Matthew R Allegretti Week 5

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Week 5 Assignment

Purpose

To create an annotated bibliography of papers related to our HIV evolution research project that we will use to interpret and discuss our results.

Methods and Results

Part 1

Bęczkowski, P., Hughes, J., Biek, R., Litster, A., Willett, B., Hosie, M. (2014). Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus. J. Gen. Virol. 96(4), 893-903. DOI:10.1099/vir.0.000035
Matsuda, Z. (2015) Recent advance in the structural analysis of HIV-1 envelope protein. Sci. China Life Sci., 58, 420. DOI:10.1007/s11427-015-4852-1
Veillette, M., Désormeaux, A., Medjahed, H., Gharsallah, N. E., Coutu, M., Baalwa, J., ... & Haynes, B. F. (2014). Interaction with cellular CD4 exposes HIV-1 envelope epitopes targeted by antibody-dependent cell-mediated cytotoxicity. Journal of virology, 88(5), 2633-2644. DOI:10.1128/JVI.03230-13.
Asbach, B., Kliche, A., Köstler, J., Perdiguero, B., Esteban, M., Jacobs, B. L., ... & Ferrari, G. (2016). Potential To Streamline Heterologous DNA Prime and NYVAC/Protein Boost HIV Vaccine Regimens in Rhesus Macaques by Employing Improved Antigens. Journal of virology, 90(8), 4133-4149. DOI:10.1128/JVI.03135-15
  • PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26865719
  • PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810551/
  • Publisher Full Text (HTML): http://jvi.asm.org/content/90/8/4133.full
  • Publisher Full Text (PDF): http://jvi.asm.org/content/90/8/4133.full.pdf+html
  • Rights and Availability
    • Copyright owned by American Society for Microbiology
    • Article is not Open Access
    • Article is freely available 4 months after publication
  • Publisher: Journal of Virology
    • Peer-reviewed Journal
  • Availability: Electronic
  • Did LMU pay a fee for this article: No, it is behind a paywall on the publisher site.
  • This article is related to the research project because it demonstrates that other scientists are using model species to examine immunodeficiency viruses in order to transfer understanding to human viruses. It is also substantial, because it may not be necessary to examine numerous species of Immunodeficiency viruses, but merely compare the same virus among different species.

Part 2

A. Keyword search
  • PubMed
    • 1. What original keyword(s) did you use? How many results did you get?
      • a) HIV-2, HIV-1, CD4, and SIV.
      • b) Number of results: 142,987-5,650
    • 2. Which terms in which combinations were most useful for to narrow down the search? How many results did you get after narrowing the search?
      • a) HIV-2 and SIV
      • b) Number of results: 22,419-638
  • Google Scholar
    • 1. What original keyword(s) did you use? How many results did you get?
      • a) HIV-2, HIV-1, CD4, and SIV.
      • b) Number of results: 2,000,000-193,000
    • 2. Which terms in which combinations were most useful for to narrow down the search? How many results did you get after narrowing the search?
      • a) HIV-2 and SIV
      • b) Number of results: 422,000-19,400
  • Web of Science
    • 1. What original keyword(s) did you use? How many results did you get?
      • a) HIV-2, HIV-1, CD4, and SIV.
      • b) Number of results: 137,473-4,214
    • 2. Which terms in which combinations were most useful for to narrow down the search? How many results did you get after narrowing the search?
      • a) HIV-2 and SIV
      • b) Number of results: 20,606-583
B. Advanced Search
  • PubMed
    • 1. Which advanced search functions were most useful to narrow down the search?
      • Title/Abstract
    • 2. How many results did you get?
      • 631
  • Google Scholar
    • 1. Which advanced search functions were most useful to narrow down the search?
      • Sorting by date and keywords within the title
    • 2. How many results did you get?
      • 747
  • Web of Science
    • 1. Which advanced search functions were most useful to narrow down the search?
      • I used the title narrowing feature, as it allowed me to narrow options to those that contain relevant titles.
    • 2. How many results did you get?
      • 1,651
C. Prospective Search
  • How many articles were cited by Markham et al. (1998)?
    • 51 articles
  • How many articles cited this article?
    • 74 articles



Acknowledgments

  • Isai Lopez
  • While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Matthew R Allegretti 10:06, 3 October 2016 (EDT)

  • I worked with my homework partner Isai Lopez in class and communicated electronically outside of class to ensure we found separate sources.

Matthew R Allegretti 21:58, 3 October 2016 (EDT)

References

  • Week 5 Instructions
  • Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A. Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., Yu, X. F. (1998) Patterns of HIV-1 Evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences USA, 95(21), 12568-12573. DOI: 10.1073/pnas.95.21.12568
  • Asbach, B., Kliche, A., Köstler, J., Perdiguero, B., Esteban, M., Jacobs, B. L., ... & Ferrari, G. (2016). Potential To Streamline Heterologous DNA Prime and NYVAC/Protein Boost HIV Vaccine Regimens in Rhesus Macaques by Employing Improved Antigens. Journal of virology, 90(8), 4133-4149. DOI:10.1128/JVI.03135-15
  • Bęczkowski, P., Hughes, J., Biek, R., Litster, A., Willett, B., Hosie, M. (2014). Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus. J. Gen. Virol. 96(4), 893-903. DOI:10.1099/vir.0.000035
  • Matsuda, Z. (2015) Recent advance in the structural analysis of HIV-1 envelope protein. Sci. China Life Sci., 58, 420. DOI:10.1007/s11427-015-4852-1
  • Veillette, M., Désormeaux, A., Medjahed, H., Gharsallah, N. E., Coutu, M., Baalwa, J., ... & Haynes, B. F. (2014). Interaction with cellular CD4 exposes HIV-1 envelope epitopes targeted by antibody-dependent cell-mediated cytotoxicity. Journal of virology, 88(5), 2633-2644. DOI:10.1128/JVI.03230-13.

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