Shaping NMDA spikes by timed synaptic inhibition on L5PC (Doron et al. 2017)

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Accession:231427
This work (published in "Timed synaptic inhibition shapes NMDA spikes, influencing local dendritic processing and global I/O properties of cortical neurons", Doron et al, Cell Reports, 2017), examines the effect of timed inhibition over dendritic NMDA spikes on L5PC (Based on Hay et al., 2011) and CA1 cell (Based on Grunditz et al. 2008 and Golding et al. 2001).
Reference:
1 . Doron M, Chindemi G, Muller E, Markram H, Segev I (2017) Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I/O Properties of Cortical Neurons. Cell Rep 21:1550-1561 [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: Neocortex;
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions:
Receptor(s): NMDA; GabaA; AMPA;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NEURON;
Model Concept(s): Active Dendrites; Detailed Neuronal Models;
Implementer(s): Doron, Michael [michael.doron at mail.huji.ac.il];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow; Gaba; Glutamate;
/
reproduction
readme.txt
ampa.mod
Ca_HVA.mod
Ca_LVAst.mod *
cad.mod *
cadiffus.mod
CaDynamics_E2.mod *
canmda.mod *
car.mod *
gabaa.mod *
gabab.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
nmda.mod *
ProbAMPA.mod
ProbAMPANMDA2_ratio.mod
ProbUDFsyn2_lark.mod
SK_E2.mod *
SKv3_1.mod *
SynExp5NMDA.mod *
cell1.asc *
cellmorphology.hoc *
create_data_for_figure_01.py
create_data_for_figure_02.py
create_data_for_figure_03.py *
create_data_for_figure_03_control.py
create_data_for_figure_03_Dt_10.py *
create_data_for_figure_03_Dt_40.py *
data_same_excitation.pickle
iniparameter.hoc
L5PCbiophys3.hoc
L5PCbiophys3_noActive.hoc
mosinit.hoc
plot_figure_01.py
plot_figure_02.py
plot_figure_03.py
plot_figure_04.py
plot_figure_05.py
plot_figure_06.py
spikes_num.pickle
spine.hoc
TTC.hoc
                            
/********************************************************************
Taken from Grunditz A, Holbro N, Tian L, Zuo Y and Oertner TG
Spine neck plasticity controls postsynaptic calcium signals through
electrical compartmentalization
J Neuroscience (2008) 28: 13457-13466
*************************************************/

/********************************************************************
section list of all apical dendrites          
*************************************************/
objref all_apicals
all_apicals = new SectionList()
dendA5_0 all_apicals.subtree()


/********************************************************************
section list of all basal dendrites            
*************************************************/
objref all_basals
all_basals = new SectionList()
dendA1_0 all_basals.subtree()
dendA2_0 all_basals.subtree()
dendA3_0 all_basals.subtree()
dendA4_0 all_basals.subtree()


/********************************************************************
section list of primary apical branch          
*************************************************/
objref primary_apical_list
primary_apical_list = new SectionList()
dendA5_0 primary_apical_list.append
dendA5_01 primary_apical_list.append
dendA5_011 primary_apical_list.append
dendA5_0111 primary_apical_list.append
dendA5_01111 primary_apical_list.append
dendA5_011111 primary_apical_list.append
dendA5_0111111 primary_apical_list.append
dendA5_01111111 primary_apical_list.append
dendA5_011111111 primary_apical_list.append
dendA5_0111111111 primary_apical_list.append
dendA5_01111111111 primary_apical_list.append
dendA5_011111111111 primary_apical_list.append
dendA5_0111111111111 primary_apical_list.append
dendA5_01111111111111 primary_apical_list.append
dendA5_011111111111111 primary_apical_list.append
dendA5_0111111111111111 primary_apical_list.append
dendA5_01111111111111111 primary_apical_list.append
dendA5_011111111111111111 primary_apical_list.append
dendA5_0111111111111111111 primary_apical_list.append

/* reset nseg in primary apical so none smaller than 5 microns */

forsec primary_apical_list { ns=int(L/5+0.5)
        if (ns==0) {
             ns=1
        }
        if ((ns-int(ns/2)*2)==0) {
             ns=ns+1
        }
        nseg = ns
}



/********************************************************************
initialize basic parameters                    
*************************************************/
celsius = 30        /* temperature */
v_init=-65
global_ra=150.00 	/* internal resistivity in ohm-cm */
Cm=0.75             /* specific membrane capacitance in uF/cm^2 */
Rm=40000            /* specific membrane resistivity in ohm-cm^2 */ 
Vleak=-65           /* leak reversal -65mV */
Vrest=-65           /* resting potential -64.6 mV*/
isegfactor=100
isegfrac=0.8
spinelimit=100      /* distance beyond which to modify for spines */
spinefactor=2.0     /* factor by which to change passive properties */


/********************************************************************
procedure to insert and initialize channels    
*************************************************/
proc initchannels(){

/* passive properties */

print "Inserting passive membrane properties"
forall {insert pas  g_pas=1/(Rm)  Ra=global_ra  e_pas=Vleak 
}

/* soma active properties */

somaA {insert pas	e_pas=Vleak  g_pas=1/Rm   Ra=global_ra  cm=Cm
}

/* basal dendrites active properties */

forsec all_basals {insert pas	e_pas=Vleak  g_pas=1/Rm   Ra=global_ra  cm=Cm
}

dendA5_00{
    insert cadiffus
}

access somaA
area(0.5)
distance()

/* procedure to insert channels and set parameters in apical dendrites */

forsec all_apicals {

    /* do passive properties; modify for spines if far enough out */    

    insert pas	e_pas=Vleak  Ra=global_ra 
    for (x) { xdist=distance(x)
              if (xdist<=spinelimit) {
                 g_pas(x)=1/Rm
                 cm(x)=Cm
              } else {
                 g_pas(x)=spinefactor/Rm
                 cm(x)=spinefactor*Cm
              }
    }
    }
}

print "Passive properties and channels are initialized"




/********************************************************************
section list of the spine - written in python code now           

objref all_spines
all_spines = new SectionList()
spine_head all_spines.append
spine_neck all_spines.append

spine_head {
    insert pas  e_pas=Vleak  g_pas=spinefactor/Rm  Ra=global_ra  cm=spinefactor*Cm 
    insert car
    insert cadiffus
    insert canmda
}
spine_neck{
    insert pas  e_pas=Vleak  g_pas=spinefactor/Rm  Ra=global_ra  cm=spinefactor*Cm 
    insert cadiffus
}
*************************************************/

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