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toy_plant_immune_system.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by COPASI version 4.12 (Build 81) on 2014-10-06 11:26 with libSBML version 5.9.0. -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model metaid="COPASI0" id="Pritchard2014_Toy_Plant_Immune_System" name="Pritchard2014_Toy_Plant_Immune_System">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This model is an abstraction of a generic interaction between microbes, and a plant host. The model reactions are generally intended to be representative of processes, not specific molecular mechanisms (except where indicated, e.g. for activation of receptors).
The model is intended to be of a similar level of abstraction as the Zig-Zag model proposed in Jones and Dangl JL (2006) Nature doi:10.1038/nature05286, but to represent a dynamic system. The model is used in Pritchard and Birch (2014) Mol. Plant. Path. [DOI to follow] to illustrate the advantages of dynamic representations of systems over expository models such as the Zig-Zag model.
To simulate the presence or absence of a particular host immune interaction:
PTI (Pattern Triggered Immunity)
----------------------------
PTI absent: In "PAMP recognition", set k1=0
PTI present: In "PAMP recognition", set k1>0
ETS (Effector Triggered Susceptibility)
--------------------------------
ETS absent: In "Callose suppression", set k1=0
ETS present: In "Callose suppression", set k1>0
ETI (Effector Triggered Immunity)
-----------------------------
ETI absent: In "Effector recognition", set k1=0
ETI present: In "Effector recognition", set k1>0</pre>
</body>
</notes>
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<listOfFunctionDefinitions>
<functionDefinition metaid="COPASI29" id="Competitive_inhibition__irr" name="Competitive inhibition (irr)">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> substrate </ci>
</bvar>
<bvar>
<ci> Inhibitor </ci>
</bvar>
<bvar>
<ci> Km </ci>
</bvar>
<bvar>
<ci> V </ci>
</bvar>
<bvar>
<ci> Ki </ci>
</bvar>
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<ci> V </ci>
<ci> substrate </ci>
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<ci> Km </ci>
<ci> substrate </ci>
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<ci> Km </ci>
<ci> Inhibitor </ci>
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<ci> Ki </ci>
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</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition id="volume" name="volume">
<listOfUnits>
<unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time" name="time">
<listOfUnits>
<unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance" name="substance">
<listOfUnits>
<unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="COPASI1" id="Cell" name="Cell" spatialDimensions="3" size="1" constant="true">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This compartment represents the host cell volume.</pre>
</body>
</notes>
<annotation>
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</compartment>
<compartment metaid="COPASI2" id="Apoplast" name="Apoplast" spatialDimensions="3" size="1" constant="true">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This compartment represents "apoplast": the fluid-filled volume adjacent to the cell. The microbe, and chemical species, occupy this volume.</pre>
</body>
</notes>
<annotation>
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</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="COPASI3" id="PAMP" name="PAMP" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PAMP is an abstraction of pathogen-associated molecular patterns, which are produced by Path in the apoplast. These may interact reversibly with the model's PRR species to produce PRR*, in a representation of PAMP detection leading (perhaps) to PTI.</pre>
</body>
</notes>
<annotation>
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</annotation>
</species>
<species metaid="COPASI4" id="R" name="R" compartment="Cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>R represents the host's Resistance protein, in its unbound state. On binding to an internalised effector E_int, it becomes activated to form R*.
There is a constant pool of R protein in this model.</pre>
</body>
</notes>
<annotation>
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</species>
<species metaid="COPASI5" id="R_0" name="R*" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
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<pre>R* represents the host's Resistance protein, activated by binding to E_int. In the activated form, this species enhances rate at which Path is lost, emulating ETI.</pre>
</body>
</notes>
<annotation>
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</species>
<species metaid="COPASI6" id="E_int" name="E_int" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
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<pre>E_int acts to reduce the effect of PTI by enhancing the rate of loss of Callose. The effector also interacts reversibly with the R protein, activating it with consequent enhanced loss of local Path, in an abstraction of ETI</pre>
</body>
</notes>
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</species>
<species metaid="COPASI7" id="Callose" name="Callose" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
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<pre>This species is a generic "Callose", abstractly representing a measurable biochemical consequence of PRR activation, at the cell wall.
Callose is also a proxy for PTI, in that it enhances the rate of loss of the species Path. This is obviously troublesome at a mechanistic level, but for the purposes of this model we equate callose deposition with ROS/peroxide production and other defences.</pre>
</body>
</notes>
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</species>
<species metaid="COPASI8" id="Path" name="Path" compartment="Apoplast" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Path is a representation of microbes local to the cell. These derive from the larger (remote) population of microbes in Path_bulk, and disappear to NULL.</pre>
</body>
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</species>
<species metaid="COPASI9" id="Path_bulk" name="Path_bulk" compartment="Apoplast" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Path_bulk represents a remote population of microbes, from which the local microbes abstracted in Path derive.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI9">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:13:05Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
<species metaid="COPASI10" id="PRR" name="PRR*" compartment="Apoplast" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PRR* represents the host's Pathogen Recognition Receptor, activated by binding to a PAMP. In the activated form, this species enhances callose production, and the rate at which Path is lost, emulating PTI.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI10">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:10:23Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
<species metaid="COPASI11" id="PRR_0" name="PRR" compartment="Apoplast" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PRR represents the host's Pathogen Recognition Receptor, in its unbound state. On binding to a PAMP, it becomes activated to form PRR*.
There is a constant pool of PRR in this model.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI11">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:10:22Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
<species metaid="COPASI12" id="E" name="E" compartment="Apoplast" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This species is an abstract Effector: a molecular species that is produced by the microbe, translocated across the cell wall to become E_int, where it acts to reduce the effect of PTI by enhancing the rate of loss of Callose. The effector also interacts with the model's R protein, activating it with consequent enhanced loss of local Path, in an abstraction of ETI.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI12">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:10:12Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="COPASI14" id="PAMP_recognition" name="PAMP recognition" reversible="true">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PAMP recognition abstracts the interaction between PAMPs(/MAMPs/other molecules), and Pattern Recognition Receptor (PRR), to produce "activated PRR" PRR*. As [PRR*] reflects the local concentration of PAMP, that might be considered to be strength of pattern-triggered signalling.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI14">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:08:09Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="PRR_0" stoichiometry="1"/>
<speciesReference species="PAMP" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="PRR" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> k1 </ci>
<ci> PRR_0 </ci>
<ci> PAMP </ci>
</apply>
<apply>
<times/>
<ci> k2 </ci>
<ci> PRR </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
<parameter id="k2" name="k2" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI15" id="Effector_recognition" name="Effector recognition" reversible="true">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Effector recognition abstracts the interaction between internalised effector E_int, and "R protein" R, to produce "activated R protein" R*. As [R*] reflects the local concentration of E_int, it might also be considered to represent the strength of effector triggered responses.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI15">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:01Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="R" stoichiometry="1"/>
<speciesReference species="E_int" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="R_0" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Cell </ci>
<apply>
<minus/>
<apply>
<times/>
<ci> k1 </ci>
<ci> R </ci>
<ci> E_int </ci>
</apply>
<apply>
<times/>
<ci> k2 </ci>
<ci> R_0 </ci>
</apply>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
<parameter id="k2" name="k2" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI16" id="Effector_removal" name="Effector removal" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This represents the loss of effector from the apoplast, necessary to obtain steady state.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI16">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:27Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="E" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Apoplast </ci>
<ci> k1 </ci>
<ci> E </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI17" id="PAMP_removal" name="PAMP removal" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This represents the loss of PAMP from the apoplast, necessary to obtain steady state.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI17">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:47Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="PAMP" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Cell </ci>
<ci> k1 </ci>
<ci> PAMP </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI18" id="Pathogen_arrival" name="Pathogen arrival" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Pathogen arrival represents movement of microbes from some (distant) 'bulk' to the locality of the cell, where they may interact.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI18">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:11:38Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path_bulk" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Path_bulk" stoichiometry="1"/>
<speciesReference species="Path" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Apoplast </ci>
<ci> k1 </ci>
<ci> Path_bulk </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI19" id="Pathogen_removal" name="Pathogen removal" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Pathogen removal represents removal of microbes from the locality of the cell, where they may interact, to some other location or state where they can no longer interact. This might be due to movement/diffusion, or microbe destruction.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI19">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:12:15Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Apoplast </ci>
<ci> k1 </ci>
<ci> Path </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI20" id="PAMP_production" name="PAMP production" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>PAMP is produced proportional to the amount of local microbe (Path) present, in the apoplast compartment.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI20">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:14:54Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="PAMP" stoichiometry="1"/>
<speciesReference species="Path" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> Path </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI21" id="Effector_production" name="Effector production" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Effector E is produced proportional to the amount of local microbe (Path) present. E is produced initially into the apoplast compartment, where it may be removed, or translocated into the cell compartment.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI21">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:18:24Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="E" stoichiometry="1"/>
<speciesReference species="Path" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Apoplast </ci>
<ci> k1 </ci>
<ci> Path </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI22" id="E_int_removal" name="E_int removal" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>E_int is removed at a constant rate, so steady state can be reached.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI22">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:22:30Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="E_int" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Cell </ci>
<ci> k1 </ci>
<ci> E_int </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI23" id="ETI" name="ETI" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>The ETI step represents reduction of local microbe concentration due to activation of the host's R protein. No molecular mechanism for this is proposed in the model.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI23">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:26:20Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path" stoichiometry="1"/>
<speciesReference species="R_0" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="R_0" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> Path </ci>
<ci> R_0 </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI24" id="Effector_translocation" name="Effector translocation" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>This step represents the translocation of effector E from the apoplast compartment to the cell compartment, where it is represented as E_int. No mechanism is reflected in the model, except that translocation rate is [E]-dependent, and slowed in response to increased Callose,</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI24">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:34:20Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="E" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="E_int" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="Callose"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> Competitive_inhibition__irr </ci>
<ci> E </ci>
<ci> Callose </ci>
<ci> Km </ci>
<ci> V </ci>
<ci> Ki </ci>
</apply>
</math>
<listOfParameters>
<parameter id="Km" name="Km" value="0.1"/>
<parameter id="V" name="V" value="0.1"/>
<parameter id="Ki" name="Ki" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI25" id="Callose_production" name="Callose production" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>The mechanism by which Callose is produced is not defined. Callose is produced at a constant rate proportional to [PRR*], so the rate of production increases with increasing PAMP detection.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI25">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:50:00Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="PRR" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="PRR" stoichiometry="1"/>
<speciesReference species="Callose" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> PRR </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI26" id="Callose_removal" name="Callose removal" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Callose is removed at a constant rate, so that a steady state can be reached.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI26">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:53:54Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Callose" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Cell </ci>
<ci> k1 </ci>
<ci> Callose </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI27" id="PTI" name="PTI" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>The PTI step represents reduction of local microbe concentration due to the activation of PRR, as an abstraction of the consequences of Pattern Triggered Immunity (PTI), represented by the amount of callose deposition. No reasonable molecular mechanism for this is proposed in the model.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI27">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:54:44Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Path" stoichiometry="1"/>
<speciesReference species="Callose" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Callose" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k1 </ci>
<ci> Path </ci>
<ci> Callose </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k1" name="k1" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI28" id="Callose_suppression" name="Callose suppression" reversible="false">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Callose suppression is represented by greater loss of Callose when there is internalised effector (E_int) present. The mechanism of this is undefined.</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI28">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T15:09:45Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="Callose" stoichiometry="1"/>
<speciesReference species="E_int" stoichiometry="1"/>