20.20(S15):Advanced topics: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(→16-220) |
(→16-220) |
||
Line 70: | Line 70: | ||
| '''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]] | ||
|-- | |-- | ||
| ''' | | '''SynBio for Science''' <br> | ||
| Week 6:<br> <font color = blue> Wed Mar 11</font color> <br>before 3 ideas presentations | | Week 6:<br> <font color = blue> Wed Mar 11</font color> <br>before 3 ideas presentations | ||
| No presentations this week (response record for one or the other paper due) | | No presentations this week (response record for one or the other paper due) | ||
|''' | | '''Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription''' <br>Forster AC. ''Biotechnol J.'' (2012) 7(7):835-45.<br> [[doi: 10.1002/biot.201200002]] | ||
| ''' | |'''Five hard truths for synthetic biology'''<br> Kwok R. ''Nature''(2010) 463(7279):288-90.<br>[[doi: 10.1038/463288a]] | ||
|-- | |-- | ||
| ''' | | '''Engineering Biology''' <br> | ||
| Week 7:<br> Wed Mar 18 | | Week 7:<br> Wed Mar 18 | ||
| <br> | | <br> | ||
| ''' | |'''Programmable biofilm-based materials from engineered curli nanofibres.'''<br> Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS.''Nat Commun.'' (2014) Sep 17;5:4945. [[doi: 10.1038/ncomms5945.]] | ||
|''' | |'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al. ''Nature'' (2013)<br> [[doi:10.1038/nature11875]] | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 23-27 | ! colspan="3" | Spring Break Mar 23-27 |
Revision as of 14:47, 28 January 2015
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 4 |
Natalie Kuldell | preview of 20.385 | Factory of Life Witze A Science News pdf Two ‘What if' experiments |
Parts™ | Week 2: Wed Feb 11 |
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 |
Advances and current limitations in transcript-level control of gene expression Leavitt JM, Alper HS. Curr Opin Biotechnol. (2015) Jan 2;34C:98-104. doi: 10.1016/j.copbio.2014.12.015. Review pdf |
Transcription-based Logic Devices |
Week 3: Wed Feb 18 |
Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules Baojun Wang and Martin Buck. Chem. Commun. (2014) 50: 11642-11644 DOI: 10.1039/C4CC05264A |
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 | |
DNA fine-tuning + evolution |
Week 4: Wed Feb 25 |
An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits. Beneš D1, Sosík P, Rodríguez-Patón A. Artif Life. (2015) Jan 26:1-14. doi:10.1162/ARTL_a_00160 |
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 4 |
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 | |
SynBio for Science |
Week 6: Wed Mar 11 before 3 ideas presentations |
No presentations this week (response record for one or the other paper due) | 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 |
Engineering Biology |
Week 7: Wed Mar 18 |
Programmable biofilm-based materials from engineered curli nanofibres. Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS.Nat Commun. (2014) Sep 17;5:4945. doi: 10.1038/ncomms5945. |
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Goldman N et al. Nature (2013) doi:10.1038/nature11875 | |
Spring Break Mar 23-27 | No class all week | |||
---|---|---|---|---|
DNA construction and editing technologies |
Week 8: Wed Apr 1 |
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 8 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 15 |
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 22 |
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 Apr 29 |
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 6 |
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 13 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 |