20.20(S10):Advanced topics
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20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
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: Sci Am summary (handout) “Two ‘What if” experiments” Ptashne, M. PMID 15055587 “Build Artificial” | |
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. |
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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 |
Elowitz, MB, and Leibler, S. A synthetic oscillatory
network of transcriptional regulators. Nature 403,
335–338 (2000) | |
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 |
Levskaya A, et al. Synthetic biology: engineering Escherichia coli to see light. PMID: 16306980 | |
Controlling System Dynamics |
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 DOI: 10.1126/science.1151153 |
Dueber JE, et al. Synthetic protein scaffolds provide modular control over metabolic flux. 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 | Tabor JJ et al. A synthetic genetic edge detection program 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). | Yokobayashi, Y, et al. Directed evolution of a genetic circuit Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002). | |
Spring Break Mar 22-26 | No class all week | |||
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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. | |
Chassis |
Thursday Apr 8 | |||
Little Red Corvette: Once you've got the DNA, where do you put it? Introducing... THE CHASSIS |
Wed Apr 14 | Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4. DOI: 10.1126/science.1154520 |
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. PMID: 16645050 | |
Secret map hidden in the peg-leg: getting DNA to speak in binary |
Wed Apr 21 | Length-based encoding of binary data in DNA. Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.
Langmuir (2008) 24(5):1613-6. |
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On your mark, get set, go: System dynamics | 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 DOI: 10.1126/science.1151153 |
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Rough consensus and running code: building patterns and memories | Tue May 4 | 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. DOI: 10.1101/gad.1586107 |
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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 |