Denizot A, Arizono M, Nägerl UV, Soula H, Berry H. (2019). Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity. PLoS computational biology. 15 [PubMed]

See more from authors: Denizot A · Arizono M · Nägerl UV · Soula H · Berry H

References and models cited by this paper

Agarwal A et al. (2017). Transient Opening of the Mitochondrial Permeability Transition Pore Induces Microdomain Calcium Transients in Astrocyte Processes. Neuron. 93 [PubMed]

Akerboom J et al. (2012). Optimization of a GCaMP calcium indicator for neural activity imaging. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32 [PubMed]

Allbritton NL, Meyer T, Stryer L. (1992). Range of messenger action of calcium ion and inositol 1,4,5-trisphosphate. Science (New York, N.Y.). 258 [PubMed]

Alzayady KJ et al. (2015). Tracing the Evolutionary History of Inositol, 1, 4, 5-Trisphosphate Receptor: Insights from Analyses of Capsaspora owczarzaki Ca2+ Release Channel Orthologs. Molecular biology and evolution. 32 [PubMed]

Anwar H, Hepburn I, Nedelescu H, Chen W, De Schutter E. (2013). Stochastic calcium mechanisms cause dendritic calcium spike variability. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]

Asada A et al. (2015). Subtle modulation of ongoing calcium dynamics in astrocytic microdomains by sensory inputs. Physiological reports. 3 [PubMed]

Bannai H, Hirose M, Niwa F, Mikoshiba K. (2019). Dissection of Local Ca2+ Signals in Cultured Cells by Membrane-targeted Ca2+ Indicators. Journal of visualized experiments : JoVE. [PubMed]

Beierlein M, Regehr WG. (2006). Brief bursts of parallel fiber activity trigger calcium signals in bergmann glia. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26 [PubMed]

Ben Haim L, Rowitch DH. (2017). Functional diversity of astrocytes in neural circuit regulation. Nature reviews. Neuroscience. 18 [PubMed]

Bezprozvanny I, Watras J, Ehrlich BE. (1991). Bell-shaped calcium-response curves of Ins(1,4,5)P3- and calcium-gated channels from endoplasmic reticulum of cerebellum. Nature. 351 [PubMed]

Bicknell BA, Goodhill GJ. (2016). Emergence of ion channel modal gating from independent subunit kinetics. Proceedings of the National Academy of Sciences of the United States of America. 113 [PubMed]

Bindocci E et al. (2017). Three-dimensional Ca2+ imaging advances understanding of astrocyte biology. Science (New York, N.Y.). 356 [PubMed]

Bosanac I et al. (2002). Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand. Nature. 420 [PubMed]

Boulay AC et al. (2017). Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface. Cell discovery. 3 [PubMed]

Breslin K et al. (2018). Potassium and sodium microdomains in thin astroglial processes: A computational model study. PLoS computational biology. 14 [PubMed]

Brunstein M, Wicker K, Hérault K, Heintzmann R, Oheim M. (2013). Full-field dual-color 100-nm super-resolution imaging reveals organization and dynamics of mitochondrial and ER networks. Optics express. 21 [PubMed]

Buscemi L et al. (2017). Homer1 Scaffold Proteins Govern Ca2+ Dynamics in Normal and Reactive Astrocytes. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]

Cahoy JD et al. (2008). A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]

Calì C et al. (2016). Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. The Journal of comparative neurology. 524 [PubMed]

Chai H et al. (2017). Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence. Neuron. 95 [PubMed]

Chen TW et al. (2013). Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature. 499 [PubMed]

Chen W, De Schutter E. (2017). Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers. Frontiers in neuroinformatics. 11 [PubMed]

De Pittà M, Goldberg M, Volman V, Berry H, Ben-Jacob E. (2009). Glutamate regulation of calcium and IP3 oscillating and pulsating dynamics in astrocytes. Journal of biological physics. 35 [PubMed]

De Young GW, Keizer J. (1992). A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration. Proceedings of the National Academy of Sciences of the United States of America. 89 [PubMed]

Dickinson GD, Swaminathan D, Parker I. (2012). The probability of triggering calcium puffs is linearly related to the number of inositol trisphosphate receptors in a cluster. Biophysical journal. 102 [PubMed]

Et AL et al. (2018). Structural Basis of Astrocytic Ca 2 Signals at Tripartite Synapses. Rochester, NY: Social Science Research Network 2018. ID 3287791.

Falcke M. (2003). Buffers and oscillations in intracellular Ca2+ dynamics. Biophysical journal. 84 [PubMed]

Falcke M, Tsimring L, Levine H. (2000). Stochastic spreading of intracellular Ca(2+) release. Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics. 62 [PubMed]

Fiacco TA, Agulhon C, McCarthy KD. (2009). Sorting out astrocyte physiology from pharmacology. Annual review of pharmacology and toxicology. 49 [PubMed]

Flegg MB, Rüdiger S, Erban R. (2013). Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release. The Journal of chemical physics. 138 [PubMed]

Fraiman D, Dawson SP. (2014). Buffer regulation of calcium puff sequences. Physical biology. 11 [PubMed]

Francis M, Waldrup J, Qian X, Taylor MS. (2014). Automated analysis of dynamic Ca2+ signals in image sequences. Journal of visualized experiments : JoVE. [PubMed]

Gillespie DT. (1977). Exact stochastic simulation of coupled chemical reactions. Journal Of Physical Chemistry. 81

Gillespie DT. (2007). Stochastic simulation of chemical kinetics. Annual review of physical chemistry. 58 [PubMed]

Gin E, Falcke M, Wagner LE, Yule DI, Sneyd J. (2009). A kinetic model of the inositol trisphosphate receptor based on single-channel data. Biophysical journal. 96 [PubMed]

Goldbeter A, Dupont G, Berridge MJ. (1990). Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 87 [PubMed]

Grosche J et al. (1999). Microdomains for neuron-glia interaction: parallel fiber signaling to Bergmann glial cells. Nature neuroscience. 2 [PubMed]

Gähwiler BH. (1981). Organotypic monolayer cultures of nervous tissue. Journal of neuroscience methods. 4 [PubMed]

Haustein MD et al. (2014). Conditions and constraints for astrocyte calcium signaling in the hippocampal mossy fiber pathway. Neuron. 82 [PubMed]

Hepburn I, Chen W, Wils S, De Schutter E. (2012). STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC systems biology. 6 [PubMed]

Hernandez-Sotomayor SM, De Los Santos-Briones C, Munoz-Sanchez JA, Loyola-Vargas VM. (1999). Kinetic analysis of phospholipase C from catharanthus roseus transformed roots using different assays Plant physiology. 120 [PubMed]

Hires SA, Tian L, Looger LL. (2008). Reporting neural activity with genetically encoded calcium indicators. Brain cell biology. 36 [PubMed]

Hituri K, Linne ML. (2013). Comparison of models for IP3 receptor kinetics using stochastic simulations. PloS one. 8 [PubMed]

Isaacson SA, Isaacson D. (2009). Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials. Physical review. E, Statistical, nonlinear, and soft matter physics. 80 [PubMed]

Jones VC, McKeown L, Verkhratsky A, Jones OT. (2008). LV-pIN-KDEL: a novel lentiviral vector demonstrates the morphology, dynamics and continuity of the endoplasmic reticulum in live neurones. BMC neuroscience. 9 [PubMed]

Kinoshita S, Goto I, Natsume K. (2004). The model of glutamate induced intracellular Ca2+ oscillation and intercellular Ca2+ wave in brain astrocytes Neurocomputing. 58-60

Kopek BG et al. (2017). Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples. Nature protocols. 12 [PubMed]

Lencesova L, O'Neill A, Resneck WG, Bloch RJ, Blaustein MP. (2004). Plasma membrane-cytoskeleton-endoplasmic reticulum complexes in neurons and astrocytes. The Journal of biological chemistry. 279 [PubMed]

Lenk K, Khalid MU, Tervonen A, Korkka I, Hyttinen J. (2017). Geometry-based Computational Modeling of Calcium Signaling in an Astrocyte. In: EMBEC & NBC 2017.

Li YX, Rinzel J. (1994). Equations for InsP3 receptor-mediated [Ca2+]i oscillations derived from a detailed kinetic model: a Hodgkin-Huxley like formalism. Journal of theoretical biology. 166 [PubMed]

Manninen T, Havela R, Linne ML. (2017). Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. Frontiers in neuroinformatics. 11 [PubMed]

Manninen T, Havela R, Linne ML. (2018). Computational Models for Calcium-Mediated Astrocyte Functions. Frontiers in computational neuroscience. 12 [PubMed]

Matyash V, Filippov V, Mohrhagen K, Kettenmann H. (2001). Nitric oxide signals parallel fiber activity to Bergmann glial cells in the mouse cerebellar slice. Molecular and cellular neurosciences. 18 [PubMed]

Mauvezin C, Neufeld TP. (2015). Bafilomycin A1 disrupts autophagic flux by inhibiting both V-ATPase-dependent acidification and Ca-P60A/SERCA-dependent autophagosome-lysosome fusion. Autophagy. 11 [PubMed]

McDougal RA et al. (2017). Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal of computational neuroscience. 42 [PubMed]

Means S et al. (2006). Reaction diffusion modeling of calcium dynamics with realistic ER geometry. Biophysical journal. 91 [PubMed]

Michailova A, DelPrincipe F, Egger M, Niggli E. (2002). Spatiotemporal features of Ca2+ buffering and diffusion in atrial cardiac myocytes with inhibited sarcoplasmic reticulum. Biophysical journal. 83 [PubMed]

Montes de Oca Balderas P, Montes de Oca Balderas H. (2018). Synaptic neuron-astrocyte communication is supported by an order of magnitude analysis of inositol tris-phosphate diffusion at the nanoscale in a model of peri-synaptic astrocyte projection. BMC biophysics. 11 [PubMed]

Morita M et al. (2003). Dual regulation of calcium oscillation in astrocytes by growth factors and pro-inflammatory cytokines via the mitogen-activated protein kinase cascade. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23 [PubMed]

Morquette P et al. (2015). An astrocyte-dependent mechanism for neuronal rhythmogenesis. Nature neuroscience. 18 [PubMed]

Nett WJ, Oloff SH, McCarthy KD. (2002). Hippocampal astrocytes in situ exhibit calcium oscillations that occur independent of neuronal activity. Journal of neurophysiology. 87 [PubMed]

Newman EA. (2001). Propagation of intercellular calcium waves in retinal astrocytes and Müller cells. The Journal of neuroscience : the official journal of the Society for Neuroscience. 21 [PubMed]

Nixon-Abell J et al. (2016). Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER. Science (New York, N.Y.). 354 [PubMed]

Okubo Y et al. (2019). Inositol 1,4,5-trisphosphate receptor type 2-independent Ca2+ release from the endoplasmic reticulum in astrocytes. Glia. 67 [PubMed]

Oschmann F, Berry H, Obermayer K, Lenk K. (2018). From in silico astrocyte cell models to neuron-astrocyte network models: A review. Brain research bulletin. 136 [PubMed]

Oura T et al. (2016). Highly Sensitive Measurement of Inositol 1,4,5-Trisphosphate by Using a New Fluorescent Ligand and Ligand Binding Domain Combination. Chembiochem : a European journal of chemical biology. 17 [PubMed]

Panatier A, Arizono M, Nägerl UV. (2014). Dissecting tripartite synapses with STED microscopy. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 369 [PubMed]

Panatier A et al. (2011). Astrocytes are endogenous regulators of basal transmission at central synapses. Cell. 146 [PubMed]

Pando B, Dawson SP, Mak DO, Pearson JE. (2006). Messages diffuse faster than messengers. Proceedings of the National Academy of Sciences of the United States of America. 103 [PubMed]

Parri HR, Crunelli V. (2003). The role of Ca2+ in the generation of spontaneous astrocytic Ca2+ oscillations. Neuroscience. 120 [PubMed]

Patrushev I, Gavrilov N, Turlapov V, Semyanov A. (2013). Subcellular location of astrocytic calcium stores favors extrasynaptic neuron-astrocyte communication. Cell calcium. 54 [PubMed]

Porter JT, McCarthy KD. (1997). Astrocytic neurotransmitter receptors in situ and in vivo. Progress in neurobiology. 51 [PubMed]

Rahman T. (2012). Dynamic clustering of IP3 receptors by IP3. Biochemical Society transactions. 40 [PubMed]

Roest G, La Rovere RM, Bultynck G, Parys JB. (2017). IP3 Receptor Properties and Function at Membrane Contact Sites. Advances in experimental medicine and biology. 981 [PubMed]

Rusakov DA. (2015). Disentangling calcium-driven astrocyte physiology. Nature reviews. Neuroscience. 16 [PubMed]

Ru¨diger S, Erban R, Dobramys lU. (2016). .Particle-Based Multiscale Modeling of Calcium Puff Dynamics. Multiscale Modeling & Simulation.

Rüdiger S, Nagaiah Ch, Warnecke G, Shuai JW. (2010). Calcium domains around single and clustered IP3 receptors and their modulation by buffers. Biophysical journal. 99 [PubMed]

Rüdiger S et al. (2007). Hybrid stochastic and deterministic simulations of calcium blips. Biophysical journal. 93 [PubMed]

Savtchenko LP et al. (2018). Disentangling astroglial physiology with a realistic cell model in silico. Nature communications. 9 [PubMed]

Schwaller B. (2010). Cytosolic Ca2+ buffers. Cold Spring Harbor perspectives in biology. 2 [PubMed]

Serysheva II, Baker MR, Fan G. (2017). Structural Insights into IP3R Function. Advances in experimental medicine and biology. 981 [PubMed]

Sherwood MW et al. (2017). Astrocytic IP3 Rs: Contribution to Ca2+ signalling and hippocampal LTP. Glia. 65 [PubMed]

Shigetomi E, Patel S, Khakh BS. (2016). Probing the Complexities of Astrocyte Calcium Signaling. Trends in cell biology. 26 [PubMed]

Shuai J, Pearson JE, Parker I. (2008). Modeling Ca2+ feedback on a single inositol 1,4,5-trisphosphate receptor and its modulation by Ca2+ buffers. Biophysical journal. 95 [PubMed]

Shuai JW, Jung P. (2003). Optimal ion channel clustering for intracellular calcium signaling. Proceedings of the National Academy of Sciences of the United States of America. 100 [PubMed]

Siekmann I, Wagner LE, Yule D, Crampin EJ, Sneyd J. (2012). A kinetic model for type I and II IP3R accounting for mode changes. Biophysical journal. 103 [PubMed]

Skupin A, Falcke M. (2008). The role of IP3R clustering in Ca2+ signalinG. Genome informatics. International Conference on Genome Informatics. 20 [PubMed]

Skupin A, Kettenmann H, Falcke M. (2010). Calcium signals driven by single channel noise. PLoS computational biology. 6 [PubMed]

Skupin A et al. (2008). How does intracellular Ca2+ oscillate: by chance or by the clock? Biophysical journal. 94 [PubMed]

Smith IF, Swaminathan D, Dickinson GD, Parker I. (2014). Single-molecule tracking of inositol trisphosphate receptors reveals different motilities and distributions. Biophysical journal. 107 [PubMed]

Smith IF, Wiltgen SM, Parker I. (2009). Localization of puff sites adjacent to the plasma membrane: functional and spatial characterization of Ca2+ signaling in SH-SY5Y cells utilizing membrane-permeant caged IP3. Cell calcium. 45 [PubMed]

Smith IF, Wiltgen SM, Shuai J, Parker I. (2009). Ca(2+) puffs originate from preestablished stable clusters of inositol trisphosphate receptors. Science signaling. 2 [PubMed]

Smith S, Grima R. (2019). Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches. Bulletin of mathematical biology. 81 [PubMed]

Srinivasan R et al. (2015). Ca(2+) signaling in astrocytes from Ip3r2(-/-) mice in brain slices and during startle responses in vivo. Nature neuroscience. 18 [PubMed]

Stobart JL et al. (2018). Long-term In Vivo Calcium Imaging of Astrocytes Reveals Distinct Cellular Compartment Responses to Sensory Stimulation. Cerebral cortex (New York, N.Y. : 1991). 28 [PubMed]

Sun MY et al. (2014). Astrocyte calcium microdomains are inhibited by bafilomycin A1 and cannot be replicated by low-level Schaffer collateral stimulation in situ. Cell calcium. 55 [PubMed]

Swaminathan D, Jung P. (2011). The role of agonist-independent conformational transformation (AICT) in IP3 cluster behavior. Cell calcium. 49 [PubMed]

Swillens S, Dupont G, Combettes L, Champeil P. (1999). From calcium blips to calcium puffs: theoretical analysis of the requirements for interchannel communication. Proceedings of the National Academy of Sciences of the United States of America. 96 [PubMed]

Tadross MR, Tsien RW, Yue DT. (2013). Ca2+ channel nanodomains boost local Ca2+ amplitude. Proceedings of the National Academy of Sciences of the United States of America. 110 [PubMed]

Tay LH et al. (2012). Nanodomain Ca²? of Ca²? channels detected by a tethered genetically encoded Ca²? sensor. Nature communications. 3 [PubMed]

Taylor CW. (2017). Regulation of IP3 receptors by cyclic AMP. Cell calcium. 63 [PubMed]

Thillaiappan NB, Chavda AP, Tovey SC, Prole DL, Taylor CW. (2017). Ca2+ signals initiate at immobile IP3 receptors adjacent to ER-plasma membrane junctions. Nature communications. 8 [PubMed]

Thrower EC, Hagar RE, Ehrlich BE. (2001). Regulation of Ins(1,4,5)P3 receptor isoforms by endogenous modulators. Trends in pharmacological sciences. 22 [PubMed]

Tu H, Wang Z, Bezprozvanny I. (2005). Modulation of mammalian inositol 1,4,5-trisphosphate receptor isoforms by calcium: a role of calcium sensor region. Biophysical journal. 88 [PubMed]

Tu H, Wang Z, Nosyreva E, De Smedt H, Bezprozvanny I. (2005). Functional characterization of mammalian inositol 1,4,5-trisphosphate receptor isoforms. Biophysical journal. 88 [PubMed]

Tønnesen J, Nadrigny F, Willig KI, Wedlich-Söldner R, Nägerl UV. (2011). Two-color STED microscopy of living synapses using a single laser-beam pair. Biophysical journal. 101 [PubMed]

Urban NT, Willig KI, Hell SW, Nägerl UV. (2011). STED nanoscopy of actin dynamics in synapses deep inside living brain slices. Biophysical journal. 101 [PubMed]

Ventura R, Harris KM. (1999). Three-dimensional relationships between hippocampal synapses and astrocytes. The Journal of neuroscience : the official journal of the Society for Neuroscience. 19 [PubMed]

Wagner LE, Yule DI. (2012). Differential regulation of the InsP3 receptor type-1 and -2 single channel properties by InsP3, Ca²? and ATP. The Journal of physiology. 590 [PubMed]

Wang X et al. (2006). Astrocytic Ca2+ signaling evoked by sensory stimulation in vivo. Nature neuroscience. 9 [PubMed]

Wang Z, Tymianski M, Jones OT, Nedergaard M. (1997). Impact of cytoplasmic calcium buffering on the spatial and temporal characteristics of intercellular calcium signals in astrocytes. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17 [PubMed]

Weerth SH, Holtzclaw LA, Russell JT. (2007). Signaling proteins in raft-like microdomains are essential for Ca2+ wave propagation in glial cells. Cell calcium. 41 [PubMed]

Wieder N, Fink R, von Wegner F. (2015). Exact stochastic simulation of a calcium microdomain reveals the impact of Ca²? fluctuations on IP3R gating. Biophysical journal. 108 [PubMed]

Wils S, De Schutter E. (2009). STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Frontiers in neuroinformatics. 3 [PubMed]

Wilson BS et al. (1998). Calcium-dependent clustering of inositol 1,4,5-trisphosphate receptors. Molecular biology of the cell. 9 [PubMed]

Xiao B, Tu JC, Worley PF. (2000). Homer: a link between neural activity and glutamate receptor function. Current opinion in neurobiology. 10 [PubMed]

Zeller S et al. (2009). Modeling of the modulation by buffers of Ca2+ release through clusters of IP3 receptors. Biophysical journal. 97 [PubMed]

Zheng K et al. (2015). Time-Resolved Imaging Reveals Heterogeneous Landscapes of Nanomolar Ca(2+) in Neurons and Astroglia. Neuron. 88 [PubMed]

Zur Nieden R, Deitmer JW. (2006). The role of metabotropic glutamate receptors for the generation of calcium oscillations in rat hippocampal astrocytes in situ. Cerebral cortex (New York, N.Y. : 1991). 16 [PubMed]

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