Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013)

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Accession:150284
"… We present a new event-driven algorithm to synchronize different neuronal models, which decreases computational time and avoids superfluous synchronizations. The algorithm is implemented in the TimeScales framework. We demonstrate its use by simulating a new multiscale model of the Medium Spiny Neuron of the Neostriatum. The model comprises over a thousand dendritic spines, where the electrical model interacts with the respective instances of a biochemical model. Our results show that a multiscale model is able to exhibit changes of synaptic plasticity as a result of the interaction between electrical and biochemical signaling. …"
Reference:
1 . Mattioni M, Le Novère N (2013) Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PLoS One 8:e66811 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse;
Brain Region(s)/Organism: Striatum;
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s): I Na,p; I Na,t; I T low threshold; I A; I K,Ca; I CAN; I Calcium; I A, slow; I Krp; I R; I Q;
Gap Junctions:
Receptor(s):
Gene(s): Kv4.2 KCND2; Kv1.2 KCNA2; Cav1.3 CACNA1D; Cav1.2 CACNA1C; Kv2.1 KCNB1;
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Synaptic Plasticity; Signaling pathways; Calcium dynamics; Multiscale;
Implementer(s): Mattioni, Michele [mattioni at ebi.ac.uk];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; I Na,p; I Na,t; I T low threshold; I A; I K,Ca; I CAN; I Calcium; I A, slow; I Krp; I R; I Q;
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</celldesigner:extension>
</annotation>
</species>
<species id="s22" name="PP2B" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr15</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species id="s27" name="PP1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr19</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re22"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species id="s52" name="s52" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>s52</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re13"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species id="s55" name="s55" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>s55</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re10"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re9" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s17" alias="sa18">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s17" alias="sa19">
<celldesigner:linkAnchor position="N"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s4" aliases="sa4" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s4" alias="sa4">
<celldesigner:linkAnchor position="ESE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference species="s17">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa18</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s17">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa19</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="s4">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa4</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction id="re10" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s19" alias="sa21">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s19" alias="sa23">
<celldesigner:linkAnchor position="N"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="MODULATION" modifiers="s55" aliases="csa6" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s55" alias="csa6">
<celldesigner:linkAnchor position="ENE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference species="s19">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa21</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s19">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa23</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="s55">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa6</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction id="re13" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s27" alias="sa35">
<celldesigner:linkAnchor position="E"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s27" alias="sa36">
<celldesigner:linkAnchor position="W"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="CATALYSIS" modifiers="s52" aliases="csa5" targetLineIndex="-1,5">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s52" alias="csa5">
<celldesigner:linkAnchor position="SSW"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference species="s27">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa35</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s27">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa36</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="s52">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa5</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction id="re20" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s17" alias="sa19">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
<celldesigner:baseReactant species="s22" alias="sa29">
<celldesigner:linkAnchor position="E"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s52" alias="csa5">
<celldesigner:linkAnchor position="W"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.5384615384615389,0.4038461538461533</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference species="s17">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa19</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference species="s22">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa29</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s52">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa5</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
<reaction id="re22" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
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<celldesigner:baseReactant species="s17" alias="sa19">
<celldesigner:linkAnchor position="ENE"/>
</celldesigner:baseReactant>
<celldesigner:baseReactant species="s18" alias="sa15">
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</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s55" alias="csa6">
<celldesigner:linkAnchor position="N"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
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<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.6930899181186211,0.3032639002788259</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
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<celldesigner:modification type="INHIBITION" modifiers="s27" aliases="sa36" targetLineIndex="2,3">
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<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s27" alias="sa36">
<celldesigner:linkAnchor position="N"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference species="s17">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa19</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference species="s18">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa15</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="s55">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa6</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="s27">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa36</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
</listOfReactions>
</model>
</sbml>

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