Spikelet generation and AP initiation in a L5 neocortical pyr neuron (Michalikova et al. 2017) Fig 1

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Accession:206398
The article by Michalikova et al. (2017) explores the generation of spikelets in cortical pyramidal neurons. The model cell, adapted from Hu et al. (2009), is a layer V pyramidal neuron. The cell is stimulated by fluctuating synaptic inputs and generates somatic APs and spikelets in response. The spikelets are initiated as APs at the AIS that do not activate the soma.
Reference:
1 . Michalikova M, Remme MW, Kempter R (2017) Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma. PLoS Comput Biol 13:e1005237 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,t;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Action Potentials; Electrotonus; Action Potential Initiation; Axonal Action Potentials;
Implementer(s): Michalikova, Martina [tinka.michalikova at gmail.com];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I Na,t;
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MichalikovaEtAl2016Fig1
morphology
Readme.html
ca.mod *
cad.mod *
Gfluct.mod
kca.mod *
km.mod *
kv.mod *
na.mod *
na12.mod *
na16.mod *
Gfluct_session.ses
mosinit.hoc
P_DensityMech.hoc
screenshot.png
Spikelets_Main.hoc
                            
/* ---------------------------------------------
     Define the Density Mechanisms 
----------------------------------------------*/

// --------------------------------------------
//  Install Passive Properties
// --------------------------------------------

proc install_passive() {
    
  // Forall
  forall {
    insert pas
    Ra = ra 
    cm = c_m 
    g_pas = 1/rm
    e_pas = v_init
  }

  soma.cm=1
  // Exceptions along the myelinated axon
  forsec "myelin" cm = cm_myelin
  forsec "node" g_pas = g_pas_node
}


// --------------------------------------------
//  Install Active Channels
// --------------------------------------------

proc  install_channels() {

  /* Add all kinds of channels to all sections*/  
    forall {
      insert na gbar_na=0
      insert na12  gbar_na12=0
      insert na16  gbar_na16=0
      insert kv    gbar_kv=0
      insert km    gbar_km=0
      insert kca   gbar_kca=0
      insert ca    gbar_ca=0
     }
  
    // Added by Hu    
    vshift_na12 = -35 - vhalf_na12 -10  // negative shift of input voltage, high threshold  -30mV    
    vshift_na16 = -35 - vhalf_na16 -10    // positive shift of input voltage, low threshold  -43mV
    vshift_na = -35 - vhalf_na -10  // the same as Na12

  
  
  /* Channel Constants */         
    forall if(ismembrane("k_ion")) ek = Ek
    forall if(ismembrane("na_ion")) ena = Ena
    forall if(ismembrane("ca_ion")) {
      eca = Eca
      ion_style("ca_ion",0,1,0,0,0)
      vshift_ca = 0
    }
  
  /* Somatodendritic */
    forsec somatodendritic {
      gbar_na = gna12_dend    // 80
      gbar_kv = gkv_dend        // 20                            
      gbar_km  = gkm            // 0.3                           
      gbar_kca = gkca           // 0.3                           
      gbar_ca = gca             // 0.3                           
      insert cad                // Internal calcium concentration mechanism only at somatodendritic region.
    }
    
    soma {
      gbar_na=gna12_soma * scale_gna_soma          // 80
      gbar_kv = gkv_soma            // 20 
      gbar_km = gkm_soma            // 0.3
      gbar_kca = gkca_soma          // 0.3
      gbar_ca = gca_soma            // 0.3
    }


  /* hill -> ais[0] -> ... -> ais[9] */
    
    // Nav 1.2   ( gna12_ais_max=3200, refer to "Nav% iseg.xls")   
    hill.gbar_na12= gna12_ais_max           *   1   *   0.8 * scale_gna12_hillais                     
    ais[0]. gbar_na12= gna12_ais_max      * 0.96    *   1 * scale_gna12_hillais                                               
    ais[1]. gbar_na12= gna12_ais_max        *   0.9 *   1 * scale_gna12_hillais                    
    ais[2]. gbar_na12= gna12_ais_max        *   0.75    *   1 * scale_gna12_hillais                  
    ais[3]. gbar_na12= gna12_ais_max        *   0.55    *   0.95 * scale_gna12_hillais               
    ais[4]. gbar_na12= gna12_ais_max        *   0.366985879 *   0.880142857 * scale_gna12_hillais  
    ais[5]. gbar_na12= gna12_ais_max        *   0.2 *   0.75 * scale_gna12_hillais                 
    ais[6]. gbar_na12= gna12_ais_max        *   0.100330761 *   0.647857143 * scale_gna12_hillais  
    ais[7]. gbar_na12= gna12_ais_max        *   0.011532125 *   0.520285714 * scale_gna12_hillais  
    ais[8]. gbar_na12= gna12_ais_max        *   0   *   0.428571429 * scale_gna12_hillais            
    ais[9]. gbar_na12= gna12_ais_max        *   0   *   0.342857143 * scale_gna12_hillais            
    
    // Nav 1.6  ( gna16_ais_max=3200, refer to "Nav% iseg.xls" )
    hill.gbar_na16 = gna16_ais_max      *   0   *   0.8 
    ais[0]. gbar_na16 = gna16_ais_max   *   0.04    *   1   
    ais[1]. gbar_na16 = gna16_ais_max   *   0.1 *   1   
    ais[2]. gbar_na16 = gna16_ais_max   *   0.25    *   1   
    ais[3]. gbar_na16 = gna16_ais_max   *   0.45    *   0.95   
    ais[4]. gbar_na16 = gna16_ais_max   *   0.633014121 *   0.880142857   
    ais[5]. gbar_na16 = gna16_ais_max   *   0.8 *   0.75   
    ais[6]. gbar_na16 = gna16_ais_max   *   0.899669239 *   0.647857143   
    ais[7]. gbar_na16 = gna16_ais_max   *   0.988467875 *   0.520285714   
    ais[8]. gbar_na16 = gna16_ais_max   *   1   *   0.428571429   
    ais[9]. gbar_na16 = gna16_ais_max   *   1   *   0.342857143   
                                     
    // Kv delayed rectifier channels  ( gkv_axon=1000 )
    hill.gbar_kv = gkv_axon *   0.1              
    ais[0]. gbar_kv = gkv_axon  *   0.2 
    ais[1]. gbar_kv = gkv_axon  *   0.3 
    ais[2]. gbar_kv = gkv_axon  *   0.4 
    ais[3]. gbar_kv = gkv_axon  *   0.5 
    ais[4]. gbar_kv = gkv_axon  *   0.6 
    ais[5]. gbar_kv = gkv_axon  *   0.7 
    ais[6]. gbar_kv = gkv_axon  *   0.8 
    ais[7]. gbar_kv = gkv_axon  *   0.9
    ais[8]. gbar_kv = gkv_axon  *   1
    ais[9]. gbar_kv = gkv_axon  *   1
    
    
  /*  Nakeaxon */
    nakeaxon  {
      gbar_na16 = 1600        // 300, artificial (ought to be 1600)
      gbar_na12 = 0
      gbar_kv = 1500
    }  
    
  /* ( Myelin[0] Node[0] ) -> ... -> ( Myelin[n_myelin] Node[n_myelin] )  */
    forsec "myelin" gbar_na = gna12_myelin    // 20
    forsec "node" gbar_na16 = gna16_ais_max/2  // 1600 

}

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