Computational analysis of NN activity and spatial reach of sharp wave-ripples (Canakci et al 2017)

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Accession:230861
Network oscillations of different frequencies, durations and amplitudes are hypothesized to coordinate information processing and transfer across brain areas. Among these oscillations, hippocampal sharp wave-ripple complexes (SPW-Rs) are one of the most prominent. SPW-Rs occurring in the hippocampus are suggested to play essential roles in memory consolidation as well as information transfer to the neocortex. To-date, most of the knowledge about SPW-Rs comes from experimental studies averaging responses from neuronal populations monitored by conventional microelectrodes. In this work, we investigate spatiotemporal characteristics of SPW-Rs and how microelectrode size and distance influence SPW-R recordings using a biophysical model of hippocampus. We also explore contributions from neuronal spikes and synaptic potentials to SPW-Rs based on two different types of network activity. Our study suggests that neuronal spikes from pyramidal cells contribute significantly to ripples while high amplitude sharp waves mainly arise from synaptic activity. Our simulations on spatial reach of SPW-Rs show that the amplitudes of sharp waves and ripples exhibit a steep decrease with distance from the network and this effect is more prominent for smaller area electrodes. Furthermore, the amplitude of the signal decreases strongly with increasing electrode surface area as a result of averaging. The relative decrease is more pronounced when the recording electrode is closer to the source of the activity. Through simulations of field potentials across a high-density microelectrode array, we demonstrate the importance of finding the ideal spatial resolution for capturing SPW-Rs with great sensitivity. Our work provides insights on contributions from spikes and synaptic potentials to SPW-Rs and describes the effect of measurement configuration on LFPs to guide experimental studies towards improved SPW-R recordings.
Reference:
1 . Canakci S, Toy MF, Inci AF, Liu X, Kuzum D (2017) Computational analysis of network activity and spatial reach of sharp wave-ripples. PLoS One 12:e0184542 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 basket cell;
Channel(s): I Na,t; I A; I K; I h;
Gap Junctions: Gap junctions;
Receptor(s): NMDA; GabaA; Glutamate;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Spatio-temporal Activity Patterns;
Implementer(s): Canakci, Sadullah [scanakci at bu.edu]; Inci, Ahmet F [afinci at sabanciuniv,edu]; Toy, Faruk [faruk.toy at metu.edu.tr]; Liu, Xin [xil432 at end.ucsd.edu]; Kuzum, Duygu [dkuzum at eng.ucsd.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; GabaA; NMDA; Glutamate; I Na,t; I A; I K; I h;
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//
// NOTICE OF COPYRIGHT AND OWNERSHIP OF SOFTWARE
//
// Copyright 2007, The University Of Pennsylvania
// 	School of Engineering & Applied Science.
//   All rights reserved.
//   For research use only; commercial use prohibited.
//   Distribution without permission of Maciej T. Lazarewicz not permitted.
//   mlazarew@seas.upenn.edu
//
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

//
// This mod file is based on the paper:
// Tort, A. B., Rotstein, H. G., Dugladze, T., et al. (2007). On the formation of gamma-coherent cell assemblies by oriens lacunosum-moleculare interneurons in the hippocampus. Proc Natl Acad Sci U S A,.
//

/*{load_file("syn.tem")}
{load_file("gap.tem")}
{load_file("iapp.tem")}*/

begintemplate Ok

external cvode

// PUBLIC VARIABLES
public x, y, z

// PUBLIC OBJECTS
public soma, spiketimes, idvec, synS, gapS, iappS, synlist

// PUBLIC METHODS
public position, getlocoS, connect2target, recordVoltage, is_art, addSynS, getTotalArea
public setScatteredVoltages, writeVoltage

create soma    

objref iappS, synS, gapS, locS, voltageRecS, recordT
objref spiketimes, idvec, nc, nil, synlist, inj

strdef cmd

// =================================================================================================
//
// init()
//
// =================================================================================================
proc init() {
    
    createCell()
        
    access soma
    
    synlist = new List()
    locS    = new SectionRef()
    iappS   = new IApp()
    synS    = new SynObj()
    gapS    = new GapObj()
    
    spiketimes  = new Vector()
    idvec       = new Vector()
    voltageRecS = new Vector()
    recordT     = new Vector()
  
    iappS.set_random_play($2, $3, $4, $1)
    
   	inj = new IClamp(0.5)
	inj.del = 0
	inj.dur = 1e9
	inj.amp = -16 * area(0.5) * 1e-5  // uA/cm2 -> nA
	
}




// =================================================================================================
//
// recordVoltage()
//
// =================================================================================================
proc recordVoltage() {
		
		//print "Started RECORDING VOLTAGE at OLM"	
		soma  cvode.record(&v(0.5), voltageRecS, recordT )
}





// =================================================================================================
//
// writeVoltage(gid)
//
// =================================================================================================
proc writeVoltage() { local i localobj fo, m

	//print "SIZE:", t, " ", recordT.size()

	m = new Matrix(recordT.size(), 6)

	m.setcol(0, recordT)
	m.setcol(1, voltageRecS)

	fo = new File()
	
	sprint(cmd,"data/%d.dat",$1)
	{fo.wopen(cmd)}
	
	{m.fprint(0, fo, "%6.3lf ")}
	
	{fo.close()}
}



// =================================================================================================
//
// connect2target()
//
// =================================================================================================
proc connect2target() { //$o1 target point process, $o2 returned NetCon
  
  soma $o2 = new NetCon(&v(0.5), $o1, 0 ,0, 0)
  
  if (numarg()==2) synS.addNetCon($o2)
}




// ========================================================================
//
// addSynS( tau1 (ms), tau2 (ms), Erev (mV), synapseName, synLoc )
//
// ========================================================================
func addSynS() {
    
    synlist.append(synS.synList.object( synS.addSyn( $1, $2, $3, $s4, $5)  ) )
	return synlist.count()-1
}




// =================================================================================================
//
// createCell()
//
// =================================================================================================
proc createCell() {

    totalArea = 100 // um2

    soma {
        nseg  = 1
        
        cm    = 1.3  // uF/cm2
        
        diam  = sqrt(totalArea) // um
        L     =  diam/PI  // um
    
    	insert pas
    		e_pas = -70     // mV
    		g_pas = 0.05e-3  // S/cm2 
  
	    insert NafOlmKop
    	insert KdrOlmKop
    	insert IhOlmKop
    	gamx_IhOlmKop = 12 // 8 or 12 I do not know
    	insert KaOlmKop	
	//insert extracellular
	//insert xtra	
    }
}




// ========================================================================
//
// getTotalArea()
//
// ========================================================================
func getTotalArea() {
	
	return totalArea
}


// =================================================================================================
//
// getlocoS()
//
// =================================================================================================
obfunc getlocoS() { return locS }



// =================================================================================================
//
// position()
//
// =================================================================================================
proc position() { x=$1 y=$2 z=$3 }




// =================================================================================================
//
// setScatteredVoltages(low, high)
//
// =================================================================================================
proc setScatteredVoltages() { localobj rand
  rand = new Random(startsw())
  rand.uniform($1,$2)

  forall v = rand.repick()
}




// =================================================================================================
//
// setIappR(mean [uA/cm2], std [uA/cm2], seed)
//
// =================================================================================================
proc setIappR() {

	locS mean_IappRrange = $1
	locS sd_IappRrange   = $2
	locS seed_IappRrange = $3
}




// =================================================================================================
//
// is_art()
//
// =================================================================================================
func is_art() { return 0}




endtemplate Ok

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