Impact of dendritic size and topology on pyramidal cell burst firing (van Elburg and van Ooyen 2010)

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Accession:114359
The code provided here was written to systematically investigate which of the physical parameters controlled by dendritic morphology underlies the differences in spiking behaviour observed in different realizations of the 'ping-pong'-model. Structurally varying dendritic topology and length in a simplified model allows us to separate out the physical parameters derived from morphology underlying burst firing. To perform the parameter scans we created a new NEURON tool the MultipleRunControl which can be used to easily set up a parameter scan and write the simulation results to file. Using this code we found that not input conductance but the arrival time of the return current, as measured provisionally by the average electrotonic path length, determines whether the pyramidal cell (with ping-pong model dynamics) will burst or fire single spikes.
Reference:
1 . van Elburg RA, van Ooyen A (2010) Impact of dendritic size and dendritic topology on burst firing in pyramidal cells. PLoS Comput Biol 6:e1000781 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,t; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Activity Patterns; Bursting; Spatio-temporal Activity Patterns; Simplified Models; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Methods;
Implementer(s): van Elburg, Ronald A.J. [R.van.Elburg at ai.rug.nl];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I Na,t; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium; 
// Author: Ronald van Elburg  (RonaldAJ at vanElburg eu)
//  
// Affiliation:
//   Department of Artificial Intelligence
//   Groningen University
//
// Parameter values used in the paper:
//
//   R.A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
//   dendritic topology on burst firing in pyramidal cells', 
//   PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
//


Reconstructed cells:
    Temperature:
        celsius   = 37
    
    Passive properties:
        General:
        ra                  = 80            ohm cm
        g_pas               = 3.3333 10^-5  S/cm^2      
        c_m                 = 0.75      uF/cm^2
        
        Exceptions:
        myelin      c_m     = 0.04      uF/cm^2
        axon nodes  g_pas   = 0.02      S/cm^2  
        
    Ion channel densities:
        Soma:   
        gna = 20            pS/um2
        gkv = 200           pS/um2
        gca = .3            pS/um2
        gkm = .1            pS/um2
        gkca = 3            pS/um2
        
        Apical dendrites:
        gna = 20            pS/um2
        gca= .3             pS/um2
        gkm = .1            pS/um2
        gkca = 3            pS/um2
        
        Basal dendrites (passive):
        gna = 0             pS/um2
        gca= 0              pS/um2
        gkm = 0             pS/um2
        gkca = 0            pS/um2
        
        Axon hillock:
        gna = 30000         pS/um2  
        gkv = 2000          pS/um2
    
        Axon initial segment:
        gkv = 2000          pS/um2 
        gna = 30000         pS/um2
        
        Axon nodes:
        gna = 30000         pS/um2
        gkv = 2000          pS/um2
        
        Myelinated axon:
        gna = 20            pS/um2
        
        Reversal potentials:
        Ek = -90                mV
        Ena = 60                mV
        Eca = 140               mV
    
        Dendritic and somatic compartment length:   
        segmentlength=50
        
        Number of myelin and node segments: 5
        

           
        // seems to be necessary for 3d cells to shift Na kinetics -5 mV
        vshift_na = -5
        
    Experiments:
        General:    
            Duration:
                tstop= 10000 ms
            Somatic stimulus:
                I=0.2 nA
                Initial delay stimulus=400 ms  
            Dendritic stimulus:
                synaptic_density=0.05 synapses/ um^2
                mean_interval=1000 ms        
                globSynapseStrength=0.0024  uS
                tau=0.5 ms 
                E_reversal=0    mV
        Pruning:
            Endsegment Pruning probability: p=0.3
            pruneSeed=1:1:20
            pruneDepth=0:1:20
            synaptic density is kept constant during pruning.
            
        ReReconstructed Cells:
            Topologies as shown.
            synaptic density is kept constant
            
        Scaling reconstructed cells:
            Length scaling factor=0.5:0.1:2.5
            For synaptic stimulation the total average current is kept 
            constant by changing the synaptic density.
            
========================================================

Simplified cells:
    Temperature:
        celsius   = 37
     
    Passive properties:
        ra                  = 80            ohm cm
        g_pas               = 3.3333 10^-5  S/cm^2      
        c_m                 = 0.75          uF/cm^2                                       
        
    Active properties:
        Dendrites:
            gca             = 0.3  pS/um2        
            gkca            =   3  pS/um2       
            gna             =  15  pS/um2                                          
            gkm             = 0.1  pS/um2         
        Soma:
            gkv             = 150  pS/um2              
            gna             =3000  pS/um2                                      
    Reversal Potentials:
        ek                  = -90           mV 
        ena                 =  60           mV  
        eca                 =  140          mV
        eleak               = -70           mV     
     
    Morphology:
        Number of Endsegments   =   8     
        somaLength              =   14      um                 
        terminalDiameter        =   0.7     um     
        rallPower               =   3/2                 
    
    Compartimentalization:
        dendNSegLength=50         um         // Maximal segment length of dendritic sections
                                             // as a consequence there are at least 15 compartments 
                                             // which are furtherdivided if the length of a section exceeds 
                                             // 50 um.
        somaNSeg=1                           // Number of segments of axo-somatic section
    Experiments:
        General
            Duration:
                tstop   = 10000 ms
            Somatic stimulus:
                I                       =0.03 nA    
                Initial delay stimulus  =400 ms         
            Dendritic stimulus:
                synapsesPerSection  =40          // number synapses per segment
                mean_interval       =1000 ms        
                globSynapseStrength =0.0024  uS
                tau                 =0.5 ms 
                E_reversal          =0  mV
            
        Rall trees:
            L       =1000:25:4000 um
            Topology=1:1:23
            
        Constant diameter trees:
            L       =500:25:2500 um
            Topology=1:1:23 
            I       =0.1 nA         (Somatic stimulus)