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toy_plant_immune_system.cps
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toy_plant_immune_system.cps
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<?xml version="1.0" encoding="UTF-8"?>
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Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant.
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<Model key="Model_3" name="Pritchard2014_Toy_Plant_Immune_System" simulationType="time" timeUnit="dimensionless" volumeUnit="dimensionless" areaUnit="m²" lengthUnit="m" quantityUnit="dimensionless" type="deterministic" avogadroConstant="6.02214179e+23">
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<vCard:EMAIL>leighton.pritchard@hutton.ac.uk</vCard:EMAIL>
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<vCard:Orgname>The James Hutton Institute</vCard:Orgname>
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<Comment>
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
</Comment>
<ListOfCompartments>
<Compartment key="Compartment_1" name="Cell" simulationType="fixed" dimensionality="3">
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<Comment>
This compartment represents the host cell volume.
</Comment>
</Compartment>
<Compartment key="Compartment_3" name="Apoplast" simulationType="fixed" dimensionality="3">
<MiriamAnnotation>
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<Comment>
This compartment represents "apoplast": the fluid-filled volume adjacent to the cell. The microbe, and chemical species, occupy this volume.
</Comment>
</Compartment>
</ListOfCompartments>
<ListOfMetabolites>
<Metabolite key="Metabolite_1" name="PAMP" simulationType="reactions" compartment="Compartment_1">
<MiriamAnnotation>
<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="#Metabolite_1">
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</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_3" name="R" simulationType="reactions" compartment="Compartment_1">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_5" name="R*" simulationType="reactions" compartment="Compartment_1">
<MiriamAnnotation>
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<rdf:Description rdf:about="#Metabolite_5">
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<dcterms:W3CDTF>2014-07-21T14:10:28Z</dcterms:W3CDTF>
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</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_7" name="E_int" simulationType="reactions" compartment="Compartment_1">
<MiriamAnnotation>
<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="#Metabolite_7">
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</rdf:RDF>
</MiriamAnnotation>
<Comment>
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
</Comment>
</Metabolite>
<Metabolite key="Metabolite_9" name="Callose" simulationType="reactions" compartment="Compartment_1">
<MiriamAnnotation>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_11" name="Path" simulationType="reactions" compartment="Compartment_3">
<MiriamAnnotation>
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<Comment>
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.
</Comment>
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<Metabolite key="Metabolite_13" name="Path_bulk" simulationType="reactions" compartment="Compartment_3">
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<Comment>
Path_bulk represents a remote population of microbes, from which the local microbes abstracted in Path derive.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_15" name="PRR*" simulationType="reactions" compartment="Compartment_3">
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</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_17" name="PRR" simulationType="reactions" compartment="Compartment_3">
<MiriamAnnotation>
<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="#Metabolite_17">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:10:22Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
<Metabolite key="Metabolite_19" name="E" simulationType="reactions" compartment="Compartment_3">
<MiriamAnnotation>
<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="#Metabolite_19">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:10:12Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
</Metabolite>
</ListOfMetabolites>
<ListOfReactions>
<Reaction key="Reaction_0" name="PAMP recognition" reversible="true" fast="false">
<MiriamAnnotation>
<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="#Reaction_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:08:09Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_17" stoichiometry="1"/>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_15" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4301" name="k1" value="0.1"/>
<Constant key="Parameter_4300" name="k2" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_14">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_62">
<SourceParameter reference="Parameter_4301"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_39">
<SourceParameter reference="Metabolite_17"/>
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_67">
<SourceParameter reference="Parameter_4300"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_71">
<SourceParameter reference="Metabolite_15"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_1" name="Effector recognition" reversible="true" fast="false">
<MiriamAnnotation>
<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="#Reaction_1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:01Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4299" name="k1" value="0.1"/>
<Constant key="Parameter_4298" name="k2" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_14">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_62">
<SourceParameter reference="Parameter_4299"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_39">
<SourceParameter reference="Metabolite_3"/>
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_67">
<SourceParameter reference="Parameter_4298"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_71">
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_2" name="Effector removal" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_2">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:27Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
This represents the loss of effector from the apoplast, necessary to obtain steady state.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_19" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4297" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4297"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_19"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_3" name="PAMP removal" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_3">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:09:47Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
This represents the loss of PAMP from the apoplast, necessary to obtain steady state.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_1" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4296" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4296"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_1"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_4" name="Pathogen arrival" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_4">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:11:38Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Pathogen arrival represents movement of microbes from some (distant) 'bulk' to the locality of the cell, where they may interact.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_13" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_13" stoichiometry="1"/>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4295" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4295"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_13"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_5" name="Pathogen removal" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_5">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:12:15Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4294" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4294"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_6" name="PAMP production" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_6">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:14:54Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
PAMP is produced proportional to the amount of local microbe (Path) present, in the apoplast compartment.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_1" stoichiometry="1"/>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4293" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4293"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_7" name="Effector production" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_7">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:18:24Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_19" stoichiometry="1"/>
<Product metabolite="Metabolite_11" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4292" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4292"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_8" name="E_int removal" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_8">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:22:30Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
E_int is removed at a constant rate, so steady state can be reached.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4291" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4291"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_9" name="ETI" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_9">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:26:20Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
<Substrate metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_5" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4290" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4290"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
<SourceParameter reference="Metabolite_5"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_10" name="Effector translocation" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_10">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:34:20Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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,
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_19" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfProducts>
<ListOfModifiers>
<Modifier metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfModifiers>
<ListOfConstants>
<Constant key="Parameter_4289" name="Km" value="0.1"/>
<Constant key="Parameter_4288" name="V" value="0.1"/>
<Constant key="Parameter_4287" name="Ki" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_4">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_32">
<SourceParameter reference="Metabolite_19"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_18">
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_28">
<SourceParameter reference="Parameter_4289"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_36">
<SourceParameter reference="Parameter_4288"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_37">
<SourceParameter reference="Parameter_4287"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_11" name="Callose production" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_11">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:50:00Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_15" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_15" stoichiometry="1"/>
<Product metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4286" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4286"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_15"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_12" name="Callose removal" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_12">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:53:54Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Callose is removed at a constant rate, so that a steady state can be reached.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfConstants>
<Constant key="Parameter_4285" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4285"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_13" name="PTI" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_13">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:54:44Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
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.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_11" stoichiometry="1"/>
<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_9" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4284" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4284"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_11"/>
<SourceParameter reference="Metabolite_9"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
<Reaction key="Reaction_14" name="Callose suppression" reversible="false" fast="false">
<MiriamAnnotation>
<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="#Reaction_14">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T15:09:45Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Callose suppression is represented by greater loss of Callose when there is internalised effector (E_int) present. The mechanism of this is undefined.
</Comment>
<ListOfSubstrates>
<Substrate metabolite="Metabolite_9" stoichiometry="1"/>
<Substrate metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfSubstrates>
<ListOfProducts>
<Product metabolite="Metabolite_7" stoichiometry="1"/>
</ListOfProducts>
<ListOfConstants>
<Constant key="Parameter_4283" name="k1" value="0.1"/>
</ListOfConstants>
<KineticLaw function="Function_13">
<ListOfCallParameters>
<CallParameter functionParameter="FunctionParameter_81">
<SourceParameter reference="Parameter_4283"/>
</CallParameter>
<CallParameter functionParameter="FunctionParameter_79">
<SourceParameter reference="Metabolite_9"/>
<SourceParameter reference="Metabolite_7"/>
</CallParameter>
</ListOfCallParameters>
</KineticLaw>
</Reaction>
</ListOfReactions>
<ListOfEvents>
<Event key="Event_0" name="Pathogen introduced" fireAtInitialTime="0" persistentTrigger="0">
<MiriamAnnotation>
<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="#Event_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2014-07-21T14:13:32Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</MiriamAnnotation>
<Comment>
Microbes are introduced to the bulk (not locally to the cell) at a specified time point, as an emulation of inoculation at some other point in the physical system.
</Comment>
<TriggerExpression>
<CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Reference=Time> > 10
</TriggerExpression>
<ListOfAssignments>
<Assignment targetKey="Metabolite_13">
<Expression>
1
</Expression>
</Assignment>
</ListOfAssignments>
</Event>
</ListOfEvents>
<ListOfModelParameterSets activeSet="ModelParameterSet_1">
<ModelParameterSet key="ModelParameterSet_1" name="Initial State">
<ModelParameterGroup cn="String=Initial Time" type="Group">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System" value="0" type="Model" simulationType="time"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Compartment Sizes" type="Group">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell]" value="1" type="Compartment" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast]" value="1" type="Compartment" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Species Values" type="Group">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell],Vector=Metabolites[PAMP]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell],Vector=Metabolites[R]" value="1" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell],Vector=Metabolites[R*]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell],Vector=Metabolites[E_int]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Cell],Vector=Metabolites[Callose]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast],Vector=Metabolites[Path]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast],Vector=Metabolites[Path_bulk]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast],Vector=Metabolites[PRR*]" value="0" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast],Vector=Metabolites[PRR]" value="1" type="Species" simulationType="reactions"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Compartments[Apoplast],Vector=Metabolites[E]" value="0" type="Species" simulationType="reactions"/>
</ModelParameterGroup>
<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
</ModelParameterGroup>
<ModelParameterGroup cn="String=Kinetic Parameters" type="Group">
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP recognition]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP recognition],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP recognition],ParameterGroup=Parameters,Parameter=k2" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector recognition]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector recognition],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector recognition],ParameterGroup=Parameters,Parameter=k2" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector removal]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector removal],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP removal]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP removal],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Pathogen arrival]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Pathogen arrival],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Pathogen removal]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Pathogen removal],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP production]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PAMP production],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector production]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector production],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[E_int removal]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[E_int removal],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[ETI]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[ETI],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector translocation]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector translocation],ParameterGroup=Parameters,Parameter=Km" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector translocation],ParameterGroup=Parameters,Parameter=V" value="0.1" type="ReactionParameter" simulationType="fixed"/>
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Effector translocation],ParameterGroup=Parameters,Parameter=Ki" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose production]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose production],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose removal]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose removal],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PTI]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[PTI],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>
<ModelParameterGroup cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose suppression]" type="Reaction">
<ModelParameter cn="CN=Root,Model=Pritchard2014_Toy_Plant_Immune_System,Vector=Reactions[Callose suppression],ParameterGroup=Parameters,Parameter=k1" value="0.1" type="ReactionParameter" simulationType="fixed"/>
</ModelParameterGroup>