Zachary T. Goldstein Week 11
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- The purpose of this week's lab is to continue working on, and finalize our HIV 1 Structure project for Week 12 class. We will finish the interpretation of our results and add background and future work slides to our presentation. Background work on amino acid properties and highly variable regions along the V3 loop will also be continued this week.
- We practiced some of our presentation in front of the class and received feedback on how we can strengthen our slides.
- Using papers previously assigned in class we compared the "nonconsensus" regions of our gp120 protein to highly variable regions found by other researchers.
- Background on the 20 standard amino acids shows the varying properties exhibited by all of them (ex: nonpolar, polar, acidic, basic)
- We redefined our question into three distinct parts:
- Does a low dS/dN ratio value result in high amino acid variation?
- Do subjects with low dS/dN ratios vary from each other?
- Do the sites of variation have non-conservative mutations?
- Titles of many slides were shortened to fit grading criteria of two lines maximum
- Color coding was added to the subject selection slide to make it more apparent which subjects belonged to the previously defined nonprogressor, moderate progressor, and rapid progressor groups in Markham et al. (1998).
- We added a slide on techniques used in BoxShade on how to alter the background colors and respective algorithms for defining nonconsensus segments.
- BoxShade figures were re-cropped and placed side-by-side to show better comparisons between amino acid sequences.
- Nonconsensus regions were highlighted on slides to make it more visually appealing and understandable.
- 3D structure was reanalyzed using 3DcN to look at where the nonconsensus regions were located within the protein. A space filling model was used and the regions in question were found to lie on the outside of the protein.
- An outline was established after all slides were nearly completed.
HIV 1 Structure Presentation: Media:HIV_Structure_Project_Zach_And_Jordan.pdf
- Throughout this weeks assignment our HIV 1 Structure project was completed for the presentation in Week 12. We received good feedback in class on what we should change in our slides. We shortened titles, reorganized our guiding question and figures, and figured out how to properly analyze our results. Six regions were found to exist as "nonconsensus" segments along the gp120 protein when we compared primary sequences from eight subjects, and six clones from each subject using Biology Workbench software. Using 3D modeling we found three of these regions exist along the V3 loop and three regions exist outside of the loop, but on the surface of the protein. The locations of these regions was understood to be very similar to variable regions found in other studies. Our presentation was completed and uploaded to this week's assignment.
- I received help on this assignment in class from User: Kam D. Dahlquist in altering titles and our guiding questions to be more succinct.
- I received help on this assignment outside of class over the weekend from User: Jordan T. Detamore in finalizing our presentation and working specifically on analyzing our results compared to other studies.
- While I received help on this assignment everything completed on this page is my work and was not coped from anybody else.
Zachary T. Goldstein 16:37, 8 November 2016 (EST)
- Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-AIDS drug design. Journal of Biomolecular Structure and Dynamics, 27(2), 179-193. DOI: 10.1080/07391102.2009.10507308
- 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
- Biology Workbench
- 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 11
All class assignments:
- Week 1 Assignment
- Week 2 Assignment
- Week 3 Assignment
- Week 4 Assignment
- Week 5 Assignment
- Week 6 Assignment
- Week 7 Assignment
- Week 8 Assignment
- Week 9 Assignment
- Week 10 Assignment
- Week 11 Assignment
- Week 14 Assignment
- Week 15 Assignment
All individual assignments:
- Zachary T. Goldstein Week 2
- Zachary T. Goldstein Week 3
- Zachary T. Goldstein Week 4
- Zachary T. Goldstein Week 5
- Zachary T. Goldstein Week 6
- Zachary T. Goldstein Week 7
- Zachary T. Goldstein Week 8
- Zachary T. Goldstein Week 9
- Zachary T. Goldstein Week 10
- Zachary T. Goldstein Week 11
- Zachary T. Goldstein Week 14
- Zachary T. Goldstein Week 15
All shared journals:
- BIOL368/F16:Class Journal Week 1
- BIOL368/F16:Class Journal Week 2
- BIOL368/F16:Class Journal Week 3
- BIOL368/F16:Class Journal Week 4
- BIOL368/F16:Class Journal Week 5
- BIOL368/F16:Class Journal Week 6
- BIOL368/F16:Class Journal Week 7
- BIOL368/F16:Class Journal Week 8
- BIOL368/F16:Class Journal Week 9
- BIOL368/F16:Class Journal Week 10
- BIOL368/F16:Class Journal Week 11
- BIOL368/F16:Class Journal Week 14
- BIOL368/F16:Class Journal Week 15