Try the new BioModels platform (beta)
BioModels Database logo

BioModels Database

spacer

BIOMD0000000299 - Leloup1999_CircadianRhythms_Neurospora

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 10643740
Leloup JC, Gonze D, Goldbeter A.
Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora.
J. Biol. Rhythms 1999 Dec; 14(6): 433-448
Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium.  [more]
Model
Original Model: CellML logo
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1101140000
Submission Date: 14 Jan 2011 14:18:45 UTC
Last Modification Date: 25 Feb 2015 13:49:51 UTC
Creation Date: 14 Jan 2011 14:22:45 UTC
Encoders:  Catherine Lloyd
   Vijayalakshmi Chelliah
set #1
bqbiol:hasTaxon Taxonomy Neurospora crassa
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
Notes

This a model from the article:
Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora.
Leloup JC, Gonze D, Goldbeter A. J Biol Rhythms. 1999 Dec;14(6):433-48. 10643740 ,
Abstract:
We examine theoretical models for circadian oscillations based on transcriptional regulation in Drosophila and Neurospora. For Drosophila, the molecular model is based on the negative feedback exerted on the expression of the per and tim genes by the complex formed between the PER and TIM proteins. For Neurospora, similarly, the model relies on the feedback exerted on the expression of the frq gene by its protein product FRQ. In both models, sustained rhythmic variations in protein and mRNA levels occur in continuous darkness, in the form of limit cycle oscillations. The effect of light on circadian rhythms is taken into account in the models by considering that it triggers degradation of the TIM protein in Drosophila, and frq transcription in Neurospora. When incorporating the control exerted by light at the molecular level, we show that the models can account for the entrainment of circadian rhythms by light-dark cycles and for the damping of the oscillations in constant light, though such damping occurs more readily in the Drosophila model. The models account for the phase shifts induced by light pulses and allow the construction of phase response curves. These compare well with experimental results obtained in Drosophila. The model for Drosophila shows that when applied at the appropriate phase, light pulses of appropriate duration and magnitude can permanently or transiently suppress circadian rhythmicity. We investigate the effects of the magnitude of light-induced changes on oscillatory behavior. Finally, we discuss the common and distinctive features of circadian oscillations in the two organisms.

This particular version of the model has been translated from equations 4a-4c (Neurospora).

This model was taken from the CellML repository and automatically converted to SBML.
The original model was: Leloup JC, Gonze D, Goldbeter A. (1999) - version02
The original CellML model was created by:
Lloyd, Catherine, May
c.lloyd@aukland.ac.nz
The University of Auckland
The Bioengineering Institute

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 10643740 Submission Date: 14 Jan 2011 14:18:45 UTC Last Modification Date: 25 Feb 2015 13:49:51 UTC Creation Date: 14 Jan 2011 14:22:45 UTC
Mathematical expressions
Rules
Rate Rule (variable: M) Rate Rule (variable: FC) Rate Rule (variable: FN) Assignment Rule (variable: Ft)
Physical entities
Compartments Species
Cytoplasm FC    
Nucleus M FN  
Global parameters
vs vm Km KI
n Ft ks vd
Kd k1 k2  
Reactions (0)
Rules (4)
 
 Rate Rule (name: M) d [ M] / d t= vs*KI^n/(KI^n+FN^n)-vm*M/(Km+M)
 
 Rate Rule (name: FC) d [ FC] / d t= (ks*M+k2*FN)-(vd*FC/(Kd+FC)+k1*FC)
 
 Rate Rule (name: FN) d [ FN] / d t= k1*FC-k2*FN
 
 Assignment Rule (name: Ft) Ft = FC+FN
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 FC
Compartment: Cytoplasm
Initial concentration: 0.1
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 M
Compartment: Nucleus
Initial concentration: 0.1
 
 FN
Compartment: Nucleus
Initial concentration: 0.1
 
Global Parameters (11)
 
 vs
Value: 1.6
Constant
 
 vm
Value: 0.505
Constant
 
 Km
Value: 0.5
Constant
 
 KI
Value: 1.0
Constant
 
 n
Value: 4.0
Constant
 
  Ft
Value: NaN
 
 ks
Value: 0.5
Constant
 
 vd
Value: 1.4
Constant
 
 Kd
Value: 0.13
Constant
 
 k1
Value: 0.5
Constant
 
 k2
Value: 0.6
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000299

Curator's comment: (updated: 14 Jan 2011 14:21:55 GMT)

The model reproduces figure 2c of the reference publication. The model was integrated and simulated using Copasi v4.6 (Build 32).

spacer
spacer