20.20(S10):Advanced topics

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings Paper 1 (10%): presented with a partner Paper 2 (15%): presented solo Response record (25%): your thoughts about the papers you don't present. Instructions for these assignment are here

Part 2: Team Mentoring Progress reports (15%): one page summaries of your freshman team's work Mentoring journal(15%): one page summary of your freshman team's 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, RW 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 Brent, R. PMID: 15055588
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. PMID: 3907859	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 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 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 pdf	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	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	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	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	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 11?		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?		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	Tue May 11?		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	Tue May 11?		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