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

 Download zip file 
Help downloading and running models
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;
/
D1signal_modelDB
images
robust
ss_bath
UchiNew
README.html
20160830_EPACsh150_100nMISO_RawRatios.xlsx *
IC_SPNspine_alcohol.xml
IC_SPNspineAChm4R_AC1_coupleGqhigh.xml
Model_SPN_STDP-protFino-isiback.xml
Model_SPN_STDP-protFino-isifor.xml
Model_SPN_STDP-protPK-isiback.xml
Model_SPN_STDP-protPK-isifor.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcCtrl.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcIC.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da_IC.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_IC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcCtrl.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcIC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da_IC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_IC.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bath_block-summary.txt
Model_SPNspineAChm4R_Gshydr5_GapD-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bathDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bathDaCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockCyA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-BlockCyA-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockOA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-BlockOA-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockPap.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockRoli.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da0.1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da0.3.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da10.xml
Model_SPNspineAChm4R_Gshydr5_GapD-noACh.xml
Model_SPNspineAChm4R_Gshydr5_GapD-nostim.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp1-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp1-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChflat.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChnoB.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChnoDip.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noCKp.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowACh.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowDaDec2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowDaDec3.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChflat.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChnoB.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChnoDip.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noCKp.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noReb_DaDec1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noReb_DaDelay.xml
Morph_1sp2umDend.xml
Morph0.9um.xml
Morph1.5um.xml *
Morph20um.xml
MSPN-mergeRateConstTable.xls
NeuroRD.bat
Neurord_stdp.bat
NeuroRDsims.bat
NeuroRDuchi.bat
Out_SPNspineCaMKII_DagL_AChm1R_AC1.xml
Out_SPNspineCaMKII_DagL_AChm1R_AC1subset.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_Glublock.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_PKAblock.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_PKAblock2.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD-CyA.xml
Stim_AChCyA.xml
Stim_AChOA.xml
Stim_AChpapaverine.xml
Stim_AChrolipram.xml
Stim_CaBathCyA.xml
Stim_CaBathOA.xml
Stim_DaBathCyA.xml
Stim20hzACh-sp1.xml
Stim20hzACh-sp2adj.xml
Stim20hzACh-sp2other.xml
Stim20hzACh-sp2sep.xml
Stim20hzACh-sp3sep.xml
StimCouple20hz_alcohol_LowDaDec3-1tr.xml
StimCouple20hz_alcoholDa_LowDaDec3-1tr.xml
StimCouple20hz_CKpblock-10sITI.xml
StimCouple20hz_DaDelay-10sITI.xml
StimCouple20hz_m1block-10sITI.xml
StimCouple20hz_m4block-10sITI.xml
StimCouple20hzAChlow_LowDaDec3-10sITI.xml
StimCouple20hzAChNoDa-10sITI.xml
StimCouple20hzAChNoDip-10sITI.xml
StimCouple20hzAChNoGlu-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec2-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec3-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec3-10sITI_onset50.xml
StimCouple20hzAChNoRebound_LowDaDec3-1tr.xml
StimCouple20hz-flatACh-10sITI.xml
StimCouple20hz-noAChburst-10sITI.xml
StimCoupleDa0.1.xml
StimCoupleDa0.3.xml
StimCoupleDa1.xml
StimCoupleDa10.xml
StimCoupleSTDP_Fino_backward.xml
StimCoupleSTDP_Fino_forward.xml
StimCoupleSTDP_PK_backward.xml
StimCoupleSTDP_PK_forward.xml
StimCoupleTheta10hz_alcohol_DaDec1-1tr.xml
StimCoupleTheta10hz_alcoholDa_DaDec1-1tr.xml
StimCoupleTheta10hz_CKpblock-15sITI.xml
StimCoupleTheta10hz_DaDelay-15sITI.xml
StimCoupleTheta10hz_m1block-15sITI.xml
StimCoupleTheta10hz_m4block-15sITI.xml
StimCoupleTheta10hzACh-15sITI.xml
StimCoupleTheta10hzAChNoDa-15sITI.xml
StimCoupleTheta10hzAChNoDip-15sITI.xml
StimCoupleTheta10hzAChNoGlu-15sITI.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-15sITI.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-15sITI_onset50.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-1tr.xml
StimCoupleTheta10hz-flatACh-15sITI.xml
StimCoupleTheta10hz-noAChburst-15sITI.xml
StimDend_CaBath.xml
StimDend_DaBath.xml
StimDend_DaCaBath.xml
StimTheta10hzACh-sp1.xml
StimTheta10hzACh-sp2adj.xml
StimTheta10hzACh-sp2other.xml
StimTheta10hzACh-sp2sep.xml
StimTheta10hzACh-sp3sep.xml
                            
<?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-GapD-CyA.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="StimDend_CaBath.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>          300000         </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>

Loading data, please wait...