Jordan T. Detamore Week 5

From OpenWetWare

Jump to: navigation, search

Contents

Annotated Bibliography Assignment

Bibliography

Cohen, C. R., Lingappa, J. R., Baeten, J. M., Ngayo, M. O., Spiegel, C. A., Hong, T., ... & Bukusi, E. A. (2012). Bacterial vaginosis associated with increased risk of female-to-male HIV-1 transmission: a prospective cohort analysis among African couples. PLoS Med, 9(6), e1001251. doi: 10.1371/journal.pmed.1001251.

  • PubMed Abstract: [1]
  • PubMed Central: [2]
  • Publisher Full Text (HTML): [3]
  • Publisher Full Text (PDF): [4]
    • Copyright: 2012 by PLOS Medicine
    • Article is Open Access
  • Publisher: PLOS Medicine
    • Open Access organization
  • Online-Only
  • No LMU Fee
  • This article studies transmission of HIV-1. It is useful because I am attempting to study the difference in HIV between those who contracted the disease sexually and those who contracted it through needles. The information in this article can provide more information about sexually transmitted HIV

Leal, E., Casseb, J., Hendry, M., Busch, M. P., & Diaz, R. S. (2012). Relaxation of adaptive evolution during the HIV-1 infection owing to reduction of CD4+ T cell counts. PloS one, 7(6), e39776. doi: 10.1371/journal.pone.0039776. PubMed Abstract: [5]

  • PubMed Central: [6]
  • Publisher Full Text (HTML): [7]
  • Publisher Full Text (PDF): [8]
    • Copyright: 2012 by PLOS Medicine
    • Article is Open Access
  • Publisher: PLOS One
    • Open Access organization
  • Online-Only
  • No LMU Fee
  • This article is very useful because it studies HIV-1 evolution similar to the Markham paper. This article also uses patients who contracted the disease sexually which will help with my specific study of comparing patients who contracted the disease sexually vs. through needles.

Rieder, P., Joos, B., Scherrer, A. U., Kuster, H., Braun, D., Grube, C., ... & Böni, J. (2011). Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection. Clinical infectious diseases, cir725. doi: 10.1093/cid/cir725.

  • PubMed Abstract: [9]
  • PubMed Central: N/A
  • Publisher Full Text (HTML): [10]
  • Publisher Full Text (PDF): [11]
  • Copyright: 2012 by Clinical Infectious Diseases
    • Not Open Access or free after period of time
    • Pay for subscriptions
  • Publisher: Oxford Journals
    • For-Profit publisher
    • Print and Online
    • LMU pays fee
  • This article will be important for its sequences. The study uses patients who contracted the disease sexually and has sequences that can be used for comparison

van Manen, D., van‘t Wout, A. B., & Schuitemaker, H. (2012). Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics. Retrovirology, 9(1), 1. doi: 10.1186/1742-4690-9-70.

  • PubMed Abstract: [12]
  • PubMed Central: [13]
  • Publisher Full Text (HTML): [14]
  • Publisher Full Text (PDF): [15]
  • Copyright 2012 by Retrovirology
    • Open-Acess
  • Publisher: BioMed Central
    • Open Accesss Publisher
  • No Fee
  • This is a review that looks at HIV susceptibility. While it studies HIV susceptibility it will be useful because there are sequences available to compare.

PubMed

  • What original keyword(s) did you use? How many results did you get?
    • Sexually Transmitted HIV-1
    • 891 results
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • HIV-1, Sexually Transmitted, and Sequences all in the Title/Abstract in the past 5 years
    • 9 results
  • Which advanced search functions were most useful to narrow down the search? How many results did you get?
    • The Title/Abstract function was most helpful giving me 9 results.

GoogleScholar

  • What original keyword(s) did you use? How many results did you get?
  • Sexually Transmitted HIV Sequences
    • 17,400
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • Sexually Transmitted HIV Sequences Moderate Progressors
    • 435
  • Which advanced search functions were most useful to narrow down the search? How many results did you get?
    • I added the full phrase "moderate progressors"
    • 3

Web of Science

  • What original keyword(s) did you use? How many results did you get?
    • Sexually Transmitted HIV-1
    • 297
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • Sexually Transmitted HIV-1 Sequences
    • 91
  • Which advanced search functions were most useful to narrow down the search? How many results did you get?
    • Narrowing the publishing years
    • 8
  • Perform a prospective search on the Markham et al. (1998) article and answer the following:
    • How many articles does the Markham et al. (1998) article cite?
      • 51
    • How many articles cite the Markham et al. (1998) article?
      • 74

HIV Evolution Project

Purpose

The purpose of our study is to compare the sequences of patients who contracted HIV sexually with the patients in Markham's study.

Methods & Results

  • This week we used the detailed instruction of the Annotated Bibliography Assignment to find articles relating to each of our HIV projects.
  • Each of us found 3 journal articles and 1 review article related to our HIV project on three different sites
  • Each paper was read in preparation for creating the methods of our HIV project in Week 6.
  • The Redd et al. paper's sequences are going to be used in comparison to a portion of the Markham et al. sequences.

HIV Project Week 6 Methods

  • Our HIV project's main purpose is to study the correlation between HIV-1 sequences of patients who contracted the virus sexually or by intravenous injection.
  • Using sequences found in the Redd et al. paper, we will compare the Markham et al. paper's sequences.
    • We will be using 25 first visit sequences of both the Redd et al. and the Markham et al. papers.
    • The sequences from the Redd et al. paper will need to cut to an appropriate length as they are around 2,500 bp long.
  • We will be using methods from BIOL368/F16:Week 4 on the Biology Workbench site to come up with our data.
    • S values, theta values, and an unrooted phylogenetic tree will be calculated and created in order to measure the relatedness of the respective sequences.
      • Theta is an estimate of the average pairwise genetic distance.
      • S values is the total number of differences in the sequences.
      • Run the multiple sequence alignment in Biology Workbench for the selected subjects and clones to postulate the unrooted tree.

Data & Files

N/A

Conclusion

We have got a start to our project by doing research about related studies. The next step is to do tests to compare the sequences we found with those form Markham's study.

Acknowledgents

  • I worked with Matthew K. Oki in class and also used parts of his Electronic Workbook that we share on this weeks assignment
  • I received instruction from Dr. Dahlquist's in class as well
  • While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
  • Jordan T. Detamore 01:10, 4 October 2016 (EDT):

References

Useful links

Introductory tutorial

OpenWetWare help pages

Bioinformatics Lab Home Page

Kam D. Dahlquist

Jordan T. Detamore

LMU Seaver College of Science and Engineering

Template:Jordan T. Detamore

Assignments

Jordan T. Detamore Week 2

Jordan T. Detamore Week 3

Jordan T. Detamore Week 4

Jordan T. Detamore Week 5

Jordan T. Detamore Week 6

Jordan T. Detamore Week 8

Jordan T. Detamore Week 9

Jordan T. Detamore Week 10

Jordan T. Detamore Week 11

Jordan T. Detamore Week 12

Jordan T. Detamore Week 13

Jordan T. Detamore Week 14

Jordan T. Detamore Week 15

Shared Journals

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 14

Week 15

Instructions

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week12

Week 13

Week 14

Week 15

Personal tools