , first visit

Subject	S	Min Difference	Max Difference
Subject 1 & 2	30	0	14

Table 4. Clustadist analysis of the sequences from Subject 1 and 2 , last visit

Subject	S	Min Difference	Max Difference
Subject 1 & 2	73	0	35

-pic of each phylogentic trees -pic of each table -pic of each multiple sequence alignment -pic of each distance matrix

Conclusion

-pic from markham paper The first visit from both subject showed that they were genetically similar with the max difference between the subjects only being 14. However, as time progressed at the last visit the max difference was measured and it was 35. The difference from the first visit in comparison to the last visit had more then doubled. (look at the two subjects in comparison visit 1 to last) Subject 2 clones are all within the same area which is indicative of a non progressor. On the other hand subject 1 tree shows plenty of divergence as time progresses which is indicative of a rapid progressor.