BIOL368/F11:HIV Evolution

Background

• BEDROCK HIV Problem Space
  • Sequence Data
• HIV Database at Los Alamos National Laboratory
• Biology Workbench
  • Orientation to the Biology Workbench

References

1. Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12568-73. Publisher Full text PDF.
2. Vlahov D, Anthony JC, Munoz A, Margolick J, Nelson KE, Celentano DD, Solomon L, Polk BF. The ALIVE study, a longitudinal study of HIV-1 infection in intravenous drug users: description of methods and characteristics of participants. NIDA Res Monogr. 1991;109:75-100. PubMed PDF.
3. Cohen MS, Hellmann N, Levy JA, DeCock K, Lange J. The spread, treatment, and prevention of HIV-1: evolution of a global pandemic. J Clin Invest. 2008 Apr;118(4):1244-54. Publisher Full text PDF.

Week 3

In-class Activity

Today you will work with the Exploring HIV Evolution handout, given out in class on 9/7/11 (an electronic copy of this handout is available on the MyLMU Connect site).

• Complete the following:
  • Activity 1/Part 2 starting on page 139
  • Activity 1/Part 3
  • Activity 2/Part 1
  • Activity 2/Part 2 ending on page 145
  • Answer the questions throughout the handout on your individual journal page, recording your methods and any files, data, and screenshots that you use to complete the exercise. Click here to see the assignment page.
• For Weeks 4 and 5, you will be working with a partner/group to carry out an HIV Evolution Research project (as described in Activity 3). You should be thinking about questions that you would like to answer in using the Markham et al. (1998) data.

Preparation for Week 4 Journal Club

"Science... is a process taking place in the minds of living scientists," (Curtis, 1983). The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings are others). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research. This is the first of three journal club discussions we will have this semester. For this first journal club, the entire class will read and present the Markham et al. (1998) paper referenced above. Each student will create an individual wiki journal page for their Week 3 assignment and also contribute to the shared journal page in preparation for the presentation in class on September 21.

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page where you found the definition is fine.
2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
   • What is the importance or significance of this work?
   • What were the limitations in previous studies that led them to perform this work?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies (See Discussion).
3. Each group of students will be assigned one table or figure. The group will be responsible for explaining the table/figure in detail to the class.
   • Figure 1:
   • Table 1:
   • Figure 2:
   • Figure 3:
   • Figure 4:

Online Biological Dictionaries

• biology-online.org dictionary
• Dictionary of Cell and Molecular Biology
• Gene Ontology
• NCI Dictionary of Cancer Terms