This investigative case module was prepared as part of a BioQUEST faculty development workshop entitled Selected Cases at Beloit College in June 1999. The cases, resources, and implementation strategies were developed by participants for use with their own students. We invite you to adopt and adapt the following materials.

The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Investigative Cases
The Case: A Multidimensional Study of HIV

Part 1. Readings taken from Barnett, Tony and Blaike,Piers. AIDS in Africa: Its Present and Future Impact. New York: The Guilford Press. 1992. (Suggested by Marion Fass, Beloit College)

Excerpts of two of these cases:

Case 1
"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..."

Case 2
"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.

TIME, Inc. MEMO: To High School Biology Students
Re: URGENT!!! Special Issue on HIV

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.

Case Author:
Jo Ann Lane St. Ignatius High School
Janice Chen North Shore High School

Case Analysis

To help you conduct your preliminary research, consider:
What do you KNOW about HIV and AIDS?
What do you WANT TO KNOW about HIV and AIDS?

Option: Include a know / need to know chart like the one below:

What do you know?
What do you need to know?

Learning Goals


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.



Investigations and Activities

See Implementation



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

Note: These three sites have excellent information.

Biology WorkBench -

Students will usually obtain additional references or resources
to help answer or explore their questions.

Special Data Items

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.

The complete Data Table is available at:

To use Biology Workbench with nucleic acid sequences, see file: AnalyzingDNA

1. MarkhamData.jpg
2. AnalyzingDNA.doc


Student Products

Know/Need to Know Charts
Biology WorkBench ClustalWs, Trees, Alignments
See Implementation

Assessment and Evaluation Plan

See Implementation



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.

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.
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 above.

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)

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?

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.
8. Have students complete post-project reflection.

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?

Course name:
Likely sequence in syllabus:
Time during term:
End of year
Classroom and Computer Lab
Students in course:
High School
Collaborative elements:
Group work, publication
Additional notes:



HIV Problem Space

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