Compartmental differences in cAMP signaling pathways in hippocam. CA1 pyr. cells (Luczak et al 2017)

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Accession:245529
Model of cAMP signaling pathways in hippocampal CA1 pyramidal neurons investigate mechanisms underlying the experimentally observed difference in cAMP and PKA FRET between proximal and distal dendrites. Simulations show that compartmental difference in PKA activity required enrichment of protein phosphatase in small compartments; neither reduced PKA subunits nor increased PKA substrates were sufficient.
Reference:
1 . Luczak V, Blackwell KT, Abel T, Girault JA, Gervasi N (2017) Dendritic diameter influences the rate and magnitude of hippocampal cAMP and PKA transients during ß-adrenergic receptor activation. Neurobiol Learn Mem 138:10-20 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism: Hippocampus; Mouse;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s): Adrenergic;
Gene(s):
Transmitter(s): Norephinephrine;
Simulation Environment:
Model Concept(s): G-protein coupled; Influence of Dendritic Geometry; Reaction-diffusion;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Adrenergic; Norephinephrine;
<?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_CaPKA_I1PP1.xml" />
          <xi:include href="Morph6.5um.xml" />
	  <xi:include href="IC_CaPKA_I1PP1_6.5u.xml" />       
          <xi:include href="IO_CaPKA_I1PP1.xml" />
    <StimulationSet>
      <InjectionStim specieID="L" injectionSite="pointA">
        <onset>           100000        </onset>
        <duration>           100       </duration>
        <rate>               170.0    </rate>
	<!-- 156.66*1000ms gives 1 uM in 6.5um dia-->
      </InjectionStim>
    </StimulationSet>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet).  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           4.0          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>

    <!-- Run time for the calculation, in milliseconds. -->
    <runtime>400000</runtime>

    <!-- Set the seed to get the same spines each time testing. Use 143, 155, 156 to calculate SEM-->
    <spineSeed>143</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
       <defaultMaxElementSide>1.0</defaultMaxElementSide> 
        
	<!-- Discretization for spines, in microns. -->
	<spineDeltaX>0.1</spineDeltaX>

    <!-- This specifies the surface layers, first implemented in v.2.1.7 -->
    <surfaceLayers>0.25,0.5</surfaceLayers>

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

    <!-- The timestep used in fixed step calculations, in milliseconds -->
    <fixedStepDt>0.005</fixedStepDt>

    <!-- Epsilong for adaptive -->
    <tolerance>0.01</tolerance>

    <outputInterval>1000</outputInterval>

    <!-- 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>

</SDRun>

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