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 37: Line 39:
|'''Related paper(s) to enjoy'''
|'''Related paper(s) to enjoy'''
|--
|--
-
| <b>A Voyage To Lilliput:</b><br>How a small number of AA substitution change activity of a protein
+
| <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]]
|  
|  
-
<b>Turning lambda Cro into a transcriptional activator.</b>Bushman FD, Ptashne M.''Cell.'' 1988 Jul 15;54(2):191-7.<br>
+
|before next week read
-
[[PMID: 2968842]]<br>
+
#''Sci Am'' summary (handout)
-
|'''Genetic Switch: Phage Lambda and Higher Organisms'''  Mark Ptashne[http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095  previewed here]<br>
+
#''Two ‘What if' experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
-
or '''Sci Am''' summary (request from NK)
+
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]] 
|--
|--
-
| <b>Slide rule optional:</b><br>Computational design of novel protein activities
+
| <b>Parts™</b>
| Wed Feb 10
| Wed Feb 10
-
|  
+
| [[Natalie Kuldell]]<br>[[User:Ron Weiss| Ron Weiss]] [[Media:20 385 Week2.ppt| ppt is here]]
-
| '''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]]
+
| '''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]]
-
|--
+
| '''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]]
-
| '''Nature heart Legos™''':<br> Proteins are modular too
+
-
| Wed Feb 17
+
-
|
+
-
|'''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]]
+
-
|
+
|--
|--
-
| '''Better odds in Vegas:'''<br>DNA elements are modular too, allowing for circuits, but circuits don't always work
+
| '''Logic Modules'''<br>  
 +
| 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'' (2007) 3:133 <br>[[PMID: 17700541]]
 +
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403,
 +
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>
 +
|--
 +
|'''Signal Connectivity'''<br>
| Wed Feb 24
| Wed Feb 24
-
|  
+
| Jose [[Media:Jose Presentation20.385.pdf]]
-
|'''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]]
+
|'''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. ''Nature'' (2005) 438(7067):441-2.<br> [[PMID: 16306980]]
|--
|--
-
| '''Darwin is alive and well:''' <br>Directed evolution at the parts and device level
+
| '''Engineered Network Dynamics''' <br>
-
| Wed Mar 3  
+
| Wed Mar 3
-
|  
+
| Kelly [[Media:Kdrinkwa week5.pdf]]
-
|'''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]]
+
|'''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. ''Nat Biotech'' (2009) 27(8):753-9.<br>[[PMID: 19648908]]
|--
|--
-
| '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design
+
| '''Functional Network Composition'''<br>  
| <font color = blue> Thursday Mar 11</font color>
| <font color = blue> Thursday Mar 11</font color>
-
|  
+
| [[Media:EdgeDetection fromHelenChen.pdf]]
-
|'''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]]
+
| '''A synthetic genetic edge detection program'''<br>Tabor JJ et al. ''Cell'' (2009) 137(7):1272-81 <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]]  
|--
|--
-
| '''Intelligent Design:'''<br> Functional composition at the device level
+
| '''Tuning the system: directed evolution''' <br>  
| Wed Mar 17  
| Wed Mar 17  
-
|
+
| Derek [[Media:Derek Ju Presentation 3-17-10.pdf]]
-
| '''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]]
+
| '''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]]
-
|
+
| '''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 86: Line 90:
|
|
|--
|--
-
| '''Writing in genetic code:'''<br> DNA construction and editing technologies
+
| '''DNA construction and editing technologies'''<br>  
| Wed Mar 31
| Wed Mar 31
-
|  
+
| Article 1 = Alie [[Media:Alie Presentation2-20385.pdf]]
-
| '''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>  
+
| '''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]]
-
| '''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]]  
+
| '''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>
|--
|--
-
| '''We're only human:''' <br>What is the state of the art? 
+
| '''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]]
-
|'''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]]
+
| '''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]]
-
|
+
|'''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]]
|--
|--
-
| '''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 (NK leaves by 3:30)
-
|  
+
| Article 2 = Alvin [[Image:Alvin 20.385 Presentation.pptx]]
-
|'''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:<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]]
-
| '''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>[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]]
|--
|--
-
| '''Secret map hidden in the peg-leg:'''<br> getting DNA to speak in binary
+
| '''Noise'''<br>  
| Wed Apr 21
| Wed Apr 21
-
|  
+
| Article 1 = Alvin [[Image:Alvin 20.385 Presentation 2.pdf]]
-
|'''Length-based encoding of binary data in DNA.''' Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.
+
|'''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]]
-
''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>[[PMID: 17189188]]
-
|
+
|--
|--
-
| '''On your mark, get set, go:''' System dynamics
+
| '''Metabolic Engineering'''  
| Wed Apr 28
| Wed Apr 28
-
|
+
| basic coverage of these articles since 310 and 330 are on overdrive this week
-
|'''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:<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]]
|--
|--
-
|'''Rough consensus and running code:''' building patterns and memories
+
|'''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: <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 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'''
 +
|
|
-
|'''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: <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: <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.]]
|--
|--
-
| '''mine mine mine:''' property rights in synthetic biology
+
|'''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]]
-
| '''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]]  
+
| '''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>
-
|'''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.]]
+
|'''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]
|--
|--
-
|'''drop it like it's hot:''' safety!
+
|'''Programming Languages'''  
-
| <font color = blue> Tue May 11? </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]]
+
|
-
|
+
| '''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'''
 +
|
 +
|
 +
|'''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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