Matthew R Allegretti Week 11
Week 11 Assignment
Purpose
- To construct a presentation for our research project.
Methods and Results
Subject 4
- 3 Clones
- 13 Clones
Subject 9
- 5 Clones
- 11 Clones
Subject 11
- 7 Clones
- 9 Clones
Subject 14
- 6 Clones
- 10 Clones
- 64 Total Clones
Variability
We measured variability at each position by identifying the locations with major mutations at them according to boxshade. We also identified positions with more than one major mutation present. Both were found by comparing them to the consensus sequence from Huang et al. (2005).
Data and Files
From Week 10
- Media:Matthew R Allegretti Markham S4V1 sequences.docx
- Media:Matthew R Allegretti Markham S4V4 sequences.docx
- Media:Matthew R Allegretti Markham S9V1 sequences.docx
- Media:Matthew R Allegretti Markham S9V4 sequences.docx
- Media:Matthew R Allegretti Markham S11V1 sequences.docx
- Media:Matthew R Allegretti Markham S11V4 sequences.docx
- Media:Matthew R Allegretti Markham S14V1 sequences.docx
- Media:Matthew R Allegretti Markham S14V4 sequences.docx
- Presentation
- Subject 4 sequence changes
From Week 11
- Media:AV-MA-s4-spacefill-allmutations.png
- Media:AV-MA-s4-spacefill-majormutations.png
- Media:AV-MA-s4-spacefill-multimajormutations.png
- Media:AV-MA-s9-spacefill-allmutations.png
- Media:AV-MA-s9-spacefill-majormutations.png
- Media:AV-MA-s9-spacefill-multimajormutations.png
- Media:AV-MA-s4-boxshade-Week11.PNG
- Media:AV-MA-s9-boxshade-Week11.PNG
- Week 12 Presentation
Conclusion
We discovered that all 4 subjects studied contained major mutations at multiple positions within the amino acid sequence. We analyzed the structural locations of each major mutation and attempted to analyze how they may affect the overall function of the protein. Upon further research, we discovered that site 317 was a key position linked with antibody interactions, Edlefsen et al. (2015). In both of the rapid progressors, this site was unchanged from the Huang et al. (2005) sequence. In both moderate progressors, however, all subjects had an identical T to A mutation. I believe that this locations may be what distinguishes the difference in progression groups between these subjects, despite having identical dS/dN values.
References
- Week 10
- Pulled my progress from last week onto this week's page
- Edlefsen, P. T., Rolland, M., Hertz, T., Tovanabutra, S., Gartland, A. J., Magaret, C. A., et al. (2015). Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol, 11(2), e1003973.
- Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., ... & Wyatt, R. (2005). Structure of a V3-containing HIV-1 gp120 core. Science, 310 (5750), 1025-1028.
- Kirchherr, J. L., Hamilton, J., Lu, X., Gnanakaran, S., Muldoon, M., Daniels, M., Kasongo, W., et al. (2011). Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology, 409(2), 163-174. DOI: 10.1016/j.virol.2010.09.031
- 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
Acknowledgements
- Anu Varshneya
- We communicated electronically and met outside of class once.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Useful links
- Stem Cell Overview
- Template
- Student Page
- Week 1 Instructions
- Journal Week 1
- Week 2 Instructions
- Week 2
- Journal Week 2
- Week 3 Instructions
- Week 3
- Journal Week 3
- Week 4 Instructions
- Week 4
- Journal Week 4
- Week 5 Instructions
- Week 5
- Journal Week 5
- Week 6 Instructions
- Week 6
- Journal Week 6
- Week 7 Instructions
- Journal Week 7
- Week 8 Instructions
- Week 8
- Journal Week 8
- Week 9 Instructions
- Week 9
- Journal Week 9
- Week 10 Instructions
- Week 10
- Journal Week 10
- Week 11 Instructions
- Week 11
- Journal Week 11
- Week 12 Instructions
- Week 14 Instructions
- Week 14 Assignment Part 1 and 2
- Journal Week 14
- Week 15 Instructions
- Week 15
- Journal Week 15
- My user page