AVM BIOL368 Week 9

Purpose

The purpose of this weeks lab is to define my HIV structure project and complete this in-class HIV structure activity.

Methods and Results

HIV Structure Project: What is your question?

• Does diversity and divergence increase within the amino acid sequences over time more within the rapid progressors compared to non-progressors?

Make a prediction about the answer to your question before you begin your analysis.

• Since divergence and diversity increases over time within the DNA sequences for all progressor types, and more so within the rapid progress ors, we would expect to see more diversity within the amino acid sequences over time within the rapid progressors.

Which subjects, visits, and clones will you use to answer your question?

• For rapid progressors we are looking at subject 3 and 10's first and last visits and for non-progressors we are looking at subject 12 and 13's first and last visits. These were chosen based on similar number of visits.

In-Class Structure Activity:

• Convert a DNA sequence into an amino acid sequence using ExPASY Translate tool.
  • You will notice you are given multiple reading frame options. Since we are not given the complete open reading frame, the option to chose will be the reading frame that does not contain a stop codon.
• Obtain the remaining sequences from the bedrock webpage.

• Open UniProt Knowledgebase (UniProt KB) and search HIV-1 and gp120.
  • If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
    • You will get 563,418 results and 207,983 results respectively.
  • 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?
      • It is the env protein gp160 (gp41 and gp120 collectively) which binds to the CD4 receptor. All known information about this protein is available through this page.
• Using PredictProtein server input an amino acid sequence from the Markham study.
  • This website gives a summary of the amino acid composition, predicted regions, etc. (Photo below).

Data and Files

• BEDROCK HIV Problem Space
  • Sequence Data

Conclusion

In this assignment, my partner, Mia, and I agreed on a second HIV project. Our project is going to be to determine if diversity and divergence increase within the amino acid sequences over time more within the rapid progressors compared to non-progressors. This differs form the first projects our classes did because we are comparing amino acid sequences rather than DNA sequences. The actual data collecting will be done next week. For the remainder of class we did activities to help familiarize ourselves with some of the programs we may use for our project. Since this week was Journal Club presentations, the assignment did not have to be completed.

Acknowledgments

• Worked in collaboration with research partner Mia Huddleston in class.
  • We agreed on our presentation topic for next week.
• Template followed from week 9 assignment BIOL368/F16
• Help from our professor, Dr. Dahlquist in class.
• Note: While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Avery Vernon-Moore 19:45, 25 October 2016 (EDT)

References

1. • 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
   • Publisher Full text
   • PDF.
   • Kwong et al. (1998) structure 1GC1
   • UniProt Knowledgebase (UniProt KB)
   • PredictProtein server
   • ExPASY Translate tool

User: Avery_Vernon-Moore

Weekly Assignments:

Assignment 1
Assignment 2
Assignment 3
Assignment 4
Assignment 5
Assignment 6
Assignment 7
Assignment 8
Assignment 9
Assignment 10
Assignment 11
Assignment 12
Assignment 14
Assignment 15

Individual Journals:

"Week 1: Create Wiki Page" 
Individual Journal 2
Individual Journal 3
Individual Journal 4
Individual Journal 5
Individual Journal 6
Individual Journal 7
Individual Journal 8
Individual Journal 9
Individual Journal 10
Individual Journal 11
Individual Journal 12
No Week 13 Assignment
Individual Journal 14
Individual Journal 15

Shared Journals:

Class Journal 1
Class Journal 2
Class Journal 3
Class Journal 4
Class Journal 5
Class Journal 6
Class Journal 7
Class Journal 8
Class Journal 9
Class Journal 10
Class Journal 11
Class Journal 12
Class Journal 14
Class Journal 15