BIOL368/F14:Chloe Jones Week 3

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Revision as of 22:35, 14 September 2014 by Chloe Jones (talk | contribs) (completion of methods)
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Annotated Bibliography for HIV Evolution Project

Questions

  1. Write three questions (or more) that you have about HIV that you would like answered.
    1. When does HIV become AIDS?
    2. If somebody infected with HIV has blood that touches you and you unknowingly tough your eye or nose, would you contract the disease?
    3. Does HIV impact your opportunity to receive employment?
  2. Keyword Search
    1. What original keyword(s) did you use? How many results did you get?
      • Web of science: HIV(264,797 results) ENV gene (4,310)
    2. Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • HIV+ENV gene: 2,305
      • HIV+ENV gene+CD4 T: 411
      • ENV gene+CD4 T: 483
      • When I added CD4 T it narrowed the results down dramatically taking the articles available from 2,305 to 411.
  3. Advanced Search - For all three, which advanced search functions were most useful to narrow down the search? How many results did you get?
    1. Web of Science
      • Using the topic: HIV-1 and ENV gene ( 1,985 results)
      • Using the topic: HIV-1 and ENV gene Author: Markham (2 results)
      • Results were able to be narrowed by incorporating an author and using the term AND to include all topics that I wanted discussed in the article. Also, by choosing the years and how many times an article had been cited allowed me to find recent articles as well as articles that seemed noteworthy to others.
    2. PubMed
      • (Hiv-1[Title/Abstract]) AND ENV[Title/Abstract] (4323 results)
      • ((HIV-1[Title/Abstract]) AND ENV gene[Title/Abstract]) AND CD4[Title/Abstract] (137 results)
      • By immediately clicking the advanced button it allows you to search using keywords found in the title and the abstract which I thought was extremely helpful. Also, by clicking the free full it allowed you to see which ones that had available.
    3. Google Scholar
      • HIV-1 and env gene: (100,000 results)
      • HIV-1 and env gene and CD4-T (31,600 results)
      • HIV-1 and env gene and CD4-T and author: Markham (2,080 results
      allintitle: env gene and HIV-1 (68; results)
      • To decrease the results in Google Scholar The drop down tool was essential because it allowed you to search keywords in the title, and or use an exact phrase. Also, allowed words to be excluded and for the time it was published to be taken into account


Article Outline

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline

  1. Methods
    • A. The Study Population
    1. Sequences of env were studied in 15 participants based on what rate there CD4 T cell count dropped. Studied from point of seroconversion, point at which antibodies introduced. 6 month interval check-up
    2. Groups defined based on level of CD4 T cells
      • a.) Rapid Progressors= fewer than 200 CD4 T cells within 2 years of contracting
      • b.) Moderate progressors= declined to 200–650 during 4 years
      • c.) Nonprogressors= maintained CD4 T cell levels above 650 during observation period
    • B. Sequencing of HIV-1 env Genes
    1. PCR used to amplify env gene from peripheral blood mononuclear cells (PBMC).
      • a.) studies how viral DNA found in great numbers in inactivated PBMC, which is the form that it is in most humans
        • hasn’t been integrated into host genome
      • b.) From the primers the restriction sites BamHI and EcoRI were used for cloning purposes
      • c.) Amplified sequences, 5 samples at the lowest level choose for 2nd round of PCR. Already had 126 input copies of viral DNA from initial round.
    • C. Plasma Viral Load
    • D. Generation of Phylogenetic Trees.
    • E. Correlation Analysis
    1. Study the connection between genetic diversity and divergence
      • a.) X0= diversity, or mutational divergence , Y0= CD4 T cell count
    • F. Determination of dS/dN Ratios
    1. Difference between the strains were labeled as synonymous (dS) or non-synonymous (nS)
      • a.) Changed because based it on where mutation could occur, remove bias of unequal sample sizes
    • G. High Genetic Variation in subjects 9 & 15
    1. Study to see if infected with two different viruses. Phylogentic tree contructed.
    2. HIV-1 seronegative 7 months before 1st visit
    3. Exclusion of subject 15; diversity higher
    • H. Comparison of the Rate of Change of Divergence and Diversity
    1. Divergence vs. Diversity over time
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