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 (15%): one page summaries of your freshman team's work
  • Mentoring journal(15%): one page summary of your freshman team's dynamics
  • Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK

Instructions for these assignments are here

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 Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164
DOI : 10.1371/journal.pcbi.0030164
Nature heart Legos™:
Proteins are modular too 		Wed Feb 18 Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1.Jin T, Inouye M.J Mol Biol. (1993)232(2):484-92.
PMID: 8393937
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:
 Article 1:

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways.
Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12
PMID: 19074487
Article 2:
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.
Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Gene. 1995 Oct 16;164(1):49-53.
PMID: 7590320

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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