BIOL398-01/S10:HIV Evolution

Background

 * BEDROCK HIV Problem Space
 * Sequence Data
 * Link to the ALIVE study listed in Reference 2 below.
 * Biology Workbench
 * Orientation to the Biology Workbench
 * HIV Database at Los Alamos National Laboratory

Lecture

 * Introduction to online biological databases, with special emphasis on literature databases
 * 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 They change frequently, and manuals go out of date quickly.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:


 * Record in your online notebook (your individual week 3 journal page) a summary paragraph of the information you already know about HIV (it's OK if you don't know much yet).
 * 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.
 * Now use your new skills to find a recent scholarly review about the HIV virus. Record the full citation of the review you found on your journal page using the wiki syntax.  (Hint:  you can see an example of how to use it in the source for this page.)
 * 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.
 * We will pool the collective class resources to choose a review article to read to accompany next week's journal club article.

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 February 9.


 * 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 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.  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.
 * 3) *What is the main result presented in this paper? (Hint:  look at the last sentence of the introduction and restate it in plain English.)
 * 4) *What is the importance or significance of this work?
 * 5) *What were the limitations in previous studies that led them to perform this work?
 * 6) *What were the methods used in the study?
 * 7) *Briefly state the result shown in each of the figures and tables.
 * 8) *How do the results of this study compare to the results of previous studies (See Discussion).
 * 9) Each group of students will be assigned one table or figure.  The pair will be responsible for explaining the table/figure in detail to the class.
 * 10) * Figure 1: Kris, Janelle, Ryan
 * 11) * Table 1: Salomon, Kevin
 * 12) * Figure 2: Michael, Alex
 * 13) * Figure 3: Bobak, J'aime
 * 14) * Figure 4: Angela, Amanda

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.

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
After Journal Club, you will work with the Exploring HIV Evolution handout, given out in class on 2/2/10 (an electronic copy of this handout is available on the MyLMUConnect 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 any files, data, and screenshots that you use to complete the exercise.
 * Write a question for the Markham et al. (1998) authors on the class journal page.
 * For Week 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.

Week 5
Now that you have finished a guided exploration of the Markham et al. (1998) data, you and a partner will ask a research question about the data and answer it using the bioinformatic tools you have practiced using. Items marked in BOLD are required for the Week 5 individual journal assignment.


 * Partners (and one threesome) will be assigned at the beginning of class.
 * Group 1: Janelle and KP
 * Group 2: Salomon and Michael
 * Group 3: Amanda, J'aime, Alex
 * Group 4: Ryan and Angela
 * Group 5: Bobak and Kris
 * 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.
 * What is your question?
 * Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
 * 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.
 * You will then answer your research question using the bioinformatics tools you practiced with in Week 4.
 * 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.
 * Use the Web of Science to do a prospective literature search on the Markham et al. (1998) paper. 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.
 * You will prepare a presentation for Week 7 showing your results. You and your partner will have the class period during Week 6 to continue to work on your project and prepare your presentation.
 * 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 6 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.