This project was prepared as part of a BioQUEST faculty development workshop entitled Mathematical and Computational Biology Education at University of Puerto Rico - Rio Piedras in July 2004. 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:

Upcoming events               BEDROCK Problem Spaces

Authors          Audiences          Overview           Materials          Resources           Future Directions



Brynne Bryan
University of Puerto Rico - Rio Piedras

Ivette Perez Chiesa
University of Puerto Rico - Rio Piedras


Possible Audiences:

Undergraduate students of the General Genetics course at the Department of Biology  


Brief Overview:

HIV is a retrovirus which infects CD4 T cells in humans. It has a high rate of mutation which makes the development of a vaccine very difficult. Furthermore, an individual may be infected with a diversity of HIV virus as reflected by their membrane protein gp120. The degree of diversity may play a role in the course of infection.

Does virus diversity increase with time in an HIV infected individual?

Is diversity at the beginning of infection correlated with the decline of CD4 within three years?

We found no statistically significant differences between PIs. With all of the data (including duplicate samples), we did find that there is a statistically significant difference between sequences: 1) affected versus unaffected subjects at the end of the trial, 2) at the beginning and at the end for affected subjects, and 3) and at the beginning and the end for unaffected subjects.  


Project Materials:

The data for this study was taken from Markham et al., (1998). Six HIV infected subjects were chosen for this study. Their CD4 counts and 666 nucleotide sequences of the env gene, from the first visit (A) and from one visit three years later (B), were used for the analysis. Workbench was used to convert the DNA sequences to amino acid sequences and a dendogram was obtained with ClustalW. We define diversity (??) as the average genetic distance between samples from the same visit. The data was analyzed with T-test.  


Resources and References:

Workbench website:

Markham, R. B. et al., 1998 Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. USA 95:12568-12573.  


Future Directions:

Add more data

Determine if there is a variant the predominates until the last visit