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BIOMD0000000295 - Akman2008_Circadian_Clock_Model1

 

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Reference Publication
Publication ID: 18277380
Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA.
Isoform switching facilitates period control in the Neurospora crassa circadian clock.
Mol. Syst. Biol. 2008; 4: 164
Centre for Systems Biology at Edinburgh, The University of Edinburgh, Edinburgh, UK [corrected]  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL8306248909
Submission Date: 03 Dec 2008 12:40:08 UTC
Last Modification Date: 28 May 2014 01:56:26 UTC
Creation Date: 03 Dec 2008 12:40:08 UTC
Encoders:  Vijayalakshmi Chelliah
   Ozgur Akman
set #1
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
Gene Ontology circadian rhythm
bqbiol:hasTaxon Taxonomy Neurospora crassa
bqmodel:isDerivedFrom BioModels Database Leloup1999_CircadianRhythms_Neurospora
Notes

This a model from the article:
Isoform switching facilitates period control in the Neurospora crassa circadian clock.
Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA Mol. Syst. Biol. 2008;Vol 4: 164 18277380 ,
Abstract:
A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic.

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: 18277380 Submission Date: 03 Dec 2008 12:40:08 UTC Last Modification Date: 28 May 2014 01:56:26 UTC Creation Date: 03 Dec 2008 12:40:08 UTC
Mathematical expressions
Reactions
MFtrn MFdeg FCtrl FCdeg
FCtrs FCptrl FCpdeg FCptrs
Rules
Assignment Rule (variable: Tot_FRQ)      
Physical entities
Compartments Species
nucleus FN FNp MF
cytoplasm FC FCp  
Global parameters
vs ki n vm
km ks vd k1n
k2n ksp vdp k1np
k2np amp dawn dusk
Tot_FRQ      
Reactions (8)
 
 MFtrn  → [MF];   {FN} , {FNp}
 
 MFdeg [MF] → ;  
 
 FCtrl  → [FC];   {MF}
 
 FCdeg [FC] → ;  
 
 FCtrs [FC] ↔ [FN];  
 
 FCptrl  → [FCp];   {MF}
 
 FCpdeg [FCp] → ;  
 
 FCptrs [FCp] ↔ [FNp];  
 
Rules (1)
 
 Assignment Rule (name: Tot_FRQ) Tot_FRQ = FC+FCp+FN+FNp
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 FN
Compartment: nucleus
Initial concentration: 1.84400040515923
 
 FNp
Compartment: nucleus
Initial concentration: 2.74224951500791
 
 MF
Compartment: nucleus
Initial concentration: 0.725579308537909
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 FC
Compartment: cytoplasm
Initial concentration: 2.46246334204771
 
 FCp
Compartment: cytoplasm
Initial concentration: 2.7123114824279
 
Global Parameters (17)
 
 vs
Value: 1.2236333742524
Constant
 
 ki
Value: 5.04543346939346
Constant
 
 n
Value: 6.3958
Constant
 
 vm
Value: 0.885376326739544
Constant
 
 km
Value: 0.0846004096489894
Constant
 
 ks
Value: 0.313846476998244
Constant
 
 vd
Value: 0.161111487362275
Constant
 
 k1n
Value: 0.222636680929471
Constant
 
 k2n
Value: 0.331484503209686
Constant
 
 ksp
Value: 0.294840169149965
Constant
 
 vdp
Value: 0.139750313979272
Constant
 
 k1np
Value: 0.272306464006464
Constant
 
 k2np
Value: 0.295420749525813
Constant
 
 amp
Constant
 
 dawn
Value: 6.0
Constant
 
 dusk
Value: 18.0
Constant
 
   Tot_FRQ
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000295

Curator's comment: (updated: 11 Jan 2011 14:25:42 GMT)

This model corresponds to "Model 1" of the reference publication. The model reproduces figure 5 in the supplementary material of the reference publication.
The model was integrated and simulated using Copasi v4.6 (Build 32).

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