Difference between revisions of "20.20(S11):Advanced topics"

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(New page: {{Template:20.20(S11)}} <div style="padding: 10px; width: 670px; border: 5px solid #CC9999;"> <center> =20.385: Advanced Topics in Synthetic Biology= ==Assignments== Homework dropbox is [h...)
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| <font color = blue> Tue May 10? </font color>  
| <font color = blue> Tue May 10? </font color>  
|'''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]]
|'''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]]
|'''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]]
|'''Engineering bacteria to solve the Burnt Pancake Problem''' <br>Haynes KA, et al. ''J Biol Eng.'' 2008 May 20;2:8.<br>[[PMID: 18492232]]

Revision as of 11:11, 29 January 2011

20.385: Advanced Topics in Synthetic Biology


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


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
  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.
Logic Modules
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,

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 23 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 2 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 10 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 16 A dual selection module for directed evolution of synthetic circuits. Yokobayashi Y, Arnold FH. Nat Comp (2005) 4:245–254
A fast, robust and tunable synthetic gene oscillator
Stricker, J. et al. Nature (2008) 456, 516–519
PMID: 18971928
Spring Break Mar 21-25 No class all week
DNA construction and editing technologies
Wed Mar 30 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
Thursday Apr 7 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 13 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
Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206
Signal Connectivity
Wed Apr 20 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 27 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 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 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 Tue May 10? 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 10? 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
Molecular and Cellular Computing Tue May 10? 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
Engineering bacteria to solve the Burnt Pancake Problem
Haynes KA, et al. J Biol Eng. 2008 May 20;2:8.
PMID: 18492232