Comparison of models for IP3 receptor kinetics using stochastic simulations

Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity

Astrocytes, a glial cell type of the central nervous system, have emerged as detectors and regulators of neuronal information processing. Astrocyte excitability resides in transient variations of free cytosolic calcium concentration over a range of temporal and spatial scales, from sub-microdomains to waves propagating throughout the cell. Despite extensive experimental approaches, it is not clear how these signals are transmitted to and integrated within an astrocyte. The localization of the main molecular actors and the geometry of the system, including the spatial organization of calcium channels IP3R, are deemed essential. However, as most calcium signals occur in astrocytic ramifications that are too fine to be resolved by conventional light microscopy, most of those spatial data are unknown and computational modeling remains the only methodology to study this issue. Here, we propose an IP3R-mediated calcium signaling model for dynamics in such small sub-cellular volumes. To account for the expected stochasticity and low copy numbers, our model is both spatially explicit and particle-based. Extensive simulations show that spontaneous calcium signals arise in the model via the interplay between excitability and stochasticity. The model reproduces the main forms of calcium signals and indicates that their frequency crucially depends on the spatial organization of the IP3R channels. Importantly, we show that two processes expressing exactly the same calcium channels can display different types of calcium signals depending on the spatial organization of the channels. Our model with realistic process volume and calcium concentrations successfully reproduces spontaneous calcium signals that we measured in calcium micro-domains with confocal microscopy and predicts that local variations of calcium indicators might contribute to the diversity of calcium signals observed in astrocytes. To our knowledge, this model is the first model suited to investigate calcium dynamics in fine astrocytic processes and to propose plausible mechanisms responsible for their variability.

Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability

The scientific community across all disciplines faces the same challenges of ensuring accessibility, reproducibility, and efficient comparability of scientific results. Computational neuroscience is a rapidly developing field, where reproducibility and comparability of research results have gained increasing interest over the past years. As the number of computational models of brain functions is increasing, we chose to address reproducibility using four previously published computational models of astrocyte excitability as an example. Although not conventionally taken into account when modeling neuronal systems, astrocytes have been shown to take part in a variety of in vitro and in vivo phenomena including synaptic transmission. Two of the selected astrocyte models describe spontaneous calcium excitability, and the other two neurotransmitter-evoked calcium excitability. We specifically addressed how well the original simulation results can be reproduced with a reimplementation of the models. Additionally, we studied how well the selected models can be reused and whether they are comparable in other stimulation conditions and research settings. Unexpectedly, we found out that three of the model publications did not give all the necessary information required to reimplement the models. In addition, we were able to reproduce the original results of only one of the models completely based on the information given in the original publications and in the errata. We actually found errors in the equations provided by two of the model publications; after modifying the equations accordingly, the original results were reproduced more accurately. Even though the selected models were developed to describe the same biological event, namely astrocyte calcium excitability, the models behaved quite differently compared to one another. Our findings on a specific set of published astrocyte models stress the importance of proper validation of the models against experimental wet-lab data from astrocytes as well as the careful review process of models. A variety of aspects of model development could be improved, including the presentation of models in publications and databases. Specifically, all necessary mathematical equations, as well as parameter values, initial values of variables, and stimuli used should be given precisely for successful reproduction of scientific results.

Inositol 1,4,5-trisphosphate receptors in the endoplasmic reticulum: A single-channel point of view

As an intracellular Ca(2+) release channel at the endoplasmic reticulum membrane, the ubiquitous inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R) plays a crucial role in the generation, propagation and regulation of intracellular Ca(2+) signals that regulate numerous physiological and pathophysiological processes. This review provides a concise account of the fundamental single-channel properties of the InsP3R channel: its conductance properties and its regulation by InsP3 and Ca(2+), its physiological ligands, studied using nuclear patch clamp electrophysiology.

Buffer regulation of calcium puff sequences

Puffs are localized Ca(2 +) signals that arise in oocytes in response to inositol 1,4,5-trisphosphate (IP3). They are the result of the liberation of Ca(2 +) from the endoplasmic reticulum through the coordinated opening of IP3 receptor/channels clustered at a functional release site. The presence of buffers that trap Ca(2 +) provides a mechanism that enriches the spatio-temporal dynamics of cytosolic calcium. The expression of different types of buffers along the cell's life provides a tool with which Ca(2 +) signals and their responses can be modulated. In this paper we extend the stochastic model of a cluster of IP3R-Ca(2 +) channels introduced previously to elucidate the effect of buffers on sequences of puffs at the same release site. We obtain analytically the probability laws of the interpuff time and of the number of channels that participate of the puffs. Furthermore, we show that under typical experimental conditions the effect of buffers can be accounted for in terms of a simple inhibiting function. Hence, by exploring different inhibiting functions we are able to study the effect of a variety of buffers on the puff size and interpuff time distributions. We find the somewhat counter-intuitive result that the addition of a fast Ca(2 +) buffer can increase the average number of channels that participate of a puff.

Astrocyte-neuron interactions: from experimental research-based models to translational medicine

In this chapter, we review the principal astrocyte functions and the interactions between neurons and astrocytes. We then address how the experimentally observed functions have been verified in computational models and review recent experimental literature on astrocyte-neuron interactions. Benefits of computational neuroscience work are highlighted through selected studies with neurons and astrocytes by analyzing the existing models qualitatively and assessing the relevance of these models to experimental data. Common strategies to mathematical modeling and computer simulation in neuroscience are summarized for the nontechnical reader. The astrocyte-neuron interactions are then further illustrated by examples of some neurological and neurodegenerative diseases, where the miscommunication between glia and neurons is found to be increasingly important.