20.20(S13):Advanced topics
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| [[Natalie Kuldell]] | | [[Natalie Kuldell]] | ||
| preview of 20.385 | | preview of 20.385 | ||
| - | |''Factory of Life ''Witze A | + | |''Factory of Life ''<br> Witze A [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life]<br> |
| - | ''Two ‘What if' experiments''Ptashne M[[PMID: 15055587]]<br> | + | ''Two ‘What if' experiments''<br> Ptashne M [[PMID: 15055587]]<br> |
| - | ''Build Artificial''Brent R [[PMID: 15055588]] | + | ''Build Artificial'' <br> Brent R [[PMID: 15055588]] |
|-- | |-- | ||
| <b>Parts™</b> | | <b>Parts™</b> | ||
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| '''Metabolic Engineering''' | | '''Metabolic Engineering''' | ||
| Week 12:<br> Wed May 1 | | Week 12:<br> Wed May 1 | ||
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| + | | '''Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs''' Na D et al. ''Nat Biotechnol'' (2013) Jan 20. <br> [[doi: 10.1038/nbt.2461]] | ||
| '''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 <br>[[PMID: 20117231]] | | '''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 <br>[[PMID: 20117231]] | ||
| - | |||
|-- | |-- | ||
|'''Systems & System Ecology''' | |'''Systems & System Ecology''' | ||
Revision as of 23:05, 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 | Factory of Life Witze A [1] Two ‘What if' experiments |
| 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 | |
| SynBio for Science | Week 7: Wed Mar 20 | Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription Forster AC. Biotechnol J. (2012) 7(7):835-45. doi: 10.1002/biot.201200002 | Five hard truths for synthetic biology Kwok R. Nature(2010) 463(7279):288-90. doi: 10.1038/463288a | |
| Spring Break Mar 26-30 | No class all week | |||
|---|---|---|---|---|
| DNA construction and editing technologies | Week 8: Wed Apr 3 | Knockout mice created by TALEN-mediated gene targeting. Sung YH et al. Nat Biotechnol (2013) 31(1):23-4. doi: 10.1038/nbt.2477 | Multiplex Genome Engineering Using CRISPR/Cas Systems Cong L et al. Science (2013) Jan 3. PMID: 23287718 | |
| Cell Physiology | Week 9: Wed Apr 10 before tech spec review | Shared control of gene expression in bacteria by transcription factors and global physiology of the cell Berthoumieux S et alMol Syst Biol (2013) 9:634 doi: 10.1038/msb.2012.70 | A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis Picotti P et al.Nature (2013) Jan 20. doi: 10.1038/nature11835 | |
| Chassis | Week 10: Wed Apr 17 | Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production Woodruff LB, May BL, Warner JR, Gill RT. Biotechnol Bioeng (2013) Jan 15. doi: 10.1002/bit.24840 | Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems Cardinale S, Arkin AP.Biotechnol J(2012) 7(7):856-66. doi: 10.1002/biot.201200085 | |
| Programming in the Noise | Week 11: Wed Apr 24 | Iterative plug-and-play methodology for constructing and modifying synthetic gene networks Litcofsky KD et al. Nat Methods(2012) 9(11):1077-80. doi: 10.1038/nmeth.2205 | 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 | Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na D et al. Nat Biotechnol (2013) Jan 20. doi: 10.1038/nbt.2461 | 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 | |
| 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 | |
