Isai Lopez Individual Journal 11

Purpose

The purpose for this week’s assignment was to take the feedback from our “work in progress” presentations from last week and finish work on the HIV-1 structure presentation. The work includes adding relevant background information slides about the function of the gp120 protein in viral entry as well as listing limitations of the study and implications of the results. Lastly, we want to highlight specific portions of the sequences that are relevant to our study to more easily visualize the amino acid residues we worked with.

We used notes and suggestions from last week’s practice run to guide the development of our PowerPoint Presentation
We wrote up an outline slide with detailed descriptions of the process of the experiment which would serve as a road map throughout the presentation
Included figures highlighting the importance of side chain interactions in producing the tertiary/ quaternary structure that allows for viral entry using gp120 proteins.
Refined the question we hoped to answer and gave our prediction, including information from the Markham study that led us to our question.
Specified the clones we chose for sequence alignment and clarified our reasons for doing so.
We also outlined the statistical techniques we used to answer our question.
We built a clear table detailing the outcome of our statistical analysis and provided p-values to support our findings
Produced a multiple sequence alignment and used Boxshade to emphasize the residues that were most pertinent to our study.
- We then highlighted these specific residues using the 3DcN program to provide a visual representation of the amino acids we analyzed.
A second slide was added from the 3DcN program that zoomed in on a distinct residues that coded for one of the more variable regions of the sequence.
We then listed the limitations of our study and offered suggestions for future studies.

For this week’s assignment, we went back and revised the work we had started in answering our question for the HIV-1 structure presentation. In doing this, we added background information on the structure of gp120, clarified how we arrived at our question and how we answered it, and provided figures detailing the residues that we used for our protein analysis using both Boxshade and 3DcN. It turned out that, under the conditions we used for our tests, there was no association between CD4 T cell decline and amino acid changes in the gp120 gene of HIV-1. Lastly, we offered reasons for why our results came out as they did, and what we could do if we weren’t limited in terms of time or resources.

I worked closely with my partner Colin Wikholm throughout the process of revising and completing our powerpoint. We are roommates and worked at home side by side.
Using feedback from Kam D. Dahlquist, we were able to refine out powerpoint and make it more effective for presentation.
While I received help on this assignment everything completed on this page is my work and was not coped from anybody else.
Isai Lopez 02:31, 15 November 2016 (EST):

Biology Workbench
Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659. DOI: 10.1038/31405
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
Week 11 Assignment Page