20.20(S11):Advanced topics

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings Paper 1 (10%) Paper 2 (15%) Response record (20%): your thoughts about the papers you don't present. Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others Instructions for these assignment are here

Part 2: Team Mentoring Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and 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 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 2	Natalie Kuldell		before next week read The promise of synthetic biology Pleiss,J. DOI:10.1007/s00253-006-0664-3 Two ‘What if' experiments Ptashne, M. PMID: 15055587 Build Artificial Brent, R. PMID: 15055588
Parts™	Wed Feb 9	Natalie Kuldell 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	Improving the Lac System for Synthetic Biology Penumetcha, P., et al. Bios (2011) 81(1):7-15. pdf
Transcription-based Logic Devices	Wed Feb 16		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
Protein Design: directed evolution	Wed Feb 23		De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth Fisher MA, et al. PLoS One (2011)6(1):e15364 DOI: 10.1371/journal.pone.0015364	Directed evolution of recombinase specificity by split gene reassembly Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543 DOI: 10.1093/nar/gkq125
RNA Engineering	Wed Mar 2		Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255 DOI: 10.1126/science.1192128	The Case for RNA Chang, CL, Arkin AP. Science (2010) 330:1185-1186 DOI: 10.1126/science.1199495
Tuning the system: Network Composition	Thursday Mar 10		A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4 DOI: 10.1186/1754-1611-4-4	A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928
(re)Programming Systems	Wed Mar 16		Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630 DOI:10.1016/j.stem.2010.08.012	Reprogramming bacteria to seek and destroy an herbicide Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470 doi:10.1038/nchembio.369
Spring Break Mar 21-25			No class all week
DNA construction and editing technologies	Wed Mar 30		Programming cells by multiplex genome engineering and accelerated evolution Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8. PMID: 19633652	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
Measurement technologies	Thursday Apr 7		Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652	Measuring the activity of BioBrick promoters using an in vivo reference standard Kelly J, et al. Journal of Biological Engineering (2009) 3:4 doi:10.1186/1754-1611-3-4
Chassis	Wed Apr 13		Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system Shin J, and Noireaux, V. JBE (2010) 4:9 DOI: 10.1186/1754-1611-4-9	Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050
Signal Connectivity	Wed Apr 20		Rewiring the specificity of two-component signal transduction systems Skerker JM, et al. Cell (2008)133(6):1043-54. PMID: 18555780	Tunable Signal Processing in Synthetic MAP Kinase Cascades O'Shaughnessy, EC, et al. Cell(2011) 144:119-131 DOI: 10.1016/j.cell.2010.12.014
Metabolic Engineering	Wed Apr 27		Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305 (2010) doi:10.1016/j.ymben.2010.01.003.	Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385
Cell Cell Communication/System Ecology	Wed May 4		Robust multicellular computing using genetically encoded NOT gates and chemical 'wires' Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215. DOI: 10.1038/nature09565	Division of logic labour Li B and You L.Nature (2011) 469:171-172 DOI:10.1038/469171a
Property rights in synthetic biology	Tue May 10?		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 Genomics Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
Safety!	Tue May 10?		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	Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article