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BIOMD0000000411 - Heiland2012_CircadianClock_C.reinhardtii

 

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Reference Publication
Publication ID: 23729908
Heiland I, Bodenstein C, Hinze T, Weisheit O, Ebenhoeh O, Mittag M, Schuster S.
Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii.
J Biol Phys 2012 Jun; 38(3): 449-464
Department of Bioinformatics, School of Biology and Pharmacy, Friedrich-Schiller University Jena, E.-Abbe-Platz 2, 07743 Jena, Germany.  [more]
Model
Original Model: BIOMD0000000411.xml.origin
Submitter: Ines Heiland
Submission ID: MODEL1201130000
Submission Date: 13 Jan 2012 08:28:40 UTC
Last Modification Date: 05 Feb 2014 12:45:08 UTC
Creation Date: 02 Apr 2012 15:49:46 UTC
Encoders:  Vijayalakshmi Chelliah
   Ines Heiland
set #1
bqbiol:isVersionOf Gene Ontology circadian temperature homeostasis
bqbiol:occursIn Taxonomy Chlamydomonas reinhardtii
Notes

This model is from the article:
Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii
Ines Heiland, Christian Bodenstein, Thomas Hinze, Olga Weisheit, Oliver Ebenhoeh, Maria Mittag and Stefan Schuster Journal of Biological Physics 4 March 2012; pp 1-16; doi: 10.1007/s10867-012-9264-x ,
Abstract:
Endogenous circadian rhythms allow living organisms to anticipate daily variations in their natural environment. Temperature regulation and entrainment mechanisms of circadian clocks are still poorly understood. To better understand the molecular basis of these processes, we built a mathematical model based on experimental data examining temperature regulation of the circadian RNA-binding protein CHLAMY1 from the unicellular green alga Chlamydomonas reinhardtii , simulating the effect of temperature on the rates by applying the Arrhenius equation. Using numerical simulations, we demonstrate that our model is temperature-compensated and can be entrained to temperature cycles of various length and amplitude. The range of periods that allow entrainment of the model depends on the shape of the temperature cycles and is larger for sinusoidal compared to rectangular temperature curves. We show that the response to temperature of protein (de)phosphorylation rates play a key role in facilitating temperature entrainment of the oscillator in Chlamydomonas reinhardtii . We systematically investigated the response of our model to single temperature pulses to explain experimentally observed phase response curves.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 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: 23729908 Submission Date: 13 Jan 2012 08:28:40 UTC Last Modification Date: 05 Feb 2014 12:45:08 UTC Creation Date: 02 Apr 2012 15:49:46 UTC
Mathematical expressions
Reactions
C3_phos C3_transk C3_mRNADegr C3_degr
C3_phos_degr C3_transl C1_transl complexformation
C1_phos C1_degr complexdegr C1_dephos
C1_phos_degr      
Rules
Assignment Rule (variable: T2) Assignment Rule (variable: EAlow) Assignment Rule (variable: EAhigh)  
Physical entities
Compartments Species
default C3_Gene C3_mRNA C_3
C_3_P C_3_pre C1
C1_mRNA C1_phos c1c3complex
junk    
Global parameters
T T2 v_phos V_dephos
R amplitude entrperiod EAlow
EAhigh vphosdegr Ephos Edephos
Reactions (13)
 
 C3_phos [C_3] → [C_3_P];  
 
 C3_transk [C3_Gene] → [C3_mRNA];   {C_3_P}
 
 C3_mRNADegr [C3_mRNA] → [junk];  
 
 C3_degr [C_3] → [junk];  
 
 C3_phos_degr [C_3_P] → [junk];  
 
 C3_transl [C_3_pre] → [C_3];   {C3_mRNA}
 
 C1_transl [C1_mRNA] → [C1];  
 
 complexformation [C1_phos] + [C_3_P] → [c1c3complex];  
 
 C1_phos [C1] → [C1_phos];  
 
 C1_degr [C1] → [junk];  
 
 complexdegr [c1c3complex] → [junk];  
 
 C1_dephos [C1_phos] → [C1];  
 
 C1_phos_degr [C1_phos] → [junk];  
 
Rules (3)
 
 Assignment Rule (name: T2) T2 = 296+parameter_4/2*sin(2*pi*time/parameter_5)
 
 Assignment Rule (name: parameter_6) EAlow = 50000
 
 Assignment Rule (name: parameter_7) EAhigh = 84000
 
Functions (5)
 
 arhenius neg feedb tempvar lambda(v, E, R, T2, T1, k, S, h, v*exp(E/R*(T2-T1)/(T1*T2))/(k+S^h))
 
 arhenius mass action tempvar lambda(v, E, R, T2, T1, S, v*exp(E/R*(T2-T1)/(T1*T2))*S)
 
 arhenius tranls temp var lambda(v, E, R, T2, T1, S, v*exp(E/R*(T2-T1)/(T1*T2))*S)
 
 arhenius michaelis menten temp var lambda(v, E, R, T2, T1, S, Km, v*exp(E/R*(T2-T1)/(T1*T2))*S/(Km+S))
 
 arhenius complexf temp var lambda(v, E, R, T2, T1, S1, S2, a, v*exp(E/R*(T2-T1)/(T1*T2))*S1*S2^a)
 
 default Spatial dimensions: 3.0  Compartment size: 1.0
 
 C3_Gene
Compartment: default
Initial concentration: 1.0
Constant
 
 C3_mRNA
Compartment: default
Initial concentration: 1.0
 
 C_3
Compartment: default
Initial concentration: 1.0
 
 C_3_P
Compartment: default
Initial concentration: 1.0
 
 C_3_pre
Compartment: default
Initial concentration: 1.0
Constant
 
 C1
Compartment: default
Initial concentration: 1.0
 
 C1_mRNA
Compartment: default
Initial concentration: 1.0
Constant
 
 C1_phos
Compartment: default
Initial concentration: 1.0
 
 c1c3complex
Compartment: default
Initial concentration: 1.0
 
 junk
Compartment: default
Initial concentration: 1.0
 
Global Parameters (12)
 
 T
Value: 291.0
Constant
 
  T2
Value: 296.0
 
 v_phos
Value: 1.0
Constant
 
 V_dephos
Value: 0.5
Constant
 
 R
Value: 8.31447
Constant
 
 amplitude
Value: 10.0
Constant
 
 entrperiod
Value: 24.0
Constant
 
  EAlow
Value: 50000.0
 
  EAhigh
Value: 84000.0
 
 vphosdegr
Value: 1.0
Constant
 
 Ephos
Value: 60000.0
Constant
 
 Edephos
Value: 67000.0
Constant
 
C3_phos (1)
 
   v
Value: 0.1
Constant
 
C3_transk (3)
 
   v
Value: 2.6
Constant
 
   k
Value: 0.4
Constant
 
   h
Value: 2.0
Constant
 
C3_mRNADegr (2)
 
   v
Value: 3.0
Constant
 
   Km
Value: 2.0
Constant
 
C3_degr (2)
 
   v
Value: 2.2
Constant
 
   Km
Value: 0.2
Constant
 
C3_phos_degr (2)
 
   v
Value: 1.5
Constant
 
   Km
Value: 1.4
Constant
 
C3_transl (1)
 
   v
Value: 5.0
Constant
 
C1_transl (2)
 
   v
Value: 19.0
Constant
 
   E
Value: 67000.0
Constant
 
complexformation (2)
 
   v
Value: 10.0
Constant
 
   a
Value: 2.0
Constant
 
C1_degr (3)
 
   v
Value: 30.0
Constant
 
   E
Value: 67000.0
Constant
 
   Km
Value: 2.0
Constant
 
complexdegr (3)
 
   v
Value: 20.0
Constant
 
   E
Value: 67000.0
Constant
 
   Km
Value: 4.0
Constant
 
C1_phos_degr (2)
 
   E
Value: 67000.0
Constant
 
   Km
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000411

Curator's comment: (updated: 02 Apr 2012 16:47:08 BST)

Figure 5d of the reference publication has been reproduced here. The model as such can reproduce the lower panel of figure 5d. The plot in the upper panel, can be obtained by changing the parameter "Ephos" to 40000J/mol (40kJ/mol).
The model was simulated using SBMLsimulator 1.0. The data were obtained and plotted using gnuplot.

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