20.20(S10):Advanced topics

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20.385: Advanced Topics in Synthetic Biology


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.

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


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
  1. Sci Am summary (handout)
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. 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,

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
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
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
Design principles for ligand-sensing, conformation-switching ribozymes.Chen X and Ellington AD. PLoS Comput Biol. (2009) Dec;5(12):e1000620. PMID: 20041206
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