20.20(S10):Advanced topics
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20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
Schedule for interviews on April 28th is here. Please sign up asap.
Interviews will run ~30' in 5-122. No response record will be due for Week 12.
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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
| |
| Parts™ | Wed Feb 10 | Natalie Kuldell Ron Weiss 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. |
Activation of prokaryotic transcription through arbitrary protein-protein contacts Dove SL, et al. Nature (1997) Apr 10;386(6625):627-30. PMID: 9121589 |
| Logic Modules |
Wed Feb 17 (RW OoT) | Alie Media:20385Presentation.ppt | 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 |
| Signal Connectivity |
Wed Feb 24 | Jose Media:Jose Presentation20.385.pdf | 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 3 | Kelly Media:Kdrinkwa week5.pdf | 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 11 | Media:EdgeDetection fromHelenChen.pdf | 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 17 | Derek Media:Derek Ju Presentation 3-17-10.pdf | 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 22-26 | No class all week | |||
|---|---|---|---|---|
| DNA construction and editing technologies |
Wed Mar 31 | Article 1 = Alie Media:Alie Presentation2-20385.pdf | 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 |
| Chassis |
Thursday Apr 8 | Article 2 = Derek File:Derek Ju Presentation 4-8-10.pdf | 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 14 (NK leaves by 3:30) | Article 2 = Alvin File:Alvin 20.385 Presentation.pptx | 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 link Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206 |
| Noise |
Wed Apr 21 | Article 1 = Alvin File:Alvin 20.385 Presentation 2.pdf | 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 28 | basic coverage of these articles since 310 and 330 are on overdrive this week | 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 5 | Article 1 = Kelly File:Kdrinkwa week13.pdf | 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 | 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 11 | Jose will focus on Article 1, but please read both File:Jose 20.385finalpresentation.pdf | 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 |
| Programming Languages | Article 1: Towards programming languages for genetic engineering of living cells Pedersen M, Phillips A J R Soc Interface 2009, 6(Suppl 4):S437-S450. PMID: 19369220 |
Article 2: Cells Are Plausible Targets for High-Level Spatial Languages Beal J, and Bachrach, J. Spatial Computing Workshop, October 2008. | ||
| Molecular and Cellular Computing | Article 1: An autonomous molecular computer for logical control of gene expression Benenson Y, et al. Nature 2004 May 27;429(6990):423-9. Epub 2004 Apr 28. PMID: 15116117 |
Article 2: Engineering bacteria to solve the Burnt Pancake Problem Haynes KA, et al. J Biol Eng. 2008 May 20;2:8. PMID: 18492232 | ||
