Neuronal morphology goes digital ... (Parekh & Ascoli 2013)

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Accession:148644
An illustration of a NEURON model and why reconstructing morphologies is useful in this regard (i.e. investigating spatial/temporal aspect of how different currents and voltage propagate in dendrites).
Reference:
1 . Parekh R, Ascoli GA (2013) Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77:1017-38 [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): Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron;
Channel(s): I Na,t; I A; I K; I h;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Tutorial/Teaching;
Implementer(s): Ferrante, Michele [mferr133 at bu.edu];
Search NeuronDB for information about:  I Na,t; I A; I K; I h;
/
ParekhAscoli2013
readme.html
distr.mod *
h.mod *
kadist.mod *
kaprox.mod *
kdrca1.mod *
na3n.mod *
naxn.mod *
netstims.mod *
85-LM-HiDe.hoc
Fig4C.hoc
fixnseg.hoc *
geo5038804.hoc *
mosinit.hoc
screenshot.png
                            
load_file("nrngui.hoc")
cvode_active(1)

numdendrite=120
numsoma=2

xopen("85-LM-HiDe.hoc")             // geometry file
xopen("fixnseg.hoc")           

Rm = 28000
RmDend = Rm
RmSoma = Rm
RmAx = Rm

Cm    = 1
CmSoma= Cm
CmAx  = Cm
CmDend = Cm

RaAll= 150
RaSoma=150  
RaAx = 50

Vrest = -65
dt = 0.1
gna =  .025
AXONM = 5
gkdr = 0.01
celsius = 35.0  
KMULT =  0.03
KMULTP = 0.03
ghd=2*0.00005

objref g, b,c, stim, distrx, distry, cdistry, p,k,o

forsec "soma" {insert pas e_pas=Vrest g_pas = 1/RmSoma Ra=RaSoma cm=CmSoma}
forsec "dendrite"{insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}

access soma

freq=50
geom_nseg()
tot=0
forall {tot=tot+nseg}
distance()

tstop=20

dend=95


b = new VBox()
b.intercept(1)
g = new Graph()
g.size(0,tstop,-70,35)
g.addvar("soma[1].v(0.5)",3,1,2*tstop,0,2)
g.addvar("dendrite[95].v(0.5)",6,1,2*tstop,0,2)
g.addvar("dendrite[84].v(.75)",4,1,2*tstop,0,2)

g.label(0.75,0.55," time (ms)",2,1,0,1,1)
g.label(0.01,0.99," voltage (mV)",2,1,0,1,1)
g.xaxis(1)

k = new Graph()
k.size(0,tstop,-0.012,0.028)
k.label(0.75,0.265," time (ms)",2,1,0,1,1)
k.label(0.01,0.99," current (nA)",2,1,0,1,1)
k.xaxis(1)

b.intercept(0)
b.map()

o = new VBox()
o.intercept(1)

p = new PlotShape()
p.exec_menu("Shape Plot")
p.size(-50,100,-500,400)
p.variable("v")
p.show(0)
p.label(0.01,0.01," 85-LM-HiDe - SLM CA3 Interneuron - Barrionuevo's lab")

c = new Graph()
c.size(0,740,0,100)
c.xaxis(1)
c.exec_menu("10% Zoom out")
c.color(1)
c.label(0.01,0.9," bAP peak (mV)")
c.label(0.6,0.1," distance from soma (microns)",2,1,0,1,1)

xpanel("")
xbutton("runm ", "runm()")
xpanel()

o.intercept(0)
o.map()

rel=0.5
soma {
stim= new IClamp(rel)
stim.amp=2.5
stim.dur=0.5
stim.del=1
}


forsec "soma" {   
		insert hd ghdbar_hd=ghd	vhalfl_hd=-73
                insert na3 gbar_na3=gna
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP
		insert ds
}


forsec "dendrite" {
	insert ds
		insert hd ghdbar_hd=ghd vhalfl_hd=-73
                insert na3 gbar_na3=gna
                insert kdr gkdrbar_kdr=gkdr
		insert kap gkabar_kap=0
		insert kad gkabar_kad=0

		for (x) if (x>0 && x<1) { xdist = distance(x)
                	ghdbar_hd(x) = ghd*(1+3*xdist/100)
                		if (xdist > 100){
					vhalfl_hd=-81
                        		gkabar_kad(x) = KMULT*(1+xdist/100)
                			} else {
					vhalfl_hd=-73
                        		gkabar_kap(x) = KMULTP*(1+xdist/100)
               				}
		}
}

proc init() {
	t=0
        forall {
        v=Vrest
        if (ismembrane("nax") || ismembrane("na3")) {ena=55}
        if (ismembrane("kdr") || ismembrane("kap") || ismembrane("kad")) {ek=-90}
        if (ismembrane("hd") ) {ehd_hd=-30}
	}
	finitialize(Vrest)
        fcurrent()

        forall {
	for (x) {
	if (ismembrane("na3")||ismembrane("nax")){e_pas(x)=v(x)+(ina(x)+ik(x))/g_pas(x)}
	if (ismembrane("hd")) {e_pas(x)=e_pas(x)+i_hd(x)/g_pas(x)}
		}
	}
	
	
	dendrite[95]{
	k.addvar("ina(1)",1,1,2*tstop,0,2)
	k.addvar("ik(1)",5,1,2*tstop,0,2)
	k.addvar("i_hd(1)",7,1,2*tstop,0,2)
	}
	
	cvode.re_init()
	cvode.event(tstop)
	access soma
	g.begin()
	k.begin()
}


proc advance() {
	fadvance()
	g.plot(t)
	g.flush()
	k.plot(t)
	k.flush()
	p.flush()
	doNotify()
}

proc runp() {
g.label(0.2,0.8," Soma",2,1,0,1,3)
g.label(0.22,0.6," Proximal dendrite",2,1,0,4,4)
g.label(0.30,0.4," Distal dendrite",2,1,0,4,6)
k.label(0.28,0.8," IK",2,1,0,1,5)
k.label(0.25,0.3," INA",2,1,0,4,1)
k.label(0.4,0.32," Ih",2,1,0,4,7)
stdinit()
continuerun(tstop)

distrx=new Vector()
	distry=new Vector()
	forall {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	distry.mark(c,distrx,"O",3,$1,2)
	c.flush()
	doNotify()


	distrx=new Vector()
	distry=new Vector()
	dendrite[95] {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	dendrite[84] {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	
	dendrite[85] {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	dendrite[93] {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	//c.label(0.55,0.55," All compartments",2,1,0,1,1)
	//c.label(0.2,0.4," Branch #6",2,1,0,1,2)
	distry.mark(c,distrx,"O",5,2,2)
	c.flush()
	doNotify()
}

proc runm() {
runp(1)
}

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