Biochemically detailed model of LTP and LTD in a cortical spine (Maki-Marttunen et al 2020)

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Accession:260971
"Signalling pathways leading to post-synaptic plasticity have been examined in many types of experimental studies, but a unified picture on how multiple biochemical pathways collectively shape neocortical plasticity is missing. We built a biochemically detailed model of post-synaptic plasticity describing CaMKII, PKA, and PKC pathways and their contribution to synaptic potentiation or depression. We developed a statistical AMPA-receptor-tetramer model, which permits the estimation of the AMPA-receptor-mediated maximal synaptic conductance based on numbers of GluR1s and GluR2s predicted by the biochemical signalling model. We show that our model reproduces neuromodulator-gated spike-timing-dependent plasticity as observed in the visual cortex and can be fit to data from many cortical areas, uncovering the biochemical contributions of the pathways pinpointed by the underlying experimental studies. Our model explains the dependence of different forms of plasticity on the availability of different proteins and can be used for the study of mental disorder-associated impairments of cortical plasticity."
Reference:
1 . Mäki-Marttunen T, Iannella N, Edwards AG, Einevoll GT, Blackwell KT (2020) A unified computational model for cortical post-synaptic plasticity. Elife [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex spiking regular (RS) neuron;
Channel(s): I Calcium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate; Norephinephrine; Acetylcholine;
Simulation Environment: NEURON; NeuroRD;
Model Concept(s): Long-term Synaptic Plasticity;
Implementer(s): Maki-Marttunen, Tuomo [tuomomm at uio.no];
Search NeuronDB for information about:  I Calcium; Acetylcholine; Norephinephrine; Glutamate;
/
synaptic
L23PC
L23_PC_cADpyr229_3
hoc_recordings
mechanisms
morphology
python_recordings
synapses
README *
biophysics.hoc *
cellinfo.json *
CHANGELOG *
constants.hoc *
creategui.hoc *
createsimulation.hoc *
current_amps.dat *
init.hoc *
LICENSE *
morphology.hoc *
mosinit.hoc *
ringplot.hoc *
run.py *
run_hoc.sh *
run_py.sh *
run_RmpRiTau.py *
run_RmpRiTau_py.sh *
template.hoc
VERSION *
                            
/*
Copyright (c) 2015 EPFL-BBP, All rights reserved.

THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJECT
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/legalcode or send a letter to Creative Commons, 171
Second Street, Suite 300, San Francisco, California, 94105, USA.
*/


/*                                                                               
 * @file creategui.hoc                                                           
 * @brief Draw the GUI                                
 * @author Werner Van Geit @ BBP                                                 
 * @date 2015                                                                    
*/        

load_file("ringplot.hoc")

pwmcnt = PWManager[0].count  // the initial GUIs should not be dismissed

objref mainhbox
objref plotvbox
objref shapehbox
objref synapsevbox
objref synapsevbox_size
objref gV, sP, rP, synapse_plot                                                               


xres = 1200
yres = 800
xstart = 50
ystart = 0

proc make_mainwindow() {
    mainhbox = new HBox(3)
    mainhbox.intercept(1)

    mainhbox.adjuster(200)
    make_runcontrol()

    mainhbox.adjuster(700)
    make_plottingpanel()

    mainhbox.adjuster(250)
    make_synapsepanel($o1)

    mainhbox.adjuster(250)
    mainhbox.intercept(0)   
    mainhbox.full_request(1) 
    mainhbox.map("Main", xstart, ystart, xres, yres)
}

proc make_plottingpanel() {
    plotvbox = new VBox()
    plotvbox.intercept(1)

    plotvbox.adjuster(300)
    make_shapepanel()
    
    plotvbox.adjuster(500)
    rP = new RingPlot()                                                         

    plotvbox.intercept(0)    
    mainhbox.full_request(1) 
    plotvbox.map("Plotting", 0, 0, -1, -1)
}


proc make_runcontrol() {                                                   
    xpanel("RunControl", 0)                                                     
    xbutton("Init & Run","restart()")                                           
    xbutton("Stop","stoprun=1")                                                 
    xvalue("Total time", "tstop")                                                 
    xvalue("Sim Time","t", 0,"", 0, 1 )                                 
    xvalue("Real Time","realtime", 0,"", 0, 1 )                                 
    xbutton("Quit","quit()")
    
    xlabel("Step current")
    xradiobutton("No step","stepcurrent=\"none\"", 1)                                                                                
    xradiobutton("Step current 1","stepcurrent=\"stepcurrent1\"")            
    xradiobutton("Step current 2","stepcurrent=\"stepcurrent2\"")               
    xradiobutton("Step current 3","stepcurrent=\"stepcurrent3\"")               
    xpanel(1498, 0)
} 
                                                                                
proc make_shapepanel() {                                                                                                                                                                                                     
    shapehbox = new HBox()
    shapehbox.intercept(1)

    shapehbox.adjuster(350)
    sP = new PlotShape(0)                                                       
    sP.variable("soma", "v(0.5)")                                               
    sP.view(-594.956, -98.0373, 1260.25, 1188.42, 573, 0, 505.92, 592)         
    sP.exec_menu("Shape Plot")                                                  

    shapehbox.adjuster(350)                                    
    synapse_plot = new Shape(0)
    synapse_plot.view(-594.956, -98.0373, 1260.25, 1188.42, 49, 0, 500.16, 592)
 
    shapehbox.intercept(0)    
    shapehbox.full_request(1) 
    plotvbox.full_request(1) 
    mainhbox.full_request(1) 
    shapehbox.map("Shapes", 1104, 0, -1, -1)                                                          
}                  

proc make_synapsepanel() { local n_of_pre_mtypes, pre_mtype_id localobj active_pre_mtypes, pre_mtype_freqs
    strdef pre_mtype_name

    synapsevbox = new HBox()
    synapsevbox.intercept(1)
    xpanel("Synapses")
    xlabel("Presyn m-types")
    for i=0, $o1.synapses.pre_mtypes.size-1 {
         pre_mtype_id = $o1.synapses.pre_mtypes.x[i]
         pre_mtype_freqs = $o1.synapses.pre_mtype_freqs
         pre_mtype_name = $o1.synapses.id_mtype_map.o(pre_mtype_id).s
         active_pre_mtypes = $o1.synapses.active_pre_mtypes
         xstatebutton(pre_mtype_name, &active_pre_mtypes.x[pre_mtype_id], "cell.synapses.update_synapses(synapse_plot)")
    }
    xpanel(100, 0)

    xpanel("Freq")
    xlabel("Frequency (Hz)")
    for i=0, $o1.synapses.pre_mtypes.size-1 {
         pre_mtype_id = $o1.synapses.pre_mtypes.x[i]
         pre_mtype_freqs = $o1.synapses.pre_mtype_freqs
         pre_mtype_name = $o1.synapses.id_mtype_map.o(pre_mtype_id).s
         active_pre_mtypes = $o1.synapses.active_pre_mtypes
         xpvalue("", &pre_mtype_freqs.x[pre_mtype_id], 0, "cell.synapses.update_synapses(synapse_plot)", 1)
    }
    xpanel(100, 0)

    synapsevbox.intercept(0)

    show_synapsepanel()
}

proc show_synapsepanel() {
    if (synapses_enabled == 1) {
        synapsevbox.map("Presynaptic activity", 0, 0, -1, -1)
    } else {
        synapsevbox.unmap()
    }
}

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