CA1 pyramidal neuron: synaptically-induced bAP predicts synapse location (Sterratt et al. 2012)

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Accession:144490
This is an adaptation of Poirazi et al.'s (2003) CA1 model that is used to measure BAP-induced voltage and calcium signals in spines after simulated Schaffer collateral synapse stimulation. In the model, the peak calcium concentration is highly correlated with soma-synapse distance under a number of physiologically-realistic suprathreshold stimulation regimes and for a range of dendritic morphologies. There are also simulations demonstrating that peak calcium can be used to set up a synaptic democracy in a homeostatic manner, whereby synapses regulate their synaptic strength on the basis of the difference between peak calcium and a uniform target value.
Reference:
1 . Sterratt DC, Groen MR, Meredith RM, van Ooyen A (2012) Spine calcium transients induced by synaptically-evoked action potentials can predict synapse location and establish synaptic democracy. PLoS Comput Biol 8:e1002545 [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): Hippocampus CA1 pyramidal GLU cell;
Channel(s): I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Synaptic Plasticity;
Implementer(s): Sterratt, David ; Groen, Martine R [martine.groen at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; AMPA; NMDA; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I Mixed; I R; I_AHP;
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bpap
CA1_multi
morphology
old20100419cell1
apical-non-trunk-list.hoc *
apical-trunk-list.hoc *
axonpoirazi.hoc *
axon-sec-list.hoc *
basal-paths.hoc *
basal-tree-list.hoc *
cell.hoc *
cell-analysis.hoc
gabab-gabaa-uniform-ratio.hoc *
n123.hoc *
nmda-ampa-ratio.hoc *
oblique-paths.hoc *
old20100419cell1_top.hoc
old20100419cell1_topadj.hoc
soma-list.hoc *
                            
// Make a set of lists, each containing the oblique sections
// that form a continuous path: starting from the section attached 
// to the trunk and ending at the apical tip section. 

// OLD CODE: ADJUSTED BY MARTINE ROSA GROEN (martine.groen@gmail.com) TO IMPLEMENT MULTIPLE MORPHOLOGIES, 
// this code refinement makes that the oblique path are traced automatically from an 
// ending to the trunk (Defined in apical-trunk-list), preventing the author to 
// manually type these paths with new morphologies (with the possible type errors)
// It is checked with the origin code. The only differences found in the original 
// code are (between brackets the new version)
// 26-109-111 (should be 25-109-111)
// 26-109-110 (should be 26-109-110)
// 104-105 (should be 103-105)
// 62-63 (double in the opl list in the Poirazi original)
// All these changes are due to typing errors in the original code. However in cell-setup 
// the first segment in the list (the trunk segment) is disregarded in the setting up of
// ion channels, because the trunk is setup before. In this trunk setup, the ion channels
// are distributed acording to distance or constants across the tree, making this 
// type errors without any effect.  

/*
objref pl[150],opl[150]
plcount=0
pl[plcount]=new SectionList()

apical_dendrite[0] pl[plcount].append()
apical_dendrite[1] pl[plcount].append()
apical_dendrite[2] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[0] pl[plcount].append()
apical_dendrite[1] pl[plcount].append()
apical_dendrite[3] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[4] pl[plcount].append()
apical_dendrite[5] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[6] pl[plcount].append()
apical_dendrite[7] pl[plcount].append()
apical_dendrite[8] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[6] pl[plcount].append()
apical_dendrite[7] pl[plcount].append()
apical_dendrite[9] pl[plcount].append()
apical_dendrite[10] pl[plcount].append()
apical_dendrite[11] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[6] pl[plcount].append()
apical_dendrite[7] pl[plcount].append()
apical_dendrite[9] pl[plcount].append()
apical_dendrite[10] pl[plcount].append()
apical_dendrite[12] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[6] pl[plcount].append()
apical_dendrite[7] pl[plcount].append()
apical_dendrite[9] pl[plcount].append()
apical_dendrite[13] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[14] pl[plcount].append()
apical_dendrite[116] pl[plcount].append()
apical_dendrite[117] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])


plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[14] pl[plcount].append()
apical_dendrite[116] pl[plcount].append()
apical_dendrite[118] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])


plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[16] pl[plcount].append()
apical_dendrite[17] pl[plcount].append()
apical_dendrite[18] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[16] pl[plcount].append()
apical_dendrite[17] pl[plcount].append()
apical_dendrite[19] pl[plcount].append()
apical_dendrite[20] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[16] pl[plcount].append()
apical_dendrite[17] pl[plcount].append()
apical_dendrite[19] pl[plcount].append()
apical_dendrite[21] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[23] pl[plcount].append()
apical_dendrite[24] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[29] pl[plcount].append()
apical_dendrite[30] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[29] pl[plcount].append()
apical_dendrite[31] pl[plcount].append()
apical_dendrite[32] pl[plcount].append()
apical_dendrite[33] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[29] pl[plcount].append()
apical_dendrite[31] pl[plcount].append()
apical_dendrite[32] pl[plcount].append()
apical_dendrite[34] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[29] pl[plcount].append()
apical_dendrite[31] pl[plcount].append()
apical_dendrite[35] pl[plcount].append()
apical_dendrite[36] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[29] pl[plcount].append()
apical_dendrite[31] pl[plcount].append()
apical_dendrite[35] pl[plcount].append()
apical_dendrite[37] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[38] pl[plcount].append()
apical_dendrite[39] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[27] pl[plcount].append()
apical_dendrite[28] pl[plcount].append()
apical_dendrite[38] pl[plcount].append()
apical_dendrite[40] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[42] pl[plcount].append()
apical_dendrite[43] pl[plcount].append()
apical_dendrite[44] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[42] pl[plcount].append()
apical_dendrite[43] pl[plcount].append()
apical_dendrite[45] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[46] pl[plcount].append()
apical_dendrite[47] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[48] pl[plcount].append()
apical_dendrite[49] pl[plcount].append()
apical_dendrite[50] pl[plcount].append()
apical_dendrite[51] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[48] pl[plcount].append()
apical_dendrite[49] pl[plcount].append()
apical_dendrite[50] pl[plcount].append()
apical_dendrite[52] pl[plcount].append()
apical_dendrite[53] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[48] pl[plcount].append()
apical_dendrite[49] pl[plcount].append()
apical_dendrite[50] pl[plcount].append()
apical_dendrite[52] pl[plcount].append()
apical_dendrite[54] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[48] pl[plcount].append()
apical_dendrite[49] pl[plcount].append()
apical_dendrite[55] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[56] pl[plcount].append()
apical_dendrite[57] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[58] pl[plcount].append()
apical_dendrite[59] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[60] pl[plcount].append()
apical_dendrite[61] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[62] pl[plcount].append()
apical_dendrite[63] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[62] pl[plcount].append()
apical_dendrite[63] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[65] pl[plcount].append()
apical_dendrite[66] pl[plcount].append()
apical_dendrite[67] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])


plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[65] pl[plcount].append()
apical_dendrite[66] pl[plcount].append()
apical_dendrite[68] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[69] pl[plcount].append()
apical_dendrite[70] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[71] pl[plcount].append()
apical_dendrite[72] pl[plcount].append()
apical_dendrite[73] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[71] pl[plcount].append()
apical_dendrite[72] pl[plcount].append()
apical_dendrite[74] pl[plcount].append()
apical_dendrite[75] pl[plcount].append()
apical_dendrite[76] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[71] pl[plcount].append()
apical_dendrite[72] pl[plcount].append()
apical_dendrite[74] pl[plcount].append()
apical_dendrite[75] pl[plcount].append()
apical_dendrite[77] pl[plcount].append()
apical_dendrite[78] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[71] pl[plcount].append()
apical_dendrite[72] pl[plcount].append()
apical_dendrite[74] pl[plcount].append()
apical_dendrite[75] pl[plcount].append()
apical_dendrite[77] pl[plcount].append()
apical_dendrite[79] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[71] pl[plcount].append()
apical_dendrite[72] pl[plcount].append()
apical_dendrite[74] pl[plcount].append()
apical_dendrite[80] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[81] pl[plcount].append()
apical_dendrite[82] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[85] pl[plcount].append()
apical_dendrite[86] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[85] pl[plcount].append()
apical_dendrite[87] pl[plcount].append()
apical_dendrite[88] pl[plcount].append()
apical_dendrite[89] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[85] pl[plcount].append()
apical_dendrite[87] pl[plcount].append()
apical_dendrite[88] pl[plcount].append()
apical_dendrite[90] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[85] pl[plcount].append()
apical_dendrite[87] pl[plcount].append()
apical_dendrite[91] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[92] pl[plcount].append()
apical_dendrite[93] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[83] pl[plcount].append()
apical_dendrite[84] pl[plcount].append()
apical_dendrite[92] pl[plcount].append()
apical_dendrite[94] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[95] pl[plcount].append()
apical_dendrite[96] pl[plcount].append()
apical_dendrite[97] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[95] pl[plcount].append()
apical_dendrite[96] pl[plcount].append()
apical_dendrite[98] pl[plcount].append()
apical_dendrite[99] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[95] pl[plcount].append()
apical_dendrite[96] pl[plcount].append()
apical_dendrite[98] pl[plcount].append()
apical_dendrite[100] pl[plcount].append()
apical_dendrite[101] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[95] pl[plcount].append()
apical_dendrite[96] pl[plcount].append()
apical_dendrite[98] pl[plcount].append()
apical_dendrite[100] pl[plcount].append()
apical_dendrite[102] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[104] pl[plcount].append()
apical_dendrite[105] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[41] pl[plcount].append()
apical_dendrite[107] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[26] pl[plcount].append()
apical_dendrite[108] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[26] pl[plcount].append()
apical_dendrite[109] pl[plcount].append()
apical_dendrite[110] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[26] pl[plcount].append()
apical_dendrite[109] pl[plcount].append()
apical_dendrite[111] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[22] pl[plcount].append()
apical_dendrite[112] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[15] pl[plcount].append()
apical_dendrite[113] pl[plcount].append()
apical_dendrite[114] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[15] pl[plcount].append()
apical_dendrite[113] pl[plcount].append()
apical_dendrite[115] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])

plcount=plcount+1
pl[plcount]=new SectionList()
apical_dendrite[64] pl[plcount].append()
apical_dendrite[106] pl[plcount].append()
opl[plcount]=new ObliquePath(pl[plcount])
forsec pl[plcount] print secname()
print plcount
*/

// START NEW CODE!! /////////////////////////////////////////////////////////////////

objref apical
apical = new SectionList()
forsec "apical_dendrite"{
  apical.append()
}

//Define new variables
objref currentsection,trunk_to_obliqueending, obliqueending_to_trunk
strdef origintrunk
trunk_to_obliqueending=new SectionList()
obliqueending_to_trunk=new List()
objref pl[150],opl[150]
plcount=-1 // to make the first counter in list pl 0

func istrunk() { local x  // return 1 if $o1.sec is the origin of the path
 //$o1.sec print secname() // if you want to see it working
  forsec apical_trunk_list{
    origintrunk=secname()
    $o1.sec x=issection(origintrunk)
    if (x==1) {
      return x
    }
  }
  return x // In this case 0 because it has not forfilled the x==1 if statement
}

obfunc trace_to_trunk() { localobj path
  //path = new SectionList()
  path = new List()
  while (istrunk(this)!=1) { // The function isorigin is defined in apical-trunk-list.hoc
    path.append(this)
    this = parsr(this) // the new this is the parent of the previous this
  }
  //this.sec path.append() // to add the trunk segment
  path.append(this)
  return path
}

obfunc reverse_list(){ localobj revlist,reftemp
  revlist=new SectionList()
  for(i=$o1.count()-1;i>=0;i=i-1) {
    reftemp=$o1.o(i)
    reftemp.sec revlist.append()
  }
  return revlist
}

forsec apical {
  secname() currentsection=new SectionRef()
  if (currentsection.nchild==0){ //endsegment
    //printf("end segment is ")
    //print secname()
    currentsection this = new SectionRef()
    obliqueending_to_trunk=trace_to_trunk()
    if(obliqueending_to_trunk.count()!=1){ // Discard the endsegment of the trunk as being an oblique
      plcount=plcount+1
      trunk_to_obliqueending=reverse_list(obliqueending_to_trunk)

      pl[plcount]=new SectionList()
      pl[plcount]=trunk_to_obliqueending
      opl[plcount]=new ObliquePath(pl[plcount])
      
      // to visually check the list of segments print to command line
      //printf("new oblique \n")      
      //print plcount
      //forsec pl[plcount]{
      //  print secname()
      //}
    
      //printf("trunk section \n")
      //opl2[plcount2].trunk_section.sec print secname()
    }
  }
}



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