Evidence map›Paper›PMID 25734493›Full record

ArticleNeural computation2015

Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model.

Samuel A Neymotin, Robert A McDougal, Mohamed A Sherif, Christopher P Fall, Michael L Hines, William W Lytton

Open access · greenAbstract read
In one paragraph

Article in Neural computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
2.7field-weighted citation impact, top 10% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed, 34 citations in OpenAlex.

  1. Article
  2. Vasodilatory Effect ofPlants (Basel, Switzerland) · 2025
    Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Endoplasmic Reticulum Calcium Pumps and Tumor Cell Differentiation.International journal of molecular sciences · 2020
    Review
  8. Review
  9. Article
  10. Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons.ACM transactions on modeling and computer simulation : a publication of the Association for Computing Machinery · 2017
    Article
  11. Article
  12. Article
  13. Reproducibility in Computational Neuroscience Models and Simulations.IEEE transactions on bio-medical engineering · 2016
    Article
  14. Article
  15. Article
  16. Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron.IEEE/ACM transactions on computational biology and bioinformatics
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 1 institution in 1 country.

Samuel A NeymotinDepartment of Physiology and Pharmacology, SUNY Downstate, Brooklyn, NY, 11203, and Department of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, U.S.A. samn@neurosim.downstate.edu.
Robert A McDougal
Mohamed A Sherif
Christopher P Fall
Michael L Hines
William W Lytton
Ain Shams University · EG

Funding

MEDICAL INFORMATICS RESEARCH TRAINING AT YALET15LM007056 · NLM · YALE UNIVERSITY · PI Mark Bender Gerstein, LUCILA OHNO-MACHADO · 1987 to 2026
$22.2M
COMPUTER METHODS FOR PHYSIOLOGICAL PROBLEMSR01NS011613 · NINDS · YALE UNIVERSITY · PI MICHAEL L HINES, Robert A. McDougal · 1985 to 2026
$10.4M
Extension of NEURON simulator for simulation of reaction-diffusion in neuronsR01MH086638 · NIMH · SUNY DOWNSTATE MEDICAL CENTER · PI LYTTON, WILLIAM W, MCDOUGAL, ROBERT A. · 2010 to 2025
$6.0M
NIMH NIH HHS R01 MH086638NINDS NIH HHS R01 NS011613NINDS NIH HHS R01 NS11613NLM NIH HHS T15 LM007056
6 · The paper itself

Abstract

Calcium (Ca²⁺) waves provide a complement to neuronal electrical signaling, forming a key part of a neuron's second messenger system. We developed a reaction-diffusion model of an apical dendrite with diffusible inositol triphosphate (IP₃), diffusible Ca²⁺, IP₃ receptors (IP₃Rs), endoplasmic reticulum (ER) Ca²⁺ leak, and ER pump (SERCA) on ER. Ca²⁺ is released from ER stores via IP₃Rs upon binding of IP₃ and Ca²⁺. This results in Ca²⁺-induced-Ca²⁺-release (CICR) and increases Ca²⁺ spread. 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 IP₃R distribution: (1) continuous homogeneous ER, (2) hotspots with increased IP₃R density (IP₃R hotspots), and (3) areas of increased ER density (ER stacks). All three modes produced Ca²⁺ waves with velocities similar to those measured in vitro (approximately 50-90 μm /sec). Continuous ER showed high sensitivity to IP₃R density increases, with time to onset reduced and speed increased. Increases in SERCA density resulted in opposite effects. The measures were sensitive to changes in density and spacing of IP₃R hotspots and stacks. Increasing the apparent diffusion coefficient of Ca²⁺ substantially increased wave speed. 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 IP₃Rs and SERCA could allow modulation of Ca²⁺ wave propagation in diseases where Ca²⁺ dysregulation has been implicated.

Indexed as

Computer SimulationModels, NeurologicalAnimalsCalcium Channels, N-TypeCalcium SignalingEndoplasmic ReticulumNeuronsPotassium ChannelsReceptors, AMPASodium ChannelsCalcium Channels, N-TypePotassium ChannelsReceptors, AMPASodium Channels

Identifiers

PMID25734493
PMCPMC4386758
OpenAlexW2057970414

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.