Hippocampus temporo-septal engram shift model (Lytton 1999)

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Accession:7400
Temporo-septal engram shift model of hippocampal memory. The model posits that memories gradually move along the hippocampus from a temporal encoding site to ever more septal sites from which they are recalled. We propose that the sense of time is encoded by the location of the engram along the temporo-septal axis.
Reference:
1 . Lytton WW, Lipton P (1999) Can the hippocampus tell time? The temporo-septal engram shift model. Neuroreport 10:2301-6 [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):
Channel(s): I Na,t; I K;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Temporal Pattern Generation; Spatio-temporal Activity Patterns; Simplified Models;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu];
Search NeuronDB for information about:  GabaA; AMPA; I Na,t; I K;
/
lytton99
README
AMPA.mod
GABAA.mod
kdr.mod
matrix.mod *
naf.mod *
passiv.mod *
pulse.mod *
sinstim.mod *
vecst.mod
vecst.mod.orig
bg.inc *
bg_cvode.inc
boxes.hoc *
declist.hoc *
decvec.hoc *
default.hoc *
directory
fig1.gif
grvec.hoc
init.hoc
ivl.vecs
labels.hoc
loadr.hoc *
local.hoc
mosinit.hoc
net.hoc
netcon.inc
nrnoc.hoc
ovl.vecs
params.hoc *
params.hoc.SAV *
proc.hoc
run.hoc
simctrl.hoc *
spkts.hoc
syncode.hoc
tmpl.hoc
                            
// $Id: nrnoc.hoc,v 1.29 2002/05/01 20:18:35 billl Exp $

proc nrnoc () {}

// Users should not edit nrnoc.hoc or default.hoc.  Any local 
// changes to these files should be made in local.hoc.

// key '*&*' is picked up by to indicate command for emacs
proc elisp () { printf("*&* %s\n",$s1) }
// if (not exists(simname)) { strdef simname, output_file, datestr, comment }

// Simctrl.hoc will automatically load stdgraph.hoc which automatically
// loads stdrun.hoc
strdef temp_string_, user_string_  // needed for simctrl
/* Global variable default values.  NOTE that stdrun.hoc, stdgraph.hoc
and simctrl.hoc all contain variable definitions and thus default.hoc
should be loaded after these files */
load_file("default.hoc")      /* Load default.hoc */

/* Allows arrays of strings */
objref hoc_obj_[2]
if (xwindows) {
  load_file("stdgui.hoc") // don't want to encounter other String tempate defs
  load_file("simctrl.hoc")
} else {
  load_file("stdlib.hoc")
  load_file("stdrunnoiv.hoc")
}

proc run () {

  stdinit()

  if (batch_flag == 1) {
    sprint(output_file,"data/b%s.%02d", datestr, runnum)
    batch_run(tstop, printStep, output_file)
    finish()
  } else {
    continueRun(tstop)
  }
}

proc continueRun() { local eventCount
  // Although this works properly "the first time" it may not properly "continue" a simulation 

  eventCount=0
  eventslow=1
  stoprun = 0

  while (t < $1 && stoprun == 0) { 
    for i = 1, nstep_steprun { fadvance() }
    outputData()
    
    eventCount = eventCount + 1
    if (xwindows && eventCount%eventStep < 0.1) { doEvents() }
  }

  finish()
}

proc stdinit() {
  realtime=0 startsw()
  t = 0
  stoprun = 0

  if (batch_flag == 1) {
    batch_save()
    batchSave()  // User defined program to set up stuff to save
  }

  init()
  init()

  if (graph_flag == 1) { 
    if (iv_flag == 1) {
      initPlot()
    } else {
      initGraph() 
    }
  }

  if (print_flag == 1) { initPrint() }
}


proc init () {
  initMech()

  initMisc1()

  /* Initialize state vars then calculate currents */
/* If user hand-set v in initMisc1() then v_init should be > 1000,
else all compartments will be set to v_init */
if (v_init < 1000) {
  finitialize(v_init)
} else {
  finitialize()
}
fcurrent()

/* Set ca pump and leak channel for steady state */
setMemb()

/* Recalculate currents with new pump and leak kinetics */
fcurrent()
fcurrent()

initMisc2()
if (cvode_active()) cvode.re_init()
}

proc initMech() { /* Initialization of mechanism variables */
/* NOTE: if any changes are made to the NEURON block of any local mod
file, the user must add the necessary inits to initMisc1() */

/** Range variables **/

forall {

  if (ismembrane("na_ion")) { 
    nai = na_init
    nai0_na_ion = na_init
  }
  
  if (ismembrane("k_ion")) {
    ki = k_init
    ki0_k_ion = k_init
  }
  
  if (ismembrane("ca_ion")) { 
    cai = ca_init
    cai0_ca_ion = ca_init
  }
}

/** Global variables **/
}

proc setMemb () { local i_forward, i_back, iSum
  // Setup steady state voltage using leak channel
  forall {
    if (ismembrane("pas")) {
      iSum = 0.0
      
      if (ismembrane("na_ion")) { iSum = iSum + ina }
      if (ismembrane("k_ion"))  { iSum = iSum + ik  }
      if (ismembrane("ca_ion")) { iSum = iSum + ica }
      if (ismembrane("ns_ion")) { iSum = iSum + ins } // Non-specific

      if (iSum == 0) {        // Pas cmp so set e_pas = v
        e_pas = v

      } else {
        if (g_pas > 0) {    // Assume g set by user, calc e
          e_pas = v + iSum/g_pas

        } else {            // Assume e set by user, calc g
          if (e_pas != v) {
            g_pas = iSum/(e_pas - v)

          } else {        // error: g_pas <= 0
            errorMsg("bad g", g_pas)
          }
        }

        if (e_pas < -100 || e_pas > 0) {
          printf(".")
          // printf("%s erev: %g %g %g\n",secname(),e_pas,ina,ik)
        }
      }

    } else if (ismembrane("Passive")) {
      iSum = 0.0
      
      if (ismembrane("na_ion")) { iSum = iSum + ina }
      if (ismembrane("k_ion"))  { iSum = iSum + ik  }
      if (ismembrane("ca_ion")) { iSum = iSum + ica }
      if (ismembrane("ns_ion")) { iSum = iSum + ins } // Non-specific

      if (iSum == 0) {        // Passive cmp so set erev_Passive = v
        erev_Passive = v

      } else {
        if (g_Passive > 0) {    // Assume g set by user, calc erev
          erev_Passive = v + iSum/g_Passive

        } else {            // Assume erev set by user, calc g
          if (erev_Passive != v) {
            g_Passive = iSum/(erev_Passive - v)

          } else {        // error: g_Passive <= 0
            errorMsg("bad g", g_Passive)
          }
        }

        if (erev_Passive < -100 || erev_Passive > 0) {
          printf(".")
          // errorMsg("erev out of bounds", erev_Passive)
        }
      }
    }
  }
  print ""
}

proc finish() {
  /* Called following completion of continueRun() */

finishMisc()

if (graph_flag == 1) {
  if (iv_flag == 1) {
    flushPlot()
  } else {
    graphmode(-1)
    plt(-1)
  }
}

if (print_flag == 1) {
  wopen("")
}
}

/*------------------------------------------------------------
User definable GRAPHICS and PRINTING routines
------------------------------------------------------------*/

proc outputData() {
  // Default procedure - if outputData() doesn't exist in the run file

  if (graph_flag == 1) {
    if (iv_flag == 1) {
      Plot()
      rt = stopsw()
      if (rt > realtime) {
        realtime = rt
        fastflushPlot()
        doNotify()
        if (realtime == 2 && eventcount > 50) {
          eventslow = int(eventcount/50) + 1
        }
        eventcount = 0
      }else{
        eventcount = eventcount + 1
        if ((eventcount%eventslow) == 0) {
          doEvents()
        }
      }

    } else {
      graph(t)
    }
  }

  if (print_flag == 1) { 
    if (t%printStep <= printStep) { printOut() }
  }
}

proc printOut() {
  /* Default procedure - if printOut() doesn't exist in the run file */
}

proc initGraph() {
  /* Default procedure - if initGraph() doesn't exist in the run file */

graph()
}

proc initPrint() {
  /* Default procedure - if initPrint() doesn't exist in the run file */

wopen(output_file)
}

/*------------------------------------------------------------
User definable BATCH RUN routines
------------------------------------------------------------*/

proc batchSave() {
  /* Default procedure - if batchSave() doesn't exist in the run file */
}

proc nextrun() {
  // Called from finishmisc() following completion of batch in an autorun
  wopen("")   
  runnum = runnum + 1
  sprint(output_file,"data/b%s.%02d", datestr, runnum)
}                       

// commands for emacs
proc update_runnum() { 
  runnum = $1
  sprint(output_file,"data/%s.%02d", datestr, runnum)
  print "^&^ (progn (sim-index-revert)(setq sim-runnum ",runnum,"))" }
proc nrn_write_index() { printf("&INDEX& %s\n",$s1) }
proc nrn_update () { elisp("nrn-update") }
proc nrn_message () { printf("!&! %s\n",$s1) } 

/*------------------------------------------------------------
User definable INITIALIZATION and FINISH routines
------------------------------------------------------------*/

// Default procedure - if initMisc1() doesn't exist in the run file 
// Initializations performed prior to finitialize() 
// This should contain point process inits and inits for any changes 
//        made to the NEURON block of any local mod file 
proc initMisc1() { }

// Default procedure - if initMisc2() doesn't exist in the run file 
// Initializations performed after finitialize() 
proc initMisc2() { }

// Default procedure - if finishMisc() doesn't exist in the run file 
proc finishMisc() { }

/*------------------------------------------------------------
Miscellaneous routines
------------------------------------------------------------*/

proc errorMsg() {
  /* Print warning, assumes arg1 is string and arg2 if present is a
  variable value */

sectionname(section)

if (numarg() == 0) {
  printf("ERROR in errorMsg(): Needs at least 1 argument.\n")
} else if (numarg() == 1) {
  printf("ERROR: %s in section %s.\n", $s1, section)
} else {
  printf("ERROR: %s in section %s (var=%g).\n", $s1, section, $2)
}
}

proc clear() {
  /* Clear non-interviews plot window */
plt(-3)
}

func mod() { local x, y
  /* Mod function for non-integers */

x=$1
y=$2

return (x/y - int(x/y))
}

proc whatSection() {
  /* Print name of section */
sectionname(section)
print section
}

proc print_pp_location() { local x //arg1 must be a point process
   x = $o1.get_loc()
   sectionname(temp_string_)
   printf("%s located at %s(%g)\n", $o1, temp_string_, x)
   pop_section()
}

//* Load local modifications to nrnoc.hoc and default.hoc
load_file("local.hoc")

if (xwindows && graph_flag) { nrnmainmenu() } // pwman_place(50,50)

print "Init complete.\n"

Lytton WW, Lipton P (1999) Can the hippocampus tell time? The temporo-septal engram shift model. Neuroreport 10:2301-6[PubMed]

References and models cited by this paper

References and models that cite this paper

Alvarez P, Squire LR (1994) Memory consolidation and the medial temporal lobe: a simple network model. Proc Natl Acad Sci U S A 91:7041-5 [PubMed]

Anderson P, Bliss TV, Skrede KK (1971) Lamellar organization of hippocampal pathways. Exp Brain Res 13:222-38 [PubMed]

Bliss TV, Lomo T (1973) Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path. J Physiol 232:331-56 [PubMed]

Cavazos JE, Golarai G, Sutula TP (1992) Septotemporal variation of the supragranular projection of the mossy fiber pathway in the dentate gyrus of normal and kindled rats. Hippocampus 2:363-72 [PubMed]

Claiborne BJ, Amaral DG, Cowan WM (1986) A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus. J Comp Neurol 246:435-58 [PubMed]

Damasio AR (1990) Category-related recognition defects as a clue to the neural substrates of knowledge. Trends Neurosci 13:95-8 [PubMed]

Davis BD (1985) Sleep and the maintenance of memory. Perspect Biol Med 28:457-64 [PubMed]

Giuditta A, Ambrosini MV, Montagnese P, Mandile P, Cotugno M, Grassi Zucconi G, Vescia S (1995) The sequential hypothesis of the function of sleep. Behav Brain Res 69:157-66 [PubMed]

Grunwald T, Lehnertz K, Heinze HJ, Helmstaedter C, Elger CE (1998) Verbal novelty detection within the human hippocampus proper. Proc Natl Acad Sci U S A 95:3193-7 [PubMed]

Hennevin E, Hars B, Maho C, Bloch V (1995) Processing of learned information in paradoxical sleep: relevance for memory. Behav Brain Res 69:125-35 [PubMed]

Holscher C, Anwyl R, Rowan MJ (1997) Stimulation on the positive phase of hippocampal theta rhythm induces long-term potentiation that can Be depotentiated by stimulation on the negative phase in area CA1 in vivo. J Neurosci 17:6470-7 [PubMed]

Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci U S A 79:2554-8 [PubMed]

Lepage M, Habib R, Tulving E (1998) Hippocampal PET activations of memory encoding and retrieval: the HIPER model. Hippocampus 8:313-22 [PubMed]

Loy R, Koziell DA, Lindsey JD, Moore RY (1980) Noradrenergic innervation of the adult rat hippocampal formation. J Comp Neurol 189:699-710 [PubMed]

Lytton WW (1998) Adapting a feedforward heteroassociative network to Hodgkin-Huxley dynamics. J Comput Neurosci 5:353-64 [Journal] [PubMed]

   Feedforward heteroassociative network with HH dynamics (Lytton 1998) [Model]

Meador-Woodruff JH, Grandy DK, Van Tol HH, Damask SP, Little KY, Civelli O, Watson SJ (1994) Dopamine receptor gene expression in the human medial temporal lobe. Neuropsychopharmacology 10:239-48 [PubMed]

Melges FT, Freeman AM (1977) Temporal disorganization and inner-outer confusion in acute mental illness. Am J Psychiatry 134:874-7 [PubMed]

Moser MB, Moser EI (1998) Distributed encoding and retrieval of spatial memory in the hippocampus. J Neurosci 18:7535-42 [PubMed]

Nyberg L, McIntosh AR, Cabeza R, Habib R, Houle S, Tulving E (1996) General and specific brain regions involved in encoding and retrieval of events: what, where, and when. Proc Natl Acad Sci U S A 93:11280-5 [PubMed]

O'Reilly RC, McClelland JL (1994) Hippocampal conjunctive encoding, storage, and recall: avoiding a trade-off. Hippocampus 4:661-82 [PubMed]

Ott BR, Saver JL (1993) Unilateral amnesic stroke. Six new cases and a review of the literature. Stroke 24:1033-42 [PubMed]

Poucet B, Thinus-Blanc C, Muller RU (1994) Place cells in the ventral hippocampus of rats. Neuroreport 5:2045-8 [PubMed]

Shen B, McNaughton BL (1996) Modeling the spontaneous reactivation of experience-specific hippocampal cell assembles during sleep. Hippocampus 6:685-92 [PubMed]

Sigala S, Missale C, Spano P (1997) Opposite effects of dopamine D2 and D3 receptors on learning and memory in the rat. Eur J Pharmacol 336:107-12 [PubMed]

Slomianka L, Geneser FA (1993) Distribution of acetylcholinesterase in the hippocampal region of the mouse. III. The area dentata. J Comp Neurol 331:225-35 [PubMed]

Squire LR (1982) Comparisons between forms of amnesia: some deficits are unique to Korsakoff's syndrome. J Exp Psychol Learn Mem Cogn 8:560-71 [PubMed]

Squire LR, Spanis CW (1984) Long gradient of retrograde amnesia in mice: continuity with the findings in humans. Behav Neurosci 98:345-8 [PubMed]

Teyler TJ, DiScenna P (1986) The hippocampal memory indexing theory. Behav Neurosci 100:147-54 [PubMed]

Treves A, Rolls ET (1994) Computational analysis of the role of the hippocampus in memory. Hippocampus 4:374-91 [PubMed]

Trimble MR (1991) Interictal psychoses of epilepsy. Adv Neurol 55:143-52 [PubMed]

Tulving E, Kapur S, Craik FI, Moscovitch M, Houle S (1994) Hemispheric encoding/retrieval asymmetry in episodic memory: positron emission tomography findings. Proc Natl Acad Sci U S A 91:2016-20 [PubMed]

Tulving E, Markowitsch HJ (1998) Episodic and declarative memory: role of the hippocampus. Hippocampus 8:198-204 [PubMed]

Verney C, Baulac M, Berger B, Alvarez C, Vigny A, Helle KB (1985) Morphological evidence for a dopaminergic terminal field in the hippocampal formation of young and adult rat. Neuroscience 14:1039-52 [PubMed]

Wilson MA, McNaughton BL (1994) Reactivation of hippocampal ensemble memories during sleep. Science 265:676-9 [PubMed]

Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [Journal] [PubMed]

   Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

Hines ML, Carnevale NT (2003) Personal Communication of NEURON bibliography

(36 refs)