20.20(S11):Advanced topics

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings Paper 1 (10%) Paper 2 (15%) Response record (20%): your thoughts about the papers you don't present. Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others Instructions for these assignment are here

Part 2: Team Mentoring Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and 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 2	Natalie Kuldell		before next week read The promise of synthetic biology Pleiss,J. DOI:10.1007/s00253-006-0664-3 Two ‘What if' experiments Ptashne, M. PMID: 15055587 Build Artificial Brent, R. PMID: 15055588
Parts™	Wed Feb 9	Natalie Kuldell ppt is here	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	Improving the Lac System for Synthetic Biology Penumetcha, P., et al. Bios (2011) 81(1):7-15. pdf
Transcription-based Logic Devices	Wed Feb 16		Environmental signal integration by a modular AND gate Anderson JC, Voigt C, Arkin, AP Molecular systems biology (2007) 3:133 PMID: 17700541	A synthetic oscillatory network of transcriptional regulators Elowitz, MB, and Leibler, S. Nature (2000) 403, 335–338 PMID: 10659856 Construction of a genetic toggle switch in Escherichia coli Gardner TS, et al.Nature(2000) 403, 339–342 PMID: 10659857
Protein Design	Wed Feb 23		De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth Fisher MA, et al. PLoS One (2011)6(1):e15364 DOI: 10.1371/journal.pone.0015364	Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 DOI: 10.1371/journal.pcbi.0030164
Tuning the system: directed evolution	Wed Mar 2		Directed evolution of recombinase specificity by split gene reassembly Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543 DOI: 10.1093/nar/gkq125	A dual selection module for directed evolution of synthetic circuits. Yokobayashi Y, Arnold FH. Nat Comp (2005) 4:245–254 pdf
RNA Engineering	Thursday Mar 10		Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255 DOI: 10.1126/science.1192128	The Case for RNA Chang, CL, Arkin AP. Science (2010) 330:1185-1186 DOI: 10.1126/science.1199495
Tuning the system: Network Composition	Wed Mar 16		A modular positive feedback-based gene amplifier Nistala GJ et. al. JBE (2010) 4:4 DOI: 10.1186/1754-1611-4-4	A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928
Spring Break Mar 21-25			No class all week
DNA construction and editing technologies	Wed Mar 30		Article 1: Programming cells by multiplex genome engineering and accelerated evolution Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8. PMID: 19633652 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	Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Stemmer WP, et al. Gene (1995) 164(1):49-53 PMID: 7590320
Chassis	Thursday Apr 7		Article 1: Formation of protocell-like vesicles in a thermal diffusion column.Budin I, Bruckner RJ, and Szostak JW. J Am Chem Soc. (2009)131(28):9628-9 PMID: 19601679 Article 2: Genome transplantation in bacteria:changing one species to another Lartigue C, et al. Science 2007, 317:632-638. PMID: 17600181	Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050
In silico and -omics	Wed Apr 13		Article 1: Design of genetic networks with specified functions by evolution in silico Francois, P. & Hakim, V. Proc. Natl Acad. Sci. USA (2004) 101, 580–585 PMID: 14704282 Article 2: Engineering transcription factors with novel DNA-binding specificity using comparative genomics Desai TA, et al. Nucleic Acids Res (2009) 37(8): 2493-503 PMID: 19264798	Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 link Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206
Signal Connectivity	Wed Apr 20		Rewiring the specificity of two-component signal transduction systems Skerker JM, et al. Cell (2008)133(6):1043-54. PMID: 18555780	Tunable Signal Processing in Synthetic MAP Kinase Cascades O'Shaughnessy, EC, et al. Cell(2011) 144:119-131 DOI: 10.1016/j.cell.2010.12.014
Metabolic Engineering	Wed Apr 27		Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385 Article 2: Synthesis of methyl halides from biomass using engineered microbes Bayer TS, et al. J Am Chem Soc (2009) 131:6508-6515. PMID: 19378995	Synthetic protein scaffolds provide modular control over metabolic flux. Dueber JE et al. Nat Biotechnol. (2009) 27(8):753-9. PMID: 19648908
Cell Cell Communication/System Ecology	Wed May 4		Article 1: A synthetic Escherichia coli predator-prey ecosystem Balagaddé FK, et al. Mol Syst Biol. 2008;4:187. PMID: 18414488 Article 2: Synthetic cooperation in engineered yeast populations Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. (2007) 104(6):1877-82. PMID: 17267602	Synthetic ecosystems based on airborne inter- and intrakingdom communication Weber, W., Daoud-El Baba, M. & Fussenegger, M. Proc. Natl Acad. Sci. USA (2007) 104, 10435–10440 PMID: 17551014
Property rights in synthetic biology	Tue May 10?		Article 1: Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173	Article 2: Patents and Translational Research in Genomics Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
Safety!	Tue May 10?		Article 1: 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	Article 2: Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article
Molecular and Cellular Computing	Tue May 10?		Robust multicellular computing using genetically encoded NOT gates and chemical 'wires' Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215. DOI: 10.1038/nature09565	Engineering bacteria to solve the Burnt Pancake Problem Haynes KA, et al. J Biol Eng. 2008 May 20;2:8. PMID: 18492232