20.20(S13):Advanced topics: Difference between revisions
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Revision as of 14:27, 21 January 2013
20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
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
|
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 | |||
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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 |