20.902(S09):Advanced topics in synthetic biology: Difference between revisions
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=20.902: Advanced Topics in Synthetic Biology= | =20.902: Advanced Topics in Synthetic Biology= | ||
==Assignments== | ==Assignments== | ||
Homework dropbox is [http://stellar.mit.edu/S/course/20/sp09/20.902/homework/index.html here] | |||
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<b>Turning lambda Cro into a transcriptional activator.</b>Bushman FD, Ptashne M.''Cell.'' 1988 Jul 15;54(2):191-7.<br> | <b>Turning lambda Cro into a transcriptional activator.</b>Bushman FD, Ptashne M.''Cell.'' 1988 Jul 15;54(2):191-7.<br> | ||
PMID 2968842<br> <br>ppt [[Media:Cro2activator.ppt| here]] | [[PMID: 2968842]]<br> <br>ppt [[Media:2020(S09) Cro2activator.ppt| here]] | ||
|'''Genetic Switch: Phage Lambda and Higher Organisms''' Mark Ptashne[http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095 previewed here]<br> | |'''Genetic Switch: Phage Lambda and Higher Organisms''' Mark Ptashne[http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095 previewed here]<br> | ||
or '''Sci Am''' summary (request from NK) | or '''Sci Am''' summary (request from NK) | ||
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| Wed Feb 11 | | Wed Feb 11 | ||
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| | | '''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]] | ||
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| Wed Feb 18 | | Wed Feb 18 | ||
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| | |'''Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1.'''Jin T, Inouye M.''J Mol Biol.'' (1993)232(2):484-92.<br>[[PMID: 8393937]] | ||
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| Wed Feb 25 | | Wed Feb 25 | ||
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| | |'''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]] | ||
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|-- | |-- | ||
| '''Darwin is alive and well:''' <br>Directed evolution at the device level | | '''Darwin is alive and well:''' <br>Directed evolution at the parts and device level | ||
| Wed Mar 4 | | Wed Mar 4 | ||
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| | |'''RNA and RNP as new molecular parts in synthetic biology.'''Saito H, Inoue, T ''Journal of biotechnology''(2007)132(1):1-7<br>[[doi:10.1016/j.jbiotec.2007.07.952]] | ||
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| <font color = blue> Thursday Mar 12</font color> | | <font color = blue> Thursday Mar 12</font color> | ||
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| | |'''Phenotypic consequences of promoter-mediated transcriptional noise.''' Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, ''Molecular cell''(2006) 24(6):853-65<br>[[DOI : 10.1016/j.molcel.2006.11.003]] | ||
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|-- | |-- | ||
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| Wed Mar 18 | | Wed Mar 18 | ||
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| | | '''Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.''' Maeder ML, et. al. ''Mol Cell.'' (2008)31(2):294-301<br>[[DOI : 10.1016/j.molcel.2008.06.016]] | ||
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| '''Writing in genetic code:'''<br> DNA construction and editing technologies | | '''Writing in genetic code:'''<br> DNA construction and editing technologies | ||
| Wed Apr 1 | | Wed Apr 1 | ||
| | | | ||
| '''DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways.'''<br> Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12<br>[[PMID: 19074487]]<br> '''Article 2:''' <br> | |||
| '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.'''<br>Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Gene. 1995 Oct 16;164(1):49-53.<br> [[PMID: 7590320]] | |||
|-- | |-- | ||
| '''We're only human:''' <br>What is the state of the art? | | '''We're only human:''' <br>What is the state of the art? | ||
| <font color = blue> Thursday Apr 9 </font color> | | <font color = blue> Thursday Apr 9 </font color> | ||
| ''' | | | ||
|'''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]] | |||
| | | | ||
|-- | |-- | ||
| '''Little Red Corvette:'''<br> Once you've got the DNA, where do you put it? Introducing... THE CHASSIS | | '''Little Red Corvette:'''<br> Once you've got the DNA, where do you put it? Introducing... THE CHASSIS | ||
| Wed Apr 15 | | Wed Apr 15 | ||
| | | | ||
|'''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]] | |||
| '''Emergent properties of reduced-genome Escherichia coli.'''Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. ''Science.'' (2006)312(5776):1044-6.<br> [[PMID: 16645050]] | |||
|-- | |-- | ||
| ''' | | '''Secret map hidden in the peg-leg:'''<br> getting DNA to speak in binary | ||
| Wed Apr 22 | | Wed Apr 22 | ||
| ''' | | | ||
|'''Length-based encoding of binary data in DNA.''' Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M. | |||
''Langmuir'' (2008) 24(5):1613-6.<br>[[DOI: 10.1021/la703235y]] | |||
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| '''On your mark, get set, go:''' System dynamics | | '''On your mark, get set, go:''' System dynamics | ||
| | | Wed Apr 29 | ||
| | | | ||
|'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' Bashor CJ, Helman NC, Yan S, Lim, WA ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]] | |||
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|-- | |-- | ||
|'''Rough consensus and running code:''' building patterns and memories | |'''Rough consensus and running code:''' building patterns and memories | ||
| | | <font color = blue>Tue May 5</font color> | ||
| | | | ||
|'''Rational design of memory in eukaryotic cells.''' Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Genes Dev. (2007):21(18):2271-6.<br> [[DOI: 10.1101/gad.1586107]] | |||
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| '''mine mine mine:''' property rights in synthetic biology | | '''mine mine mine:''' property rights in synthetic biology | ||
| <font color = blue> Tue May 12 </font color> | | <font color = blue> Tue May 12 </font color> | ||
| | | | ||
| '''Synthetic biology: caught between property rights, the public domain, and the commons''' Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[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.]] | ||
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|-- | |-- | ||
|'''drop it like it's hot:''' safety! | |'''drop it like it's hot:''' safety! | ||
| | | <font color = blue> Tue May 12 </font color> | ||
| | | | ||
| '''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.<br>[[DOI: 10.1038/embor.2008.232]] | |||
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|-- | |-- | ||
|} | |} |
Latest revision as of 05:30, 3 February 2009
<html> <style>#en2020 a {color:black;}</style> </html>
Home | Lecture and Studio schedule |
20.902 Reading Schedule | |
Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 | |||
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Expectations | Guidelines: 3 Ideas Presentation | Guidelines: Tech Spec Review | Guidelines: Final Presentations |
Team Building Resources | Teacher Resources |
20.902: 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 |
A Voyage To Lilliput: How a small number of AA substitution change activity of a protein |
Wed Feb 4 | Natalie Kuldell |
Turning lambda Cro into a transcriptional activator.Bushman FD, Ptashne M.Cell. 1988 Jul 15;54(2):191-7. |
Genetic Switch: Phage Lambda and Higher Organisms Mark Ptashnepreviewed here or Sci Am summary (request from NK) |
Slide rule optional: Computational design of novel protein activities |
Wed Feb 11 | Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 DOI : 10.1371/journal.pcbi.0030164 |
||
Nature heart Legos™: Proteins are modular too |
Wed Feb 18 | Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1.Jin T, Inouye M.J Mol Biol. (1993)232(2):484-92. PMID: 8393937 |
||
Better odds in Vegas: DNA elements are modular too, allowing for circuits, but circuits don't always work |
Wed Feb 25 | Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173 |
||
Darwin is alive and well: Directed evolution at the parts and device level |
Wed Mar 4 | RNA and RNP as new molecular parts in synthetic biology.Saito H, Inoue, T Journal of biotechnology(2007)132(1):1-7 doi:10.1016/j.jbiotec.2007.07.952 |
||
I demand the cone of silence: nature's constraints on genetic circuit design |
Thursday Mar 12 | Phenotypic consequences of promoter-mediated transcriptional noise. Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, Molecular cell(2006) 24(6):853-65 DOI : 10.1016/j.molcel.2006.11.003 |
||
Intelligent Design: Functional composition at the device level |
Wed Mar 18 | Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Maeder ML, et. al. Mol Cell. (2008)31(2):294-301 DOI : 10.1016/j.molcel.2008.06.016 |
||
Spring Break Mar 24-28 | No class all week | |||
---|---|---|---|---|
Writing in genetic code: DNA construction and editing technologies |
Wed Apr 1 | DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12 PMID: 19074487 Article 2: |
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Gene. 1995 Oct 16;164(1):49-53. PMID: 7590320 | |
We're only human: What is the state of the art? |
Thursday Apr 9 | 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 |
||
Little Red Corvette: Once you've got the DNA, where do you put it? Introducing... THE CHASSIS |
Wed Apr 15 | Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4. DOI: 10.1126/science.1154520 |
Emergent properties of reduced-genome Escherichia coli.Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. Science. (2006)312(5776):1044-6. PMID: 16645050 | |
Secret map hidden in the peg-leg: getting DNA to speak in binary |
Wed Apr 22 | Length-based encoding of binary data in DNA. Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.
Langmuir (2008) 24(5):1613-6. |
||
On your mark, get set, go: System dynamics | Wed Apr 29 | Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor CJ, Helman NC, Yan S, Lim, WA Science (2008)319: 1539-1543 DOI: 10.1126/science.1151153 |
||
Rough consensus and running code: building patterns and memories | Tue May 5 | Rational design of memory in eukaryotic cells. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Genes Dev. (2007):21(18):2271-6. DOI: 10.1101/gad.1586107 |
||
mine mine mine: property rights in synthetic biology | Tue May 12 | 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 12 | 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 |