BIOL368/F14:Week 4

This journal entry is due on Wednesday, September 24 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

NOTE that this assignment is UNDER CONSTRUCTION.

Background for HIV Evolution Project

• BEDROCK HIV Problem Space
  • Sequence Data
  • Media:Visit_1_Subjects_1_thru_9_HIV.txt
  • Media:Visit_1_Subjects_10_thru_15_HIV.txt
• HIV Database at Los Alamos National Laboratory
• Biology Workbench
  • Orientation to the Biology Workbench
• Sigma notation calculator

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.
2. Vlahov, D., Anthony, J.C., Munoz, A., Margolick, J., Nelson, K.E., Celentano, D.D., Solomon, L., Polk, B.F. (1991). The ALIVE study, a longitudinal study of HIV-1 infection in intravenous drug users: description of methods and characteristics of participants. NIDA Res Monogr 109, 75-100.
   • PubMed
   • PDF.

Individual Journal Assignment

• Store this journal entry as "username Week 4" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "BIOL368/F14" category to the end of your wiki page.
• Complete your electronic notebook for the Exploring HIV Evolution In-Class Activity below.
• Define your research project by answering the questions below.

Exploring HIV Evolution In-Class Activity

Your electronic notebook entry for this portion should contain:

• Record your methods, results, and interpretations for the in-class activity using the Exploring HIV Evolution handout on your individual journal page (an electronic copy of this handout is available on the MyLMU Connect site).
  • 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.
  • Write a scientific conclusion that summarizes your overall findings for this exercise.

Defining Your Research Project

For this portion of your journal assignment, your electronic lab notebook entry should contain the answers to the following:

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 (see the Week 5 Assignment). Although the project is not due until October 1, you should work ahead. Your electronic notebook should contain your notes, methods, results, and interpretations as you carry out your project. You should document as you work, taking your notes on the wiki as much as possible. Post data, figures, screenshots, to support your project. You can post files that are in progress; remember, you can upload a new version of the file and the wiki will automatically link to the new version (while keeping the old).

Shared Journal Assignment

• Store your journal entry in the shared BIOL368/F14:Class Journal Week 4 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Link to the shared journal entry from your user page.
• Link the shared journal page to this assignment page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL368/F14" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer these questions on the shared page:

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
2. Have your views about what it means to do original research in biology changed as a result of discussing this article? Why or why not?