Jordan T. Detamore Week 9

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Purpose

The purpose of this assignment was to get acclimated with new website technologies and get ideas flowing about what programs will be useful for our upcoming project.

Defining HIV Structure Research Project

  1. What is your question?
    • Will subjects demonstrating a low dS/dN ratio value show high variation and dissimilar relationships between each other when examining their respective amino acid sequences and will subjects demonstrating high dS/dN ratio values show low variation and closer relationships when examining their amino acid sequences both individually and comparatively.
  2. What is your prediction before performing analysis?
    • If we extract and compare subjects from the Markham paper who exhibited very high and very low non-synonymous mutation rates and compare the amino acid sequences from their last visits, we will find high variation between them both structurally and functionally because the subjects with lower ratios will have experienced more mutations which caused changes in their amino acid sequencing.
  3. Which subjects, visits, and clones will you use to answer your question?
    • Subjects were selected with the same criteria from week 6 presentation Media:HIV1Presentaionzachandshivum.pdf due to selection for "extreme" dS/dN values. Eight subjects were chosen, the four exhibiting the highest dS/dN ratios and the four exhibiting the lowest dS/dN ratios. Due to inconsistencies in subject's visits, we decided to use three clones from the subjects' first (of which everyone's is the same) visit and last (of which some subjects were different) visit. For example, Subject 2's last visit was after 4 years, but subjects 4's last visit was only after 1.5 years. Random selection was used to determine which 3 clone sequences were compared within each visit. The specific clones chosen are:
      • Subject 2
        • First visit clones: 1,6,4
        • Last visit clones: 8,6,1
      • Subject 4
        • First visit clones: 1,2,3
        • Last visit clones: 8,10,7
      • Subject 5
        • First visit clones: 2,5,1
        • Last visit clones: 3,4,5
      • Subject 7
        • First visit clones: 7,9,3
        • Last visit clones: 7,4,5
      • Subject 9
        • First visit clones: 4,2,5
        • Last visit clones: 1,4,7
      • Subject 11
        • First visit clones: 7,5,4
        • Last visit clones: 7,6,3
      • Subject 13
        • First visit clones: 2,1,3
        • Last visit clones: 2,5,6
      • Subject 14
        • First visit clones: 6,1,2
        • Last visit clones: 4,9,13

Methods/Results: HIV Structure In-Class Activity

  1. Convert one of your DNA sequences into protein sequences using either the NCBI Open Reading Frame Finder or the ExPASY Translate tool.
    • How do you know which of the six frames is the correct reading frame (without looking up the answer)?
      • It is the only sequence that does not have a stop codon. No stop codon should be present because this is the middle segment of a protein sequence.
  2. Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgebase (UniProt KB).
    • If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
      • HIV: 723,401 results
      • gp120: 207,983 results
      • HIV gp120: 206,278 results
    • Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
    • What types of information are provided about this protein in this database entry?
      • The entry provides information about the functions of both gp120 and gp41 as the HIV virus attacks cells.
  3. We are going to use the PredictProtein server to analyze just the V3 region from Markham et al. (1998).
    • Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit.
    • Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
      • UniProt provides more information than the Protein server however the protein server provides a more visual and interactive display.

UniprotJD109.png ProteinserverJD109.png

Conclusion

I was not able to get all of the assignment done, but I did complete a couple of the prompts and navigate a few sites and programs. These programs may be useful in further research. Additionally Zach and I settled on our research project and chose our subjects of study. We will be looking at dS/dN ratios which Zach has worked with in the past and look at the protein sequences of subjects from the Markham paper.

Acknowledgements

  • I worked with Zachary T. Goldstein 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 19:51, 25 October 2016 (EDT):

References

Week 9 Assignment Page

UniProt Knowledgebase (UniProt KB)

PredictProtein server

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

Useful links

Introductory tutorial

OpenWetWare help pages

Bioinformatics Lab Home Page

Kam D. Dahlquist

Jordan T. Detamore

LMU Seaver College of Science and Engineering

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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

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