MDCK EMT D

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This model is used in the publication by Mukhtar et al. under review.

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<?xml version='1.0' encoding='UTF-8'?>
<MorpheusModel version="4">
    <Description>
        <Details>Naba Mukhtar, Eric N Cytrynbaum, and Leah Edelstein-Keshet (2022) A Multiscale computational model of YAP signaling in epithelial fingering behaviour

Produced SI Figure 13

ODE model for the Tian et al model for epithelial-mesenchymal transition (EMT) governed by TGF-beta.

Tian, X.J., Zhang, H. and Xing, J. (2013) Coupled reversible and irreversible bistable switches underlying TGFβ-induced epithelial to mesenchymal transition. Biophysical journal, 105(4), pp.1079-1089.

This file was constructed by Leah Edelstein-Keshet using an XPP .ode file kindly supplied by Prof. Xiaojun Tian. </Details> <Title>TianODEs</Title> </Description> <Time> <StartTime value="0"/> <StopTime value="500" symbol="stoptime"/> <TimeSymbol symbol="time"/> <RandomSeed value="1"/> </Time> <Space> <Lattice class="linear"> <Size value="1, 0, 0" symbol="size"/> <Neighborhood> <Order>1</Order> </Neighborhood> </Lattice> <SpaceSymbol symbol="space"/> </Space> <Global> <Variable name="TGF" value="0" symbol="TGF"/> <Variable name="snail" value="0.01" symbol="snail"/> <Variable name="SNAIL" value="0.01" symbol="SNAIL"/> <Variable name="miR34" value="0.4" symbol="miR34"/> <Variable name="zeb" value="0.01" symbol="zeb"/> <Variable name="ZEB" value="0.01" symbol="ZEB"/> <Variable name="miR200" value="0.4" symbol="miR200"/> <Variable name="E-cadherin" value="4" symbol="Ecadherin"/> <Variable name="N-cadherin" value="0" symbol="Ncadherin"/> <System solver="Runge-Kutta [fixed, O(4)]" time-step="0.1"> <Constant name="TGF0" value="3" symbol="TGF0"/> <Constant name="k0TGF" value="0.06" symbol="k0TGF"/> <Constant name="kTGF" value="1.2" symbol="kTGF"/> <Constant name="JTGF" value="0.06" symbol="JTGF"/> <Constant name="kdTGF" value="0.6" symbol="kdTGF"/> <Constant name="Jsnail" value="1.6" symbol="Jsnail"/> <Constant name="kdsnail" value="0.09" symbol="kdsnail"/> <Constant name="k0snail" value="0.0006" symbol="k0snail"/> <Constant name="ksnail" value="0.03" symbol="ksnail"/> <Constant name="kSNAIL" value="17.0" symbol="kSNAIL"/> <Constant name="JSNAIL" value="0.08" symbol="JSNAIL"/> <Constant name="kdSNAIL" value="1.66" symbol="kdSNAIL"/> <Constant value="0.2" symbol="Jsnailcad1"/> <Constant name="k034" value="0.0012" symbol="k034"/> <Constant name="k34" value="0.012" symbol="k34"/> <Constant name="J134" value="0.15" symbol="J134"/> <Constant name="J234" value="0.36" symbol="J234"/> <Constant name="kd34" value="0.035" symbol="kd34"/> <Constant name="k0zeb" value="0.003" symbol="k0zeb"/> <Constant name="kzeb" value="0.06" symbol="kzeb"/> <Constant name="Jzeb" value="3.5" symbol="Jzeb"/> <Constant name="kdzeb" value="0.09" symbol="kdzeb"/> <Constant name="kZEB" value="17" symbol="kZEB"/> <Constant name="JZEB" value="0.06" symbol="JZEB"/> <Constant name="kdZEB" value="1.66" symbol="kdZEB"/> <Constant name="k02" value="0.0002" symbol="k02"/> <Constant name="k2" value="0.012" symbol="k2"/> <Constant name="kd2" value="0.035" symbol="kd2"/> <Constant name="J12" value="5.0" symbol="J12"/> <Constant name="J22" value="0.2" symbol="J22"/> <Constant value="0.1" symbol="kecad1"/> <Constant value="0.06" symbol="kecad2"/> <Constant value="0.2" symbol="Jecad1"/> <Constant value="0.5" symbol="Jecad2"/> <Constant value="0.05" symbol="kdecad"/> <Constant value="0.1" symbol="kncad1"/> <Constant value="0.06" symbol="kncad2"/> <Constant value="0.2" symbol="Jncad1"/> <Constant value="0.5" symbol="Jncad2"/> <Constant value="0.05" symbol="kdncad"/> <DiffEqn symbol-ref="TGF" name="Equation for TGF"> <Expression>k0TGF+kTGF/(1+(miR200/JTGF)^2)-kdTGFTGF</Expression> </DiffEqn> <DiffEqn symbol-ref="snail" name="Equation for snail"> <Expression>k0snail+ksnail(((TGF+TGF0)/Jsnail)^2)/(1+((TGF+TGF0)/Jsnail)^2)-kdsnailsnail</Expression> </DiffEqn> <DiffEqn symbol-ref="SNAIL" name="Equation for SNAIL"> <Expression>kSNAILsnail/(1+(miR34/JSNAIL)^2)-kdSNAILSNAIL</Expression> </DiffEqn> <DiffEqn symbol-ref="miR34" name="Equation for miR34"> <Expression>k034+k34/(1+(SNAIL/J134)^2+(ZEB/J234)^2)-kd34miR34</Expression> </DiffEqn> <DiffEqn symbol-ref="zeb" name="Equation for zeb"> <Expression>k0zeb+kzeb*(SNAIL/Jzeb)^2/(1+(SNAIL/Jzeb)^2)-kdzebzeb</Expression> </DiffEqn> <DiffEqn symbol-ref="ZEB" name="Equation for ZEB"> <Expression>kZEBzeb/(1+(miR200/JZEB)^2)-kdZEBZEB</Expression> </DiffEqn> <DiffEqn symbol-ref="miR200" name="Equation for miR200"> <Expression>k02+k2/(1+(SNAIL/J12)^2+(ZEB/J22)^2)-kd2miR200</Expression> </DiffEqn> <DiffEqn symbol-ref="Ecadherin" name="Equation for E-cadherin"> <Expression>kecad1/((SNAIL/Jecad1)^2+1)+kecad2/((ZEB/Jecad2)^2+1)-kdecadEcadherin</Expression> </DiffEqn> <DiffEqn symbol-ref="Ncadherin" name="Equation for N_cadherin"> <Expression>kncad1((SNAIL/Jncad1)^2)/((SNAIL/Jncad1)^2+1)+kncad2*((ZEB/Jncad2)^2)/((ZEB/Jncad2)^2+1)-kdncad*Ncadherin</Expression> </DiffEqn> </System> </Global> <Analysis> <Logger time-step="0.1"> <Plots> <Plot title="EMT Model" time-step="-1"> <Style decorate="true" style="lines" line-width="2.0" grid="true"/> <Terminal terminal="png"/> <X-axis> <Symbol symbol-ref="time"/> </X-axis> <Y-axis minimum="0.0" maximum="4"> <Symbol symbol-ref="TGF"/> <!– <Disabled> <Symbol symbol-ref="miR200"/> </Disabled> –> <!– <Disabled> <Symbol symbol-ref="miR34"/> </Disabled> –> <Symbol symbol-ref="SNAIL"/> <Symbol symbol-ref="snail"/> <Symbol symbol-ref="ZEB"/> <Symbol symbol-ref="zeb"/> <Symbol symbol-ref="Ecadherin"/> <Symbol symbol-ref="Ncadherin"/> </Y-axis> </Plot> </Plots> <Output> <TextOutput/> </Output> <Input/> </Logger> <ModelGraph include-tags="#untagged" format="dot" reduced="false"/> </Analysis> </MorpheusModel>

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