Olfactory bulb mitral cell gap junction NN model: burst firing and synchrony (O`Connor et al. 2012)

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Accession:146030
In a network of 6 mitral cells connected by gap junction in the apical dendrite tuft, continuous current injections of 0.06 nA are injected into 20 locations in the apical tufts of two of the mitral cells. The current injections into one of the cells starts 10 ms after the other to generate asynchronous firing in the cells (Migliore et al. 2005 protocol). Firing of the cells is asynchronous for the first 120 ms. However after the burst firing phase is completed the firing in all cells becomes synchronous.
Reference:
1 . O'Connor S, Angelo K, Jacob TJC (2012) Burst firing versus synchrony in a gap junction connected olfactory bulb mitral cell network model. 6:75. Frontiers in Computational Neuroscience 6:75:1-18
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell;
Channel(s): I Na,t; I L high threshold; I A; I K; I K,Ca;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Bursting; Oscillations; Synchronization; Active Dendrites; Influence of Dendritic Geometry; Calcium dynamics; Olfaction;
Implementer(s):
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; I Na,t; I L high threshold; I A; I K; I K,Ca;
/
oconnoretal2012
README
AMPA.mod
Ca_mit_conc_ChannelML.mod
CurrentClampExt.mod
KA_ChannelML.mod
KCa3_ChannelML_new.mod
Kdr_ChannelML.mod
LCa3_mit_usb_ChannelML.mod
LeakConductance.mod
NaxSH0_ChannelML.mod
NaxSH10_ChannelML.mod
SynForRndSpike.mod
Cell1.hoc
Cell2.hoc
Cell3.hoc
Cell4.hoc
Cell5.hoc
Cell6.hoc
cellCheck.hoc
CellPositions.dat
ElectricalInputs.dat
gap.hoc
init.hoc
mosinit.hoc *
nCtools.hoc
NetworkConnections.dat
regenerateMods
simulation.props
                            
COMMENT

   **************************************************
   File generated by: neuroConstruct v1.3.8 
   **************************************************

   This file holds the implementation in NEURON of the Cell Mechanism:
   Ca_mit_conc_ChannelML (Type: Ion concentration, Model: ChannelML based process)

   with parameters: 
   /channelml/@units = SI Units 
   /channelml/notes = A channel from Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:     simulations of the mitral and granule cells ... 
   /channelml/ion/@name = ca 
   /channelml/ion/@charge = 2 
   /channelml/ion/@role = SignallingSubstance 
   /channelml/ion/notes = Signifies that the ion is involved in a process which alters its concentration 
   /channelml/ion_concentration/@name = Ca_mit_conc_ChannelML 
   /channelml/ion_concentration/status/@value = stable 
   /channelml/ion_concentration/status/contributor/name = Simon O'Connor 
   /channelml/ion_concentration/notes = An expontially decaying pool of calcium 
   /channelml/ion_concentration/publication/fullTitle = Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:     simulations of the mitral and granule cells of the olfacto ... 
   /channelml/ion_concentration/publication/pubmedRef = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7688798&dopt=Abstract 
   /channelml/ion_concentration/ion_species = ca 
   /channelml/ion_concentration/decaying_pool_model/resting_conc = 5.2e-6 
   /channelml/ion_concentration/decaying_pool_model/decay_constant = 0.01 
   /channelml/ion_concentration/decaying_pool_model/pool_volume_info/shell_thickness = 0.00001 

// File from which this was generated: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/Ca_mit_conc_ChannelML/CaPool.xml

// XSL file with mapping to simulator: /home/Simon/nC_projects/Rat_Mitral_Cell_Gap_Network_copy4/cellMechanisms/Ca_mit_conc_ChannelML/ChannelML_v1.8.0_NEURONmod.xsl

ENDCOMMENT


?  This is a NEURON mod file generated from a ChannelML file

?  Unit system of original ChannelML file: SI Units

COMMENT
    A channel from Bhalla, U.S.and Bower, J.M. Exploring parameter space in detailed single neuron models:
    simulations of the mitral and granule cells of the olfactory bulb
ENDCOMMENT

    

? Creating ion concentration

TITLE Channel: Ca_mit_conc_ChannelML

COMMENT
    An expontially decaying pool of calcium
ENDCOMMENT


UNITS {
    (mV) = (millivolt)
    (mA) = (milliamp)
    (um) = (micrometer)
    (l) = (liter)
    (molar) = (1/liter)
    (mM) = (millimolar)
}

    
NEURON {
    SUFFIX Ca_mit_conc_ChannelML
    USEION ca READ ica WRITE cai VALENCE 2
    
    RANGE cai
    
    RANGE rest_conc
    
    
    RANGE tau
    
    
    GLOBAL total_current
    
    
    RANGE thickness, F
    
    GLOBAL volume, surf_area
    
    
}

ASSIGNED {

    ica (mA/cm2)
    diam (um)
}

INITIAL {
    
        
    LOCAL shell_inner_diam

    shell_inner_diam = diam - (2*thickness)
    
    volume = (diam*diam*diam)*3.14159/6 - (shell_inner_diam*shell_inner_diam*shell_inner_diam)*3.14159/6
    
    surf_area = (diam*diam)*3.14159
    
    cai = rest_conc

}

PARAMETER {

    total_current
    rest_conc = 0.0000052 (mM)
          
    
    tau = 10 (ms)
   
    F = 96494 (C)
    
    thickness = 10 (um)   
                
    volume
    surf_area
    
    
}

STATE {

    cai (mM)

}

BREAKPOINT {

    SOLVE conc METHOD derivimplicit
    

}

DERIVATIVE conc {
    
    LOCAL thickness_cm, surf_area_cm2, volume_cm3 ? Note, normally dimensions are in um, but curr dens is in mA/cm2, etc
    
    thickness_cm = thickness *(1e-4)
    surf_area_cm2 = surf_area * 1e-8
    volume_cm3 = volume * 1e-12
    
    total_current = ica * surf_area_cm2


    cai' =  ((-1 * total_current)/(2 * F * volume_cm3)) - ((cai - rest_conc)/tau)
    

}


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