BIO/CSC295 2009F, Class 09: Gene Alignments (4)

Admin:
* Did anyone attend convo today?  What did you think?
* For Monday, read through Chapter 4 of St. Clair and Visick.
* You have a new assignment for next Thursday which replaces the 
  "on your own" part of Chapter 3.
* Tomorrow's CS Table is on Software and Intellectual Property.  
  For those who have thought about patenting of genes, it provides 
  an another domain to think about appropriateness of patent.
  + I brought copies of the paper we'll discuss.

Overview:
* Lab, continued.
* Exploring the HIV env gene.

Thinking ahead
* What do you expect about successful variants of the gene?
  * They will be more abundant in the population
* "Cool" system
  * Information on sickness
  * Information on 
* Hypotheses
  * More variability confers an advantage
  * A successful variant will be more abundant
  * Sam can't type fast enough
* Background
  * You get infected with the virus
  * The virus mutates over time
  * Classic evolutionary theory says: If you have three variants,
    A, B, and C and C is a little more successful, over time, you'll 
    have much more C (and diversity decreases)
  * Acting against all of this is your immune system defense
    * You have antibodies for specific protein.  If an antibody "sees"
      a foreign protein, it attaches to that protein and marks it for
      destruction
    * Maybe the immune system will respond better to more abundant
      things
    * The immune system is pretty darn specific
  * Do we know whether HIV infection is a variety of viruses and they
    get selected, or that it mutates over time?
    * It looks like you get infected by one and it mutates over time
* The data
  * 14 IV drug users all infected with IV
  * Look at virus sequence for a particular gene over time
    * Visits every six months or so
  * Using an amplification thingy to see how abundant each variation is
  * How?  Take blood sample, PCR amplification, sequence product
    * Gives them a few variants
    * May not be representative
* You get access to the data.  Ooh
  * So you can ask some questions about it
  * Do you see a pattern in an individual?
  * You see a pattern across individuals?
  * Do changes in the sequence of the virus help it avoid predation
    (that is, keep it safe from the immune response)
  * "You can get an inkling of the battle that is going on between the
    virus and the immune system."
* Remember: It's biology, so it's bound to be messy!
  * And you're using computers, so something will go wrong.