20.20(S11):Advanced topics

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|'''Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system'''<br> Shin J, and Noireaux, V. ''JBE'' (2010) 4:9<br> [[DOI: 10.1186/1754-1611-4-9]]
|'''Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system'''<br> Shin J, and Noireaux, V. ''JBE'' (2010) 4:9<br> [[DOI: 10.1186/1754-1611-4-9]]
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| ''''''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: ]]
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| '''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]]
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| '''Signal Connectivity'''<br>
| '''Signal Connectivity'''<br>
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| '''Metabolic Engineering'''  
| '''Metabolic Engineering'''  
| Wed Apr 27
| Wed Apr 27
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|'''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]]
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| '''Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.'''Moon TS et al. ''Metabolic Engineering'' (2010) 12: 298-305 (2010) [[doi:10.1016/j.ymben.2010.01.003.]]
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| '''Synthetic protein scaffolds provide modular control over metabolic flux.'''<br> Dueber JE et al. ''Nat Biotechnol.'' (2009) 27(8):753-9. [[PMID: 19648908]]
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|'''Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]
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|'''Cell Cell Communication/System Ecology'''  
|'''Cell Cell Communication/System Ecology'''  
| Wed May 4  
| Wed May 4  
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|'''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]]
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|'''Robust multicellular computing using genetically encoded NOT gates and chemical 'wires''''<br>Tamsir, a., Tabor, J.J., Voigt, C.A. ''Nature'' 2011 Jan 13;469:212-215.<br>[[DOI: 10.1038/nature09565]]
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| ''' 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]]
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| ''' Division of logic labour''' <br> Li B and You L.''Nature'' (2011) 469:171-172<br>[[DOI:10.1038/469171a]]
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| '''Property rights in synthetic biology'''  
| '''Property rights in synthetic biology'''  
|  <font color = blue> Tue May 10? </font color>  
|  <font color = blue> Tue May 10? </font color>  
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|''' 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>
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|''' 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>
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|'''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.]]
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|'''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.]]
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|'''Safety!'''  
|'''Safety!'''  
| <font color = blue> Tue May 10? </font color>  
| <font color = blue> Tue May 10? </font color>  
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| '''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>
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| '''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>
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|'''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]
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|'''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]
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|'''Molecular and Cellular Computing'''
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| <font color = blue> Tue May 10? </font color>
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|'''Robust multicellular computing using genetically encoded NOT gates and chemical 'wires''''<br>Tamsir, a., Tabor, J.J., Voigt, C.A. ''Nature'' 2011 Jan 13;469:212-215.<br>[[DOI: 10.1038/nature09565]]
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|'''Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]]
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Revision as of 18:47, 29 January 2011

Contents

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%)
  • Paper 2 (15%)
  • Response record (20%): your thoughts about the papers you don't present.
  • Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and 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 2 Natalie Kuldell before next week read
  1. The promise of synthetic biology
    Pleiss,J.
    DOI:10.1007/s00253-006-0664-3
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. Build Artificial
    Brent, R.
    PMID: 15055588
Parts™ Wed Feb 9 Natalie Kuldell
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

Improving the Lac System for Synthetic Biology
Penumetcha, P., et al. Bios (2011) 81(1):7-15.
pdf
Transcription-based Logic Devices
Wed Feb 16 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

Protein Design: directed evolution
Wed Feb 23 De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth
Fisher MA, et al. PLoS One (2011)6(1):e15364
DOI: 10.1371/journal.pone.0015364
Directed evolution of recombinase specificity by split gene reassembly
Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543
DOI: 10.1093/nar/gkq125
RNA Engineering
Wed Mar 2 Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins
Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255
DOI: 10.1126/science.1192128
The Case for RNA
Chang, CL, Arkin AP. Science (2010) 330:1185-1186
DOI: 10.1126/science.1199495
Tuning the system: Network Composition
Thursday Mar 10 A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4
DOI: 10.1186/1754-1611-4-4
A fast, robust and tunable synthetic gene oscillator
Stricker, J. et al. Nature (2008) 456, 516–519
PMID: 18971928
(re)Programming Systems
Wed Mar 16 Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630
DOI:10.1016/j.stem.2010.08.012
Reprogramming bacteria to seek and destroy an herbicide
Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470
doi:10.1038/nchembio.369
Spring Break Mar 21-25 No class all week
DNA construction and editing technologies
Wed Mar 30 Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8.
PMID: 19633652
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
Measurement technologies
Thursday Apr 7 Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652 Measuring the activity of BioBrick promoters using an in vivo reference standard
Kelly J, et al. Journal of Biological Engineering (2009) 3:4
doi:10.1186/1754-1611-3-4
Chassis
Wed Apr 13 Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system
Shin J, and Noireaux, V. JBE (2010) 4:9
DOI: 10.1186/1754-1611-4-9
Emergent properties of reduced-genome Escherichia coli.
Pósfai G, et al. Science.(2006)312(5776):1044-6.
PMID: 16645050
Signal Connectivity
Wed Apr 20 Rewiring the specificity of two-component signal transduction systems
Skerker JM, et al. Cell (2008)133(6):1043-54.
PMID: 18555780
Tunable Signal Processing in Synthetic MAP Kinase Cascades
O'Shaughnessy, EC, et al. Cell(2011) 144:119-131
DOI: 10.1016/j.cell.2010.12.014
Metabolic Engineering Wed Apr 27 Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305 (2010) doi:10.1016/j.ymben.2010.01.003. Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro DK, et al. Nature (2006) 440, 940–943
PMID: 16612385
Cell Cell Communication/System Ecology Wed May 4 Robust multicellular computing using genetically encoded NOT gates and chemical 'wires'
Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215.
DOI: 10.1038/nature09565
Division of logic labour
Li B and You L.Nature (2011) 469:171-172
DOI:10.1038/469171a
Property rights in synthetic biology Tue May 10? 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 Genomics
Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
Safety! Tue May 10? 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
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?
Michael Specter New Yorker article
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