Layer V PFC pyramidal neuron used to study persistent activity (Sidiropoulou & Poirazi 2012)

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Accession:144089
"... Here, we use a compartmental modeling approach to search for discriminatory features in the properties of incoming stimuli to a PFC pyramidal neuron and/or its response that signal which of these stimuli will result in persistent activity emergence. Furthermore, we use our modeling approach to study cell-type specific differences in persistent activity properties, via implementing a regular spiking (RS) and an intrinsic bursting (IB) model neuron. ... Collectively, our results pinpoint to specific features of the neuronal response to a given stimulus that code for its ability to induce persistent activity and predict differential roles of RS and IB neurons in persistent activity expression. "
Reference:
1 . Sidiropoulou K, Poirazi P (2012) Predictive features of persistent activity emergence in regular spiking and intrinsic bursting model neurons. PLoS Comput Biol 8:e1002489 [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;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I A; I K; I K,Ca; I CAN;
Gap Junctions:
Receptor(s): GabaA; GabaB; AMPA; NMDA; IP3;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Detailed Neuronal Models;
Implementer(s): Sidiropoulou, Kyriaki [sidirop at imbb.forth.gr];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; GabaA; GabaB; AMPA; NMDA; IP3; I Na,p; I Na,t; I L high threshold; I A; I K; I K,Ca; I CAN; Gaba; Glutamate;
/* ---------------------   PROCEEDURES USED IN CELL SETUP  -------------------------*/
/*-----------------------------------PFC-cell---------------------------------------*/

//Rm is sigmoidally decreased by half along the basal and apical dendrites and Cm is doubled, Ra is constant, kiki july 2008

/*  To make the distal membrane less conductive, vis-a-vis Stuart G.
and Spruston N., J. Neuroscience 18(10) 3501-3510, 1998, we deceay Rm 
from proximal to distal sigmoidally
*/

proc Rm_sigmoid_basal() { local rm
	Rm_soma = Rm_default
	Rm_end=  Rm_default*0.5
	Rm_dhalf=10 
	Rm_steep=5

     for (x) {  
	
       xdist = distance(x)    // calc. path distance     
	  rm = Rm_soma + (Rm_end - Rm_soma)/(1.0 + exp((Rm_dhalf-xdist)/Rm_steep))
       g_pas(x) = 1.0/rm
     }
}

proc Rm_sigmoid_apical() { local rm
	Rm_soma = Rm_default
	Rm_end=  Rm_default*0.5
	Rm_dhalf=300 //was 500
	Rm_steep=50

     for (x) {  
       xdist = distance(x)    
	 rm = Rm_soma + (Rm_end - Rm_soma)/(1.0 + exp((Rm_dhalf-xdist)/Rm_steep))
       g_pas(x) = 1.0/rm
     }

}


//==================================================================
//June 2006
//In Day et al, 2005, J Neuroscience,  25(38):8776-8787
// Ih was increased by a factor of 10 towards the apical and basilar dendrites

/* 
===================================================================
In cortical layer V neurons, it is reported that K+ currents (A, D, and K) 
decrease with increasing distance 
based on Korngreen and Sakmann, 2000
All three types of K+ currents decrease with distance from the soma
*/


/* Inserting K(Ca++)-type channels and calcium pumps along the
apical trunk with maximum conductances in 100<xdist<500
*/


/* Inserting LVA Ca++ T-type channels along the apical trunk in
a linearly increasing manner, for xdist > 100 um 
*/


/* Inserting HVAm Ca++ R-type and HVA L-type channesls along
the apical trunk. The R-type current is distributed in a fixed
conductance while the L-type current is distributed in a
maximum fixed conductance for distances xdist > 50 um and in a very
small conductance for xdist < 50 um
*/

proc apical_mechanisms(){


	//Insert h-current, sigmoidally increasing in the dendrites
	gh_soma=soma_hbar
	gh_end=soma_hbar*10
	H_dhalf=300
	H_steep=50

     for (x) {  
       xdist = distance(x)  //calc. perpedicular distance
       insert h
       gbar_h(x) = gh_soma + (gh_end - gh_soma)/(1.0 + exp((H_dhalf-xdist)/H_steep))
	}

	kap_distal_maxfactor=1
	kap_distal_distance=100
	kad_distal_maxfactor=0.1
	kad_distal_distance=300  

//for cortical cell, data is up to 400um
	for (x) {  
       xdist=distance(x)
       fr1= kad_distal_distance/xdist
       insert kad
       insert Ks
     
 
       if (xdist < kap_distal_distance ) {
          gkabar_kad(x) = kad_init*kap_distal_maxfactor
          gKsbar_Ks(x) = soma_kdBG*kap_distal_maxfactor  
	

       } else if (xdist < kad_distal_distance ) {
          gkabar_kad(x) = kad_distal_maxfactor*kad_init*fr1
          gKsbar_Ks(x) = soma_kdBG*kad_distal_maxfactor*fr1
	
          
       } else {
          gkabar_kad(x) = kad_distal_maxfactor*kad_init
          gKsbar_Ks(x) = soma_kdBG*kad_distal_maxfactor  
	
       }
     }

      
      	insert cad    // calsium pump/buffering mechanism
       
//insert calcium mechanisms and persistent sodium
        
	insert car	
	insert nap
	insert cal
	insert can
	insert cat
	insert kca
	insert mykca

 for (x) {  
         xdist = distance(x)
	 fr = xdist/200
       
         if (xdist < 200) {                	
		gcabar_car(x) = soma_car*0.5 	
		gnabar_nap(x) = soma_nap
		gcalbar_can(x) = soma_caN/30
     	    	gcalbar_cal(x) soma_caL
		gcatbar_cat(x) = soma_caT
		gbar_kca = soma_kca*0.1
		gkbar_mykca = mykca_init*0.05

         } else {
		
		gcabar_car(x) = soma_car*fr   
		gnabar_nap(x) = soma_nap*fr*5
		gcalbar_can(x) = soma_caN*fr*3.2
	   	gcalbar_cal(x) = soma_caL/(30*fr)
		gcatbar_cat(x) = soma_caT*fr  			
		gbar_kca = soma_kca*0.001
		gkbar_mykca = mykca_init *0.001
         }
     		
	}
		
}


/* Seting conductance values in all basal dendrites to be the
same as the values in the soma, except for the A
current conductance which is 0.6 times higher.  
*/

proc khbasal_fixed() { local i,x,d

forsec basal {


//increase H along the basal dendrites	
	
       insert h   //no gradient in somatosensory according to schiller
	   gbar_h = soma_hbar
	
 	insert kad
        insert can
        insert cad
	insert nap	
		gnabar_nap=soma_nap
	

	

for (x) {  
         xdist = distance(x)
	 fr = xdist/50
       
         if (xdist < 50) {        
        	
		gcalbar_can(x) = soma_caN/30
 		gkabar_kad(x) = kad_init*2 

         } else {
		
 		gkabar_kad(x) = kad_init*5  
		gcalbar_can(x) = soma_caN*0.1
         }
     		
	}
  }
}


/* The Na channels developed Mel and modified by Brannon,
Poirazi (hha2 and hha_old) both reduce activation as function
of voltage. In other words, they show actvity-dependent
attenuation of conductance.  Within both of these mechanisms,
ar2 ([0..1]) is used to inversely describe the intensity of
voltage-dependent attenuation. 0 is maximum attenuation, 1 is
no attenuation.

Within the cell model, we vary the amount of attenuation along
the apical trunk as a function of distance from the cell body
such that proximal sections show little attenuation and distal
sections show comparably more (with the exception of distal
obliques).

We typically decay ar2 linearly from proximal to distal with
the maximum and minimum values of decay as
parameters. Initialize these parameters: 
*/

max_ar2=0
min_ar2=0
decay_start=0 /* The distance at which decay starts. 
              The distance at which decay ends.
              */
decay_end=0

strdef ar24_tmp_str
objref  strobj, ar24_f
strobj=new StringFunctions()
ar2_firsttime=1

proc ar2_log() {

  if (!ar2_firsttime) { return }

  ar24_f=new File() 
  sprint($o3.tmp_str3, "%s/ar2_log", $o3.generic_dir)
  ar24_f.wopen($o3.tmp_str3)
  ar24_f.printf("%s:",$s1)

  while (strobj.substr($s2, "*") > -1) {
    //printf("substr:%d\n", strobj.substr($s2, "*"))

      index=strobj.head($s2, "\\*", ar24_tmp_str)
    //printf("index:%d\n", index)

      strobj.right($s2, 1+index)
     //printf("%s ... %s \n", ar24_tmp_str, $s2)

      $o3.create_variable("ar24_val", ar24_tmp_str)
      ar24_f.printf("%s:%g:", ar24_tmp_str, ar24_val)
     //printf("%s:%g", ar24_tmp_str, ar24_val)
  }

  $o3.create_variable("ar24_val", $s2)
  ar24_f.printf("%s:%g\n", $s2, ar24_val)
  

  ar24_f.close()
  ar2_firsttime=0
}



/*_______ END OF PROCEEDURES ROUTINELY USED IN CELL SETUP______*/

//__________________________________________________________________________________________________________


/* ____________      CELL SET-UP PROCEEDURE      _____________ */

maximum_segment_length=75
strdef sectype
objref CAN_temp, CAL_temp, CAT_temp, KAD_temp, KAP_temp, NA_temp

proc cell_setup() {

  // Set passive membrane properties
 	Rm_default=30000 
	Rm_dend=15000
	Ra_default= 100			
 	Cm_default = 1.2	
	Cm_dend = 2.0
	v_init = -66		
	
  // SEVERELY affects experiment results
    $o1.defvar("general", "celsius", "34","Temperature of slice.")        
    $o1.xopen_library("Terrence","cut-sections")
    cut_sections(maximum_segment_length)

// make 3-d mapping of cell sections
    $o1.xopen_library("Terrence","map-segments-to-3d")
    map_segments_to_3d()

// prepare to make a graph with cell configuration
    $o1.tmpo2=new Shape()
        
// Set initial conductance values 
      
  //Sodium - Potassium properties
	gna_default = 0.031 	
	gkdrbar_default=0.045 
 
//Calcium currents
	soma_caN = 0.3e-4
	soma_caL = 3e-4  
	soma_car = 3e-5*25  //*0.5 FOR RS	
	soma_caT = 1e-5*10 	
    
//Calcium activated K+ currents
	soma_kca =  0.005*5*0.5    		
 	mykca_init =0.006*5*0.001  

//Potassium current
	soma_km = 0.00022*0
	kad_init = 0.00075*1.2  	 	
	soma_kdBG = 0.0012*4.4  
 	soma_hbar = 1.872e-5*0.5    	
	
//Persistent sodium
	soma_nap = 1.2e-5  //*0.5 //for RS1
//----------------------------------------------------------------------------    
//for sadp induction	  
    gCAN = 0.0001 	 		 	
//=====================================================================================
 
// Start inserting mechanisms in cell
	   
      forsec somatic {
		nseg = 21
            		
		insert Naf
			gnafbar_Naf = gna_default*5  
		insert kdr
			gkdrbar_kdr = gkdrbar_default

           insert pas    // leak conductance
                    g_pas =  1/Rm_default
                    e_pas = v_init
                    Ra    = Ra_default
		         cm = Cm_default

           insert h     // h current 
                   gbar_h  = soma_hbar
                   K_h     = 8.8
                   vhalf_h = -82

  	    	 insert km
			gbar_km=soma_km

	    	  insert kad  // proximal A current
                   gkabar_kad = kad_init
                  
            insert cal 
  	      		gcalbar_cal=soma_caL

            insert can
			gcalbar_can=soma_caN  
 
            insert kca
			gbar_kca = soma_kca
     
         	 insert mykca 
			gkbar_mykca = mykca_init
         
	     	insert cad
	    
		insert Ks
			gKsbar_Ks = soma_kdBG
		    
         	insert cat 
                   gcatbar_cat = soma_caT   
	    
	   	 insert car
			gcabar_car=soma_car
	    insert nap	
		gnabar_nap=soma_nap*0.1
 
	    insert ican
                 gbar_ican  = gCAN
		
		//==========================================
	
            $o1.tmpo2.color(2)            
      }

//  Configure Axon

        forsec axonal {
		nseg=5

		insert Naf
			gnafbar_Naf = gna_default*10
		insert kdr
			gkdrbar_kdr = gkdrbar_default  
              insert pas  // leak conductance
                    g_pas       = 1/Rm_default
                    e_pas       = v_init
                    Ra          = Ra_default
                    cm          = Cm_default
		                                           
               $o1.tmpo2.color(1)
      }
	
    
//Include all apical dendrites


//  Configure apical trunk
 access soma[0]
distance()

       
       forsec apical {
	
           insert Naf
			gnafbar_Naf = gna_default*0.2 
		insert kdr 
			gkdrbar_kdr=gkdrbar_default*0.001   
                    
          insert pas // leak conductance
                  
		    e_pas          = v_init                    
		    Ra             = Ra_default*0.5	
               cm             = 1.2  
         	    Rm_sigmoid_apical($o1)         	 
	
	//add ICAN  in dendrites but smaller
	 insert ican
         gbar_ican  = gCAN*0.1
	  
	apical_mechanisms()   

           
// Set the Na+ spike attenuation variable (linearly decreasing from soma to 300 um)

         $o1.defvar("channel:na", "max_ar2", "0.95", "Somatic value of ar2")  //original 0.95
         $o1.defvar("channel:na", "min_ar2", "0.30", "Minimum value of ar2")
         $o1.defvar("channel:na", "decay_end", "300.0", "Distance beyond which all values are min_ar2") //800 for pfc
         $o1.defvar("channel:na", "decay_start", "50.0", "Distance at which ar2 starts to decrease")
         m_ar2 = (max_ar2 - min_ar2)/(decay_start - decay_end)
            for (x) {
                xdist = distance(x)
                if (xdist < decay_start) { 
                  ar2_Naf(x) = max_ar2 
                } else if (xdist > decay_end) {               
                  ar2_Naf(x) = min_ar2 
                } else {               
               ar2_Naf(x) = max_ar2 + m_ar2*xdist
                }
            }
            ar2_log("linear", "min_ar2*max_ar2*m_ar2*decay_start*decay_end",$o1)
	}

	

// Configure the basal dendrites

	access soma[0]
	distance()
   forsec basal {
            
		insert Naf
			gnafbar_Naf = gna_default*0.1
		insert kdr
			gkdrbar_kdr=gkdrbar_default*0.09  

            insert pas // passive properties
                    e_pas          = v_init
                    Ra             = Ra_default  
                    cm             = Cm_dend
			    Rm_sigmoid_basal($o1)  

	//add ICAN  in dendrites but smaller
	 insert ican
         gbar_ican  = gCAN*0.1
	  

                
// Set the Na+ spike attenuation variable (linearly decreasing from soma to 300 um)

         $o1.defvar("channel:na", "max_ar2", "0.95", "Somatic value of ar2")  //original 0.95
         $o1.defvar("channel:na", "min_ar2", "0.30", "Minimum value of ar2")
         $o1.defvar("channel:na", "decay_end", "50.0", "Distance beyond which all values are min_ar2") 
         $o1.defvar("channel:na", "decay_start", "20.0", "Distance at which ar2 starts to decrease")
         m_ar2 = (max_ar2 - min_ar2)/(decay_start - decay_end)
            for (x) {
                xdist = distance(x)
                if (xdist < decay_start) { 
                  ar2_Naf(x) = max_ar2 
                } else if (xdist > decay_end) {               
                  ar2_Naf(x) = min_ar2 
                } else {               
               ar2_Naf(x) = max_ar2 + m_ar2*xdist
                }
            }
            ar2_log("linear", "min_ar2*max_ar2*m_ar2*decay_start*decay_end",$o1)
             
	
        $o1.tmpo2.color(5)
     } 
   
	khbasal_fixed($o1) // Configure basal dendrites         
   
  

  forsec somatic { g_pas=1/Rm_default } // force Rm at all soma sections

    
forall {
	if (ismembrane("Naf")) {ena = 55}
	if (ismembrane("k_ion")) { ek = -85}
     
     if(ismembrane("ca_ion")) {
      eca = 140
     cai0_ca_ion =  2.4e-6 // for pump  
     cao = 2
     ion_style("ca_ion",3,2,1,1,1)
     }

  }

 
  //print the cell shape in the experiment folder
   sprint($o1.tmp_str2, "%s/configure_sections.eps", $o1.generic_dir)
   $o1.tmpo2.printfile($o1.tmp_str2)
  
   $o1.xopen_library("Terrence","current-balance") // balance current to -66 mV
   current_balance(v_init)

}
proc init() {
finitialize(v_init)
fcurrent()
}