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,"%sTreePlot = $Revision: 1.14 $, ",pkgversions)

load_file("RPlot.hoc")

begintemplate TreePlot

public plot, lines, marks, errorbars
public view, size, family, erase_all
public getline, line_info, view_info
public getmarks
public graph

public rprintfile, rp
public set_xlab, get_xlab
public set_ylab, get_ylab
public view_equal_plot, auto_limits_on, set_limits, get_limit

objref graph, xvec, yvec, diamvec, parentsvec, errorvec
objref tmpxvec, tmpyvec
objref xmarklist, ymarklist
strdef xlab, ylab
objref rp
objref this

double manual_limits[4]
double auto_limits[4]
double auto_flag[4]
double limits[4]

proc init() { local i 
    // Allow not to map, similar to Graph object
    if (numarg()== 1) {
        graph = new Graph($1)
    } else {
        graph = new Graph()
    }
    tmpxvec = new Vector(2)
    tmpyvec = new Vector(2)
    xmarklist = new List()
    ymarklist = new List()
    colour = 1
    lines(1)                              // Show lines
    marks(0)                              // Don't show marks
    errorbars(1)                          // Show errorbars
    family_flag = 0                       // Whether to keep lines
    for i=0,3 { auto_flag[i] = 1 }
    xlab = ""
    ylab = ""
    rp = new RPlot()
}

proc plot() { local i, s
    xvec = $o1
    yvec = $o2
    parentsvec = $o3
    if (numarg() >= 4) { errorvec = $o4 }
    
    // Clear graph if required
    if (!family_flag) { 
        erase_all()
        colour = 1
    }
    
    // So that crosshair_action works, do invisible line
    yvec.line(graph,xvec,0,1)
    if (lines_flag) {
        for i=0, xvec.size()-1 { 
            tmpxvec.x(0) = xvec.x(i)
            tmpxvec.x(1) = xvec.x(parentsvec.x(i))
            tmpyvec.x(0) = yvec.x(i)
            tmpyvec.x(1) = yvec.x(parentsvec.x(i))
            tmpyvec.line(graph,tmpxvec,colour,1)
        }
    }
    if (marks_flag) { 
        yvec.mark(graph,xvec,"o",6,colour)
        xmarklist.append(xvec)
        ymarklist.append(yvec)
    }
    if ((numarg() >= 4) && (errorbars_flag == 1)) {
        for i=0, errorvec.size()-1 {
            tmpxvec.x(0) = xvec.x(i)
            tmpxvec.x(1) = xvec.x(i)
            tmpyvec.x(0) = yvec.x(i)-errorvec.x(i)
            tmpyvec.x(1) = yvec.x(i)+errorvec.x(i)
            tmpyvec.line(graph,tmpxvec,colour,1)
        }
    }
    colour += 1
    if (colour == 10) colour=1
}

proc erase_all() {
    graph.erase_all() 
    s = xmarklist.remove_all()
    s = ymarklist.remove_all()
}    

// turn lines on or off
proc lines() { lines_flag = $1 }

// turn marks on or off
proc marks() { marks_flag = $1 }

// turn errorbars on or off
proc errorbars() { errorbars_flag = $1 } 

// mleft, mbottom, mwidth, mheight, wleft, wtop, wwidth, wheight
proc view() { graph.view($1,$2,$3,$4,$5,$6,$7,$8) }

// Clone of Graph.size()
proc size() { graph.size($1,$2,$3,$4) }

// Part of functionality of Graph.family()
proc family() { family_flag = $1 }

// Clone of Graph.getline()
func getline() { return graph.getline($1,$o2,$o3) }

// Analogue of getline() for marks
func getmarks() { local i
    i = $1
    i += 1
    if (i <= (xmarklist.count()-1)) {
        $o2 = xmarklist.object(i).cl
        $o3 = ymarklist.object(i).cl
    } else {
        i = -1
    }
    return i 
}

// Clone of Graph.view_info()
func view_info() {
    if (numarg() == 0 ) { return graph.view_info() }
    if (numarg() == 2 ) { return graph.view_info($1,$2) }
    return -1
}

// Clone of Graph.line_info()
func line_info() {
    return graph.line_info($1,$o2)
}

// Set manual limits which will be respected by view_equal_plot() in
// directions for which auto_limits = 0
proc set_limits() { local i
    for i=1,4 { manual_limits[i-1] = $i }
}

// turn on automatic setting of limit when argument corresponding to
// argument in size() is 1
proc auto_limits_on() { local i 
    for i=1,4 { auto_flag[i-1] = $i }
}

// Fit graph to plot (apart from manually-set limits)
proc view_equal_plot() { local i
    graph.size(&auto_limits)
    for i=0,3 {
        if (auto_flag[i]) {
            limits[i] = auto_limits[i]
        } else {
            limits[i] = manual_limits[i]
        }
    }
    size(limits[0], limits[1], limits[2], limits[3])
}

func get_limit() { 
    return limits[$1-1] 
}

proc set_xlab() { xlab = $s1 } 
proc get_xlab() { $s1 = xlab }
proc set_ylab() { ylab = $s1 } 
proc get_ylab() { $s1 = ylab }

// rprintfile(String epsfilename, Double SaveFile)
proc rprintfile() { local i, j
    if (numarg() == 1) { rp.create_rfile() }
    if (numarg() == 2) {
        if ($2 != 0) { rp.create_rfile($s1) }
    }
    rp.start_plot($s1)
    rp.add_graph(this)
    rp.end_plot()
    rp.run()
}

endtemplate TreePlot

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