Nav1.6 sodium channel model in globus pallidus neurons (Mercer et al. 2007)

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Accession:105385
Model files for the paper Mercer JN, Chan CS, Tkatch T, Held J, Surmeier DJ. Nav1.6 sodium channels are critical to pacemaking and fast spiking in globus pallidus neurons.,J Neurosci. 2007 Dec 5;27(49):13552-66.
Reference:
1 . Mercer JN, Chan CS, Tkatch T, Held J, Surmeier DJ (2007) Nav1.6 sodium channels are critical to pacemaking and fast spiking in globus pallidus neurons. J Neurosci 27:13552-66 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Globus pallidus neuron;
Channel(s): I Na,p; I Na,t; I K; I h; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s): Nav1.6 SCN8A;
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Action Potentials; Parkinson's;
Implementer(s): Held, Joshua [j-held at northwestern.edu];
Search NeuronDB for information about:  I Na,p; I Na,t; I K; I h; I K,Ca; I Sodium; I Calcium; I Potassium;
create soma, initial, dend[4], unmyelin, axon[5], node[4], hillock

connect dend[0](0), soma(0)
connect dend[1](0), soma(0)
connect dend[2](0), soma(0)
connect dend[3](0), soma(0)
connect hillock(0), soma(1)
connect initial(0), hillock(1)
connect unmyelin(0), initial(1)
connect axon[0](0), unmyelin(1)
connect node[0](0), axon[0](1)
connect axon[1](0), node[0](1)
connect node[1](0), axon[1](1)
connect axon[2](0), node[1](1)
connect node[2](0), axon[2](1)
connect axon[3](0), node[2](1)
connect node[3](0), axon[3](1)
connect axon[4](0), node[3](1)

v_init = -54
tstop = 7000
celsius = 23

g0_kir2 = .00006
g1_kir2 = .0006
g0_hcn12 = 0.0012
g1_hcn12 = 0.0045
g0_hcn2 = 6e-6
g1_hcn2 = 6e-5

g0_na1 = 0.08
g1_na1 = 0.008
g0_na6 = 0.02
g1_na6 = 0.002

access soma

soma {
   	L = 25
	diam = 25
	cm = 0.75
	insert hcn12_gp
		gbar_hcn12_gp = 0
		ehcn_hcn12_gp = -20
	insert hcn2_gp
		gbar_hcn2_gp = 0
		ehcn_hcn2_gp = -20
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
	insert na1_gp
		gbar_na1_gp = 0.2
	insert na6_gp
		gbar_na6_gp = 0.08
	insert kv1_gp
		gbar_kv1_gp = 0.008
	insert kv2_gp
		gbar_kv2_gp = 10
	insert kv3_gp
		gbar_kv3_gp = 0.1
	insert kv4_gp
		gbar_kv4_gp = 0.001
	insert kir2_gp
		gbar_kir2_gp = 0
	insert kcnq_gp
		gbar_kcnq_gp = 0
	insert bk_gp
		gbar_bk_gp = 0
	insert sk_gp
		gbar_sk_gp = 0.05
	insert cal_gp
		gbar_cal_gp = 0
	insert cap_gp
		gbar_cap_gp = 2e-06
	insert ca_gp
}

hillock {nseg = 3
   	L = 15
	diam = 3.2
	cm = 0.75
	insert hcn12_gp
		gbar_hcn12_gp = 0
		ehcn_hcn12_gp = -20
	insert hcn2_gp
		gbar_hcn2_gp = 0
		ehcn_hcn2_gp = -20
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
	insert na1_gp
		gbar_na1_gp = 0.1
	insert na6_gp
		gbar_na6_gp = 0.1
	insert kv1_gp
		gbar_kv1_gp = 0.01
	insert kv2_gp
		gbar_kv2_gp = 2
	insert kv3_gp
		gbar_kv3_gp = 0.03
	insert kv4_gp
		gbar_kv4_gp = 0
	insert kir2_gp
		gbar_kir2_gp = 0
	insert kcnq_gp
		gbar_kcnq_gp = 0
	insert bk_gp
		gbar_bk_gp = 0
	insert sk_gp
		gbar_sk_gp = 0
	insert cal_gp
		gbar_cal_gp = 0
	insert cap_gp
		gbar_cap_gp = 0
	insert ca_gp
}

initial {
   	L = 30
	diam = 1.4
	cm = 0.75
	insert hcn12_gp
		gbar_hcn12_gp = 0
		ehcn_hcn12_gp = -20
	insert hcn2_gp
		gbar_hcn2_gp = 0
		ehcn_hcn2_gp = -20
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -20
	insert na1_gp
		gbar_na1_gp = 0
	insert na6_gp
		gbar_na6_gp = 2
	insert kv1_gp
		gbar_kv1_gp = 0.015
	insert kv2_gp
		gbar_kv2_gp = 5
	insert kv3_gp
		gbar_kv3_gp = 0.1
	insert kv4_gp
		gbar_kv4_gp = 0
	insert kir2_gp
		gbar_kir2_gp = 0
	insert kcnq_gp
		gbar_kcnq_gp = 0.001
	insert bk_gp
		gbar_bk_gp = 0
	insert sk_gp
		gbar_sk_gp = 0.0
	insert cal_gp
		gbar_cal_gp = 0
	insert cap_gp
		gbar_cap_gp = 0
	insert ca_gp
}

forsec "dend" {
   	nseg = 9
   	L = 800
	diam = 1
	cm = 0.75
	insert hcn12_gp
		gbar_hcn12_gp(0:1) = g0_hcn12:g1_hcn12
		ehcn_hcn12_gp = -20
	insert hcn2_gp
		gbar_hcn2_gp(0:1) = g0_hcn2:g1_hcn2
		ehcn_hcn2_gp = -20
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
	insert na1_gp
		gbar_na1_gp(0:1) = g0_na1:g1_na1
	insert na6_gp
		gbar_na6_gp(0:1) = g0_na6:g1_na6
	insert kv1_gp
		gbar_kv1_gp = 0
	insert kv2_gp
		gbar_kv2_gp = 0
	insert kv3_gp
		gbar_kv3_gp = 0
	insert kv4_gp
		gbar_kv4_gp = 0.002
	insert kir2_gp
		gbar_kir2_gp(0:1) = g0_kir2:g1_kir2
	insert kcnq_gp
		gbar_kcnq_gp = 0
	insert bk_gp
		gbar_bk_gp = 0
	insert sk_gp
		gbar_sk_gp = 0.008
	insert cal_gp
		gbar_cal_gp = 3e-05
	insert cap_gp
		gbar_cap_gp = 0
	insert ca_gp
}

unmyelin {
	L = 50
	diam = 1
	cm = 0.75
	insert na1_gp
		gbar_na1_gp = 0
	insert na6_gp
		gbar_na6_gp = 0
	insert kv1_gp
		gbar_kv1_gp = 0
	insert kv2_gp
		gbar_kv2_gp = 0
	insert kv3_gp
		gbar_kv3_gp = 0
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
}

forsec "axon" {
	L = 100
	diam = 1
	cm = 0.04
	insert na1_gp
		gbar_na1_gp = 0
	insert na6_gp
		gbar_na6_gp = 0
	insert kv1_gp
		gbar_kv1_gp = 0
	insert kv2_gp
		gbar_kv2_gp = 0
	insert kv3_gp
		gbar_kv3_gp = 0
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
}

forsec "node" {
	L = 1
	diam = 1
	cm = 0.75
	insert na1_gp
		gbar_na1_gp = 0
	insert na6_gp
		gbar_na6_gp = 0.1
	insert kv1_gp
		gbar_kv1_gp = 0.06
	insert kv2_gp
		gbar_kv2_gp = 0
	insert kv3_gp
		gbar_kv3_gp = 0.6
	insert kcnq_gp
		gbar_kcnq_gp = 0
	insert leak_gp
		gbar_leak_gp = 0
		e_leak_gp = -65
}

forall {
	ek = -77
	ena = 50
	Ra = 150
}

cvode.active(1)

access soma
objref iramp
iramp = new IRamp(0.5)
iramp.del = 6000
iramp.dur = 1000
iramp.amp0 = 0
iramp.amp1 = 1

// *** Voltage Plot Panel ***

objref VoltagePlot
	VoltagePlot = new Graph(0)
	VoltagePlot.size(0,7000,-80,40)
	VoltagePlot.view(0,-80,7000,120,650,300,400,200)
	graphList[0].append(VoltagePlot)
	VoltagePlot.save_name("graphList[0].")
	VoltagePlot.addexpr("soma.v",1,1,0.8,0.9,2)



// *** Run Panel ***

		t = 0
		dt = 0.1
		realtime = 0
		na16remove = 0
		na16replace = 0

objref RunPanel
RunPanel = new HBox()
RunPanel.intercept(1)
	xpanel("")
		xbutton("Init & Run","run()")
		xbutton("Stop","stoprun=1")
		xlabel("")
		xstatebutton("Remove Na1.6",&na16remove,"remove16()")
		xlabel("Remove Na1.6 from all locations")
		xlabel("")
		xstatebutton("Replace Na1.6",&na16replace,"replace16()")
		xlabel("Replace Na1.6 with Na1.1")
	xpanel()
	xpanel("")
		xvalue("t","t", 2 )
		xvalue("Real Time","realtime", 0,"", 0, 1 )
		xlabel("")
		xvalue("gNa 1.1 (soma)","soma.gbar_na1_gp",1)
		xlabel("")
		xvalue("gNa 1.6 (soma)","soma.gbar_na6_gp",1)
		xlabel("The sodium conductances change throughout.")
		xlabel("Use the somatic values to keep track of changes.")
	xpanel()
RunPanel.intercept(0)
RunPanel.map("Run Panel",0,300,500,200)


// *** REMOVE16() ***
proc remove16() {
	if (soma.gbar_na6_gp == 0.08) {
		na16remove = 1
		forall gbar_na6_gp = 0
	} else {
		na16remove = 0
		soma.gbar_na6_gp = 0.08
		hillock.gbar_na6_gp = 0.1
		initial.gbar_na6_gp = 2
		forsec "dend" {gbar_na6_gp(0:1) = 0.02:0.002}
		forsec "node" {gbar_na6_gp = 0.1}
	}
}

// *** REPLACE16() ***
proc replace16() {
	if (soma.gbar_na1_gp == 0.2) {
		na16replace = 1
		soma.gbar_na1_gp = 0.28
		hillock.gbar_na1_gp = 0.2
		initial.gbar_na1_gp = 2
		forsec "dend" {gbar_na1_gp(0:1) = 0.1:0.01}
		forsec "node" {gbar_na1_gp = 0.1}

	} else {
		na16replace = 0
		soma.gbar_na1_gp = 0.2
		hillock.gbar_na1_gp = 0.1
		initial.gbar_na1_gp = 0
		forsec "dend" {gbar_na1_gp(0:1) = 0.08:0.008}
		forsec "node" {gbar_na1_gp = 0}
	}
}

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