IGEM:IMPERIAL/2006/Bibliography & Papers
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
Biology
Molecular Biology of the Cell, 4th ed. (Alberts, et al.) - Online Textbook
Presentation on Chemostats - Vincent's favorite new toy
Oscillators
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
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))
