20.20(S11):Advanced topics: Difference between revisions
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335–338 <br>[[PMID: 10659856]] <br>'''Construction of a genetic toggle switch in Escherichia coli'''<br> Gardner TS, et al.''Nature''(2000) 403, 339–342 <br>[[PMID: 10659857]]<br> | 335–338 <br>[[PMID: 10659856]] <br>'''Construction of a genetic toggle switch in Escherichia coli'''<br> Gardner TS, et al.''Nature''(2000) 403, 339–342 <br>[[PMID: 10659857]]<br> | ||
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|'''Protein Design'''<br> | |'''Protein Design: directed evolution'''<br> | ||
| Wed Feb 23 | | Wed Feb 23 | ||
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|'''De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth''' <br>Fisher MA, et al. ''PLoS One'' (2011)6(1):e15364<br>[[DOI: 10.1371/journal.pone.0015364]] | |'''De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth''' <br>Fisher MA, et al. ''PLoS One'' (2011)6(1):e15364<br>[[DOI: 10.1371/journal.pone.0015364]] | ||
|''' | |'''Directed evolution of recombinase specificity by split gene reassembly''' <br>Gersbach, CA, et al. ''NAR'' (2010) 38(12): 4198-4206-1543 <br> [[DOI: 10.1093/nar/gkq125]] | ||
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| ''' | |'''RNA Engineering'''<br> | ||
| Wed Mar 2 | | Wed Mar 2 | ||
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|''' | | '''Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins'''<br>Culler, SJ, Hoff, KG, Smolke, CD. ''Science'' (2010) 330:1251-1255 <br>[[DOI: 10.1126/science.1192128]] | ||
| ''' | | '''The Case for RNA''' <br>Chang, CL, Arkin AP. ''Science'' (2010) 330:1185-1186<br>[[DOI: 10.1126/science.1199495]] | ||
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| ''' | | '''Tuning the system: Network Composition''' <br> | ||
| <font color = blue> Thursday Mar 10</font color> | | <font color = blue> Thursday Mar 10</font color> | ||
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| ''' | | '''A modular positive feedback-based gene amplifier''' Nistala GJ et al. ''JBE'' (2010) 4:4<br>[[DOI: 10.1186/1754-1611-4-4]] | ||
|''' | |'''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]] | ||
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| ''' | | '''System Composition''' <br> | ||
| Wed Mar 16 | | Wed Mar 16 | ||
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| ''' | | '''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<br>[[DOI:10.1016/j.stem.2010.08.012]] | ||
| '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]] | | '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]] | ||
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| Wed Mar 30 | | Wed Mar 30 | ||
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| | | '''Programming cells by multiplex genome engineering and accelerated evolution'''<br>Wang HH, et al. ''Nature'' (2009) Aug 13;460(7257):894-8. <br>[[PMID: 19633652 ]] | ||
| '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides'''<br>Stemmer WP, et al. ''Gene'' (1995) 164(1):49-53 <br>[[PMID: 7590320]] <br> | | '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides'''<br>Stemmer WP, et al. ''Gene'' (1995) 164(1):49-53 <br>[[PMID: 7590320]] <br> | ||
|-- | |-- |
Revision as of 14:58, 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 | before next week read
| |
Parts™ | Wed Feb 9 | Natalie Kuldell ppt is here |
A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor
Brent R, Ptashne M.Cell (1985) Dec;43(3 Pt 2):729-36. |
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 | |
System Composition |
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 |
A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928 | |
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 | |
Chassis |
Thursday Apr 7 | Article 1: Formation of protocell-like vesicles in a thermal diffusion column.Budin I, Bruckner RJ, and Szostak JW. J Am Chem Soc. (2009)131(28):9628-9 PMID: 19601679 Article 2: Genome transplantation in bacteria:changing one species to another Lartigue C, et al. Science 2007, 317:632-638. PMID: 17600181 |
Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050 | |
In silico and -omics |
Wed Apr 13 | Article 1: Design of genetic networks with specified functions by evolution in silico Francois, P. & Hakim, V. Proc. Natl Acad. Sci. USA (2004) 101, 580–585 PMID: 14704282 Article 2: Engineering transcription factors with novel DNA-binding specificity using comparative genomics Desai TA, et al. Nucleic Acids Res (2009) 37(8): 2493-503 PMID: 19264798 |
Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 link Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206 | |
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 | Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385 Article 2: Synthesis of methyl halides from biomass using engineered microbes Bayer TS, et al. J Am Chem Soc (2009) 131:6508-6515. PMID: 19378995 |
Synthetic protein scaffolds provide modular control over metabolic flux. Dueber JE et al. Nat Biotechnol. (2009) 27(8):753-9. PMID: 19648908 | |
Cell Cell Communication/System Ecology | Wed May 4 | Article 1: A synthetic Escherichia coli predator-prey ecosystem Balagaddé FK, et al. Mol Syst Biol. 2008;4:187. PMID: 18414488 Article 2: Synthetic cooperation in engineered yeast populations Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. (2007) 104(6):1877-82. PMID: 17267602 |
Synthetic ecosystems based on airborne inter- and intrakingdom communication Weber, W., Daoud-El Baba, M. & Fussenegger, M. Proc. Natl Acad. Sci. USA (2007) 104, 10435–10440 PMID: 17551014 | |
Property rights in synthetic biology | Tue May 10? | Article 1: Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173 |
Article 2: 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? | Article 1: 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 |
Article 2: Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article | |
Molecular and Cellular Computing | Tue May 10? | 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 |
Engineering bacteria to solve the Burnt Pancake Problem Haynes KA, et al. J Biol Eng. 2008 May 20;2:8. PMID: 18492232 |