BIO/CSC295 2011F, Class 23: Guest/Goetz Lecture

Overview:
* Jillian Goetz
* Elevator Presentations, Revisited
  * Helpful critiques from JG

Admin:
* Today at 4:15: Chats with Jillian Goetz
* EC Monday at noon: Biology seminar on cool stuff
* EC for Swim Meet Saturday @ 1pm in RKO
* EC for first meeting of G-FOSS Club 4:15 next Monday
* EC for Latin-American festival on Friday
* EC for another installment of FreeSound concert series; punk
  Gardner 9pm Saturday, but only if you abstain from alcohol all day
  Saturday, including the party
* EC for Fetish Harris on Saturday, but only if you abstain from alcohol 
  all day Saturday, including the party
* EC for Collegium Concert Sunday at 2pm

Welcome to Jillian Goetz: Single-Cell Isolation in the Retina
* How I became a molecular biologist in two short rotations
* Cute pictures - These are the model things we torture.
* Interpreting data - Bioinformatics rears its beautful head
* Eye overview
  * Lots of diversity in cells in the retina  
    * Even though there are only seven or so basic cell types  
    * Partiuclar diversity in the ganglion
* All of these cells come from the same progenitor
* What makes the progenitors develop into different cells?
  * What are the cues in the gene works
  * How do we differentiate cells
* Ganglion cells have many different functions; How are they different
  genetically?  What are their different signatures and when do they
  develop.
* ...
* Lots of data: 45K data points for each of 200+ cells
* How do you analyze that much data?
  * Computationally
  * Bioinfomratically
  * Biologically
* Followup question: Is what we found on the microarray true?
  * The cool stuff: What happens if we overexpress a gene or knock 
    it out?
* More cool stuff (heat map)
  * You can see gradual increase in expression of genes as
    progenitors mature and get closer and closer to ganglion
    cells.
* Electroporation - In developing cells, add DNA and hope for update,
  leading to overexpression
* iPS - Induced pluripotent stem cells
  * Induced from a somatic cell; bypasses moral quandaries
  * Uses four known transcription factors
* Jill's question: Can we turn these back into the wide variety of 
  ganglion cells?
  * E.g., to recover from glaucoma
* Wouldn't this be a cool research question for this class?

Research questions
* How far are you?  Not very.
* Have there been studies on the interaction of the generated ganglion
  cells with other nerve cells?  No.  But we care a lot about how they
  do connect.
* How can you be reproducible from single-cell isolates?  Are you seeing
  a few general patterns or infinite variability or ...?
  * That's part of what the computational analysis is supposed to tell us.
  * The patterns they are seeing are reproducible

Lessons from JG
* You need to learn lots of skills!  And you can do it.
* How big is biology at ISU?  1000 students in intro course.
* How does grad school compare to Grinnell in terms of amount and kind?
  * "My program may not be typical."
  * "I'm busy."
  * "I read more primary literature at Grinnell." 
    * But other grad schools differ.  E.g., at MIT there's the required
      paper group, 7pm until it finishes.
  * I took more multiple choice tests and did less homework
  * But all of your free time is in lab.  
  * A key to rotations - make sure you're comfortable in the lab
* What's the balance between self-directed and advisor-directed lab?
  * "I'm a special case" - Less molbio background than most, so perhaps
    asks more questions
  * But now has her own projects, so "It's just down for me."

Elevator Presentations
* Jay, Noelle, Marcus, and Radhika - Want to identify nociceptors; look
  for motifs.  Test against known database.  Then test against unknown
  to see if can predict.  A few snags.
  * There are three kinds of receptors; nociceptors fall into all three
    kinds
  * One they've looked at reacts to temps over 43 degrees celsius
  * TRPC
  * Currently narrowing search to a set that have been identified in
    a range of organisms, and it's likely to have a conserved region
  * Look for about six alpha helices and conserved coil regions
    * How are you going to look for alpha helices if you don't do
      strucure prediction?
  * Concerns about scope
  * Talk to Katherine