Shivum Desai Journal Week 9

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Week 9 Individual Journal


The purpose of this week's journal club is to determine a scientific question and project structure for a research project on HIV that focuses on amino acid change and HIV function.


  1. The first step taken this week involved the determination of a scientific question for our HIV evolution project based upon amino acid structure and the HIV virus.
  2. Next a hypothesis was formed and a general outline of the experiment was formed, including the subjects that are too be used and why.
    • The subjects were determined because of their distance apart from each other in time. We elected based upon the beginning of the project and the end.
  3. Next I answered questions 1 through 3 in the HIV starchier in-class activity. This included translating a DNA sequences using the ExPASY translate tool, using Unipot knowledgeable to research HIV and gp120, and then using the predict protein server to analyze the V3 region from Markham et al. paper.
  4. Lastly, the wikipage was formatted correctly and an acknowledgments sections was added. There were no data files that needed to be attached this week.

Scientific Conclusion

This weeks journal club involved two different assignments that had related content. The first step included determining a scientific question, purpose, hypothesis, and methods for a future HIV evolution project involving amino acid change and disease progression. This section was careered out quite easily with the help of Dr. Dahlqvist who helped to clarify the scientific question when it was in its infancy stages. After this was determined, I moved onto the In-class activity for which i started with the translation of a DNA sequence using the exPASY translate tool. This was interesting and I found out the reasoning to determine which of the six reading frames is the correct reading frame. The next step was using the UniPot Knowldgebase for HIV and gp120. The last step that was reached was using the Predict Protein to analyze the V3 region from the Markham et al. paper. The predict protein website was interesting and will be beneficial for the HIV evolution project because it determines the amino acids present in a amino acid chain and groups them, which will make it easier to determine the presence of amino acids and how they have mutated from the subjects first visit, to last visit.

Defining Your HIV Structure Research Project

Scientific Question

Is there a correlation between the mutation of a subject's amino acids, comparing first and last visits, and CD4 cell count.


It is hypothesized that the more mutations in a subjects amino acids from first visit to last, will correlate to a decrease in CD4 cell count.


For this experiment subjects 1 through 3 will be used. Specifically the first and last visits for each subject 1-3 and their corresponding clones. This results in the study of 51 DNA sequences. We did this because subjects 1 and 3 are rapid progress ors based on CD4 cell count and subject 2 is a non progressor. Thus, if my hypothesis is true we should see an obvious decline in two of the subjects and we can use those examples to compare to the nonprogressor subject, subject 2.

HIV Structure In-class Activity

1.Convert one of your DNA sequences into protein sequences using either the NCBI Open Reading Frame Finder or the ExPASY Translate tool.

  • The correct frame is the reading from that does not have a start or stop codon because this area under question is the middle of the gp120 area, not the beginning or end. It is the V3 region.
  • Sequences obtained for experiment.

2. Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgebase (UniProt KB). UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases.

  • I get 206, 278 results when I search "HIV gp120" together.
  • P04578: The function of the Env gene is given. Its molecular function and biological process. It also gives protein names, gene names, organism, taxonomic lineage, virus host, proteomes. It also gives the general sub cellular location and its general interactions with other molecules.

3. We are going to use the PredictProtein server to analyze just the V3 region from Markham et al. (1998).

  • The main information provided by this system is the ratio and amount of amino acids present in ta AA chain relative to one another. This will be beneficial to my HIV evolution project. It also provides a projection of the amino acids and there relative positions along a DNA strand.

Useful Links

Useful Links


I would like to thank my partner Courtney Merriam for her help collaborating on this weeks HIV evolution project. Also I would like to thank Dr. Dahlquist for her guidance in formulating a plan and purpose for our future HIV evolution project. Lastly, While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.


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

BIOL368/F16:Week 9