Zebrafish Mauthner-cell model (Watanabe et al 2017)

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Accession:232813
The NEURON model files encode the channel generator and firing simulator for simulating development and differentiation of the Mauthner cell (M-cell) excitability in zebrafish. The channel generator enables us to generate arbitrary Na+ and K+ channels by changing parameters of a Hodgkin-Huxley model under emulation of two-electrode voltage-clamp recordings in Xenopus oocyte system. The firing simulator simulates current-clamp recordings to generate firing patterns of the model M-cell, which are implemented with arbitrary-generated basic Na+ and K+ conductances and low-threshold K+ channels Kv7.4/KCNQ4 and sole Kv1.1 or Kv1.1 coexpressed with Kvbeta2.
Reference:
1 . Watanabe T, Shimazaki T, Oda Y (2017) Coordinated Expression of Two Types of Low-Threshold K+ Channels Establishes Unique Single Spiking of Mauthner Cells among Segmentally Homologous Neurons in the Zebrafish Hindbrain. eNeuro [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism: Brainstem;
Cell Type(s): Mauthner cell;
Channel(s): I Potassium; I A; I_KLT; I_KHT; I M; I Sodium;
Gap Junctions:
Receptor(s):
Gene(s): Kv1.1 KCNA1; Kv7.4 KCNQ4; Kvb2 KCNAB2;
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Spike Frequency Adaptation; Bursting; Ion Channel Kinetics;
Implementer(s): Watanabe, Takaki [wtakaki at m.u-tokyo.ac.jp];
Search NeuronDB for information about:  I A; I M; I Sodium; I Potassium; I_KHT; I_KLT;
// Graphs panels.hoc generates firing pattern, conductance and ionic dynamics of
// the model M-cell firing produced by firing simulator.hoc.
// Each firing model can be activated by step currents with 1pA increments (Figures 6,7,8) or 
// 500Hz pulse currents with 20pA increments(Figure 9). 
// Comprehensive implementation of kcnq and kcna or kcnq and kcnab2 are executed
// ranging from 0 to 2000 nS and from 0 to 1000 nS, respectively (Figure 7). 
// Almost all parameters can be changed to test how it affect to the model firing.
// Representative firing traces at 1T, 1.5T, 2T, 2.5T and 3T are shown.  
//
// Takaki Watanabe
// wtakaki@m.u-tokyo.ac.jp


proc graph1(){
yt.x[6]=40
yb.x[6]=-5
ana[3]= new Graph()
ana[3].size(iint, icur.max()*1.2, yb.x[6], yt.x[6])
ana[3].label(0.1,0.95,"#AP vs I")
}

proc graph2(){
yt.x[7]=ncur
yb.x[7]=0
ana[4]= new Graph()
ana[4].size(xscale0, xscale1, yb.x[7], icamp)
ana[4].exec_menu("10% Zoom out")
ana[4].label(0.2,0.9,"Raster plot")
}

proc graph3(){
yt.x[2]=0.01
yb.x[2]=0
plotwin= new Graph(0)
plotwin.size(xscale0,xscale1, yb.x[2], yt.x[2])
gp[2]=plotwin
{plotwin.view(xscale0, yb.x[2], xscale1, (yt.x[2]-yb.x[2]), 0, 450, 400, 200, 400, 40)}
graphList[0].append(plotwin)
plotwin.save_name("graphList[2].")
plotwin.addexpr("soma.gna_na(0.5)",1,1,0.8,0.9,2)
plotwin.addexpr("soma.gkcna_kcna(0.5)",6,1,0.8,0.9,2)
plotwin.addexpr("soma.gkht_kht(0.5)",3,1,0.8,0.9,2)
plotwin.addexpr("soma.gka_ka(0.5)",4,1,0.8,0.9,2)
plotwin.addexpr("soma.gkcnq_kcnq(0.5)",2,1,0.8,0.9,2)
}
proc graph4(){
yt.x[1]=0.4
yb.x[1]=-0.4
plotwin= new Graph(0)
plotwin.size(xscale0,xscale1, yb.x[1], yt.x[1])
gp[1]=plotwin
{plotwin.view(xscale0, yb.x[1], xscale1, (yt.x[1]-yb.x[1]), 0,250, 400, 200, 400, 40)}
graphList[0].append(plotwin)
plotwin.save_name("graphList[1].")
plotwin.addexpr("soma.ina(0.5)",1,1,0.8,0.9,2)
plotwin.addexpr("soma.ik(0.5)",2,1,0.8,0.9,2)
}

proc graph5(){
yt.x[8]=500
yb.x[8]=-50
ana[5]= new Graph()
ana[5].size(0, 10, yb.x[8], yt.x[8])
ana[5].label(0.2,0.9,"Instant frequency")
}

proc graph6(){
yt.x[9]=6
yb.x[9]=-1
ana[6]= new Graph()
ana[6].size(iint, icamp, yb.x[9], yb.x[9])
ana[6].exec_menu("10% Zoom out")
ana[6].label(0.2,0.9,"1stAP latency")
}

proc graph7(){
ana[7]= new Graph()
ana[7].size(0, 4, yb.x[6], yb.x[6])
ana[7].exec_menu("10% Zoom out")
ana[7].label(0.2,0.9,"#AP vs I @T")
}

proc graph8(){
ana[8]= new Graph()
ana[8].size(xscale0, xscale1, yb.x[7], icamp)
ana[8].exec_menu("10% Zoom out")
ana[8].label(0.2,0.9,"Raster plot @T")
}

proc graph9(){
ana[9]= new Graph()
ana[9].size(0, 4, yb.x[8], yt.x[8])
ana[9].exec_menu("10% Zoom out")
ana[9].label(0.2,0.9,"Instant frequency @T")
}

proc graph10(){
ana[10]= new Graph()
ana[10].size(0, 10, yb.x[9], yb.x[9])
ana[10].exec_menu("10% Zoom out")
ana[10].label(0.2,0.9,"1stAP latency @T")
}

num=21
num1=21

proc newtraces(){
w[num1]=new VBox()
w[num1].intercept(1)
	ana[num+4] = new Graph()
    ana[num+4].size(xscale0,xscale1, yb.x[0], yt.x[0])
	ana[num+4].label(0.1,0.9,"3T")
	ana[num+3] = new Graph()
    ana[num+3].size(xscale0,xscale1, yb.x[0], yt.x[0])
	ana[num+3].label(0.1,0.9,"2.5T")
	ana[num+2] = new Graph()
    ana[num+2].size(xscale0,xscale1, yb.x[0], yt.x[0])
	ana[num+2].label(0.1,0.9,"2T (Fig.6)")
	ana[num+1] = new Graph()
	ana[num+1].size(xscale0,xscale1, yb.x[0], yt.x[0])
	ana[num+1].label(0.1,0.9,"1.5T (Fig.6)")
	ana[num] = new Graph()
	ana[num].size(xscale0,xscale1, yb.x[0], yt.x[0])
	ana[num].label(0.1,0.9,"1T (Fig.6)")
w[num1].intercept(0)
w[num1].map("Firing traces(1-3T)",50,300,220,500)
}

num2=470
num4=470

w[3]=new HBox()
w[3].intercept(1)
w[4]= new VBox()
w[4].intercept(1)
{
xscale0=3
xscale1=120
yt.x[0]=10
yb.x[0]=-90
plotwin= new Graph(0)
plotwin.size(xscale0,xscale1, yb.x[0], yt.x[0])
gp[0]=plotwin
{plotwin.view(xscale0, yb.x[0], xscale1, (yt.x[0]-yb.x[0]), 300, 600, 400,300, 5, 5)}
graphList[0].append(plotwin)
plotwin.save_name("graphList[0].")
plotwin.addexpr("soma.v(0.5)",1,1,0.8,0.9,2)
plotwin.exec_menu("Keep Lines")
}
graph3()
graph4()

w[4].intercept(0)
w[4].map()

//Main control panel
w[0]= new VBox()
w[0].intercept(1)
{
xpanel("Control panel",0)
xlabel("M-cell firing")
xradiobutton("gKv1.1,gKv7.4(0,0)","access soma set_Mauthner0() set_original()",1)
xradiobutton("gKv1.1,gKv7.4(150,0)","access soma set_Mauthner3() set_original()",0)
xradiobutton("gKv1.1,gKv7.4(0,700)","access soma set_Mauthner4() set_original()",0)
xradiobutton("gKv1.1,gKv7.4(150,700)","access soma set_Mauthner2() set_original()",0)
xradiobutton("gKv1.1+beta2, gKv7.4(700,0)","access soma set_Mauthner5() set_original()",0)
xradiobutton("gKv1.1+beta2, gKv7.4(0,1400)","access soma set_Mauthner6() set_original()",0)
xradiobutton("gKv1.1+beta2, gKv7.4(700,1400)","access soma set_Mauthner1() set_original()",0)
xbutton("Run(Step), Fig.6,8","iclamp2() run1()")
xbutton("Run(Step), Fig.7(Kv1.1)  ","iclamp2() mode=3 run1()")
xbutton("Run(Step), Fig.7(Kv1.1+beta2)","iclamp2() mode=4 run1()")
xbutton("Run(500Hz), Fig.9 ","iclamp500() run1()")
xbutton("Stop","excute stoprun=1")
xpanel()
}

w[1]= new Deck()
w[1].intercept(1)
{
xpanel("IClamp parameters")
xlabel("IClamp parameters")
xvalue("Initial I (pA)","iint",1,"",0,0)
xvalue("Isteps (#)","ncur",1,"",0,0)
xvalue("Idelta (pA)","idelta",1,"",0,0)
xpanel()
}
w[1].intercept(0)
w[1].map()

xpanel("Graph control",0)
xlabel("Graph control")
xradiobutton("Firing graph","w[5].flip_to(0)",1)
xradiobutton("Conductance graph","w[5].flip_to(1)",0)
xradiobutton("Current graph","w[5].flip_to(2)",0)
xradiobutton("Phase Plane","w[5].flip_to(4)",0)
xpanel()

w[5]= new Deck()
w[5].intercept(1)
{
xpanel("")
xlabel("Firing graph")
xvalue("xaxis0","xscale0",1,"",0,0)
xvalue("xaxis1","xscale1",1,"",0,0)
xvalue("y0top","yt.x[0]",1,"",0,0)
xvalue("y0bottom","yb.x[0]",1,"",0,0)
xpanel()
xpanel("")
xlabel("Conductance graph")
xvalue("xaxis0","xscale0",1,"",0,0)
xvalue("xaxis1","xscale1",1,"",0,0)
xvalue("y2top","yt.x[2]",1,"",0,0)
xvalue("y2bottom","yb.x[2]",1,"",0,0)
xpanel()
xpanel("")
xlabel("Current graph")
xvalue("xaxis0","xscale0",1,"",0,0)
xvalue("xaxis1","xscale1",1,"",0,0)
xvalue("y1top","yt.x[1]",1,"",0,0)
xvalue("y1bottom","yb.x[1]",1,"",0,0)
xpanel()
xpanel("")
xlabel("Firing trance")
xvalue("xaxis0","xscale0",1,"",0,0)
xvalue("xaxis1","xscale1",1,"",0,0)
xvalue("y4top","yt.x[4]",1,"",0,0)
xvalue("y4bottom","yb.x[4]",1,"",0,0)
xpanel()
xpanel("")
xlabel("Phase Plane")
xvalue("x3left","xl.x[3]",1,"",0,0)
xvalue("x3right","xr.x[3]",1,"",0,0)
xvalue("y3top","yt.x[3]",1,"",0,0)
xvalue("y3bottom","yb.x[3]",1,"",0,0)
xpanel()
}
w[5].intercept(0)
w[5].map()

{
xl.x[3]=-100
xr.x[3]=50
yt.x[3]=0.85
yb.x[3]=-0.45
plotwin= new Graph(0)
plotwin.size(xl.x[3],xr.x[3], yb.x[3], yt.x[3])
gp[3]=plotwin
{plotwin.view(xl.x[3], yb.x[3], (xr.x[3]-xl.x[3]), (yt.x[3]-yb.x[3]), 150, 650, 150, 150, 200, 40)}
graphList[0].append(plotwin)
plotwin.save_name("graphList[3].")
plotwin.addexpr("soma.i_cap(0.5)",2,1,0.8,0.9,2)
plotwin.xexpr("soma.v(0.5)")

}
w[0].intercept(0)
w[0].map("Control panel",550,0,200,400)

w[2]= new VBox()
w[2].intercept(1)
{
xpanel("M-cell parameters",0)
xlabel("M-cell parameters")
xvalue("Total cap pF","totcap",1,"totalcap() set_original()  run1()",0,0)
xvalue("L um","soma.L",100,"capcalL() set_original()  run1()",0,0)
xvalue("diam um","soma.diam",1,"capcalD() set_original()  run1()",0,0)
xvalue("cm","soma.cm",1," run1()",0,0)
xvalue("Ra","soma.Ra",1,"soma.Ra += 0 run1()",0,0)
xvalue("celsius","celsius",1,"set_original()  run1()",0,0)
xpanel()
}
{
xpanel("Channel integration",0)
xlabel("Channel integration (nS)")
xvalue("gnabar_na","gnabar_na1",1,"set_original() run1()",0,0)
xvalue("gkhtbar_kht","gkhtbar_kht1",1,"set_original() run1()",0,0)
xvalue("gkabar_ka","gkabar_ka1",1,"set_original() run1()",0,0)
xvalue("g_leak","g_leak1",1,"set_original() run1()",0,0)
xvalue("gkcnqbar_kcnq","gkcnqbar_kcnq1",1,"set_original() run1()",0,0)
xvalue("gkcnabar_kcna","gkcnabar_kcna1",1,"set_original() run1()",0,0)
xvalue("gkcnab2bar_kcnab2","gkcnab2bar_kcnab21",1,"set_original() run1()",0,0)
xpanel()
}
{
xpanel("Current injection",0)
xlabel("Current injection")
xbutton("delta 20pA","access soma delta20pA() run1()",1)
xbutton("delta 1pA","access soma delta1pA() run1()",0)
xlabel("Firing trace control")
xvalue("Color","color5",1,"",0,0)
xbutton("Clear analysis","Clearrecord()")
xbutton("New traces","num=num+5 num1=num1+1 newtraces()")
xbutton("graph control","w[5].flip_to(3)",0)
xpanel()
}

w[2].intercept(0)
w[2].map("Parameters",1300,0,200,350)

w[3].intercept(0)
w[3].map("Firing simulator",10,10,650,650)

w[9]=new HBox()
w[9].intercept(1)

w[7]=new VBox()
w[7].intercept(1)
graph1()
graph2()
graph5()
graph6()
w[7].intercept(0)
w[7].map("",1000,450,300,500)

w[8]=new VBox()
w[8].intercept(1)
graph7()
graph8()
graph9()
graph10()
w[8].intercept(0)
w[8].map("",1200,450,300,500)

w[9].intercept(0)
w[9].map("Firing analysis(Fig.7, 9)",300,300,300,500)

newtraces()

proc reGraph(){
for i=0,2 {
	gp[i].erase_all()
	gp[i].yaxis(0)
	gp[i].size(xscale0, xscale1, yb.x[i], yt.x[i])
	}
	gp[3].erase_all()
	gp[3].yaxis(0)
	gp[3].size(xl.x[3], xr.x[3], yb.x[3], yt.x[3])
	gp[0].label(0.15,0.95,modename)
	gp[0].label(0.35,0.95,modelname)
	gp[1].color(1)
	gp[1].label("Ionic dynamics")
	gp[1].label("soma ina")
	gp[1].color(2)
	gp[1].label("soma ik")
	gp[2].label("Fig.8")
	gp[2].label("Conductance dynamics")
	ana[num+4].size(xscale0,xscale1, yb.x[0], yt.x[0]+20)
    ana[num+3].size(xscale0,xscale1, yb.x[0], yt.x[0]+20)
    ana[num+2].size(xscale0,xscale1, yb.x[0], yt.x[0]+20)
	ana[num+1].size(xscale0,xscale1, yb.x[0], yt.x[0]+20)
	ana[num].size(xscale0,xscale1, yb.x[0], yt.x[0]+20)
	color=1
	color2=2
	color3=3
	color4=1
	threcur=0.01
    spiken=0
}

proc Clearrecord(){
for i=3,10{
    ana[i].erase_all()
    ana[i].yaxis(0)
	}
	ana[3].size(iint, icur.x[i]*1.2, yb.x[6], yt.x[6])
	ana[4].size(-xscale1*0.1, xscale1,-icur.x[i]*0.2, icur.x[i]*1.2)
	ana[5].size(0, spiken, yb.x[8], yt.x[8])
	ana[6].size(-icur.x[i]*0.1, icur.x[i]*1.2, yb.x[9], yt.x[9])
	ana[7].size(1, 3, yb.x[6], yt.x[6])
	ana[8].size(-xscale1*0.1, xscale1,0, 4)
	ana[9].size(0, spiken, yb.x[8], yt.x[8])
	ana[10].size(1, 3, yb.x[9], yt.x[9])
	ana[3].label(0.2,0.9,"#AP vs I")
	ana[4].label(0.2,0.9,"Raster plot")
	ana[6].label(0.2,0.9,"1stAP latency")
	ana[5].label(0.2,0.9,"Interspike interval")
	ana[7].label(0.2,0.9,"#AP vs I @T")
	ana[8].label(0.2,0.9,"Raster plot @T")
	ana[10].label(0.2,0.9,"1stAP latency @T")
	ana[9].label(0.2,0.9,"Interspike interval @T")
}

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