Bursting respiratory net: clustered architecture gives large phase diff`s (Fietkiewicz et al 2011)

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Accession:139418
Using a previous model of respiratory rhythm generation, we modified the network architecture such that cells can be segregated into two clusters. Cells within a given cluster burst with smaller phase differences than do cells from different clusters. This may explain the large phase differences seen experimentally, as reported in the paper.
Reference:
1 . Fietkiewicz C, Loparo KA, Wilson CG (2011) Drive latencies in hypoglossal motoneurons indicate developmental change in the brainstem respiratory network. J Neural Eng 8:065011 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Bursting;
Implementer(s):
// Load channel files
load_file("pmchannels.ses")
load_file("hgchannels.ses")
load_file("calciumchannels.ses")

//********************* RandomStream Template***************************
random_stream_offset_ = 1000

begintemplate RandomStream
public r, repick, start, stream
external random_stream_offset_
objref r
proc init() {
	stream = $1
	r = new Random()
	start()
}
func start() {
	return r.MCellRan4(stream*random_stream_offset_ + 1)
}
func repick() {
	return r.repick()
}
endtemplate RandomStream

//******************************Pacemaker Template***************************
begintemplate PM
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target

public soma
public all

objref synlist

proc init() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
  synlist = new List()
  synapses()
  x = y = z = 0 // only change via position
}

create soma

proc topol() { local i
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()
    soma all.append()

}
proc geom() {
  forsec all {  /*area = 3000 */ L = diam = 30.9019  }
  soma {  /*area = 3000 */ L = diam = 30.9019  }
}
external lambda_f
proc geom_nseg() {
  forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}
proc biophys() {
  soma {
    Ra = 100
    insert na
      gmax_na = 0.0013333
    insert nap
      gmax_nap = 0.00002907
    insert k
      gmax_k = 0.000533333
    insert leak
      gmax_leak = 0.00003091
      e_leak = -65
    insert K_Leak
      gmax_K_Leak = 0.000021428
    insert potassium
      kbath_potassium = 6
      fhspace_potassium = 300
      txfer_potassium = 50
      bmax_potassium = 50
      k1N_potassium = 1.1
      k1_potassium = 0.0008
      d_potassium = 1.5e-07
    insert pump
      kbath_pump = 6
      ipumpmax_pump = 0.0005
  }
}
proc biophys_inhomo(){}
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 = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  soma nc = new NetCon(&v(1), $o1)
  nc.threshold = 0
  if (numarg() == 2) { $o2 = nc } // for backward compatibility
  return nc
}
objref syn_
proc synapses() {
  /* Itonic0 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
  /* Isyn1 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
}
func is_art() { return 0 }

endtemplate PM

//******************************Hypoglossal Template***************************
begintemplate HG
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target

public soma
public all

objref synlist

proc init() {
  topol() 
  subsets()
  geom()
  biophys()
  geom_nseg()
  synlist = new List()
  synapses()
  x = y = z = 0 // only change via position
}

create soma

proc topol() { local i
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()
    soma all.append()

}
proc geom() {
  forsec all {  /*area = 4000 */ L = diam = 35.6825  }
}
external lambda_f
proc geom_nseg() {
  forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}
proc biophys() {
  soma {
    Ra = 100
    insert H
      gmax_H = 0.000125
      e_H = -38.8
    insert A
      gmax_A = 0.025
    insert P
      gmax_P = 0.00125
    insert N
      gmax_N = 0.00125
    insert leak_hg
      gmax_leak_hg = 0.001476
      e_leak_hg = -50
    insert T
      gmax_T = 0.0025
    insert K_hg
      gmax_K_hg = 0.0325
    insert NaP_hg
      gmax_NaP_hg = 0.000039747
    insert Na_hg
      gmax_Na_hg = 0.0175
    insert sk
      gbar_sk = 0.0075
      ztau_sk = 1
      i_sk = 0
    insert cax
      K1_cax = 0.02
      K2_cax = 0.04
  }
}
proc biophys_inhomo(){}
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 = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  soma nc = new NetCon(&v(1), $o1)
  nc.threshold = 0
  if (numarg() == 2) { $o2 = nc } // for backward compatibility
  return nc
}
objref syn_
proc synapses() {
  /* Isyn0 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
}
func is_art() { return 0 }

endtemplate HG

//********************* Premotoneuron/intermediate-cell Template***************************
begintemplate IC
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target

public soma
public all

objref synlist

proc init() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
  synlist = new List()
  synapses()
  x = y = z = 0 // only change via position
}

create soma

proc topol() { local i
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()
    soma all.append()

}
proc geom() {
  forsec all {  /*area = 3000 */ L = diam = 37.847  }
  soma {  /*area = 3000 */ L = diam = 37.847  }
}
external lambda_f
proc geom_nseg() {
  forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}
proc biophys() {
  soma {
    Ra = 100
    insert na
      gmax_na = 0.0013333
    insert nap
      gmax_nap = 0.00002467
    insert k
      gmax_k = 0.000533333
    insert leak
      gmax_leak = 0.00006667
      e_leak = -65
    insert K_Leak
      gmax_K_Leak = 0.000021428
    insert potassium
      kbath_potassium = 6
      fhspace_potassium = 300
      txfer_potassium = 50
      bmax_potassium = 50
      k1N_potassium = 1.1
      k1_potassium = 0.0008
      d_potassium = 1.5e-07
    insert pump
      kbath_pump = 6
      ipumpmax_pump = 0.0005
//    insert HVA
//      gmax_HVA = 1.1743-05
//    insert CaT
//      gmax_CAT = 1.2228e-05
//    insert CaL
//      gmax_CaL = 2.347e-05  
//    insert cadyn
//      depth_cadyn = 0.1
//      tayr_cadyn = 2
//      cainf_cadyn = 5e-05
//      kt_cadyn = 0.0001
//      kd_cadyn = 0.0001

  }
}
proc biophys_inhomo(){}
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 = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  soma nc = new NetCon(&v(1), $o1)
  nc.threshold = 0
  if (numarg() == 2) { $o2 = nc } // for backward compatibility
  return nc
}
objref syn_
proc synapses() {
  /* Itonic0 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
  /* Isyn1 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
}
func is_art() { return 0 }

endtemplate IC

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