1 / 16

Analyzing Base Pair Differences Between Subjects with Significantly Different T-Cell Rate

This study analyzes the base pair differences between subjects with significantly different T-cell rates. The research aims to identify specific nucleotide differences that contribute to the increase or decline of CD4 T-cells.

sritchie
Download Presentation

Analyzing Base Pair Differences Between Subjects with Significantly Different T-Cell Rate

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 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 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. 2003. 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 1998 Oct 13; 95(21) 12568-73. pmid:9770526.

More Related