20.20(S13):Advanced topics
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| '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]] | | '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]] | ||
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| - | | ''' | + | | '''Engineering Biology''' <br> |
| Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations | | Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations | ||
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| - | |''' | + | |'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al. ''Nature'' (2013)<br> [[doi:10.1038/nature11875]] |
| - | | '''A | + | | '''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast''' <br>Jaschke PR et al. ''Virology''(2012)434(2):278-84. <br> [[doi: 10.1016/j.virol.2012.09.020]] |
|-- | |-- | ||
| '''(re)Programming Systems''' <br> | | '''(re)Programming Systems''' <br> | ||
Revision as of 22:09, 29 January 2013
Contents |
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
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| 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 | Synthetic biology devices as tools for metabolic engineering Shiue E, Prather K. Biochemical Engineering Journal (2012) 65:82–89 doi:10.1016/j.bej.2012.04.006 |
| DNA fine-tuning + evolution | Week 3: Wed Feb 20 | Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology Blount BA, Weenink T, Vasylechko S, Ellis T. PLoS ONE (2012) 7(3): e33279. doi:10.1371/journal.pone.0033279 | Directed evolution as a powerful synthetic biology tool Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23. PMID: 22465795 | |
| Transcription-based Logic Devices | Week 4: Wed Feb 27 | 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 | 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 | |
| RNA Engineering | Week 5: Wed Mar 6 | De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Rodrigo G, Landrain TE, Jaramillo A. PNAS(2012) 109(38):15271-6. PMID: 22949707 | RNA synthetic biology Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54. PMID: 16680139 | |
| Engineering Biology | Week 6: Wed Mar 13 before 3 ideas presentations | Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Goldman N et al. Nature (2013) doi:10.1038/nature11875 | A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Jaschke PR et al. Virology(2012)434(2):278-84. doi: 10.1016/j.virol.2012.09.020 | |
| (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 | |
