Matthew K. Oki Individual Journal 5

From OpenWetWare
Jump to: navigation, search

Matthew K. Oki Week 5

Week 5 Assignment

Annotated Bibliography

Assignment 5 Questions

  1. Keyword Search and Advanced Search Questions
    • PubMed
      • What original keyword(s) did you use? How many results did you get?
        • I used the key words HIV-1 and sexual transmission at first. The resulting articles were much too many to get a handle on, as there were 2,566 articles.
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • The most useful combination without the use of the advanced search was the combination of HIV-1 and sexual interaction. These gave a total result of 105 articles. This was much easier to go through, but the articles weren't exactly what I was looking for.
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • Instead of using HIV-1 and sexual transmission in any field, I narrowed it to Title/Abstract only. This reduced the total articles to 319. Even though this is still a fairly large number, the articles were much closer to what I was looking for. I think this field function is the most useful.
    • GoogleScholar
      • What original keyword(s) did you use? How many results did you get?
        • I used the key words HIV-1 and sexual transmission again at first. However, this gave a massive return of about 19,000 articles. Clearly this was much too many to go through.
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • Without using the advanced functions for GoogleScholar, it is very difficult to get a reasonable number of results. Even after using the combination of HIV-1 and sexual interaction, the results were still in the 17,000s. This is much too high to get a good read on any potential articles.
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • When I ran the advanced search, I made the time range from 2011-2016. I also made the results only ones who displayed HIV-1 and sexual transmission in the title. This severely cut the results to 19. This was not nearly enough to give an accurate picture of all the articles on this topic.
    • Web of Science
      • What original keyword(s) did you use? How many results did you get?
        • The keywords of HIV-1 and sexual transmission turned up 1,808 articles. This is a very large number for the Web of Science page. Using the advanced search was very helpful on this website as well.
      • 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 and sexual interaction was searched in an attempt to narrow down the results. It cut down the results to 141 articles, a very large improvement.
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • I liked this website because I think it fit our project the best. When using the advanced function, it cut down the results just enough without taking away too many articles. I used the keywords HIV-1 and sexual transmission, but I selected it only for those words appearing in the title of the article. This cut the total results down to 81 with most of them being close to what I needed.
  2. Prospective Search on Markham et al. (1998)
    • How many articles does the Markham et al. (1998) article cite?
      • The Markham et al. (1998) article cites 51 other articles.
    • How many articles cite the Markham et al. (1998) article?
      • The Markham et al. (1998) article is cited by 74 other articles.

HIV Project Week 5 Electronic Lab Notebook

Purpose

  • The purpose of this week's assignment was to get more familiar with research tools. These tools will enable us to become more effective researchers by finding relevant articles and reviews quicker and more efficiently. We were also tasked with giving a general outline for our HIV project's methods.

Methods

  • This week we used the detailed instruction of the Annotated Bibliography Assignment to find articles relating to each of our HIV projects.
  • We found 3 journal articles and 1 review article related to our HIV project on three different sites: PubMed, GoogleScholar,Web of Science
  • 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 and Files

  • There were no data and files used in this project.

Scientific Conclusion

In our correlation analysis of the HIV-1 patients who contracted the virus sexually or by intravenous injection, we expect there to be no significant difference. Even though the virus is transmitted in two separate ways, there shouldn't be a significant difference in the sequences variability. The unrooted tree will be our most telling data given that it is a good visual of the total relatedness of the sequences.

Acknowledgments

  • I would like to thank my partner, Jordan Detamore, for assistance on this project.
    • We collaborated in class on the searching for sources.
    • We also worked on our HIV project together in class.
  • I would also like to thank Kam D. Dahlquist, Ph.D. for providing the instructions and information for this assignment both in class and on these documents: BIOL368/F16:Week 5 and Annotated Bibliography Assignment.
  • Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
  • Matthew K. Oki 01:48, 3 October 2016 (EDT):

References

  • BIOL368/F16:Week 5
  • Annotated Bibliography Assignment
  • PubMed
  • GoogleScholar
  • Web of Science
  • 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. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568
  • Frange, P., Meyer, L., Jung, M., Goujard, C., Zucman, D., Abel, S., ... & Chaix, M. L. (2013). Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner. PloS one, 8(7), e69144. doi: 10.1371/journal.pone.0069144
  • Redd, A. D., Collinson-Streng, A. N., Chatziandreou, N., Mullis, C. E., Laeyendecker, O., Martens, C., ... & Grabowski, M. K. (2012). Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions. Journal of Infectious Diseases, jis503. doi: 10.1093/infdis/jis503
  • Vrancken, B., Rambaut, A., Suchard, M. A., Drummond, A., Baele, G., Derdelinckx, I., ... & Lemey, P. (2014). The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates. PLoS Comput Biol, 10(4), e1003505. doi: 10.1371/journal.pcbi.1003505
  • Brenner, B., Wainberg, M. A., & Roger, M. (2013). Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS (London, England), 27(7), 1045. doi: 10.1097/QAD.0b013e32835cffd9.

Class Homework Links

Weekly Assignments

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 14

Week 15

Individual 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 14

Week 15

Class 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 14

Week 15

Other Links

My Home Page: Matthew K. Oki

Class Home Page: Bioinformatics Home Page

My Paper Resume: Matthew K. Oki Resume