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.

1. How do the various viral proteins associated with HIV work to infect a host cell?
2. How is HIV either similar or different from other retro-viruses?
3. 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).

1. 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:

1. A comparative study of HIV-1 clade C env evolution in a Zambian infant with an infected rhesus macaque during disease progression
2. Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women
3. HIV-1 evolution in gag and env is highly correlated but exhibits different relationships with viral load and the immune response
4. Relationship of Injection Drug Use, Antiretroviral Therapy Resistance, and Genetic Diversity in the HIV-1 pol Gene
5. Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression

Preparation for Week 4 Journal Club

Question 1

Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.

1. Nonsynonymous mutation: A nucleotide substitution that that changes the amino acid specified (i.e., AGC to AGA, or serine Æ arginine). (Compare with synonymous mutation which is a nucleotide sustituion which does not change the amino acid specified). http://www.whfreeman.com/thelifewire6e/content/glossary_htm/gloss_n.html
2. Variant: a group of organisms within a species that differ in trivial ways from similar groups; a new strain of microorganisms. http://www.biology-online.org/dictionary/Variant
3. Frequency dependent selection is the term given to an evolutionary process where the fitness of a phenotype is dependent on its frequency relative to other phenotypes in a given population. In positive frequency dependent selection, the fitness of a phenotype increases as it becomes more common. In negative frequency dependent selection, the fitness of a phenotype increases as it becomes less common. Negative frequency dependent selection is a particular mechanism of balancing selection. http://en.wikipedia.org/wiki/Frequency_dependent_selection
4. 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. Following seroconversion, a person tests positive in tests based on the presence of antibodies (such as ELISA). http://www.medterms.com/script/main/art.asp?articlekey=9388
5. Peripheral Blood Mononuclear Cell (PBMC) is any blood cell having a round nucleus[1]. For example: a lymphocyte, a monocyte or a macrophage. These blood cells are a critical component in the immune system to fight infection and adapt to intruders. The lymphocyte population consists of T cells (CD4 and CD8 positive ~75%), B cells and NK cells (~25% combined). http://en.wikipedia.org/wiki/PBMC
6. Consensus Sequence: In molecular biology and bioinformatics, a consensus sequence is a way of representing the results of a multiple sequence alignment, where related sequences are compared to each other, and similar functional sequence motifs are found. The consensus sequence shows which residues are most abundant in the alignment at each position. http://en.wikipedia.org/wiki/Consensus_sequence
7. Monophyletic means common descent form a single ancestor. Biologists have introduced a taxonomy. If there is a group, that is made of a common ancestor (or parent), and all its descendants (children), they call that group monophyletic (Greek: "of one race"). http://simple.wikipedia.org/wiki/Monophyletic
8. Divergent evolution: the accumulation of differences between groups which can lead to the formation of new species, usually a result of diffusion of the same species adapting to different environments, leading to natural selection defining the success of specific mutations. Primarily difussion is the basis of molecular division can be seen in some higher-level characters of structure and function that are readily observable in organisms. For example, the vertebrate limb is one example of divergent evolution. The limb in many different species has a common origin, but has diverged somewhat in overall structure and function. Alternatively, "divergent evolution" can be applied to molecular biology characteristics. This could apply to a pathway in two or more organisms or cell types, for example. This can apply to genes and proteins, such as nucleotide sequences or protein sequences that derive from two or more homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication within a population) can be said to display divergent evolution. Because of the latter, it is possible for divergent evolution to occur between two genes within a species. http://en.wikipedia.org/wiki/Divergent_evolution
9. Phylogenetic tree: A tree showing the evolutionary relationships among various biological species or other entities that are known to have a common ancestor. In a rooted phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and the edge lengths in some trees correspond to time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed. http://en.wikipedia.org/wiki/Phylogenetic_tree
10. Primer: a strand of nucleic acid that serves as a starting point for DNA replication. They are required because the enzymes that catalyze replication, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. In most cases of natural DNA replication, the primer for DNA synthesis and replication is a short strand of RNA (which can be made de novo). This RNA is produced by primase, and is later removed and replaced with DNA by a repair polymerase. Many of the laboratory techniques of biochemistry and molecular biology that involve DNA polymerase, such as DNA sequencing and the polymerase chain reaction (PCR), require DNA primers. These primers are usually short, chemically synthesized oligonucleotides, with a length of about twenty bases. They are hybridized to a target DNA, which is then copied by the polymerase. http://en.wikipedia.org/wiki/Primer_(molecular_biology)

• Question 2: Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.

1. Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, and Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12568-73. DOI:10.1073/pnas.95.21.12568 |

Janelle N. Ruiz

Class Links

BIOL 398.01/Spring 2010

Journal Assignments

Janelle N. Ruiz Assignment 2	Janelle N. Ruiz Assignment 5	Janelle N. Ruiz Assignment 8	Janelle N. Ruiz Assignment 12	Janelle N. Ruiz Assignment 14
Janelle N. Ruiz Assignment 3	Janelle N. Ruiz Assignment 6	Janelle N. Ruiz Assignment 9	Janelle N. Ruiz Assignment 13	Janelle N. Ruiz Assignment 15
Janelle N. Ruiz Assignment 4	Janelle N. Ruiz Assignment 7	Janelle N. Ruiz Assignment 11

• 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

• 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