20.20(S10):Advanced topics
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 (request from NK) | |
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. |
Ptashne “Two ‘What if” experiments” PMID 15055587 Brent “Build Artificial” PMID 15055588 |
Logic Modules |
Wed Feb 17 | Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173 |
Elowitz, M. B. & 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 |
Synthetic biology: engineering Escherichia coli to see light. Levskaya A, et al. Nature (2005) 438(7067):441-2. | |
Circuit Design |
Wed Mar 3 | Bashor, C. J., Helman, N. C., Yan, S. & Lim, W. A.
Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319, 1539–1543 (2008). |
Stricker, J. et al. A fast, robust and tunable synthetic
gene oscillator. Nature 456, 516–519 (2008). | |
I demand the cone of silence: nature's constraints on genetic circuit design |
Thursday Mar 11 | 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 DOI : 10.1016/j.molcel.2006.11.003 |
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Intelligent Design: Functional composition at the device level |
Wed Mar 17 | 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 DOI : 10.1016/j.molcel.2008.06.016 |
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Spring Break Mar 22-26 | No class all week | |||
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Writing in genetic code: DNA construction and editing technologies |
Wed Mar 31 | DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12 PMID: 19074487 Article 2: |
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Gene. 1995 Oct 16;164(1):49-53. PMID: 7590320 | |
We're only human: What is the state of the art? |
Thursday Apr 8 | 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 |
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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 |