Dataset Information

Multi-scale data-driven modeling and observation of calcium puffs.

ABSTRACT: The spatiotemporal dynamics of elementary Ca(2+) release events, such as "blips" and "puffs" shapes the hierarchal Ca(2+) signaling in many cell types. Despite being the building blocks of Ca(2+) patterning, the mechanism responsible for the observed properties of puffs, especially their termination is incompletely understood. In this paper, we employ a data-driven approach to gain insights into the complex dynamics of blips and puffs. We use a model of inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R) derived directly from single channel patch clamp data taken at 10 ?M concentration of IP(3) to simulate calcium puffs. We first reproduce recent observations regarding puffs and blips and then investigate the mechanism of puff termination. Our model suggests that during a puff, IP(3)R s proceed around a loop through kinetic states from "rest" to "open" to "inhibited" and back to "rest". A puff terminates because of self-inhibition. Based on our simulations, we rule out the endoplasmic reticulum (ER) Ca(2+) depletion as a possible cause for puff termination. The data-driven approach also enables us to estimate the current through a single IP(3)R and the peak Ca(2+) concentration near the channel pore.

SUBMITTER: Ullah G

PROVIDER: S-EPMC3560535 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Multi-scale data-driven modeling and observation of calcium puffs.

Ullah Ghanim G Parker Ian I Mak Don-On Daniel DO Pearson John E JE

Cell calcium 20120606 2

The spatiotemporal dynamics of elementary Ca(2+) release events, such as "blips" and "puffs" shapes the hierarchal Ca(2+) signaling in many cell types. Despite being the building blocks of Ca(2+) patterning, the mechanism responsible for the observed properties of puffs, especially their termination is incompletely understood. In this paper, we employ a data-driven approach to gain insights into the complex dynamics of blips and puffs. We use a model of inositol 1,4,5-trisphosphate (IP(3)) recep ...[more]

PMID: 22682010

Similar Datasets

Project description:In synapses, calcium is required for modulating synaptic transmission, plasticity, synaptogenesis, and synaptic pruning. The regulation of calcium dynamics within neurons involves cellular mechanisms such as synaptically activated channels and pumps, calcium buffers, and calcium sequestrating organelles. Many experimental studies tend to focus on only one or a small number of these mechanisms, as technical limitations make it difficult to observe all features at once. Computational modeling enables incorporation of many of these properties together, allowing for more complete and integrated studies. However, the scale of existing detailed models is often limited to synaptic and dendritic compartments as the computational burden rapidly increases when these models are integrated in cellular or network level simulations. In this article we present a computational model of calcium dynamics at the postsynaptic spine of a CA1 pyramidal neuron, as well as a methodology that enables its implementation in multi-scale, large-scale simulations. We first present a mechanistic model that includes individually validated models of various components involved in the regulation of calcium at the spine. We validated our mechanistic model by comparing simulated calcium levels to experimental data found in the literature. We performed additional simulations with the mechanistic model to determine how the simulated calcium activity varies with respect to presynaptic-postsynaptic stimulation intervals and spine distance from the soma. We then developed an input-output (IO) model that complements the mechanistic calcium model and provide a computationally efficient representation for use in larger scale modeling studies; we show the performance of the IO model compared to the mechanistic model in terms of accuracy and speed. The models presented here help achieve two objectives. First, the mechanistic model provides a comprehensive platform to describe spine calcium dynamics based on individual contributing factors. Second, the IO model is trained on the main dynamical features of the mechanistic model and enables nonlinear spine calcium modeling on the cell and network level simulation scales. Utilizing both model representations provide a multi-level perspective on calcium dynamics, originating from the molecular interactions at spines and propagating the effects to higher levels of activity involved in network behavior.

Dataset Information

Multi-scale data-driven modeling and observation of calcium puffs.

Publications

Multi-scale data-driven modeling and observation of calcium puffs.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets