20.902(S09):Advanced topics in synthetic biology

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20.902: Advanced Topics in Synthetic Biology

Assignments

Part 1: Readings

  • Paper 1 (10%): presented with a partner
  • Paper 2 (15%): presented solo
  • Response record (25%): your thoughts about the papers you don't present.

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress reports (25%): 2x one page summary of your freshman team's work, due Wednesday March 11th, and Wednesday April 8th
  • Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 11th, and Wednesday April 8th
  • Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK

Reading Schedule

Discussions will be 1 hour long during Wednesday 2-5 studio block

26-152

TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
A Voyage To Lilliput:
How a small number of AA substitution change activity of a protein 		Wed Feb 4 Natalie Kuldell

Turning lambda Cro into a transcriptional activator.Bushman FD, Ptashne M.Cell. 1988 Jul 15;54(2):191-7.
PMID 2968842

ppt here

Genetic Switch: Phage Lambda and Higher Organisms Mark Ptashnepreviewed here

or Sci Am summary (request from NK)

Slide rule optional:
Computational design of novel protein activities 		Wed Feb 11
Nature heart Legos™:
Proteins are modular too 		Wed Feb 18
Better odds in Vegas:
DNA elements are modular too, allowing for circuits, but circuits don't always work 		Wed Feb 25
Darwin is alive and well:
Directed evolution at the device level 		Wed Mar 4
I demand the cone of silence:
nature's constraints on genetic circuit design 		Thursday Mar 12
Intelligent Design:
Functional composition at the device level 		Wed Mar 18
Spring Break Mar 24-28 No class all week
Writing in genetic code:
DNA construction and editing technologies 		Wed Apr 1 article 1:

article 2:
We're only human:
What is the state of the art? 		Thursday Apr 9 article 1:

article 2:
Little Red Corvette:
Once you've got the DNA, where do you put it? Introducing... THE CHASSIS 		Wed Apr 15 article 1:

article 2:
(R)evolution:
Can we understand it? Can we program it? 		Wed Apr 22 article 1:

article 2:
On your mark, get set, go: System dynamics Thur Apr 30 article 1:

article 2:
Rough consensus and running code: building patterns and memories article 1:

article 2:
mine mine mine: property rights in synthetic biology Tue May 12 article 1:
2020: Empire of Reason article 2:
drop it like it's hot: safety! article 3:
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