Salomon Garcia: Week 3

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Week 3 Entry

What are the certain aspects that I know about the HIV virus?

  • I know that HIV virus attacks the functions of the immune system. It is acquired sexually. It is a virus that can't be destroyed. There are ways to control some of the symptoms of the disease by treating it with certain drugs, but it doesn't assure that the symptoms won't comeback in a later time. Other than the basic issues related to the HIV virus such as in the case of health there aren't any other specific things that I know about the virus. I also know that people who have this disease are able to live a healthy life with no problems or symptoms as is the case of a famous basketball player. I also know that there are many studies gong on to try to find a way to cure this disease but at the moment not one exists.
  1. How did it arise?
  2. What are the current treatments against the virus?
  3. Are there any other viruses that have risen from the HIV virus?


  • In the first portion it's to familiarize with the website this is done by looking and reading the "Bioinformatics for Dummies Book" and entering the site name which is

screen looks like this:

PubMed Website
  • Then after this I typed in my search which was HIV virus and the search came out I clicked on one of the links and an abstract came up which looked something like this:
Abstract Picture
  • After this I found an article that seemed interesting and it followed certain things that I was looking for it had an abstract and a tab at the bottom of the abstract where it takes you to a page with the full text in pdf format:
Full Text Option


These were the articles that were acquired from PubMed

  • Edathodu J, Halim MM, Dahham MB, and Alrajhi AA. Mother-to-child transmission of HIV: experience at a referral hospital in Saudi Arabia. Ann Saudi Med. 2010 Jan-Feb;30(1):15-7. DOI:10.4103/0256-4947.59367 | PubMed ID:20103953 | HubMed [Paper2]
  • All Medline abstracts: PubMed | HubMed

    Article Assignment

    10 Definitions

    1. Seroconverting- Development of antibodies in blood serum as a result of infection or immunization.
    2. CD4 Tcells- A form of T lymphocyte with CD4 receptor on the cell surface that recognizes antigens of a virus-infected cell.
    3. Cytokines- A family of glycoproteins derived from human cells which normally has a role in fighting viral infections by preventing virus multiplication in cells.
    4. LTNP(Long-term nonprogressors)-are rare individuals who are infected with HIV, but whose infection progresses to AIDS only very slowly, after a long delay, or not at all.
    5. Antiretroviral- the group of medications used to treat HIV/AIDS
    6. Adenovirus vector vaccines- is a vaccine against Adenovirus and adenovirus is a disease that affects respiratory tract.
    7. HAART- When several such drugs, typically three or four, are taken in combination, the approach is known as highly active antiretroviral therapy, or HAART
    8. Microbicides- is any compound or substance whose purpose is to reduce the infectivity of microbes
    9. Azidothymidine- is a type of retroviral drug used to help in the fight against aids.
    10. CTL-that are capable of inducing the death of infected somatic or tumor cells; they kill cells that are infected with viruses
    11. CD8 T- T cell with CD8 receptor that recognizes antigens on the surface of a virus-infected cell and binds to the infected cell and kill it



    • The main point of this study was to continue the research that is currently going on with the HIV-1 virus. What are some of the new apects of the disease that are known.


    • For this experiment 15 individuals were selected at random for this study. there blood was tested every 6 months and they were catergoized into three categories: Rapid Progressors, Moderate Progressors, and Non-Progressors and this was based on their CD4 T cell decline.


    • No significant correlation between diversity and divergence.
    • There was CD4 T cell decline because there was an increase in diversity and divergence.


    • Table 1:
      • Seperated the 15 individuals that were used in this study into 3 different categories:Rapid Progressors, Moderate Progressors, and Non-Progressors.
      • Some changes occurred on the 15 individuals on their CD4 T cell count it ranged from 53 to 593 (increase to decrease).
      • Since subject 7 had a decline in a coarse of 392 days his CD4 T cell count never fell below the 200 range and the reason for why he remained in the Moderate progressor section of this study.
      • Categorization of subjects was based on the lowest level of CD4 T cell counts attained during the period of observation.

    BIOL 398-01: Bioinformatics Lab

    • Lab Journal
    Salomon Garcia: Week 2 Salomon Garcia: Week 6 Salomon Garcia: Week 11
    Salomon Garcia: Week 3 Salomon Garcia: Week 7 Salomon Garcia: Week 12
    Salomon Garcia: Week 4 Salomon Garcia: Week 8 Salomon Garcia: Week 13
    Salomon Garcia: Week 5 Salomon Garcia: Week 9 Salomon Garcia: Week 14

    • Shared Journal
    1. BIOL398-01/S10:Class Journal Week 2
    2. BIOL398-01/S10:Class Journal Week 3
    3. BIOL398-01/S10:Class Journal Week 4
    4. BIOL398-01/S10:Class Journal Week 5
    5. BIOL398-01/S10:Class Journal Week 6
    6. BIOL398-01/S10:Class Journal Week 7
    7. BIOL398-01/S10:Class Journal Week 8
    8. BIOL398-01/S10:Class Journal Week 9
    9. BIOL398-01/S10:Class Journal Week 11
    10. BIOL398-01/S10:Class Journal Week 12
    11. BIOL398-01/S10:Class Journal Week 13
    12. BIOL398-01/S10:Class Journal Week 14

    • Assignments
    1. BIOL398-01/S10:Week 2
    2. BIOL398-01/S10:Week 3
    3. BIOL398-01/S10:Week 4
    4. BIOL398-01/S10:Week 5
    5. BIOL398-01/S10:Week 6
    6. BIOL398-01/S10:Week 7
    7. BIOL398-01/S10:Week 8
    8. BIOL398-01/S10:Week 9
    9. BIOL398-01/S10:Week 11
    10. BIOL398-01/S10:Week 12
    11. BIOL398-01/S10:Week 13
    12. BIOL398-01/S10:Week 14