20.20(S10):Advanced topics

20.385: Advanced Topics in Synthetic Biology

Assignments

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

26-152

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 (request from NK)
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	Ptashne “Two ‘What if” experiments” PMID 15055587 Brent “Build Artificial” PMID 15055588
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
Chassis	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