20.20(S11):Advanced topics: Difference between revisions
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| <b>Parts™</b> | | <b>Parts™</b> | ||
| Wed Feb 9 | | Wed Feb 9 | ||
| [[Natalie Kuldell]]<br>[[ ppt is here]] | | [[Natalie Kuldell]]<br>[[Media:2020(S11) Cro2activator.ppt| ppt is here]] | ||
| ''' | | '''Turning lambda Cro into a transcriptional activator'''Bushman FD, Ptashne M.''Cell.'' (1988) Jul 15;54(2):191-7.<br>[[PMID: 2968842]]<br> | ||
| '''Improving the Lac System for Synthetic Biology''' <br>Penumetcha, P., et al. ''Bios'' (2011) 81(1):7-15.<br>[[Media:Penumetcha etal 2010.pdf| pdf]] | | '''Improving the Lac System for Synthetic Biology''' <br>Penumetcha, P., et al. ''Bios'' (2011) 81(1):7-15.<br>[[Media:Penumetcha etal 2010.pdf| pdf]] | ||
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Revision as of 17:53, 29 January 2011
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
26-152
TOPIC | DATE | Discussion leader(s) | Discussion paper(s) | Related paper(s) to enjoy |
Preview of 20.385 | Wed Feb 2 | Natalie Kuldell | preview of 20.385 | before next week read
|
Parts™ | Wed Feb 9 | Natalie Kuldell ppt is here |
Turning lambda Cro into a transcriptional activatorBushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7. PMID: 2968842 |
Improving the Lac System for Synthetic Biology Penumetcha, P., et al. Bios (2011) 81(1):7-15. |
Transcription-based Logic Devices |
Wed Feb 16 | Environmental signal integration by a modular AND gate Anderson JC, Voigt C, Arkin, AP Molecular systems biology (2007) 3:133 PMID: 17700541 |
A synthetic oscillatory network of transcriptional regulators Elowitz, MB, and Leibler, S. Nature (2000) 403, 335–338 | |
Protein Design: directed evolution |
Wed Feb 23 | 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 | |
RNA Engineering |
Wed Mar 2 | Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255 DOI: 10.1126/science.1192128 |
The Case for RNA Chang, CL, Arkin AP. Science (2010) 330:1185-1186 DOI: 10.1126/science.1199495 | |
Tuning the system: Network Composition |
Thursday Mar 10 | A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4 DOI: 10.1186/1754-1611-4-4 |
A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928 | |
(re)Programming Systems |
Wed Mar 16 | Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630 DOI:10.1016/j.stem.2010.08.012 |
Reprogramming bacteria to seek and destroy an herbicide Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470 doi:10.1038/nchembio.369 | |
Spring Break Mar 21-25 | No class all week | |||
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DNA construction and editing technologies |
Wed Mar 30 | Programming cells by multiplex genome engineering and accelerated evolution Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8. PMID: 19633652 |
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Stemmer WP, et al. Gene (1995) 164(1):49-53 PMID: 7590320 | |
Measurement technologies |
Thursday Apr 7 | Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652 | Measuring the activity of BioBrick promoters using an in vivo reference standard Kelly J, et al. Journal of Biological Engineering (2009) 3:4 doi:10.1186/1754-1611-3-4 | |
Chassis |
Wed Apr 13 | Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system Shin J, and Noireaux, V. JBE (2010) 4:9 DOI: 10.1186/1754-1611-4-9 |
Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050 | |
Signal Connectivity |
Wed Apr 20 | Rewiring the specificity of two-component signal transduction systems Skerker JM, et al. Cell (2008)133(6):1043-54. PMID: 18555780 |
Tunable Signal Processing in Synthetic MAP Kinase Cascades O'Shaughnessy, EC, et al. Cell(2011) 144:119-131 DOI: 10.1016/j.cell.2010.12.014 | |
Metabolic Engineering | Wed Apr 27 | 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 (2010) doi:10.1016/j.ymben.2010.01.003. | Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385 | |
Cell Cell Communication/System Ecology | Wed May 4 | Robust multicellular computing using genetically encoded NOT gates and chemical 'wires' Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215. DOI: 10.1038/nature09565 |
Division of logic labour Li B and You L.Nature (2011) 469:171-172 DOI:10.1038/469171a | |
Property rights in synthetic biology | Tue May 10? | 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! | Tue May 10? | 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 |