Spatiotemporal patterning of IP3-mediated Ca2+ signals in Xenopus oocytes by Ca2+-binding proteins

Automated denoising software for calcium imaging signals using deep learning

Dynamic Ca2+ signaling is crucial for cell survival and death, and Ca2+ imaging approaches are commonly used to study and measure cellular Ca2+ patterns within cells. However, the presence of image noise from instrumentation and experimentation protocols can impede the accurate extraction of Ca2+ signals. Removing noise from Ca2+ Spatio-Temporal Maps (STMaps) is essential for precisely analyzing Ca2+ datasets. Current methods for denoising STMaps can be time-consuming and subjective and rely mainly on image processing protocols. To address this, we developed CalDenoise, an automated software that employs robust image processing and deep learning models to remove noise and enhance Ca2+ signals in STMaps effectively. CalDenoise integrates four pipelines capable of efficiently removing salt-and-pepper, impulsive, and periodic noise and detecting and removing background noise. Comprising both an image-processing-based pipeline and three generative-adversarial-network-based (GAN) deep learning models, CalDenoise proficiently removes complex noise patterns. The software features adjustable parameters to enhance accuracy and is integrated into a user-friendly graphical interface for easy access and streamlined usage. CalDenoise can serve as a robust platform for denoising complex dynamic fluorescence signal images across diverse cell types, including Ca2+, voltage, ions, and pH signals.

Ca2+ dynamics in interstitial cells: foundational mechanisms for the motor patterns in the gastrointestinal tract

The gastrointestinal (GI) tract displays multiple motor patterns that move nutrients and wastes through the body. Smooth muscle cells (SMCs) provide the forces necessary for GI motility, but interstitial cells, electrically coupled to SMCs, tune SMC excitability, transduce inputs from enteric motor neurons, and generate pacemaker activity that underlies major motor patterns, such as peristalsis and segmentation. The interstitial cells regulating SMCs are interstitial cells of Cajal (ICC) and PDGF receptor (PDGFR)α+ cells. Together these cells form the SIP syncytium. ICC and PDGFRα+ cells express signature Ca2+-dependent conductances: ICC express Ca2+-activated Cl- channels, encoded by Ano1, that generate inward current, and PDGFRα+ cells express Ca2+-activated K+ channels, encoded by Kcnn3, that generate outward current. The open probabilities of interstitial cell conductances are controlled by Ca2+ release from the endoplasmic reticulum. The resulting Ca2+ transients occur spontaneously in a stochastic manner. Ca2+ transients in ICC induce spontaneous transient inward currents and spontaneous transient depolarizations (STDs). Neurotransmission increases or decreases Ca2+ transients, and the resulting depolarizing or hyperpolarizing responses conduct to other cells in the SIP syncytium. In pacemaker ICC, STDs activate voltage-dependent Ca2+ influx, which initiates a cluster of Ca2+ transients and sustains activation of ANO1 channels and depolarization during slow waves. Regulation of GI motility has traditionally been described as neurogenic and myogenic. Recent advances in understanding Ca2+ handling mechanisms in interstitial cells and how these mechanisms influence motor patterns of the GI tract suggest that the term "myogenic" should be replaced by the term "SIPgenic," as this review discusses.

T cell Ca2+ microdomains through the lens of computational modeling

Cellular Ca2+ signaling is highly organized in time and space. Locally restricted and short-lived regions of Ca2+ increase, called Ca2+ microdomains, constitute building blocks that are differentially arranged to create cellular Ca2+ signatures controlling physiological responses. Here, we focus on Ca2+ microdomains occurring in restricted cytosolic spaces between the plasma membrane and the endoplasmic reticulum, called endoplasmic reticulum-plasma membrane junctions. In T cells, these microdomains have been finely characterized. Enough quantitative data are thus available to develop detailed computational models of junctional Ca2+ dynamics. Simulations are able to predict the characteristics of Ca2+ increases at the level of single channels and in junctions of different spatial configurations, in response to various signaling molecules. Thanks to the synergy between experimental observations and computational modeling, a unified description of the molecular mechanisms that create Ca2+ microdomains in the first seconds of T cell stimulation is emerging.

Physiology of intracellular calcium buffering

Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.

Modeling IP3-induced Ca2+ signaling based on its interspike interval statistics

Inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ signaling is a second messenger system used by almost all eukaryotic cells. Recent research demonstrated randomness of Ca2+ signaling on all structural levels. We compile eight general properties of Ca2+ spiking common to all cell types investigated and suggest a theory of Ca2+ spiking starting from the random behavior of IP3 receptor channel clusters mediating the release of Ca2+ from the endoplasmic reticulum capturing all general properties and pathway-specific behavior. Spike generation begins after the absolute refractory period of the previous spike. According to its hierarchical spreading from initiating channel openings to cell level, we describe it as a first passage process from none to all clusters open while the cell recovers from the inhibition which terminated the previous spike. Our theory reproduces the exponential stimulation response relation of the average interspike interval Tav and its robustness properties, random spike timing with a linear moment relation between Tav and the interspike interval SD and its robustness properties, sensitive dependency of Tav on diffusion properties, and nonoscillatory local dynamics. We explain large cell variability of Tav observed in experiments by variability of channel cluster coupling by Ca2+-induced Ca2+ release, the number of clusters, and IP3 pathway component expression levels. We predict the relation between puff probability and agonist concentration and [IP3] and agonist concentration. Differences of spike behavior between cell types and stimulating agonists are explained by the different types of negative feedback terminating spikes. In summary, the hierarchical random character of spike generation explains all of the identified general properties.

Termination of Ca2+ puffs during IP3-evoked global Ca2+ signals

We previously described that cell-wide cytosolic Ca²⁺ transients evoked by inositol trisphosphate (IP₃) are generated by two modes of Ca²⁺ liberation from the ER; 'punctate' release via an initial flurry of transient Ca²⁺ puffs from local clusters of IP₃ receptors, succeeded by a spatially and temporally 'diffuse' Ca²⁺ liberation. Those findings were derived using statistical fluctuation analysis to monitor puff activity which is otherwise masked as global Ca²⁺ levels rise. Here, we devised imaging approaches to resolve individual puffs during global Ca²⁺ elevations to better investigate the mechanisms terminating the puff flurry. We find that puffs contribute about 40% (∼90 attomoles) of the total Ca²⁺ liberation, largely while the global Ca²⁺ signal rises halfway to its peak. The major factor terminating punctate Ca²⁺ release is an abrupt decline in puff frequency. Although the amplitudes of large puffs fall during the flurry, the amplitudes of more numerous small puffs remain steady, so overall puff amplitudes decline only modestly (∼30%). The Ca²⁺ flux through individual IP₃ receptor/channels does not measurably decline during the flurry, or when puff activity is depressed by pharmacological lowering of Ca²⁺ levels in the ER lumen, indicating that the termination of punctate release is not a simple consequence of reduced driving force for Ca²⁺ liberation. We propose instead that the gating of IP₃ receptors at puff sites is modulated such that their openings become suppressed as the bulk [Ca²⁺] in the ER lumen falls during global Ca²⁺ signals.

High rates of calcium-free diffusion in the cytosol of living cells

Calcium (Ca²⁺) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca²⁺ concentration spread in space and time is key for the versatility of the signals. Ca²⁺ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca²⁺ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca²⁺-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.

Revealing the Precise Role of Calretinin Neurons in Epilepsy: We Are on the Way

Epilepsy is a common neurological disorder characterized by hyperexcitability in the brain. Its pathogenesis is classically associated with an imbalance of excitatory and inhibitory neurons. Calretinin (CR) is one of the three major types of calcium-binding proteins present in inhibitory GABAergic neurons. The functions of CR and its role in neural excitability are still unknown. Recent data suggest that CR neurons have diverse neurotransmitters, morphologies, distributions, and functions in different brain regions across various species. Notably, CR neurons in the hippocampus, amygdala, neocortex, and thalamus are extremely susceptible to excitotoxicity in the epileptic brain, but the causal relationship is unknown. In this review, we focus on the heterogeneous functions of CR neurons in different brain regions and their relationship with neural excitability and epilepsy. Importantly, we provide perspectives on future investigations of the role of CR neurons in epilepsy.

Quantification of fluctuations from fluorescence correlation spectroscopy experiments in reaction-diffusion systems

Fluorescence correlation spectroscopy (FCS) is commonly used to estimate diffusion and reaction rates. In FCS the fluorescence coming from a small volume is recorded and the autocorrelation function (ACF) of the fluorescence fluctuations is computed. Scaling out the fluctuations due to the emission process, this ACF can be related to the ACF of the fluctuations in the number of observed fluorescent molecules. In this paper the ACF of the molecule number fluctuations is studied theoretically, with no approximations, for a reaction-diffusion system in which the fluorescence changes with binding and unbinding. Theoretical ACFs are usually derived assuming that fluctuations in the number of molecules of one species are instantaneously uncorrelated to those of the others and obey Poisson statistics. Under these assumptions, the ACF derived in this paper is characterized only by the diffusive timescale of the fluorescent species and its total weight is the inverse of the mean number of observed fluorescent molecules. The theory is then scrutinized in view of previous experimental results which, for a similar system, gave a different total weight and correct estimates of other diffusive timescales. The total weight mismatch is corrected by assuming that the variance of the number of fluorescent molecules depends on the variance of the particle numbers of the other species, as in the variance decomposition formula. Including the finite acquisition time in its computation, it is shown that the ACF depends on various timescales of the system and that its total weight coincides with the one obtained with the variance decomposition formula. This calculation implies that diffusion coefficients of nonobservable species can be estimated with FCS experiments performed in reaction-diffusion systems. Ways to proceed in future experiments are also discussed.

A high throughput machine-learning driven analysis of Ca2+ spatio-temporal maps

High-resolution Ca2+ imaging to study cellular Ca2+ behaviors has led to the creation of large datasets with a profound need for standardized and accurate analysis. To analyze these datasets, spatio-temporal maps (STMaps) that allow for 2D visualization of Ca2+ signals as a function of time and space are often used. Methods of STMap analysis rely on a highly arduous process of user defined segmentation and event-based data retrieval. These methods are often time consuming, lack accuracy, and are extremely variable between users. We designed a novel automated machine-learning based plugin for the analysis of Ca2+ STMaps (STMapAuto). The plugin includes optimized tools for Ca2+ signal preprocessing, automated segmentation, and automated extraction of key Ca2+ event information such as duration, spatial spread, frequency, propagation angle, and intensity in a variety of cell types including the Interstitial cells of Cajal (ICC). The plugin is fully implemented in Fiji and able to accurately detect and expeditiously quantify Ca2+ transient parameters from ICC. The plugin's speed of analysis of large-datasets was 197-fold faster than the commonly used single pixel-line method of analysis. The automated machine-learning based plugin described dramatically reduces opportunities for user error and provides a consistent method to allow high-throughput analysis of STMap datasets.

IP3 mediated global Ca2+ signals arise through two temporally and spatially distinct modes of Ca2+ release

The 'building-block' model of inositol trisphosphate (IP3)-mediated Ca2+ liberation posits that cell-wide cytosolic Ca2+ signals arise through coordinated activation of localized Ca2+ puffs generated by stationary clusters of IP3 receptors (IP3Rs). Here, we revise this hypothesis, applying fluctuation analysis to resolve Ca2+ signals otherwise obscured during large Ca2+ elevations. We find the rising phase of global Ca2+ signals is punctuated by a flurry of puffs, which terminate before the peak by a mechanism involving partial ER Ca2+ depletion. The continuing rise in Ca2+, and persistence of global signals even when puffs are absent, reveal a second mode of spatiotemporally diffuse Ca2+ signaling. Puffs make only small, transient contributions to global Ca2+ signals, which are sustained by diffuse release of Ca2+ through a functionally distinct process. These two modes of IP3-mediated Ca2+ liberation have important implications for downstream signaling, imparting spatial and kinetic specificity to Ca2+-dependent effector functions and Ca2+ transport.

Pacemaker function and neural responsiveness of subserosal interstitial cells of Cajal in the mouse colon

KEY POINTS

Rhythmic action potentials and intercellular Ca²⁺ waves are generated in smooth muscle cells of colonic longitudinal muscles (LSMC). Longitudinal muscle excitability is tuned by input from subserosal ICC (ICC-SS), a population of ICC with previously unknown function. ICC-SS express Ano1 channels and generate spontaneous Ca²⁺ transients in a stochastic manner. Release of Ca²⁺ and activation of Ano1 channels causes depolarization of ICC-SS and LSMC, leading to activation of L-type Ca²⁺ channels, action potentials, intercellular Ca²⁺ waves and contractions in LSMC. Nitrergic neural inputs regulate the Ca²⁺ events in ICC-SS. Pacemaker activity in longitudinal muscle is an emergent property as a result of integrated processes in ICC-SS and LSMC.

ABSTRACT

Much is known about myogenic mechanisms in circular muscle (CM) in the gastrointestinal tract, although less is known about longitudinal muscle (LM). Two Ca²⁺ signalling behaviours occur in LM: localized intracellular waves not causing contractions and intercellular waves leading to excitation-contraction coupling. An Ano1 channel antagonist inhibited intercellular Ca²⁺ waves and LM contractions. Ano1 channels are expressed by interstitial cells of Cajal (ICC) but not by smooth muscle cells (SMCs). We investigated Ca²⁺ signalling in a novel population of ICC that lies along the subserosal surface of LM (ICC-SS) in mice expressing GCaMP6f in ICC. ICC-SS fired stochastic localized Ca²⁺ transients. Such events have been linked to activation of Ano1 channels in ICC. Ca²⁺ transients in ICC-SS occurred by release from stores most probably via inositol trisphosphate receptors. This activity relied on influx via store-operated Ca²⁺ entry and Orai channels. No voltage-dependent mechanism that synchronized Ca²⁺ transients in a single cell or between cells was found. Nitrergic agonists inhibited Ca²⁺ transients in ICC-SS, and stimulation of intrinsic nerves activated nitrergic responses in ICC-SS. Cessation of stimulation resulted in significant enhancement of Ca²⁺ transients compared to the pre-stimulus activity. No evidence of innervation by excitatory, cholinergic motor neurons was found. Our data suggest that ICC-SS contribute to regulation of LM motor activity. Spontaneous Ca²⁺ transients activate Ano1 channels in ICC-SS. Resulting depolarization conducts to SMCs, depolarizing membrane potential, activating L-type Ca²⁺ channels and initiating contraction. Rhythmic electrical and mechanical behaviours of LM are an emergent property of SMCs and ICC-SS.

Noise analysis of cytosolic calcium image data

Cellular Ca²⁺ signals are often constrained to cytosolic micro- or nano-domains where stochastic openings of Ca²⁺ channels cause large fluctuations in local Ca²⁺ concentration (Ca²⁺ 'noise'). With the advent of TIRF microscopy to image the fluorescence of Ca²⁺-sensitive probes from attoliter volumes it has become possible to directly monitor these signals, which closely track the gating of plasmalemmal and ER Ca²⁺-permeable channels. Nevertheless, it is likely that many physiologically important Ca²⁺ signals are too small to resolve as discrete events in fluorescence recordings. By analogy with noise analysis of electrophysiological data, we explore here the use of statistical approaches to detect and analyze such Ca²⁺ noise in images obtained using Ca²⁺-sensitive indicator dyes. We describe two techniques - power spectrum analysis and spatio-temporal correlation - and demonstrate that both effectively identify discrete, spatially localized calcium release events (Ca²⁺ puffs). Moreover, we show they are able to detect localized noise fluctuations in a case where discrete events cannot directly be resolved.

Changes in Ca2+ Removal Can Mask the Effects of Geometry During IP3R Mediated Ca2+ Signals

Calcium (Ca²⁺) signals are ubiquitous. Most intracellular Ca²⁺ signals involve the release of Ca²⁺ from the endoplasmic reticulum (ER) through Inositol 1,4,5-Trisphosphate Receptors (IP₃Rs). The non-uniform spatial organization of IP₃Rs and the fact that their individual openings are coupled via cytosolic Ca²⁺ are key factors for the variety of spatio-temporal distributions of the cytosolic [Ca²⁺] and the versatility of the signals. In this paper we combine experiments performed in untreated and in progesterone-treated Xenopus laevis oocytes and mathematical models to investigate how the interplay between geometry (the IP₃R spatial distribution) and dynamics (the processes that characterize the release, transport, and removal of cytosolic Ca²⁺) affects the resulting signals. Signal propagation looks more continuous and spatially uniform in treated (mature) than in untreated (immature) oocytes. This could be due to the different underlying IP₃R spatial distribution that has been observed in both cell types. The models, however, show that the rate of cytosolic Ca²⁺ removal, which is also different in both cell types, plays a key role affecting the coupling between Ca²⁺ release sites in such a way that the effect of the underlying IP₃R spatial distribution can be modified.

All three IP3 receptor isoforms generate Ca2+ puffs that display similar characteristics

Inositol 1,4,5-trisphosphate (IP₃) evokes Ca²⁺ release through IP₃ receptors (IP₃Rs) to generate both local Ca²⁺ puffs arising from concerted openings of clustered IP₃Rs and cell-wide Ca²⁺ waves. Imaging Ca²⁺ puffs with single-channel resolution yields information on the localization and properties of native IP₃Rs in intact cells, but interpretation has been complicated because cells express varying proportions of three structurally and functionally distinct isoforms of IP₃Rs. Here, we used TIRF and light-sheet microscopy to image Ca²⁺ puffs in HEK-293 cell lines generated by CRISPR-Cas9 technology to express exclusively IP₃R type 1, 2, or 3. Photorelease of the IP₃ analog i-IP₃ in all three cell lines evoked puffs with largely similar mean amplitudes, temporal characteristics, and spatial extents. Moreover, the single-channel Ca²⁺ flux was similar among isoforms, indicating that clusters of different IP₃R isoforms contain comparable numbers of active channels. Our results show that all three IP₃R isoforms cluster to generate local Ca²⁺ puffs and, contrary to findings of divergent properties from in vitro electrophysiological studies, display similar conductances and gating kinetics in intact cells.

Using two dyes to observe the competition of Ca2+ trapping mechanisms and their effect on intracellular Ca2+ signals

The specificity and universality of intracellular [Formula: see text] signals rely on the variety of spatio-temporal patterns that the [Formula: see text] concentration can display. [Formula: see text] liberation through inositol 1,4,5-trisphosphate receptors ([Formula: see text]) is key for this variety. In this paper, we study how the competition between buffers of different kinetics affects [Formula: see text] signals that involve [Formula: see text] release through [Formula: see text]. The study also provides insight into the underlying spatial distribution of the channels that participate in the signals. Previous works on the effects of [Formula: see text] buffers have drawn conclusions 'indirectly' by observing the [Formula: see text]-bound dye distributions in the presence of varying concentrations of exogenous buffers and using simulations to interpret the results. In this paper, we make visible the invisible by observing the signals simultaneously with two dyes, [Formula: see text] and [Formula: see text], each of which plays the role of a slow or fast [Formula: see text] buffer, respectively. Our observations obtained for different concentrations of [Formula: see text] highlight the dual role that fast buffers exert on the dynamics, either reducing the intracluster channel coupling or preventing channel inhibition and allowing the occurrence of relatively long cycles of [Formula: see text] release. Our experiments also show that signals with relatively high [Formula: see text] release rates remain localized in the presence of large [Formula: see text] concentrations, while the mean speed of the elicited waves increases. We interpret this as a consequence of the more effective uncoupling between [Formula: see text] clusters as the slow dye concentration increases. Combining the analysis of the experiments with numerical simulations, we also conclude that [Formula: see text] release not only occurs within the close vicinity of the centers of the clearly identifiable release sites ([Formula: see text] clusters) but there are also functional [Formula: see text] in between them.

Wave failure at strong coupling in intracellular Ca^{2+} signaling system with clustered channels

As an important intracellular signal, Ca^{2+} ions control diverse cellular functions. In this paper, we discuss the Ca^{2+} signaling with a two-dimensional model in which the inositol 1,4,5-trisphosphate (IP_{3}) receptor channels are distributed in clusters on the endoplasmic reticulum membrane. The wave failure at large Ca^{2+} diffusion coupling is discussed in detail in the model. We show that with varying model parameters the wave failure is a robust behavior with either deterministic or stochastic channel dynamics. We suggest that the wave failure should be a general behavior in inhomogeneous diffusing systems with clustered excitable regions and may occur in biological Ca^{2+} signaling systems.

Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching

Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.

Fluorescence correlation spectroscopy experiments to quantify free diffusion coefficients in reaction-diffusion systems: The case of Ca^{2+} and its dyes

Many cell signaling pathways involve the diffusion of messengers that bind and unbind to and from intracellular components. Quantifying their net transport rate under different conditions then requires having separate estimates of their free diffusion coefficient and binding or unbinding rates. In this paper, we show how performing sets of fluorescence correlation spectroscopy (FCS) experiments under different conditions, it is possible to quantify free diffusion coefficients and on and off rates of reaction-diffusion systems. We develop the theory and present a practical implementation for the case of the universal second messenger, calcium (Ca^{2+}) and single-wavelength dyes that increase their fluorescence upon Ca^{2+} binding. We validate the approach with experiments performed in aqueous solutions containing Ca^{2+} and Fluo4 dextran (both in its high and low affinity versions). Performing FCS experiments with tetramethylrhodamine-dextran in Xenopus laevis oocytes, we infer the corresponding free diffusion coefficients in the cytosol of these cells. Our approach can be extended to other physiologically relevant reaction-diffusion systems to quantify biophysical parameters that determine the dynamics of various variables of interest.

Distinct Neural Properties in the Low-Frequency Region of the Chicken Cochlear Nucleus Magnocellularis

Topography in the avian cochlear nucleus magnocellularis (NM) is represented as gradually increasing characteristic frequency (CF) along the caudolateral-to-rostromedial axis. In this study, we characterized the organization and cell biophysics of the caudolateral NM (NMc) in chickens (Gallus gallus). Examination of cellular and dendritic architecture first revealed that NMc contains small neurons and extensive dendritic processes, in contrast to adendritic, large neurons located more rostromedially. Individual dye-filling study further demonstrated that NMc is divided into two subregions, with NMc2 neurons having larger and more complex dendritic fields than NMc1. Axonal tract tracing studies confirmed that NMc1 and NMc2 neurons receive afferent inputs from the auditory nerve and the superior olivary nucleus, similar to the adendritic NM. However, the auditory axons synapse with NMc neurons via small bouton-like terminals, unlike the large end bulb synapses on adendritic NM neurons. Immunocytochemistry demonstrated that most NMc2 neurons express cholecystokinin but not calretinin, distinct from NMc1 and adendritic NM neurons that are cholecystokinin negative and mostly calretinin positive. Finally, whole-cell current clamp recordings revealed that NMc neurons require significantly lower threshold current for action potential generation than adendritic NM neurons. Moreover, in contrast to adendritic NM neurons that generate a single-onset action potential, NMc neurons generate multiple action potentials to suprathreshold sustained depolarization. Taken together, our data indicate that NMc contains multiple neuron types that are structurally, connectively, molecularly, and physiologically different from traditionally defined NM neurons, emphasizing specialized neural properties for processing low-frequency sounds.

FCS experiments to quantify Ca2+ diffusion and its interaction with buffers

Ca²⁺ signals are ubiquitous. One of the key factors for their versatility is the variety of spatio-temporal distributions that the cytosolic Ca²⁺ can display. In most cell types Ca²⁺ signals not only depend on Ca²⁺ entry from the extracellular medium but also on Ca²⁺ release from internal stores, a process which is in turn regulated by cytosolic Ca²⁺ itself. The rate at which Ca²⁺ is transported, the fraction that is trapped by intracellular buffers, and with what kinetics are thus key features that affect the time and spatial range of action of Ca²⁺ signals. The quantification of Ca²⁺ diffusion in intact cells is quite challenging because the transport rates that can be inferred using optical techniques are intricately related to the interaction of Ca²⁺ with the dye that is used for its observation and with the cellular buffers. In this paper, we introduce an approach that uses Fluorescence Correlation Spectroscopy (FCS) experiments performed at different conditions that in principle allows the quantification of Ca²⁺ diffusion and of its reaction rates with unobservable (non-fluorescent) Ca²⁺ buffers. To this end, we develop the necessary theory to interpret the experimental results and then apply it to FCS experiments performed in a set of solutions containing Ca²⁺, a single wavelength Ca²⁺ dye, and a non-fluorescent Ca²⁺ buffer. We show that a judicious choice of the experimental conditions and an adequate interpretation of the fitting parameters can be combined to extract information on the free diffusion coefficient of Ca²⁺ and of some of the properties of the unobservable buffer. We think that this approach can be applied to other situations, particularly to experiments performed in intact cells.

The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca2+ Signals and the Harmonization of Ca2+-Related Cellular Responses

Calcium ions (Ca²⁺) are important mediators of a great variety of cellular activities e.g. in response to an agonist activation of a receptor. The magnitude of a cellular response is often encoded by frequency modulation of Ca²⁺ oscillations and correlated with the stimulation intensity. The stimulation intensity highly depends on the sensitivity of a cell to a certain agonist. In some cases, it is essential that neighboring cells produce a similar and synchronized response to an agonist despite their different sensitivity. In order to decipher the presumed function of Ca²⁺ waves spreading among connecting cells, a mathematical model was developed. This model allows to numerically modifying the connectivity probability between neighboring cells, the permeability of gap junctions and the individual sensitivity of cells to an agonist. Here, we show numerically that strong gap junctional coupling between neighbors ensures an equilibrated response to agonist stimulation via formation of Ca²⁺ phase waves, i.e. a less sensitive neighbor will produce the same or similar Ca²⁺ signal as its highly sensitive neighbor. The most sensitive cells within an ensemble are the wave initiator cells. The Ca²⁺ wave in the cytoplasm is driven by a sensitization wave front in the endoplasmic reticulum. The wave velocity is proportional to the cellular sensitivity and to the strength of the coupling. The waves can form different patterns including circular rings and spirals. The observed pattern depends on the strength of noise, gap junctional permeability and the connectivity probability between neighboring cells. Our simulations reveal that one highly sensitive region gradually takes the lead within the entire noisy system by generating directed circular phase waves originating from this region.

The calcium ion (Ca²⁺), a universal signaling molecule, is widely recognized to play a fundamental role in the regulation of various biological processes. Agonist–evoked Ca²⁺ signals often manifest as rhythmic changes in the cytosolic free Ca²⁺ concentration (c_cyt) called Ca²⁺ oscillations. Stimuli intensity was found to be proportional to the oscillation frequency and the evoked down-steam cellular response. Stochastic receptor expression in individual cells in a cell population inevitably leads to individually different oscillation frequencies and individually different Ca²⁺-related cellular responses. However, in many organs, the neighboring cells have to overcome their individually different sensitivity and produce a synchronized response. Gap junctions are integral membrane structures that enable the direct cytoplasmic exchange of Ca²⁺ ions and InsP₃ molecules between neighboring cells. By simulations, we were able to demonstrate how the strength of intercellular gap junctional coupling in relation to stimulus intensity can modify the spatiotemporal patterns of Ca²⁺ signals and harmonize the Ca²⁺-related cellular responses via synchronization of oscillation frequency. We demonstrate that the most sensitive cells are the wave initiator cells and that a highly sensitive region plays an important role in the determination of the Ca²⁺ phase wave direction. This sensitive region will then also progressively determine the global behavior of the entire system.

Microdomain [Ca(2+)] Fluctuations Alter Temporal Dynamics in Models of Ca(2+)-Dependent Signaling Cascades and Synaptic Vesicle Release

Ca(2+)-dependent signaling is often localized in spatially restricted microdomains and may involve only 1 to 100 Ca(2+) ions. Fluctuations in the microdomain Ca(2+) concentration (Ca(2+)) can arise from a wide range of elementary processes, including diffusion, Ca(2+) influx, and association/dissociation with Ca(2+) binding proteins or buffers. However, it is unclear to what extent these fluctuations alter Ca(2+)-dependent signaling. We construct Markov models of a general Ca(2+)-dependent signaling cascade and Ca(2+)-triggered synaptic vesicle release. We compare the hitting (release) time distribution and statistics for models that account for [Ca(2+)] fluctuations with the corresponding models that neglect these fluctuations. In general, when Ca(2+) fluctuations are much faster than the characteristic time for the signaling event, the hitting time distributions and statistics for the models with and without Ca(2+) fluctuation are similar. However, when the timescale of Ca(2+) fluctuations is on the same order as the signaling cascade or slower, the hitting time mean and variability are typically increased, in particular when the average number of microdomain Ca(2+) ions is small, a consequence of a long-tailed hitting time distribution. In a model of Ca(2+)-triggered synaptic vesicle release, we demonstrate the conditions for which [Ca(2+)] fluctuations do and do not alter the distribution, mean, and variability of release timing. We find that both the release time mean and variability can be increased, demonstrating that Ca(2+) fluctuations are an important aspect of microdomain Ca(2+) signaling and further suggesting that Ca(2+) fluctuations in the presynaptic terminal may contribute to variability in synaptic vesicle release and thus variability in neuronal spiking.

Ca²⁺ images obtained in different experimental conditions shed light on the spatial distribution of IP₃ receptors that underlie Ca²⁺ puffs

Many intracellular Ca(2+) signals involve Ca(2+) release from the endoplasmic reticulum through inositol 1,4,5-trisphosphate receptors (IP3Rs). The open probability of IP3Rs depends on cytosolic Ca(2+) so that these signals involve Ca(2+)-induced Ca(2+)-release (CICR). IP3Rs are organized in clusters. The signals they mediate are observed using single-wavelength dyes and, often, a slow Ca(2+) buffer (EGTA) is added to disrupt CICR between clusters and keep the signals spatially restricted. It is assumed that the presence of the dye or of EGTA does not alter the intra-cluster Ca(2+) dynamics. In this paper we analyze this issue combining experiments and numerical simulations. We compare the properties of local signals known as puffs observed with different dyes and EGTA concentrations. We determine that although the dye or EGTA does not alter the intra-cluster dynamics, the set of observable events is different depending on the degree of inter-cluster uncoupling of the experiment. An analysis of the observations shows that the events that are missed for insufficient inter-cluster uncoupling are those of fastest amplitude growth rate. This agrees with a spatial organization in which the largest amplitude events correspond to clusters with densely packed active IP3Rs.

Calretinin: from a "simple" Ca(2+) buffer to a multifunctional protein implicated in many biological processes

The hexa-EF-hand Ca(2+)-binding protein calretinin (CR) is predominantly expressed in specific neurons of the central and peripheral nervous system. However, CR expression is also observed in non-neuronal cells, e.g., during embryonic development and in mesothelioma cells. Of the 6 EF-hand domains, 5 are functional; the first 4 domains form 2 pairs showing high cooperativity within a pair that results in non-linear modulation of intracellular Ca(2+) signals by CR. EF-hand domain 5 has a low affinity and represents the identified interaction site with CR-binding partners present in mouse cerebellar granule cells. CR binding to other targets including the pore-forming α1 subunit of the Ca(2+) channel Ca V 2.1, as well as to huntingtin indicates additional Ca(2+) sensor functions besides the well-known Ca(2+)-buffering functions. The absence of CR in cerebellar granule cells of CR(-/-) mice results in increased excitability and altered firing of Purkinje cells and promotes cerebellar 160-Hz oscillations impairing motor coordination. The putative role of CR in neuroprotection is still highly discussed. Altogether, CR emerges as a multi-functional protein also associated with development, i.e., cell proliferation, differentiation, and cell death.

Buffer regulation of calcium puff sequences

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

Inverse problems in neuronal calcium signaling

Calcium is the most important of the brain's second messengers. Thanks to engineered fluorescent indicators and caged compounds we have an excellent qualitative picture of its regulation and impact.With the advent of new scanning technology that permits one to observe the calcium signal throughout a highly branched neuron the potential exists for functional, single cell, quantitative calcium imaging. To help realize that potential we analyze a sequence of four inverse problems that infer the parameters of the cytosolic calcium buffers and plasma membrane calcium pumps and channels from the light shed by fluorescent indicators following specific stimulus protocols. Our analyses lead in each case to practical algorithms that we illustrate and test on synthetic data.

Bidirectional Ca²⁺ signaling occurs between the endoplasmic reticulum and acidic organelles

After acidic organelles induce signaling to activate ER calcium ion release, local microdomains of high calcium at ER–acidic organelle junctions feed back to activate further acidic organelle calcium release.

The endoplasmic reticulum (ER) and acidic organelles (endo-lysosomes) act as separate Ca²⁺ stores that release Ca²⁺ in response to the second messengers IP₃ and cADPR (ER) or NAADP (acidic organelles). Typically, trigger Ca²⁺ released from acidic organelles by NAADP subsequently recruits IP₃ or ryanodine receptors on the ER, an anterograde signal important for amplification and Ca²⁺ oscillations/waves. We therefore investigated whether the ER can signal back to acidic organelles, using organelle pH as a reporter of NAADP action. We show that Ca²⁺ released from the ER can activate the NAADP pathway in two ways: first, by stimulating Ca²⁺-dependent NAADP synthesis; second, by activating NAADP-regulated channels. Moreover, the differential effects of EGTA and BAPTA (slow and fast Ca²⁺ chelators, respectively) suggest that the acidic organelles are preferentially activated by local microdomains of high Ca²⁺ at junctions between the ER and acidic organelles. Bidirectional organelle communication may have wider implications for endo-lysosomal function as well as the generation of Ca²⁺ oscillations and waves.

Effects of calretinin on Ca2+ signals in cerebellar granule cells: implications of cooperative Ca2+ binding

Calretinin is thought to be the main endogenous calcium buffer in cerebellar granule cells (GrCs). However, little is known about the impact of cooperative Ca(2+) binding to calretinin on highly localized and more global (regional) Ca(2+) signals in these cells. Using numerical simulations, we show that an essential property of calretinin is a delayed equilibration with Ca(2+). Therefore, the amount of Ca(2+), which calretinin can accumulate with respect to equilibrium levels, depends on stimulus conditions. Based on our simulations of buffered Ca(2+) diffusion near a single Ca(2+) channel or a large cluster of Ca(2+) channels and previous experimental findings that 150 μM 1,2-bis(o-aminophenoxy) ethane-N, N, N', N'-tetraacetic acid (BAPTA) and endogenous calretinin have similar effects on GrC excitability, we estimated the concentration of mobile calretinin in GrCs in the range of 0.7-1.2 mM. Our results suggest that this estimate can provide a starting point for further analysis. We find that calretinin prominently reduces the action potential associated increase in cytosolic free Ca(2+) concentration ([Ca(2+)]( i )) even at a distance of 30 nm from a single Ca(2+) channel. In spite of a buildup of residual Ca(2+), it maintains almost constant maximal [Ca(2+)]( i ) levels during repetitive channel openings with a frequency less than 80 Hz. This occurs because of accelerated Ca(2+) binding as calretinin binds more Ca(2+). Unlike the buffering of high Ca(2+) levels within Ca(2+) nano/microdomains sensed by large conductance Ca(2+)-activated K(+) channels, the buffering of regional Ca(2+) signals by calretinin can never be mimicked by certain concentration of BAPTA under all different experimental conditions.

Do calcium buffers always slow down the propagation of calcium waves?

Calcium buffers are large proteins that act as binding sites for free cytosolic calcium. Since a large fraction of cytosolic calcium is bound to calcium buffers, calcium waves are widely observed under the condition that free cytosolic calcium is heavily buffered. In addition, all physiological buffered excitable systems contain multiple buffers with different affinities. It is thus important to understand the properties of waves in excitable systems with the inclusion of buffers. There is an ongoing controversy about whether or not the addition of calcium buffers into the system always slows down the propagation of calcium waves. To solve this controversy, we incorporate the buffering effect into the generic excitable system, the FitzHugh-Nagumo model, to get the buffered FitzHugh-Nagumo model, and then to study the effect of the added buffer with large diffusivity on traveling waves of such a model in one spatial dimension. We can find a critical dissociation constant (K = K(a)) characterized by system excitability parameter a such that calcium buffers can be classified into two types: weak buffers (K ∈ (K(a), ∞)) and strong buffers (K ∈ (0, K(a))). We analytically show that the addition of weak buffers or strong buffers but with its total concentration b(0)(1) below some critical total concentration b(0,c)(1) into the system can generate a traveling wave of the resulting system which propagates faster than that of the origin system, provided that the diffusivity D1 of the added buffers is sufficiently large. Further, the magnitude of the wave speed of traveling waves of the resulting system is proportional to √D1 as D1 --> ∞. In contrast, the addition of strong buffers with the total concentration b(0)(1) > b(0,c)(1) into the system may not be able to support the formation of a biologically acceptable wave provided that the diffusivity D1 of the added buffers is sufficiently large.

The probability of triggering calcium puffs is linearly related to the number of inositol trisphosphate receptors in a cluster

Puffs are local Ca(2+) signals that arise by Ca(2+) liberation from the endoplasmic reticulum through concerted opening of tightly clustered inositol trisphosphate receptor/channels (IP(3)R). They serve both local signaling functions and trigger global Ca(2+) waves. The numbers of functional IP(3)R within clusters differ appreciably between different puff sites, and we investigated how the probability of puff occurrence varies with cluster size. We imaged puffs in SH-SY5Y cells using total internal fluorescence microscopy, and estimated cluster sizes from the magnitude of the largest puff observed at each site relative to the signal from a single channel. We find that the initial triggering rate of puffs following photorelease of IP(3), and the average frequency of subsequent repetitive puffs, vary about linearly with cluster size. These data accord well with stochastic simulations in which opening of any individual IP(3)R channel within a cluster triggers a puff via Ca(2+)-induced Ca(2+) release. An important consequence is that the signaling power of a puff site (average amount of Ca(2+) released per puff × puff frequency) varies about the square of cluster size, implying that large clusters contribute disproportionately to cellular signaling and, because of their higher puff frequency, preferentially act as pacemakers to initiate Ca(2+) waves.

Calretinin regulates Ca2+-dependent inactivation and facilitation of Ca(v)2.1 Ca2+ channels through a direct interaction with the α12.1 subunit

Voltage-gated Ca(v)2.1 Ca(2+) channels undergo dual modulation by Ca(2+), Ca(2+)-dependent inactivation (CDI), and Ca(2+)-dependent facilitation (CDF), which can influence synaptic plasticity in the nervous system. Although the molecular determinants controlling CDI and CDF have been the focus of intense research, little is known about the factors regulating these processes in neurons. Here, we show that calretinin (CR), a Ca(2+)-binding protein highly expressed in subpopulations of neurons in the brain, inhibits CDI and enhances CDF by binding directly to α(1)2.1. Screening of a phage display library with CR as bait revealed a highly basic CR-binding domain (CRB) present in multiple copies in the cytoplasmic linker between domains II and III of α(1)2.1. In pulldown assays, CR binding to fusion proteins containing these CRBs was largely Ca(2+)-dependent. α(1)2.1 coimmunoprecipitated with CR antibodies from transfected cells and mouse cerebellum, which confirmed the existence of CR-Ca(v)2.1 complexes in vitro and in vivo. In HEK293T cells, CR significantly decreased Ca(v)2.1 CDI and increased CDF. CR binding to α(1)2.1 was required for these effects, because they were not observed upon substitution of the II-III linker of α(1)2.1 with that from the Ca(v)1.2 α(1) subunit (α(1)1.2), which lacks the CRBs. In addition, coexpression of a protein containing the CRBs blocked the modulatory action of CR, most likely by competing with CR for interactions with α(1)2.1. Our findings highlight an unexpected role for CR in directly modulating effectors such as Ca(v)2.1, which may have major consequences for Ca(2+) signaling and neuronal excitability.

Termination of Ca²+ release for clustered IP₃R channels

In many cell types, release of calcium ions is controlled by inositol 1,4,5-trisphosphate () receptor channels. Elevations in concentration after intracellular release through receptors (R) can either propagate in the form of waves spreading through the entire cell or produce spatially localized puffs. The appearance of waves and puffs is thought to implicate random initial openings of one or a few channels and subsequent activation of neighboring channels because of an “autocatalytic” feedback. It is much less clear, however, what determines the further time course of release, particularly since the lifetime is very different for waves (several seconds) and puffs (around 100 ms). Here we study the lifetime of signals and their dependence on residual microdomains. Our general idea is that microdomains are dynamical and mediate the effect of other physiological processes. Specifically, we focus on the mechanism by which binding proteins (buffers) alter the lifetime of signals. We use stochastic simulations of channel gating coupled to a coarse-grained description for the concentration. To describe the concentration in a phenomenological way, we here introduce a differential equation, which reflects the buffer characteristics by a few effective parameters. This non-stationary model for microdomains gives deep insight into the dynamical differences between puffs and waves. It provides a novel explanation for the different lifetimes of puffs and waves and suggests that puffs are terminated by inhibition while unbinding is responsible for termination of waves. Thus our analysis hints at an additional role of and shows how cells can make use of the full complexity in R gating behavior to achieve different signals.

Calcium signals are important for a host of cellular processes such as neurotransmitter release, cell contraction and gene expression. While the principles of activation and spreading of calcium signals have been largely understood, it is much less clear how their spatio-temporal appearance is shaped. This issue is of high relevance since the spatio-temporal signature is thought to carry the information content. In our paper we study the dynamical mechanisms that determine the time course of calcium release from receptor channels. We use a stochastic channel description combined with a recently developed model for the distribution of released calcium in a microdomain. The simulations uncover a complex control mechanism, which allows for the tuning of release from short frequent puffs to extended and less frequent wave-like release. Unexpectedly, the model predicts that for wave-like release the dissociation of from the receptors leads to termination of the calcium signal. This effect relies on a well-known gating property of R channels, which earlier has been regarded as superfluous in studies for groups of channels. Our results also provide a missing link to understand cellular response to calcium-binding proteins and present a novel mechanism for information processing by R channels.

Visualizing metal ions in cells: an overview of analytical techniques, approaches, and probes

Quantifying the amount and defining the location of metal ions in cells and organisms are critical steps in understanding metal homeostasis and how dyshomeostasis causes or is a consequence of disease. A number of recent advances have been made in the development and application of analytical methods to visualize metal ions in biological specimens. Here, we briefly summarize these advances before focusing in more depth on probes for examining transition metals in living cells with high spatial and temporal resolution using fluorescence microscopy. This article is part of a Special Issue entitled: Cell Biology of Metals.

The activation state of the inositol 1,4,5-trisphosphate receptor regulates the velocity of intracellular Ca2+ waves in bovine aortic endothelial cells

Ca(2+) is a highly versatile second messenger that plays a key role in the regulation of many cell processes. This versatility resides in the fact that different signals can be encoded spatio-temporally by varying the frequency and amplitude of the Ca(2+) response. A typical example of an organized Ca(2+) signal is a Ca(2+) wave initiated in a given area of a cell that propagates throughout the entire cell or within a specific subcellular region. In non-excitable cells, the inositol 1,4,5-trisphosphate receptor (IP(3) R) is responsible for the release of Ca(2+) from the endoplasmic reticulum. IP(3) R activity can be directly modulated in many ways, including by interacting molecules, proteins, and kinases such as PKA, PKC, and mTOR. In the present study, we used a videomicroscopic approach to measure the velocity of Ca(2+) waves in bovine aortic endothelial cells under various conditions that affect IP(3) R function. The velocity of the Ca(2+) waves increased with the intensity of the stimulus while extracellular Ca(2+) had no significant impact on wave velocity. Forskolin increased the velocity of IP(3) R-dependent Ca(2+) waves whereas PMA and rapamycin decreased the velocity. We used scatter plots and Pearson's correlation test to visualize and quantify the relationship between the Ca(2+) peak amplitude and the velocity of Ca(2+) waves. The velocity of IP(3) R-dependent Ca(2+) waves poorly correlated with the amplitude of the Ca(2+) response elicited by agonists in all the conditions evaluated, indicating that the velocity depended on the activation state of IP(3) R, which can be modulated in many ways.

Endogenous cytosolic Ca(2+) buffering is necessary for TRPM4 activity in cerebral artery smooth muscle cells

The melastatin transient receptor potential (TRP) channel, TRPM4, is a critical regulator of smooth muscle membrane potential and arterial tone. Activation of the channel is Ca(2+)-dependent, but prolonged exposures to high global Ca(2+) causes rapid inactivation under conventional whole-cell patch clamp conditions. Using amphotericin B perforated whole cell patch clamp electrophysiology, which minimally disrupts cytosolic Ca(2+) dynamics, we recently showed that Ca(2+) released from 1,2,5-triphosphate receptors (IP(3)R) on the sarcoplasmic reticulum (SR) activates TRPM4 channels, producing sustained transient inward cation currents (TICCs). Thus, Ca(2+)-dependent inactivation of TRPM4 may not be inherent to the channel itself but rather is a result of the recording conditions. We hypothesized that under conventional whole-cell configurations, loss of intrinsic cytosolic Ca(2+) buffering following cell dialysis contributes to inactivation of TRPM4 channels. With the inclusion of the Ca(2+) buffers ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA, 10mM) or bis-ethane-N,N,N',N'-tetraacetic acid (BAPTA, 0.1mM) in the pipette solution, we mimic endogenous Ca(2+) buffering and record novel, sustained whole-cell TICC activity from freshly-isolated cerebral artery myocytes. Biophysical properties of TICCs recorded under perforated and whole-cell patch clamp were nearly identical. Furthermore, whole-cell TICC activity was reduced by the selective TRPM4 inhibitor, 9-phenanthrol, and by siRNA-mediated knockdown of TRPM4. When a higher concentration (10mM) of BAPTA was included in the pipette solution, TICC activity was disrupted, suggesting that TRPM4 channels on the plasma membrane and IP(3)R on the SR are closely opposed but not physically coupled, and that endogenous Ca(2+) buffer proteins play a critical role in maintaining TRPM4 channel activity in native cerebral artery smooth muscle cells.

Measuring the kinetics of calcium binding proteins with flash photolysis

BACKGROUND

Calcium-binding proteins (CBPs) are instrumental in the control of Ca2+ signaling. They are the fastest players within the Ca2+ toolkit responding within microseconds to [Ca2+] changes. The CBPs compete for Ca2+ which plays a direct role in modulating Ca2+ transients and the resulting biochemical message. The kinetic properties of the CBPs have to be known to have a good understanding of Ca2+ signaling.

SCOPE OF REVIEW

Most techniques used to measure binding kinetics are too slow to accurately determine the fast kinetics of most CBP. Furthermore, many CBPs bind Ca2+ in a cooperative way, which should be incorporated in the kinetic modeling. Here we will review a new ultra-fast in vitro technique for measuring Ca2+ binding properties of CBPs following flash photolysis of caged Ca2+. Compartmental modeling is used to resolve the kinetics of fast cooperative Ca2+ binding to CBPs.

MAJOR CONCLUSIONS

Currently this technique has only been used to quantify the kinetics of three CBPs (calbindin, calretinin and calmodulin), but has already provided remarkable insights into the specific role that these kinetics in Ca2+ signaling.

GENERAL SIGNIFICANCE

The potential to gain novel insights into Ca2+ signaling by quantifying kinetics of other CBPs using this technique is very promising. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signaling.

Inositol (1,4,5)-trisphosphate receptor microarchitecture shapes Ca2+ puff kinetics

Inositol (1,4,5)-trisphosphate receptors (IP(3)Rs) release intracellular Ca(2+) as localized Ca(2+) signals (Ca(2+) puffs) that represent the activity of small numbers of clustered IP(3)Rs spaced throughout the endoplasmic reticulum. Although much emphasis has been placed on estimating the number of active Ca(2+) release channels supporting Ca(2+) puffs, less attention has been placed on understanding the role of cluster microarchitecture. This is important as recent data underscores the dynamic nature of IP(3)R transitions between heterogeneous cellular architectures and the differential behavior of IP(3)Rs socialized into clusters. Here, we applied a high-resolution model incorporating stochastically gating IP(3)Rs within a three-dimensional cytoplasmic space to demonstrate: 1), Ca(2+) puffs are supported by a broad range of clustered IP(3)R microarchitectures; 2), cluster ultrastructure shapes Ca(2+) puff characteristics; and 3), loosely corralled IP(3)R clusters (>200 nm interchannel separation) fail to coordinate Ca(2+) puffs, owing to inefficient triggering and impaired coupling due to reduced Ca(2+)-induced Ca(2+) release microwave velocity (<10 nm/s) throughout the channel array. Dynamic microarchitectural considerations may therefore influence Ca(2+) puff occurrence/properties in intact cells, contrasting with a more minimal role for channel number over the same simulated conditions in shaping local Ca(2+) dynamics.

Calcium domains around single and clustered IP3 receptors and their modulation by buffers

We study Ca(2+) release through single and clustered IP(3) receptor channels on the ER membrane under presence of buffer proteins. Our computational scheme couples reaction-diffusion equations and a Markovian channel model and allows our investigating the effects of buffer proteins on local calcium concentrations and channel gating. We find transient and stationary elevations of calcium concentrations around active channels and show how they determine release amplitude. Transient calcium domains occur after closing of isolated channels and constitute an important part of the channel's feedback. They cause repeated openings (bursts) and mediate increased release due to Ca(2+) buffering by immobile proteins. Stationary domains occur during prolonged activity of clustered channels, where the spatial proximity of IP(3)Rs produces a distinct [Ca(2+)] scale (0.5-10 microM), which is smaller than channel pore concentrations (>100 microM) but larger than transient levels. While immobile buffer affects transient levels only, mobile buffers in general reduce both transient and stationary domains, giving rise to Ca(2+) evacuation and biphasic modulation of release amplitude. Our findings explain recent experiments in oocytes and provide a general framework for the understanding of calcium signals.

Cytosolic Ca2+ buffers

"Ca(2+) buffers," a class of cytosolic Ca(2+)-binding proteins, act as modulators of short-lived intracellular Ca(2+) signals; they affect both the temporal and spatial aspects of these transient increases in [Ca(2+)](i). Examples of Ca(2+) buffers include parvalbumins (α and β isoforms), calbindin-D9k, calbindin-D28k, and calretinin. Besides their proven Ca(2+) buffer function, some might additionally have Ca(2+) sensor functions. Ca(2+) buffers have to be viewed as one of the components implicated in the precise regulation of Ca(2+) signaling and Ca(2+) homeostasis. Each cell is equipped with proteins, including Ca(2+) channels, transporters, and pumps that, together with the Ca(2+) buffers, shape the intracellular Ca(2+) signals. All of these molecules are not only functionally coupled, but their expression is likely to be regulated in a Ca(2+)-dependent manner to maintain normal Ca(2+) signaling, even in the absence or malfunctioning of one of the components.

Cytosolic calcium regulates liver regeneration in the rat

Liver regeneration is regulated by growth factors, cytokines, and other endocrine and metabolic factors. Calcium is important for cell division, but its role in liver regeneration is not known. The purpose of this study was to understand the effects of cytosolic calcium signals in liver growth after partial hepatectomy (PH). The gene encoding the calcium-binding protein parvalbumin (PV) targeted to the cytosol using a nuclear export sequence (NES), and using a discosoma red fluorescent protein (DsR) marker, was transfected into rat livers by injecting it, in recombinant adenovirus (Ad), into the portal vein. We performed two-thirds PH 4 days after Ad-PV-NES-DsR or Ad-DsR injection, and liver regeneration was analyzed. Calcium signals were analyzed with fura-2-acetoxymethyl ester in hepatocytes isolated from Ad-infected rats and in Ad-infected Hela cells. Also, isolated hepatocytes were infected with Ad-DsR or Ad-PV-NES-DsR and assayed for bromodeoxyuridine incorporation. Ad-PV-NES-DsR injection resulted in PV expression in the hepatocyte cytosol. Agonist-induced cytosolic calcium oscillations were attenuated in both PV-NES-expressing Hela cells and hepatocytes, as compared to DsR-expressing cells. Bromodeoxyuridine incorporation (S phase), phosphorylated histone 3 immunostaining (mitosis), and liver mass restoration after PH were all significantly delayed in PV-NES rats. Reduced cyclin expression and retinoblastoma protein phosphorylation confirmed this observation. PV-NES rats exhibited reduced c-fos induction and delayed extracellular signal-regulated kinase 1/2 phosphorylation after PH. Finally, primary PV-NES-expressing hepatocytes exhibited less proliferation and agonist-induced cyclic adenosine monophosphate responsive element binding and extracellular signal-regulated kinase 1/2 phosphorylation, as compared with control cells.

CONCLUSION

Cytosolic calcium signals promote liver regeneration by enhancing progression of hepatocytes through the cell cycle.

Recording single-channel activity of inositol trisphosphate receptors in intact cells with a microscope, not a patch clamp

Optical single-channel recording is a novel tool for the study of individual Ca2+-permeable channels within intact cells under minimally perturbed physiological conditions. As applied to the functioning and spatial organization of IP3Rs, this approach complements our existing knowledge, which derives largely from reduced systems - such as reconstitution into lipid bilayers and patch clamping of IP3Rs on the membrane of excised nuclei - where the spatial arrangement and interactions among IP3Rs via CICR are disrupted. The ability to image the activity of single IP3R channels with millisecond resolution together with localization of their positions with a precision of a few tens of nanometers both raises several intriguing questions and holds promise of answers. In particular, what mechanism underlies the anchoring of puffs and blips to static locations; why do these Ca2+ release events appear to involve only a very small fraction of the IP3Rs within a cell; and how can we reconcile the relative immotility of functional IP3Rs with numerous studies reporting free diffusion of IP3R protein in the ER membrane?

Inositol trisphosphate 3-kinases: focus on immune and neuronal signaling

The localized control of second messenger levels sculpts dynamic and persistent changes in cell physiology and structure. Inositol trisphosphate [Ins(1,4,5)P(3)] 3-kinases (ITPKs) phosphorylate the intracellular second messenger Ins(1,4,5)P(3). These enzymes terminate the signal to release Ca(2+) from the endoplasmic reticulum and produce the messenger inositol tetrakisphosphate [Ins(1,3,4,5)P(4)]. Independent of their enzymatic activity, ITPKs regulate the microstructure of the actin cytoskeleton. The immune phenotypes of ITPK knockout mice raise new questions about how ITPKs control inositol phosphate lifetimes within spatial and temporal domains during lymphocyte maturation. The intense concentration of ITPK on actin inside the dendritic spines of pyramidal neurons suggests a role in signal integration and structural plasticity in the dendrite, and mice lacking neuronal ITPK exhibit memory deficits. Thus, the molecular and anatomical features of ITPKs allow them to regulate the spatiotemporal properties of intracellular signals, leading to the formation of persistent molecular memories.

Puff-wave transition in an inhomogeneous model for calcium signals

In many cell types, calcium ion channels on the endoplasmic reticulum membrane occur in a clustered distribution. The channels generate either localized puffs, each comprising channels of only one cluster, or global calcium waves. In this work we model the calcium system as a two-dimensional lattice of active elements distributed regularly in an otherwise passive space. We address an important feature of the puff-wave transition, which is the difference in lifetime of puffs at a few hundred milliseconds and long-lived global waves with periods of several seconds. We show that such a lifetime difference between puffs and waves can be understood with strongly reduced ordinary differential equations modified by a time-scale factor that takes into account the coupling strength of active and passive regions determined by the Ca2+ diffusion coefficient. Furthermore, we show that the point model can also describe very well the dependence of Ca2+ oscillation characteristics on the cluster-cluster distance in the case of large diffusivity.

Modeling of the modulation by buffers of Ca2+ release through clusters of IP3 receptors

Intracellular Ca(2+) release is a versatile second messenger system. It is modeled here by reaction-diffusion equations for the free Ca(2+) and Ca(2+) buffers, with spatially discrete clusters of stochastic IP(3) receptor channels (IP(3)Rs) controlling the release of Ca(2+) from the endoplasmic reticulum. IP(3)Rs are activated by a small rise of the cytosolic Ca(2+) concentration and inhibited by large concentrations. Buffering of cytosolic Ca(2+) shapes global Ca(2+) transients. Here we use a model to investigate the effect of buffers with slow and fast reaction rates on single release spikes. We find that, depending on their diffusion coefficient, fast buffers can either decouple clusters or delay inhibition. Slow buffers have little effect on Ca(2+) release, but affect the time course of the signals from the fluorescent Ca(2+) indicator mainly by competing for Ca(2+). At low [IP(3)], fast buffers suppress fluorescence signals, slow buffers increase the contrast between bulk signals and signals at open clusters, and large concentrations of buffers, either fast or slow, decouple clusters.

The carboxy-terminal tail of human cytomegalovirus (HCMV) US28 regulates both chemokine-independent and chemokine-dependent signaling in HCMV-infected cells

The human cytomegalovirus (HCMV)-encoded G-protein-coupled receptor (GPCR) US28 is a potent activator of a number of signaling pathways in HCMV-infected cells. The intracellular carboxy-terminal domain of US28 contains residues critical for the regulation of US28 signaling in heterologous expression systems; however, the role that this domain plays during HCMV infection remains unknown. For this study, we constructed an HCMV recombinant virus encoding a carboxy-terminal domain truncation mutant of US28, FLAG-US28/1-314, to investigate the role that this domain plays in US28 signaling. We demonstrate that US28/1-314 exhibits a more potent phospholipase C-beta (PLC-beta) signal than does wild-type US28, indicating that the carboxy-terminal domain plays an important role in regulating agonist-independent signaling in infected cells. Moreover, HMCV-infected cells expressing the US28/1-314 mutant exhibit a prolonged calcium signal in response to CCL5, indicating that the US28 carboxy-terminal domain also regulates agonist-dependent signaling. Finally, while the chemokine CX3CL1 behaves as an inverse agonist or inhibitor of constitutive US28 signaling to PLC-beta, we demonstrate that CX3CL1 functions as an agonist with regard to US28-stimulated calcium release. This study is the first to demonstrate that the carboxy terminus of US28 controls US28 signaling in the context of HCMV infection and indicates that chemokines such as CX3CL1 can decrease constitutive US28 signals and yet simultaneously promote nonconstitutive US28 signals.