20.20(S10):Advanced topics

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| [[Natalie Kuldell]]<br>[[Ron Weiss]]
| [[Natalie Kuldell]]<br>[[Ron Weiss]]
|  
|  
-
|before next week read: '''Sci Am''' summary (handout)<br>“Two ‘What if” experiments”<br>Ptashne, M. <br>[[PMID 15055587]]<br>
+
|before next week read
-
“Build Artificial”<br> Brent, R. <br> [[PMID: 15055588]]   
+
#''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>
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| '''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
+
|'''A synthetic oscillatory network of transcriptional regulators.'''<br>Elowitz, MB, and Leibler, S. ''Nature'' 403,
-
network of transcriptional regulators.'' 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>
+
-
Gardner TS, et al.<br> ''Construction of a genetic toggle switch in Escherichia
+
-
coli'' Nature 403, 339–342 (2000).<br>
+
<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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| 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]]
-
|Levskaya A, et al.<br>''Synthetic biology: engineering Escherichia coli to see light.''<br> [[PMID: 16306980]]
+
|'''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, 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''' <br>Bashor CJ, et al. ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]]
-
| Dueber JE, et al. <br>''Synthetic protein scaffolds provide modular control over metabolic flux.'' <br>[[PMID: 19648908]]
+
| '''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''  
-
| Tabor JJ et al. <br>''A synthetic genetic edge detection program''<br>[[PMID: 19563759]]
+
| '''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).
-
|Yokobayashi, Y, et al.<br> ''Directed evolution of a genetic circuit'' Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002).
+
| '''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
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| Wed Mar 31
| Wed Mar 31
|  
|  
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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]]
+
| '''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]]
|--
|--
-
| '''Little Red Corvette:'''<br> Once you've got the DNA, where do you put it?  Introducing... THE CHASSIS
+
| '''In silico and -omics'''<br>  
| Wed Apr 14
| Wed Apr 14
|  
|  
-
|'''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]]
+
|'''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
-
| '''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]]  
+
| '''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]]
|--
|--
-
| '''Secret map hidden in the peg-leg:'''<br> getting DNA to speak in binary
+
| '''Noise'''<br>  
| Wed Apr 21
| Wed Apr 21
|  
|  
-
|'''Length-based encoding of binary data in DNA.''' Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.
+
|'''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>
-
''Langmuir'' (2008) 24(5):1613-6.<br>[[DOI: 10.1021/la703235y]]
+
|'''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]]
-
|
+
|--
|--
-
| '''On your mark, get set, go:''' System dynamics
+
| '''Metabolic Engineering'''  
| Wed Apr 28
| 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 <br> [[DOI: 10.1126/science.1151153]]
+
|'''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>
|  
|  
|--
|--
-
|'''Rough consensus and running code:''' building patterns and memories
+
|'''Cell Cell Communication/System Ecology'''  
| <font color = blue>Tue May 4</font color>  
| <font color = blue>Tue May 4</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]]
+
|'''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 16:21, 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
  1. Sci Am summary (handout)
  2. Two ‘What if” experiments
    Ptashne, M.
    PMID: 15055587
  3. Build Artificial
    Brent, R.
    PMID: 15055588
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

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)
Construction of a genetic toggle switch in Escherichia coli
Gardner TS, et al.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.
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.

PMID: 7590320

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.
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.
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
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