20.20(S11):Advanced topics

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Contents

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
  1. The promise of synthetic biology
    Pleiss,J.
    DOI:10.1007/s00253-006-0664-3
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. 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
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
Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164
DOI: 10.1371/journal.pcbi.0030164
Tuning the system: directed evolution
Wed Mar 2 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
A dual selection module for directed evolution of synthetic circuits. Yokobayashi Y, Arnold FH. Nat Comp (2005) 4:245–254
pdf
RNA Engineering
Thursday Mar 10 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
Wed Mar 16 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
Spring Break Mar 21-25 No class all week
DNA construction and editing technologies
Wed Mar 30 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 7 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 13 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
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 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 4 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 10? 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 10? 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
Molecular and Cellular Computing Tue May 10? 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
Engineering bacteria to solve the Burnt Pancake Problem
Haynes KA, et al. J Biol Eng. 2008 May 20;2:8.
PMID: 18492232
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