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	before next week read Innovation at the intersection of synthetic and systems biology Lanza AM, Crook NC, and HS Alper doi:10.1016/j.copbio.2011.12.026 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	Computational tools for the synthetic design of biochemical pathways Medema, M, et al. Nature Rev Micro (2012) January 23 doi:10.1038/nrmicro2717
Transcription-based Logic Devices	Week 3: Wed Feb 20		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	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
RNA Engineering	Week 4: Wed Feb 27		Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction Goldfless SJ, et al. NAR (2012) 1-12 DOI: 10.1093/nar/gks028	Versatile RNA-sensing transcriptional regulators for engineering genetic networks Lucks JB, et al. PNAS (2011) 108(21): 8617-8622 DOI: 10.1073/pnas.1015741108
Protein Design: directed evolution	Week 5: Wed Mar 6		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	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
Modularity	Week 6: Wed Mar 13 before 3 ideas presentations		Modularity of a carbon-fixing protein organelle Bonacci W et al. PNAS (2012)109(2):478-483 DOI: 10.1073/pnas.1108557109	A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4 DOI: 10.1186/1754-1611-4-4]
(re)Programming Systems	Week 7: Wed Mar 20		Reprogramming bacteria to seek and destroy an herbicide Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470 doi:10.1038/nchembio.369	Scaling up synthetic biology: Do not forget the chassis A Danchin FEBS letters (2012) pdf here
Spring Break Mar 26-30			No class all week
DNA construction and editing technologies	Week 8: Wed Apr 3		Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs FJ et al. Science (2011) 333(6040):348-353 DOI: 10.1126/science.1205822	Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Cermak T et al. NAR (2011) 39(12):7879 PMID: 21493687
Feedback and Insulation	Week 9: Wed Apr 10 before tech spec review		A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches Cantone I et alCell (2009)137(1):172-181 PMID: 19327819	In silico feedback for in vivo regulation of a gene expression circuit Milias-Argeitis A et al.Nature BioTech (2011) 29(12):1114–1116 doi:10.1038/nbt.2018
Chassis	Week 10: Wed Apr 17		An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells Shin J, and Noireaux, V. ACS Synthetic Biology (2012) 1(1):29–41 DOI: 10.1021/sb200016s	Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs Csorgo B et al. Microbial Cell Factories (2012)11:11 doi:10.1186/1475-2859-11-11
Programming with Models & Noise	Week 11: Wed Apr 24		Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression Carothers JM et al. Science (2011)334(6063):1716-1719 DOI: 10.1126/science.1212209	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		Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305 PMID: 20117231	Organization of Intracellular Reactions with Rationally Designed RNA Assemblies Delebecqu CJ et al. Science (2011) 333:470 DOI: 10.1126/science.1206938
Systems & System Ecology	Week 13: Wed May 8		Synthetic chromosome arms function in yeast and generate phenotypic diversity by design Dymond JS et al. Nature (2011) 477: 471–476 doi:10.1038/nature10403	Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium Brenner K PNAS (2007) 104(44):17300-17304 DOI: 10.1073/pnas.0704256104
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	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!	Week 14: Wed May 16 before final presentations		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	Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article