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<front>
<journal-meta><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="nlm-ta">PLoS Comput Biol</journal-id><journal-id journal-id-type="pmc">ploscomp</journal-id><!--===== Grouping journal title elements =====--><journal-title-group><journal-title>PLoS Computational Biology</journal-title></journal-title-group><issn pub-type="ppub">1553-734X</issn><issn pub-type="epub">1553-7358</issn><publisher>
<publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta>
<article-meta><article-id pub-id-type="publisher-id">09-PLCB-RA-1300R3</article-id><article-id pub-id-type="doi">10.1371/journal.pcbi.1000870</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Cell Biology/Cell Signaling</subject><subject>Computational Biology</subject><subject>Computational Biology/Molecular Dynamics</subject><subject>Computational Biology/Signaling Networks</subject><subject>Computational Biology/Systems Biology</subject><subject>Physics/Interdisciplinary Physics</subject></subj-group></article-categories><title-group><article-title>Calcium Signals Driven by Single Channel Noise</article-title><alt-title alt-title-type="running-head">Ca<sup>2+</sup> Signals Driven by Noise</alt-title></title-group><contrib-group>
<contrib contrib-type="author" xlink:type="simple"><name name-style="western"><surname>Skupin</surname><given-names>Alexander</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name name-style="western"><surname>Kettenmann</surname><given-names>Helmut</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib>
<contrib contrib-type="author" xlink:type="simple"><name name-style="western"><surname>Falcke</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib>
</contrib-group><aff id="aff1"><label>1</label><addr-line>Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany</addr-line>       </aff><aff id="aff2"><label>2</label><addr-line>Molecular Neuroscience, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany</addr-line>       </aff><aff id="aff3"><label>3</label><addr-line>Mathematical Cell Physiology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany</addr-line>       </aff><contrib-group>
<contrib contrib-type="editor" xlink:type="simple"><name name-style="western"><surname>Stelling</surname><given-names>Jorg</given-names></name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"/></contrib>
</contrib-group><aff id="edit1">ETH Zurich, Switzerland</aff><author-notes>
<corresp id="cor1">* E-mail: <email xlink:type="simple">skupin@mpimp-golm.mpg.de</email></corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: AS HK MF. Performed the experiments: AS. Analyzed the data: AS MF. Contributed reagents/materials/analysis tools: AS. Wrote the paper: AS HK MF.</p></fn>
<fn fn-type="conflict"><p>The authors have declared that no competing interests exist.</p></fn></author-notes><pub-date pub-type="collection"><month>8</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>5</day><month>8</month><year>2010</year></pub-date><volume>6</volume><issue>8</issue><elocation-id>e1000870</elocation-id><history>
<date date-type="received"><day>28</day><month>10</month><year>2009</year></date>
<date date-type="accepted"><day>29</day><month>6</month><year>2010</year></date>
</history><!--===== Grouping copyright info into permissions =====--><permissions><copyright-year>2010</copyright-year><copyright-holder>Skupin et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract>
<p>Usually, the occurrence of random cell behavior is appointed to small copy numbers of molecules involved in the stochastic process. Recently, we demonstrated for a variety of cell types that intracellular Ca<sup>2+</sup> oscillations are sequences of random spikes despite the involvement of many molecules in spike generation. This randomness arises from the stochastic state transitions of individual Ca<sup>2+</sup> release channels and does not average out due to the existence of steep concentration gradients. The system is hierarchical due to the structural levels channel - channel cluster - cell and a corresponding strength of coupling. Concentration gradients introduce microdomains which couple channels of a cluster strongly. But they couple clusters only weakly; too weak to establish deterministic behavior on cell level. Here, we present a multi-scale modelling concept for stochastic hierarchical systems. It simulates active molecules individually as Markov chains and their coupling by deterministic diffusion. Thus, we are able to follow the consequences of random single molecule state changes up to the signal on cell level. To demonstrate the potential of the method, we simulate a variety of experiments. Comparisons of simulated and experimental data of spontaneous oscillations in astrocytes emphasize the role of spatial concentration gradients in Ca<sup>2+</sup> signalling. Analysis of extensive simulations indicates that frequency encoding described by the relation between average and standard deviation of interspike intervals is surprisingly robust. This robustness is a property of the random spiking mechanism and not a result of control.</p>
</abstract><abstract abstract-type="summary"><title>Author Summary</title>
<p>The number of proteins organizing cellular processes is huge. The challenge for systems biology is to connect the properties of all these proteins to cellular behavior. Do individual state changes of molecules matter for cell behavior despite these large numbers? Recently, we have experimentally shown for four cell types that intracellular Ca<sup>2+</sup> signalling is driven by single channel dynamics. Molecular fluctuations are used constructively for a stochastic spike generation mechanism. The hierarchical structure of Ca<sup>2+</sup> signalling prevents averaging of fluctuations and, consequently, the sequence of global spikes still reflects this molecular noise. Here we present a stochastic 3-D multiscale modelling tool living up to these findings by following the consequences of individual channel state changes up to cell level. We simulate the variety of cell responses in different experiments. The stochastic spike generation mechanism is surprisingly robust, providing new insights into the relation of function and robustness. The modelling concept can be applied to a large class of reaction-diffusion processes including other pathways like cAMP.</p>
</abstract><funding-group><funding-statement>A.S. was supported by the International Research Training Group (IRTG) “Genomics and Systems Biology of Molecular Networks” of the German Research Association (DFG) and by the GoFORSYS project no. 0313924 of the Federal Ministry of Education and Research (BMBF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="13"/></counts></article-meta>
</front>
<body><sec id="s1">
<title>Introduction</title>
<p>Cellular behavior is the dynamics emerging out of molecular properties and molecular interactions. Hence, cells are indispensably subject to intrinsic noise due to the randomness of diffusion and molecule state transitions in gene expression <xref ref-type="bibr" rid="pcbi.1000870-Elowitz1">[1]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Suel1">[2]</xref>, signaling pathways and control mechanisms. It drives noise induced cell differentiation <xref ref-type="bibr" rid="pcbi.1000870-Chang1">[3]</xref>, cell-to-cell variability of cloned cells <xref ref-type="bibr" rid="pcbi.1000870-Nakumura1">[4]</xref> or second messenger dynamics <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. While noise in gene expression can be attributed to small molecule numbers, we consider here noise in signalling pathways which occurs even in systems with large molecule numbers.</p>
<p>Molecular interactions create nonlinear feedback like substrate depletion and allosteric regulation in enzyme kinetics or mutual activation of ion channels in membrane potential dynamics. They also couple active molecules inside cells spatially by diffusion of product and substrate or electric currents. If this coupling is strong enough, cells respond spatially homogeneous. Otherwise, we observe dynamic spatial structures formed by concentrations of molecules in specific states. These structures are often called microdomains <xref ref-type="bibr" rid="pcbi.1000870-Berridge1">[6]</xref>–<xref ref-type="bibr" rid="pcbi.1000870-Tovey1">[9]</xref>.</p>
<p>The existence of these dynamic structures determines in some systems whether the cell obeys deterministic or stochastic mechanisms. The dynamic compartmentalization of the cell by concentration gradients may prevent the establishment of deterministic dynamics by the law of large numbers even if the total number of molecules in the cell would suggest it otherwise. Microdomains are too small to behave deterministically. Not even the whole ensemble of microdomains will behave deterministically, if they are only weakly coupled or if there are only a few of them. Consequently, noise is not averaged out on cell level.</p>
<p>To determine whether we deal with a deterministic or stochastic system is important since these regimes may exhibit very different dependencies of behavior on system parameters <xref ref-type="bibr" rid="pcbi.1000870-Kummer1">[10]</xref>. For instance, repetitive spiking in intracellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e001" xlink:type="simple"/></inline-formula> signalling would be restricted to parameter values providing oscillatory dynamics with a deterministic mechanism <xref ref-type="bibr" rid="pcbi.1000870-Thul1">[11]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Thul2">[12]</xref>. It may occur with a stochastic system also for parameters which would lead to bistable or excitable dynamics in the deterministic limit, i.e. for larger or different parameter ranges <xref ref-type="bibr" rid="pcbi.1000870-Falcke1">[13]</xref>. In the non-oscillatory parameter ranges, the mechanism creating almost regular spike sequences can be coherence resonance <xref ref-type="bibr" rid="pcbi.1000870-Pikovsky1">[14]</xref>–<xref ref-type="bibr" rid="pcbi.1000870-Lindner1">[16]</xref> rather than the existence of a limit cycle in phase space of the local dynamics. Noisy systems with gradients usually show also a dependency of system characteristics on parameters of spatial coupling which spatially homogeneous systems do not exhibit. An example is the dependency of the spiking frequency on diffusion properties (see below and <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>).</p>
<p>In summary, the interaction between noise and gradients determines parameter dependencies and mechanisms. Recent experimental and theoretical studies on intracellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e002" xlink:type="simple"/></inline-formula> dynamics taught us that cells may indeed work in this regime and may exhibit repetitive spiking with non-oscillatory local dynamics. Functionally relevant gradients are also observed with intracellular cAMP <xref ref-type="bibr" rid="pcbi.1000870-Zaccolo1">[8]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Karpen1">[17]</xref>–<xref ref-type="bibr" rid="pcbi.1000870-Leroy1">[19]</xref>, pH <xref ref-type="bibr" rid="pcbi.1000870-Cardone1">[20]</xref> and in phosphorylation/dephosphorylation dynamics <xref ref-type="bibr" rid="pcbi.1000870-Kholodenko1">[21]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Kholodenko2">[22]</xref> suggesting that the lessons learned from <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e003" xlink:type="simple"/></inline-formula> dynamics may also apply to other systems.</p>
<p>One of these lessons is that the randomness of single molecule state changes is carried up from the molecular level to cell level <xref ref-type="bibr" rid="pcbi.1000870-Marchant1">[23]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Marchant2">[24]</xref>. Cellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e004" xlink:type="simple"/></inline-formula> concentration spikes form random sequences of interspike intervals (ISIs) and that randomness arises from the randomness of single molecule state transitions <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Dupont1">[25]</xref>. Consequently, the fluctuations of cellular signals contain information on single molecule behavior. It is a task for modelling now to establish the relation between these fluctuations and single molecule properties to decode this information.</p>
<p>Systems exhibiting the interaction between noise and gradients require modelling tools which can deal efficiently with the large concentration gradients and with the time scale range from molecular transitions to cell behavior. Here, we present such a modelling concept with the example of intracellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e005" xlink:type="simple"/></inline-formula> dynamics. It simulates all active molecules as stochastic Markov chains with all the individual state transitions and describes diffusion and some bulk reactions deterministically. Active molecules are those carrying the crucial feedbacks and nonlinearities. That allows for linearization of passive bulk reactions and the application of a multi-component Green's function to solve the partial differential equations in the cell analytically. We combine Green's functions with a local quasi-static approximation for the fast concentration changes and diffusion processes at the location of active molecules. That is possible due to the short diffusion time on the molecular length scale of a few nanometers. Since we use Green's functions for the long range concentration profiles we can restrict the calculation of concentration values to the location of active molecules. That renders this method extremely efficient even in 3 spatial dimensions.</p>
<p>We will apply this concept to intracellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e006" xlink:type="simple"/></inline-formula> dynamics and compare simulated time dependent concentrations with single cell time series obtained from cultured astrocytes all measured under the same condition without any stimulation. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e007" xlink:type="simple"/></inline-formula> is a ubiquitous second messenger in eukaryotic cells that transmits a variety of extracellular signals to intracellular targets. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e008" xlink:type="simple"/></inline-formula> controls fertilization, cell differentiation, gene expression, learning and memory <xref ref-type="bibr" rid="pcbi.1000870-Berridge2">[26]</xref>. It triggers secretion in glands, muscle contractions in the heart and transmits apoptosis signals <xref ref-type="bibr" rid="pcbi.1000870-Berridge3">[27]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Orrenius1">[28]</xref>.</p>
<p>A main mechanism to increase the cytosolic <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e009" xlink:type="simple"/></inline-formula> concentration is release from intracellular stores, especially from the sarcoplasmic reticulum by ryanodine receptor channels (RyRs) or the endoplasmic reticulum (ER) by inositol 1,4,5-trisphosphate receptor channels (<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e010" xlink:type="simple"/></inline-formula>). These channels open in a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e011" xlink:type="simple"/></inline-formula> dependent fashion - a self amplifying effect known as <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e012" xlink:type="simple"/></inline-formula> induced <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e013" xlink:type="simple"/></inline-formula> release (CICR) <xref ref-type="bibr" rid="pcbi.1000870-Berridge3">[27]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Bootman2">[29]</xref>. If a single channel opens, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e014" xlink:type="simple"/></inline-formula> is released into the cytosol, diffuses to adjacent channels and increases their open probability. Thus release may spread into the entire cell leading to a global cytosolic <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e015" xlink:type="simple"/></inline-formula> concentration spike.</p>
<p>The inositol 1,4,5-trisphosphate (<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e016" xlink:type="simple"/></inline-formula>) pathway initiates <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e017" xlink:type="simple"/></inline-formula> release from the ER in many cell types (including astrocytes <xref ref-type="bibr" rid="pcbi.1000870-Fiacco1">[30]</xref>), since binding of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e018" xlink:type="simple"/></inline-formula> to the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e019" xlink:type="simple"/></inline-formula> primes them for activation by <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e020" xlink:type="simple"/></inline-formula> (Figure 1 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). The spatial arrangement of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e021" xlink:type="simple"/></inline-formula> in channel clusters leads to a hierarchical system with the structural levels channel, channel cluster and cluster array, which is the cell level. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e022" xlink:type="simple"/></inline-formula> pumps and buffers generate large gradients close to open channel clusters. Thus, channels within a cluster are strongly coupled and the coupling between clusters is only weak - the geometrical hierarchy entails a hierarchy of coupling strengths.</p>
<p>Stochastic binding of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e023" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e024" xlink:type="simple"/></inline-formula> to the binding sites of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e025" xlink:type="simple"/></inline-formula> leads to random opening of a single channel in a cluster <xref ref-type="bibr" rid="pcbi.1000870-Falcke3">[31]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Shuai1">[32]</xref>. This causes other channels of the same cluster to open also leading to a puff. An individual cluster is stochastic due to the small number of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e026" xlink:type="simple"/></inline-formula> per cluster <xref ref-type="bibr" rid="pcbi.1000870-Smith1">[33]</xref>–<xref ref-type="bibr" rid="pcbi.1000870-TaufiqUrRahman1">[35]</xref>. The opening of a single cluster can only be detected by adjacent clusters due to the strong <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e027" xlink:type="simple"/></inline-formula> gradients <xref ref-type="bibr" rid="pcbi.1000870-Marchant1">[23]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Marchant2">[24]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Berridge3">[27]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Yao1">[36]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Falcke4">[37]</xref>. Since they are again only a few, it remains random whether they are opened by the initial puff. If a supercritical number of puffs arises, release spreads into the whole cell causing a global spike. Thus, due to the hierarchy of coupling strength, randomness is carried up from the channel level to the cell level.</p>
<p>In order to model the hierarchical system, we have to consider the stochastic behavior of individual <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e028" xlink:type="simple"/></inline-formula> and the spatial heterogeneity of cells induced by <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e029" xlink:type="simple"/></inline-formula> clustering. That leads to a reaction diffusion system (RDS) with local stochastic source terms. For sufficient fast simulations, we decompose the system into local stochastic dynamics comprising channel state transitions and fast local concentration changes and a deterministic global dynamics for which we derive an analytical solution in form of a three component Green's function (<xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). The solution is driven by stochastic channel behavior described by a hybrid deterministic-stochastic algorithm. We apply the model to a variety of experiments to demonstrate its potential.</p>
</sec><sec id="s2">
<title>Results</title>
<sec id="s2a">
<title>Multi-scale modelling exploiting the hierarchical organization of Ca<sup>2+</sup> signals</title>
<p>Our modelling concept simulates active molecules individually by Markov chains, the concentration dynamics in the range of the molecule locally quasi-statically and the diffusional long range coupling by Green's functions. Simulations are orders of magnitude faster than numerical schemes based on spatial grids. Their efficiency derives from the methods which we apply. The use of hybrid deterministic-stochastic algorithms for the Markov chains allows for time steps much larger than traditional Gillespie algorithms. In between stochastic molecule state transitions, we integrate the concentration dynamics. The local quasi-static approximation reduces clusters to spatial <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e030" xlink:type="simple"/></inline-formula>-function sources which turns integrals into sums. It also substantially reduces the number of modes to be used in the Green's function. And finally Green's function enables us to restrict the calculation of concentration values to the locations of active molecules.</p>
</sec><sec id="s2b">
<title>Channel and cluster level</title>
<p><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e031" xlink:type="simple"/></inline-formula> dynamics and spatial channel clustering lead to the hierarchical system depicted in <xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1</xref>. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e032" xlink:type="simple"/></inline-formula> channels are tetrameres <xref ref-type="bibr" rid="pcbi.1000870-Nucifora1">[38]</xref>. A single channel opens and closes in dependence on binding and dissociation of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e033" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e034" xlink:type="simple"/></inline-formula> to the binding sites of its subunits (see below). An open channel conducts a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e035" xlink:type="simple"/></inline-formula> current from the ER into the cytosol which is due to the huge concentration difference of up to 4 orders of magnitude across the ER membrane.</p>
<fig id="pcbi-1000870-g001" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.g001</object-id><label>Figure 1</label><caption>
<title>IP<sub>3</sub>R properties and clustering generate a hierarchical system.</title>
<p><bold>A</bold>: <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e036" xlink:type="simple"/></inline-formula> form channel clusters (green dots) that are randomly scattered across the membrane of the ER and separated by 1 to 7 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e037" xlink:type="simple"/></inline-formula> in the cell. <bold>B</bold>: Compared with inter-cluster distances, channels (orange) within a cluster are tightly packed in the ER membrane and are strongly coupled by <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e038" xlink:type="simple"/></inline-formula> (red). Channels within a cluster are lumped into one source term (green sphere) with radius <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e039" xlink:type="simple"/></inline-formula>, which depends on the number of open channels (see text). <bold>C</bold>: Single <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e040" xlink:type="simple"/></inline-formula> consist of four subunits the dynamics of which is described by the DeYoung-Keizer model. The 8 subunit states form a cube and subunit state transitions correspond to the edges. <bold>D</bold>: The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e041" xlink:type="simple"/></inline-formula> dependent activation and inhibition of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e042" xlink:type="simple"/></inline-formula> are key elements of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e043" xlink:type="simple"/></inline-formula> induced <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e044" xlink:type="simple"/></inline-formula> release. Combined with the spatial clustering, the resulting hierarchical structure transforms fast fluctuating single channel dynamics (blips) first into locally amplified cluster signals (puffs) and then into cellular release spikes. (Local concentrations are determined 10 nm apart from the release site.)</p>
</caption><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.g001" xlink:type="simple"/></fig>
<p><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e045" xlink:type="simple"/></inline-formula> form clusters on the membrane of the ER consisting of 1 to 10 channels <xref ref-type="bibr" rid="pcbi.1000870-Smith1">[33]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-TaufiqUrRahman1">[35]</xref>. They physically interact within a cluster and are consequently separated by a few nanometers only <xref ref-type="bibr" rid="pcbi.1000870-TaufiqUrRahman1">[35]</xref>. The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e046" xlink:type="simple"/></inline-formula> in a cluster are strongly coupled by the large local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e047" xlink:type="simple"/></inline-formula> concentration close to open channels.</p>
<p>Typical inter-cluster distances found experimentally are in the range of 1–7 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e048" xlink:type="simple"/></inline-formula> <xref ref-type="bibr" rid="pcbi.1000870-Tateishi1">[39]</xref>. <xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1A</xref> shows a representative example of cluster arrangement used in simulations. Due to cytosolic buffers and SERCAs, the local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e049" xlink:type="simple"/></inline-formula> concentrations close to an open channel cluster exhibit large gradients such that coupling between clusters is weak compared to intra-cluster coupling. This leads to the hierarchical organization of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e050" xlink:type="simple"/></inline-formula> signals. Stochastic opening of a single channel (blip) is locally amplified by CICR leading to a puff (<xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1B and D</xref>). The concentration gradients keep the probability for activation of adjacent clusters small and only a fraction of puffs activates several neighboring clusters. Once a supercritical number of open clusters is reached, more of them open forming a global signal. In that way, the triggering random opening of a single <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e051" xlink:type="simple"/></inline-formula> is carried up to the macroscopic scale. The mechanism transforms the fast noise of channel state changes on a millisecond time scale into fluctuations of interspike intervals of tens of seconds as shown in <xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1D</xref>.</p>
<p>An early and widely used channel state model is the DeYoung-Keizer model <xref ref-type="bibr" rid="pcbi.1000870-DeYoung1">[40]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Sneyd1">[41]</xref>. It assumes independent subunit dynamics and allocates three binding sites to each subunit as shown in <xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1C</xref>. One site for <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e052" xlink:type="simple"/></inline-formula> and one for <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e053" xlink:type="simple"/></inline-formula> that cooperatively activate the subunit. Another binding site with lower affinity for <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e054" xlink:type="simple"/></inline-formula> inhibits the subunit dominantly. These two different affinities lead to a biphasic dependence of the stationary open probability on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e055" xlink:type="simple"/></inline-formula> concentration (see Figure 1 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). Only the state <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e056" xlink:type="simple"/></inline-formula> out of the 8 possible subunit states <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e057" xlink:type="simple"/></inline-formula> corresponds to an active subunit (<xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1C</xref>), where the first index refers to the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e058" xlink:type="simple"/></inline-formula> binding and is 1, if <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e059" xlink:type="simple"/></inline-formula> is bound and 0 otherwise. Analogously, the second and third index describe <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e060" xlink:type="simple"/></inline-formula> binding to the activating and inhibiting site, respectively. A channel opens, if at least 3 subunits are in the active state.</p>
<p>The 12 possible transitions between the 8 subunit states correspond to transitions in a state scheme forming a cube (<xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1C</xref>). Some of the transition probabilities depend on the local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e061" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e062" xlink:type="simple"/></inline-formula> concentrations (Figure 1 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). In simulations, the transitions are realized by a hybrid deterministic-stochastic algorithm <xref ref-type="bibr" rid="pcbi.1000870-Rdiger1">[42]</xref>, which uses the local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e063" xlink:type="simple"/></inline-formula> concentrations and the dissociation rates and binding rate constants given in Table 1 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>.</p>
<p>Since <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e064" xlink:type="simple"/></inline-formula> within one cluster are close to each other, a cluster can be approximated by one spatial <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e065" xlink:type="simple"/></inline-formula>-source for the purpose of simulating the cluster current in the long range cellular dynamics. The current depends on the number of open channels <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e066" xlink:type="simple"/></inline-formula>, the time course of which comes out of the stochastic simulation of channel states. It is proportional to the concentration difference <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e067" xlink:type="simple"/></inline-formula> across the ER membrane at the location of the channel molecule. Hence, we actually need to solve the complete reaction-diffusion problem to determine it. But the concentration difference at the cluster is not well defined with a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e068" xlink:type="simple"/></inline-formula>-source term. Therefore, we calculate the cluster current using a spatially extended cluster with radius <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e069" xlink:type="simple"/></inline-formula> as described in detail in Ref. <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref>. The solution of that problem converges within fractions of a millisecond to its stationary state in the range of the channel molecule <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref>. That part of the solution is all we need to calculate the current of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e070" xlink:type="simple"/></inline-formula>th cluster. Using the stationary concentration profiles we obtain:<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e071" xlink:type="simple"/><label>(1)</label></disp-formula>with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e072" xlink:type="simple"/></inline-formula> where <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e073" xlink:type="simple"/></inline-formula> denotes the channel flux constant. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e074" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e075" xlink:type="simple"/></inline-formula> are the diffusion coefficients of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e076" xlink:type="simple"/></inline-formula> in the ER and the cytosol. The cluster radius <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e077" xlink:type="simple"/></inline-formula> depends on the number of open channels <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e078" xlink:type="simple"/></inline-formula> and the single channel radius <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e079" xlink:type="simple"/></inline-formula>. The advantage of the approximation is that it takes local ER depletion into account but only depends on the the spatially averaged concentrations <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e080" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e081" xlink:type="simple"/></inline-formula>, which form the boundary conditions for the local quasi-static approximation (see <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref> for details). If channel distances within a cluster are of the order of magnitude of the diffusion length of free <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e082" xlink:type="simple"/></inline-formula>, the internal cluster geometry becomes relevant. In that case, several <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e083" xlink:type="simple"/></inline-formula>-functions can be used for one cluster.</p>
<p>The approximation allows as well for determination of the local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e084" xlink:type="simple"/></inline-formula> concentration at an open channel cluster resulting from its own current (1) as<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e085" xlink:type="simple"/><label>(2)</label></disp-formula>the validity of which had been shown for the buffer concentrations used here <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref>. Note that the total concentration at a cluster is the sum of the concentration (2) and the concentrations induced by currents of other open channel clusters. After closing, the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e086" xlink:type="simple"/></inline-formula> concentration is determined by the cellular concentration dynamics (see below) 10 nm apart from the release site.</p>
</sec><sec id="s2c">
<title>Cellular concentration dynamics</title>
<p>The modelling strategy for the cellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e087" xlink:type="simple"/></inline-formula> dynamics is based on the separation of two length scales. On the microscopic scale of channel clusters, we use a detailed and stochastic channel model to determine local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e088" xlink:type="simple"/></inline-formula> currents. On the macroscopic scale of the cell, we use a linearized spatial bi-domain model, and Green's function to integrate it. The microscopic scale determines the currents representing the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e089" xlink:type="simple"/></inline-formula> sources of the macroscopic scale. We implement ideas proposed in <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref> and use the currents <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e090" xlink:type="simple"/></inline-formula> of Eq. (1) as the amplitudes of the spatial <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e091" xlink:type="simple"/></inline-formula>-functions representing the cluster source terms in Eqs. (3). A similar approach was taken by Solovey <italic>et al.</italic> <xref ref-type="bibr" rid="pcbi.1000870-Solovey1">[44]</xref>. We circumvent the concentration divergence at <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e092" xlink:type="simple"/></inline-formula>-function sources by using Eq. (2) for the value of the local concentration at open clusters. Vice versa, the macroscopic scale affects the concentration values entering the transition rates of the microscopic state schemes.</p>
<p>The ER is a tubular network spreading throughout the cell <xref ref-type="bibr" rid="pcbi.1000870-Roderick1">[45]</xref>. Diffusion in such a geometry can be described by diffusion in unrestricted space with a decreased diffusion coefficient <xref ref-type="bibr" rid="pcbi.1000870-lveczky1">[46]</xref>. Subsequently, we can superimpose the ER and the cytosol leading to a bi-domain model. Due to the quasi-static approximation (Eq. 1), we do not need to determine the spatially resolved concentration in the ER. Lumenal and cytosolic domains are coupled by a homogeneous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e093" xlink:type="simple"/></inline-formula> leak flux <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e094" xlink:type="simple"/></inline-formula> through the ER membrane, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e095" xlink:type="simple"/></inline-formula> re-uptake <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e096" xlink:type="simple"/></inline-formula> of the ER by SERCA pumps and by the stochastic channel currents <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e097" xlink:type="simple"/></inline-formula>. Within the cytosol we take free <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e098" xlink:type="simple"/></inline-formula>, one mobile buffer <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e099" xlink:type="simple"/></inline-formula> and one immobile buffer <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e100" xlink:type="simple"/></inline-formula> with the total concentrations <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e101" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e102" xlink:type="simple"/></inline-formula> into account leading to the reaction diffusion equations<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e103" xlink:type="simple"/><label>(3a)</label></disp-formula><disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e104" xlink:type="simple"/><label>(3b)</label></disp-formula><disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e105" xlink:type="simple"/><label>(3c)</label></disp-formula>where we used buffer conservation and linear pump and leak fluxes with the flux constants <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e106" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e107" xlink:type="simple"/></inline-formula>. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e108" xlink:type="simple"/></inline-formula> is the stochastic channel cluster current of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e109" xlink:type="simple"/></inline-formula>th cluster with strength defined by Equation (1).</p>
<p>Scaling concentrations, space and time with typical values reveals the number of independent parameters. It entails the definitions of <xref ref-type="table" rid="pcbi-1000870-t002">Table 2</xref>. We linearize Eqs. (3), since we would like to use Green's function to solve them. Our parameter values are in the range of the applicability of the linearization to the buffer dynamics as described by Smith <italic>et al.</italic> <xref ref-type="bibr" rid="pcbi.1000870-Smith3">[47]</xref> for the stationary profiles. We additionally have linearized the pump dynamics. The linearization does not exhibit saturation, which is relevant for calcium concentrations above <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e110" xlink:type="simple"/></inline-formula>, with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e111" xlink:type="simple"/></inline-formula> being the dissociation constant of the pump (Figure 2 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). These concentrations occur close to open clusters. In that area, the dynamics are dominated by the diffusion term and the channel term, which reduces the relative error due to the linearization of pump and buffer rates substantially. However, if precise knowledge of concentration values close to open channels or clusters is required, the complete non-linear reaction diffusion equations must be solved like e.g. in <xref ref-type="bibr" rid="pcbi.1000870-Rdiger1">[42]</xref>. The scaled linear reaction diffusion system (<xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>) describes the spatially resolved concentration dynamics by:<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e112" xlink:type="simple"/><label>(4a)</label></disp-formula><disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e113" xlink:type="simple"/><label>(4b)</label></disp-formula><disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e114" xlink:type="simple"/><label>(4c)</label></disp-formula>where the leak flux depends on the average lumenal concentration, only. All the reaction rate constants depend on the resting state concentration <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e115" xlink:type="simple"/></inline-formula>, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e116" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e117" xlink:type="simple"/></inline-formula> due to the linearization: <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e118" xlink:type="simple"/></inline-formula>, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e119" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e120" xlink:type="simple"/></inline-formula>. For simplicity we subsumed also <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e121" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e122" xlink:type="simple"/></inline-formula> under <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e123" xlink:type="simple"/></inline-formula>.</p>
<p>The cytosolic concentrations <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e124" xlink:type="simple"/></inline-formula> are determined by the 3-component Green's function with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e125" xlink:type="simple"/></inline-formula> clusters localized at <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e126" xlink:type="simple"/></inline-formula> (see also Figure 3 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>)<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e127" xlink:type="simple"/><label>(5)</label></disp-formula>with the Bessel function of the first kind <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e128" xlink:type="simple"/></inline-formula> and the Legendre polynomial <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e129" xlink:type="simple"/></inline-formula>, where <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e130" xlink:type="simple"/></inline-formula> is the angle between the source location <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e131" xlink:type="simple"/></inline-formula> and the point <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e132" xlink:type="simple"/></inline-formula> given by<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e133" xlink:type="simple"/><label>(6)</label></disp-formula></p>
<p>The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e134" xlink:type="simple"/></inline-formula> are determined by the boundary conditions at the plasma membrane (see <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>).</p>
<p>The three-component response functions <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e135" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e136" xlink:type="simple"/></inline-formula> include the time integration over the source history, i.e. the time dependent channel flux strength <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e137" xlink:type="simple"/></inline-formula>, and take the buffer reactions as well as the coupling with the ER into account:<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e138" xlink:type="simple"/><label>(7a)</label></disp-formula><disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e139" xlink:type="simple"/><label>(7b)</label></disp-formula>with the dimensionless cell radius <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e140" xlink:type="simple"/></inline-formula> and the normalization factors <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e141" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e142" xlink:type="simple"/></inline-formula> given in the <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>. The coupling between the cytosol and the ER by <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e143" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e144" xlink:type="simple"/></inline-formula> as well as the reaction rates of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e145" xlink:type="simple"/></inline-formula> with the two buffers determine the time constants <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e146" xlink:type="simple"/></inline-formula> of the response functions (0), which are implicitly given by the roots of the determinant of the coupling matrix<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e147" xlink:type="simple"/><label>(8)</label></disp-formula></p>
<p>The method allows for spatially resolved concentration dynamics as shown in <xref ref-type="fig" rid="pcbi-1000870-g002">Figure 2</xref> and in the <xref ref-type="supplementary-material" rid="pcbi.1000870.s002">Video S1</xref> by an iso-concentration surface of 2 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e148" xlink:type="simple"/></inline-formula>. An initially opening cluster increases the open probability of adjacent <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e149" xlink:type="simple"/></inline-formula> clusters and release is spreading through the cell until inhibition stops release.</p>
<fig id="pcbi-1000870-g002" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.g002</object-id><label>Figure 2</label><caption>
<title>Spatially resolved Ca<sup>2+</sup> dynamics.</title>
<p>An initial puff induces <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e150" xlink:type="simple"/></inline-formula> release of adjacent clusters by diffusion and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e151" xlink:type="simple"/></inline-formula> induced <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e152" xlink:type="simple"/></inline-formula> release leading to a global <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e153" xlink:type="simple"/></inline-formula> spike. The puff to spike transition is visualized by the iso-concentration surface of 2 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e154" xlink:type="simple"/></inline-formula> during a spike. Time is indicated on the panels (see <xref ref-type="supplementary-material" rid="pcbi.1000870.s002">Video S1</xref>).</p>
</caption><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.g002" xlink:type="simple"/></fig>
<p>For the global <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e155" xlink:type="simple"/></inline-formula> dynamics, the average concentrations are obtained by spatial integration of the analytical solution (9) as<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e156" xlink:type="simple"/><label>(9)</label></disp-formula>where <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e157" xlink:type="simple"/></inline-formula> denotes the cell radius. The first component of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e158" xlink:type="simple"/></inline-formula> describes the cytosolic average concentration <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e159" xlink:type="simple"/></inline-formula>. With this, the lumenal average <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e160" xlink:type="simple"/></inline-formula> concentration <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e161" xlink:type="simple"/></inline-formula> in dimensionless units is determined by<disp-formula><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e162" xlink:type="simple"/><label>(10)</label></disp-formula>which takes into account the leak, pump and channel fluxes, and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e163" xlink:type="simple"/></inline-formula> is the volume ratio <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e164" xlink:type="simple"/></inline-formula> of the cytosol and the ER. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e165" xlink:type="simple"/></inline-formula> denotes the equilibrium average lumenal concentration at <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e166" xlink:type="simple"/></inline-formula>. The difference between the average cytosolic and lumenal concentration <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e167" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e168" xlink:type="simple"/></inline-formula> determines the cluster current according to Eq. (1) (see <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>).</p>
<p>The two main approximations of our method are the local quasi-static approximation and the linearization of the passive bulk processes. These assumptions do not allow for a precise study of the intra-cluster concentration dynamics. That can be done with finite element methods like in ref. <xref ref-type="bibr" rid="pcbi.1000870-Rdiger1">[42]</xref>. The structure of the Green's function solution enables an elegant parallel algorithm that we call the Green's cell. It is orders of magnitude faster than finite element methods and able to simulate long lasting whole cell dynamics in feasible computing time. In the Green's cell algorithm the actual concentration of each cluster is calculated with the Green's function and local quasi-static approximation in dependence on the source history of all clusters by a single process. The concentrations are sent to the master process which determines the corresponding state transition and reaction time by the hybrid algorithm and also calculates the average concentrations. The transition times are re-distributed to the cluster processes where they are used to update the concentrations. For further details see Figure 4 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>.</p>
</sec><sec id="s2d">
<title>Stochasticity in measured and simulated Ca<sup>2+</sup> signals</title>
<p>Our recent experimental investigation started from the assumption of a random spike generation by wave nucleation followed by a deterministic refractory time. This prediction yields in a linear dependence of the standard deviation on the average period which was also experimentally confirmed <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. Previous studies report a possible feedback of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e169" xlink:type="simple"/></inline-formula> on PKC activity in glutamate stimulated rat astrocytes <xref ref-type="bibr" rid="pcbi.1000870-Codazzi1">[48]</xref>–<xref ref-type="bibr" rid="pcbi.1000870-Pasti1">[50]</xref>. This may lead to a positive feedback on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e170" xlink:type="simple"/></inline-formula> level by activation of PLC<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e171" xlink:type="simple"/></inline-formula>. The measured relation between standard deviation and average of interspike intervals for spontaneous spiking has a slope equal to 1 <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>, demonstrating that spike generation is poissonian and the spike generation probability is constant on the time scale of ISI. Clearly, there is no feedback on that time scale.</p>
<p>To show that the experimental findings are indeed consistent with our ideas of spike generation, we use our modelling tool to study how molecular noise of single channels can be translated into global signals and whether it is sufficient to cause the observed randomness of spike sequences. <xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3A</xref> shows an example of single cell measurements, where the upper panel exhibits the fluorescent signal <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e172" xlink:type="simple"/></inline-formula> related to the cytosolic <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e173" xlink:type="simple"/></inline-formula> concentration and the lower panel the individual ISIs. It demonstrates the stochasticity of spiking, since variations in ISIs are in the range of their average. Simulations of a cell with 47 clusters each containing a random number of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e174" xlink:type="simple"/></inline-formula> between 4 and 16 exhibit a behavior very similar to experiments showing that single channel noise can lead to time varying ISIs, since there are not any other sources of noise in the simulations (<xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3B and C</xref>). The simulated <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e175" xlink:type="simple"/></inline-formula> oscillations exhibit in accordance with experimental observations different flavors ranging from rare and irregular spiking to fast and more periodic spiking. The standard deviation <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e176" xlink:type="simple"/></inline-formula> depends linearly on the average period <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e177" xlink:type="simple"/></inline-formula> <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. Recently we have shown that this linear dependence is not a self-evident relation <xref ref-type="bibr" rid="pcbi.1000870-Skupin2">[51]</xref>. In particular, it was found that self-sustained oscillatory systems exhibit a different relation than the one observed in <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e178" xlink:type="simple"/></inline-formula> spiking experiments. The dependence of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e179" xlink:type="simple"/></inline-formula> on <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e180" xlink:type="simple"/></inline-formula> obtained here in simulations is shown in <xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3D</xref> and exhibits a linear dependence with a slope of 1 which was found in experiments for spontaneous oscillations <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Skupin3">[52]</xref>. The offset of the regression line on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e181" xlink:type="simple"/></inline-formula> -axis of about 20 s is the deterministic recovery time.</p>
<fig id="pcbi-1000870-g003" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.g003</object-id><label>Figure 3</label><caption>
<title>Stochasticity of Ca<sup>2+</sup> oscillations.</title>
<p><bold>A</bold>: An experimental example of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e182" xlink:type="simple"/></inline-formula> oscillations in an astrocyte. The varying ISIs demonstrate the stochasticity of spiking. <bold>B,C</bold>: Simulations of the cellular <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e183" xlink:type="simple"/></inline-formula> dynamics of a cell with 47 clusters each having a random number of channels between 4 and 16 for different <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e184" xlink:type="simple"/></inline-formula> base level <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e185" xlink:type="simple"/></inline-formula> concentrations and the standard parameters given in <xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref>. For a low <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e186" xlink:type="simple"/></inline-formula> base level of 30 nM spiking is rather slow and irregular (B). For an increased <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e187" xlink:type="simple"/></inline-formula> base level of 50 nM spiking becomes faster and more regular (C). <bold>D</bold>: The simulated <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e188" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e189" xlink:type="simple"/></inline-formula> relation, where dots correspond to spike trains of single cells having different <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e190" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e191" xlink:type="simple"/></inline-formula> concentration (see Figure 5 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>), is in accordance with the experimentally observed one <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref> supporting the wave nucleation mechanism. <bold>E,F</bold>: The dependence of the average period <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e192" xlink:type="simple"/></inline-formula> on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e193" xlink:type="simple"/></inline-formula> concentration and the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e194" xlink:type="simple"/></inline-formula> resting concentration obtained in simulations show that regular spiking is more likely if one concentration is high.</p>
</caption><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.g003" xlink:type="simple"/></fig></sec><sec id="s2e">
<title>Dependence on IP<sub>3</sub> and Ca<sup>2+</sup> concentrations</title>
<p>The different <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e195" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e196" xlink:type="simple"/></inline-formula> data points in <xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3D</xref> result from different combinations of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e197" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e198" xlink:type="simple"/></inline-formula> base level concentrations, which are both parameters in the model. <italic>In vivo</italic> the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e199" xlink:type="simple"/></inline-formula> concentration is related to the stimulation level by activation of Phospholipase C and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e200" xlink:type="simple"/></inline-formula> production. The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e201" xlink:type="simple"/></inline-formula> base level is determined by the leak and the pump flux through the ER membrane. In simulations, we adjust the leak flux according to <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e202" xlink:type="simple"/></inline-formula> and the pump strength. If both concentrations are rather high in the range of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e203" xlink:type="simple"/></inline-formula> no spiking occurs since channels are activated as soon as they are in the excitable state (Figure 5 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). We observe fast and regular spiking (Figure 3C,E and F and Figure 5 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>) for intermediate concentrations. The ISIs have a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e204" xlink:type="simple"/></inline-formula> close to the deterministic refractory time, since a new spike is initiated as soon as the recovery time has elapsed. Regular spiking corresponds to cells with small <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e205" xlink:type="simple"/></inline-formula> in <xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3D</xref>. A further decrease in one of the concentrations increases <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e206" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e207" xlink:type="simple"/></inline-formula>, in a way depending on the other concentration (<xref ref-type="fig" rid="pcbi-1000870-g003">Figure 3B,E and F</xref>). If both concentrations are small, global spiking vanishes and the signal consists of uncorrelated blips.</p>
</sec><sec id="s2f">
<title>Different Ca<sup>2+</sup> signals in dependence on physiologic parameters</title>
<p>In the previous analysis of the dependence of oscillations on the concentrations, we have already seen that the modelling tool can generate a large spectrum of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e208" xlink:type="simple"/></inline-formula> signals ranging from stochastic spiking to almost periodic oscillations. Here, we show that the model can produce all known <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e209" xlink:type="simple"/></inline-formula> -induced forms of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e210" xlink:type="simple"/></inline-formula> signals in dependence on physiologic parameters. <xref ref-type="fig" rid="pcbi-1000870-g004">Figure 4</xref> exhibits different experimental signal forms and the corresponding simulation results for a cell with 32 clusters. The variety of signals is achieved by varying cell parameters leading to distinct cell responses as shown by the behavior of open channels (black) and number of inhibited subunits (magenta) as well as by the resulting average <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e211" xlink:type="simple"/></inline-formula> concentration in the cytosol (red) and in the ER (blue). Fast and rather regular oscillations occur by the interplay of activation and inhibition leading to array enhanced coherence resonance as was hypothesized before <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. This can be seen in the behavior of the channel state dynamics. The number of inhibited subunits (magenta) increases dramatically during a spike and finally inhibition terminates it (<xref ref-type="fig" rid="pcbi-1000870-g004">Figure 4A</xref>). In the following the number of inhibited subunits relaxes slowly towards its resting level. Only very few channels open directly after a spike and these openings do not initiate a new spike, since the number of inhibited subunits is still to high (higher than approximately 220). That causes the deterministic time <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e212" xlink:type="simple"/></inline-formula> also observed experimentally <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Skupin3">[52]</xref>. But a spike occurs very soon after the number of inhibited subunits has fallen below a critical range since the open probability is rather high with these parameter values. That keeps the stochastic part of the ISI small and spike sequences regular. Moreover, the amplitude of the spike of open channels seems to be smaller, if the spike is initiated at times where the number of inhibited subunits is still high.</p>
<fig id="pcbi-1000870-g004" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.g004</object-id><label>Figure 4</label><caption>
<title>Spontaneous Ca<sup>2+</sup> signals in individual astrocytes measured under identical conditions (upper row) and simulations of a cell with 32 clusters with different parameters (red line, middle row) exhibit good agreement in the cytosolic Ca<sup>2+</sup> concentration.</title>
<p>The parameter changes between the simulations account for the variability of the cells in the experiment. The lumenal concentration is shown in blue (middle row). The channel dynamics (lower row) is shown as the number of open channels (black) and inhibited subunits (magenta). <bold>A</bold>: Fast and regular spiking occurs by array enhanced coherence resonance where the simulated cell spikes as soon as enough channels are in the excitable state again. Spikes occur before the cell reaches its resting state as can be seen from the time course of the fraction of inhibited subunits. This is caused in simulations by a high <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e213" xlink:type="simple"/></inline-formula> base level concentration <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e214" xlink:type="simple"/></inline-formula> nM and a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e215" xlink:type="simple"/></inline-formula> concentration of 0.12 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e216" xlink:type="simple"/></inline-formula>. <bold>B</bold>: Spontaneous oscillations exhibit often a more irregular spiking. This is achieved in simulation for the same cellular setup as in A by a <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e217" xlink:type="simple"/></inline-formula> base level concentration of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e218" xlink:type="simple"/></inline-formula> nM, which is lower than the standard value of 50 nM (<xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref>). That decreases the probabilities for an initial event and spikes compared to panel A. The cell reaches the resting state before some of the spikes. <bold>C</bold>: A bursting like behavior is observed for decreased SERCA activity (<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e219" xlink:type="simple"/></inline-formula>) in simulations, since <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e220" xlink:type="simple"/></inline-formula> remains longer in the cytosol. <bold>D</bold>: For a even smaller SERCA activity of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e221" xlink:type="simple"/></inline-formula>, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e222" xlink:type="simple"/></inline-formula> signals obtained in simulations exhibit plateau responses with superimposed oscillations which are also found in experiments. Simulation parameters are given in <xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref> if not stated here.</p>
</caption><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.g004" xlink:type="simple"/></fig>
<p>We find longer and more irregular ISIs for decreased <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e223" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e224" xlink:type="simple"/></inline-formula> base level concentrations, since the probability of a channel opening is decreased. As a consequence, the cell relaxes to a resting state between spikes with only a few inhibited subunits (<xref ref-type="fig" rid="pcbi-1000870-g004">Figure 4B</xref>). The spike amplitudes of both the number of open channels and of the average <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e225" xlink:type="simple"/></inline-formula> concentration are slightly increased compared to the regular spiking.</p>
<p>SERCA pumps also shape <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e226" xlink:type="simple"/></inline-formula> signals. Recent studies have shown that different phenotypes of cloned cells with regard to <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e227" xlink:type="simple"/></inline-formula> signalling occur due to small variations in SERCA expression levels and activity of RyR <xref ref-type="bibr" rid="pcbi.1000870-Nakumura1">[4]</xref>. Here, we find that a decreased SERCA activity leads to a burst like behavior (<xref ref-type="fig" rid="pcbi-1000870-g004">Figure 4C</xref>), since <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e228" xlink:type="simple"/></inline-formula> is removed slower from the cytosol and thus can activate channels which have recovered early from inhibition or channels which have not been activated before.</p>
<p>For even smaller SERCA activity, cells exhibit long lasting plateau <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e229" xlink:type="simple"/></inline-formula> signals often with superimposed oscillations (<xref ref-type="fig" rid="pcbi-1000870-g004">Figure 4D</xref>). In these cases, released <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e230" xlink:type="simple"/></inline-formula> stays within the cytosol and reactivates <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e231" xlink:type="simple"/></inline-formula> again and again. Cooperativeness induced by inhibition leads to superimposed oscillations on the high <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e232" xlink:type="simple"/></inline-formula> level. The panels of <xref ref-type="fig" rid="pcbi-1000870-g004">Fig. 4</xref> provide also an idea of cell variability within one cell type and even within one experiment.</p>
</sec><sec id="s2g">
<title>Increased randomness by Ca<sup>2+</sup> buffers</title>
<p>A direct consequence of the diffusion mediated signal mechanism is the dependence on the strength of spatial coupling by <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e233" xlink:type="simple"/></inline-formula> diffusion. That coupling strength can be modulated by exogenous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e234" xlink:type="simple"/></inline-formula> buffers, since they reduce the diffusion length of free <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e235" xlink:type="simple"/></inline-formula>. We took advantage of this property of buffers to demonstrate the spatial character of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e236" xlink:type="simple"/></inline-formula> oscillations <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. Note that we used concentrations of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e237" xlink:type="simple"/></inline-formula> buffers much smaller than usually applied in order to suppress any kind of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e238" xlink:type="simple"/></inline-formula> signal. We measured spiking for several minutes to obtain reference values for ISIs, loaded additional buffer and continued measuring (see <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5A</xref>). The individual ISIs (blue crosses) are increased and exhibit a larger variability after buffer loading.</p>
<fig id="pcbi-1000870-g005" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.g005</object-id><label>Figure 5</label><caption>
<title>Buffers render spiking more irregular by decreasing spatial coupling.</title>
<p><bold>A</bold>: Astrocytes were measured several minutes for reference values (red) before loading with 20 nM BAPTA-AM during the break and restarting the measurement (blue). Fast and regular spiking is shifted to a slower and more irregular one. <bold>B</bold>: Simulation of a cell containing 32 clusters with two different EGTA concentrations shown in red and blue respectively exhibit an analogous behavior. <bold>C</bold>: An increase of 10 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e239" xlink:type="simple"/></inline-formula> EGTA increases <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e240" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e241" xlink:type="simple"/></inline-formula> for a population of simulated cells with different cell properties, very similar to experimental observations. <bold>D</bold>: <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e242" xlink:type="simple"/></inline-formula> increases with increasing EGTA (magenta) and BAPTA (black) concentration for a given cell. The value of the increase depends on the single channel current. Squares correspond to 0.12 pA and dots to 1.2 pA. <bold>E</bold>: Corresponding <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e243" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e244" xlink:type="simple"/></inline-formula> dependence of simulations in panel D. BAPTA and EGTA lead to a similar <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e245" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e246" xlink:type="simple"/></inline-formula> dependence for the smaller current (squares), whereas the increased current decreases the slope to 0.6. <bold>F</bold>: A single channel current of 0.12 pA leads to a population slope <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e247" xlink:type="simple"/></inline-formula> of 1 rather independent of spatial arrangement of clusters (gray), stimulation strength (light red) and pump strength (light blue) where the population slopes arise due to 10 different buffer concentrations (<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e248" xlink:type="simple"/></inline-formula> simulations for each condition). For the larger current of 1.2 pA the slope decreases to 0.6 and is again relatively independent of other physiologic parameters. This may explain the experimentally observed cell specific slopes <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. Parameters used in simulations are given in <xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref> if not explicitly stated here.</p>
</caption><graphic mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.g005" xlink:type="simple"/></fig>
<p>To understand the experimental observation in more detail, we use simulations to analyze the response to additional buffer. Analogously to the experiment, we simulate a fixed cellular arrangement with different mobile buffer concentrations. <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5B</xref> shows a representative example, where the red and the blue parts correspond to 25 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e249" xlink:type="simple"/></inline-formula> and 250 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e250" xlink:type="simple"/></inline-formula> EGTA, respectively. Like in the experiment, larger buffer concentration leads to less and more irregular spiking. In the part with the higher buffer concentration, we observe isolated events which do not lead to global waves since coupling of clusters is too weak. These local events are rare in the reference measurements, since a triggering event initiates a global wave very likely.</p>
<p>From population simulations, where individual cells differ in their spatial arrangement of clusters, initial buffer and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e251" xlink:type="simple"/></inline-formula> base level concentrations, we obtain the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e252" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e253" xlink:type="simple"/></inline-formula> relation shown in <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5C</xref>, where cells are shifted by an increase of 10 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e254" xlink:type="simple"/></inline-formula> in the EGTA concentration. Similar to experiment <xref ref-type="bibr" rid="pcbi.1000870-Skupin3">[52]</xref>, cells exhibit individual increases of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e255" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e256" xlink:type="simple"/></inline-formula> with a slope of the shift close to 1 comparable with the population slopes for the two measuring periods.</p>
</sec><sec id="s2h">
<title>Influence of buffer kinetics</title>
<p>BAPTA and EGTA are common <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e257" xlink:type="simple"/></inline-formula> buffers to suppress <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e258" xlink:type="simple"/></inline-formula> signals and we have used both in experiments <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. Cells responded much more sensitive to BAPTA than to EGTA. BAPTA has much larger binding and dissociation rate constants than EGTA (<xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref>). A disadvantage of the experiment is that the buffer is loaded into a cell by its esterificated form and the total amount that has entered is unknown and difficult to control. Here, we use modelling to illuminate the influence of the different buffer kinetics and concentrations of EGTA and BAPTA.</p>
<table-wrap id="pcbi-1000870-t001" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.t001</object-id><label>Table 1</label><caption>
<title>Physiologic standard parameters used in simulation if not stated otherwise.</title>
</caption><!--===== Grouping alternate versions of objects =====--><alternatives><graphic id="pcbi-1000870-t001-1" mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.t001" xlink:type="simple"/><table><colgroup span="1"><col align="left" span="1"/><col align="center" span="1"/><col align="center" span="1"/></colgroup>
<tbody>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e259" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">10 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e260" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">cell radius <xref ref-type="bibr" rid="pcbi.1000870-CornellBell1">[62]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e261" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">8 nm</td>
<td align="left" colspan="1" rowspan="1">channel radius <xref ref-type="bibr" rid="pcbi.1000870-Suhara1">[63]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e262" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e263" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">diffusion coefficient of cytosolic <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e264" xlink:type="simple"/></inline-formula> <xref ref-type="bibr" rid="pcbi.1000870-Allbritton1">[64]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e265" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e266" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">estimated diffusion coefficient of lumenal <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e267" xlink:type="simple"/></inline-formula> <xref ref-type="bibr" rid="pcbi.1000870-Thul3">[65]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e268" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e269" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">diffusion coefficient of mobile buffer <xref ref-type="bibr" rid="pcbi.1000870-Jafri1">[66]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e270" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">50 nM</td>
<td align="left" colspan="1" rowspan="1">standard <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e271" xlink:type="simple"/></inline-formula> base level concentration <xref ref-type="bibr" rid="pcbi.1000870-Irvine1">[67]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1">[IP<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e272" xlink:type="simple"/></inline-formula>]</td>
<td align="left" colspan="1" rowspan="1">0.1 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e273" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">standard <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e274" xlink:type="simple"/></inline-formula> concentration <xref ref-type="bibr" rid="pcbi.1000870-Irvine1">[67]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e275" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e276" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">estimated pump rate constant <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e277" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e278" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">leak flux constant <xref ref-type="bibr" rid="pcbi.1000870-Meldolesi1">[68]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e279" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e280" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">channel flux constant <xref ref-type="bibr" rid="pcbi.1000870-Bentele1">[43]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e281" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">50 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e282" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">total mobile buffer concentration</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e283" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e284" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">capture rate of EGTA <xref ref-type="bibr" rid="pcbi.1000870-Pape1">[69]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e285" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e286" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dissociation rate of EGTA <xref ref-type="bibr" rid="pcbi.1000870-Pape1">[69]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e287" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e288" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">capture rate of BAPTA <xref ref-type="bibr" rid="pcbi.1000870-Richardson1">[70]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e289" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e290" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dissociation rate of BAPTA <xref ref-type="bibr" rid="pcbi.1000870-Richardson1">[70]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e291" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">30 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e292" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">total immobile buffer concentration</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e293" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e294" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">capture rate of the immobile buffer <xref ref-type="bibr" rid="pcbi.1000870-Richardson1">[70]</xref></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e295" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e296" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dissociation rate of the immobile buffer <xref ref-type="bibr" rid="pcbi.1000870-Richardson1">[70]</xref></td>
</tr>
</tbody>
</table></alternatives><table-wrap-foot><fn id="nt101"><label/><p>The definitions for the dissociation constants read <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e297" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e298" xlink:type="simple"/></inline-formula>.</p></fn></table-wrap-foot></table-wrap><table-wrap id="pcbi-1000870-t002" position="float"><object-id pub-id-type="doi">10.1371/journal.pcbi.1000870.t002</object-id><label>Table 2</label><caption>
<title>Definition of scaling factors and non-dimensional parameters.</title>
</caption><!--===== Grouping alternate versions of objects =====--><alternatives><graphic id="pcbi-1000870-t002-2" mimetype="image" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.t002" xlink:type="simple"/><table><colgroup span="1"><col align="left" span="1"/><col align="center" span="1"/><col align="center" span="1"/></colgroup>
<tbody>
<tr>
<td align="left" colspan="3" rowspan="1">Rescaling of time and space</td>
</tr>
<tr>
<td align="left" colspan="2" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e299" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">scaling time t with reaction time <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e300" xlink:type="simple"/></inline-formula></td>
</tr>
<tr>
<td align="left" colspan="2" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e301" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">scaling space r with diffusion length <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e302" xlink:type="simple"/></inline-formula></td>
</tr>
<tr>
<td align="left" colspan="3" rowspan="1">Dimensionless parameter definition</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e303" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e304" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dimensionless free <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e305" xlink:type="simple"/></inline-formula> concentration</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e306" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e307" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dimensionless free mobile buffer concentration</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e308" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e309" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dimensionless free immobile buffer concentration</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e310" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e311" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dimensionless free <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e312" xlink:type="simple"/></inline-formula> concentration within the ER</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e313" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e314" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">ratio of the diffusion coefficients</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e315" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e316" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">time separation of the mobile buffer</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e317" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e318" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">time separation of the immobile buffer</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e319" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e320" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">ratio of buffer influence</td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e321" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e322" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">scaled fluxes of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e323" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e324" xlink:type="simple"/></inline-formula></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e325" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e326" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">scaled channel cluster current <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e327" xlink:type="simple"/></inline-formula></td>
</tr>
<tr>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e328" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1"><inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e329" xlink:type="simple"/></inline-formula></td>
<td align="left" colspan="1" rowspan="1">dissociation constants ratio of the mobile and immobile buffer</td>
</tr>
</tbody>
</table></alternatives></table-wrap>
<p><xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5D</xref> shows the dependence of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e330" xlink:type="simple"/></inline-formula> for fixed cell parameters on the buffer concentration in magenta for EGTA and in black for BAPTA, where squares denote simulations with a single channel current of 0.12 pA and the dots correspond to 1.2 pA. The larger current was achieved by an increased lumenal <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e331" xlink:type="simple"/></inline-formula> concentration. Cells only differ in the buffer type. We see that increasing BAPTA has a stronger effect than EGTA, which is mainly caused by the larger capture rate. Moreover, we observe a nonlinear dependence of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e332" xlink:type="simple"/></inline-formula> on the buffer concentration. The nonlinearity explains the individual shifts of cells in the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e333" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e334" xlink:type="simple"/></inline-formula> plane shown <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5D</xref>. The comparison of the two different current strengths for BAPTA (black) indicates the role of spatial coupling. Higher currents lead to stronger coupling, and subsequently increasing buffer concentrations have a smaller effect on <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e335" xlink:type="simple"/></inline-formula>.</p>
</sec><sec id="s2i">
<title>Cell characteristics in dependence on single channel currents</title>
<p>From the buffer simulations, we can determine the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e336" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e337" xlink:type="simple"/></inline-formula> relation shown in <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5E</xref>. For the smaller currents, there is no qualitative difference between EGTA and BAPTA. Both exhibit a slope close to 1 as shown by the regression lines and an estimated deterministic time of 20 s. The simulations with higher cluster currents indicate a similar deterministic refractory period but the slope of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e338" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e339" xlink:type="simple"/></inline-formula> relation decreases to approximately 0.6. This might explain the experimentally found differences between cell types. Larger currents lead to stronger coupling on the macroscopic length scale and hence to smaller variations.</p>
<p>To confirm these findings and to test the dependency of the slope on other parameters, we analyze spiking of cells for the two different single channel currents. In each simulation set the cells have identical properties and differ only with respect to the buffer content leading to the distinct <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e340" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e341" xlink:type="simple"/></inline-formula> values in <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5E</xref> (see also Section 6 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). From these values we determine the population slopes <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e342" xlink:type="simple"/></inline-formula>. <xref ref-type="fig" rid="pcbi-1000870-g005">Figure 5F</xref> shows <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e343" xlink:type="simple"/></inline-formula> averaged over different spatial arrangements, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e344" xlink:type="simple"/></inline-formula> concentrations (stimulation levels) and pump strengths (see Figure 6 in <xref ref-type="supplementary-material" rid="pcbi.1000870.s001">Text S1</xref>). Analogously, we investigated <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e345" xlink:type="simple"/></inline-formula>, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e346" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e347" xlink:type="simple"/></inline-formula> (data not shown). The results are very similar to those with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e348" xlink:type="simple"/></inline-formula>. For smaller single channel current we obtain always a slope close to 1 when varying all 4 cell properties and for the larger current a slope to 0.6. Varying the buffer concentration, spatial arrangement of clusters, <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e349" xlink:type="simple"/></inline-formula> concentration or pump strength (within certain limits) does not change the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e350" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e351" xlink:type="simple"/></inline-formula> relation but only the position of the system on it.</p>
</sec></sec><sec id="s3">
<title>Discussion</title>
<p>We have presented here an efficient modelling concept for <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e352" xlink:type="simple"/></inline-formula> dynamics in 3 spatial dimensions. It simulates cell behavior starting from individual channels in full detail. Using Green's function and multiscale techniques allow for taking concentration gradients into account and thus for capturing the hierarchy of coupling strengths. The method can simulate up to 4000 seconds real time within 24 h on 8 CPUs for a cell with 32 clusters and 10 channels per cluster. In comparison to grid-based numerical methods, its main advantage is a gain of computational speed of several orders of magnitude, which enables us to simulate whole spike sequences. We demonstrate the potential of this modelling concept by simulating a variety of experiments. We compare the <italic>in silico</italic> data with time series obtained from spontaneous oscillations in cultured astrocytes, but several of the results will also apply to other cell types like those analyzed in <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>.</p>
<p>These recent experiments showed for 4 different cell types that the sequences of interspike intervals in <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e353" xlink:type="simple"/></inline-formula> signalling are random <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. In line with the ideas on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e354" xlink:type="simple"/></inline-formula> signalling mechanisms, we assumed single molecule state transitions to be a sufficient source of noise. We confirm this assumptions with our simulations here in which these state transitions are the only source of randomness. The fluctuations are carried up through the structural levels due to the existence of concentration gradients and hierarchies of coupling strength.</p>
<p>With our bottom-up modelling approach, we were able to generate all experimentally known <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e355" xlink:type="simple"/></inline-formula> signal types in dependence on physiologic parameters. Spiking exhibits the random ISI sequences observed experimentally with fast regular sequences and slow irregular ones. In particular, the dependency on parameters of spatial coupling observed in experiments is reproduced. We find a sigmoidal response of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e356" xlink:type="simple"/></inline-formula> concentration upon very strong stimulation or strong spatial coupling, which is well known as over stimulation. We observe also bursting. We do not compare our bursting simulations with specific experiments here, but we would like to mention a general aspect. This signal type is usually ascribed to the existence of a dynamic feedback like store depletion or inhibition of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e357" xlink:type="simple"/></inline-formula> production which terminates bursts. Such a feedback is not required with a stochastic model. The random length of bursts in our stochastic model offers also a simple explanation for the irregular burst length observed in experiments.</p>
<p>With our method we are able to follow the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e358" xlink:type="simple"/></inline-formula> dynamics from the molecular to the cellular level. The single molecule fluctuations determine the global behavior, since they initiate cellular signals. Simultaneously, the local rough channel signal is smoothed on the cell level by the hierarchical system due to diffusion. The universality and variety of signalling cross talks between <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e359" xlink:type="simple"/></inline-formula> signalling and other pathways render <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e360" xlink:type="simple"/></inline-formula> a potential source of noise in cellular systems. The fluctuations can be used for cell variability <xref ref-type="bibr" rid="pcbi.1000870-Nakumura1">[4]</xref> with regards to gene regulation <xref ref-type="bibr" rid="pcbi.1000870-Capite1">[53]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Cai1">[54]</xref> and cell differentiation <xref ref-type="bibr" rid="pcbi.1000870-Chang1">[3]</xref> and provides a flexibility to changing external conditions which is needed during evolution <xref ref-type="bibr" rid="pcbi.1000870-Reanney1">[55]</xref>.</p>
<sec id="s3a">
<title>The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e361" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e362" xlink:type="simple"/></inline-formula> relation and functional robustness</title>
<p>Both the experiments and simulations show a simple linear relation between the standard deviation of ISI <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e363" xlink:type="simple"/></inline-formula> and the average ISI <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e364" xlink:type="simple"/></inline-formula>. The existence of this linear relation turned out to be surprisingly robust. It survives even an increase of the single channel current by an order of magnitude. This relation describes for each individual cell the response to stimulation changes. Cells shift the spike pattern from slow and irregular to fast and regular along the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e365" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e366" xlink:type="simple"/></inline-formula> relation when we increase stimulation. That supplements the current ideas on frequency encoding <xref ref-type="bibr" rid="pcbi.1000870-Cai1">[54]</xref>, <xref ref-type="bibr" rid="pcbi.1000870-Dolmetsch1">[56]</xref>.</p>
<p>At the same time, the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e367" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e368" xlink:type="simple"/></inline-formula> relation describes the outcome of spiking experiments with a group of cells. In the experiments, we subjected a sample of cells to the same protocol, and we obtained as many different responses as there are cells in the sample <xref ref-type="bibr" rid="pcbi.1000870-Skupin1">[5]</xref>. That set of responses is not arbitrarily scattered across the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e369" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e370" xlink:type="simple"/></inline-formula> -plane but aligns along the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e371" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e372" xlink:type="simple"/></inline-formula> relation. All the variability among individual cells with respect to expression levels of pathway components, cell volume, ER volume, shape, ion concentration, etc. does not lead to severe deviations from this <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e373" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e374" xlink:type="simple"/></inline-formula> relation. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e375" xlink:type="simple"/></inline-formula> spiking is robust against variability of many pathway components in the sense that the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e376" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e377" xlink:type="simple"/></inline-formula> relation is robust. We learn from the simulations here, that it is rather the stochastic spike generation mechanism than control and regulation which provides for this robustness.</p>
<p>If we call the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e378" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e379" xlink:type="simple"/></inline-formula> relation from a single cell obtained by parameter changes individual relation and that obtained from a sample of cells population relation, we can describe our findings as identity of individual and population relation.</p>
<p>We could reproduce the variability within a population of cells in simulations by varying cluster array geometry, pump strength, stimulation or buffering conditions. Changing these parameter values simply shifted the system on the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e380" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e381" xlink:type="simple"/></inline-formula> relation and did not modify the relation. But changing the single channel current by one order of magnitude did change the slope of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e382" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e383" xlink:type="simple"/></inline-formula> relation.</p>
<p>That suggests a mathematical definition of robustness which accounts for the fact that cells should be able to execute certain functions (e.g. to spike with a range of ISI), but not necessarily at the same strength of stimulation or normalized values of other parameters. We denote with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e384" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e385" xlink:type="simple"/></inline-formula> two variables describing the function (e.g. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e386" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e387" xlink:type="simple"/></inline-formula>), and with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e388" xlink:type="simple"/></inline-formula>,…,<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e389" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e390" xlink:type="simple"/></inline-formula>,…,<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e391" xlink:type="simple"/></inline-formula> two sets of parameters (e.g. stimulation strength, temperature, cell volume). The relation between <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e392" xlink:type="simple"/></inline-formula> and <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e393" xlink:type="simple"/></inline-formula> is robust with respect to value changes of parameters <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e394" xlink:type="simple"/></inline-formula>, if it has the structure <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e395" xlink:type="simple"/></inline-formula>. The parameters <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e396" xlink:type="simple"/></inline-formula> change only the value of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e397" xlink:type="simple"/></inline-formula> while the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e398" xlink:type="simple"/></inline-formula> control also the properties of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e399" xlink:type="simple"/></inline-formula>, i.e. the properties of the pathway. We call this robustness of the function <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e400" xlink:type="simple"/></inline-formula> functional robustness (in difference to the robustness of the value of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e401" xlink:type="simple"/></inline-formula>). If we identify the stimulation strength with <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e402" xlink:type="simple"/></inline-formula>, all cells distinguished by the values of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e403" xlink:type="simple"/></inline-formula> only can realize frequency encoding with the same <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e404" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e405" xlink:type="simple"/></inline-formula> relation by varying <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e406" xlink:type="simple"/></inline-formula>. They can realize this function also by varying another <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e407" xlink:type="simple"/></inline-formula>-parameter or several of them: function and functional robustness are closely related.</p>
<p>The statement on robustness can also be interpreted with respect to identity of pathways converging onto <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e408" xlink:type="simple"/></inline-formula> spiking. <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e409" xlink:type="simple"/></inline-formula> signals can be caused by many different stimuli. The pathways upstream from <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e410" xlink:type="simple"/></inline-formula> responding to the stimuli must differ with respect to their value of the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e411" xlink:type="simple"/></inline-formula>, in order to be distinguishable by pathways downstream from <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e412" xlink:type="simple"/></inline-formula>.</p>
<p>In summary, cells realize frequency encoding - the function of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e413" xlink:type="simple"/></inline-formula> spiking - by mainly moving up and down the relation between standard deviation and average of ISI and to some degree by modulating the deterministic part of the ISI <xref ref-type="bibr" rid="pcbi.1000870-Skupin3">[52]</xref>. The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e414" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e415" xlink:type="simple"/></inline-formula> relation exists for a stochastic process only, since <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e416" xlink:type="simple"/></inline-formula> holds for deterministic systems. The <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e417" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e418" xlink:type="simple"/></inline-formula> relation turned out to be functionally robust with respect to changes of values of one set of parameters. That set may describe cell variability within one cell type or pathway. Changing substantially another set of parameters modified the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e419" xlink:type="simple"/></inline-formula>−<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e420" xlink:type="simple"/></inline-formula> relation. That set appears rather to specify the identity of pathways converging on <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e421" xlink:type="simple"/></inline-formula> spiking.</p>
</sec><sec id="s3b">
<title>The role of IP<sub>3</sub>R clusters for astrocyte Ca<sup>2+</sup> signalling</title>
<p>Our model predicts that close proximity of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e422" xlink:type="simple"/></inline-formula> clusters is a prerequisite for a spontaneous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e423" xlink:type="simple"/></inline-formula> response to spread throughout a cell. Indeed, there are types of astrocytes in which <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e424" xlink:type="simple"/></inline-formula> responses spread within the cell and those, such as Bergmann glia where this is not observed. Interestingly local, subcellular spontaneous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e425" xlink:type="simple"/></inline-formula> responses have been recorded which represent functional microdomains <xref ref-type="bibr" rid="pcbi.1000870-Grosche1">[57]</xref>. Complementary to the functional units, morphological units are described which are separated from each other by fine processes <xref ref-type="bibr" rid="pcbi.1000870-Grosche2">[58]</xref>. It is well conceivable that these thin processes separate endoplasmic reticulum between microdomains by more than 2 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e426" xlink:type="simple"/></inline-formula> and according to our model this separation would prevent the spread of a local <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e427" xlink:type="simple"/></inline-formula> signal to other parts of the cell. In contrast, in cultured astrocytes, the endoplasmic reticulum is preferentially arranged around the cell center without apparent discontinuity <xref ref-type="bibr" rid="pcbi.1000870-Pivneva1">[59]</xref> and these cells frequently exhibit spontaneous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e428" xlink:type="simple"/></inline-formula> responses. In situ, spontaneous <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e429" xlink:type="simple"/></inline-formula> responses are reported for hippocampal astrocytes and these astrocytes are less polarized as compared to Bergmann glial cells and we would predict that they are less compartimentalized. Indeed, morphological studies indicate that hippocampal astrocytes have five to ten main processes from which smaller extensions branch off <xref ref-type="bibr" rid="pcbi.1000870-Bushhong1">[60]</xref>. The synchronized activity obviously can spread within the volume of the main processes and soma of hippocampal astrocytes. Moreover, in contrast to culture, the endoplasmic reticulum in astrocytes in hippocampus tissue is preferentially located close to the plasma membrane <xref ref-type="bibr" rid="pcbi.1000870-Pivneva1">[59]</xref>. These different morphological arrangements result in distinct patterns of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e430" xlink:type="simple"/></inline-formula> responses and as a consequence in different gene expression patterns <xref ref-type="bibr" rid="pcbi.1000870-Capite1">[53]</xref>.</p>
</sec><sec id="s3c">
<title>Do we need such a modelling tool beyond intracellular Ca<sup>2+</sup> dynamics</title>
<p>The rise of cell imaging during the last decades illustrated the spatial structure of cells and protein localization. Obviously, cells are not homogeneous and active molecules coupled by diffusional transport are very common. Concentration gradients are functionally relevant, if they create microdomains inside which a pathway is in a state different from its state at other locations in the cell. They have been shown to exist for ‘the other’ fast diffusing intracellular messenger cAMP and in phosphorylation/dephosphorylation dynamics.</p>
<p>Hence, the need for spatially resolved cell models exists and we can apply the modelling concept, if all essential non-linearities are in the discrete active molecules or the boundary conditions and we can linearize remaining bulk reactions. The excellent validity of the linearization for the buffer reactions of <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e431" xlink:type="simple"/></inline-formula> dynamics has been shown by Smith <italic>et al.</italic> <xref ref-type="bibr" rid="pcbi.1000870-Smith3">[47]</xref>. We expect a degradation reaction like the cAMP degradation by PDEs also to be linearizable in good approximation. If local concentrations at active molecules should be outside the range of validity of the linearization, that can be fixed by the choice of the local quasi-static approximation of the diffusion process there in many cases. The non-linearities of cAMP production by membrane-bound adenylyl cyclase can be formulated as boundary condition and Green's function must then be used iteratively with an update of the boundary condition in each time step. These remarks illustrate that there is flexibility in the choice of reactions to be linearized which crucially expands the applicability of the concept.</p>
</sec></sec><sec id="s4" sec-type="methods">
<title>Methods</title>
<sec id="s4a">
<title>Cell preparation</title>
<p>Astrocyte cell cultures were prepared from cortex of newborn NMRI mice <xref ref-type="bibr" rid="pcbi.1000870-Lyon1">[61]</xref>. Briefly, brain tissue was freed from blood vessels and meninges, trypsinised and gently triturated with a fire-polished pipette in the presence of 0.05% DNAase (Worthington Biochem. Corp., Freehold, NY, USA). Cells were washed twice and plated directly on poly-L-lysine (PLL; 100 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e432" xlink:type="simple"/></inline-formula> ; Sigma, Deisenhofen, Germany) coated glass coverslips (<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e433" xlink:type="simple"/></inline-formula>) at densities of 3 to <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e434" xlink:type="simple"/></inline-formula> cells/coverslip, kept in <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e435" xlink:type="simple"/></inline-formula>-10-cm-dishes using Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 units/ml penicillin, and 100 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e436" xlink:type="simple"/></inline-formula> streptomycin. One day later, cultures were washed twice with Hank's balanced salt solution (HBSS).</p>
<p>Cells were maintained for at least 4 days and after reaching a subconfluent state, microglial cells and oligodendrocytes as well as their early precursors were dislodged by manual shaking and removed by washing with HBSS. The purity of the astrocytes was routinely determined by immunofluorescence using an antibody against glial fibrillary acidic protein (GFAP, Sigma), a specific astrocytic marker. The cultures typically exhibited more than 90% cells positive for GFAP.</p>
</sec><sec id="s4b">
<title>Cell imaging</title>
<p>Cultured cells plated on glass coverslips were measured between p4 and p6. Cells were incubated with the <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e437" xlink:type="simple"/></inline-formula> indicator dye Fluo-4-acetoxymethyl-ester (Fluo-4 AM, 5 <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e438" xlink:type="simple"/></inline-formula>, Molecular Probes, Eugene, USA) for 30 min at room temperature in HEPES buffer (148.9 mM NaCl, 5.4 mM KCl, 1 mM <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e439" xlink:type="simple"/></inline-formula>, 10 mM <inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e440" xlink:type="simple"/></inline-formula>, 10 mM HEPES, 5 mM D-glucose, pH 7.4) containing 0.01% Pluronic-127 (Molecular Probes). Subsequently cells were washed and kept in HEPES buffer for 15–20 min prior to the measurements with the conventional imaging system at a frequency of 0.33 Hz. Cultures were fixed within the microscope chamber of an upright microscope (Axioskop FS, Zeiss, Oberkochen, Germany) equipped with a 20× water immersion objective (UMPlanFl, numeric aperture: 0.5, Olympus, Hamburg, Germany) by a U-shaped platinum wire and superfused with HEPES buffer at 20<inline-formula><inline-graphic mimetype="image" xlink:href="info:doi/10.1371/journal.pcbi.1000870.e441" xlink:type="simple"/></inline-formula>. Substances were applied by changing the perfusate. Cells were illuminated (495 nm) from a monochromator (T.I.L.L. Photonics) and fluorescent images (515–545 nm) collected every 3 s with a 12 bit camera (SensiCam) on an upright microscope. At this state, no intercellular waves were observed. Single cell time series were extracted from these images with ImagingCellsEasily software.</p>
</sec></sec><sec id="s5">
<title>Supporting Information</title>
<supplementary-material id="pcbi.1000870.s001" mimetype="application/pdf" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.s001" xlink:type="simple"><label>Text S1</label><caption>
<p>Detailed mathematical model and supporting results.</p>
<p>(0.75 MB PDF)</p>
</caption></supplementary-material><supplementary-material id="pcbi.1000870.s002" mimetype="video/x-msvideo" position="float" xlink:href="info:doi/10.1371/journal.pcbi.1000870.s002" xlink:type="simple"><label>Video S1</label><caption>
<p>The movie shows the free cytosolic calcium concentration during a spike lasting 15 s by an iso-concentration surface of 2 µM. The initial puff activates adjacent channel clusters by increasing their open probability. The clusters open and close randomly until inhibition terminates the release. Parameter values are in <xref ref-type="table" rid="pcbi-1000870-t001">Table 1</xref>, the spatial arrangement of clusters is shown in <xref ref-type="fig" rid="pcbi-1000870-g001">Figure 1</xref>.</p>
<p>(9.94 MB AVI)</p>
</caption></supplementary-material></sec></body>
<back>
<ack>
<p>We thank Irene Haupt for excellent cell preparation and Carola Schipke for experimental advice.</p>
</ack>
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