BIOL368/F14:Isabel Gonzaga Week 5: Difference between revisions

==Determining Genetic Relationships==

In Figure 1 we see that virus strains from each subject are genetically similar to each other, with the exception of one sequence in Subject 15. The three categories (AIDS diagnosed, progressing and no trend) are dispersed fairly evenly throughout the tree, thus no strong relationships between their genes may be determined. In Figure 2, the sequences of the viral strains from the last visit show a much different distribution pattern. The non-trending subjects are together and uninterrupted by other subjects. This shows that they are more genetically similar to one another, than the others. Subject 9 (progress or) and Subject 13 (no trend) also branched from the the same ancestor, however, this genetic connection may contribute to subject 9's resilience and ability to raise CD4 C Cell counts despite dropping below 200. <br>Most interestingly, Subject 10 and 15, both AIDS Diagnosed, cluster and overlap each other, showing much genetic overlap. They are most genetically similar to Subject 14, whom developed AIDS one year later. These observations support that AIDS development may be due to the development of specific genetic identities of the viral strains. That is, AIDS developing HIV-1 strains are similar to each other.

==Analyzing Diversity Within Groups==

[[Image:AIDSV1alignment.jpg|thumb|left|300px|<b>Figure 3.</b> ClustalW alignment for all AIDS-diagnosed sequences at the time of the first visit. Black, non-asterisked segments denote individual base pair differences between the 9 strands. These differences were counted and used to calculated the S and θ values to determine differences between the AIDS Diagnosed groups.]]

[[Image:Nonclustadistvf.png|thumb|left|300px|<b>Figure 13.</b> Clustadist analysis for all Non-Trending sequences at the time of their final visits. Minimum and Maximum base pair values were calculated using this matrix]]

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| No Trend  || 64 || 24 || 1 || 47

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<b>Table 3: </b>Diversity Within Categories at Final Visit<Br>

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| No Trend  || 61 || 22 || 1 || 43

==Analyzing Diversity Between Groups==

Groupings were further analyzed in comparison to each other. ClustalW was performed for AIDS diagnosed and AIDS progressing subjects. The sequences were aligned and a Clustaldist was performed to calculate minimum and maximum differences between strains within the two groups. This was repeated for AIDS diagnosed and No Trend, as well as AIDS progressing and no trend. These processes were repeated for the Final Visit sequences. The findings and calculations are as follows:

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| AIDS Progressing <br>vs.<br>No Trend  || 13 || 43

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| AIDS Progressing <br>vs.<br>No Trend  || 25 || 49

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=Discussion and Conclusion=

{{Template:Isabel Gonzaga}}