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
[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 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

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

[http://mic.sgmjournals.org/cgi/reprint/150/7/2023 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))