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;
/
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
                            
/* This is the primary file for creating the MSP cell - this file calls all
	of the hoc files necessary to build one cell and sets the default
	parameter values.
	
	Usually this file is called by a hoc file in /input_params/.
	
	Jason Moyer 2005 - jtmoyer@seas.upenn.edu
*/
	

//****************************************************************************
//Load all the baseline parameters to start with

sprint(dirstr, "%s/baseline_values.txt", preface)
//print dirstr
xopen(dirstr)
//load_file("../input_params/baseline_values.txt")
//****************************************************************************



//****************************************************************************
// all_tau_vecs.hoc loads the tables used to define the taus for many channels

sprint(dirstr, "%s/all_tau_vecs.hoc", preface)
//print dirstr
xopen(dirstr)
//load_file("all_tau_vecs.hoc")
//****************************************************************************



//****************************************************************************
//load the templates for the synapses - AMPA, GABA, and NMDA

sprint(dirstr, "%s/synapse_templates.hoc", preface)
xopen(dirstr)
//load_file("synapse_templates.hoc")
//****************************************************************************




//****************************************************************************
// load cell template - builds the cell topology, including inserting
// channels and synapses; dlambda code is in here (under geom()) along 
// with code to output the number of compartments in cell

sprint(dirstr, "%s/msp_template.hoc", preface)
xopen(dirstr)
//load_file ("msp_template.hoc")
//****************************************************************************



create acell_home_



//****************************************************************************
// load netstims template, sets default interval, number, noise

sprint(dirstr, "%s/netstims_template.hoc", preface)
xopen(dirstr)
//load_file("netstims_template.hoc")
//****************************************************************************



//****************************************************************************
// create msp cells using cell_append(), nc_append()
// set number of segments using geom_nseg() (in fixnseg.hoc)
// create shunt for sharp electrode

sprint(dirstr, "%s/create_mspcells.hoc", preface)
xopen(dirstr)
//load_file("create_mspcells.hoc")
//****************************************************************************





//**********************************************************************
// calculate membrane area, access soma by default
A1 = 0
Ad = 0

forsec "dendrite[1]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}

forsec "dendrite[14]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}

forsec "dendrite[26]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[27]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[29]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[32]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[35]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[42]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[52]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[53]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[54]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[2]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[9]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[15]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[18]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[23]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[30]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[31]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[36]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[39]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[43]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[44]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[3]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[8]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[10]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[11]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[16]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[17]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[19]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[20]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[37]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[38]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[40]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[41]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[45]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[50]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[4]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[7]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[12]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[13]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[21]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[22]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[46]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[47]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[5]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[6]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[48]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}
forsec "dendrite[49]" {
	for i = 1, nseg {
		Ad = Ad + area( i/(nseg+1) )
	}
}

forsec "MSP_Cell[0]"  {
	for i = 1, nseg {
		A1 = A1 + area( i/(nseg+1) )
	}
}

Ap = A1 - Ad

print "Total cell membrane area = ", A1		// equals whole cell membrane area
print "Mid + Dist mem area = ", Ad
print "Soma + Prox mem area = ", Ap 

//**********************************************************************
load_file("set_synapse.hoc")
//****************************************************************************
// specify cell's active properties using constants listed in
// input_params/baseline_values.txt
//

sprint(dirstr, "%s/basic_procs.hoc", preface)
xopen(dirstr)


set_pas(G_PAS)

set_naf(G_NAF)
set_nafd(G_NAFD)
set_nap(G_NAP)
set_napd(G_NAPD)

set_kir(G_KIR)
set_kas(G_KAS)
set_kasd(G_KASD)
set_kaf(G_KAF)
set_kafd(G_KAFD)
set_krp(G_KRP)
set_bkkca(G_BKKCA)
set_skkca(G_SKKCA)

set_caL(P_CAL)
set_caL13(P_CAL13)
set_can(P_CAN)
set_caq(P_CAQ)
set_car(P_CAR)
set_cat(P_CAT)

set_cainf(CAINF)
set_taur(TAUR)
set_cadrive(CA_DRIVE)
set_pump(CA_PUMP)

//set_mu()

set_ek(EK)
forsec "MSP_Cell" {Ra = RA    cm = CM}
//Mid 
F=1.3
//    forsec "Mid_Dend" {Ra = RA cm = CM*F}
forsec "dendrite[1]" {Ra = RA cm = CM*F}
forsec "dendrite[14]" {Ra = RA cm = CM*F}
forsec "dendrite[26]" {Ra = RA cm = CM*F}
forsec "dendrite[27]" {Ra = RA cm = CM*F}
forsec "dendrite[29]" {Ra = RA cm = CM*F}
forsec "dendrite[32]" {Ra = RA cm = CM*F}
forsec "dendrite[35]" {Ra = RA cm = CM*F}
forsec "dendrite[42]" {Ra = RA cm = CM*F}
forsec "dendrite[52]" {Ra = RA cm = CM*F}
forsec "dendrite[53]" {Ra = RA cm = CM*F}
forsec "dendrite[54]" {Ra = RA cm = CM*F}
//***
forsec "dendrite[2]" {Ra = RA cm = CM*F}
forsec "dendrite[9]" {Ra = RA cm = CM*F}
forsec "dendrite[15]" {Ra = RA cm = CM*F}
forsec "dendrite[18]" {Ra = RA cm = CM*F}
forsec "dendrite[23]" {Ra = RA cm = CM*F}
forsec "dendrite[30]" {Ra = RA cm = CM*F}
forsec "dendrite[31]" {Ra = RA cm = CM*F}
forsec "dendrite[36]" {Ra = RA cm = CM*F}
forsec "dendrite[39]" {Ra = RA cm = CM*F}
forsec "dendrite[43]" {Ra = RA cm = CM*F}
forsec "dendrite[44]" {Ra = RA cm = CM*F}

forsec "spine[0]" {Ra = RA cm = CM*F}

//Dist 
F=3
forsec "dendrite[3]" {Ra = RA cm = CM*F}
forsec "dendrite[8]" {Ra = RA cm = CM*F}
forsec "dendrite[10]" {Ra = RA cm = CM*F}
forsec "dendrite[11]" {Ra = RA cm = CM*F}
forsec "dendrite[16]" {Ra = RA cm = CM*F}
forsec "dendrite[17]" {Ra = RA cm = CM*F}
forsec "dendrite[19]" {Ra = RA cm = CM*F}
forsec "dendrite[20]" {Ra = RA cm = CM*F}
forsec "dendrite[37]" {Ra = RA cm = CM*F}
forsec "dendrite[38]" {Ra = RA cm = CM*F}
forsec "dendrite[40]" {Ra = RA cm = CM*F}
forsec "dendrite[41]" {Ra = RA cm = CM*F}
forsec "dendrite[45]" {Ra = RA cm = CM*F}
forsec "dendrite[50]" {Ra = RA cm = CM*F}
//***
forsec "dendrite[4]" {Ra = RA cm = CM*F}
forsec "dendrite[7]" {Ra = RA cm = CM*F}
forsec "dendrite[12]" {Ra = RA cm = CM*F}
forsec "dendrite[13]" {Ra = RA cm = CM*F}
forsec "dendrite[21]" {Ra = RA cm = CM*F}
forsec "dendrite[22]" {Ra = RA cm = CM*F}
forsec "dendrite[46]" {Ra = RA cm = CM*F}
forsec "dendrite[47]" {Ra = RA cm = CM*F}
//**
forsec "dendrite[5]" {Ra = RA cm = CM*F}
forsec "dendrite[6]" {Ra = RA cm = CM*F}
forsec "dendrite[48]" {Ra = RA cm = CM*F}
forsec "dendrite[49]" {Ra = RA cm = CM*F}


forsec "spine[1]" {Ra = RA cm = CM*F}


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



//*************************************************************************
// create and set netstims using champawt(), chnmdawt(), chint()

sprint(dirstr, "%s/make_netstims.hoc", preface)
xopen(dirstr)

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



access MSP_Cell[0].soma





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