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 I	Discussion or Related paper II
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	Heejo and Tushar ppt is here	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	Gabi and Ellie ppt is here	Evolution-guided optimization of biosynthetic pathways Raman S, Rogers JK, Taylor ND, Church GM.Proc Natl Acad Sci U S A. (2014) Dec 16;111(50):17803-8. doi: 10.1073/pnas.1409523111	Directed evolution as a powerful synthetic biology tool Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23. PMID: 22465795
Top down vs. Bottom up	Week 5: Wed Mar 4	No presentations this week (response record for one or the other paper due)	Five hard truths for synthetic biology Kwok R. Nature(2010) 463(7279):288-90. doi: 10.1038/463288a	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
RNA Engineering	Week 6: Wed Mar 11 day of 3 ideas presentations	Marianne and Jenn ppt is here	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
Engineering Materials with Biology	Week 7: Wed Mar 18	Paper #1: Gabi ppt is here	Engineering living functional materials Chen AY1, Zhong C, Lu TK.ACS Synth Biol. (2015) Jan 16;4(1):8-11. doi: 10.1021/sb500113b*AND Synthesis and patterning of tunable multiscale materials with engineered cells Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK.(2014) Nat Mater. 13(5):515-23. doi: 10.1038/nmat3912	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.
Spring Break Mar 23-27			No class all week
Genome editing technologies	Week 8: Wed Apr 1	Paper #2: Jenn ppt is here also...bacon anyone?	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 #1: Tushar ppt is here	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
Setting Standards	Week 11: Wed Apr 22	Paper #1: Ellie ppt is here	SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology. Wang L, et.al. Wang D.Sci Rep. (2015) Jan 28;5:8090. doi: 10.1038/srep08090	Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K1, Zhao D, Voigt CA.Proc Natl Acad Sci U S A. (2012) May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109 (moved from week 12)
Methods for Metabolic Engineering	Week 12: Wed Apr 29	Paper #1: Heejo ppt is here	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 (moved from week 11)	CONSTRICTOR: constraint modification provides insight into design of biochemical networks Erickson KE, Gill RT, Chatterjee A. PLoS One (2014) Nov 25;9(11):e113820.doi: 10.1371/journal.pone.0113820
Synthetic Systems at Play	Week 13: Wed May 6	Paper #1: Marianne ppt is here	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 last day of class	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