20.20(S10):Advanced topics

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20.385: 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
Preview of 20.385 Wed Feb 3 Natalie Kuldell
Ron Weiss
before next week read: Sci Am summary (handout)
“Two ‘What if” experiments”
Ptashne, M.
PMID 15055587
“Build Artificial”
Brent, R.
PMID: 15055588
Parts™ Wed Feb 10 Natalie Kuldell
Ron Weiss
A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.

Brent R, Ptashne M.Cell. 1985 Dec;43(3 Pt 2):729-36.
PMID: 3907859

Logic Modules
Wed Feb 17 (RW OoT) Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007
DOI : 10.1038/msb4100173
Elowitz, MB, and Leibler, S. A synthetic oscillatory

network of transcriptional regulators. Nature 403, 335–338 (2000)
Gardner TS, et al.
Construction of a genetic toggle switch in Escherichia coli Nature 403, 339–342 (2000).
May also want non-DNA, non-protein based logic paper (RNAi logic?)

Signal Specificity
Wed Feb 24 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
Levskaya A, et al.
Synthetic biology: engineering Escherichia coli to see light.
PMID: 16306980
Controlling System Dynamics
Wed Mar 3 (RW OoT) 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
Dueber JE, et al.
Synthetic protein scaffolds provide modular control over metabolic flux.
PMID: 19648908
Functional Network Composition
Thursday Mar 11 Diversity-based, model-guided construction of synthetic gene networks with predicted functions Ellis T, Wang X, and Collins JJ. Nat Biotech Tabor JJ et al.
A synthetic genetic edge detection program
PMID: 19563759
Tuning the system: directed evolution
Wed Mar 17 A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature 456, 516–519 (2008). Yokobayashi, Y, et al.
Directed evolution of a genetic circuit Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002).
Spring Break Mar 22-26 No class all week
DNA construction and editing technologies
Wed Mar 31 Article 1:
Programming cells by multiplex genome engineering and accelerated evolution.
Wang HH, et al. Nature. 2009 Aug 13;460(7257):894-8.
Article 2:
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.Gibson DG, et al. Science. 2008 Feb 29;319(5867):1215-20.
PMID: 18218864
Stemmer WP, et al. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.

PMID: 7590320

Thursday Apr 8
Little Red Corvette:
Once you've got the DNA, where do you put it? Introducing... THE CHASSIS
Wed Apr 14 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 21 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 28 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 4 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 11 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 11? 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