Kristoffer Chin: Week 5

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Question

The question we are asking for week 5 is if there are specific differences nucleotide sequences that cause an increase in the rate of CD4 T cells decline in rapid progressors compared to non-progressors.

Hypothesis

We believe that there will be a difference in the nucleotide sequences found in the nucleotide sequences in rapid progressors and non-progressors

Subjects

  • For the group of rapid progressors, we have chosen 4-V2, 4-V3, 4-V4, 10-V4, 10-V5, 10-V6, 11-V2, 11-V3, 11-V4. These subjects were chosen because they had the highest frequencies of visit which allowed a better variable of CD4 T cells to choose from. These specific visits were chosen because they had the highest rate of CD4 T Cell decline
  • For the group of non-progressors, we have chosen 2-V1, 2-V3, 2-V4, 12-V3, 12-V4, 12-V5, 13-V2, 13-V3, 13-V5. These subjects were chosen because they were the only recorded nonprogressors in the experiment. These visits were chosen because they had the highest CD4 T cell count among all visits.
  • All clones will also be analyzed for each visit to find a difference in the nucleotide sequence.

Journal articles

  1. Borrego P, Marcelino JM, Rocha C, Doroana M, Antunes F, Maltez F, Gomes P, Novo C, Barroso H, and Taveira N. The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients. Retrovirology. 2008 Sep 8;5:78. DOI:10.1186/1742-4690-5-78 | PubMed ID:18778482 | HubMed [Paper1]
  2. Hill MD and Hernández W. Nucleotide and amino acid mutations in human immunodeficiency virus corresponding to CD4+ decline. Arch Virol. 2006 Jun;151(6):1149-58. DOI:10.1007/s00705-005-0693-8 | PubMed ID:16385396 | HubMed [Paper2]
  3. Templeton AR, Reichert RA, Weisstein AE, Yu XF, and Markham RB. Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics. 2004 Aug;167(4):1547-61. DOI:10.1534/genetics.103.023945 | PubMed ID:15342497 | HubMed [Paper3]
  4. Deckers R, Quesson B, Arsaut J, Eimer S, Couillaud F, and Moonen CT. Image-guided, noninvasive, spatiotemporal control of gene expression. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1175-80. DOI:10.1073/pnas.0806936106 | PubMed ID:19164593 | HubMed [Paper4]
  5. Deckers R, Quesson B, Arsaut J, Eimer S, Couillaud F, and Moonen CT. Image-guided, noninvasive, spatiotemporal control of gene expression. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1175-80. DOI:10.1073/pnas.0806936106 | PubMed ID:19164593 | HubMed [Paper5]
All Medline abstracts: PubMed | HubMed

BIOL398-01: Bioinformatics Lab

  • Lab Journal
Kristoffer Chin: Week 2 Kristoffer Chin: Week 6 Kristoffer Chin: Week 11
Kristoffer Chin: Week 3 Kristoffer Chin: Week 7 Kristoffer Chin: Week 12
Kristoffer Chin: Week 4 Kristoffer Chin: Week 8 Kristoffer Chin: Week 13
Kristoffer Chin: Week 5 Kristoffer Chin: Week 9 Kristoffer Chin: Week 14


  • Shared Journal
BIOL398-01/S10:Class Journal Week 2 BIOL398-01/S10:Class Journal Week 6 BIOL398-01/S10:Class Journal Week 11
BIOL398-01/S10:Class Journal Week 3 BIOL398-01/S10:Class Journal Week 7 BIOL398-01/S10:Class Journal Week 12
BIOL398-01/S10:Class Journal Week 4 BIOL398-01/S10:Class Journal Week 8 BIOL398-01/S10:Class Journal Week 13
BIOL398-01/S10:Class Journal Week 5 BIOL398-01/S10:Class Journal Week 9 BIOL398-01/S10:Class Journal Week 14


  • Assignments
BIOL398-01/S10:Week 2 BIOL398-01/S10:Week 6 BIOL398-01/S10:Week 11
BIOL398-01/S10:Week 3 BIOL398-01/S10:Week 7 BIOL398-01/S10:Week 12
BIOL398-01/S10:Week 4 BIOL398-01/S10:Week 8 BIOL398-01/S10:Week 13
BIOL398-01/S10:Week 5 BIOL398-01/S10:Week 9 BIOL398-01/S10:Week 14

Links