Calcium response prediction in the striatal spines depending on input timing (Nakano et al. 2013)

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Accession:151458
We construct an electric compartment model of the striatal medium spiny neuron with a realistic morphology and predict the calcium responses in the synaptic spines with variable timings of the glutamatergic and dopaminergic inputs and the postsynaptic action potentials. The model was validated by reproducing the responses to current inputs and could predict the electric and calcium responses to glutamatergic inputs and back-propagating action potential in the proximal and distal synaptic spines during up and down states.
Reference:
1 . Nakano T, Yoshimoto J, Doya K (2013) A model-based prediction of the calcium responses in the striatal synaptic spines depending on the timing of cortical and dopaminergic inputs and post-synaptic spikes. Front Comput Neurosci 7:119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse;
Brain Region(s)/Organism:
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I A; I K; I K,leak; I K,Ca; I CAN; I Sodium; I Calcium; I Potassium; I A, slow; I Krp; I R; I Q; I Na, leak; I Ca,p; Ca pump;
Gap Junctions:
Receptor(s): D1; AMPA; NMDA; Glutamate; Dopaminergic Receptor; IP3;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Reinforcement Learning; STDP; Calcium dynamics; Reward-modulated STDP;
Implementer(s): Nakano, Takashi [nakano.takashi at gmail.com];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; D1; AMPA; NMDA; Glutamate; Dopaminergic Receptor; IP3; I Na,p; I Na,t; I L high threshold; I A; I K; I K,leak; I K,Ca; I CAN; I Sodium; I Calcium; I Potassium; I A, slow; I Krp; I R; I Q; I Na, leak; I Ca,p; Ca pump;
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Nakano_FICN_model
stim_files2
tau_tables
readme.html
AMPA.mod
bkkca.mod *
cadyn.mod
caL.mod
caL13.mod
caldyn.mod
can.mod
caq.mod
car.mod *
cat.mod
damsg.mod
ER.mod
GABA.mod *
kaf.mod *
kas.mod *
kir.mod
krp.mod *
MGLU.mod
naf.mod
nap.mod *
NMDA.mod
skkca.mod *
stim.mod *
_control.hoc
_IVsaveplot.hoc
_paper_condition.hoc
_plot_post02.hoc
_plot_pre_spine.hoc
_reset.hoc
_run_me.hoc
_saveIVplot.hoc
_saveplots.hoc
_timed_input_1AP_spine_post.hoc
_timed_input_Glu.hoc
all_tau_vecs.hoc *
baseline_values.txt
basic_procs.hoc
create_mspcells.hoc *
current_clamp.ses
fig4a.png
make_netstims.hoc
mosinit.hoc
msp_template.hoc
nacb_main.hoc
netstims_template.hoc *
posttiming.txt
set_synapse.hoc
set_synapse_caL.hoc
set_synapse_caL13.hoc
set_synapse_can.hoc
set_synapse_caq.hoc
set_synapse_ER.hoc
set_synapse_kir.hoc
set_synapse_naf.hoc
set_synapse_NMDA.hoc
stimxout_jns_sqwave_noinput.dat
synapse_templates.hoc
                            
//****************************************************************************
// basic_procs.hoc defines procedures for setting conductances and range
// variables of channels - these are primarily used to change variables
// from the gui

proc set_pas() {    NEW_GPAS = $1
    forall if (ismembrane("pas")) {g_pas = NEW_GPAS}
	nG_PAS = NEW_GPAS

//*******************Mid*******************
	MSP_Cell[0].dendrite[1] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[14] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[26] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[27] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[29] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[32] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[35] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[42] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[52] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[53] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[54] g_pas = nG_PAS*1.3

	MSP_Cell[0].dendrite[2] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[9] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[15] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[18] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[23] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[30] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[31] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[36] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[39] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[43] g_pas = nG_PAS*1.3
	MSP_Cell[0].dendrite[44] g_pas = nG_PAS*1.3
	
//*******************Dist*******************
	MSP_Cell[0].dendrite[3] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[8] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[10] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[11] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[16] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[17] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[19] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[20] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[37] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[38] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[40] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[41] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[45] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[50] g_pas = nG_PAS*3
	
	MSP_Cell[0].dendrite[4] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[7] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[12] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[13] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[21] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[22] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[46] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[47] g_pas = nG_PAS*3
	
	MSP_Cell[0].dendrite[5] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[6] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[48] g_pas = nG_PAS*3
	MSP_Cell[0].dendrite[49] g_pas = nG_PAS*3
	
	MSP_Cell[0].spine[0] g_pas = nG_PAS*1.3
	MSP_Cell[0].spine[1] g_pas = nG_PAS*3

}


//*****************
// Sodium conductance settings

proc set_naf() {		NEW_GBAR = $1
	nG_NAF = NEW_GBAR
	forsec "soma" {gnabar_naf = nG_NAF}

 }

proc set_nafd() {		NEW_GBAR = $1
	nG_NAFD = NEW_GBAR
//	forsec "dend.*" {gnabar_naf = nG_NAFD}
	forsec "dendrite.*" {gnabar_naf = nG_NAFD}
	forsec "spine.*" {gnabar_naf = nG_NAFD}
}

proc set_nap() {		NEW_GBAR = $1
	nG_NAP = NEW_GBAR
	forsec "soma" {gnabar_nap = nG_NAP}
	}

proc set_napd() {		NEW_GBAR = $1
	nG_NAPD = NEW_GBAR
//	forsec "dend.*" {gnabar_nap = nG_NAPD}
	forsec "dendrite.*" {gnabar_nap = nG_NAPD}
	forsec "spine.*" {gnabar_nap = nG_NAPD}
}

//*****************


	


//*****************
// Potassium conductance settings

proc set_ek() {	newEK = $1
	forsec "MSP" {ek = newEK}
	EK = newEK
}

proc set_kir() {		NEW_GBAR = $1
	nG_KIR = NEW_GBAR
	forall if (ismembrane("kir")) {gkbar_kir = nG_KIR}
}

proc set_kas() {		NEW_GBAR = $1
	nG_KAS = NEW_GBAR
	forsec "soma" {gkbar_kas = nG_KAS}
	MSP_Cell[0].dendrite[0] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[24] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[25] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[28] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[33] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[34] gkbar_kas = nG_KAS
	MSP_Cell[0].dendrite[51] gkbar_kas = nG_KAS
 }

proc set_kasd() {		NEW_GBAR = $1
	nG_KASD = NEW_GBAR
	//forsec "dend._.*" {gkbar_kas = nG_KASD}
	MSP_Cell[0].dendrite[1] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[14] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[26] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[27] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[29] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[32] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[35] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[42] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[52] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[53] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[54] gkbar_kas = nG_KASD

	MSP_Cell[0].dendrite[2] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[9] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[15] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[18] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[23] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[30] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[31] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[36] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[39] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[43] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[44] gkbar_kas = nG_KASD
	
//*******************Dist*******************
	MSP_Cell[0].dendrite[3] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[8] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[10] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[11] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[16] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[17] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[19] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[20] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[37] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[38] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[40] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[41] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[45] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[50] gkbar_kas = nG_KASD
	
	MSP_Cell[0].dendrite[4] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[7] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[12] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[13] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[21] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[22] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[46] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[47] gkbar_kas = nG_KASD
	
	MSP_Cell[0].dendrite[5] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[6] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[48] gkbar_kas = nG_KASD
	MSP_Cell[0].dendrite[49] gkbar_kas = nG_KASD
	
	MSP_Cell[0].spine[0] gkbar_kas = nG_KASD
	MSP_Cell[0].spine[1] gkbar_kas = nG_KASD

}
proc set_kaf() {		NEW_GBAR = $1
	nG_KAF = NEW_GBAR
	forsec "soma" {gkbar_kaf = nG_KAF}
	MSP_Cell[0].dendrite[0] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[24] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[25] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[28] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[33] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[34] gkbar_kaf = nG_KAF
	MSP_Cell[0].dendrite[51] gkbar_kaf = nG_KAF


}

proc set_kafd() {		NEW_GBAR = $1
	nG_KAFD = NEW_GBAR
	forsec "dend._.*" {gkbar_kaf = nG_KAFD}
	MSP_Cell[0].dendrite[1] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[14] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[26] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[27] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[29] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[32] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[35] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[42] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[52] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[53] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[54] gkbar_kaf = nG_KAFD

	MSP_Cell[0].dendrite[2] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[9] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[15] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[18] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[23] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[30] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[31] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[36] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[39] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[43] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[44] gkbar_kaf = nG_KAFD
	
//*******************Dist*******************
	MSP_Cell[0].dendrite[3] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[8] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[10] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[11] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[16] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[17] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[19] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[20] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[37] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[38] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[40] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[41] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[45] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[50] gkbar_kaf = nG_KAFD
	
	MSP_Cell[0].dendrite[4] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[7] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[12] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[13] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[21] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[22] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[46] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[47] gkbar_kaf = nG_KAFD
	
	MSP_Cell[0].dendrite[5] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[6] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[48] gkbar_kaf = nG_KAFD
	MSP_Cell[0].dendrite[49] gkbar_kaf = nG_KAFD
	
	MSP_Cell[0].spine[0] gkbar_kaf = nG_KAFD
	MSP_Cell[0].spine[1] gkbar_kaf = nG_KAFD
}

proc set_krp() {		NEW_GBAR = $1
	nG_KRP = NEW_GBAR
	forall if (ismembrane("krp")) {gkbar_krp = NEW_GBAR}
}

proc set_bkkca() {		NEW_GBAR = $1
	nG_BKKCA = NEW_GBAR
	forall if(ismembrane("bkkca")) {gkbar_bkkca = NEW_GBAR}
}

proc set_skkca() {		NEW_GBAR = $1
	nG_SKKCA = NEW_GBAR
	forall if(ismembrane("skkca")) {gkbar_skkca = NEW_GBAR}
}

//*****************





//******************
// Calcium conductance settings


proc set_caL() {		NEW_PBAR = $1
	nP_CAL = NEW_PBAR
	forall if (ismembrane("caL")) {pbar_caL = NEW_PBAR}
}

proc set_caL13() {		NEW_PBAR = $1
	nP_CAL13 = NEW_PBAR
	forall if (ismembrane("caL13")) {pcaLbar_caL13 = NEW_PBAR}
}

proc set_can() {		NEW_PBAR = $1
	nP_CAN = NEW_PBAR
	forall if (ismembrane("can")) {pbar_can = NEW_PBAR}
}

proc set_caq() {		NEW_PBAR = $1
	nP_CAQ = NEW_PBAR
	forall if (ismembrane("caq")) {pcaqbar_caq = NEW_PBAR}
}

proc set_car() {		NEW_PBAR = $1
	nP_CAR = NEW_PBAR
	forall if (ismembrane("car")) {pcarbar_car = NEW_PBAR}
}
proc set_cat() {		NEW_PBAR = $1
	nP_CAT = NEW_PBAR
	forall if (ismembrane("cat")) {pcatbar_cat = NEW_PBAR}
}

//******************





//******************
// Calcium dynamics procs

proc set_cainf() {	NEW_CAINF = $1
	nCA_INF = NEW_CAINF
	forall if (ismembrane("cadyn")) {cainf_cadyn = NEW_CAINF}
	forall if (ismembrane("caldyn")) {cainf_caldyn = NEW_CAINF}
}

proc set_taur() {	NEW_TAUR = $1
	nCA_TAUR = NEW_TAUR
	forall if (ismembrane("cadyn")) {taur_cadyn = NEW_TAUR}
	forall if (ismembrane("caldyn")) {taur_caldyn = NEW_TAUR}
}
proc set_cadrive() { 	NEW_DRIVE = $1
	nCA_DRIVE = NEW_DRIVE
	forall if (ismembrane("cadyn")) {drive_cadyn = NEW_DRIVE}
	forall if (ismembrane("caldyn")) {drive_caldyn = NEW_DRIVE}
}
proc set_pump() {	NEW_PUMP = $1
	nCA_PUMP = NEW_PUMP
	forall if (ismembrane("cadyn")) {pump_cadyn = NEW_PUMP}
	forall if (ismembrane("caldyn")) {pump_caldyn = NEW_PUMP}
}
//******************


proc set_mu(){//	NEW_mu = $1
	//mu=1
	forall if (issection("caL")) {
		for (x,0) { // skip the nodes at 0 and 1
			//setpointer mu_caL(x), mu
			setpointer mu_caL(x), DAsyn[0].msg
		}
	}
	
	forall if (issection("kir")) {
		for (x,0) { // skip the nodes at 0 and 1
			//setpointer mu_kir(x), mu
			setpointer mu_kir(x), DAsyn[0].msg
		}
	}
}
 
 

 
//******************
// synaptic gbar procs
proc gampa() {	NEW = $1		// AMPA conductance
	nG_AMPA = NEW
	for j = 0, NGLU-1 {AMPA[j].gbar = NEW}
	for j = NGLU-2, NGLU-1 {AMPA[j].ca_ratio = 0.0001}
}

proc gnmda() {	NEW = $1		// NMDA conductance
	nG_NMDA = NEW
	for j = 0, NGLU-1 {NMDA[j].gbar = NEW}
	for j = NGLU-2, NGLU-1 {NMDA[j].ca_ratio = 0.002}
}

proc nmda_mg() {	NEW = $1		// NMDA conductance
//	MG_NMDA = NEW
	for j = 0, NGLU-1 {NMDA[j].mg = NEW}
}

//proc gmglu() {	NEW = $1		// mGluR conductance
//	nG_MGLU = NEW
//	for j = 0, NGLU-1 {MGLU[j].gbar = NEW}
//}

proc ggaba() {	NEW = $1		// GABA conductance
	nG_GABA = NEW
	for j = 0, NGABA-1 {GABA[j].gbar = nG_GABA}
}
//******************




//******************
// netstim variables
proc tstart() {		NEW = $1	// time of netstims to start spiking
	nT_START = NEW
	for i = 0, NSYN-1 {NS_NetStim[i].pp.start = NEW}
}

proc setnetn() {	NEW = $1	// number of times a netstim will spike
	nNET_N = NEW
	for i = 0, NSYN-1 { NS_NetStim[i].pp.number = nNET_N }
}

proc setnoise() { NEW = $1		// netstim noise - 1 = random, 0 = not
	nNOISE = NEW
	for i = 0, NSYN-1 { NS_NetStim[i].pp.noise = nNOISE }
}
//******************



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