Janelle N. Ruiz Assignment 3
In Class Activity
- Question 1: Record in your online notebook (your individual week 3 journal page) a summary paragraph of the information you already know about HIV (it's OK if you don't know much yet).
Human Immunodeficiency Virus (HIV) is a retrovirus, more specifically a lentivirus, which means that its genetic material is composed of RNA rather than DNA. To infect a host cell, HIV utilizes its RNA in conjunction with reverse transcriptase (as well as other viral proteins) to integrate its genome into an infected host’s DNA. In this way, the virus is able to exploit the mechanisms and cellular components of the host’s cell in order to transcribe more viral RNA/protein and ultimately infect more cells. The disease caused by HIV is called Acquired Immune Deficiency Syndrome which causes devastating immune dysfunction. HIV primarily infects a host’s CD4+ T cells, which are central to proper function of the entire adaptive immune system; however, HIV can also infect macrophages and dendritic cells. HIV is transmitted through bodily fluids via sexual contact, intravenous drug use, blood transfusions, etc. It is considered a world-wide pandemic, with the majority of infections being present in Sub-Sahara Africa where both access to healthcare and proper education regarding viral transmission and prevention are lacking.
- Question 2: Write three questions (or more) that you have about HIV that you would like answered.
- How do the various viral proteins associated with HIV work to infect a host cell?
- How is HIV either similar or different from other retro-viruses?
- What is the current status of progress on the HIV vaccine and/or how is the scientific community currently exploiting the mechanisms of "elite controllers" of HIV infection to produce a vaccine that would protect against the devastating effects of the virus?
- Question 3: In Chapter 2 of Bioinformatics for Dummies, follow the protocol on "Becoming an Instant Expert with PubMed/Medline", using the examples shown in the book. Notice the differences between the instructions and screenshots shown in the book and what you see on today's version of PubMed.
The layout of PubMed has changed slightly since the Bioinformatics book was published. For example, suggestions for articles similar to the search article are given. Also, the links to reviews, etc have changed location and format on the screen. When I type in dUTPase, 404 references rather than 200 references are found. Though the book states that on the Results list, the author's name is able to be clicked, in fact, now, the title of the article must be clicked before you are able to link to the authors' names (though they are still shown on the screen).
When I typed "Abergel", 100 more results came up than are listed in the book. Also, when "Abergel dUTPase" was inputted, two results rather than one were found.
Instead of searching with the "limits" link, you know need to go to "advanced search" to narrow your search results to specific categories.
- Question 4: Now use your new skills to find a recent scholarly review about the HIV virus. Record the full citation of the review you found on your journal page using the wiki syntax. (Hint: you can see an example of how to use it in the source for this page.) Compare your search results with Google Scholar and the ISI Web of Science (a commercial site that LMU subscribes to).
- Hariri S and McKenna MT. Epidemiology of human immunodeficiency virus in the United States. Clin Microbiol Rev. 2007 Jul;20(3):478-88, table of contents. DOI:10.1128/CMR.00006-07 |
The three search engines/online databases gave me many results; however I thought that PubMed gave me the best results in terms of specificity when I used the "advanced search" features. Google Scholar did not give me results in the order of most recent to least recent, like Pubmed and Web of Science. With Google Scholar, you need to restrict the search settings to do this, whereas the other databases do this automatically. Though I restricted my searched on PubMed and Web of Science to FullText, when I did not do this, typically I could find the fulltext article on Google Scholar when I could not find it on PubMed and/or Web of Science.
- Question 5: Using ISI Web of Science perform a prospective search on the Markham et al. (1998) article to find out what articles cite that article since its publication in 1998.
- The Markaim article was cited 52 times. The top 5 articles that included the citation were:
- A comparative study of HIV-1 clade C env evolution in a Zambian infant with an infected rhesus macaque during disease progression
- Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women
- HIV-1 evolution in gag and env is highly correlated but exhibits different relationships with viral load and the immune response
- Relationship of Injection Drug Use, Antiretroviral Therapy Resistance, and Genetic Diversity in the HIV-1 pol Gene
- Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
Class Links
Journal Assignments
- Shared Journal
- BIOL398-01/S10:Class Journal Week 2
- BIOL398-01/S10:Class Journal Week 3
- BIOL398-01/S10:Class Journal Week 4
- BIOL398-01/S10:Class Journal Week 5
- BIOL398-01/S10:Class Journal Week 6
- BIOL398-01/S10:Class Journal Week 7
- BIOL398-01/S10:Class Journal Week 8
- BIOL398-01/S10:Class Journal Week 9
- BIOL398-01/S10:Class Journal Week 11
- BIOL398-01/S10:Class Journal Week 12
- BIOL398-01/S10:Class Journal Week 13
- Assignments
