20.20(S12):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	Wed Feb 8	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™	Wed Feb 15	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	Wed Feb 22	article 1 = Jamal and Queenie, ppt is here	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	Wed Feb 29	article 1 = Lauren and Alfred, ppt is here	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	Wed Mar 7	article 1 = Hannah and Sabina ppt is here	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	Wed Mar 14 before 3 ideas presentations	article 1 = Shelley and Donnie ppt is here and pdf is here	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	Wed Mar 21	article 1 (+2 as needed) = PJ, Nahum and Shlomiya ppt is here and pdf is here	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	Wed Apr 4	article 1 = PJ ppt pdf article 2 = Shelley ppt pdf	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	Wed Apr 11 before tech spec review,	article 1 = Alfred, pptx pdf article 2 = Jamal pptx pdf	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	Wed Apr 18	article 1 = Hannah article 2= Queenie ppt pdf	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	Wed Apr 25	article 1 = Lauren pptx pdf article 2 = Sabina pptx pdf	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	Wed May 2	Guest discussion leader for paper 1 = Tae Seok Moon discussion to start @4:15	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	Wed May 9	article 1 from April 18th = Hannah ppt and pdf article 2 (here) = Shlomiya ppt and pdf	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	Wed May 16 before final presentations,	article 1 = Nahum ppt	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!	Wed May 16 before final presentations,	article 2 = Donnie ppt	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