20.902(S09):Advanced topics in synthetic biology

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20.902: Advanced Topics in Synthetic Biology


Homework dropbox is here

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


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 Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007
DOI : 10.1038/msb4100173
Darwin is alive and well:
Directed evolution at the parts and device level
Wed Mar 4 RNA and RNP as new molecular parts in synthetic biology.Saito H, Inoue, T Journal of biotechnology(2007)132(1):1-7
I demand the cone of silence:
nature's constraints on genetic circuit design
Thursday Mar 12 Phenotypic consequences of promoter-mediated transcriptional noise. Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, Molecular cell(2006) 24(6):853-65
DOI : 10.1016/j.molcel.2006.11.003
Intelligent Design:
Functional composition at the device level
Wed Mar 18 Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Maeder ML, et. al. Mol Cell. (2008)31(2):294-301
DOI : 10.1016/j.molcel.2008.06.016
Spring Break Mar 24-28 No class all week
Writing in genetic code:
DNA construction and editing technologies
Wed Apr 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 Rewiring the specificity of two-component signal transduction systems. Skerker JM, et al. Cell (2008)133(6):1043-54.
DOI: 10.1016/j.cell.2008.04.040
Little Red Corvette:
Once you've got the DNA, where do you put it? Introducing... THE CHASSIS
Wed Apr 15 Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4.
DOI: 10.1126/science.1154520
Emergent properties of reduced-genome Escherichia coli.Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. Science. (2006)312(5776):1044-6.
PMID: 16645050
Secret map hidden in the peg-leg:
getting DNA to speak in binary
Wed Apr 22 Length-based encoding of binary data in DNA. Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.

Langmuir (2008) 24(5):1613-6.
DOI: 10.1021/la703235y

On your mark, get set, go: System dynamics Wed Apr 29 Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor CJ, Helman NC, Yan S, Lim, WA Science (2008)319: 1539-1543
DOI: 10.1126/science.1151153
Rough consensus and running code: building patterns and memories Tue May 5 Rational design of memory in eukaryotic cells. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Genes Dev. (2007):21(18):2271-6.
DOI: 10.1101/gad.1586107
mine mine mine: property rights in synthetic biology Tue May 12 Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173
Patents and Translational Research in GenomicsKaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
drop it like it's hot: safety! Tue May 12 Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics. Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11.
DOI: 10.1038/embor.2008.232