20.20(S13):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

16-220

TOPIC	DATE	Discussion leader(s)	Discussion paper(s)	Related paper(s) to enjoy
Preview of 20.385	Week 1: Wed Feb 6	Natalie Kuldell	preview of 20.385	Factory of Life Witze A Science News Two ‘What if' experiments Ptashne M PMID: 15055587 Build Artificial Brent R PMID: 15055588
Parts™	Week 2: Wed Feb 13	Natalie Kuldell ppt is here	Turning lambda Cro into a transcriptional activator Bushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7. PMID: 2968842	Synthetic biology devices as tools for metabolic engineering Shiue E, Prather K. Biochemical Engineering Journal (2012) 65:82–89 doi:10.1016/j.bej.2012.04.006
DNA fine-tuning + evolution	Week 3: Wed Feb 20		Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology Blount BA, Weenink T, Vasylechko S, Ellis T. PLoS ONE (2012) 7(3): e33279. doi:10.1371/journal.pone.0033279	Directed evolution as a powerful synthetic biology tool Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23. PMID: 22465795
Transcription-based Logic Devices	Week 4: Wed Feb 27		Genetic programs constructed from layered logic gates in single cells Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA Nature (2012) 491: 249–253 doi:10.1038/nature11516	Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology Wang B, et al. Nat. Commun. (2011) 2 : 508 doi: 10.1038/ncomms1516
RNA Engineering	Week 5: Wed Mar 6		De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Rodrigo G, Landrain TE, Jaramillo A. PNAS(2012) 109(38):15271-6. PMID: 22949707	RNA synthetic biology Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54. PMID: 16680139
Engineering Biology	Week 6: Wed Mar 13 before 3 ideas presentations		Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Goldman N et al. Nature (2013) doi:10.1038/nature11875	A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Jaschke PR et al. Virology(2012)434(2):278-84. doi: 10.1016/j.virol.2012.09.020
SynBio for Science	Week 7: Wed Mar 20		Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription Forster AC. Biotechnol J. (2012) 7(7):835-45. doi: 10.1002/biot.201200002	Five hard truths for synthetic biology Kwok R. Nature(2010) 463(7279):288-90. doi: 10.1038/463288a
Spring Break Mar 26-30			No class all week
DNA construction and editing technologies	Week 8: Wed Apr 3		Knockout mice created by TALEN-mediated gene targeting. Sung YH et al. Nat Biotechnol (2013) 31(1):23-4. doi: 10.1038/nbt.2477	Multiplex Genome Engineering Using CRISPR/Cas Systems Cong L et al. Science (2013) Jan 3. PMID: 23287718
Cell Physiology	Week 9: Wed Apr 10 before tech spec review		Shared control of gene expression in bacteria by transcription factors and global physiology of the cell Berthoumieux S et alMol Syst Biol (2013) 9:634 doi: 10.1038/msb.2012.70	A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis Picotti P et al.Nature (2013) Jan 20. doi: 10.1038/nature11835
Chassis	Week 10: Wed Apr 17		Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production Woodruff LB, May BL, Warner JR, Gill RT. Biotechnol Bioeng (2013) Jan 15. doi: 10.1002/bit.24840	Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems Cardinale S, Arkin AP.Biotechnol J(2012) 7(7):856-66. doi: 10.1002/biot.201200085
Programming in the Noise	Week 11: Wed Apr 24		Iterative plug-and-play methodology for constructing and modifying synthetic gene networks Litcofsky KD et al. Nat Methods(2012) 9(11):1077-80. doi: 10.1038/nmeth.2205	A sensing array of radically coupled genetic ‘biopixels’ Prindle A et al. Nature(2012)481:39–44 doi:10.1038/nature10722
Metabolic Engineering	Week 12: Wed May 1		Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na D et al. Nat Biotechnol (2013) Jan 20. doi: 10.1038/nbt.2461	Synthetic protein scaffolds provide modular control over metabolic fluxDueber JE et al. Nat Biotechnol (2009) 27(8):753-9. doi: 10.1038/nbt.1557
Systems & Communities	Week 13: Wed May 8		Engineered cell-cell communication via DNA messaging Ortiz ME, Endy D. JBE (2012) 6(1):16. doi: 10.1186/1754-1611-6-16	Autonomous bacterial localization and gene expression based on nearby cell receptor density Wu HC et al. Mol Syst Biol (2013) 9:636. doi: 10.1038/msb.2012.71
Property rights in synthetic biology	Week 14: Wed May 15 before final presentations		Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173	Preparing synthetic biology for the world Moe-Behrens GH, Davis R, Haynes KA. Front Microbiol (2013) 4:5 doi: 10.3389/fmicb.2013.00005