User:Anthony Salvagno/Notebook/Research/2009/10/15/Talk 1.5

Candidacy Exam Practice Presentation View more presentations from Anthony Salvagno.

Audio will come tonight!

Change of plans. Apparently there is a time limit to how long you have to add audio. I recorded it, but it will have to be done in the morning cause I am tired. If you don't want to wait till then let me give you a sneak preview...

..it is awesome. The amount of hesitating and stuttering provides a glimpse into my awesome potential. I actually think I did a rather bad job and my streak of each presentation being worse than the last continues. Hopefully it starts to get better starting tomorrow. We'll see.

Steve Comments
(Continued after practice talk)
 * Slide 8: As already mentioned, practice what you want to say here (or move to the unzipping data slide)
 * Slide 10: You used the term "RNA" for "RNA Polymerase." To avoid doing this, you should call it "Pol II".
 * Slide 11: Don't forget that SNPs (single-nucleotide polymorphisms (single-base changes)) account for a lot of variation. In your practice talk, you didn't mention these.  It's been shown that you can detect some of these by unzipping too, but it's a lot harder, of course.
 * Slide 12: You may not have time to prepare for this. But it would be really good to explain the ChIP process as a way that information is currently obtained.  As it is right now, I don't think people will appreciate that biologists have really clever ways to get information that they REALLY want...but that there are still drawbacks to these methods.  The Fleming et al. Osley paper would be a good one to show a figure from.  Or Mason & Struhl transcription paper.  In some of my old talks from 2007 (on private wiki), I have slides explaining ChIP.
 * Reminder that tetrasome is H3H4 dimer.
 * Before slide 15, need transition (I think we talked about this on Friday)
 * When you talk about the match score, make sure you know the exact formula. You say "deviation," but make sure you know how that's defined, how it's scaled, and why.
 * Practice the Optical Trap slide (as we discussed while grilling you)
 * I don't think you defined "QPD," but mentioned it a few times
 * I'd show a picture of the whole OT before going through the piece by piece slide
 * After slide 24, I'd say, "Next step: calibration, then unzipping." And you should be prepared to discuss how we calibrate (stuck bead; free bead: see Richard Yeh's master's thesis)
 * Slide 26 you went through too fast. I think on Friday we had ideas of how to improve this, right?
 * Slide 27 go slower and use laser pointer to show the sticky ends and explain how "NNN" turns into a specific site for us. Although, to be honest, non-palindromic sticky ends may be quite confusing for people.  Keep in mind that "palindromic" is sort of a misnomer that confuses people at first.
 * At the top of slide 28, you should label the sticky ends. i.e., "here is BstXI sticky end."
 * I think you used the phrase "ligating construct to unzippable DNA" and I thought people would be confused without more explanation. Remember, a term like "ligate" is confusing to non-biologists
 * I think you need to define "what is cloning" too.
 * As discussed, after slide 35, should spell out what's next (prove SDM)
 * You can mention Adelman lab on slide 37
 * And finally, reminder to keep in mind that at least Sally will be viewing this as a proposal, and should be prepared to give a good guess as to what the bulk of your dissertation will be.