1. Loyola Marymount University
Analyzing Base Pair Differences Between Subjects with Significantly Different T-Cell Rate
Alex George
J’aime Moehlman
Amanda Wavrin
Loyola Marymount University
March 2, 2010

2. Outline
Introduction
Materials/Methods
Results
Discussion
References

3. Introduction to HIV-1 HIV-1 relation to CD4 T-Cells.
Significance of the Env gene
gp 120
Studies suggest adaptation leads to pathogenicity of HIV-1.

4. Our Proposed Question
Is there a specific base pair difference between the subjects with a high rate of CD4 T-Cell decline versus the subjects with an increase in CD4 T-Cells?

5. 1st Hypothesis
H1: There will be a specific nucleotide difference between each group that is responsible for CD4 T-Cell increase or decline.
Two Groups:
Group 1 (Decline): Subjects 10, 11, 15
Group 2 (Increase): Subjects 6, 12 13

6. Methods for Hypothesis 1
We selected all clones from all subjects from Visit 4.
Unrooted Tree of all Six Subjects.
Multiple Sequence Alignment within groups on Biology Workbench.
Compared similarities within Group 1 to similarities within Group 2.

7. Unrooted Tree for S6,10,11,12,13,15 S6
S12
S10
S11
S15
S13

8. Example Comparison between S10 and S6
S10,V4-1
S6, V4-1

9. Results The similar sequences were identical for both groups.
Our hypothesis is rejected:
H0: There was no constant DNA sequence in Group 1 that differed from sequences in Group 2.
These results led us to formulate a second hypothesis.

10. 2nd Hypothesis
H2: The range of difference in Group 1 will be larger than the range of difference for Group 2.
Two Groups:
Group 1 (Decline): Subjects 10, 11, 15
Group 2 (Increase): Subjects 6, 12, 13

11. Methods for Hypothesis 2
Observed differences from original Unrooted Tree.
Use Clustdist tool in Biology Workbench to generate distance matrices for each group.
Multiplied Min. and Max. by 285 to calculate raw number of differences.

12. Unrooted Tree for S6,10,11,12,13,15 S6
S12
S10
S11
S15
S13

13. Table Comparing Minimum and Maximum Difference between Groups 1 and 2
# of Clones
Min. Diff.
Max. Diff. 1 35
.855
54.43 2 25
1.14
47.88
Data table shows no convincing difference in range between the two groups.

14. Results
The range difference of Group 1 was larger than Group 2, but is not convincing.
In the V3 region, the similarities within Group 1 were identical to the similarities within Group 2.

15. Discussion The V3 region does not have the most adaptive events.
The base pair differences could lie in a different region of the gene.
Future Research:
Analyze other regions of the gene in a similar manner to find differences in base pairs.

16. References
Williamson, Scott Adaptation in the env Gene of HIV-1 and Evolutionary Theories of Disease Progression. Molecular Biology Evolution. 20(8):1318–1325
Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, and Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A Oct 13; 95(21) pmid: