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
Cell-free Synthetic Biology	Week 10: Wed Apr 15		Paper-based synthetic gene networks Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Cell (2014) Nov 6;159(4):940-54. doi: 10.1016/j.cell.2014.10.004	Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system Sun ZZ1, Yeung E, Hayes CA, Noireaux V, Murray RM. ACS Synth Biol. (2014) Jun 20;3(6):387-97. doi: 10.1021/sb400131a
Standardization and Measurement	Week 11: Wed Apr 22		Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P. PLoS One (2012) 7(7):e39407. doi: 10.1371/journal.pone.0039407	The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts Alnahhas RN, Slater B, Huang Y, Mortensen C, Monk JW, Okasheh Y, Howard MD, Gottel NR, Hammerling MJ, Barrick JE.J Biol Eng. (2014) Dec 1;8(1):28. doi: 10.1186/1754-1611-8-28
'Metabolic Engineering'Pattern Formation'Minimal Cell'Noise	Week 12: Wed Apr 29
Synthetic Systems at Play	Week 13: Wed May 6		Towards synthetic biological approaches to resource utilization on space missions Menezes AA, Cumbers J, Hogan JA, Arkin AP.J R Soc Interface (2015) Jan 6;12(102):20140715. doi: 10.1098/rsif.2014.0715	Programmable bacteria detect and record an environmental signal in the mammalian gut Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. Proc Natl Acad Sci U S A. (2014) Apr 1;111(13):4838-43. doi: 10.1073/pnas.1321321111
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