Isai Lopez Individual Journal 5

Purpose

To construct an annotated bibliography for our HIV project and to begin work on the project itself, documenting steps as we continue.
ILopezAnnotatedBibHIV.pdf
ILopezPartIIAnnotatedBib.pdf

We are going to have to compare sequence data between species we've found where the env gene has been sequenced. The FIV is proving to be most helpful for this.
We will need similar data for other species of animals to humans to compare, so sequencing information alone will not be enough. We need to find trends of CD4+ T cell changes over time, hopefully decline, in order to compare the two.
We will compare sequences of RNA between subjects in the Markham study using the ClustalW tool
We can also use the ClustalW tool to build an unrooted tree to compare species, and compare divergence between the clones found in each study, to see if similar patterns of divergence are found.
We will calculate θ values for the data we have on the set of subjects we choose and build a table.
Using dS/dN and comparing to CD4+ T cell rate of decline, we may be able to say something about the similarities between how immunodeficiency viruses act on host species even when they are different organisms entirely.

As of now, phylogenetic trees for FIV positive cats have been found within literature. It will take some digging to find the pieces of RNA that are similar/ analogous to their human counterparts and compare them. However, the research I've done as of now gives me confidence that this part of the assignment will be completed without an enormous amount of difficulty.

I worked with partner Matthew R Allegretti in class and we texted multiple times outside of class to work on this project and direct it, as well as to make sure we had different citations
Kam D. Dahlquist answered questions in class regarding our project and suggested types of articles we should look for
while I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Isai Lopez 02:29, 4 October 2016 (EDT):

Week 5 Homework Page
Bęczkowski, P. M., Hughes, J., Biek, R., Litster, A., Willett, B. J., & Hosie, M. J. (2014). Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology, 11, 80. http://doi.org/10.1186/s12977-014-0080-1
Kenyon, J. C., & Lever, A. M. L. (2011). The Molecular Biology of Feline Immunodeficiency Virus (FIV). Viruses, 3(11), 2192–2213. http://doi.org/10.3390/v3112192
Kraase, M., Sloan, R., Klein, D., Logan, N., McMonagle, L., Biek, R., ... & Hosie, M. J. (2010). Feline immunodeficiency virus env gene evolution in experimentally infected cats. Veterinary immunology and immunopathology,134(1), 96-106. 10.1016/j.vetimm.2009.10.015
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. Proceedings of the National Academy of Sciences USA, 95(21), 12568-12573. DOI: 10.1073/pnas.95.21.12568
Sanou, M. P., Roff, S. R., Mennella, A., Sleasman, J. W., Rathore, M. H., Yamamoto, J. K., & Levy, J. A. (2013). Evolutionarily Conserved Epitopes on Human Immunodeficiency Virus Type 1 (HIV-1) and Feline Immunodeficiency Virus Reverse Transcriptases Detected by HIV-1-Infected Subjects. Journal of Virology, 87(18), 10004–10015. http://doi.org/10.1128/JVI.00359-13