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

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.

Abstract

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.

Introduction

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.

Results

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.

Discussion

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.

References

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

Guest Lecture

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

• Introduction to online literature databases and library resources
  • LMU Library Guide for Biology 478 (but also useful for this class)

In-class 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 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?
• Choose one article from any of your searches that you believe is relevant to your research project question. You will read this article and use it in your project and presentation.