20.20(S11):Advanced topics: Difference between revisions
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*Response record (20%): your thoughts about the papers you don't present. | *Response record (20%): your thoughts about the papers you don't present. | ||
*Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others | *Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others | ||
Instructions for these assignment are [[20.385(S11): | Instructions for these assignment are [[20.385(S11): About your reading assignments| here]] | ||
</div> | </div> | ||
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*Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team | *Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team | ||
*Instructor Leverage (5%): discretionary adjustment by NK | *Instructor Leverage (5%): discretionary adjustment by NK | ||
Instructions for these assignments are [[20.385(S11): | Instructions for these assignments are [[20.385(S11): About the team mentoring| here]] | ||
</div> | </div> | ||
|} | |} | ||
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| Wed Feb 2 | | Wed Feb 2 | ||
| [[Natalie Kuldell]] | | [[Natalie Kuldell]] | ||
| | | preview of 20.385 | ||
|before next week read | |before next week read | ||
#''The promise of synthetic biology''<br>Pleiss,J.<br>[[DOI:10.1007/s00253-006-0664-3]] | #''The promise of synthetic biology''<br>Pleiss,J.<br>[[DOI:10.1007/s00253-006-0664-3]] | ||
Line 49: | Line 49: | ||
| <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]] | ||
|-- | |-- | ||
| '''Logic | | '''Transcription-based Logic Devices'''<br> | ||
| Wed Feb 16 | | Wed Feb 16 | ||
| | | Pei-Ann, Jessica<br>[[Media:2 16 Jessica and Pei.ppt| ppt is here]] | ||
|'''Environmental signal integration by a modular AND gate'''<br> Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology'' (2007) 3:133 <br>[[PMID: 17700541]] | |'''Environmental signal integration by a modular AND gate'''<br> Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology'' (2007) 3:133 <br>[[PMID: 17700541]] | ||
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403, | |'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403, | ||
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> | ||
|-- | |-- | ||
|''' | |'''Protein Design: directed evolution'''<br> | ||
| Wed Feb 23 | | Wed Feb 23 | ||
| | | Yuan, Amber<br>[[Media:Amber yuan.ppt| ppt is here]] | ||
|''' | |'''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]] | ||
| | |- | ||
| ''' | |'''RNA Engineering'''<br> | ||
| Wed Mar 2 | | Wed Mar 2 | ||
| | | Andrew, Tina<br> [[Media:Tinaandrew20.385.ppt| ppt is here]] | ||
|''' | | '''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]] | ||
|-- | |-- | ||
| ''' | | '''Tuning the system: Network Composition''' <br> | ||
| <font color = blue> | | <font color = blue> Wed Mar 10</font color> <br>before 3 ideas presentations, meet in 4-163 | ||
| | | Colin, Raven<br> [[Media:Raven 20110309Presentation.pptx| ppt is here]] | ||
| '''A | | '''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]] | ||
|-- | |-- | ||
| ''' | | '''(re)Programming Systems''' <br> | ||
| Wed Mar 16 | | Wed Mar 16 | ||
| | | Patrick, Nick<br>[[Media:Presentation 3.16.2011.pptx| ppt is here]] | ||
| ''' | | '''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]] | ||
| ''' | | '''Reprogramming bacteria to seek and destroy an herbicide''' <br>Sinha, J. et al. ''Nature Chemical Biology'' (2010)6: 464–470<br>[[doi:10.1038/nchembio.369]] | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 21-25 | ! colspan="3" | Spring Break Mar 21-25 | ||
Line 91: | Line 90: | ||
| '''DNA construction and editing technologies'''<br> | | '''DNA construction and editing technologies'''<br> | ||
| Wed Mar 30 | | Wed Mar 30 | ||
| | | Raven, Andrew<br> [[Media:Yang20.385SingleStepAssembly.pptx| Andrew's ppt is here]]<br> [[Media:Raven 20110330Presentation.pptx| Raven's ppt is here]] | ||
| ' | | '''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> | ||
|-- | |-- | ||
| ''' | | '''Measurement technologies''' <br> | ||
| <font color = blue> | | <font color = blue> Wed Apr 6 </font color><br> before tech spec review, meet in 56-114 | ||
| | | Nick<br> [[Media:Nick paper 2.pptx| ppt is here]] | ||
| '''Nascent transcript sequencing visualizes transcription at nucleotide resolution'''Churchman 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''' <br> Kelly J, et al. ''Journal of Biological Engineering'' (2009) 3:4<br> [[doi:10.1186/1754-1611-3-4]] | ||
| | |- | ||
| ''' | | '''Chassis''' <br> | ||
| Wed Apr 13 | | Wed Apr 13 | ||
| | | Jessica, Tina<br> [[Media:Tina Presentation 20.385 4.13.2011-1.pptx| Tina's ppt is here]]<br> Jessica will present next week | ||
|'''Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system'''<br> Shin J, and Noireaux, V. ''JBE'' (2010) 4:9<br> [[DOI: 10.1186/1754-1611-4-9]] | |||
| ''' | | '''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]] | ||
|-- | |-- | ||
| '''Signal Connectivity'''<br> | | '''Signal Connectivity'''<br> | ||
| Wed Apr 20 | | Wed Apr 20 | ||
| | | Amber (will present Skerker paper next week)<br> [[Media:4 20 Journal Club Presentation.pptx| Jessica's ppt is here]] | ||
|'''Rewiring the specificity of two-component signal transduction systems'''<br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[PMID: 18555780]] | |||
|''' | |'''Tunable Signal Processing in Synthetic MAP Kinase Cascades''' <br>O'Shaughnessy, EC, et al. ''Cell''(2011) 144:119-131<br>[[DOI: 10.1016/j.cell.2010.12.014]] | ||
|-- | |-- | ||
| '''Metabolic Engineering''' | | '''Metabolic Engineering''' | ||
| Wed Apr 27 | | Wed Apr 27 | ||
| | | Yuan<br> [[Media:Amber 20385 presentation2 signal specificity.ppt| Amber's ppt is here]]<br>[[Media:Yuan 385 talk.ppt| Yuan's ppt is here]] | ||
| '''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) [[PMID: 20117231]] | |||
| ''' | |'''Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]] | ||
|-- | |-- | ||
|'''Cell Cell Communication/System Ecology''' | |'''Cell Cell Communication/System Ecology''' | ||
| Wed May 4 | | Wed May 4 | ||
| | | Colin <br> [[Media:Multicellular computing CMR.pptx| ppt is here]] | ||
|''' | |'''Robust multicellular computing using genetically encoded NOT gates and chemical 'wires''''<br>Tamsir, a., Tabor, J.J., Voigt, C.A. ''Nature'' 2011 Jan 13;469:212-215.<br>[[DOI: 10.1038/nature09565]]<br>[[Media:NORgate+ChemWires SuppInfo nature09565-s1.pdf| + supplementary info]] | ||
| ''' | | ''' Division of logic labour''' <br> Li B and You L.''Nature'' (2011) 469:171-172<br>[[DOI:10.1038/469171a]] | ||
|-- | |-- | ||
| '''Property rights in synthetic biology''' | | '''Property rights in synthetic biology''' | ||
| <font color = blue> | | <font color = blue> Wed May 11 </font color><br> before final presentations, meet in 56-114 | ||
| | | Pei <br> [[Media:PeiPresentationBoyle.pptx| ppt is here]] | ||
|''' | |''' Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br> | ||
|''' | |'''Patents and Translational Research in Genomics'''<br>Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]] | ||
|-- | |-- | ||
|'''Safety!''' | |'''Safety!''' | ||
| <font color = blue> | | <font color = blue> Wed May 11 </font color> <br> before final presentations, meet in 56-114 | ||
| | | Patrick <br> [[Media:Darwin’s Surprise.pptx| ppt is here]] | ||
| ''' | | '''Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' <br>Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]<br> | ||
|''' | |'''Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' <br>Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article] | ||
|} | |} |
Latest revision as of 06:43, 14 May 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 | Pei-Ann, Jessica ppt is here |
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 | Yuan, Amber ppt is here |
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 | Andrew, Tina ppt is here |
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 |
Wed Mar 10 before 3 ideas presentations, meet in 4-163 |
Colin, Raven ppt is here |
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 | Patrick, Nick ppt is here |
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 | |||
---|---|---|---|---|
DNA construction and editing technologies |
Wed Mar 30 | Raven, Andrew Andrew's ppt is here Raven's ppt is here |
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 |
Wed Apr 6 before tech spec review, meet in 56-114 |
Nick ppt is here |
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 | Jessica, Tina Tina's ppt is here Jessica will present next week |
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 | Amber (will present Skerker paper next week) Jessica's ppt is here |
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 | Yuan Amber's ppt is here Yuan's ppt is here |
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) PMID: 20117231 | 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 | Colin ppt is here |
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 + supplementary info |
Division of logic labour Li B and You L.Nature (2011) 469:171-172 DOI:10.1038/469171a |
Property rights in synthetic biology | Wed May 11 before final presentations, meet in 56-114 |
Pei 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 |
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! | Wed May 11 before final presentations, meet in 56-114 |
Patrick ppt is here |
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 |