20.20(S13):Advanced topics
From OpenWetWare
Jump to navigationJump to search
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 Science News 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 |
| Transcription-based Logic Devices |
Week 3: Wed Feb 20 |
Paula + NK ppt is here |
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 |
| DNA fine-tuning + evolution |
Week 4: Wed Feb 27 |
Jessica + NK ppt is here |
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 |
| RNA Engineering |
Week 5: Wed Mar 6 |
Kristine + Ryan ppt is here |
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 |
Divya + NK ppt is here |
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 |
Holly + Gonzo ppt is here |
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 |
Jessica (Sung et al paper) ppt is here |
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 |
No presentations this week (response record for one or the other paper due) | 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 |
Kristine (Woodruff paper) ppt is here Ryan (Cardinale paper) ppt is here |
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 |
Divya (Litcofsky paper) May 1st Gonzo (Prindle paper) May 8th |
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 |
| Property rights in synthetic biology | Week 12: Wed May 1 |
Holly (Rai paper) ppt is here + Divya ppt is here |
Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173 |
Preparing synthetic biology for the world Moe-Behrens GH, Davis R, Haynes KA. Front Microbiol (2013) 4:5 doi: 10.3389/fmicb.2013.00005 |
| Systems & Communities | Week 13: Wed May 8 |
Paula (Oritz paper) ppt is here + Gonzo (Prindle paper) ppt is here |
Engineered cell-cell communication via DNA messaging Ortiz ME, Endy D. JBE (2012) 6(1):16. doi: 10.1186/1754-1611-6-16 |
Autonomous bacterial localization and gene expression based on nearby cell receptor density Wu HC et al. Mol Syst Biol (2013) 9:636. doi: 10.1038/msb.2012.71 |
| Metabolic Engineering | Week 14: Wed May 15 before final presentations |
no presentations this week (response record only if you've missed a different discussion this term) | Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na D et al. Nat Biotechnol (2013) Jan 20. doi: 10.1038/nbt.2461 |
Synthetic protein scaffolds provide modular control over metabolic fluxDueber JE et al. Nat Biotechnol (2009) 27(8):753-9. doi: 10.1038/nbt.1557 |
