IGEM:IMPERIAL/2006/Bibliography & Papers

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This site contains all of the papers and books which may be of interest and may be used in the final report.

Synthetic Biology/General Papers

Engineered Gene Circuits (Hasty, McMillin, and Collins) Nature (14 November 2002)

Designer Gene Networks: Towards Fundamental Cellular Control (Hasty et al.) Chaos (13 March 2001)

Biological Modelling

Modelling Gene Expression with Differential Equations (Ching, He, and Church), Pacific Symposium on Biocomputing, 1999, p. 29-40.

Michaelis-Menten Kinetics on Wikipedia


Molecular Biology of the Cell, 4th ed. (Alberts, et al.) - Online Textbook

Presentation on Chemostats - Vincent's favorite new toy


Synchronizing Genetic Relaxation Oscillators by Intercell Signalling (David McMillen, Nancy Kopell, Jeff Hasty and J.J. Collins)

A Synthetic Oscillatory Network of Transcriptional Regulators (Michael B. Elowitz & Stanislas Leibler) NATURE, 20 January 2000, vol 403

A Synthetic Gene–Metabolic Oscillator (Eileen Fung, Wilson W. Wong, Jason K. Suen, Thomas Bulter, Sun-gu Lee & James C. Liao) NATURE, 5 May 2005, vol 435

Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability (James E Ferrell Jr) Current Opinion in Chemical Biology 12 February 2002

Modelling the Lux/AiiA Relaxion Oscillator (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory

Presentation from MIT's Synthetic Biology Competition of 2004 - Previous version of iGEM competition, describes oscillator

Specification paper from MIT's Synthetic Biology Competition of 2004 - Details for their design and methology

Lotka-Volterra Model - Implementation in Chemcial Systems

Lotka-Volterra Equations on Wikipedia

Quorum Sensing/Quenching

Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones (Cynthia H. Collins, Frances H. Arnold and Jared R. Leadbetter) Molecular Microbiology 2005

Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes (Yi-Han Lin, Jin-Ling Xu, Jiangyong Hu, Lian-Hui Wang, Say Leong, Jared Renton Leadbetter and Lian-Hui Zhang) Molecular Microbiology 2003

Quorum Sensing and Quorum-quenching enzymes (Yi-Hu Dong and Lian-Hui Zhang) Journal of Microbiology 2005

AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria (Park, et. al) Microbiology 2003

AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora PNAS 2000

The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase (Kim et al.) PNAS 2005

Communications blackout? Do N-acylhomoserine-lactone degrading enzymes have any role in quorum sensing? (Declan M. Roche, Joseph T. Byers, Debra S. Smith, Freija G. Glansdorp, David R. Spring and Martin Welch) Microbiology 2004

Quorum Sensing and Signal Interference: Diverse Implications (Lian-Hui Zhang, and Yi-Hu Dong) Molecular Microbiology 2004

The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein (Wang, L. H., et al.) PubMed 2004

The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase (Kim et al.) PNAS 2005

Flourescent Proteins

Living Colors User Manual (Clontech) - Gives half-lives and information on flourescent proteins (GFP, EGFP, EYFP, RFP, ECFP, etc.) 2001

Tags and Modifiers

Antibodies to Epitome Tags (Sigma-Aldrich)

Lotka Volterra Model

Individual based modeling and parameter estimation for a Lotka Volterra system (Waniewski, Mathematical Biosciences (1999))