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My advice on the matters for the day (as listed in the calendar):
- Gene Regulation: This is your chance to make sure that you understand how the regulation of cI and cro work to regulate the lysis/lysogeny decision by phage lambda. The notes on this topic may help, particularly pages 4 through 8. Question 5 of Problem Set 7 may help you understand Fig. 6 of the notes. The goal is to go beyond fuzzy concepts and understand how real proteins and actual DNA sequences achieve complex regulatory outcomes.
- Problem Set 7: Question 5 of Problem Set 7 is intended to help you understand Fig. 6 of the notes by giving you the opportunity to put your fingers on the relevant sequences.
- Past proposals: This time for sure (maybe). It will help the class discussion if you read a couple old proposals. It shouldn't take long, since there is no need to read for deep understanding. Rather, the idea is to see how others approach the task.
I. Basic Information
A. Your name
II. Old business
- Brenner et al (1961) - the rationale and the experiment
Regarding Brenner et al (1961) and its companion, do you understand the three hypotheses they were trying to test? Do you understand the nature of the experiment(s) they performed? Given your understanding of the experiments, can you understand the results found in the different figures and draw conclusions from them?
- Gene regulation
Any concerns about the notes on Gene Regulation and Bacteriophage, particularly:
- The different levels of gene regulation?
- The relationship between transcriptional proteins (like RNA polymerase and repressors) and specific DNA sequences (like promoters and operators)?
- Common features of the sequences of actual promoters and operators in the cI-cro region of lambda?
- The power of regulatory feedback loops?
- How the interplay between the lambda repressor and Cro protein might achieve a stable decision of lysogeny vs lysis?
- Problem Set 7, question 5 (finding regulatory motifs in a phage that isn't lambda)?
- Any other regulation-related issues?
- Problem Set 7
Any concerns about
Problem Set 7, question 3 (redrawing figures from Brenner et al (1961))?
Question 5 (lambda regulation)? Anything else?
- Semester Project
What do you need to bring your project to the finish line?
III. Old research proposals
Have you looked over any proposals from past years? If so, which ones? In brief, what do you think -- good models for your own (or your colleague's)? If not, explore. If none strike your fancy, you might look at the last three of 2013 and/or 2016. If enough people have looked at them, we'll spend time discussing them in class
IV. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?
(nb. Issues concerning your proposal are always welcome)
Thanks!
REMEMBER TO CLICK SUBMIT!
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