Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:139883
The model allows reconstruction of evoked local field potentials as seen in the cerebellar granular layer. The approach uses a detailed model of cerebellar granule neuron to generate data traces and then uses a "ReConv" or jittered repetitive convolution technique to reproduce post-synaptic local field potentials in the granular layer. The algorithm was used to generate both in vitro and in vivo evoked LFP and reflected the changes seen during LTP and LTD, when such changes were induced in the underlying neurons by modulating release probability of synapses and sodium channel regulated intrinsic excitability of the cells.
Reference:
1 . Diwakar S, Lombardo P, Solinas S, Naldi G, D'Angelo E (2011) Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control. PLoS One 6:e21928 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Cerebellum interneuron granule GLU cell;
Channel(s): I K; I M; I K,Ca; I Sodium; I Calcium; I Cl, leak;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB; Octave;
Model Concept(s): Extracellular Fields; Evoked LFP;
Implementer(s): Diwakar, Shyam [shyam at amrita.edu];
Search NeuronDB for information about:  Cerebellum interneuron granule GLU cell; GabaA; AMPA; NMDA; I K; I M; I K,Ca; I Sodium; I Calcium; I Cl, leak;
/
ReConv
data
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_NA.mod *
NmdaS.mod *
Pregen.mod *
ComPanel.hoc
Grc_Cell.hoc
mosinit.hoc
Parametri.hoc
ReConv_GrC.jpg
ReConv_invitro.jpg
ReConv_invivo.jpg
Record_vext.hoc
Start.hoc
                            
// ReConv algorithm for reconstructing evoked LFP in cerebellar granular layer
// Uses Multicompartmental GrC model (see http://senselab.med.yale.edu/ModelDb/showmodel.asp?model=116835)
// Last updated 11-June-2011
// Model developer: Shyam Diwakar M.
// Developed at Amrita School of Biotechnology (India) and at Prof. Egidio D'Angelo's Lab at Univ of Pavia (Italy)
// Amrita School of Biotechnology, Amritapuri
// Clappana P.O., Kollam, 690 525, Kerala, India.
// http://research.amrita.edu/compneuro
// Email:shyam@amrita.edu

 
/* Model published as [Diwakar et al., 2011, manuscript accepted, PLoS ONE]
Shyam Diwakar, Paola Lombardo, Sergio Solinas, Giovanni Naldi, Egidio D'Angelo. "Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control", PLoS ONE, 2011.
*/
 
begintemplate GrC 

	          ndend = 4 
              nsg = 5
	      	  naxon = 30	
	 
              public soma,synA,synNS,synG,Area,CC,dend_1,dend_2,dend_3,dend_4,hillock,axon 
              public connect_pre,rescale,Us 
              public list_go_grc,list_con_inhib 
	          public branch0,branch1,branch2,branch3
              public SpikeTrain 
              create soma,hillock[1],axon[1],dend_1[1],dend_2[1],dend_3[1],dend_4[1],branch0,branch1,branch2,branch3 
              objref synNS[4],synA[4],synG[4] 
              objref list_go_grc,list_con_inhib 
              objref Inhib[4],CC
	    
	    	  objref SpikeTrain,nil,netcon 
		 
              proc init() {  
				list_go_grc=new List() 
				list_con_inhib=new List() 
				if(numarg()==4){ndend=$1 nsg =$2 nbut=$3 naxon=$4} else {ndend=4 nsg=5 nbut=20 naxon=30} 
				create soma, hillock[nsg], axon[naxon], dend_1[ndend], dend_2[ndend], dend_3[ndend], dend_4[ndend],branch0,branch1,branch2,branch3  
			
				soma {
			     access soma 
                             nseg = 1 
                             diam = 5.8//6.06 
                             L = 5.8//6.16 
                             cm = 1 
                             Ra = 100
			     celsius=30
			         
			     // 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	 
                             usetable_GRC_KIR 	= 0	 
                             usetable_GRC_KM 	= 0	
			     
			    			 insert GRC_NA 
	                     	 insert GRC_KV 
		
	 		     			 usetable_GRC_NA 	= 0	
			      			 usetable_GRC_KV 	= 0	     

                             insert GRC_KCA 
                             usetable_GRC_KCA 	= 0	
                             gkbar_GRC_KCA = 0
 
                             insert GRC_CA 
                             usetable_GRC_CA 	= 0	
                             gcabar_GRC_CA        = 0
 
                             insert GRC_CALC 
			     			 beta_GRC_CALC = 1.5

			     			 ena = 87.39	
			     			 ek = -84.69 
                             eca = 129.33 
                             ecl = -65
			     
			     
			     
                        } 
                      // 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_NA 
	                     	    insert GRC_KV 
		
	 		     	    		usetable_GRC_NA 	= 0	 
	                     	    usetable_GRC_KV 	= 0	
				    				     	\
				    			ena = 87.39
				    			ek = -84.69 
				        }
		      		}
 
		      
		      for(w3=0;w3<naxon;w3=w3+1) { 
                      	axon[w3] {   // Axon definition
				 			access axon[w3] 
	                         nseg = 1 
	                         diam = 0.3 
	                         L = 2.3367 
	                         cm = 1 
	                         Ra = 100
				 
	                         // Axon Channels 
	                         insert GRC_LKG1
				 			 insert GRC_NA 
	                     	 insert GRC_KV 
		
	 		     	 		 usetable_GRC_NA 	= 0	 
	                     	 usetable_GRC_KV 	= 0	
  

   		  	  	 			 ena = 87.39 
				 			 ek = -84.69  
						} 
				  
                }
	
            // Dendrite definition: first compartment     
			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 
	                           gkbar_GRC_KIR=0 

				               insert GRC_KA 
	                           usetable_GRC_KA 	= 0 
	                           gkbar_GRC_KA=0 
 
                               insert GRC_KCA 
                               usetable_GRC_KCA 	= 0
                               gkbar_GRC_KCA = 0
 
                               insert GRC_CA 
                               usetable_GRC_CA 	= 0
                               gcabar_GRC_CA    = 0
 
                               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
				  
				               // Dendritic Channels 
	                           	insert GRC_LKG1
				   			   	insert GRC_LKG2
			      	   			ggaba_GRC_LKG2 = 3e-05	 
                                   
				   				insert GRC_KIR 
	                           	usetable_GRC_KIR 	= 0
	                           	gkbar_GRC_KIR=0 
 
	                           	insert GRC_KA 
	                           	usetable_GRC_KA = 0	
                                gkbar_GRC_KA=0 
 
                                insert GRC_KCA 
                                usetable_GRC_KCA = 0
                                gkbar_GRC_KCa = 0
 
                                insert GRC_CA 
                                usetable_GRC_CA 	= 0	
                                gcabar_GRC_CA        = 0
 
                                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
	                           	gkbar_GRC_KIR=0 
 				   
	                           	insert GRC_KA 
	                           	usetable_GRC_KA 	= 0
	                           	gkbar_GRC_KA=0 
 
                                insert GRC_KCA 
                                usetable_GRC_KCA 	= 0
                                gkbar_GRC_KCA = 0
 
                                insert GRC_CA 
                                usetable_GRC_CA 	= 0	
                                gcabar_GRC_CA        = 0
 
                                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
				                                           
	                           			// 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) 
					
                            }
			    }

			//Passive compartments -to maintain propagation delay and to avoid spike reflection     
			branch0 {
			     			access branch0 
                 			nseg = 1 
                            diam = 0.3
                            L = 3
                            cm = 0.5 
                            Ra = 100
						    celsius=30
			     			insert GRC_LKG1 	
				   
			}
			branch1 {
			     			access branch1 
                            nseg = 1 
                            diam = 0.2
                            L = 5
                            cm = 0.45 
                            Ra = 100
			     			celsius=30
			     			insert GRC_LKG1 	
				   
			}
			branch2 {
			     			access branch2 
                            nseg = 1 
                            diam = 0.1
                            L = 10
                            cm = 1 
                            Ra = 90
			     			celsius=30
			     			insert GRC_LKG1 	
				   
			}
	 		branch3 {
			     			access branch3 
                            nseg = 1 
                            diam = 0.1
                            L = 200
                            cm = 1 
                            Ra = 100
			     			celsius=30
			     			insert GRC_LKG1
			}	 
			
			//Connect all compartments
                        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),branch0(0)
			connect branch0(1),branch1(0)
 			connect branch1(1),branch2(0)
 			connect branch2(1),branch3(0)

                        
      } 
endtemplate GrC

Loading data, please wait...