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BIOMD0000000298 - Leloup1999_CircadianRhythms_Drosophila

 

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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: MODEL0478965170
Submission Date: 28 Apr 2009 15:31:24 UTC
Last Modification Date: 18 Jan 2011 15:52:44 UTC
Creation Date: 28 Apr 2009 15:31:24 UTC
Encoders:  Catherine Lloyd
   Vijayalakshmi Chelliah
set #1
bqmodel:isDerivedFrom BioModels Database Leloup1998_CircClock_LD
set #2
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #3
bqbiol:isPartOf KEGG Pathway dme04710
set #4
bqbiol:occursIn Taxonomy Drosophila melanogaster
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 1a-1j (Drosophila).

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) 2005-2011 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: 28 Apr 2009 15:31:24 UTC Last Modification Date: 18 Jan 2011 15:52:44 UTC Creation Date: 28 Apr 2009 15:31:24 UTC
Mathematical expressions
Rules
Rate Rule (variable: MP) Rate Rule (variable: P0) Rate Rule (variable: P1) Rate Rule (variable: P2)
Rate Rule (variable: MT) Rate Rule (variable: T0) Rate Rule (variable: T1) Rate Rule (variable: T2)
Rate Rule (variable: C) Rate Rule (variable: CN) Assignment Rule (variable: Pt)  
Physical entities
Compartments Species
Compartment MP CN C
T2 T1 T0
MT P0 P1
P2    
Global parameters
vsP vmP KmP KIP
Pt ksP vdP KdP
vsT vmT KmT KIT
ksT vdT KdT kdC
kdN k1 k2 k3
k4 kd V1P V1T
V2P V2T V3P V3T
V4P V4T K1P K1T
K2P K2T K3P K3T
K4P K4T n  
Reactions (0)
Rules (11)
 
 Rate Rule (name: MP) d [ MP] / d t= vsP*KIP^n/(KIP^n+CN^n)-(vmP*MP/(KmP+MP)+kd*MP)
 
 Rate Rule (name: P0) d [ P0] / d t= ksP*MP+V2P*P1/(K2P+P1)-(V1P*P0/(K1P+P0)+kd*P0)
 
 Rate Rule (name: P1) d [ P1] / d t= V1P*P0/(K1P+P0)+V4P*P2/(K4P+P2)-(V2P*P1/(K2P+P1)+V3P*P1/(K3P+P1)+kd*P1)
 
 Rate Rule (name: P2) d [ P2] / d t= V3P*P1/(K3P+P1)+k4*C-(V4P*P2/(K4P+P2)+k3*P2*T2+vdP*P2/(KdP+P2)+kd*P2)
 
 Rate Rule (name: MT) d [ MT] / d t= vsT*KIT^n/(KIT^n+CN^n)-(vmT*MT/(KmT+MT)+kd*MT)
 
 Rate Rule (name: T0) d [ T0] / d t= ksT*MT+V2T*T1/(K2T+T1)-(V1T*T0/(K1T+T0)+kd*T0)
 
 Rate Rule (name: T1) d [ T1] / d t= V1T*T0/(K1T+T0)+V4T*T2/(K4T+T2)-(V2T*T1/(K2T+T1)+V3T*T1/(K3T+T1)+kd*T1)
 
 Rate Rule (name: T2) d [ T2] / d t= V3T*T1/(K3T+T1)+k4*C-(V4T*T2/(K4T+T2)+k3*P2*T2+vdT*T2/(KdT+T2)+kd*T2)
 
 Rate Rule (name: C) d [ C] / d t= k3*P2*T2+k2*CN-(k4*C+k1*C+kdC*C)
 
 Rate Rule (name: CN) d [ CN] / d t= k1*C-(k2*CN+kdN*CN)
 
 Assignment Rule (name: Pt) Pt = P0+P1+P2+C+CN
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 MP
Compartment: Compartment
Initial concentration: 0.0614368
 
 CN
Compartment: Compartment
Initial concentration: 1.34728
 
 C
Compartment: Compartment
Initial concentration: 0.207614
 
 T2
Compartment: Compartment
Initial concentration: 0.0145428
 
 T1
Compartment: Compartment
Initial concentration: 0.0213384
 
 T0
Compartment: Compartment
Initial concentration: 0.0217261
 
 MT
Compartment: Compartment
Initial concentration: 0.0860342
 
 P0
Compartment: Compartment
Initial concentration: 0.0169928
 
 P1
Compartment: Compartment
Initial concentration: 0.0141356
 
 P2
Compartment: Compartment
Initial concentration: 0.0614368
 
Global Parameters (39)
 
 vsP
Value: 1.1
Constant
 
 vmP
Value: 1.0
Constant
 
 KmP
Value: 0.2
Constant
 
 KIP
Value: 1.0
Constant
 
  Pt
Value: NaN
 
 ksP
Value: 0.9
Constant
 
 vdP
Value: 2.2
Constant
 
 KdP
Value: 0.2
Constant
 
 vsT
Value: 1.0
Constant
 
 vmT
Value: 0.7
Constant
 
 KmT
Value: 0.2
Constant
 
 KIT
Value: 1.0
Constant
 
 ksT
Value: 0.9
Constant
 
 vdT
Value: 3.0
Constant
 
 KdT
Value: 0.2
Constant
 
 kdC
Value: 0.01
Constant
 
 kdN
Value: 0.01
Constant
 
 k1
Value: 0.8
Constant
 
 k2
Value: 0.2
Constant
 
 k3
Value: 1.2
Constant
 
 k4
Value: 0.6
Constant
 
 kd
Value: 0.01
Constant
 
 V1P
Value: 8.0
Constant
 
 V1T
Value: 8.0
Constant
 
 V2P
Value: 1.0
Constant
 
 V2T
Value: 1.0
Constant
 
 V3P
Value: 8.0
Constant
 
 V3T
Value: 8.0
Constant
 
 V4P
Value: 1.0
Constant
 
 V4T
Value: 1.0
Constant
 
 K1P
Value: 2.0
Constant
 
 K1T
Value: 2.0
Constant
 
 K2P
Value: 2.0
Constant
 
 K2T
Value: 2.0
Constant
 
 K3P
Value: 2.0
Constant
 
 K3T
Value: 2.0
Constant
 
 K4P
Value: 2.0
Constant
 
 K4T
Value: 2.0
Constant
 
 n
Value: 4.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000298

Curator's comment: (updated: 14 Jan 2011 14:20:07 GMT)

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

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