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 |
A Voyage To Lilliput: How a small number of AA substitution change activity of a protein |
Wed Feb 3 | Natalie Kuldell Ron Weiss |
Turning lambda Cro into a transcriptional activator.Bushman FD, Ptashne M.Cell. 1988 Jul 15;54(2):191-7. |
Genetic Switch: Phage Lambda and Higher Organisms Mark Ptashnepreviewed here or Sci Am summary (request from NK) |
Slide rule optional: Computational design of novel protein activities |
Wed Feb 10 | Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164 DOI : 10.1371/journal.pcbi.0030164 |
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Nature heart Legos™: 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. PMID: 8393937 |
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Better odds in Vegas: DNA elements are modular too, allowing for circuits, but circuits don't always work |
Wed Feb 24 | Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007 DOI : 10.1038/msb4100173 |
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Darwin is alive and well: Directed evolution at the parts and device level |
Wed Mar 3 | RNA and RNP as new molecular parts in synthetic biology.Saito H, Inoue, T Journal of biotechnology(2007)132(1):1-7 doi:10.1016/j.jbiotec.2007.07.952 |
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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 |