Modelling a Genetic Oscillator
Catherine
Lloyd
Auckland Bioengineering Institute, The University of Auckland
Model Status
This CellML modelis known to run in OpenCell and COR to reproduce the results published in the paper on which it is based (figures 2 and 3).
Model Structure
ABSTRACT: A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The integration of these "circuits" at the cellular level imposes strong constraints on their functioning and design. Here, we study a recently proposed model [Barkai, N. and Leibler, S. (2000) Nature (London), 403, 267-268] that incorporates just the essential elements found experimentally. We show that this type of oscillator is driven mainly by two elements: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor. Thus, the clock does not need to rely on mRNA dynamics to oscillate, which makes it especially resistant to fluctuations. Oscillations can be present even when the time average of the number of mRNA molecules goes below one. Under some conditions, this oscillator is not only resistant to but, paradoxically, also enhanced by the intrinsic biochemical noise.
The original paper reference is cited below:
Mechanisms of noise-resistance in genetic oscillators, Jose M. G. Vilar, Hao Yuan Kueh, Naama Barkai, and Stanislas Leibler, 2002,Proceedings of the National Academy of Sciences of the United States of America, 99, 5988-5992. PubMed ID: 11972055
reaction diagram
Biochemical network of the circadian oscillator model.
circadian rhythms
noise-resistance
signal transduction
gene regulation
genetic oscillator
James
Lawson
Richard
400
10000
5
2008-09-03T14:33:04+12:00
James Lawson
keyword
2003-11-03T00:00:00+00:00
PNAS
added cmeta:id's to some variables
James
Lawson
Jose
Vilar
G.
M.
Catherine
Lloyd
May
Catherine Lloyd
2008-09-01T13:12:26+12:00
Hao
Kueh
Yuan
This model has been recoded using the Biomodels Database model as a template
This model is known to run in PCEnv and COR reproduce the results published in the paper on which it is based (figures 2 and 3)
Vilar et al.'s 2002 mathematical model of a genetic oscillator.
James
Lawson
Richard
This is the CellML description of Vilar et al.'s 2002 mathematical model of a genetic oscillator.
2008-02-05T11:39:57+13:00
Added some cmeta:ids to varibles to allow referencing by a PCEnv session
2008-02-20T14:54:14+13:00
The University of Auckland
Auckland Bioengineering Institute
c.lloyd@auckland.ac.nz
Added CellML 1.0 namespace
Removed extraneous code: initial_value=""
Removed unnecessary initial values from RXN_X* variables with public_interface="in"
* - X is 1-16
Mechanisms of noise-resistance in genetic oscillators
99
5988
5992
2002-04-30
The University of Auckland, Auckland Bioengineering Institute
Naama
Barkai
11972055
Stanislas
Leibler
Vignesh
Kumar
B