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]
Citations  Citation Browser
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
                            
/*-----------------------------------------------------
Model used in the article by Michalikova et al. (2016)
to explore the generation of spikelets in cortical pyramidal neurons.
The model was adapted from Hu et al. (2009).

The following script simulates a layer V pyramidal cell stimulated with 
fluctuating synaptic input that results in somatic APs and spikelets.
To run this script, first compile the .mod files (e.g. with "nrnivmodl"),
then open this script in GUI ("nrngui Spikelets_Main.hoc"). 
Press "Init & Run" to start the simulation. The graph shows voltage traces
at the soma (black) and at the AIS (red). Somatic spikelets correspond to 
APs at the AIS.
---------------------------------------------------- */



/* -----------------------------------------------------
    Layer V Cortical Pyramidal Cell
    
    Based on Yu Yuguo ( May 1, 2008)
----------------------------------------------------- */


objref somatodendritic, dendritic




// --------------------------------------------------
//    Parameter Settings
// --------------------------------------------------

/* Global */
  dt = 0.01
  celsius   = 37
  steps_per_ms = 1/dt
  tstop = 10000
  v_init = -70
  
/* Others */
  axonOnSoma=1
  
/* Passive membrane */
  ra        = 150  
  global_ra = ra
  rm        = 30000   // g_pas=1/rm
  c_m       = 0.5
  cm_myelin = 0.02
  g_pas_node = 0.02

/* Active channels */
  // Nav
  Ena = 60
  gna12_soma = 80
  gna12_dend = 80 
  gna12_ais_max = 3200   // Nav1.2 
  gna16_ais_max = 3200   // Nav1.6
  gna16_nakeaxon= 300    
  gna12_myelin=20       // Nav1.2 at myelins
  gna16_node = 3200     // Nav1.6 at node
  
  vhalf_na12 = -30
  vhalf_na16 = -43
  vhalf_na = -30
  
  // Kv
  Ek = -90  
  gkv_soma = 20
  gkv_dend = 10 
  gkv_axon = 1000
  
  // Km
  gkm = .3
  gkm_soma = gkm
  
  // Kca
  gkca = 3
  gkca_soma = gkca
  
  // Ca
  Eca=140
  gca = .3
  gca_soma = gca

/* MM: downscale gNa */
scale_gna_soma = 0.8           //factor to scale gbar_na in soma
scale_gna_dend = 0.6          //factor to scale gbar_na in dendrites
scale_gna12_hillais = 0.8    //factor to scale the na12 conductance in hill and ais


// ------------------------------------------------
//    Cell Geometry
// ------------------------------------------------
 

/* Clean up */  
  forall delete_section()

/* Soma and Dendrites */
  load_file("morphology/P_Soma_Dendrites.hoc")

  // build a sectionlist for soma and dendrites
  somatodendritic = new SectionList()
  forall {
    if (L/nseg>40) {
      nseg = L/40 + 1 
    }    // make sure no segments exceed 40 uM length. Note, soma.nseg remains 10.
    somatodendritic.append()  // soma and dendrites are all included
  }

    
  // build a sectionlist for dendrites only
  dendritic = new SectionList()
  forsec somatodendritic dendritic.append()
  soma  dendritic.remove()     // remove soma for pure dendritic sectionlist

/* Axon - MM: diameters corrected to avoid a discontinuity */
  load_file("morphology/P_Axon_corrected.hoc") 
  create_axon()

  
/* Spines */
  aspiny = 0  // 0 for spiny
  if (!aspiny) {
    load_file ("morphology/P_Spines.hoc")
    add_spines(dendritic,spine_dens)
  }
  
  
  distance(0,axonOnSoma)  // set the point where axon seated on soma as the origin


// ----------------------------------------------------
//  Insert Density Mechanisms
// ----------------------------------------------------

load_file ("P_DensityMech.hoc") 

// Install passive membrane properties
install_passive()  
// Install active channels
install_channels()

    
// -------------------------------------------------------------------
// MM: insert fluctuating synaptic conductance from Destexhe et al. (2001)
// -------------------------------------------------------------------
objref fl
soma fl = new Gfluct2(0.5)

    
/* MM: load the session */
xopen("Gfluct_session.ses")