BNFO 301 
Introduction to Bioinformatics
Questionnaire on Gene Regulation and Bacteriophage
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(and please don't use quotation marks in your answers. They break the questionnaire program!)
Spring 2011 

I. Basic Information

A. Your name 
II. Genome Sequencing in action (Myers et al)

A. How comfortable are you in calculating the amount of a genome has been sequenced from the coverage? For example, How many of the ~120 million nucleotides in the Drosophila genome would you expect to have been sequenced if the coverage were 10x?

B. Do you have any remaining issues regarding Myers et al that warrent discussion?
     

III. Lifestyles of bacteriophage
  1. Do you understand what lysogeny is and why it might serve the bacteriophage?
  2. Do you understand the need for a general repressor in lysogenic phage?
  3. Anything other phage-related issues?
     

Do you have any favorite study questions (SQ1-SQ5) you think need discussion?  

IV. Gene regulation
  1. Do you understand the different levels of gene regulation?
  2. Do you understand the relationship between transcriptional proteins (like RNA polymerase and repressors) and specific DNA sequences?
  3. Can you recognize sequences to which lambda repressor binds?
  4. Do you understand the power of regulatory feedback loops?
  5. DO you understand how the interplay between the lambda repressor and Cro protein might achieve a stable decision of lysogeny vs lysis?
  6. Anything other regulation-related issues?
     

Do you have any favorite study questions (SQ6-SQ21) you think need discussion?  

V. Miscellaneous

A. There will be a talk/discussion Friday, February 25, some time between 9AM and 11AM, by David Harper, Chief Scientific Officer of BioControl a subsidiary of Targeted Genetics. He is the founder of his company, which has the goal of targeting bacteriophage to human pathogens. You can read a bit more here about BioControl's approach and Sulakvelidze et al (2001) for a general account of phage therapy.

  1. Would you be interested and able to attend?
  2. Do you have a preference as to the format and nature of the encounter? He is willing to give a conventional talk or lead a more informal discussion of biotechnology and your possible roles in it.
     

B. Any miscellaneous comments, questions, suggestions, concerns?
     

Thanks!

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