20.20(S10):Advanced topics

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=20.385: Advanced Topics in Synthetic Biology=
=20.385: Advanced Topics in Synthetic Biology=
==Assignments==
==Assignments==
-
Homework dropbox is [http://stellar.mit.edu/S/course/20/sp10/20.385/homework/index.html here]
+
Homework dropbox is [http://stellar.mit.edu/S/course/20/sp10/20.385/homework/index.html here]<br>
 +
Schedule for interviews on April 28th is [[20.385(S10):Interview Schedule| here.]] Please sign up asap.<br> Interviews will run ~30' in 5-122. No response record will be due for Week 12.
{| cellspacing="2"  
{| cellspacing="2"  
|- valign="top"
|- valign="top"
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*Paper 2 (15%): presented solo
*Paper 2 (15%): presented solo
*Response record (25%): your thoughts about the papers you don't present.  
*Response record (25%): your thoughts about the papers you don't present.  
-
Instructions for these assignment are [[20.902(S09):Assignments on readings| here]]
+
Instructions for these assignment are [[20.385(S10):Assignments on readings| here]]
</div>
</div>
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*Mentoring journal(15%): one page summary of your freshman team's dynamics
*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
*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, RW
-
Instructions for these assignments are [[20.902(S09): Team mentoring assignments| here]]
+
Instructions for these assignments are [[20.385(S10): Team mentoring assignments| here]]
</div>
</div>
|}
|}
 +
==Reading Schedule==
==Reading Schedule==
===Discussions will be 1 hour long during Wednesday 2-5 studio block===  
===Discussions will be 1 hour long during Wednesday 2-5 studio block===  
Line 39: Line 41:
| <b>Preview of 20.385</b>
| <b>Preview of 20.385</b>
| Wed Feb 3  
| Wed Feb 3  
-
| [[Natalie Kuldell]]<br>[[Ron Weiss]]
+
| [[Natalie Kuldell]]<br>[[User:Ron Weiss| Ron Weiss]]
|  
|  
|before next week read
|before next week read
#''Sci Am'' summary (handout)
#''Sci Am'' summary (handout)
-
#''Two ‘What if” experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
+
#''Two ‘What if' experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]]   
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]]   
|--
|--
| <b>Parts™</b>
| <b>Parts™</b>
| Wed Feb 10
| Wed Feb 10
-
| [[Natalie Kuldell]]<br>[[Ron Weiss]]
+
| [[Natalie Kuldell]]<br>[[User:Ron Weiss| Ron Weiss]] [[Media:20 385 Week2.ppt| ppt is here]]
-
| '''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]]
+
| '''Activation of prokaryotic transcription through arbitrary protein-protein contacts''' <br>Dove SL, et al. ''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)
-
|  
+
| Alie [[Media:20385Presentation.ppt]]
-
|'''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]]
+
|'''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'' 403,
+
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403,
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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 <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>
-
<font color = red>May also want non-DNA, non-protein based logic paper (RNAi logic?)</font color>
+
|--  
|--  
-
|'''Signal Specificity'''<br>  
+
|'''Signal Connectivity'''<br>  
| Wed Feb 24
| Wed Feb 24
-
|  
+
| Jose [[Media:Jose Presentation20.385.pdf]]
-
|'''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]]
+
|'''Rewiring the specificity of two-component signal transduction systems''' <br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[PMID: 18555780]]
-
|'''Synthetic biology: engineering Escherichia coli to see light.'''<br>Levskaya A, et al.<br> [[PMID: 16306980]]
+
|'''Synthetic biology: engineering Escherichia coli to see light'''<br>Levskaya A, et al. ''Nature'' (2005) 438(7067):441-2.<br> [[PMID: 16306980]]
|--
|--
-
| '''Controlling System Dynamics''' <br>
+
| '''Engineered Network Dynamics''' <br>
-
| Wed Mar 3 (RW OoT)
+
| Wed Mar 3
-
|  
+
| Kelly [[Media:Kdrinkwa week5.pdf]]
-
|'''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]]
+
|'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' <br>Bashor CJ, et al. ''Science'' (2008) 319: 1539-1543 <br> [[PMID: 18339942]]
-
| '''Synthetic protein scaffolds provide modular control over metabolic flux.'''<br> Dueber JE, et al. <br>[[PMID: 19648908]]
+
| '''Synthetic protein scaffolds provide modular control over metabolic flux'''<br> Dueber JE, et al. ''Nat Biotech'' (2009) 27(8):753-9.<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>
-
|  
+
| [[Media:EdgeDetection fromHelenChen.pdf]]
-
| '''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' <br>Ellis T, Wang X, and Collins JJ.  ''Nat Biotech''  
+
| '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. ''Cell'' (2009) 137(7):1272-81 <br>[[PMID: 19563759]]
-
| '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. <br>[[PMID: 19563759]]
+
|'''Diversity-based, model-guided construction of synthetic gene networks with predicted functions''' <br>Ellis T, Wang X, and Collins JJ.  ''Nat Biotech'' (2009) 27(5):465-71<br>[[PMID: 19377462]]  
|--
|--
| '''Tuning the system: directed evolution''' <br>  
| '''Tuning the system: directed evolution''' <br>  
| Wed Mar 17  
| Wed Mar 17  
-
|
+
| Derek [[Media:Derek Ju Presentation 3-17-10.pdf]]
-
| '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' 456, 516–519 (2008).
+
| '''A dual selection module for directed evolution of synthetic circuits.''' Yokobayashi Y, Arnold FH. ''Nat Comp'' (2005) 4:245–254<br>[[Media:DirEvolTuning NaturalComputing05.pdf| pdf]]
-
| '''Directed evolution of a genetic circuit''' <br>Yokobayashi, Y, et al.''Proc. Natl Acad. Sci. USA'' 99, 16587–16591 (2002).
+
| '''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]]
|--
|--
! colspan="3" | Spring Break Mar 22-26
! colspan="3" | Spring Break Mar 22-26
Line 91: Line 92:
| '''DNA construction and editing technologies'''<br>  
| '''DNA construction and editing technologies'''<br>  
| Wed Mar 31
| Wed Mar 31
-
|  
+
| Article 1 = Alie [[Media:Alie Presentation2-20385.pdf]]
-
| '''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>[[PMID: 19633652 ]]<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>
+
| '''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>
-
[[PMID: 7590320]] <br>
+
|--
|--
| '''Chassis''' <br>
| '''Chassis''' <br>
| <font color = blue> Thursday Apr 8 </font color>
| <font color = blue> Thursday Apr 8 </font color>
-
|
+
| Article 2 = Derek [[Image:Derek Ju Presentation 4-8-10.pdf]]
-
| '''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:
+
| '''Article 1: <br>Formation of protocell-like vesicles in a thermal diffusion column.'''Budin I, Bruckner RJ, and Szostak JW. ''J Am Chem Soc.'' (2009)131(28):9628-9 [[PMID: 19601679]] <br> '''Article 2:<br> Genome transplantation in bacteria:changing one species to another'''<br>Lartigue C, et al. ''Science'' 2007, 317:632-638.<br>[[PMID: 17600181]]
-
changing one species to another.'''<br>Lartigue C, et al. ''Science'' 2007, 317:632-638.
+
|'''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]]
-
|'''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]]
+
|--
|--
| '''In silico and -omics'''<br>  
| '''In silico and -omics'''<br>  
-
| Wed Apr 14
+
| Wed Apr 14 (NK leaves by 3:30)
-
|  
+
| Article 2 = Alvin [[Image:Alvin 20.385 Presentation.pptx]]
-
|'''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  
+
|'''Article 1:<br>Design of genetic networks with specified functions by evolution in silico'''<br> Francois, P. & Hakim, V. ''Proc. Natl Acad. Sci. USA'' (2004) 101, 580–585<br> [[PMID: 14704282]]<br>'''Article 2:<br>Engineering transcription factors with novel DNA-binding specificity using comparative genomics''' <br> Desai TA, et al. ''Nucleic Acids Res'' (2009) 37(8): 2493-503<br>[[PMID: 19264798]]
-
| '''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]]
+
| '''Design of multi-specificity in protein interfaces'''Humphris, EL; Kortemme, T. ''PLoS computational biology'' (2007) 3(8):e164<br>[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030164 link]<br>'''Design principles for ligand-sensing, conformation-switching ribozymes.'''Chen X and Ellington AD. ''PLoS Comput Biol.'' (2009) Dec;5(12):e1000620. [[PMID: 20041206]]
|--
|--
| '''Noise'''<br>  
| '''Noise'''<br>  
| Wed Apr 21
| Wed Apr 21
-
|  
+
| Article 1 = Alvin [[Image:Alvin 20.385 Presentation 2.pdf]]
-
|'''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>
+
|'''Article 1: <br>Gene regulation at the single-cell level'''<br>Rosenfeld N, et al. ''Science'' (2005) 307, 1962–1965 <br>[[PMID: 15790856]]<br> '''Article 2: <br>Stochastic switching as a survival strategy in fluctuating environments'''<br> Acar M. et al.  ''Nature Genetics'' (2008) 40, 471 – 475<br>[[PMID: 18362885]]
-
|'''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]]
+
|'''Phenotypic consequences of promoter-mediated transcriptional noise.''' <br>Blake WJ, et al. ''Molecular Cell''(2006) 24(6):853-65<br>[[PMID: 17189188]]
|--
|--
| '''Metabolic Engineering'''  
| '''Metabolic Engineering'''  
| Wed Apr 28
| Wed Apr 28
-
|
+
| basic coverage of these articles since 310 and 330 are on overdrive this week
-
|'''Article 1: Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]<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>[[PMID: 19378995]]
+
|'''Article 1:<br> Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]<br> '''Article 2: <br>Synthesis of methyl halides from biomass using engineered microbes''' <br> Bayer TS, et al. ''J Am Chem Soc'' (2009) 131:6508-6515.<br>[[PMID: 19378995]]
-
|  
+
| '''Synthetic protein scaffolds provide modular control over metabolic flux.'''<br> Dueber JE et al. ''Nat Biotechnol.'' (2009) 27(8):753-9. [[PMID: 19648908]]
|--
|--
|'''Cell Cell Communication/System Ecology'''  
|'''Cell Cell Communication/System Ecology'''  
-
| <font color = blue>Tue May 4</font color>
+
| Wed May 5
-
|
+
| Article 1 = Kelly [[Image:Kdrinkwa week13.pdf]]
-
|'''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'' (2007) 104, 10435–10440 <br>[[PMID: 17551014]]
+
|'''Article 1: <br>A synthetic Escherichia coli predator-prey ecosystem'''<br> Balagaddé FK, et al. ''Mol Syst Biol.'' 2008;4:187. <br>[[PMID: 18414488]]<br> '''Article 2:<br>Synthetic cooperation in engineered yeast populations'''<br> Shou W, Ram S, Vilar JM. ''Proc Natl Acad Sci U S A.'' (2007) 104(6):1877-82. <br>[[PMID: 17267602]]
-
| '''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. <br>[[PMID: 17267602]]
+
| ''' Synthetic ecosystems based on airborne inter- and intrakingdom communication''' <br> Weber, W., Daoud-El Baba, M. & Fussenegger, M. ''Proc. Natl Acad. Sci. USA'' (2007) 104, 10435–10440 <br>[[PMID: 17551014]]
|--
|--
| '''Property rights in synthetic biology'''  
| '''Property rights in synthetic biology'''  
-
<font color = blue> Tue May 11? </font color>
+
|   
|
|
-
|''' Article 1: 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>
+
|''' Article 1: <br>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>
-
|'''Article 2: 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.]]
+
|'''Article 2: <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> Tue May 11? </font color>  
+
| <font color = blue> Tue May 11 </font color>  
-
|  
+
| Jose will focus on Article 1, but please read both [[Image:Jose 20.385finalpresentation.pdf]]
-
| '''Article 1: 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>
+
| '''Article 1:<br> 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>
-
|'''Article 2: 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]
+
|'''Article 2: <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]
|--
|--
|'''Programming Languages'''  
|'''Programming Languages'''  
-
| <font color = blue> Tue May 11? </font color>
 
|  
|  
-
| '''Article 1: Towards programming languages for genetic engineering of living cells'''<br> Pedersen M, Phillips A  ''J R Soc Interface'' 2009, 6(Suppl 4):S437-S450.<br>[[PMID: 19369220]]<br>
+
|
-
|'''Article 2: Cells Are Plausible Targets for High-Level Spatial Languages'''<br> Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008.
+
| '''Article 1: <br>Towards programming languages for genetic engineering of living cells'''<br> Pedersen M, Phillips A  ''J R Soc Interface'' 2009, 6(Suppl 4):S437-S450.<br>[[PMID: 19369220]]<br>
 +
|'''Article 2: <br>Cells Are Plausible Targets for High-Level Spatial Languages'''<br> Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008.
|--
|--
|'''Molecular and Cellular Computing'''
|'''Molecular and Cellular Computing'''
-
| <font color = blue> Tue May 11? </font color>
+
|  
-
|
+
-
|'''Article 1: An autonomous molecular computer for logical control of gene expression'''<br>Benenson Y, et al. ''Nature'' 2004 May 27;429(6990):423-9. Epub 2004 Apr 28.<br>[[PMID: 15116117]]
+
-
|'''Article 2: Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]]
+
|
|
 +
|'''Article 1: <br>An autonomous molecular computer for logical control of gene expression'''<br>Benenson Y, et al. ''Nature'' 2004 May 27;429(6990):423-9. Epub 2004 Apr 28.<br>[[PMID: 15116117]]
 +
|'''Article 2: <br>Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]]
|}
|}

Current revision

Contents

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here
Schedule for interviews on April 28th is here. Please sign up asap.
Interviews will run ~30' in 5-122. No response record will be due for Week 12.

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, RW

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 ppt is here
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) Alie Media:20385Presentation.ppt 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
PMID: 10659856
Construction of a genetic toggle switch in Escherichia coli
Gardner TS, et al.Nature(2000) 403, 339–342
PMID: 10659857

Signal Connectivity
Wed Feb 24 Jose Media:Jose Presentation20.385.pdf Rewiring the specificity of two-component signal transduction systems
Skerker JM, et al. Cell (2008)133(6):1043-54.
PMID: 18555780
Synthetic biology: engineering Escherichia coli to see light
Levskaya A, et al. Nature (2005) 438(7067):441-2.
PMID: 16306980
Engineered Network Dynamics
Wed Mar 3 Kelly Media:Kdrinkwa week5.pdf Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
Bashor CJ, et al. Science (2008) 319: 1539-1543
PMID: 18339942
Synthetic protein scaffolds provide modular control over metabolic flux
Dueber JE, et al. Nat Biotech (2009) 27(8):753-9.
PMID: 19648908
Functional Network Composition
Thursday Mar 11 Media:EdgeDetection fromHelenChen.pdf A synthetic genetic edge detection program
Tabor JJ et al. Cell (2009) 137(7):1272-81
PMID: 19563759
Diversity-based, model-guided construction of synthetic gene networks with predicted functions
Ellis T, Wang X, and Collins JJ. Nat Biotech (2009) 27(5):465-71
PMID: 19377462
Tuning the system: directed evolution
Wed Mar 17 Derek Media:Derek Ju Presentation 3-17-10.pdf A dual selection module for directed evolution of synthetic circuits. Yokobayashi Y, Arnold FH. Nat Comp (2005) 4:245–254
pdf
A fast, robust and tunable synthetic gene oscillator
Stricker, J. et al. Nature (2008) 456, 516–519
PMID: 18971928
Spring Break Mar 22-26 No class all week
DNA construction and editing technologies
Wed Mar 31 Article 1 = Alie Media:Alie Presentation2-20385.pdf Article 1:
Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8.
PMID: 19633652
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
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
Chassis
Thursday Apr 8 Article 2 = Derek Image:Derek Ju Presentation 4-8-10.pdf Article 1:
Formation of protocell-like vesicles in a thermal diffusion column.
Budin I, Bruckner RJ, and Szostak JW. J Am Chem Soc. (2009)131(28):9628-9 PMID: 19601679
Article 2:
Genome transplantation in bacteria:changing one species to another

Lartigue C, et al. Science 2007, 317:632-638.
PMID: 17600181
Emergent properties of reduced-genome Escherichia coli.
Pósfai G, et al. Science.(2006)312(5776):1044-6.
PMID: 16645050
In silico and -omics
Wed Apr 14 (NK leaves by 3:30) Article 2 = Alvin Image:Alvin 20.385 Presentation.pptx Article 1:
Design of genetic networks with specified functions by evolution in silico

Francois, P. & Hakim, V. Proc. Natl Acad. Sci. USA (2004) 101, 580–585
PMID: 14704282
Article 2:
Engineering transcription factors with novel DNA-binding specificity using comparative genomics

Desai TA, et al. Nucleic Acids Res (2009) 37(8): 2493-503
PMID: 19264798
Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164
link
Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206
Noise
Wed Apr 21 Article 1 = Alvin Image:Alvin 20.385 Presentation 2.pdf Article 1:
Gene regulation at the single-cell level

Rosenfeld N, et al. Science (2005) 307, 1962–1965
PMID: 15790856
Article 2:
Stochastic switching as a survival strategy in fluctuating environments

Acar M. et al. Nature Genetics (2008) 40, 471 – 475
PMID: 18362885
Phenotypic consequences of promoter-mediated transcriptional noise.
Blake WJ, et al. Molecular Cell(2006) 24(6):853-65
PMID: 17189188
Metabolic Engineering Wed Apr 28 basic coverage of these articles since 310 and 330 are on overdrive this week Article 1:
Production of the antimalarial drug precursor artemisinic acid in engineered yeast

Ro DK, et al. Nature (2006) 440, 940–943
PMID: 16612385
Article 2:
Synthesis of methyl halides from biomass using engineered microbes

Bayer TS, et al. J Am Chem Soc (2009) 131:6508-6515.
PMID: 19378995
Synthetic protein scaffolds provide modular control over metabolic flux.
Dueber JE et al. Nat Biotechnol. (2009) 27(8):753-9. PMID: 19648908
Cell Cell Communication/System Ecology Wed May 5 Article 1 = Kelly Image:Kdrinkwa week13.pdf Article 1:
A synthetic Escherichia coli predator-prey ecosystem

Balagaddé FK, et al. Mol Syst Biol. 2008;4:187.
PMID: 18414488
Article 2:
Synthetic cooperation in engineered yeast populations

Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. (2007) 104(6):1877-82.
PMID: 17267602
Synthetic ecosystems based on airborne inter- and intrakingdom communication
Weber, W., Daoud-El Baba, M. & Fussenegger, M. Proc. Natl Acad. Sci. USA (2007) 104, 10435–10440
PMID: 17551014
Property rights in synthetic biology Article 1:
Synthetic biology: caught between property rights, the public domain, and the commons

Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173
Article 2:
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! Tue May 11 Jose will focus on Article 1, but please read both Image:Jose 20.385finalpresentation.pdf Article 1:
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
Article 2:
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?

Michael Specter New Yorker article
Programming Languages Article 1:
Towards programming languages for genetic engineering of living cells

Pedersen M, Phillips A J R Soc Interface 2009, 6(Suppl 4):S437-S450.
PMID: 19369220
Article 2:
Cells Are Plausible Targets for High-Level Spatial Languages

Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008.
Molecular and Cellular Computing Article 1:
An autonomous molecular computer for logical control of gene expression

Benenson Y, et al. Nature 2004 May 27;429(6990):423-9. Epub 2004 Apr 28.
PMID: 15116117
Article 2:
Engineering bacteria to solve the Burnt Pancake Problem

Haynes KA, et al. J Biol Eng. 2008 May 20;2:8.
PMID: 18492232
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