20.20(S15):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 4	Natalie Kuldell	preview of 20.385	Factory of Life Witze A Science News pdf Two ‘What if' experiments Ptashne M PMID: 15055587 pdf Build Artificial Brent R PMID: 15055588 pdf
Parts™	Week 2: Wed Feb 11	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	Advances and current limitations in transcript-level control of gene expression Leavitt JM, Alper HS. Curr Opin Biotechnol. (2015) Jan 2;34C:98-104. doi: 10.1016/j.copbio.2014.12.015. Review pdf
Transcription-based Logic Devices	Week 3: Wed Feb 18		Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules Baojun Wang and Martin Buck. Chem. Commun. (2014) 50: 11642-11644 DOI: 10.1039/C4CC05264A	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
DNA fine-tuning + evolution	Week 4: Wed Feb 25		An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits. Beneš D1, Sosík P, Rodríguez-Patón A. Artif Life. (2015) Jan 26:1-14. doi:10.1162/ARTL_a_00160	Directed evolution as a powerful synthetic biology tool Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23. PMID: 22465795
RNA Engineering	Week 5: Wed Mar 4		Protein-responsive ribozyme switches in eukaryotic cells. Kennedy AB, Vowles JV, d'Espaux L, Smolke CD.Nucleic Acids Res. (2014) Oct 29;42(19):12306-21. doi: 10.1093/nar/gku875	RNA synthetic biology Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54. PMID: 16680139
SynBio for Science	Week 6: Wed Mar 11 day of 3 ideas presentations	No presentations this week (response record for one or the other paper due)	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
Engineering Biology	Week 7: Wed Mar 18		Programmable biofilm-based materials from engineered curli nanofibres. Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS.Nat Commun. (2014) Sep 17;5:4945. doi: 10.1038/ncomms5945.	Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Goldman N et al. Nature (2013) doi:10.1038/nature11875
Spring Break Mar 23-27			No class all week
Genome editing technologies	Week 8: Wed Apr 1		Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Mitchell LA, Boeke JD.Proc Natl Acad Sci U S A. (2014) Dec 2;111(48):17003-10. doi: 10.1073/pnas.1414399111	Multiplex Genome Engineering Using CRISPR/Cas Systems Cong L et al. Science (2013) Jan 3. PMID: 23287718
Recoded Organisms	Week 9: Wed Apr 8 day of tech spec review	No presentations this week (response record for one or the other paper due)	Recoded organisms engineered to depend on synthetic amino acids. Rovner AJ, et. al...Isaacs FJ. Nature (2015) Jan 21. doi: 10.1038/nature14095	A bacterial strain with a unique quadruplet codon specifying non-native amino acids Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG. Chembiochem (2014) Aug 18;15(12):1782-6 doi: 10.1002/cbic.201402104
Chassis	Week 10: Wed Apr 15		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 22		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 Apr 29
Systems & Communities	Week 13: Wed May 6		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 13 day of final presentations	no presentations this week (response record only if you've missed a different discussion this term) Bringing Standards to Life: Synthetic Biology Standards and Intellectual Property AW Torrance and LJ Kahl Santa Clara High Technology Law Journal(2014) 30(2) link]	Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173