Neuronal dendrite calcium wave model (Neymotin et al, 2015)

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Accession:168874
"... We developed a reaction-diffusion model of an apical dendrite with diffusible inositol triphosphate (IP3 ), diffusible Ca2+, IP3 receptors (IP3 Rs), endoplasmic reticulum (ER) Ca2+ leak, and ER pump (SERCA) on ER. ... At least two modes of Ca2+ wave spread have been suggested: a continuous mode based on presumed relative homogeneity of ER within the cell; and a pseudo-saltatory model where Ca2+ regeneration occurs at discrete points with diffusion between them. We compared the effects of three patterns of hypothesized IP3 R distribution: 1. continuous homogeneous ER, 2. hotspots with increased IP3R density (IP3 R hotspots), 3. areas of increased ER density (ER stacks). All three modes produced Ca2+ waves with velocities similar to those measured in vitro (~50 - 90µm /sec). ... The measures were sensitive to changes in density and spacing of IP3 R hotspots and stacks. ... An extended electrochemical model, including voltage gated calcium channels and AMPA synapses, demonstrated that membrane priming via AMPA stimulation enhances subsequent Ca2+ wave amplitude and duration. Our modeling suggests that pharmacological targeting of IP3 Rs and SERCA could allow modulation of Ca2+ wave propagation in diseases where Ca2+ dysregulation has been implicated. "
Reference:
1 . Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model Neural Computation 27(4):898-924 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal cell; Hippocampus CA3 pyramidal cell; Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell;
Channel(s): I T low threshold; I A; I K; I K,Ca; I CAN; I Sodium; I Calcium; I_SERCA; I_KD; Ca pump;
Gap Junctions:
Receptor(s): AMPA;
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Calcium waves; Reaction-diffusion;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; McDougal, Robert [robert.mcdougal at yale.edu]; Sherif, Mohamed [mohamed.sherif.md at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; Hippocampus CA3 pyramidal cell; Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell; AMPA; I T low threshold; I A; I K; I K,Ca; I CAN; I Sodium; I Calcium; I_SERCA; I_KD; Ca pump; Glutamate;
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ca1dDemo
data
readme.txt
cagk.mod *
cal_mig.mod
can_mig.mod
cat_mig.mod
kaprox.mod *
kdrca1.mod *
km.mod *
misc.mod *
na3n.mod *
naf.mod
NMDA.mod
stats.mod *
vecst.mod *
AMPA0.cfg
AMPA150.cfg
analysisCode.py
batch.py
cawave.cfg
cawave.py
conf.py
geneval_cvode.inc *
misc.h *
netcon.inc *
nqs.hoc
nqs.py
plot_fig11.py
setup.hoc *
vector.py *
                            
[set]
electrical = 0
boost_every = 20.0
boost_halfw = 5.0
er_scale = 1.0
ca_stim = 0.0
ca_stimt = 2000.0
ip3rtau = 400
#ip3_notorigin = 120400.0
ip3_notorigin = 96320.0
ip3_origin = 120400.0
gserca = 1.9565
gleak = 18.06
stim_minx = 498
stim_maxx = 502
ip3_stim = 1.25
ip3_stimt = 2e3
ip3_init = 0.1
IP3ForceInit = 0
cacyt_init = 0.0001
caAvg_init = 0.0017
cadiff = 0.080 
ip3diff = 1.415
gCaChannels = 1.e-6
spaceum = 1.0
synLoclist = [0.5]
nstimStart = 3000
nstimInterval = 25
nstimNumber = 5
nconnThreshold = 0
nconnDelay = 0
nconnWeight = 0.5
nconnActive = 1

[sstvars]
m_cal = 4.1795192885229201e-06
l_kap = 0.89323822223885241
m_na3 = 0.0062508484631504874
n_kap = 0.00032432496528686684
ca_er = 0.01226866096200032
s_na3 = 1.0
ip3r_gate_state = 0.90225558792959659
ip3 = 0.1
ca_cyt = 4.3436305123460646e-05
n_kdr = 5.179579756650326e-05
h_na3 = 0.99803815375138849
v = -68.927645500091074
m_cat = 0.012531992943261227
h_can = 0.97000895856793268
h_cat = 0.57329440713169955
o_cagk = 0.0020172659561742911
m_can = 0.0018959716051689464

[run]
recdt = 5
tstop = 5000
dt = 1
cvodeactive = 1
runit = 0
simstr = 14sep23_A
saveout = 0
dodraw = 0
loadState = 0
ipydebug = 0
statestr = 14aug12_3000s_save_C
savestate = 0
useInitDict = 0
loadRXDStateOnly = 0