HIV - MIMM-386D Bioinformatics Project Human...

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MIMM-386D Bioinformatics Project Human Immunodeficiency Virus Fall 2009 - Winter 2010 Department of Microbiology and Immunology, McGill University Recommended Reading: The following provides you with references to start with. You may need information contained in these in order to write a solid report. We count on your curiosity to find more references to back your paper. Alternatively, you may talk with your TAs for further reading suggestions. 1. http://www.hiv.lanl.gov/ (The HIV Databases - One of the top sites on the web for HIV research and operated by the University of California. Explore the “Publications” section from the “Sequence Database”.) 2. Retroviruses, by Coffin, Hugues and Varmus, Cold Spring Harbor Lab Press (1997) and (since it’s a fairly large book) it is available online for free: 3. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=rv or just Google “retroviruses” 4. Journal of Antimicrobial Chemotherapy (2003) 51, 229-240 (A review article written by a group led by Mark Wainberg, a member of this department and world-renowned HIV scientist. The “Geo-graphical spread” section contains an outline of the geographical distribution of HIV Group M subtypes, useful for Part 2. The article is the first hit on Google when searching for “clade diversity”.) 5. Ou et al, Science, Vol 256, No 5060 (May 22, 1992), 1165-1171. (The article on which the bonus of this assignment is based. Find it in the Science Magazine (science.com) archives provided by JSTOR, to which McGill subscribes.) 6. http://www.rcsb.org/pdb/molecules/pdb33 1.html (The HIV reverse transcriptase was the molecule of the month at the Protein Data Bank in September 2002. Comes along with it, a nice walkthrough of RT’s structure.) 7. http://www.iasusa.org/resistance mutations/ (List of resistance mutations published by the International AIDS Society-USA.) 8. http://resdb.lanl.gov/resist db/ (Drug Resistance Database at Los Alamos) Introduction HIV and AIDS
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The Human Immunodeficiency Virus (HIV) was discovered jointly in the 1980s by Dr Luc Montagnier of France and Dr Robert Gallo of the USA. It is largely accepted by the scientific community as the causative agent of the Acquired Immunodeficiency Syndrome (AIDS). Retroviruses HIV is a member of the retroviridae family of RNA viruses. The name given to this class of viruses comes from the reverse transcription step of its life cycle when a retrovirus’ RNA genome is converted to DNA and consequently integrated into its host’s genome. One interesting story relating to this particularity of retroviral biology is the one of the evolution of amylase expression by salivary glands in primates. In 1990, a group from the University of Michigan proposed that a retrovirus inserted in the region upstream of a repeated pancreatic amylase gene 40 million years ago and changed its tissue specificity1. This single event triggered by a virus, a so-called parasite, would’ve had a significant effect on the diet of our ancestors and spawns even more questions about the “sanctity” of the human genome. [1] HIV’s high rate of mutation
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