20.20(S10):Advanced topics: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
Line 41: | Line 41: | ||
| [[Natalie Kuldell]]<br>[[Ron Weiss]] | | [[Natalie Kuldell]]<br>[[Ron Weiss]] | ||
| | | | ||
|before next week read | |before next week read | ||
#''Sci Am'' summary (handout) | |||
#''Two ‘What if” experiments''<br>Ptashne, M. <br>[[PMID: 15055587]] | |||
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]] | |||
|-- | |-- | ||
| <b>Parts™</b> | | <b>Parts™</b> | ||
Line 49: | Line 51: | ||
| '''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.''' | | '''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.<br> [[PMID: 3907859]] | Brent R, Ptashne M.''Cell.'' 1985 Dec;43(3 Pt 2):729-36.<br> [[PMID: 3907859]] | ||
| | | '''Activation of prokaryotic transcription through arbitrary protein-protein contacts''' <br>Dove SL, et al.<br> Nature. 1997 Apr 10;386(6625):627-30.<br>[[PMID: 9121589]] | ||
|-- | |-- | ||
| '''Logic Modules'''<br> | | '''Logic Modules'''<br> | ||
| Wed Feb 17 (RW OoT) | | Wed Feb 17 (RW OoT) | ||
| | | | ||
|'''Environmental signal integration by a modular AND gate.'''Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology''3 133 2007<br>[[DOI : 10.1038/msb4100173]] | |'''Environmental signal integration by a modular AND gate.'''<br> Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology''3 133 2007<br>[[DOI : 10.1038/msb4100173]] | ||
|Elowitz, MB, and Leibler, S. '' | |'''A synthetic oscillatory network of transcriptional regulators.'''<br>Elowitz, MB, and Leibler, S. ''Nature'' 403, | ||
335–338 (2000)<br>'''Construction of a genetic toggle switch in Escherichia coli'''<br> Gardner TS, et al.''Nature'' 403, 339–342 (2000)<br> | |||
335–338 (2000)<br> | |||
coli'' Nature 403, 339–342 (2000) | |||
<font color = red>May also want non-DNA, non-protein based logic paper (RNAi logic?)</font color> | <font color = red>May also want non-DNA, non-protein based logic paper (RNAi logic?)</font color> | ||
|-- | |-- | ||
Line 65: | Line 64: | ||
| Wed Feb 24 | | Wed Feb 24 | ||
| | | | ||
|'''Rewiring the specificity of two-component signal transduction systems.''' Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[DOI: 10.1016/j.cell.2008.04.040]] | |'''Rewiring the specificity of two-component signal transduction systems.''' <br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[DOI: 10.1016/j.cell.2008.04.040]] | ||
| | |'''Synthetic biology: engineering Escherichia coli to see light.'''<br>Levskaya A, et al.<br> [[PMID: 16306980]] | ||
|-- | |-- | ||
| '''Controlling System Dynamics''' <br> | | '''Controlling System Dynamics''' <br> | ||
| Wed Mar 3 (RW OoT) | | Wed Mar 3 (RW OoT) | ||
| | | | ||
|'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' Bashor CJ, | |'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' <br>Bashor CJ, et al. ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]] | ||
| | | '''Synthetic protein scaffolds provide modular control over metabolic flux.'''<br> Dueber JE, et al. <br>[[PMID: 19648908]] | ||
|-- | |-- | ||
| '''Functional Network Composition'''<br> | | '''Functional Network Composition'''<br> | ||
| <font color = blue> Thursday Mar 11</font color> | | <font color = blue> Thursday Mar 11</font color> | ||
| | | | ||
| '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' Ellis T, Wang X, and Collins JJ. ''Nat Biotech'' | | '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' <br>Ellis T, Wang X, and Collins JJ. ''Nat Biotech'' | ||
| | | '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. <br>[[PMID: 19563759]] | ||
|-- | |-- | ||
| '''Tuning the system: directed evolution''' <br> | | '''Tuning the system: directed evolution''' <br> | ||
| Wed Mar 17 | | Wed Mar 17 | ||
| | | | ||
| '''A fast, robust and tunable synthetic gene oscillator''' Stricker, J. et al. ''Nature'' 456, 516–519 (2008). | | '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' 456, 516–519 (2008). | ||
| | | '''Directed evolution of a genetic circuit''' <br>Yokobayashi, Y, et al.''Proc. Natl Acad. Sci. USA'' 99, 16587–16591 (2002). | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 22-26 | ! colspan="3" | Spring Break Mar 22-26 | ||
Line 93: | Line 92: | ||
| Wed Mar 31 | | Wed Mar 31 | ||
| | | | ||
| '''Article 1:''' <br>'''Programming cells by multiplex genome engineering and accelerated evolution.'''<br>Wang HH, et al. Nature | | '''Article 1:''' <br>'''Programming cells by multiplex genome engineering and accelerated evolution.'''<br>Wang HH, et al. ''Nature'' 2009 Aug 13;460(7257):894-8. <br>'''Article 2:''' <br> '''Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.'''Gibson DG, et al. Science. 2008 Feb 29;319(5867):1215-20. <br>[[PMID: 18218864]] | ||
| Stemmer WP, et al. ''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.''<br> | | Stemmer WP, et al. ''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.''<br> | ||
[[PMID: 7590320]] <br> | [[PMID: 7590320]] <br> | ||
Line 99: | Line 98: | ||
| '''Chassis''' <br> | | '''Chassis''' <br> | ||
| <font color = blue> Thursday Apr 8 </font color> | | <font color = blue> Thursday Apr 8 </font color> | ||
| | | | ||
| Article 1: '''Towards synthesis of a minimal cell'''<br>Forster, A. C. & Church, G. M. <br> ''Mol. Syst. Biol.'' 2, 45 (2006). <br> alternative Article 1:? '''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]] <br> '''Article 2:''' '''Genome transplantation in bacteria: | |||
changing one species to another.'''<br>Lartigue C, et al. ''Science'' 2007, 317:632-638. | |||
|'''Reconstitution of contractile FtsZ rings in liposomes.''' Osawa M, Anderson DE, Erickson HP.''Science'' (2008)320(5877):792-4.<br>[[DOI: 10.1126/science.1154520]] | |||
|-- | |-- | ||
| ''' | | '''In silico and -omics'''<br> | ||
| Wed Apr 14 | | Wed Apr 14 | ||
| | | | ||
|''' | |'''Article 1:''' '''Design of genetic networks with specified functions by evolution in silico'''<br> Francois, P. & Hakim, V. ''Proc. Natl Acad. Sci. USA'' 101, 580–585 (2004). <br> '''Article 2:''''''Engineering transcription factors with novel DNA-binding specificity using comparative genomics''' <br> Desai TA, et al. ''Nucleic Acids Res'' 2009 | ||
| ''' | | '''Design of multi-specificity in protein interfaces'''Humphris, EL; Kortemme, T. ''PLoS computational biology'' (2007) 3(8):e164<br>[[DOI : 10.1371/journal.pcbi.0030164]] | ||
|-- | |-- | ||
| ''' | | '''Noise'''<br> | ||
| Wed Apr 21 | | Wed Apr 21 | ||
| | | | ||
|''' | |'''Article 1: Gene regulation at the single-cell level'''<br>Rosenfeld N, et al. ''Science'' 307, 1962–1965 (2005).<br> '''Article 2: Stochastic switching as a survival strategy in fluctuating environments.'''<br> Acar M. et al. ''Nature Genetics'' 40, 471 – 475 (2008) <br> | ||
'' | |'''Phenotypic consequences of promoter-mediated transcriptional noise.''' <br>Blake WJ, et al. ''Molecular Cell''(2006) 24(6):853-65<br>[[DOI : 10.1016/j.molcel.2006.11.003]] | ||
|-- | |-- | ||
| ''' | | '''Metabolic Engineering''' | ||
| Wed Apr 28 | | Wed Apr 28 | ||
| | | | ||
|''' | |'''Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro, D. K. et al. ''Nature'' 440, 940–943 (2006).<br> '''Article 2: Synthesis of methyl halides from biomass using engineered microbes.''' <br> Bayer TS, et al. ''J Am Chem Soc'' 2009, 131:6508-6515.<br> | ||
| | | | ||
|-- | |-- | ||
|''' | |'''Cell Cell Communication/System Ecology''' | ||
| <font color = blue>Tue May 4</font color> | | <font color = blue>Tue May 4</font color> | ||
| | | | ||
|''' | |'''Article 1: A synthetic Escherichia coli predator-prey ecosystem'''<br> Balagaddé FK, et al. ''Mol Syst Biol.'' 2008;4:187. <br>[[PMID: 18414488]] '''Article 2: Synthetic ecosystems based on airborne inter- and intrakingdom communication.''' <br> Weber, W., Daoud-El Baba, M. & Fussenegger, M. ''Proc. Natl Acad. Sci. USA'' 104, 10435–10440 (2007). | ||
| '''Synthetic cooperation in engineered yeast populations'''<br> Shou W, Ram S, Vilar JM. ''Proc Natl Acad Sci U S A.'' 2007 Feb 6;104(6):1877-82. | |||
|-- | |-- | ||
| '''mine mine mine:''' property rights in synthetic biology | | '''mine mine mine:''' property rights in synthetic biology |
Revision as of 13:21, 18 January 2010
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 3 | Natalie Kuldell Ron Weiss |
before next week read
| |
Parts™ | Wed Feb 10 | Natalie Kuldell Ron Weiss |
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. |
Activation of prokaryotic transcription through arbitrary protein-protein contacts Dove SL, et al. Nature. 1997 Apr 10;386(6625):627-30. PMID: 9121589 |
Logic Modules |
Wed Feb 17 (RW OoT) | Environmental signal integration by a modular AND gate. Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173 |
A synthetic oscillatory network of transcriptional regulators. Elowitz, MB, and Leibler, S. Nature 403, 335–338 (2000) | |
Signal Specificity |
Wed Feb 24 | Rewiring the specificity of two-component signal transduction systems. Skerker JM, et al. Cell (2008)133(6):1043-54. DOI: 10.1016/j.cell.2008.04.040 |
Synthetic biology: engineering Escherichia coli to see light. Levskaya A, et al. PMID: 16306980 | |
Controlling System Dynamics |
Wed Mar 3 (RW OoT) | Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor CJ, et al. Science (2008)319: 1539-1543 DOI: 10.1126/science.1151153 |
Synthetic protein scaffolds provide modular control over metabolic flux. Dueber JE, et al. PMID: 19648908 | |
Functional Network Composition |
Thursday Mar 11 | Diversity-based, model-guided construction of synthetic gene networks with predicted functions Ellis T, Wang X, and Collins JJ. Nat Biotech |
A synthetic genetic edge detection program Tabor JJ et al. PMID: 19563759 | |
Tuning the system: directed evolution |
Wed Mar 17 | A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature 456, 516–519 (2008). |
Directed evolution of a genetic circuit Yokobayashi, Y, et al.Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002). | |
Spring Break Mar 22-26 | No class all week | |||
---|---|---|---|---|
DNA construction and editing technologies |
Wed Mar 31 | Article 1: Programming cells by multiplex genome engineering and accelerated evolution. Wang HH, et al. Nature 2009 Aug 13;460(7257):894-8. Article 2: Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.Gibson DG, et al. Science. 2008 Feb 29;319(5867):1215-20. PMID: 18218864 |
Stemmer WP, et al. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. | |
Chassis |
Thursday Apr 8 | Article 1: Towards synthesis of a minimal cell Forster, A. C. & Church, G. M. Mol. Syst. Biol. 2, 45 (2006). alternative Article 1:? Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050 Article 2: Genome transplantation in bacteria: changing one species to another. |
Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4. DOI: 10.1126/science.1154520 | |
In silico and -omics |
Wed Apr 14 | 'Article 1: Design of genetic networks with specified functions by evolution in silico Francois, P. & Hakim, V. Proc. Natl Acad. Sci. USA 101, 580–585 (2004). Article 2:'Engineering transcription factors with novel DNA-binding specificity using comparative genomics Desai TA, et al. Nucleic Acids Res 2009 |
Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 DOI : 10.1371/journal.pcbi.0030164 | |
Noise |
Wed Apr 21 | Article 1: Gene regulation at the single-cell level Rosenfeld N, et al. Science 307, 1962–1965 (2005). Article 2: Stochastic switching as a survival strategy in fluctuating environments. Acar M. et al. Nature Genetics 40, 471 – 475 (2008) |
Phenotypic consequences of promoter-mediated transcriptional noise. Blake WJ, et al. Molecular Cell(2006) 24(6):853-65 DOI : 10.1016/j.molcel.2006.11.003 | |
Metabolic Engineering | Wed Apr 28 | Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro, D. K. et al. Nature 440, 940–943 (2006). Article 2: Synthesis of methyl halides from biomass using engineered microbes. Bayer TS, et al. J Am Chem Soc 2009, 131:6508-6515. |
||
Cell Cell Communication/System Ecology | Tue 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 ecosystems based on airborne inter- and intrakingdom communication. Weber, W., Daoud-El Baba, M. & Fussenegger, M. Proc. Natl Acad. Sci. USA 104, 10435–10440 (2007). |
Synthetic cooperation in engineered yeast populations Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1877-82. | |
mine mine mine: property rights in synthetic biology | Tue May 11 | 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 GenomicsKaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739. | |
drop it like it's hot: safety! | Tue May 11? | 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 |