BIOL368/F11:HIV Evolution

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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  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, including the methods used to obtain that figure/table.
    • Figure 1 & first five data columns of Table 1: Alex and Robert
    • Figure 2 & last three data columns of Table 1: Chris and Nicki
    • Figures 3 & 4: Isaiah, Samantha, Zeb

Online Biological Dictionaries

How to Read a Primary Research Article

A primary research article is divided into sections that each have a different purpose. Articles in Science and Nature are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.


The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on PubMed and may be the only part of the text publicly available.


The introduction gives the background information necessary to understand the paper. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

  • States importance of the problem
  • States what is known about the problem
  • States what is unknown about the problem
  • States clues that suggest how to approach the unknown
  • States the question the paper is trying to address
  • States the experimental approach
  • Sometimes briefly states the answer they found

Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.


Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.


States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.


List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

Week 4

The Journal Club presentation will take place at the beginning of class.

Now that you have finished the journal club (today) and a guided exploration of the Markham et al. (1998) data (last week), you and a partner will ask a research question about the data and answer it using the bioinformatic tools you have practiced using. Items 1-3 are required for the Week 4 individual journal assignment. You will work on this project during Weeks 4 and 5 and will present your report in class during Week 6.

  • Partners (and one threesome) will be assigned at the beginning of class.
    • Group 1: Robert, Zeb, Alex
    • Group 2: Chris & Nicki
    • Group 3: Isaiah & Samantha
  • You and your partners will come up with a research question that you want to answer regarding the Markham et al. (1998) data and discuss it with Dr. Dahlquist.
    1. What is your question?
    2. Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
    3. Which subjects, visits, and clones will you use to answer your question?
      • You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
      • Justify why you chose the subjects, visits, and clones you did.

Once you have your question, hypothesis, and data you will use, you should then move on to answering your question (shown below in Week 5). Although the project is not due until the Week 5 journal assignment, you should work ahead.

Week 5

Guest Lecture

The reference librarian for the sciences, Glenn Johnson-Grau will be giving a guest lecture.

Literature Search Activity

Bioinformatics servers and online biological databases are a moving target. They change frequently, and manuals go out of date quickly. Today we will explore online literature databases because the first step in any research project is to find out what is previously known about the subject in the published literature. Your goal is to find out published information about the HIV virus that will help you understand the HIV evolution project. To begin:

  • Write three questions (or more) that you have about HIV that you would like answered.
  • In Chapter 2 of Bioinformatics for Dummies, follow the protocol on "Becoming an Instant Expert with PubMed/Medline", using the examples shown in the book. Notice the differences between the instructions and screenshots shown in the book and what you see on today's version of PubMed.
  • The Markham et al. article that we have read was published in 1998, 13 years ago. Now use your new skills to find a recent scholarly areticle about the evolution of the gp120 protein of the HIV virus. Record the full citation of the article you found on your journal page using the Guidelines for Literature Citations in a Scientific Paper handout.
    • Compare your search results with Google Scholar and the ISI Web of Science (a commercial site that LMU subscribes to).
    • Using ISI Web of Science perform a prospective search on the Markham et al. (1998) article to find out what articles cite that article since its publication in 1998. How many are there? Did your article that you found from a keyword search show up in the list of articles that cite the Markham et al. (1998) article?
    • Select a paper that was published within the last 5 years that studies the evolution of the env gene, in particular the V3 region, if possible. Include the bibilographic reference to this paper in your Week 5 journal (you will also need it for your project).

Continue Research Project

The following is due for your Week 5 Journal Assignment.

  1. You will then answer your research question from Week 4 using the bioinformatics tools you practiced with in Week 3.
    • You must create a multiple sequence alignment and tree using ClustalW.
    • You must also use one of the statistics you calculated, S, θ, or the Min and Max distances (or some other statistic mentioned in the Markham et al. (1998) paper.
  2. Use your Web of Science prospective literature search results from the in-class activity to select a paper that was published within the last 5 years that studies the evolution of the env gene, in particular the V3 region, if possible. Include the bibilographic reference to this paper in your Week 5 journal.
    • Interpret your results in light of the data in this new paper.
  3. You will prepare a presentation for Week 6 showing your results.
    • Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
      • Title slide
      • Outline slide
      • Background that led you to ask your research question (summary of Markham et al. 1998)
      • Your question
      • How you answered your question, method/results
      • Interpretation of your results; answer to your question
      • Discussion and interprettion of your results in light of the new paper you found.
    • Upload your slides to the OpenWetware wiki by the Week 5 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.