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BIOMD0000000273 - Pokhilko2010_CircClock

 

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Reference Publication
Publication ID: 20865009
Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ.
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model.
Mol. Syst. Biol. 2010 Sep; 6: 416
School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, UK.  [more]
Model
Original Model: BIOMD0000000273.origin
Submitter: Alexandra Pokhilko
Submission ID: MODEL1007240000
Submission Date: 24 Jul 2010 16:04:47 UTC
Last Modification Date: 08 Apr 2016 16:18:49 UTC
Creation Date: 21 Oct 2010 17:09:01 UTC
Encoders:  Vijayalakshmi Chelliah
   Alexandra Pokhilko
set #1
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
set #2
bqmodel:isDerivedFrom BioModels Database Locke2006_CircClock_LL
set #3
bqbiol:hasTaxon Taxonomy Arabidopsis thaliana
Notes

This a model from the article:
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model.
Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ. Mol Syst Biol.2010 Sep 21;6:416. 20865009,
Abstract:
Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation.

Model
Publication ID: 20865009 Submission Date: 24 Jul 2010 16:04:47 UTC Last Modification Date: 08 Apr 2016 16:18:49 UTC Creation Date: 21 Oct 2010 17:09:01 UTC
Mathematical expressions
Reactions
cL_m_trscr cL_m_degr cL_trsl cL_degr
cL_modif cLm_degr cT_m_trscr cT_m_degr
cT_trsl cT_degr cT_modif cTm_degr
cY_m_trscr cY_m_degr cY_trsl cY_degr
cP_trsl cP_degr cP9_m_trscr cP9_m_degr
cP9_trsl cP9_degr cP7_m_trscr cP7_m_degr
cP7_trsl cP7_degr cNI_m_trscr cNI_m_degr
cNI_trsl cNI_degr cG_m_trscr cG_m_degr
cG_trsl cG_degr cG_cZTL_assoc cZTL_trsl
cZTL_degr cZG_degr    
Rules
Assignment Rule (variable: L) Assignment Rule (variable: D)    
Physical entities
Compartments Species
def cG cG_m cL
cL_m cLm cNI
cNI_m cP cP7
cP7_m cP9 cP9_m
cT cT_m cTm
cY cY_m cZG
cZTL    
Global parameters
n0 n1 n2 n3
n4 n5 n6 n7
n8 n9 n10 n11
n12 g1 g2 g3
g4 g5 g6 g7
g8 g9 g10 g11
g12 g13 g14 g15
g16 m1 m2 m3
m4 m5 m6 m7
m8 m9 m10 m11
m12 m13 m14 m15
m16 m17 m18 m19
m20 m21 m22 m23
m24 m25 m26 a
b c d e
f h g i
j k l m
n o s p1
p2 p3 p4 p5
p6 p7 p8 p9
p10 p11 p12 p13
p14 p15 q1 q2
q3 q4 dawn dusk
dawn1 dusk1 dawn2 dusk2
L D quantity  
Reactions (38)
 
 cL_m_trscr  → [cL_m];   {cNI} , {cP} , {cP7} , {cP9} , {cTm}
 
 cL_m_degr [cL_m] → ;  
 
 cL_trsl  → [cL];   {cL_m}
 
 cL_degr [cL] → ;  
 
 cL_modif  → [cLm];   {cL}
 
 cLm_degr [cLm] → ;  
 
 cT_m_trscr  → [cT_m];   {cL} , {cY}
 
 cT_m_degr [cT_m] → ;  
 
 cT_trsl  → [cT];   {cT_m}
 
 cT_degr [cT] → ;   {cZG} , {cZTL}
 
 cT_modif  → [cTm];   {cT}
 
 cTm_degr [cTm] → ;  
 
 cY_m_trscr  → [cY_m];   {cL} , {cP} , {cT}
 
 cY_m_degr [cY_m] → ;  
 
 cY_trsl  → [cY];   {cY_m}
 
 cY_degr [cY] → ;  
 
 cP_trsl  → [cP];  
 
 cP_degr [cP] → ;  
 
 cP9_m_trscr  → [cP9_m];   {cL} , {cP} , {cT}
 
 cP9_m_degr [cP9_m] → ;  
 
 cP9_trsl  → [cP9];   {cP9_m}
 
 cP9_degr [cP9] → ;  
 
 cP7_m_trscr  → [cP7_m];   {cL} , {cLm} , {cP9}
 
 cP7_m_degr [cP7_m] → ;  
 
 cP7_trsl  → [cP7];   {cP7_m}
 
 cP7_degr [cP7] → ;  
 
 cNI_m_trscr  → [cNI_m];   {cLm} , {cP7}
 
 cNI_m_degr [cNI_m] → ;  
 
 cNI_trsl  → [cNI];   {cNI_m}
 
 cNI_degr [cNI] → ;  
 
 cG_m_trscr  → [cG_m];   {cL} , {cP} , {cT}
 
 cG_m_degr [cG_m] → ;  
 
 cG_trsl  → [cG];   {cG_m}
 
 cG_degr [cG] → ;  
 
 cG_cZTL_assoc [cG] + [cZTL] ↔ [cZG];  
 
 cZTL_trsl  → [cZTL];  
 
 cZTL_degr [cZTL] → ;  
 
 cZG_degr [cZG] → ;  
 
Rules (2)
 
 Assignment Rule (name: L) L = 0.5*(((1+tanh((t-24*floor(t/24))/0.5))-(1+tanh(((t-24*floor(t/24))-12)/0.5)))+1+tanh(((t-24*floor(t/24))-24)/0.5))
 
 Assignment Rule (name: D) D = 1-L
 
Functions (38)
 
 function_4_cT_degr lambda(D, L, cT, cZG, cZTL, def, m6, m7, m8, p5, ((m6*L+m7*D)*cT*(p5*cZTL+cZG)+m8*cT)/def)
 
 function_4_cNI_m_degr lambda(cNI_m, def, m16, m16*cNI_m/def)
 
 function_4_cNI_m_trscr lambda(cLm, cP7, def, g12, g13, l, m, n10, n11, (n10*cLm^l/(cLm^l+g12^l)+n11*cP7^m/(cP7^m+g13^m))/def)
 
 function_4_cY_trsl lambda(cY_m, def, p6, p6*cY_m/def)
 
 function_4_cP7_degr lambda(D, L, cP7, def, m15, m23, (m15*L+m23*D)*cP7/def)
 
 function_4_cT_trsl lambda(cT_m, def, p4, p4*cT_m/def)
 
 function_4_cY_m_trscr lambda(D, L, cL, cP, cT, def, g, g16, g7, n5, n6, q2, s, (L*q2*cP+(n5*L+n6*D)*g7^s/(cT^s+g7^s)*g16^g/(cL^g+g16^g))/def)
 
 function_4_cT_m_trscr lambda(cL, cY, d, def, e, g4, g5, n2, n3, (n2*cY^d/(cY^d+g4^d)+n3)*g5^e/(cL^e+g5^e)/def)
 
 function_4_cT_m_degr lambda(cT_m, def, m5, m5*cT_m/def)
 
 function_4_cNI_trsl lambda(cNI_m, def, p10, p10*cNI_m/def)
 
 function_4_cZTL_trsl lambda(def, p14, p14/def)
 
 function_4_cP7_m_degr lambda(cP7_m, def, m14, m14*cP7_m/def)
 
 function_4_cY_m_degr lambda(cY_m, def, m9, m9*cY_m/def)
 
 function_4_cLm_degr lambda(cLm, def, m4, m4*cLm/def)
 
 function_4_cL_modif lambda(c, cL, def, g3, p3, p3*cL^c/(cL^c+g3^c)/def)
 
 function_4_cL_degr lambda(c, cL, def, g3, m3, p3, (m3*cL+p3*cL^c/(cL^c+g3^c))/def)
 
 function_4_cL_trsl lambda(D, L, cL_m, def, p1, p2, cL_m*(p1*L+p2*D)/def)
 
 function_4_cP9_m_degr lambda(cP9_m, def, m12, m12*cP9_m/def)
 
 function_4_cY_degr lambda(cY, def, m10, m10*cY/def)
 
 function_4_cP_degr lambda(L, cP, def, m11, m11*cP*L/def)
 
 function_4_cTm_degr lambda(D, L, cTm, def, m25, m26, (m25*L+m26*D)*cTm/def)
 
 function_4_cP_trsl lambda(D, cP, def, p7, p7*D*(1-cP)/def)
 
 function_4_cG_cZTL_assoc lambda(D, L, cG, cZG, cZTL, def, p12, p13, (p12*L*cZTL*cG-p13*D*cZG)/def)
 
 function_4_cG_m_trscr lambda(L, cL, cP, cT, def, g14, g15, n, n12, o, q4, (L*q4*cP+n12*L*g15^o/(cL^o+g15^o)*g14^n/(cT^n+g14^n))/def)
 
 function_4_cG_degr lambda(cG, def, m19, m19*cG/def)
 
 function_4_cZG_degr lambda(cZG, def, m21, m21*cZG/def)
 
 function_4_cL_m_trscr lambda(L, a, b, cNI, cP, cP7, cP9, cTm, def, g1, g2, n0, n1, q1, (n0*L+L*q1*cP+n1*cTm^b/(cTm^b+g2^b))*g1^a/((cP9+cP7+cNI)^a+g1^a)/def)
 
 function_4_cL_m_degr lambda(D, L, cL_m, def, m1, m2, (m1*L+m2*D)*cL_m/def)
 
 function_4_cG_trsl lambda(cG_m, def, p11, p11*cG_m/def)
 
 function_4_cP9_m_trscr lambda(L, cL, cP, cT, def, g8, g9, h, i, n4, n7, q3, (L*q3*cP+(n4*L+n7*cL^i/(cL^i+g9^i))*g8^h/(cT^h+g8^h))/def)
 
 function_4_cP9_degr lambda(D, L, cP9, def, m13, m22, (m13*L+m22*D)*cP9/def)
 
 function_4_cP7_trsl lambda(cP7_m, def, p9, p9*cP7_m/def)
 
 function_4_cP7_m_trscr lambda(cL, cLm, cP9, def, g10, g11, j, k, n8, n9, (n8*(cLm+cL)^j/((cLm+cL)^j+g10^j)+n9*cP9^k/(cP9^k+g11^k))/def)
 
 function_4_cNI_degr lambda(D, L, cNI, def, m17, m24, (m17*L+m24*D)*cNI/def)
 
 function_4_cG_m_degr lambda(cG_m, def, m18, m18*cG_m/def)
 
 function_4_cP9_trsl lambda(cP9_m, def, p8, p8*cP9_m/def)
 
 function_4_cZTL_degr lambda(cZTL, def, m20, m20*cZTL/def)
 
 function_4_cT_modif lambda(cT, def, f, g6, p15, p15*cT^f/(cT^f+g6^f)/def)
 
 def Spatial dimensions: 3.0  Compartment size: 1.0
 
 cG
Compartment: def
Initial concentration: 0.0238
 
 cG_m
Compartment: def
Initial concentration: 0.119
 
 cL
Compartment: def
Initial concentration: 0.416
 
 cL_m
Compartment: def
Initial concentration: 1.0
 
 cLm
Compartment: def
Initial concentration: 0.054
 
 cNI
Compartment: def
Initial concentration: 0.044
 
 cNI_m
Compartment: def
Initial concentration: 0.0065
 
 cP
Compartment: def
Initial concentration: 0.825
 
 cP7
Compartment: def
Initial concentration: 0.019
 
 cP7_m
Compartment: def
Initial concentration: 0.075
 
 cP9
Compartment: def
Initial concentration: 0.056
 
 cP9_m
Compartment: def
Initial concentration: 0.35
 
 cT
Compartment: def
Initial concentration: 0.393
 
 cT_m
Compartment: def
Initial concentration: 0.25
 
 cTm
Compartment: def
Initial concentration: 0.24
 
 cY
Compartment: def
Initial concentration: 0.1
 
 cY_m
Compartment: def
Initial concentration: 0.093
 
 cZG
Compartment: def
Initial concentration: 0.0774
 
 cZTL
Compartment: def
Initial concentration: 0.323
 
Global Parameters (99)
 
 n0
Value: 0.4
Constant
 
 n1
Value: 1.8
Constant
 
 n2
Value: 0.7
Constant
 
 n3
Value: 0.06
Constant
 
 n4
Constant
 
 n5
Value: 3.4
Constant
 
 n6
Value: 1.25
Constant
 
 n7
Value: 0.2
Constant
 
 n8
Value: 0.42
Constant
 
 n9
Value: 0.26
Constant
 
 n10
Value: 0.18
Constant
 
 n11
Value: 0.71
Constant
 
 n12
Value: 2.3
Constant
 
 g1
Value: 0.1
Constant
 
 g2
Value: 0.28
Constant
 
 g3
Value: 0.4
Constant
 
 g4
Value: 0.91
Constant
 
 g5
Value: 0.3
Constant
 
 g6
Value: 0.3
Constant
 
 g7
Value: 0.18
Constant
 
 g8
Value: 0.14
Constant
 
 g9
Value: 0.3
Constant
 
 g10
Value: 0.7
Constant
 
 g11
Value: 0.7
Constant
 
 g12
Value: 0.5
Constant
 
 g13
Value: 0.6
Constant
 
 g14
Value: 0.17
Constant
 
 g15
Value: 0.4
Constant
 
 g16
Value: 0.2
Constant
 
 m1
Value: 0.54
Constant
 
 m2
Value: 0.24
Constant
 
 m3
Value: 0.2
Constant
 
 m4
Value: 0.2
Constant
 
 m5
Value: 0.3
Constant
 
 m6
Value: 0.25
Constant
 
 m7
Value: 0.5
Constant
 
 m8
Value: 0.1
Constant
 
 m9
Value: 1.0
Constant
 
 m10
Value: 0.3
Constant
 
 m11
Value: 1.0
Constant
 
 m12
Value: 1.0
Constant
 
 m13
Value: 0.32
Constant
 
 m14
Value: 0.28
Constant
 
 m15
Value: 0.31
Constant
 
 m16
Value: 0.5
Constant
 
 m17
Value: 0.3
Constant
 
 m18
Value: 1.0
Constant
 
 m19
Value: 0.2
Constant
 
 m20
Value: 1.2
Constant
 
 m21
Value: 0.2
Constant
 
 m22
Value: 2.0
Constant
 
 m23
Value: 1.0
Constant
 
 m24
Value: 0.405
Constant
 
 m25
Value: 0.28
Constant
 
 m26
Value: 0.14
Constant
 
 a
Value: 2.0
Constant
 
 b
Value: 3.0
Constant
 
 c
Value: 3.0
Constant
 
 d
Value: 2.5
Constant
 
 e
Value: 2.0
Constant
 
 f
Value: 3.0
Constant
 
 h
Value: 2.0
Constant
 
 g
Value: 2.0
Constant
 
 i
Value: 3.0
Constant
 
 j
Value: 3.0
Constant
 
 k
Value: 3.0
Constant
 
 l
Value: 2.0
Constant
 
 m
Value: 2.0
Constant
 
 n
Value: 1.0
Constant
 
 o
Value: 2.0
Constant
 
 s
Value: 3.0
Constant
 
 p1
Value: 0.4
Constant
 
 p2
Value: 0.27
Constant
 
 p3
Value: 0.1
Constant
 
 p4
Value: 0.268
Constant
 
 p5
Value: 1.0
Constant
 
 p6
Value: 0.44
Constant
 
 p7
Value: 0.3
Constant
 
 p8
Value: 0.7
Constant
 
 p9
Value: 0.4
Constant
 
 p10
Value: 0.36
Constant
 
 p11
Value: 0.23
Constant
 
 p12
Value: 30.0
Constant
 
 p13
Value: 0.4
Constant
 
 p14
Value: 0.45
Constant
 
 p15
Value: 0.05
Constant
 
 q1
Value: 0.8
Constant
 
 q2
Value: 0.5
Constant
 
 q3
Value: 2.9
Constant
 
 q4
Value: 0.6
Constant
 
   dawn
Constant
 
   dusk
Value: 12.0
Constant
 
   dawn1
Constant
 
   dusk1
Value: 3.0
Constant
 
   dawn2
Value: 9.0
Constant
 
   dusk2
Value: 12.0
Constant
 
   L
Value: 0.5
 
   D
Value: 0.5
 
   quantity
Value: 0.5
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000273

Curator's comment: (updated: 04 Nov 2010 11:54:38 GMT)

The figure 2A of the reference publication has been reproduced. The model was integrated and simulated using Copasi v4.6 (Build 32).

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