Signaling pathways In D1R containing striatal spiny projection neurons (Blackwell et al 2018)

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Accession:239744
We implemented a mechanistic model of signaling pathways activated by dopamine D1 receptors, acetylcholine receptors, and glutamate. We use our novel, computationally efficient simulator, NeuroRD, to simulate stochastic interactions both within and between dendritic spines. Results show that the combined activity of several key plasticity molecules correctly predicts the occurrence of either LTP, LTD or no plasticity for numerous experimental protocols.
Reference:
1 . Blackwell KT, Salinas AG, Tewatia P, English B, Hellgren Kotaleski J, Lovinger DM (2019) Molecular mechanisms underlying striatal synaptic plasticity: relevance to chronic alcohol consumption and seeking. Eur J Neurosci 49:768-783 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network; Synapse;
Brain Region(s)/Organism: Basal ganglia; Striatum;
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s):
Gap Junctions:
Receptor(s): D1; mGluR5; M1; M4;
Gene(s):
Transmitter(s): Acetylcholine; Dopamine; Endocannabinoid; Glutamate;
Simulation Environment: NeuroRD;
Model Concept(s): G-protein coupled; Long-term Synaptic Plasticity; Signaling pathways; Alcohol Use Disorder;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; M1; M4; mGluR5; D1; Acetylcholine; Dopamine; Glutamate; Endocannabinoid;
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<SDRun xmlns:xi="http://www.w3.org/2001/XInclude" xmlns="http://stochdiff.textensor.org">
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

          <xi:include href="Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapDdhpg.xml" />
          <xi:include href="../Morph_1sp2umDend.xml" />
	  <xi:include href="../IC_SPNspineAChm4R_AC1_coupleGqhigh.xml" />       
          <xi:include href="../Out_SPNspineCaMKII_DagL_AChm1R_AC1.xml" />
          <xi:include href="UchiStim5s25dhpg20sCa12-3-3-2-2.xml" />

    <!--2D means the morphology is interpreted like a flatworm, 3D for
	roundworms. The 2D case is good for testing as it is eas/Stry to visualize the
results (also, 3D may not work yet...)  -->
    <geometry>          2D           </geometry>
    <depth2D>           0.6          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    123       </simulationSeed>
    <outputQuantity>NUMBER</outputQuantity>


    <!-- run time for the calculation, milliseconds -->
    <runtime>          150000         </runtime>
<!-- 100001 -->
    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>          123          </spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
       <defaultMaxElementSide>0.3</defaultMaxElementSide> 
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>   0.1           </spineDeltaX>

	<!-- This specifies the surface layers, first implemented in v.2.1.7 -->
	<surfaceLayers>0.1,0.2</surfaceLayers>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds -->
    <fixedStepDt>         1       </fixedStepDt>

    <!-- interval at which stuff should be saved to the output file(s) -->
    <outputInterval>      500.0   </outputInterval>

    <!-- the tolerace is used for adaptive sims -->
    <tolerance>           0.002       </tolerance>
    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <!--calculation>GRID_STEPPED_STOCHASTIC</calculation-->
    <!--use the following for adaptive: -->
    <calculation>GRID_ADAPTIVE</calculation>

</SDRun>

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