CA1 pyramidal neuron: synaptically-induced bAP predicts synapse location (Sterratt et al. 2012)

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Accession:144490
This is an adaptation of Poirazi et al.'s (2003) CA1 model that is used to measure BAP-induced voltage and calcium signals in spines after simulated Schaffer collateral synapse stimulation. In the model, the peak calcium concentration is highly correlated with soma-synapse distance under a number of physiologically-realistic suprathreshold stimulation regimes and for a range of dendritic morphologies. There are also simulations demonstrating that peak calcium can be used to set up a synaptic democracy in a homeostatic manner, whereby synapses regulate their synaptic strength on the basis of the difference between peak calcium and a uniform target value.
Reference:
1 . Sterratt DC, Groen MR, Meredith RM, van Ooyen A (2012) Spine calcium transients induced by synaptically-evoked action potentials can predict synapse location and establish synaptic democracy. PLoS Comput Biol 8:e1002545 [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,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Synaptic Plasticity;
Implementer(s): Sterratt, David ; Groen, Martine R [martine.groen at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; AMPA; NMDA; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
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bpap
CA1_multi
datastore
pars
plots
poirazi-nmda-car
tests
validation-plots
README.txt
ampa_forti.mod
cacum.mod
cad.mod *
cagk.mod
cal.mod
calH.mod
car.mod
car_mag.mod
cat.mod
d3.mod *
h.mod
hha_old.mod
hha2.mod
kadist.mod
kaprox.mod
kca.mod
km.mod
nap.mod
nmda_andr.mod
somacar.mod
binaverages.m
bpap-cell.hoc
bpap-data.hoc
bpap-dendburst.hoc
bpap-graphics.hoc
bpap-gui.hoc
bpap-gui.ses
bpap-pars.hoc
bpap-record.hoc
bpap-run.hoc
bpap-scaling.hoc
bpap-sims.hoc
bpap-sims-cell1.hoc
bpap-sims-cell2.hoc
bpap-sims-scaling.hoc
bpap-somainj.hoc
bpap-spiketrain.hoc
ca1_mrg_cell1.hoc
ca1_mrg_cell2.hoc
ca1_poirazi.hoc
ChannelBlocker.hoc
CrossingFinder.hoc
epspsizes.hoc
figure-example.R
figures.R
figures-common.R
FileUtils.hoc
FormatFile.hoc
ghk.inc
GraphUtils.hoc
Integrator.hoc
Makefile
mosinit.hoc
NmdaAmpaSpineSynStim.hoc
NmdaAmpaSynStim.hoc
ObjectClass.hoc
plotscalingresults_pergroup1.m
plotscalingresults5.m
PointProcessDistributor.hoc
ReferenceAxis.hoc
removezeros.m
RPlot.hoc
scaling_plots.m
Segment.hoc
SimpleSpine.hoc
Spine.hoc
TreePlot.hoc
TreePlotArray.hoc
triexpsyn.inc
units.inc
utils.hoc
validate-bpap.hoc
VarList.hoc
VCaGraph.hoc
                            
if (name_declared("pkgversions") != 4 ) {  execute("strdef pkgversions") }
sprint(pkgversions,"%sRPlot = $Revision: 1.14 $, ",pkgversions)

load_file("FormatFile.hoc")
load_file("ObjectClass.hoc")
load_file("FileUtils.hoc")

begintemplate RPlot

public create_rfile, start_plot, add_graph, end_plot
public run
public plot
public clear
public set_mfrow
public set_width, set_height

objref xvec, yvec
objref xveclist, yveclist
objref rfile
strdef rfilename, tmpdir
objref li, lilist
strdef xlab, ylab, rxlab, rylab
strdef cmd
objref oc
strdef texlab, rlab, tmp
objref sf, fu

proc init() {
    sf = new StringFunctions()
    fu = new FileUtils()
    fu.tempdirname(tmpdir)
    
    if (numarg() == 0) { create_rfile() }
    if (numarg() == 1) { create_rfile($s1) }
    
    // Initialise variables and objects
    width=6
    height=4
    oc = new ObjectClass()
    xvec = new Vector()
    yvec = new Vector()
    li = new Vector()
}

proc create_rfile() {
    // Overide filename with argument
    fu.tempfilename(rfilename)
    if (numarg() == 1) { rfilename = $s1 }
    rfile = new FormatFile(rfilename,"R")
}

func getline() { local i 
    $o2.line_info($1, li)
    i = $o2.getline($1, xvec, yvec)
    return i
}

proc set_mfrow() {
    rfile.aopen()
    rfile.f.printf("par(mfrow=c(%g,%g))\n",$1,$2)
    rfile.close()
}

proc start_plot() {
    rfile.wopen()
    rfile.f.printf("postscript(file=\"%s\"",$s1)
    rfile.f.printf(", width=%g", width)  
    rfile.f.printf(", height=%g",height) 
    rfile.f.printf(", horizontal = FALSE, onefile = FALSE, paper = \"special\")\n")
    rfile.close()
}

// add_graph(Graph g, String filename, String xlabel, String ylabel) 
proc add_graph() { local limits_set
    limits_set = 0
    xlab = ""
    ylab = ""
    if (oc.object_is($o1,"TreePlot")) { 
        $o1.get_xlab(xlab)
        $o1.get_ylab(ylab)
    }
    if (numarg() >= 2) { xlab = $s2 }
    if (numarg() >= 3) { ylab = $s3 }
    
    xveclist = new List()
    yveclist = new List()
    lilist = new List()
    
    for ( i=-1; ( i = getline(i, $o1)) != -1 ; ) {
        // xvec and yvec contain the line with Graph internal index i.
        // and can be associated with the sequential index j.
        xveclist.append(xvec.c)
        yveclist.append(yvec.cl)
        lilist.append(li.c)
    }
    vi = $o1.view_info()
    if (vi != -1) {
        limits_set = 1
        xmin = $o1.view_info(vi,5)
        xmax = $o1.view_info(vi,6)
        ymin = $o1.view_info(vi,7)
        ymax = $o1.view_info(vi,8)
    }
    if (oc.object_is($o1,"TreePlot")) { 
        limits_set = 1
        xmin = $o1.get_limit(1)
        xmax = $o1.get_limit(2)
        ymin = $o1.get_limit(3)
        ymax = $o1.get_limit(4)
    }
    textoRtext(xlab, rxlab)
    textoRtext(ylab, rylab)
    
    rfile.aopen()
    rfile.print_VectorList("xvec",xveclist)
    rfile.print_VectorList("yvec",yveclist)
    rfile.print_VectorList("li",lilist)

    if (limits_set) {
        rfile.f.printf("plot(NA,NA,xlim=c(%g,%g),ylim=c(%g,%g),xlab=%s,ylab=%s)\n",xmin,xmax,ymin,ymax,rxlab,rylab) 
    } else {
        rfile.printf("plot(NA,NA,")
        rfile.printf("xlim=c(min(sapply(xvec,min)),max(sapply(xvec,max))),                            ylim=c(min(sapply(yvec,min)),max(sapply(yvec,max))),")
        rfile.f.printf("xlab=%s,ylab=%s)\n",rxlab,rylab)
    }
    rfile.printf("\
    for (i in 1:length(xvec)) {\
        lines(xvec[[i]],yvec[[i]],col=li[[i]][1])\
    }\n")
    if (oc.object_is($o1,"TreePlot")) {
        for ( i=-1; ( i = $o1.getmarks(i, xvec, yvec)) != -1 ; ) {
            rfile.printvec("xvec",xvec)
            rfile.printvec("yvec",yvec)
            rfile.printf("points(xvec,yvec)\n")
        }
    }
    rfile.close()
}

proc end_plot() {
    rfile.aopen()
    rfile.printf("dev.off()\n")
    rfile.close()
}

proc run() {
    fu.basename(rfilename,tmp)
    sprint(cmd,"R --vanilla CMD BATCH %s.R %s/%s.Rout", rfilename,tmpdir,tmp)
    system(cmd)
}

// plot(Graph g, String name) 
proc plot() {
    clear()
    start_plot($s2)
    if (numarg() == 2) { add_graph($o1) }
    if (numarg() == 3) { add_graph($o1, $s3) }
    if (numarg() == 4) { add_graph($o1, $s3, $s4) }
    end_plot()
    run()
}

proc clear() {
    rfile.unlink()
}

proc textoRtext() {
    texlab = $s1
    sprint(texlab,"%s ",texlab) // Hack to fix bug with tex symbol at end of string
    rlab = "expression(paste("
    while (( ind = sf.substr(texlab,"\\")) != -1) {
        // print texlab, "]"
        // print rlab, "]"
        sf.head(texlab,"\\\\",tmp) 
        if (sf.len(tmp)) {
            sprint(rlab,"%s\"%s\",",rlab,tmp)
        }
        sf.right(texlab,ind+1)               // Get rid of backslash with +1
        ind = sf.substr(texlab," ")
        if (ind==0) {
            sf.right(texlab,ind)      // Keep space straight after backslash
            //        print "space"
            continue
        }
        ind = sf.head(texlab,"[ \\\\]",tmp) 
        sprint(rlab,"%s%s,",rlab,tmp)
        if (sf.substr(texlab,"\\") == ind) { 
            sf.right(texlab,ind)         // backslash; don't remove
        } else {
            sf.right(texlab,ind+1)            // space; remove
        }
    }
    sprint(rlab,"%s\"%s\"))",rlab,texlab)
    $s2 = rlab
}

proc set_width() { width = $1 }
proc set_height() { height = $1 }
    

endtemplate RPlot

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