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
old20100922cell2
apical-non-trunk-list.hoc *
apical-trunk-list.hoc *
axonpoirazi.hoc *
axon-sec-list.hoc *
basal-paths.hoc *
basal-tree-list.hoc *
cell-analysis.hoc
gabab-gabaa-uniform-ratio.hoc *
nmda-ampa-ratio.hoc *
oblique-paths.hoc *
old20100922cell2_top.hoc
old20100922cell2_topadj.hoc *
soma-list.hoc *
                            
// This function makes a set of lists, each containing the basal sections
// that form a continuous path: starting from the section attached 
// to the trunk and ending at the basal tip section. 
// written by Yiota Poirazi, July 2001, poirazi@LNC.usc.edu



// 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)

// The new code automatically trace back. This showed that the list below is tracing 
// some of the obliques all the way back to the soma (e.g. 5-4-3-2-1-0) while others
// are only partially traced (e.g. 52-51-35 in stead of 52-51-35-21-19-18). It is not
// clear why this is the case. However in the simulations of Sterratt et al, this 
// basal-paths list is not used, so all the code is commented out.   

/*
objref bl[150],obl[150]

blcount=0
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[16] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[3] bl[blcount].append()
dendrite[4] bl[blcount].append()
dendrite[5] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[3] bl[blcount].append()
dendrite[4] bl[blcount].append()
dendrite[6] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[3] bl[blcount].append()
dendrite[7] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[8] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[9] bl[blcount].append()
dendrite[10] bl[blcount].append()
dendrite[11] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[0] bl[blcount].append()
dendrite[1] bl[blcount].append()
dendrite[2] bl[blcount].append()
dendrite[9] bl[blcount].append()
dendrite[10] bl[blcount].append()
dendrite[12] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[13] bl[blcount].append()
dendrite[14] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[54] bl[blcount].append()
dendrite[55] bl[blcount].append()
dendrite[57] bl[blcount].append()
dendrite[13] bl[blcount].append()
dendrite[15] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[15] bl[blcount].append()
dendrite[17] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])


blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[23] bl[blcount].append()
dendrite[24] bl[blcount].append()
dendrite[25] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])


blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[23] bl[blcount].append()
dendrite[24] bl[blcount].append()
dendrite[26] bl[blcount].append()
dendrite[27] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[23] bl[blcount].append()
dendrite[24] bl[blcount].append()
dendrite[26] bl[blcount].append()
dendrite[28] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[23] bl[blcount].append()
dendrite[29] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[37] bl[blcount].append()
dendrite[38] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[37] bl[blcount].append()
dendrite[39] bl[blcount].append()
dendrite[40] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])


blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[37] bl[blcount].append()
dendrite[39] bl[blcount].append()
dendrite[41] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[42] bl[blcount].append()
dendrite[43] bl[blcount].append()
dendrite[44] bl[blcount].append()
dendrite[45] bl[blcount].append()
dendrite[46] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[42] bl[blcount].append()
dendrite[43] bl[blcount].append()
dendrite[44] bl[blcount].append()
dendrite[45] bl[blcount].append()
dendrite[47] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[49] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[36] bl[blcount].append()
dendrite[50] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])


blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[51] bl[blcount].append()
dendrite[52] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[35] bl[blcount].append()
dendrite[51] bl[blcount].append()
dendrite[53] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])


blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[54] bl[blcount].append()
dendrite[56] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[54] bl[blcount].append()
dendrite[55] bl[blcount].append()
dendrite[57] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])

blcount=blcount + 1
bl[blcount]=new SectionList()
dendrite[54] bl[blcount].append()
dendrite[58] bl[blcount].append()
obl[blcount]=new BasalPath(bl[blcount])
*/


/*

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

//Define new variables
objref currentsection,soma_to_basalending, basalending_to_soma
strdef soma_compartment
soma_to_basalending=new SectionList()
basalending_to_soma=new List()
objref bl2[150],obl2[150]
blcount2=-1 // to make the first counter in list pl 0

func issoma() { local x  // return 1 if $o1.sec is the origin of the path
  forsec soma_list{
    soma_compartment=secname()
    $o1.sec x=issection(soma_compartment)
    if (x==1) {
      return x
    }
  }
  return x // In this case 0 because it has not forfilled the x==1 if statement
}

obfunc trace_to_soma() { localobj path
  //path = new SectionList()
  path = new List()
  while (issoma(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_listbasal(){ 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 basal_tree_list {
  secname() currentsection=new SectionRef()
  if (currentsection.nchild==0){ //endsegment
    currentsection this = new SectionRef()
    basalending_to_soma=trace_to_soma()
    if(basalending_to_soma.count()!=1){ // Discard the endsegment of the trunk as being an oblique
      blcount2=blcount2+1
      soma_to_basalending=reverse_listbasal(basalending_to_soma)

      bl2[blcount2]=new SectionList()
      bl2[blcount2]=soma_to_basalending
      obl2[blcount2]=new BasalPath(bl2[blcount2])
      
      // to visually check the list of segments print to command line
      printf("new basal \n")      
      print blcount2
      forsec bl2[blcount2]{
        print secname()
      }
    }
  }
}

*/




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