Dentate gyrus network model pattern separation and granule cell scaling in epilepsy (Yim et al 2015)

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Accession:185355
The dentate gyrus (DG) is thought to enable efficient hippocampal memory acquisition via pattern separation. With patterns defined as spatiotemporally distributed action potential sequences, the principal DG output neurons (granule cells, GCs), presumably sparsen and separate similar input patterns from the perforant path (PP). In electrophysiological experiments, we have demonstrated that during temporal lobe epilepsy (TLE), GCs downscale their excitability by transcriptional upregulation of ‘leak’ channels. Here we studied whether this cell type-specific intrinsic plasticity is in a position to homeostatically adjust DG network function. We modified an established conductance-based computer model of the DG network such that it realizes a spatiotemporal pattern separation task, and quantified its performance with and without the experimentally constrained leaky GC phenotype. ...
Reference:
1 . Yim MY, Hanuschkin A, Wolfart J (2015) Intrinsic rescaling of granule cells restores pattern separation ability of a dentate gyrus network model during epileptic hyperexcitability. Hippocampus 25:297-308 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Dentate gyrus;
Cell Type(s): Dentate gyrus granule GLU cell; Dentate gyrus mossy cell; Dentate gyrus basket cell; Dentate gyrus hilar cell; Dentate gyrus MOPP cell;
Channel(s): I Chloride; I K,leak; I Cl, leak; Kir; Kir2 leak;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s): IRK; Kir2.1 KCNJ2; Kir2.2 KCNJ12; Kir2.3 KCNJ4; Kir2.4 KCNJ14;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Spatio-temporal Activity Patterns; Intrinsic plasticity; Pathophysiology; Epilepsy; Homeostasis; Pattern Separation;
Implementer(s): Yim, Man Yi [manyi.yim at googlemail.com]; Hanuschkin, Alexander ; Wolfart, Jakob ;
Search NeuronDB for information about:  Dentate gyrus granule GLU cell; GabaA; AMPA; I Chloride; I K,leak; I Cl, leak; Kir; Kir2 leak; Gaba; Glutamate; 
//**********************       BASKET CELL         ****************************************

// extracted from
// Dentate gyrus network model 
// Santhakumar V, Aradi I, Soltesz I (2005) J Neurophysiol 93:437-53 
// https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=51781&file=\dentategyrusnet2005\DG500_M7.hoc

// ModelDB file along with publication:
// Yim MY, Hanuschkin A, Wolfart J (2015) Hippocampus 25:297-308.
// http://onlinelibrary.wiley.com/doi/10.1002/hipo.22373/abstract

// modified by 
// Man Yi Yim / 2015
// Alexander Hanuschkin / 2011

objref Bcell[nbcell]

begintemplate BasketCell

ndend1=4
ndend2=4
ndend3=4
ndend4=4

public  pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, bcdend1, bcdend2, bcdend3, bcdend4
public all, adend, bdend, cdend, ddend
create soma, bcdend1[ndend1], bcdend2[ndend2], bcdend3[ndend3], bcdend4[ndend4]
objref syn, pre_list


//to include steady state current injection
nst=1
objectvar stim[nst]

objref syn
proc init() {
	pre_list = new List()
	subsets()
	temp()
	synapse()
}

objref all, adend, bdend, cdend, ddend

proc subsets() { local i
	objref all, adend, bdend, cdend, ddend
	all = new SectionList()
		soma all.append()
		for i=0, 3 bcdend1 [i] all.append()
		for i=0, 3 bcdend2 [i] all.append()
		for i=0, 3 bcdend3 [i] all.append()
		for i=0, 3 bcdend4 [i] all.append()

	adend  = new SectionList()
		bcdend1 [0] adend.append()
		bcdend2 [0] adend.append()
		bcdend3 [0] adend.append()
		bcdend4 [0] adend.append()

	bdend  = new SectionList()
		bcdend1 [1] bdend.append()
		bcdend2 [1] bdend.append()
		bcdend3 [1] bdend.append()
		bcdend4 [1] bdend.append()

	cdend  = new SectionList()
		bcdend1 [2] cdend.append()
		bcdend2 [2] cdend.append()
		bcdend3 [2] cdend.append()
		bcdend4 [2] cdend.append()

	ddend  = new SectionList()
		bcdend1 [3] ddend.append()
		bcdend2 [3] ddend.append()
		bcdend3 [3] ddend.append()
		bcdend4 [3] ddend.append()
}

proc temp() {

	soma {nseg=1 L=20 diam=15} // changed L & diam
		
	bcdend1 [0] {nseg=1 L=75 diam=4}	// bcdend 1 and 2 are apical
	bcdend1 [1] {nseg=1 L=75 diam=3}
	bcdend1 [2] {nseg=1 L=75 diam=2}
 	bcdend1 [3] {nseg=1 L=75 diam=1}

	bcdend2 [0] {nseg=1 L=75 diam=4}
	bcdend2 [1] {nseg=1 L=75 diam=3}
	bcdend2 [2] {nseg=1 L=75 diam=2}
	bcdend2 [3] {nseg=1 L=75 diam=1}
 		 
	bcdend3 [0] {nseg=1 L=50 diam=4} 	// bcdend 3 and 4 are basal
	bcdend3 [1] {nseg=1 L=50 diam=3}
	bcdend3 [2] {nseg=1 L=50 diam=2}
	bcdend3 [3] {nseg=1 L=50 diam=1} 
	
	bcdend4 [0] {nseg=1 L=50 diam=4}
	bcdend4 [1] {nseg=1 L=50 diam=3}
	bcdend4 [2] {nseg=1 L=50 diam=2}
	bcdend4 [3] {nseg=1 L=50 diam=1} 	

    
	forsec all {
		insert ccanl
	catau_ccanl = 10
	caiinf_ccanl = 5.e-6
		insert ka
	gkabar_ka=0.00015
		insert nca  
	gncabar_nca=0.0008   
		insert lca 
	glcabar_lca=0.005
		insert sk
	gskbar_sk=0.000002
		insert bk
	gkbar_bk=0.0002
	}

	soma {insert ichan2  
	gnatbar_ichan2=0.12  // Santhakumar et al (2005) tab2
	gkfbar_ichan2=0.013  // Santhakumar et al (2005) tab2
	gl_ichan2 = 0.00018
	cm=1.4
	} 

	forsec adend {insert ichan2
	gnatbar_ichan2=0.12  // Santhakumar et al (2005) tab2
	gkfbar_ichan2=0.013
	gl_ichan2 = 0.00018
	cm=1.4
	}		
	forsec	bdend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00018
	cm=1.4}
		
	forsec 	cdend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00018
	cm=1.4}

	forsec	ddend {insert ichan2
	gnatbar_ichan2=0.0
	gkfbar_ichan2=0.00
	gl_ichan2 = 0.00018
	cm=1.4}


	connect bcdend1[0](0), soma(1)
	connect bcdend2[0](0), soma(1)
	connect bcdend3[0](0), soma(0)
	connect bcdend4[0](0), soma(0)
	for i=1,3 {
	connect bcdend1[i](0), bcdend1[i-1](1)
	}
	for i=1,3 {
	connect bcdend2[i](0), bcdend2[i-1](1)
	}
	for i=1,3 {
	connect bcdend3[i](0), bcdend3[i-1](1)
	}
	for i=1,3 {
	connect bcdend4[i](0), bcdend4[i-1](1)
	}


	forsec all {Ra=100}
	forsec all {	ena 	= 	50 	// ena was unified from enat=55 (BC, HIPP, MC) and enat=45 (GC) in Santhakumar et al. (2005) <ah>
		    	ek 	= 	-90  	// simplified ekf=eks=ek=esk; note the eK was erroneously reported as -105mV in the Yim et al. 2015 <ah>
		 	el_ichan2 =	-60.06 
			cao_ccanl =	2 }   
}


//Defining Synapses on to Basket Cells
proc synapse() {
	bcdend1 [3] syn = new Exp2Syn(0.5)	//PP(AMPA) syn to apical dist dend Dingledine '95
	syn.tau1 = 2	syn.tau2 = 6.3	syn.e = 0 
	pre_list.append(syn)

	bcdend2 [3] syn = new Exp2Syn(0.5)	//PP(AMPA) syn to apical dist dend Dingledine '95
	syn.tau1 = 2	syn.tau2 = 6.3	syn.e = 0  
	pre_list.append(syn)

	bcdend1 [0] syn = new Exp2Syn(0.5)	//GC(AMPA) syn to prox dend Geiger '97
	syn.tau1 = .3	syn.tau2 = .6	syn.e = 0
	pre_list.append(syn)

	bcdend2 [0] syn = new Exp2Syn(0.5)	//GC(AMPA) syn to prox dend Geiger '97
	syn.tau1 = .3	syn.tau2 = .6	syn.e = 0
	pre_list.append(syn)

	bcdend3 [0] syn = new Exp2Syn(0.5)	//GC(AMPA) syn to prox dend Geiger '97
	syn.tau1 = .3	syn.tau2 = .6	syn.e = 0
	pre_list.append(syn)

	bcdend4 [0] syn = new Exp2Syn(0.5)	//GC(AMPA) syn to prox dend Geiger '97
	syn.tau1 = .3	syn.tau2 = .6	syn.e = 0
	pre_list.append(syn)

	bcdend1 [1] syn = new Exp2Syn(0.5)	//MC(AMPA) syn to apical IML dend
	syn.tau1 = 0.9	syn.tau2 = 3.6	syn.e = 0 // *** Estimated based on CA3>BC min stim Dingledine '95
	pre_list.append(syn)

	bcdend2 [1] syn = new Exp2Syn(0.5)	//MC(AMPA) syn to apical IML dend
	syn.tau1 = 0.9	syn.tau2 = 3.6	syn.e = 0 // *** Estimated based on CA3>BC min stim Dingledine '95
	pre_list.append(syn)

	bcdend1 [1] syn = new Exp2Syn(0.5)	//BC(GABA) syn to apical IML dend Bartos
	syn.tau1 = 0.16		syn.tau2 = 1.8	syn.e = -70
	pre_list.append(syn)

	bcdend2 [1] syn = new Exp2Syn(0.5)	//BC(GABA) syn to apical IML dend Bartos
	syn.tau1 = 0.16		syn.tau2 = 1.8	syn.e = -70
	pre_list.append(syn)

	bcdend1 [3] syn = new Exp2Syn(0.5)	//HIPP(GABA) syn to apical distal dend 
	syn.tau1 = 0.4	syn.tau2 = 5.8	syn.e = -70 // *** Estimated as HIPP>GC
	pre_list.append(syn)

	bcdend2 [3] syn = new Exp2Syn(0.5)	//HIPP(GABA) syn to apical distal dend 
	syn.tau1 = 0.4	syn.tau2 = 5.8	syn.e = -70 // *** Estimated as HIPP>GC
	pre_list.append(syn)

// Total of 12 synapses 	0,1 PP; 	2-5 GC; 	6,7 MC; 	8,9 BC; 	10,11 HIPP 
	}

proc connect_pre() {  
	soma $o2 = new NetCon (&v(1), $o1)
	}

func is_art() { return 0 }

endtemplate BasketCell

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