Ryan N. Willhite Week 3

In-Class Activity
BIOL398-01/S10:Week 3

What I know about HIV

I know that this is a virus that is extremely difficult to cure because of such diversity in each person's immune system. There are some people that are immune to this virus. They may acquire this virus, however, the virus is somewhat dormant and the effects of the virus do not show up. These people are being tested so that scientist can see why this virus does not have the same effects it does in others. This virus is transmitted sexually as well as through cuts in the skin, etc. This virus can be lethal and as of now incurable although treatment is available to slow down the processes of this virus. Also, I know that this disease involves T-cells in our body.

Questions I have about HIV
 * 1) I have heard about the people who have the disease who show know symptoms or are not affected by the disease, where are these people located and what do we know about their immunity to the virus?
 * 2) What exactly happens to the body once acquiring this virus?
 * 3) How do the drugs that slow down the process work? What are the side effects?
 * 4) What are all the different ways people have acquired this virus?
 * 5) How do homosexual men acquire the virus?

Bioinformatics for Dummies Protocol Chapter 2


 * 1) www.ncbi.nlm.nih.gov/entrez/
 * After putting this site in, I was taken to another site different than PubMed, NCBI. I then tried dUTPase in the search engine on the website.
 * Nothing is coming up the same as in the book.
 * On the search engine, I have typed in examples from the book, and have gotten the hang of things on this site.
 * Google Scholar seems to be a much easier database to use. They gave me exactly what I wanted, using more specific search engines. It allows me to be a bit more specific in what I am looking for.
 * Google scholar helped me find articles that I was trying to find but could not on PubMed.
 * Although I loved how Google Scholar worked the best for me, there is also an advanced search in PubMed as well by going to advanced search, search builder and finally index for specific terms.
 * Search builder also allows one to search by journal or author, etc.
 * Go to advanced search and go to limit by topics, etc. This will allow one to only select review articles once going to type of articles.


 * 1) Paper1 pmid=20118674
 * 2) Paper2 pmid=20103765
 * 3) Paper3 pmid=19630581


 * The papers I found were so interesting, however, the last is I believe the only review article that I found eventually. I learned a great new way to find review articles using the advanced search.

Unfamiliar words in Markham Article

 * 1) seroconversion- The development of detectable antibodies in the blood directed against an infectious agent. It normally takes some time for antibodies to develop after the initial exposure to the agent.(MedicineNet.com)
 * 2) progressors- Someone who has been infected with the Human Immunodeficiency Virus (HIV) for seven to 12 years and eventually developing full blown AIDS.
 * 3) nonsynonymous mutations-A nucleotide substitution that that changes the amino acid specified
 * 4) nonprogressor-A non-progressor is someone who has been infected with the Human Immunodeficiency Virus (HIV) for seven to 12 years without developing full-blown AIDS (wisegeek.com)
 * 5) PBMC-Peripheral Blood Mononuclear Cell (freedictionary.com)
 * 6) epidemiologically- a branch of medical science that deals with the incidence, distribution, and control of disease in a population (merriam-webster.com)
 * 7) seronegative/positive- having or being a negative serum reaction especially in a test for the presence of an antibody (merriam-webster.com)
 * 8) predominance-being most frequent or common (merriam-webster.com)
 * 9) stratification-to form, deposit, or arrange in strata (merriam-webster.com)
 * 10) monophyletic-developed from a single common ancestral form (meeriam-webster.com)

Article Outline
a) Significance of the experiment b) Limitations in previous studies a) Methods used a) Main result b) Results in figure/tables c) Comparing Results
 * I. Introduction
 * The significance is to study to HIV-1 env sequence evolution
 * In previous studies they used techniques unsuitable for this type of experiment because it did not involved direct examination of sewuence patterns.
 * Another issue was that what was analyzed was very limited due to the number of time points in each subject.
 * II. Methods
 * 1) They created a study group of injection drug users.
 * 15 individuals were chosen
 * They were infected or injection drug users
 * 4 year observation
 * 1) Sequenced HIV-env genes using methods such as PCR.
 * Nested PCR was used to amplify the env gene
 * This is from PBMC because it is closely related to the viral RNA in the plasma
 * Different cycles of PCR were done at different temperatures
 * After PCR, cloning and sequencing were done
 * 1) reverse transcription-PCR was used in order to find the plasmid viral load
 * 2) Construction of phylogenetic trees
 * MEGA computer package was used
 * Taxons were labeled by color in order to record time of isolation as well as viewing replicates.
 * 1) Correlation analysis
 * units of analysis were defined
 * 1) dS/dN ratios were determined
 * averaged over all strains
 * 1) They compared the rate of change of divergence as well as diversity.
 * A regression line was placed of divergence and diversity over time
 * The slopes were then averaged
 * III. Results
 * There was a greater decline in CD4+ T cells when there were higher levels of both genetic diversity and divergence in the HIV-1 variants present.
 * Figure 1- Shows patterns of Cd4 T cell decline
 * it also shows diversity and divergence through nucleotide differences.
 * Table 1- This table shows annual changes in CD4 T cell number
 * It is a summary of seroconverters.
 * Figure 2- Compares the different professor groups
 * Those of the mean slope/year of intravisit geentic diversity as well as the mean slope/year of nucleotides mutated from the virus.
 * Figure 3- Phylogenetic tree from subject 9.
 * The horrizontal distance at the bottom of this tree shows a single mutation
 * Figure 4- Phylogenetic trees of the evolution of the virus in 4 randomly selected individuals (Markham).
 * Once again, the horizontal distance shows a single mutation.
 * In McDonald's experiment, there was a similarity when seeing greater diversity and divergence in the rapid progressors found in 3/5 of them studied.
 * However, differences in diversity were not conclusive since there were fewer time points were analyzed as well as not following from time of seroconversion.
 * In Wolinsky's experiment, there was an observation that concluded that perhaps genetic diversity is not associated with declining CD4 T cells.
 * Nowak's experiment was closest to the current study because it's results showed an association with viral genetic diversity and T-cell decline.


 * IV. Discussion
 * Overall, HIV-1- infected individuals with higher levels of genetic diversity and divergence showed signs of major CD4 T cell decline in the HIV-1 variants.