User:Anthony Salvagno/Notebook/Research/2009/10/07/A-Exam Outline

As far as webcasting goes. I think I could do it live, but I don't know what the best method is. I did find ustream, which broadcasts live streaming video. I can also use the digital cameras in lab to record and save it. I could also just use google chat probably. My laptop also has a webcam built into it, but that might not be the best option because powerpoint for mac doesn't get along with powerpoint for windows. (Steve Koch 02:14, 8 October 2009 (EDT):It's probably 100x easier to just record it and then figure out how to broadcast it later. Given time frame, that's my recommendation. A quick message to J-C, though, would possibly be worth it, because I know he's somehow linked syncronized slides / speaking.)

Outline

Here is my tentative plan for my talk:

Welcome to the Lab

^{SJK 02:17, 8 October 2009 (EDT)}

02:17, 8 October 2009 (EDT)
In all of the candidacy exams I've seen, I've never seen a lab overview like this. I love it! I can't imagine a good scientist not appreciating this overview of what's going on in a lab. In my opinion, will be a major sign of a good scientist for you to show that you understand the whole lab, even the parts that you're not involved with day to day.

1. Maybe have a slide of lab members
2. Slide of Lab Research Focuses
   • SDM
   • Kinesin
3. Current Kinesin Experiments
   • Bulk Assays of ATP Hydrolysis - Brigette
   • Gliding Motility
   • Surface Passivation - Andy
   • Kinesin Simulation - Larry

Introduction

Intro to DNA and problems with DNA

1. What is DNA
   • This might be a couple of slides
2. Chromatin and higher orders
3. DNA to people
   • Central Dogma explanation
   • Maybe talk about transcription here
4. Cancer is bad
   • Errors in DNA
   • Post Translational Modifications
   • Telomeres

SDM

^{SJK 02:19, 8 October 2009 (EDT)}

02:19, 8 October 2009 (EDT)
I like the intro above, and using cancer as transcription gone haywire as a motivation. In my NSF CAREER 2009 proposal I put in some stuff about "single-molecule genetics." I still like that, so you may want to take a look at the 2x2 matrix figure I have and think about whether it'd be good for you to try to sell in your candidacy exam.

1. Single molecule studies
   • Unzipping Data of nucleosome, and Koch's protein studies
2. What is SDM
3. Simulation Info
   • "Tether" creation
   • Unzipping based on Ewlc, Efjc, Ebp
4. Detection Capabilities
   • Larry Data from alt. splicing
   • Now what? - go to next section

Optical Tweezers

1. Image of OT
2. Basics of OT
3. our OT design (Steve Koch 02:21, 8 October 2009 (EDT): Definitely show picture(s) here, because it looks very cool. Also, make sure to give props to people who worked on this design an various parts of it (Andy, Larry, Linh).

Molecular Biology

1. Start from Yeast
2. digest genome
3. clone fragments
4. create unzipping construct
5. ligate fragments and unzip construct
6. tether and unzip

(Steve Koch 02:23, 8 October 2009 (EDT): Make sure to give props here, too -- Kelly, Diego, Brandon...It's a big challenge, but try to make this part interesting to both the biologists and the physicists. I think this can be accomplished by explaining things that can and / or did go wrong.)

Future Plans

1. Addition of nucleosomes
   • in vitro nucleosome unzipping
   • in vivo nucleosome unzipping
   • transcriptional studies
     • unzip profile of RNA Pol II
     • study RNA Pol II in different scenarios
   • telomere mapping