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
                            
// _run_me.hoc runs a current clamp experiment
// "play_netstims" activates synaptic input - the current clamp will be turned
//    - ampa, gaba, and nmda weight can be changed in the panel

//****************************************************************************
// create cells, load appropriate session file
strdef preface, dirstr
preface = "."
 
xopen("./nacb_main.hoc")
print "main hoc loaded"

xopen("./current_clamp.ses")

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




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

NSYN = 471//310//168//252
maxcol = 21
//maxcol = 101//21
strdef input_file
objref stimx, stimxout

stimx = new Matrix(NSYN, maxcol)
sprint(input_file,"./stim_files2/stimxout_s0_preNO_DANO.txt")		// input file with 
													// synaptic input times

proc play_stimx() {							// turns on synaptic inputs
	stimxout = new File()
	stimxout.ropen(input_file)				// read in input times
	stimx.scanf(stimxout,NSYN,maxcol-1)
	stimxout.close()


	for cntrw = 0, NSYN-1 {					// assign spike times to synapses
		cntcl = 0
		while (stimx.x[cntrw][cntcl] > 0) {
			ConnectFAKE_[cntrw].event(stimx.x[cntrw][cntcl])
			cntcl = cntcl + 1
		}
	}
}




proc init() {
	finitialize(v_init)

	// play synaptic input
	if (playstim == 1) {
		setnetn(0)
		play_stimx()
		recordstim = 0
//		IClamp[0].amp = 1
		tstop = 2000
	} else { setnetn(1e7) }
	
	frecord_init()

	if (cvode.active()) {
		cvode.re_init()
	} else {
		fcurrent()
	}
}

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



// intialize some variables
cvode.active(1)
dt = 0.025
IClamp[0].amp = 0//0.8//0.2481		// 0.271
tstop = 1000	
playstim = 0


objectvar stim1
stim1 = new IClamp(0.5)
stim1.del = 100000
stim1.dur = 1000
stim1.amp =0.2


objectvar stim2
stim2 = new IClamp(0.5)
stim2.del = 10000//200
stim2.dur = 0.1
stim2.amp =300


objectvar stim2a
stim2a = new IClamp(0.5)
stim2a.del = 10000//210
stim2a.dur = 0.1
stim2a.amp =300


objectvar stim2b
stim2b = new IClamp(0.5)
stim2b.del = 10000//220
stim2b.dur = 0.1
stim2b.amp =300


objectvar stim3
stim3 = new IClamp(0.5)
stim3.del = 10000//178
stim3.dur = 30
stim3.amp =0.48


objectvar stim3u
stim3u = new IClamp(0.5)
stim3u.del = 10000//182
stim3u.dur = 30
stim3u.amp =0.12


objectvar stim4
stim4 = new IClamp(0.5)
stim4.del = 10000//199
stim4.dur = 2
stim4.amp =2.5

objectvar stim4a
stim4a = new IClamp(0.5)
stim4a.del = 10000//209
stim4a.dur = 2
stim4a.amp =2.5

objectvar stim4b
stim4b = new IClamp(0.5)
stim4b.del = 10000//219
stim4b.dur = 2
stim4b.amp =2.5

objectvar stim4u
stim4u = new IClamp(0.5)
stim4u.del = 10000//199
stim4u.dur = 2
stim4u.amp =1.3

objectvar stim4ua
stim4ua = new IClamp(0.5)
stim4ua.del = 10000//209
stim4ua.dur = 2
stim4ua.amp =1.3

objectvar stim4ub
stim4ub = new IClamp(0.5)
stim4ub.del = 10000//219
stim4ub.dur = 2
stim4ub.amp =1.3


objectvar stim5
stim5 = new IClamp(0.5)
stim5.del = 10000//197
stim5.dur = 5
stim5.amp =1.5

objectvar stim5a
stim5a = new IClamp(0.5)
stim5a.del = 10000//207
stim5a.dur = 5
stim5a.amp =1.5

objectvar stim5b
stim5b = new IClamp(0.5)
stim5b.del = 10000//217
stim5b.dur = 5
stim5b.amp =1.5

objectvar stim5u
stim5u = new IClamp(0.5)
stim5u.del = 10000//197
stim5u.dur = 5
stim5u.amp =0.5


objectvar stim5ua
stim5ua = new IClamp(0.5)
stim5ua.del = 10000//207
stim5ua.dur = 5
stim5ua.amp =0.5


objectvar stim5ub
stim5ub = new IClamp(0.5)
stim5ub.del = 10000//217
stim5ub.dur = 5
stim5ub.amp =0.5


objectvar stim6
stim6 = new IClamp(0.5)
stim6.del = 100000
stim6.dur = 1000
stim6.amp =0.2


//****************************************************************************
// Define the user interface
xpanel("cell settings")
xvalue("prox naf bar","nG_NAF", 1,"set_naf(nG_NAF)", 1, 1 )
xvalue("distal naf bar","nG_NAFD", 1,"set_nafd(nG_NAFD)", 1, 1 )
xvalue("prox nap bar","nG_NAP", 1,"set_nap(nG_NAP)", 1, 1 )
xvalue("distal nap bar","nG_NAPD", 1,"set_napd(nG_NAPD)", 1, 1 )
xlabel("--------------------")
xvalue("gkbar_kir","nG_KIR", 1,"set_kir(nG_KIR)", 1, 1 )
xvalue("prox kas bar","nG_KAS", 1,"set_kas(nG_KAS)", 1, 1 )
xvalue("distal kas bar","nG_KASD", 1,"set_kasd(nG_KASD)", 1, 1 )
xvalue("prox kaf bar","nG_KAF", 1,"set_kaf(nG_KAF)", 1, 1 )
xvalue("distal kaf bar","nG_KAFD", 1,"set_kafd(nG_KAFD)", 1, 1 )
xvalue("gkbar_krp","nG_KRP", 1,"set_krp(nG_KRP)", 1, 1 )
xvalue("gkbar_bkkca","nG_BKKCA", 1,"set_bkkca(nG_BKKCA)", 1, 1 )
xvalue("gkbar_skkca","nG_SKKCA",1,"set_skkca(nG_SKKCA)",1,1)
xlabel("--------------------")
xvalue("g_pas","nG_PAS", 1,"set_pas(nG_PAS)", 1, 1 )
xvalue("P_CAL","nP_CAL", 1,"set_caL(nP_CAL)", 1, 1 )
xvalue("P_CAL13","nP_CAL13", 1,"set_caL13(nP_CAL13)", 1, 1 )
xvalue("P_CAN","nP_CAN", 1,"set_can(nP_CAN)", 1, 1 )
xvalue("P_CAQ","nP_CAQ", 1,"set_caq(nP_CAQ)", 1, 1 )
xvalue("P_CAR","nP_CAR", 1,"set_car(nP_CAR)", 1, 1 )
xvalue("P_CAT","nP_CAT", 1,"set_cat(nP_CAT)", 1, 1 )
xlabel("--------------------")
xvalue("ampa weight","nAMPA_WT", 1,"champawt(nAMPA_WT)", 1, 1 )
xvalue("nmda weight","nNMDA_WT", 1,"chnmdawt(nNMDA_WT)", 1, 1 )
xvalue("mglu weight","nMGLU_WT", 1,"chmgluwt(nMGLU_WT)", 1, 1 )
xvalue("gaba weight","nGABA_WT", 1,"chgabawt(nGABA_WT)", 1, 1 )
xvalue("dr weight","nDR_WT", 1,"chdrwt(nDR_WT)", 1, 1 )
xlabel("--------------------")
xstatebutton("play netstims",&playstim, "init()")
xlabel("--------------------")
xpanel(1262,22)




///////////////
objref gplot1
gplot1=new Graph(0)
addplot(gplot1,0)
//gplot1.size(0,1000,0,0.02)
gplot1.view(0, 0, 1000, 0.01, 300, 450, 300.48, 200.32)
gplot1.addvar("MSP_Cell[0].dendrite[1].cali(0.5)", 2, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MGLU[7].ip3i", 5, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[0].cali(0.5)", 1, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[0].mu_caL(0.5)", 4, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[0].ip3im_ER(0.5)", 3, 1, 0.383706, 0.947923, 2)
//gplot1.exec_menu("Keep Lines")

objref gplot2
gplot2=new Graph(0)
addplot(gplot2,0)
gplot2.view(0, -1e-3, 1000, 1e-3, 600, 450, 300.48, 200.32)
gplot2.addvar("MSP_Cell[0].dendrite[1].ical_ER", 5, 1, 0.383706, 0.947923, 2)
gplot2.addvar("MSP_Cell[0].dendrite[1].ical_caL", 4, 1, 0.383706, 0.947923, 2)
gplot2.addvar("MSP_Cell[0].dendrite[1].ical_cat", 2, 1, 0.383706, 0.947923, 2)
gplot2.addvar("NMDA[7].ical", 7, 1, 0.383706, 0.947923, 2)
gplot2.addvar("AMPA[7].ical", 8, 1, 0.383706, 0.947923, 2)

objref gplot3
gplot3=new Graph(0)
addplot(gplot3,0)
gplot3.view(0, 0, 1000, 1, 900, 450, 300.48, 200.32)
gplot3.addvar("MSP_Cell[0].dendrite[1].h_cat", 1, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[1].h_caL", 2, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[1].m_cat", 4, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[1].m_caL", 5, 1, 0.383706, 0.947923, 2)
//gplot3.addvar("DAsyn[7].msg", 1, 1, 0.383706, 0.947923, 2)

objref gplot4
gplot4=new Graph(0)
addplot(gplot4,0)
gplot4.view(0, 0, 1000, 0.002, 1200, 450, 300, 200)
gplot4.addvar("MSP_Cell[0].dendrite[0].cali(0.5)", 1, 1, 0.383706, 0.947923, 2)
gplot4.addvar("MSP_Cell[0].dendrite[1].cali(0.5)", 2, 1, 0.383706, 0.947923, 2)
gplot4.addvar("MSP_Cell[0].dendrite[2].cali(0.5)", 3, 1, 0.383706, 0.947923, 2)
gplot4.addvar("MSP_Cell[0].dendrite[3].cali(0.5)", 4, 1, 0.383706, 0.947923, 2)
gplot4.addvar("MSP_Cell[0].dendrite[4].cali(0.5)", 5, 1, 0.383706, 0.947923, 2)
gplot4.addvar("MSP_Cell[0].dendrite[5].cali(0.5)", 6, 1, 0.383706, 0.947923, 2)


///////////////
objref gplot1
gplot1=new Graph(0)
addplot(gplot1,0)
//gplot1.size(0,1000,0,0.02)
gplot1.view(0, 0, 1000, 0.01, 300, 700, 300.48, 200.32)
gplot1.addvar("MSP_Cell[0].dendrite[4].cali(0.5)", 2, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MGLU[107].ip3i", 5, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[1].cali(0.5)", 1, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[1].mu_caL(0.5)", 4, 1, 0.383706, 0.947923, 2)
gplot1.addvar("MSP_Cell[0].spine[1].ip3im_ER(0.5)", 3, 1, 0.383706, 0.947923, 2)
//gplot1.exec_menu("Keep Lines")

objref gplot2
gplot2=new Graph(0)
addplot(gplot2,0)
gplot2.view(0, -1e-3, 1000, 1e-3, 600, 700, 300.48, 200.32)
gplot2.addvar("MSP_Cell[0].dendrite[4].ical_ER", 5, 1, 0.383706, 0.947923, 2)
gplot2.addvar("MSP_Cell[0].dendrite[4].ical_caL", 4, 1, 0.383706, 0.947923, 2)
gplot2.addvar("MSP_Cell[0].dendrite[4].ical_cat", 2, 1, 0.383706, 0.947923, 2)
gplot2.addvar("NMDA[107].ical", 7, 1, 0.383706, 0.947923, 2)
gplot2.addvar("AMPA[107].ical", 8, 1, 0.383706, 0.947923, 2)

objref gplot3
gplot3=new Graph(0)
addplot(gplot3,0)
gplot3.view(0, 0, 1000, 1, 900, 700, 300.48, 200.32)
gplot3.addvar("MSP_Cell[0].dendrite[4].h_cat", 1, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[4].h_caL", 2, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[4].m_cat", 4, 1, 0.383706, 0.947923, 2)
gplot3.addvar("MSP_Cell[0].dendrite[4].m_caL", 5, 1, 0.383706, 0.947923, 2)
//gplot3.addvar("DAsyn[107].msg", 1, 1, 0.383706, 0.947923, 2)

xopen("./_saveplots.hoc")
playstim = 1
/////////////////////////////

////change condition
xopen("./_control.hoc")

////conditioning
//xopen("./_conditioning.hoc")

////reset default condition
//xopen("./_reset.hoc")


////plot IV curve
//xopen("./_IV.hoc")

//STDP
//xopen("./_timed_input_Glu.hoc")


////1AP
////pre timing = 0
//xopen("./_timed_input_1AP_pre.hoc")
////post timing = 0
//xopen("./_timed_input_1AP_post.hoc")
//xopen("./_timed_input_1AP_post_PostNO.hoc")
//xopen("./_timed_input_1AP_spine_post.hoc")
////xopen("./_timed_input_1AP_spine_post_PostNO.hoc")


////3APs
////pre timing = 0
//xopen("./_timed_input_3APs_pre.hoc")
////post timing = 0
//xopen("./_timed_input_3APs_post.hoc")
//xopen("./_timed_input_3APs_post_PostNO.hoc")
//xopen("./_timed_input_3APs_spine_post.hoc")
//xopen("./_timed_input_3APs_spine_post_PostNO.hoc")

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