20.20(S10):Advanced topics

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|'''Related paper(s) to enjoy'''
|'''Related paper(s) to enjoy'''
|--
|--
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| <b>A Voyage To Lilliput:</b><br>How a small number of AA substitution change activity of a protein
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| <b>Preview of 20.385</b>
| Wed Feb 3  
| Wed Feb 3  
| [[Natalie Kuldell]]<br>[[Ron Weiss]]
| [[Natalie Kuldell]]<br>[[Ron Weiss]]
|  
|  
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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>
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|before next week read: '''Sci Am''' summary (request from NK)
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[[PMID: 2968842]]<br>
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|'''Genetic Switch: Phage Lambda and Higher Organisms'''  Mark Ptashne[http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095  previewed here]<br>
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or '''Sci Am''' summary (request from NK)
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|--
|--
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| <b>Slide rule optional:</b><br>Computational design of novel protein activities
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| <b>Parts™</b>
| Wed Feb 10
| Wed Feb 10
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|  
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| [[Natalie Kuldell]]<br>[[Ron Weiss]]
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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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| '''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.'''
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|  
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Brent R, Ptashne M.''Cell.'' 1985 Dec;43(3 Pt 2):729-36.<br>
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PMID 3907859
 +
 
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|Ptashne “Two ‘What if” experiments” PMID 15055587<br>
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Brent “Build Artificial” PMID 15055588
|--
|--
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| '''Nature heart Legos™''':<br> Proteins are modular too
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| '''Logic Modules'''<br>  
| Wed Feb 17
| Wed Feb 17
|  
|  
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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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|'''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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|
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|Elowitz, M. B. & Leibler, S. A synthetic oscillatory
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|--
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network of transcriptional regulators. Nature 403,
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| '''Better odds in Vegas:'''<br>DNA elements are modular too, allowing for circuits, but circuits don't always work
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335–338 (2000)<br>
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Gardner, T. S., Cantor, C. R. & Collins, J. J.
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Construction of a genetic toggle switch in Escherichia
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coli. Nature 403, 339–342 (2000).<br>
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<font color = red>May also want non-DNA, non-protein based logic paper (RNAi logic?)</font color>
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|--  
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|'''Signal Specificity'''<br>  
| Wed Feb 24
| Wed Feb 24
|  
|  
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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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|'''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]]
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|
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|'''Synthetic biology: engineering Escherichia coli to see light.''' Levskaya A, et al. ''Nature'' (2005) 438(7067):441-2.
|--
|--
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| '''Darwin is alive and well:''' <br>Directed evolution at the parts and device level
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| '''Circuit Design''' <br>
| Wed Mar 3  
| Wed Mar 3  
|  
|  
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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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|Bashor, C. J., Helman, N. C., Yan, S. & Lim, W. A.
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|
+
Using engineered scaffold interactions to reshape
 +
MAP kinase pathway signaling dynamics. Science
 +
319, 1539–1543 (2008).
 +
|Stricker, J. et al. A fast, robust and tunable synthetic
 +
gene oscillator. Nature 456, 516–519 (2008).
|--
|--
| '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design
| '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design

Revision as of 07:45, 18 January 2010

Contents

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%): presented with a partner
  • Paper 2 (15%): presented solo
  • Response record (25%): your thoughts about the papers you don't present.

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress reports (15%): one page summaries of your freshman team's work
  • Mentoring journal(15%): one page summary of your freshman team's dynamics
  • 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

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: Sci Am summary (request from NK)
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.
PMID 3907859

Ptashne “Two ‘What if” experiments” PMID 15055587

Brent “Build Artificial” PMID 15055588

Logic Modules
Wed Feb 17 Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007
DOI : 10.1038/msb4100173
Elowitz, M. B. & Leibler, S. A synthetic oscillatory

network of transcriptional regulators. Nature 403, 335–338 (2000)
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
May also want non-DNA, non-protein based logic paper (RNAi logic?)

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. Nature (2005) 438(7067):441-2.
Circuit Design
Wed Mar 3 Bashor, C. J., Helman, N. C., Yan, S. & Lim, W. A.

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319, 1539–1543 (2008).

Stricker, J. et al. A fast, robust and tunable synthetic

gene oscillator. Nature 456, 516–519 (2008).

I demand the cone of silence:
nature's constraints on genetic circuit design
Thursday Mar 11 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 17 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 22-26 No class all week
Writing in genetic code:
DNA construction and editing technologies
Wed Mar 31 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 8 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 14 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 21 Length-based encoding of binary data in DNA. Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.

Langmuir (2008) 24(5):1613-6.
DOI: 10.1021/la703235y

On your mark, get set, go: System dynamics Wed Apr 28 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 4 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 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
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