Granule Cells of the Olfactory Bulb (Simoes_De_Souza et al. 2014)

 Download zip file 
Help downloading and running models
Electrical responses of three classes of granule cells of the olfactory bulb to synaptic activation in different dendritic locations. The constructed models were based on morphological detailed compartmental reconstructions of three granule cell classes of the olfactory bulb with active dendrites described by Bhalla and Bower (J. Neurophysiol. 69: 1948-1965, 1993) and dendritic spine distributions described by Woolf et al. (J. Neurosci. 11: 1837-1854, 1991). The computational studies with the model neurons showed that different quantities of spines have to be activated in each dendritic region to induce an action potential, which always was originated in the active terminal dendrites, independently of the location of the stimuli and the morphology of the dendritic tree.
1 . Bhalla US, Bower JM (1993) Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb. J Neurophysiol 69:1948-65 [PubMed]
2 . Woolf TB, Shepherd GM, Greer CA (1991) Local information processing in dendritic trees: subsets of spines in granule cells of the mammalian olfactory bulb. J Neurosci 11:1837-54 [PubMed]
3 . Simões-de-Souza FM, Antunes G, Roque AC (2014) Electrical responses of three classes of granule cells of the olfactory bulb to synaptic inputs in different dendritic locations. Front Comput Neurosci 8:128 [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): Olfactory bulb main interneuron granule MC GABA cell; Olfactory bulb main interneuron granule TC GABA cell;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Simulation Environment: GENESIS;
Model Concept(s): Dendritic Action Potentials; Active Dendrites; Synaptic Integration; Olfaction;
Implementer(s): Simoes-de-Souza, Fabio [fabio.souza at];
Search NeuronDB for information about:  Olfactory bulb main interneuron granule MC GABA cell; Olfactory bulb main interneuron granule TC GABA cell; AMPA; NMDA;
// genesis 2.3 

include defaults

int hflag = 1    // use hsolve if hflag = 1
int chanmode = 1

float tmax = 0.1               // simulation time in sec
float dt = 1e-7              // simulation time step in sec
setclock  0  {dt}               // set the simulation clock
float injcurr = 0

setclock 1 1e-4 //clock for plots 

// Create a library of prototype elements to be used by the cell reader

/* file for standard compartments */
include compartments 
//* file for Hodgkin-Huxley Squid Na and K channels */
include hhchan 

/* file for Upi's mitral cell channels */
include mitchan 
include newbulbchan

/* file for Upi's mitral cell synaptic channels */
include mitsynC2 // for now use channelC2 version
// file for Fabio's prototype 
include fabioproto

**  2	Invoking functions to make prototypes in the /library element

//create neutral /library

disable /library

	pushe /library

	/* Make the standard types of compartments  */

	make_cylind_compartment		/* makes "compartment" */
	make_sphere_compartment		/* makes "compartment_sphere" */
	make_cylind_symcompartment	/* makes "symcompartment" */
	make_sphere_symcompartment	/* makes "symcompartment_sphere" */

	/* These are some standard channels used in .p files */
	make_Na_squid_hh		/* makes "Na_squid_hh" */
	make_K_squid_hh			/* makes "K_squid_hh" */
	make_Na_mit_hh			/* makes "Na_mit_hh" */
	make_K_mit_hh			/* makes "K_mit_hh" */

make_Na_rat_smsnn	// Na current
make_K_mit_usb  // K-current     

make_GABA_A //fabioproto
make_AMPA_NMDA // fabioproto
make_Ca_conc /fabioproto

	/* These are some synaptic channels for the mitral cell */
	make_glu_mit_upi		/* makes "glu_mit_upi" */
	make_GABA_mit_upi		/* makes "GABA_mit_upi" */


enable /library

//      Function Definitions

function step_tmax
    step {tmax} -time

//    Graphics Functions

function make_control
    create xform /control [10,50,300,200]
    create xlabel /control/label -hgeom 50 -bg cyan -label "CONTROL PANEL"
    create xbutton /control/RESET -wgeom 25%       -script reset
    create xbutton /control/RUN  -xgeom 0:RESET -ygeom 0:label -wgeom 19% \
         -script step_tmax
    create xbutton /control/STOP  -xgeom 0:RUN -ygeom 0:label -wgeom 19% \
         -script stop
    create xbutton /control/QUIT -xgeom 0:STOP -ygeom 0:label -wgeom 19% \
        -script quit
    create xbutton /control/STIM -xgeom 0:QUIT -ygeom 0:label -wgeom 19% \
        -script stim
    create xdialog /control/Injection -label "Injection (amperes)" \
		-value {injcurr}  -script "set_inject <widget>"
    create xdialog /control/stepsize -title "dt (sec)" -value {dt} \
                -script "change_stepsize <widget>"
    create xdialog /control/tempo -label "Tmax (sec)" \
                -value {tmax} -script "set_time <widget>"
    create xtoggle /control/overlay  \
           -script "overlaytoggle <widget>"
    setfield /control/overlay offlabel "Overlay OFF" onlabel "Overlay ON" state 0
    xshow /control

function make_Vmgraph
    float vmin = -0.100
    float vmax = 0.05
    create xform /data [265,50,350,350]
    create xlabel /data/label -hgeom 10% -label "Granule cell "
    create xgraph /data/voltage  -hgeom 90%  -title "Membrane Potential"
    setfield ^ XUnits sec YUnits Volts
    setfield ^ xmax {tmax} ymin {vmin} ymax {vmax}
    xshow /data
    useclock /data/## 1 

function make_Gkgraph
    float gmin = 0
    float gmax = 1e-9
    create xform /data2 [265,50,350,350]
    create xlabel /data2/label -hgeom 10% -label "Granule cell"
    create xgraph /data2/conductance  -hgeom 90%  -title "Conductances"
    setfield ^ XUnits sec YUnits Siemens
    setfield ^ xmax {tmax} ymin {gmin} ymax {gmax}
    xshow /data2
    useclock /data2/## 1 

function make_xcell
    create xform /cellform [620,50,400,400]
    create xdraw /cellform/draw [0,0,100%,100%]
    setfield /cellform/draw xmin -3e-3 xmax 3e-3 ymin -3e-3 ymax 3e-3 zmin -3e-2 zmax 3e-2 transform p
    xshow /cellform
    echo creating xcell
    create xcell /cellform/draw/cell
    setfield /cellform/draw/cell colmin -0.1 colmax 0.1 \
        path /cell/##[TYPE=compartment] field Vm \
        script "echo <w> <v>"
    useclock /cellform/## 1 

function set_time(dialog)
    str dialog
    tmax={getfield {dialog} value}

function set_inject(dialog)
    str dialog
    setfield /cell/soma inject {getfield {dialog} value}

function change_stepsize(dialog)
   str dialog
   dt =  {getfield {dialog} value}
   setclock 0 {dt}
   echo "Changing step size to "{dt}

function stim
step 0.010 -time
echo "Firing synapse"
setfield presyn z {1/{getclock 0}}
step 1
setfield presyn z 0
step 1
step 0.9 -time
echo "End of simulation"

// Use of the wildcard sets overlay field for all graphs
function overlaytoggle(widget)
    str widget
    setfield /##[TYPE=xgraph] overlay {getfield {widget} state}

//         Main Script
// Build the cell from a parameter file using the cell reader

readcell granII_fabio.p /cell -hsolve 

setfield /cell path "/cell/##[][TYPE=compartment]"
setfield /cell chanmode {chanmode}
call /cell SETUP
setmethod 11
echo "Using hsolve"

setfield /cell/soma inject {injcurr}

//setting up ca_fraction and Enmda
function set_Cafraction
//fractional Ca2+ (Schneggenburger et al., 1996)
float Caout=2 //mM extracelular calcium
float M=155  //mM extracelular monovalent ion concentration
float PCaPM=3.6  //permeability ration of Ca2+ over monovalent ions
float T=298.15 //273.15+25 Celcius Temperature
float R=8.314 //J.K-1.mol-1 gas constant
float F=96485 //C.mol-1 Farady constant
float V
float f

//GHK approach for Enmda
float Enmda
float a
Enmda= {{R*T}/F}*{log {a}}
setfield /cell/periph11[20]/head[20]/AMPA_NMDA Ek Enmda
setfield /cell/periph122[11]/head[11]/AMPA_NMDA Ek Enmda
setfield /cell/periph21[5]/head[5]/AMPA_NMDA Ek Enmda

V={getfield /cell/periph11[20]/head[20] Vm}
f={Caout}/{Caout+{1/PCaPM}*{M/4}*{1-{exp {2*V*F/{R*T}}}}}
setfield /cell/periph11[20]/head[20]/AMPA_NMDA/Ca_fraction x {f}

V={getfield /cell/periph122[11]/head[11] Vm}
f={Caout}/{Caout+{1/PCaPM}*{M/4}*{1-{exp {2*V*F/{R*T}}}}}
setfield /cell/periph122[11]/head[11]/AMPA_NMDA/Ca_fraction x {f}

V={getfield /cell/periph21[5]/head[5] Vm}
f={Caout}/{Caout+{1/PCaPM}*{M/4}*{1-{exp {2*V*F/{R*T}}}}}
setfield /cell/periph21[5]/head[5]/AMPA_NMDA/Ca_fraction x {f}

create script_out /set_Cafraction_nmda
setfield /set_Cafraction_nmda command set_Cafraction

// make the control panel

// make the graph to display soma Vm and pass messages to the graph

addmsg /cell/soma /data/voltage PLOT Vm *soma *black
addmsg /cell/trunk[8] /data/voltage PLOT Vm *trunk *red 


/* comment out the line below to disable the cell display (faster)  */
make_xcell // create and display the xcell

//Granule cell stimulation
ce /

/* create presynaptic element for NMDA and AMPA channels */

create neutral presyn
setfield presyn z 0

//O que esta sendo estimulado
/* a trick: we use coordinate field to set activation */

//Stimulation patterns

//Dedritos distais

//Spines on the tip of the terminal dendrites
addmsg /presyn /cell/periph11[20]/##[][TYPE=synchan] ACTIVATION z
addmsg /presyn /cell/periph122[11]/##[][TYPE=synchan] ACTIVATION z
addmsg /presyn /cell/periph21[5]/##[][TYPE=synchan] ACTIVATION z

//Setting maximum conductances
setfield /cell/##[][TYPE=compartment]/head[]/AMPA_NMDA gmax 1e-9
setfield /cell/##[][TYPE=compartment]/head[]/AMPA_NMDA/NMDA gmax 0.593e-9

//Ploting variables
addmsg /cell/periph11[20]/head[]/AMPA_NMDA/NMDA /data2/conductance PLOT Gk *GNMDA *green
addmsg /cell/periph11[20]/head[]/AMPA_NMDA /data2/conductance PLOT Gk *GAMPA *red

//Magnesium concentration
setfield /cell/##[][TYPE=Mg_block] CMg 1.2



Loading data, please wait...