Mitral cell activity gating by respiration and inhibition in an olfactory bulb NN (Short et al 2016)

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Accession:183300
To explore interactions between respiration, inhibition, and olfaction, experiments using light to active channel rhodopsin in sensory neurons expressing Olfactory Marker Protein were performed in mice and modeled in silico. This archive contains NEURON models that were run on parallel computers to explore the interactions between varying strengths of respiratory activity and olfactory sensory neuron input and the roles of periglomerular, granule, and external tufted cells in shaping mitral cell responses.
Reference:
1 . Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV (2016) Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb. PLoS One 11:e0168356 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell; Olfactory bulb main tufted cell external;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Sensory processing; Sensory coding; Bursting; Oscillations; Olfaction;
Implementer(s): Morse, Tom [Tom.Morse at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell;
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ShortEtAl2016
early_theta_version
event_generator
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batch_run_first_NSG.py
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cell_properties_for_ET_from_standalone.txt
cells_volt_graphs.ses
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et.hoc
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mitral.hoc
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pre_init.py
pre_init_first_NSG.py
pre_init_no_changes_in_weights.py
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run_on_serial.hoc
runcntrl.ses
sample_gc1_v_graph.ses
sample_mitral_pg_space_plots.ses
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begintemplate Mitral

// ls - long secondary dendrites 

public soma, priden, secden, tuftden, hillock, initialseg
public dendritic, somatic, second, somden, synodor, external_syn
public dampa
public position, x, y, z


create soma, priden, secden[2], tuftden, hillock, initialseg

forall {Ra = 150}

objref dendritic, somatic, somden, synodor, external_syn
objref dampa

proc init() {

dendritic = new SectionList()
forsec "priden" dendritic.append()
forsec "secden" dendritic.append()
forsec "tuftden" dendritic.append()

somatic = new SectionList()
soma somatic.append
hillock somatic.append

somden = new SectionList()
forsec somatic somden.append()
forsec dendritic somden.append()

topol()
segments()
geometry()
memb()
	x = y = z = 0 // only change via position
}


proc topol() {local i
	connect secden[0](0), soma(.5)
	connect secden[1](0), soma(.5)
	connect priden(0), soma(1)
	connect tuftden(0), priden(1)

	connect hillock(0), soma(0)
	connect initialseg(0), hillock(1)
}

proc segments() {local i
	soma.nseg= 1
	priden.nseg = 5
	forsec "tuftden" nseg = 10
	forsec "secden" nseg = 50
	initialseg.nseg = 3
	hillock.nseg = 3
}

proc geometry() {local i
	basic_shape()
	soma { L = 25  diam = 20 }
	priden { L = 300  diam = 3 }
	//forsec "tuftden" {rallbranch=20 L=300  diam(0:1)=.4:.4 }
	forsec "tuftden" {rallbranch=10 L=200  diam(0:1)=1:1 }
	forsec "secden" { L=1000  diam=2 }
	initialseg{ L=30  diam=1.5}
	hillock { L=5  diam(0:1) = soma.diam(0) : initialseg.diam(0) }
	//define_shape()
}
	
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  priden {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  tuftden {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  secden[0] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(1, 0, 0, 1)}
  secden[1] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-1, 0, 0, 1)}
  hillock {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, -1, 0, 1)}
  initialseg {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, -1, 0, 1)}
}

proc memb() {
	forall {insert pas }
	forsec somden {
		insert nax  insert kamt insert kdrmt
		ek = -90
		ena = 50
		gbar_nax = 0.04 sh_nax=10
	 	gbar_kdrmt = 0.0001
		gbar_kamt = 0.004
		}

	forall {Ra = 150}

	totarea=0
	forall {
		for (x) {totarea=totarea+area(x)}
		cm = 1.8
		g_pas = 1/12000
		e_pas = -65
	}

	initialseg {
		insert nax  insert kamt insert kdrmt
		ek = -90
		ena = 50
	        g_pas = 1/1000
	        gbar_nax = 0.8
		sh_nax = 0
	        gbar_kamt = 0.08
	        gbar_kdrmt = 0.0001
	}       

  
	tuftden {
	synodor = new Exp2Syn(.2)
	synodor.e=0
	synodor.tau1 = 20
            	synodor.tau2 = 200

}
            soma {
                external_syn = new Exp2Syn(.5)
                external_syn.e=0
                external_syn.tau1 = 5
                external_syn.tau2 = 50  
            }

}

proc position() { local i
  soma for i = 0, n3d()-1 {
    pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
  }
  x = $1  y = $2  z = $3
}

endtemplate Mitral

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