Cerebellum granule cell FHF (Dover et al. 2016)

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Accession:206267
"Neurons in vertebrate central nervous systems initiate and conduct sodium action potentials in distinct subcellular compartments that differ architecturally and electrically. Here, we report several unanticipated passive and active properties of the cerebellar granule cell's unmyelinated axon. Whereas spike initiation at the axon initial segment relies on sodium channel (Nav)-associated fibroblast growth factor homologous factor (FHF) proteins to delay Nav inactivation, distal axonal Navs show little FHF association or FHF requirement for high-frequency transmission, velocity and waveforms of conducting action potentials. ...'
Reference:
1 . Dover K, Marra C, Solinas S, Popovic M, Subramaniyam S, Zecevic D, D'Angelo E, Goldfarb M (2016) FHF-independent conduction of action potentials along the leak-resistant cerebellar granule cell axon. Nat Commun 7:12895 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum interneuron granule cell;
Channel(s): I A; I Calcium; I K; I K,Ca; I M; I Na,p; I Na,t; I Potassium; I Sodium; Kir;
Gap Junctions:
Receptor(s): AMPA; Gaba; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s):
Implementer(s): Solinas, Sergio [solinas at unipv.it]; Subramaniyam, Sathyaa [sakthisathyaa at gmail.com]; D'Angelo, Egidio [dangelo at unipv.it]; Goldfarb, Mitchell goldfarb at genectr.hunter.cuny.edu];
Search NeuronDB for information about:  Cerebellum interneuron granule cell; AMPA; NMDA; Gaba; I Na,p; I Na,t; I A; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium; Kir;
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GrC_FHF_ModelDB
images
README.html
AmpaCOD.mod
GRC_CA.mod *
GRC_CALC.mod *
GRC_GABA.mod *
GRC_KA.mod *
GRC_KCA.mod *
GRC_KIR.mod *
GRC_KM.mod
GRC_KV.mod *
GRC_LKG1.mod *
GRC_LKG2.mod *
GRC_LKG3.mod
GRC_NA.mod
Grc_sine.mod
NmdaS.mod
Pregen.mod *
CClamp_soma.ses
ComPanel.hoc
Fig5.ses
Grc_Cell.hoc
helper_procedures.hoc
Ina.ses
KOFHF.DAPF.slowalfabeta.REV5.30.2016.ses
modComPanel.hoc
mosinit.hoc
Parametri.hoc
Start.hoc
WTFHF.DAPF.slowalfabeta.REV5.30.2016.ses
                            
// New version of Granule cell with Calcium in dendrites
// Multicompartmental model - cell template 
// Shyam Diwakar M. 
// Last modified 5-Feb-2007 
 
begintemplate GrC 

	      ndend = 4 
              nsg = 5
	      naxon = 56
	      npf=500  		
	 
              public soma,synA,synNS,synG,Area,CC,dend_1,dend_2,dend_3,dend_4,hillock,axon,pf
              public connect_pre,rescale,Us 
              public list_go_grc,list_con_inhib 
	      public branch0,branch1,branch2,branch3,br0,br1,br2,br3
              public SpikeTrain 
              create soma,hillock[1],axon[1],dend_1[1],dend_2[1],dend_3[1],dend_4[1],pf[1]//,branch0,branch1,branch2,branch3,br0,br1,br2,br3
              objref synNS[4],synA[4],synG[4] 
              objref list_go_grc,list_con_inhib 
              objref Inhib[4],CC
	    
	    	//objref gol_rec
              objref SpikeTrain,nil,netcon 
		 
              proc init() {  
			list_go_grc=new List() 
			list_con_inhib=new List() 
			//gol_rec=new Vector() 
			if(numarg()==5){ndend=$1 nsg =$2 nbut=$3 naxon=$4 npf=$5} else {ndend=4 nsg=5 nbut=20 naxon=56 npf=500} 
			create soma, hillock[nsg],axon[naxon],dend_1[ndend],dend_2[ndend],dend_3[ndend],dend_4[ndend],pf[npf]//,branch0,branch1,branch2,branch3,br0,br1,br2,br3  
			
					 
                        soma {
			     access soma 
                             nseg = 1 
                             diam = 5.8//6.06 
                             L = 5.8//6.16 
                             cm = 1 
                             Ra = 100
			     celsius=30
			     //for membrane current
			     //insert extracellular    
			     
			     
			     // Soma Channels 
                             insert GRC_LKG1 
                             insert GRC_LKG2
			     ggaba_GRC_LKG2 = 3e-05
 	 
                             insert GRC_KIR 
                             insert GRC_KA 
                             insert GRC_KM 
                              
 	 		     usetable_GRC_KA 	= 0	// 1 
                             usetable_GRC_KIR 	= 0	// 1 
                             usetable_GRC_KM 	= 0	// 1
			     
			     insert GRC_NA 
	                     insert GRC_KV 
		
	 		     usetable_GRC_NA 	= 0	// 1
			     usetable_GRC_KV 	= 0	// 1     

                             insert GRC_KCA 
                             usetable_GRC_KCA 	= 0	// 1 
                             gkbar_GRC_KCA = 0//0.010041491     // 1 
 
                             insert GRC_CA 
                             usetable_GRC_CA 	= 0	// 1 
                             gcabar_GRC_CA        = 0//0.001154771    // 1 
 
                             insert GRC_CALC 
			     beta_GRC_CALC = 1.5

			     ena = 87.39	
			     ek = -84.69 
                             eca = 129.33 
                             ecl = -65
			     
			     //CC =new VClamp(0.5)
	   
			     Area = L*diam*PI*1e-8	 
                        } 
                      // Hillock definition 
 
                      for(w1=0;w1<nsg;w1=w1+1) {
			hillock[w1] {
				    access hillock[w1]
                                    nseg = 1 
	                            diam = 2.3-0.5*w1 
	                            L = 0.5 
	                            cm = 1 
	                            Ra = 100
				    
 
	                            // Hillock Channels 
	                            insert GRC_LKG1 
	                            // insert GRC_Lkg2
				    //insert extracellular    
				    insert GRC_NA 
	                     	    insert GRC_KV 
		
	 		     	    usetable_GRC_NA 	= 0	// 1 
	                     	    usetable_GRC_KV 	= 0	// 1
				    				     	
				    ena = 87.39
				    ek = -84.69 
				    //Area = PI*L*diam*1e-8		  
	                         }
		      }
 
		      
		      for(w3=0;w3<naxon;w3=w3+1) { 
                      	axon[w3] {   // Axon definition
				 access axon[w3] 
	                         nseg = 1 
	                         diam = 0.15 
	                         L = 2.3367 
	                         cm = 1 
	                         Ra = 100
				 
				  
	                         // Axon Channels 
	                         insert GRC_LKG3
				 insert GRC_NA 
	                     	 insert GRC_KV 
		
	 		     	 usetable_GRC_NA 	= 0	// 1 
	                     	 usetable_GRC_KV 	= 0	// 1
  

   		  	  	 //insert extracellular    					
				 ena = 87.39 
				 ek = -84.69  
			} 
				  
                    }
	
			for(w2=0;w2<ndend;w2=w2+1) { 
                            dend_1[w2] {
				   access dend_1[w2]  
	                           nseg = 1 
	                           diam = 0.75 
	                           L = 5 
	                           cm = 1 
	                           Ra = 100
				    
 
	                           // Dendritic Channels 
	                           insert GRC_LKG1 
				   insert GRC_LKG2
			      	   ggaba_GRC_LKG2 = 3e-05	 
 
	                           insert GRC_KIR 
	                           usetable_GRC_KIR 	= 0	// 1 
	                           gkbar_GRC_KIR=0 

				   //insert extracellular     
	                           insert GRC_KA 
	                           usetable_GRC_KA 	= 0	// 1 
	                           gkbar_GRC_KA=0 
 
                                   insert GRC_KCA 
                                   usetable_GRC_KCA 	= 0	// 1 
                                   gkbar_GRC_KCA = 0//0.010041491     // 1 
 
                                   insert GRC_CA 
                                   usetable_GRC_CA 	= 0	// 1 
                                   gcabar_GRC_CA        = 0//0.001154771    // 1 
 
                                   insert GRC_CALC 
				   beta_GRC_CALC = 1.5
 
                                   eca = 129.33 
                                   ek = -84.69 
				    
                             }
			} 
                      	 
                        // Dendrite definition: second compartment 
                        for(w2=0;w2<ndend;w2=w2+1) { 
                            dend_2[w2] { 
				   access dend_2[w2]
                                   nseg = 1 
                                   diam = 0.75 
                                   L = 5 
                                   cm = 1 
                                   Ra = 100
				  
				    //insert extracellular    				    
	                           // Dendritic Channels 
	                           insert GRC_LKG1
				   insert GRC_LKG2
			      	   ggaba_GRC_LKG2 = 3e-05	 
                                   
				   insert GRC_KIR 
	                           usetable_GRC_KIR 	= 0	// 1 
	                           gkbar_GRC_KIR=0 
 
	                           insert GRC_KA 
	                           usetable_GRC_KA 	= 0	// 1 
                                   gkbar_GRC_KA=0 
 
                                   insert GRC_KCA 
                                   usetable_GRC_KCA 	= 0	// 1 
                                   gkbar_GRC_KCa = 0//.010041491     // 1 
 
                                   insert GRC_CA 
                                   usetable_GRC_CA 	= 0	// 1 
                                   gcabar_GRC_CA        = 0//.001154771     // 1 
 
                                   insert GRC_CALC 
				   beta_GRC_CALC = 1.5
 
                                   eca = 129.33 
                                   ek = -84.69
				    
                               } 
                        }
			  
                        // Dendrite definition: third compartment 
                        // 
			  for(w2=0;w2<ndend;w2=w2+1) {	 
                            dend_3[w2] {
				   access dend_3[w2] 
                                   nseg = 1 
	                           diam = 0.75 
	                           L = 2.5 
	                           cm = 1 
	                           Ra = 100
                                   
 
	                           // Dendritic Channels 
 
	                           insert GRC_LKG1
				   insert GRC_LKG2
			      	   ggaba_GRC_LKG2 = 3e-05	 
 
	                           insert GRC_KIR 
	                           usetable_GRC_KIR 	= 0	// 1 
	                           gkbar_GRC_KIR=0 
 				   //insert extracellular    
	                           insert GRC_KA 
	                           usetable_GRC_KA 	= 0	// 1 
	                           gkbar_GRC_KA=0 
 
                                   insert GRC_KCA 
                                   usetable_GRC_KCA 	= 0	// 1 
                                   gkbar_GRC_KCA = 0//.010041491     // 1 
 
                                   insert GRC_CA 
                                   usetable_GRC_CA 	= 0	// 1 
                                   gcabar_GRC_CA        = 0//.001154771     // 1 
 
                                   insert GRC_CALC 
				   beta_GRC_CALC = 1.5
 
                                   eca = 129.33 
                                   ek = -84.69  
 
                                   synG[w2] = new GRC_GABA(0.5)  
                               }
			    }	 
				 
                        // Dendrite definition: fourth compartment 
                        // 
                        for(w2=0;w2<ndend;w2=w2+1) { 
                            dend_4[w2] {
				   access dend_4[w2] 
                                   nseg = 1 
	                           diam = 0.75 
	                           L = 2.5 
	                           cm = 1 
	                           Ra = 100
				   
				   //insert extracellular                                        
	                           // Dendritic Channels 
	                           insert GRC_LKG1
				   insert GRC_LKG2
			      	   ggaba_GRC_LKG2 = 3e-05	 
 
				   insert GRC_CA
 
	                           insert GRC_KIR 
	                           usetable_GRC_KIR 	= 0	// 1 
	                           gkbar_GRC_KIR=0 
 
	                           insert GRC_KA 
	                           usetable_GRC_KA 	= 0	// 1 
	                           gkbar_GRC_KA=0 
 
                                   insert GRC_KCA 
                                   usetable_GRC_KCA 	= 0	// 1 
 
                                   insert GRC_CA 
                                   usetable_GRC_CA 	= 0	// 1 
                                  
                                   insert GRC_CALC
				   beta_GRC_CALC = 1.5  
 
                                   eca = 129.33 
                                   ek = -84.69 
 
	                           synA[w2] = new AmpaCOD(0.5) 
                                   synNS[w2] = new NMDAS(0.5) 
					//synNES[i] = new NMDAES(0.5)  
 
                               }
			    }
	    	        for(p1=0;p1<npf;p1=p1+1) { 
                      	   pf[p1] {   // pf definition
				 access pf[p1] 
	                         nseg = 1 
	                         diam = 0.15 
	                         L = 10
	                         cm = 1
	                         Ra = 100
				 
				  
	                         // Pf Channels 
	                         insert GRC_LKG3
				 insert GRC_NA 
	                     	 insert GRC_KV 
		
	 		     	 usetable_GRC_NA 	= 0	// 1 
	                     	 usetable_GRC_KV 	= 0	// 1
  

   		  	  	 //insert extracellular    					
				 ena = 87.39 
				 ek = -84.69  
			} 
				  
                    }/*
	
			branch0 {
			     access branch0 
                             nseg = 1 
                             diam = 0.15//0.1//6.06 
                             L = 3//100//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
			branch1 {
			     access branch1 
                             nseg = 1 
                             diam = 0.1//0.1//6.06 
                             L = 5//100//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
			branch2 {
			     access branch2 
                             nseg = 1 
                             diam = 0.05//0.1//6.06 
                             L = 10//100//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
	 		branch3 {
			     access branch3 
                             nseg = 1 
                             diam = 0.025//0.1//6.06 
                             L = 20//200//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
			br0 {
			     access br0 
                             nseg = 1 
                             diam = 0.15//0.1//6.06 
                             L = 3//100//6.16 
                             cm = 1
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
			br1 {
			     access br1 
                             nseg = 1 
                             diam = 0.1//0.1//6.06 
                             L = 5//100//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
			br2 {
			     access br2 
                             nseg = 1 
                             diam = 0.05//0.1//6.06 
                             L = 10//100//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}
	 		br3 {
			     access br3 
                             nseg = 1 
                             diam = 0.025//0.1//6.06 
                             L = 20//200//6.16 
                             cm = 1 
                             Ra = 100//e3
			     celsius=30
			     insert GRC_LKG3 	
				   // insert extracellular    
			}*/	 
                        	 
                        for(i=0;i<ndend;i=i+1){ 
                                 connect dend_4[i](1), dend_3[i](0) 
                                 connect dend_3[i](1), dend_2[i](0) 
                                 connect dend_2[i](1), dend_1[i](0) 
                                 connect dend_1[i](1), soma(0)
			}	 
			connect soma(1), hillock[0](0)
			connect hillock[0](1), hillock[1](0)
			connect hillock[1](1), hillock[2](0)
			connect hillock[2](1), hillock[3](0)
			connect hillock[3](1), hillock[4](0)
			connect hillock[4](1), axon[0](0)


			for(i=0;i<naxon-1;i=i+1) {
				connect axon[i](1), axon[i+1](0)
			}
						
			connect axon[naxon-1](1),pf[250](0.5)
			
			connect pf[0](1), pf[1](0)

			for(i=1;i<npf-1;i=i+1) {
				connect pf[i](1), pf[i+1](0)
			}
			//connect axon[naxon-1](1),branch0(0)

			/*connect branch0(0), pf[0](0)
			connect branch0(1),branch1(0)
 			connect branch1(1),branch2(0)
 			connect branch2(1),branch3(0)
						
			connect pf[npf-1](1),br0(0)
			connect br0(1),br1(0)
 			connect br1(1),br2(0)
 			connect br2(1),br3(0)*/

                        Area_soma = PI*soma.diam*soma.L*1e-8 
                        //Area_axon = 0 //not necessary (seems) 
                        //Area_dendrites = 0 //not necessary

			

		
                } 
endtemplate GrC

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