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		Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173	Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000) Gardner, T. S., Cantor, C. R. & Collins, J. J. 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
Physical Organization	Wed Mar 3		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. Nat Biotechnol. 2009 Aug;27(8):753-9.
Functional Network Composition	Thursday Mar 11		Ellis, Tom, Xiao Wang, and James J Collins. “Diversity-based, model-guided construction of synthetic gene networks with predicted functions.” Nat Biotech advanced online publication (April 19, 2009).	Tabor JJ et al. A synthetic genetic edge detection program PMID: 19563759
Tuning the system: directed evolution	Wed Mar 17		Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008).	Yokobayashi, Y., Weiss, R. & Arnold, F. H. 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		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 8		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 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