20.20(S10):Advanced topics

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| '''Logic Modules'''<br>  
| '''Logic Modules'''<br>  
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| Wed Feb 17
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| Wed Feb 17 (RW OoT)
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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]]
|'''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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|Elowitz, M. B. & Leibler, S. A synthetic oscillatory
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|Elowitz, MB, and Leibler, S. ''A synthetic oscillatory
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network of transcriptional regulators. Nature 403,
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network of transcriptional regulators.'' Nature 403,
335–338 (2000)<br>
335–338 (2000)<br>
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Gardner, T. S., Cantor, C. R. & Collins, J. J.
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Gardner TS, et al.<br> ''Construction of a genetic toggle switch in Escherichia
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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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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>
<font color = red>May also want non-DNA, non-protein based logic paper (RNAi logic?)</font color>
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Line 69: Line 68:
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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]]
|'''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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|Levskaya A, et al.''Synthetic biology: engineering Escherichia coli to see light.''<br> [[PMID: 16306980]]
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|Levskaya A, et al.<br>''Synthetic biology: engineering Escherichia coli to see light.''<br> [[PMID: 16306980]]
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|--
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| '''Physical Organization''' <br>
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| '''Controlling System Dynamics''' <br>
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| Wed Mar 3  
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| Wed Mar 3 (RW OoT)
|  
|  
|'''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]]
|'''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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| Dueber JE, et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol. 2009 Aug;27(8):753-9.
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| Dueber JE, et al. <br>''Synthetic protein scaffolds provide modular control over metabolic flux.'' <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>
|  
|  
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| Ellis, Tom, Xiao Wang, and James J Collins. “Diversity-based, model-guided construction of synthetic gene networks with predicted functions.Nat Biotech advanced online publication (April 19, 2009).
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| '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' Ellis T, Wang X, and Collins JJ. ''Nat Biotech''
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| Tabor JJ et al. ''A synthetic genetic edge detection program''<br>[[PMID: 19563759]]
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| Tabor JJ et al. <br>''A synthetic genetic edge detection program''<br>[[PMID: 19563759]]
|--
|--
| '''Tuning the system: directed evolution''' <br>  
| '''Tuning the system: directed evolution''' <br>  
| Wed Mar 17  
| Wed Mar 17  
|
|
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| Stricker, J. et al. A fast, robust and tunable synthetic
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| '''A fast, robust and tunable synthetic gene oscillator''' Stricker, J. et al. ''Nature'' 456, 516–519 (2008).
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gene oscillator. Nature 456, 516–519 (2008).
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|Yokobayashi, Y, et al.<br> ''Directed evolution of a genetic circuit'' Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002).
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|Yokobayashi, Y., Weiss, R. & Arnold, F. H. Directed
+
-
evolution of a genetic circuit. Proc. Natl Acad. Sci. USA
+
-
99, 16587–16591 (2002).
+
|--
|--
! colspan="3" | Spring Break Mar 22-26
! colspan="3" | Spring Break Mar 22-26
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| Wed Mar 31
| Wed Mar 31
|  
|  
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| '''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>  
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| '''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]]
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| '''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]]  
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| Stemmer WP, et al. ''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.''<br>
 +
[[PMID: 7590320]] <br>
|--
|--
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| '''We're only human:''' <br>What is the state of the art? 
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| '''Chassis''' <br>
| <font color = blue> Thursday Apr 8 </font color>
| <font color = blue> Thursday Apr 8 </font color>
|  
|  
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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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Revision as of 15:18, 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 (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
Elowitz, MB, and Leibler, S. A synthetic oscillatory

network of transcriptional regulators. Nature 403, 335–338 (2000)
Gardner TS, et al.
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
Levskaya A, et al.
Synthetic biology: engineering Escherichia coli to see light.
PMID: 16306980
Controlling System Dynamics
Wed Mar 3 (RW OoT) 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
Dueber JE, et al.
Synthetic protein scaffolds provide modular control over metabolic flux.
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 Tabor JJ et al.
A synthetic genetic edge detection program
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). Yokobayashi, Y, et al.
Directed evolution of a genetic circuit 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.

PMID: 7590320

Chassis
Thursday Apr 8
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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