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]
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)
//
// NEURON script for the paper:
//
//   Ronald 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.
//
// Please consult readme.txt or instructions on the usage of this file.
//
// This software is released under the GNU GPL version 3: 
// http://www.gnu.org/copyleft/gpl.html
//
// func LTree:
//      Calculate the combined length of the sections whose name starts with the
//      sectionname specified as input.
//
//      parameters:
//          $s1 sectionname

strdef tstr
func LTree(){local NewParents, NoEndSegments,sum,mean  localobj allSections, endSections, parentSections, intermediateSections, tmpSecRef,tmpSecRefParent
    allSections=new SectionList()
    endSections=new SectionList()
    NewParents=0
    NoEndSegments=0
    sum=0
    mean=0
    // Put sectionname into a search string
    sprint(tstr,".*%s.*",$s1)
    
    // Create a sectionlist containing all sections corresponding to the sectionname and 
    // initialize the section diameters (i.e. set it to 0). We will (ab)use diam to store the 
    // number of endsegments of the subtree of the present section.
    forsec $s1 {
        allSections.append()
    }

    // Find terminal segments and put them in the endSections sectionlist 
    forsec allSections {
        tmpSecRef=new SectionRef()
        if (tmpSecRef.nchild==0) {
            NewParents=1
            NoEndSegments=NoEndSegments+1
            endSections.append()
            
        }                          
    } 
    
    // Move through tree from endsegments to soma and electrotonic path of every 
    // section to the sum which will at the end of the evaluation contain the 
    // sum of all path from endsegemnt to soma
    
    intermediateSections=endSections
    while(NewParents==1){
              
        NewParents=0
        parentSections=new SectionList()
        
        forsec intermediateSections {
            tmpSecRef=new SectionRef()
            sum=sum+L
            if (tmpSecRef.has_parent==1) {
                tmpSecRef.parent { 
                    tmpSecRef if (issection(tstr)){
                        NewParents=1
                        parentSections.append()
                    } 
                }
            }  
        }
        intermediateSections=parentSections
        
    }

    mean=sum
    return mean
    
}

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