HHMI Teacher Institute July 2000

Authors Janice Chen and Jo Ann Lane


A three-part unit that examines HIV and AIDS from biological/medical, cultural, economic,
and political perspectives



Part 1. A Case Study Analysis of the Cultural Impact of AIDS:

Readings taken from Barnett, Tony and Blaike,Piers. AIDS in Africa: Its Present and Future Impact. New York: The Guilford Press. 1992. (Marion Fass, Beloit College)

Excerpts of two of these cases:

The man lived alone in a bare hut, sleeping on the floor. His possessions appear to be little beyond a blanket and a pot over a meagre fire upon which he was cooking some bananas. He was said to be 45 years old but looked considerably older. He was clearly very disturbed and could not be interviewed. Information was obtained from others nearby.
Only a few years ago, this was a substantial household with a reasonable farm supplemented by fishing. His wife and eight of his teenage and adult children had died of AIDS within the last few years. He had no relatives living in the village and supported himself by cultivating and selling some of his bananas...

There are five siblings, three girls and two boys aged 14, 12, 11, 10 and nine years. They live in an isolated house on the edge of the village. Their parents died of AIDS two years ago. The house remains half completed, without windows, the kitchen has collapsed to the ground and the remains of an old car stand in the area behind the house. The children have a small plot measuring 20 metres by 30 metres on which they grow some tomatoes and onions. These they sell to generate income. For food they maintain a small patch of bananas and they also grow beans and potatoes. As soon as their parents died, they dropped out of school because there was no money. The only relative they know is a maternal uncle who lives in another county. They are fond of him but he is not dependable because he drinks excessively...

Part II. Memorandum

TIME, Inc.

MEMO: To High School Biology Students
Re: URGENT!!! Special Issue on HIV
From: John Doe, Senior Editor

Congratulations! You have been carefully selected from a strong group of applicants to write articles for the next special issue of Time. This issue will focus on updating the public about HIV and AIDS. Recently, it has come to our attention that high school students are not particularly concerned about HIV infections. We decided to ask high school students to write the stories in order to find a voice that could reach a larger audience among the young adults in the United States.



This activity is designed as an end-of-year project that incorporates skills such as Internet research and using Biology Workbench. Students should already have learned molecular biology and the basics of virology and immunology.


Part 1--Analysis of the Cultural Impact of AIDS:

Time Required: One 40-minute period

Teacher should:
1. Discuss how science cannot be separated from its cultural context.
We are going to depart from our usual discussions of "hard" science and look at how science relates to its cultural context. To do this, we will examine the effects of AIDS on a community in Uganda.

2. Pass out the readings/case studies about the effects of AIDS on different families.

Readings are taken from Barnett, Tony and Blaike,Piers. AIDS in Africa: Its Present and Future Impact. New York: The Guilford Press. 1992.

3. Ask students to read the cases to themselves and to write their thoughts about the impact of AIDS in the margins. Be sure that each student answers the question at the end of the readings.

4. Give the students a few minutes to work in groups to compare their thoughts.

5. As a class, discuss the issues that were raised and list them on the board.

Possible answers may include (NOTE: this is not an exhaustive list):
Less food because there are fewer people to farm
Fewer money crops and decreased quality of crops (more starch, less protein)
Family structure drastically changed
Less schooling and decreased ability to pass on social norms
Money must go towards medicines rather than schooling

6. Assess students based on their written and spoken contributions to the class.

7. Pass out the "TIME, Inc." memorandum and send students home to begin filling in the reporter's preliminary research worksheet. Teachers should emphasize that students should interview at least two other students. Allow two to three days for the students to complete this.


To help you conduct your preliminary research, use the form below:

 REPORTER: _______________

 DATE: ___________

 What do you KNOW about HIV and AIDS?










 What do you WANT TO KNOW about HIV and AIDS?











Part 2-An Update on HIV

Time Required: Ten minutes for introduction
One period for web searching
One period for sharing findings

Teacher should:
Note: at the end of the previous activity, the teacher already passed out the instructional memo to the students, complete with due dates for each part of the assignment.

1. Ask students to state the results of their preliminary research. Teacher should record the findings on the board or overhead.

2. Pair up students based on their interest in doing further research on a particular topic. Have students try to focus their question/topic on a particular issue. For example, if the students wanted to study the effects of drugs on the spread of HIV, the teacher could ask them which drug or which particular drug regimen they would like to address.

3. Schedule at least one period for Internet research, if possible.

Note: These three sites have excellent information.
CDC -www.cdc.gov/hiv/pubs/facts.htm
UN -www.unaids.org

4. Allow students time out of class to finish writing the articles.

5. Collect drafts of articles and graphics and give feedback.

6. Collect final copies of articles and graphics. Depending on their computer skills, the students can compile the articles into an actual magazine that could be shared with other classes

7. Assess all parts of the project based on the rubrics that follow.


Students will be able to:

· Analyze the effects of AIDS on a specific Ugandan community.

· Identify questions or information concerning AIDS and HIV.

· Research those questions about AIDS and HIV.

· Relate HIV molecular data to the numbers of clones found in AIDS patients.

· Compare and interpret the phylogenetic trees based on HIV DNA from pairs of patients.

· Discuss the implications of having many clones of HIV in each individual patient.

Problem Solving

Part 3-DNA Analysis of HIV

Time Required: two 40-minute periods

Teacher should:
1. Remind students of the utility of looking at DNA sequence data using Biology Workbench.

2. If necessary, give a brief explanation of the types of genes that are contained in the HIV genome.

3. Pass out handout "The Markham, et al., HIV-1 env Sequence Data Set" and allow the students to read and mark up their copies of the document. (Sam Donovan et. al., Beloit College)


The Markham et al. HIV-1 env Sequence Dataset

Richard Markham and his colleagues (1998), published some research on the pattern of HIV evolution and the rate of CD4 T-cell decline in the Proceedings of the National Academy of Sciences. In addition to the journal article they submitted 666 nucleotide sequences to the GenBank database. They studied a 285 base pair region of the env gene. The gene product, membrane protein gp120, binds to the CD4 receptor site on T-lymphocytes and is involved with the entry of the virus into those cells. Markham et al. followed the evolution of this viral gene sequence in 15 subjects by collecting blood samples at six month intervals for up to four years. For each visit all the forms of the gene (clones) were sequenced and CD4 T-cell counts were made. This data set provides a rich resource for looking closely at the patterns of change in HIV over time.


NOTE: Summary table of information available on the subjects studied in Markham et al. (1998).

1 The CD4 count for time 1 is reported in Table 1. of Markham et al. (1998), the others values are estimated from the Figure 1. of the same publication.
2 The paper reports 5 visits for subject 2, only 3 visits were identified in the GenBank records.

4. Discuss the following:

What questions do you have based on the data set?
What kinds of questions could you answer by examining this data set?
What additional information would you want to know?

NOTE: The number of clones listed for each visit is the number of new clones found at each visit, so the total number of clones is the total number of different clones that were identified in each patient.

If student screens in the Biology Workbench are not showing their commands as buttons, then scroll up to the top of the pages where the title screen is located and click on the area labeled "click here to toggle between menus and buttons" until all the commands are shown as buttons.

5. Have students choose one question that each would like to answer from the above discussion.

6. Have students look over the summary data set and choose two subjects whose data might best help them answer their questions.

7. Pass out "Analyzing DNA Sequences for HIV env Protein" worksheet and have students follow the directions, and answer the italicized questions on the back of the sequence alignment printout.

Analyzing DNA Sequences for HIV env Protein



1. Open Netscape Navigator application.

2. Type the following URL into the Location box into the navigator window.



3. Click on the hotlink "Enter the Biology Workbench 3.2," which is blue and is large and underlined. This will bring up a small screen.

4. Supply your username and password.

5. Click on the "OK" button. This will give you a new screen.


6. Scroll down and click on the "Session Tools" button.

7. Check to make sure that all the commands are shown as buttons. If you are having trouble, ask your teacher.

8. Click on the "NEW" button.

9. At the next screen, name the session "HIV env" in the white box to the right of the words "Session Description."

10. Click on the "Start New Session" button.


11. Click on the "Nucleic Tools" button.

12. Scroll down and click on the "Add" button in the middle of the top line of buttons.

13. Click the "Browse" button.

14. Find the Desktop and double click on the "HIV env Sequences" folder. This will open the folder. Go to the popup menu for "Files of type:". Select "All Files" from the menu. This will bring up the data for all subjects. Choose your first subject by double clicking on that subject's number.

15. Click on the "Upload File" button. At this point, you will be able to see the sequences on your screen.

16. IMPORTANT!!!! Click the "SAVE" button at the top of the page.

17. Repeat steps 12-16 to add the data for a second subject.


18. Click on 4 DNA sequences PER SUBJECT to activate them. A small checkmark should appear in the box to the left of all the sequences that you will want to analyze. You should have eight total checkmarks.

Note: The names of the files will look like the following: S10V5-6. This stands for subject 10, visit 5, clone 6.

19. Click on the "CLUSTALW" button on the right of the second row of buttons at the bottom of the screen. This will give you a new screen with the selected sequences listed.

20. On this screen, click the "Submit" button.

21. Go to the "File" menu and print the sequence alignment. Write your name on the printout. Use a highlighter to mark those areas where the 8-10 sequences are different.

22. Answer the following questions on the back of the printout.
A. Does there seem to be any pattern to the mutations in the sequences?

B. Compare the sequences between the two individuals. How are they similar and how are they different?



23. Scroll to the top of the page and click on the "Import Alignment(s)" button.

24. In the next screen, click in the box to the left of "CLUSTALW-Nucleic" to activate the set of aligned sequences.

25. Click on the "DRAWGRAM" button.

26. Click on the "Submit" button. Then scroll down to see your tree.

27. Print your tree by choosing "Print" under the "File" menu.
C. How did your tree compare to that of your neighbors? Are both trees consistent with each other?

D. Using at least two phylogenetic trees, answer your original research question in a complete paragraph.

E. How does your data highlight the difficulties facing those who are seeking a cure or treatments for AIDS?


8. Have students complete post-project reflection.


Barnett, Tony and Blaike,Piers. AIDS in Africa: Its Present and Future Impact. New York: The Guilford Press. 1992.

Richard Markham and his colleagues (1998), published research on the pattern of HIV evolution and the rate of CD4 T-cell decline in the Proceedings of the National Academy of Sciences



CDC - http://www.cdc.gov/hiv/pubs/facts.htm
UN - http://www.unaids.org
BBC - http://www.bbc.co.uk/worldservice/sci_tech/teachers/health

Biology WorkBench - http://workbench.sdsc.edu



Answer the following questions in complete sentences.

1. When you hear the terms HIV and AIDS, what comes to mind?

2. In the future what do you think you will remember the most about this project? Why?

3. Evaluate your work habits throughout this project (i.e., timeliness, cooperation with others, class participation, ability to stay on task).

4. Was there anything you were uncomfortable with during this project?

5. How do you think that this project could be improved in the future?