Complex CA1-neuron to study AP initiation (Wimmer et al. 2010)

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Accession:123927
Complex model of a pyramidal CA1-neuron, adapted from Royeck, M., et al. Role of axonal NaV1.6 sodium channels in action potential initiation of CA1 pyramidal neurons. Journal of neurophysiology 100, 2361-2380 (2008). It contains a biophysically realistic morphology comprising 265 compartments (829 segments) and 15 different distributed Ca2+- and/or voltage-dependent conductances.
Reference:
1 . Wimmer VC, Reid CA, Mitchell S, Richards KL, Scaf BB, Leaw BT, Hill EL, Royeck M, Horstmann MT, Cromer BA, Davies PJ, Xu R, Lerche H, Berkovic SF, Beck H, Petrou S (2010) Axon initial segment dysfunction in a mouse model of genetic epilepsy with febrile seizures plus. J Clin Invest 120:2661-71 [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 CA1 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I N; I T low threshold; I p,q; I A; I K; I K,leak; I M; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s):
Gene(s): Nav SCN1B;
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Detailed Neuronal Models; Epilepsy;
Implementer(s): Horstmann, Marie-Therese [mhorstma at uni-bonn.de];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; I Na,p; I Na,t; I L high threshold; I N; I T low threshold; I p,q; I A; I K; I K,leak; I M; I h; I K,Ca; I Calcium;
load_file("stdlib.hoc")
load_file("stdrun.hoc")
load_file("nrngui.hoc") 

//load morphology
load_file("morphology.hoc")

//Some simulation parameters
stdrun=1
celsius=30
v_init=-75 
cai0_ca_ion=5e-06 
cao0_ca_ion=2
ca2i0_ca2_ion=5e-06
ca2o0_ca2_ion=2

//integration time step
dt = 0.025 //0.01 was the original simulation time step 
tstop = 520

//inserting current clamp at soma
access soma
objectvar stim
stim = new IClamp(0.5)
stim.del = 500 //this model needs quite a long time to achieve an equilibrium state
stim.dur = 20
stim.amp = 0.6

//for writing result files
objref somav, ahv, isav
somav = new Vector(52000)
ahv = new Vector(52000)
isav = new Vector(52000)
somav.record(&soma.v(0.5), dt)
ahv.record(&AH.v(0.5), dt)
isav.record(&isa.v(0.5), dt)

objref all
all = new File()
strdef datei

//defining some functions
proc run_sim_graph_coarse() {
    dt = 0.025
    init()
    run()
}

proc run_sim_graph() {
    dt = 0.01
    print "running simulation please wait"
    init()
    run()
    print "writing data file of soma, axon hillock, and initial segment voltages"
    write_file()
    print "done"
}

proc write_file() {
    sprint(datei, "outputfilename") 
    all.wopen(datei)

    for i=0, ahv.size()-1 {
        all.printf("%g %g %g \r\n", somav.x(i), ahv.x(i), isav.x(i))
    }

    all.close
}


//building gui controls for easy access to changed model parameters

objref vbox
vbox = new VBox()
vbox.intercept(1)
xpanel("")
xlabel("shift at AIS varied from 0 to -15 in the publication")
xvalue("shift at AIS", "isa.sh_naxMig")
xlabel("Na density at AIS varied from 0.05 to 0.75 in the publication")
xvalue("Na density at AIS", "isa.gbar_naxMig")
xpanel()
vbox.intercept(0)
vbox.map("adjust model parameters", 100, 150, -1, -1)

objref vbox3
vbox3 = new VBox()
vbox3.intercept(1)
xpanel("Wimmer et al 2009")
xlabel("Re-create figure 8A")
xlabel("The first button runs at a coarse resolution of dt = 0.025 ms")
xlabel("The second button runs at pulication resolution of dt = 0.01 ms")
xlabel("")
xbutton("Demo Simulation/graph", "run_sim_graph_coarse()")
xbutton("Run Simulation/graph then write file", "run_sim_graph()")
xlabel("simulation time")
xvalue("t")
xpanel()
vbox3.intercept(0)
vbox3.map("run the simulation", 100,350,-1,-1)

objref vbox2
vbox2 = new VBox()
vbox2.intercept(1)

newPlot(505,520,-80,40)
graphItem.save_name("graphList[0].")
graphList[0].append(graphItem)
graphItem.addexpr("AH.v(0.5)")

vbox2.intercept(0)
vbox2.map("mebrane voltage at axon hillock", 600,150,500,350)









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