An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging

Systemic nimodipine affects pericyte calcium signaling, resting hemodynamics and neurovascular coupling in healthy mouse brain

Nimodipine is a L-type voltage gated calcium channel blocker commonly given to patients after a sub-arachnoid hemorrhage. It is known to dilate cerebral arteries and affect brain pericytes that express voltage gated calcium channels. Here, we systemically administered nimodipine (1 ​mg/kg; i.p.) and measured brain pericyte calcium transients and single-vessel hemodynamics in the brains of mice by two-photon microscopy. We find that nimodipine reduces calcium transients in all types of pericytes, from ensheathing to thin-strand cells, at different locations in the vascular network. This induces local vasodilation of vessels closer to penetrating arterioles but decreases blood cell velocity. These vascular consequences are due to systemic nimodipine effects because direct brain application of nimodipine caused blood cell velocity to increase. Nimodipine treatment also reduced further dilation during neurovascular coupling throughout the vascular network. Overall, this suggests that nimodipine can change cerebrovascular hemodynamics by altering pericyte physiology and these are important considerations for the clinical use of this drug.

Single-particle tracking reveals heterogeneous PIEZO1 diffusion

The mechanically activated ion channel PIEZO1 is critical to numerous physiological processes, and is activated by diverse mechanical cues. The channel is gated by membrane tension and has been found to be mobile in the plasma membrane. We employed single-particle tracking (SPT) of endogenous, tdTomato-tagged PIEZO1 using total internal reflection fluorescence microscopy in live cells. Application of SPT unveiled a surprising heterogeneity of diffusing PIEZO1 subpopulations, which we labeled "mobile" and "immobile." We sorted these trajectories into the two aforementioned categories using trajectory spread. To evaluate the effects of the plasma membrane composition on PIEZO1 diffusion, we manipulated membrane composition by depleting or supplementing cholesterol, or by adding margaric acid to stiffen the membrane. To examine effects of channel activation on PIEZO1 mobility, we treated cells with Yoda1, a PIEZO1 agonist, and GsMTx-4, a channel inhibitor. We collected thousands of trajectories for each condition, and found that cholesterol removal and Yoda1 incubation increased the channel's propensity for mobility. Conversely, we found that GsMTx-4 incubation and cholesterol supplementation resulted in a lower chance of mobile trajectories, whereas margaric acid incubation did not have a significant effect on PIEZO1 mobility. The mobile trajectories were analyzed further by fitting the time-averaged mean-squared displacement as a function of lag time to a power law model, revealing that mobile PIEZO1 puncta exhibit anomalous subdiffusion. These studies illuminate the fundamental properties governing PIEZO1 diffusion in the plasma membrane and set the stage to determine how cellular processes and interactions may influence channel activity and mobility.

Dual regulation of IP3 receptors by IP3 and PIP2 controls the transition from local to global Ca2+ signals

The spatial organization of inositol 1,4,5-trisphosphate (IP3)-evoked Ca2+ signals underlies their versatility. Low stimulus intensities evoke Ca2+ puffs, localized Ca2+ signals arising from a few IP3 receptors (IP3Rs) within a cluster tethered beneath the plasma membrane. More intense stimulation evokes global Ca2+ signals. Ca2+ signals propagate regeneratively as the Ca2+ released stimulates more IP3Rs. How is this potentially explosive mechanism constrained to allow local Ca2+ signaling? We developed methods that allow IP3 produced after G-protein coupled receptor (GPCR) activation to be intercepted and replaced by flash photolysis of a caged analog of IP3. We find that phosphatidylinositol 4,5-bisphosphate (PIP2) primes IP3Rs to respond by partially occupying their IP3-binding sites. As GPCRs stimulate IP3 formation, they also deplete PIP2, relieving the priming stimulus. Loss of PIP2 resets IP3R sensitivity and delays the transition from local to global Ca2+ signals. Dual regulation of IP3Rs by PIP2 and IP3 through GPCRs controls the transition from local to global Ca2+ signals.

Astrocytes adopt a progenitor-like migratory strategy for regeneration in adult brain

Mature astrocytes become activated upon non-specific tissue damage and contribute to glial scar formation. Proliferation and migration of adult reactive astrocytes after injury is considered very limited. However, the regenerative behavior of individual astrocytes following selective astroglial loss, as seen in astrocytopathies, such as neuromyelitis optica spectrum disorder, remains unexplored. Here, we performed longitudinal in vivo imaging of cortical astrocytes after focal astrocyte ablation in mice. We discovered that perilesional astrocytes develop a remarkable plasticity for efficient lesion repopulation. A subset of mature astrocytes transforms into reactive progenitor-like (REPL) astrocytes that not only undergo multiple asymmetric divisions but also remain in a multinucleated interstage. This regenerative response facilitates efficient migration of newly formed daughter cell nuclei towards unoccupied astrocyte territories. Our findings define the cellular principles of astrocyte plasticity upon focal lesion, unravelling the REPL phenotype as a fundamental regenerative strategy of mature astrocytes to restore astrocytic networks in the adult mammalian brain. Promoting this regenerative phenotype bears therapeutic potential for neurological conditions involving glial dysfunction.

Two-pore channel-2 and inositol trisphosphate receptors coordinate Ca2+ signals between lysosomes and the endoplasmic reticulum

Lysosomes and the endoplasmic reticulum (ER) are Ca2+ stores mobilized by the second messengers NAADP and IP3, respectively. Here, we establish Ca2+ signals between the two sources as fundamental building blocks that couple local release to global changes in Ca2+. Cell-wide Ca2+ signals evoked by activation of endogenous NAADP-sensitive channels on lysosomes comprise both local and global components and exhibit a major dependence on ER Ca2+ despite their lysosomal origin. Knockout of ER IP3 receptor channels delays these signals, whereas expression of lysosomal TPC2 channels accelerates them. High-resolution Ca2+ imaging reveals elementary events upon TPC2 opening and signals coupled to IP3 receptors. Biasing TPC2 activation to a Ca2+-permeable state sensitizes local Ca2+ signals to IP3. This increases the potency of a physiological agonist to evoke global Ca2+ signals and activate a downstream target. Our data provide a conceptual framework to understand how Ca2+ release from physically separated stores is coordinated.

Novel algorithms for improved detection and analysis of fluorescent signal fluctuations

Fluorescent dyes and genetically encoded fluorescence indicators (GEFI) are common tools for visualizing concentration changes of specific ions and messenger molecules during intra- as well as intercellular communication. Using advanced imaging technologies, fluorescence indicators are a prerequisite for the analysis of physiological molecular signaling. Automated detection and analysis of fluorescence signals require to overcome several challenges, including correct estimation of fluorescence fluctuations at basal concentrations of messenger molecules, detection, and extraction of events themselves as well as proper segmentation of neighboring events. Moreover, event detection algorithms need to be sensitive enough to accurately capture localized and low amplitude events exhibiting a limited spatial extent. Here, we present two algorithms (PBasE and CoRoDe) for accurate baseline estimation and automated detection and segmentation of fluorescence fluctuations.

Dissociation of inositol 1,4,5-trisphosphate from IP3 receptors contributes to termination of Ca2+ puffs

Ca²⁺ puffs are brief, localized Ca²⁺ signals evoked by physiological stimuli that arise from the coordinated opening of a few clustered inositol 1,4,5-trisphosphate receptors (IP₃Rs). However, the mechanisms that control the amplitude and termination of Ca²⁺ puffs are unresolved. To address these issues, we expressed SNAP-tagged IP₃R3 in HEK cells without endogenous IP₃Rs and used total internal reflection fluorescence microscopy to visualize the subcellular distribution of IP₃Rs and the Ca²⁺ puffs that they evoke. We first confirmed that SNAP-IP₃R3 were reliably identified and that they evoked normal Ca²⁺ puffs after photolysis of a caged analog of IP₃. We show that increased IP₃R expression caused cells to assemble more IP₃R clusters, each of which contained more IP₃Rs, but the mean amplitude of Ca²⁺ puffs (indicative of the number of open IP₃Rs) was unaltered. We thus suggest that functional interactions between IP₃Rs constrain the number of active IP₃Rs within a cluster. Furthermore, Ca²⁺ puffs evoked by IP₃R with reduced affinity for IP₃ had undiminished amplitude, but the puffs decayed more quickly. The selective effect of reducing IP₃ affinity on the decay times of Ca²⁺ puffs was not mimicked by exposing normal IP₃R to a lower concentration of IP₃. We conclude that distinct mechanisms constrain recruitment of IP₃Rs during the rising phase of a Ca²⁺ puff and closure of IP₃Rs during the falling phase, and that only the latter is affected by the rate of IP₃ dissociation.

Algorithm for biological second messenger analysis with dynamic regions of interest

Physiological function is regulated through cellular communication that is facilitated by multiple signaling molecules such as second messengers. Analysis of signal dynamics obtained from cell and tissue imaging is difficult because of intricate spatially and temporally distinct signals. Signal analysis tools based on static region of interest analysis may under- or overestimate signals in relation to region of interest size and location. Therefore, we developed an algorithm for biological signal detection and analysis based on dynamic regions of interest, where time-dependent polygonal regions of interest are automatically assigned to the changing perimeter of detected and segmented signals. This approach allows signal profiles to be rigorously and precisely tracked over time, eliminating the signal distortion observed with static methods. Integration of our approach with state-of-the-art image processing and particle tracking pipelines enabled the isolation of dynamic cellular signaling events and characterization of biological signaling patterns with distinct combinations of parameters including amplitude, duration, and spatial spread. Our algorithm was validated using synthetically generated datasets and compared with other available methods. Application of the algorithm to volumetric time-lapse hyperspectral images of cyclic adenosine monophosphate measurements in rat microvascular endothelial cells revealed distinct signal heterogeneity with respect to cell depth, confirming the utility of our approach for analysis of 5-dimensional data. In human tibial arteries, our approach allowed the identification of distinct calcium signal patterns associated with atherosclerosis. Our algorithm for automated detection and analysis of second messenger signals enables the decoding of signaling patterns in diverse tissues and identification of pathologic cellular responses.

Missense mutations in inositol 1,4,5-trisphosphate receptor type 3 result in leaky Ca2+ channels and activation of store-operated Ca2+ entry

Mutations in all subtypes of the inositol 1,4,5-trisphosphate receptor Ca2+ release channel are associated with human diseases. In this report, we investigated the functionality of three neuropathy-associated missense mutations in IP3R3 (V615M, T1424M, and R2524C). The mutants only exhibited function when highly over-expressed compared to endogenous hIP3R3. All variants resulted in elevated basal cytosolic Ca2+ levels, decreased endoplasmic reticulum Ca2+ store content, and constitutive store-operated Ca2+ entry in the absence of any stimuli, consistent with a leaky IP3R channel pore. These variants differed in channel function; when stably over-expressed the R2524C mutant was essentially dead, V615M was poorly functional, and T1424M exhibited activity greater than that of the corresponding wild-type following threshold stimulation. These results demonstrate that a common feature of these mutations is decreased IP3R3 function. In addition, these mutations exhibit a novel phenotype manifested as a constitutively open channel, which inappropriately gates SOCE in the absence of stimulation.

Functional determination of calcium-binding sites required for the activation of inositol 1,4,5-trisphosphate receptors

Inositol 1,4,5-trisphosphate receptors (IP3Rs) initiate a diverse array of physiological responses by carefully orchestrating intracellular calcium (Ca2+) signals in response to various external cues. Notably, IP3R channel activity is determined by several obligatory factors, including IP3, Ca2+, and ATP. The critical basic amino acid residues in the N-terminal IP3-binding core (IBC) region that facilitate IP3 binding are well characterized. In contrast, the residues conferring regulation by Ca2+ have yet to be ascertained. Using comparative structural analysis of Ca2+-binding sites identified in two main families of intracellular Ca2+-release channels, ryanodine receptors (RyRs) and IP3Rs, we identified putative acidic residues coordinating Ca2+ in the cytosolic calcium sensor region in IP3Rs. We determined the consequences of substituting putative Ca2+ binding, acidic residues in IP3R family members. We show that the agonist-induced Ca2+ release, single-channel open probability (P0), and Ca2+ sensitivities are markedly altered when the negative charge on the conserved acidic side chain residues is neutralized. Remarkably, neutralizing the negatively charged side chain on two of the residues individually in the putative Ca2+-binding pocket shifted the Ca2+ required to activate IP3R to higher concentrations, indicating that these residues likely are a component of the Ca2+ activation site in IP3R. Taken together, our findings indicate that Ca2+ binding to a well-conserved activation site is a common underlying mechanism resulting in increased channel activity shared by IP3Rs and RyRs.

KRAP is required for diffuse and punctate IP3-mediated Ca2+ liberation and determines the number of functional IP3R channels within clusters

KRas-induced actin-interacting protein (KRAP) has been identified as crucial for the appropriate localization and functioning of the inositol trisphosphate receptors (IP₃Rs) that mediate Ca²⁺ release from the endoplasmic reticulum. Here, we used siRNA knockdown of KRAP expression in HeLa and HEK293 cells to examine the roles of KRAP in the generation of IP₃-mediated local Ca²⁺ puffs and global, cell-wide Ca²⁺ signals. High resolution Ca²⁺ imaging revealed that the mean amplitude of puffs was strongly reduced by KRAP knockdown, whereas the Ca²⁺ flux during openings of individual IP₃R channels was little affected. In both control and KRAP knockdown cells the numbers of functional channels in the clusters underlying puff sites were stochastically distributed following a Poisson relationship, but the mean number of functional channels per site was reduced by about two thirds by KRAP knockdown. We conclude that KRAP is required for activity of IP₃R channels at puff sites and stochastically 'licenses' the function of individual channels on a one-to-one basis, rather than determining the functioning of the puff site as a whole. In addition to puff activity ('punctate' Ca²⁺ release), global, cell-wide Ca²⁺ signals evoked by higher levels of IP₃ are further composed from a discrete 'diffuse' mode of Ca²⁺ release. By applying fluctuation analysis to isolate the punctate component during global Ca²⁺ signals, we find that KRAP knockdown suppresses to similar extents punctate and diffuse Ca²⁺ release in wild-type cells and in HEK293 cells exclusively expressing type 1 and type 3 IP3Rs. Thus, KRAP appears essential for the functioning of the IP₃Rs involved in diffuse Ca²⁺ release as well as the clustered IP₃Rs that generate local Ca²⁺ puffs.

Segregated cation flux by TPC2 biases Ca2+ signaling through lysosomes

Two-pore channels are endo-lysosomal cation channels with malleable selectivity filters that drive endocytic ion flux and membrane traffic. Here we show that TPC2 can differentially regulate its cation permeability when co-activated by its endogenous ligands, NAADP and PI(3,5)P₂. Whereas NAADP rendered the channel Ca²⁺-permeable and PI(3,5)P₂ rendered the channel Na⁺-selective, a combination of the two increased Ca²⁺ but not Na⁺ flux. Mechanistically, this was due to an increase in Ca²⁺ permeability independent of changes in ion selectivity. Functionally, we show that cell permeable NAADP and PI(3,5)P₂ mimetics synergistically activate native TPC2 channels in live cells, globalizing cytosolic Ca²⁺ signals and regulating lysosomal pH and motility. Our data reveal that flux of different ions through the same pore can be independently controlled and identify TPC2 as a likely coincidence detector that optimizes lysosomal Ca²⁺ signaling.

TPC2 is a lysosomal ion channel permeable to both calcium and sodium ions. Here, the authors show that TPC2 can selectively increase its calcium permeability when simultaneously challenged by both its natural activators- NAADP and PI(3,5)P₂.

Computational Methods for Neuron Segmentation in Two-Photon Calcium Imaging Data: A Survey

Calcium imaging has rapidly become a methodology of choice for real-time in vivo neuron analysis. Its application to large sets of data requires automated tools to annotate and segment cells, allowing scalable image segmentation under reproducible criteria. In this paper, we review and summarize the most recent methods for computational segmentation of calcium imaging. The contributions of the paper are three-fold: we provide an overview of the main algorithms taxonomized in three categories (signal processing, matrix factorization and machine learning-based approaches), we highlight the main advantages and disadvantages of each category and we provide a summary of the performance of the methods that have been tested on public benchmarks (with links to the public code when available).

Decoupling astrocytes in adult mice impairs synaptic plasticity and spatial learning

The mechanisms by which astrocytes modulate neural homeostasis, synaptic plasticity, and memory are still poorly explored. Astrocytes form large intercellular networks by gap junction coupling, mainly composed of two gap junction channel proteins, connexin 30 (Cx30) and connexin 43 (Cx43). To circumvent developmental perturbations and to test whether astrocytic gap junction coupling is required for hippocampal neural circuit function and behavior, we generate and study inducible, astrocyte-specific Cx30 and Cx43 double knockouts. Surprisingly, disrupting astrocytic coupling in adult mice results in broad activation of astrocytes and microglia, without obvious signs of pathology. We show that hippocampal CA1 neuron excitability, excitatory synaptic transmission, and long-term potentiation are significantly affected. Moreover, behavioral inspection reveals deficits in sensorimotor performance and a complete lack of spatial learning and memory. Together, our findings establish that astrocytic connexins and an intact astroglial network in the adult brain are vital for neural homeostasis, plasticity, and spatial cognition.

TREM2 regulates purinergic receptor-mediated calcium signaling and motility in human iPSC-derived microglia

The membrane protein TREM2 (Triggering Receptor Expressed on Myeloid cells 2) regulates key microglial functions including phagocytosis and chemotaxis. Loss-of-function variants of TREM2 are associated with increased risk of Alzheimer's disease (AD). Because abnormalities in Ca2+ signaling have been observed in several AD models, we investigated TREM2 regulation of Ca2+ signaling in human induced pluripotent stem cell-derived microglia (iPSC-microglia) with genetic deletion of TREM2. We found that iPSC-microglia lacking TREM2 (TREM2 KO) show exaggerated Ca2+ signals in response to purinergic agonists, such as ADP, that shape microglial injury responses. This ADP hypersensitivity, driven by increased expression of P2Y12 and P2Y13 receptors, results in greater release of Ca2+ from the endoplasmic reticulum stores, which triggers sustained Ca2+ influx through Orai channels and alters cell motility in TREM2 KO microglia. Using iPSC-microglia expressing the genetically encoded Ca2+ probe, Salsa6f, we found that cytosolic Ca2+ tunes motility to a greater extent in TREM2 KO microglia. Despite showing greater overall displacement, TREM2 KO microglia exhibit reduced directional chemotaxis along ADP gradients. Accordingly, the chemotactic defect in TREM2 KO microglia was rescued by reducing cytosolic Ca2+ using a P2Y12 receptor antagonist. Our results show that loss of TREM2 confers a defect in microglial Ca2+ response to purinergic signals, suggesting a window of Ca2+ signaling for optimal microglial motility.

Distinct movement patterns generate stages of spider web building

The geometric complexity and stereotypy of spider webs have long generated interest in their algorithmic origin. Like other examples of animal architecture, web construction is the result of several assembly phases that are driven by distinct behavioral stages coordinated to build a successful structure. Manual observations have revealed a range of sensory cues and movement patterns used during web construction, but methods to systematically quantify the dynamics of these sensorimotor patterns are lacking. Here, we apply an analytical pipeline to quantify web-making behavior of the orb-weaver Uloborus diversus. Position tracking revealed stereotyped stages of construction that could occur in typical or atypical progressions across individuals. Using an unsupervised clustering approach, we identified general and stage-specific leg movements. A hierarchical hidden Markov model revealed that web-building stages are characterized by stereotyped sequences of actions largely shared across individuals, regardless of whether these stages progress in a typical or an atypical fashion. Web stages could be predicted based on action sequences alone, revealing that web-stage geometries are a physical manifestation of behavioral transition regimes.

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.

CREB regulates the expression of type 1 inositol 1,4,5-trisphosphate receptors

Inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) play a central role in regulating intracellular Ca2+ signals in response to a variety of internal and external cues. Dysregulation of IP3R signaling is the underlying cause for numerous pathological conditions. It is well established that the activities of IP3Rs are governed by several post-translational modifications, including phosphorylation by protein kinase A (PKA). However, the long-term effects of PKA activation on expression of IP3R subtypes remains largely unexplored. In this report, we investigate the effects of chronic stimulation and tonic activity of PKA on the expression of IP3R subtypes. We demonstrate that expression of the type 1 IP3R (IP3R1) is augmented upon prolonged activation of PKA or upon ectopic overexpression of cyclic AMP-response element-binding protein (CREB) without altering IP3R2 and IP3R3 abundance. By contrast, inhibition of PKA or blocking CREB diminished IP3R1 expression. We also demonstrate that agonist-induced Ca2+-release mediated by IP3R1 is significantly attenuated upon blocking of CREB. Moreover, CREB - by regulating the expression of KRAS-induced actin-interacting protein (KRAP) - ensures correct localization and licensing of IP3R1. Overall, we report a crucial role for CREB in governing both the expression and correct localization of IP3R1. This article has an associated First Person interview with the first author of the paper.

A protocol for detecting elemental calcium signals (Ca2+ puffs) in mammalian cells using total internal reflection fluorescence microscopy

This protocol outlines steps to visualize and detect Ca2+ puffs following photo-liberation of caged inositol-1,4,5-trisphosphate (IP3) from HEK-293 cells expressing only the native IP3R type 1 receptor using total internal reflection fluorescence (TIRF) microscopy. TIRF microscopy offers high axial resolution and allows imaging at high speed, with a higher signal-to-background ratio. Additionally, we shed light on commonly encountered pitfalls, which should be considered while recording Ca2+ puffs using TIRF microscopy. For complete details on the use and execution of this protocol, please refer to Emrich et al. (2021) and Lock et al. (2015a).

The Mitochondrial Ca2+ uniporter is a central regulator of interorganellar Ca2+ transfer and NFAT activation

Mitochondrial Ca²⁺ uptake tailors the strength of stimulation of plasma membrane phospholipase C–coupled receptors to that of cellular bioenergetics. However, how Ca²⁺ uptake by the mitochondrial Ca²⁺ uniporter (MCU) shapes receptor-evoked interorganellar Ca²⁺ signaling is unknown. Here, we used CRISPR/Cas9 gene knockout, subcellular Ca²⁺ imaging, and mathematical modeling to show that MCU is a universal regulator of intracellular Ca²⁺ signaling across mammalian cell types. MCU activity sustains cytosolic Ca²⁺ signaling by preventing Ca²⁺-dependent inactivation of store-operated Ca²⁺ release–activated Ca²⁺ channels and by inhibiting Ca²⁺ extrusion. Paradoxically, MCU knockout (MCU-KO) enhanced cytosolic Ca²⁺ responses to store depletion. Physiological agonist stimulation in MCU-KO cells led to enhanced frequency of cytosolic Ca²⁺ oscillations, endoplasmic reticulum Ca²⁺ refilling, nuclear translocation of nuclear factor for activated T cells transcription factors, and cell proliferation, without altering inositol-1,4,5-trisphosphate receptor activity. Our data show that MCU has dual counterbalancing functions at the cytosol–mitochondria interface, whereby the cell-specific MCU-dependent cytosolic Ca²⁺ clearance and buffering capacity of mitochondria reciprocally regulate interorganellar Ca²⁺ transfer and nuclear factor for activated T cells nuclear translocation during receptor-evoked signaling. These findings highlight the critical dual function of the MCU not only in the acute Ca²⁺ buffering by mitochondria but also in shaping endoplasmic reticulum and cytosolic Ca²⁺ signals that regulate cellular transcription and function.

KRAP tethers IP3 receptors to actin and licenses them to evoke cytosolic Ca2+ signals

Regulation of IP₃ receptors (IP₃Rs) by IP₃ and Ca²⁺ allows regenerative Ca²⁺ signals, the smallest being Ca²⁺ puffs, which arise from coordinated openings of a few clustered IP₃Rs. Cells express thousands of mostly mobile IP₃Rs, yet Ca²⁺ puffs occur at a few immobile IP₃R clusters. By imaging cells with endogenous IP₃Rs tagged with EGFP, we show that KRas-induced actin-interacting protein (KRAP) tethers IP₃Rs to actin beneath the plasma membrane. Loss of KRAP abolishes Ca²⁺ puffs and the global increases in cytosolic Ca²⁺ concentration evoked by more intense stimulation. Over-expressing KRAP immobilizes additional IP₃R clusters and results in more Ca²⁺ puffs and larger global Ca²⁺ signals. Endogenous KRAP determines which IP₃Rs will respond: it tethers IP₃R clusters to actin alongside sites where store-operated Ca²⁺ entry occurs, licenses IP₃Rs to evoke Ca²⁺ puffs and global cytosolic Ca²⁺ signals, implicates the actin cytoskeleton in IP₃R regulation and may allow local activation of Ca²⁺ entry.

Distinct signatures of calcium activity in brain mural cells

Pericytes have been implicated in various neuropathologies, yet little is known about their function and signaling pathways in health. Here, we characterized calcium dynamics of cortical mural cells in anesthetized or awake Pdgfrb-CreERT2;Rosa26< LSL-GCaMP6s > mice and in acute brain slices. Smooth muscle cells (SMCs) and ensheathing pericytes (EPs), also named as terminal vascular SMCs, revealed similar calcium dynamics in vivo. In contrast, calcium signals in capillary pericytes (CPs) were irregular, higher in frequency, and occurred in cellular microdomains. In the absence of the vessel constricting agent U46619 in acute slices, SMCs and EPs revealed only sparse calcium signals, whereas CPs retained their spontaneous calcium activity. Interestingly, chemogenetic activation of neurons in vivo and acute elevations of extracellular potassium in brain slices strongly decreased calcium activity in CPs. We propose that neuronal activation and an extracellular increase in potassium suppress calcium activity in CPs, likely mediated by Kir2.2 and KATP channels.

Glucose and NAADP trigger elementary intracellular β-cell Ca2+ signals

Pancreatic β-cells release insulin upon a rise in blood glucose. The precise mechanisms of stimulus-secretion coupling, and its failure in Diabetes Mellitus Type 2, remain to be elucidated. The consensus model, as well as a class of currently prescribed anti-diabetic drugs, are based around the observation that glucose-evoked ATP production in β-cells leads to closure of cell membrane ATP-gated potassium (K_ATP) channels, plasma membrane depolarisation, Ca²⁺ influx, and finally the exocytosis of insulin granules. However, it has been demonstrated by the inactivation of this pathway using genetic and pharmacological means that closure of the K_ATP channel alone may not be sufficient to explain all β-cell responses to glucose elevation. We have previously proposed that NAADP-evoked Ca²⁺ release is an important step in stimulus-secretion coupling in pancreatic β-cells. Here we show using total internal reflection fluorescence (TIRF) microscopy that glucose as well as the Ca²⁺ mobilising messenger nicotinic acid adenine dinucleotide phosphate (NAADP), known to operate in β-cells, lead to highly localised elementary intracellular Ca²⁺ signals. These were found to be obscured by measurements of global Ca²⁺ signals and the action of powerful SERCA-based sequestration mechanisms at the endoplasmic reticulum (ER). Building on our previous work demonstrating that NAADP-evoked Ca²⁺ release is an important step in stimulus-secretion coupling in pancreatic β-cells, we provide here the first demonstration of elementary Ca²⁺ signals in response to NAADP, whose occurrence was previously suspected. Optical quantal analysis of these events reveals a unitary event amplitude equivalent to that of known elementary Ca²⁺ signalling events, inositol trisphosphate (IP₃) receptor mediated blips, and ryanodine receptor mediated quarks. We propose that a mechanism based on these highly localised intracellular Ca²⁺ signalling events mediated by NAADP may initially operate in β-cells when they respond to elevations in blood glucose.

Comparative Effects of Event Detection Methods on the Analysis and Interpretation of Ca2+ Imaging Data

Calcium imaging has gained substantial popularity as a tool to profile the activity of multiple simultaneously active cells at high spatiotemporal resolution. Among the diverse approaches to processing of Ca²⁺ imaging data is an often subjective decision of how to quantify baseline fluorescence or F ₀. We examine the effect of popular F ₀ determination methods on the interpretation of neuronal and astrocyte activity in a single dataset of rats trained to self-administer intravenous infusions of cocaine and compare them with an F ₀-independent wavelet ridgewalking event detection approach. We find that the choice of the processing method has a profound impact on the interpretation of widefield imaging results. All of the dF/F ₀ thresholding methods tended to introduce spurious events and fragment individual transients, leading to smaller calculated event durations and larger event frequencies. Analysis of simulated datasets confirmed these observations and indicated substantial intermethod variability as to the events classified as significant. Additionally, most dF/F ₀ methods on their own were unable to adequately account for bleaching of fluorescence, although the F ₀ smooth approach and the wavelet ridgewalking algorithm both did so. In general, the choice of the processing method led to dramatically different quantitative and sometimes opposing qualitative interpretations of the effects of cocaine self-administration both at the level of individual cells and at the level of cell networks. Significantly different distributions of event duration, amplitude, frequency, and network measures were found across the majority of dF/F ₀ approaches. The wavelet ridgewalking algorithm broadly outperformed dF/F ₀-based methods for both neuron and astrocyte recordings. These results indicate the need for heightened awareness of the limitations and tendencies associated with decisions to use particular Ca²⁺ image processing pipelines. Both quantification and interpretation of the effects of experimental manipulations are strongly sensitive to such decisions.

Omnitemporal choreographies of all five STIM/Orai and IP3Rs underlie the complexity of mammalian Ca2+ signaling

Stromal-interaction molecules (STIM1/2) sense endoplasmic reticulum (ER) Ca²⁺ depletion and activate Orai channels. However, the choreography of interactions between native STIM/Orai proteins under physiological agonist stimulation is unknown. We show that the five STIM1/2 and Orai1/2/3 proteins are non-redundant and function together to ensure the graded diversity of mammalian Ca²⁺ signaling. Physiological Ca²⁺ signaling requires functional interactions between STIM1/2, Orai1/2/3, and IP₃Rs, ensuring that receptor-mediated Ca²⁺ release is tailored to Ca²⁺ entry and nuclear factor of activated T cells (NFAT) activation. The N-terminal Ca²⁺-binding ER-luminal domains of unactivated STIM1/2 inhibit IP₃R-evoked Ca²⁺ release. A gradual increase in agonist intensity and STIM1/2 activation relieves IP₃R inhibition. Concomitantly, activated STIM1/2 C termini differentially interact with Orai1/2/3 as agonist intensity increases. Thus, coordinated and omnitemporal functions of all five STIM/Orai and IP₃Rs translate the strength of agonist stimulation to precise levels of Ca²⁺ signaling and NFAT induction, ensuring the fidelity of complex mammalian Ca²⁺ signaling.

ER-luminal [Ca2+] regulation of InsP3 receptor gating mediated by an ER-luminal peripheral Ca2+-binding protein

Modulating cytoplasmic Ca2+ concentration ([Ca2+]i) by endoplasmic reticulum (ER)-localized inositol 1,4,5-trisphosphate receptor (InsP3R) Ca2+-release channels is a universal signaling pathway that regulates numerous cell-physiological processes. Whereas much is known regarding regulation of InsP3R activity by cytoplasmic ligands and processes, its regulation by ER-luminal Ca2+ concentration ([Ca2+]ER) is poorly understood and controversial. We discovered that the InsP3R is regulated by a peripheral membrane-associated ER-luminal protein that strongly inhibits the channel in the presence of high, physiological [Ca2+]ER. The widely-expressed Ca2+-binding protein annexin A1 (ANXA1) is present in the nuclear envelope lumen and, through interaction with a luminal region of the channel, can modify high-[Ca2+]ER inhibition of InsP3R activity. Genetic knockdown of ANXA1 expression enhanced global and local elementary InsP3-mediated Ca2+ signaling events. Thus, [Ca2+]ER is a major regulator of InsP3R channel activity and InsP3R-mediated [Ca2+]i signaling in cells by controlling an interaction of the channel with a peripheral membrane-associated Ca2+-binding protein, likely ANXA1.

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.

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.

QuantiMus: A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology

Skeletal muscle injury provokes a regenerative response, characterized by the de novo generation of myofibers that are distinguished by central nucleation and re-expression of developmentally restricted genes. In addition to these characteristics, myofiber cross-sectional area (CSA) is widely used to evaluate muscle hypertrophic and regenerative responses. Here, we introduce QuantiMus, a free software program that uses machine learning algorithms to quantify muscle morphology and molecular features with high precision and quick processing-time. The ability of QuantiMus to define and measure myofibers was compared to manual measurement or other automated software programs. QuantiMus rapidly and accurately defined total myofibers and measured CSA with comparable performance but quantified the CSA of centrally-nucleated fibers (CNFs) with greater precision compared to other software. It additionally quantified the fluorescence intensity of individual myofibers of human and mouse muscle, which was used to assess the distribution of myofiber type, based on the myosin heavy chain isoform that was expressed. Furthermore, analysis of entire quadriceps cross-sections of healthy and mdx mice showed that dystrophic muscle had an increased frequency of Evans blue dye+ injured myofibers. QuantiMus also revealed that the proportion of centrally nucleated, regenerating myofibers that express embryonic myosin heavy chain (eMyHC) or neural cell adhesion molecule (NCAM) were increased in dystrophic mice. Our findings reveal that QuantiMus has several advantages over existing software. The unique self-learning capacity of the machine learning algorithms provides superior accuracy and the ability to rapidly interrogate the complete muscle section. These qualities increase rigor and reproducibility by avoiding methods that rely on the sampling of representative areas of a section. This is of particular importance for the analysis of dystrophic muscle given the "patchy" distribution of muscle pathology. QuantiMus is an open source tool, allowing customization to meet investigator-specific needs and provides novel analytical approaches for quantifying muscle morphology.

Increased Vascular Contractility in Hypertension Results From Impaired Endothelial Calcium Signaling

Supplemental Digital Content is available in the text.

Endothelial cells line all blood vessels and are critical regulators of vascular tone. In hypertension, disruption of endothelial function alters the release of endothelial-derived vasoactive factors and results in increased vascular tone. Although the release of endothelial-derived vasodilators occurs in a Ca²⁺-dependent manner, little is known on how Ca²⁺ signaling is altered in hypertension. A key element to endothelial control of vascular tone is Ca²⁺ signals at specialized regions (myoendothelial projections) that connect endothelial cells and smooth muscle cells. This work describes disruption in the operation of this key Ca²⁺ signaling pathway in hypertension. We show that vascular reactivity to phenylephrine is increased in hypertensive (spontaneously hypertensive rat) when compared with normotensive (Wistar Kyoto) rats. Basal endothelial Ca²⁺ activity limits vascular contraction, but that Ca²⁺-dependent control is impaired in hypertension. When changes in endothelial Ca²⁺ levels are buffered, vascular contraction to phenylephrine increased, resulting in similar responses in normotension and hypertension. Local endothelial IP₃(inositol trisphosphate)-mediated Ca²⁺ signals are smaller in amplitude, shorter in duration, occur less frequently, and arise from fewer sites in hypertension. Spatial control of endothelial Ca²⁺ signaling is also disrupted in hypertension: local Ca²⁺ signals occur further from myoendothelial projections in hypertension. The results demonstrate that the organization of local Ca²⁺ signaling circuits occurring at myoendothelial projections is disrupted in hypertension, giving rise to increased contractile responses.

TraceSpecks: A Software for Automated Idealization of Noisy Patch-Clamp and Imaging Data

Experimental records of single molecules or ion channels from fluorescence microscopy and patch-clamp electrophysiology often include high-frequency noise and baseline fluctuations that are not generated by the system under investigation and have to be removed. Moreover, multiple channels or conductance levels can be present at a time in the data that need to be quantified to accurately understand the behavior of the system. Manual procedures for removing these fluctuations and extracting conducting states or multiple channels are laborious, prone to subjective bias, and likely to hinder the processing of often very large data sets. We introduce a maximal likelihood formalism for separating signal from a noisy and drifting background such as fluorescence traces from imaging of elementary Ca²⁺ release events called puffs arising from clusters of channels, and patch-clamp recordings of ion channels. Parameters such as the number of open channels or conducting states, noise level, and background signal can all be optimized using the expectation-maximization algorithm. We implement our algorithm following the Baum-Welch approach to expectation-maximization in the portable Java language with a user-friendly graphical interface and test the algorithm on both synthetic and experimental data from the patch-clamp electrophysiology of Ca²⁺ channels and fluorescence microscopy of a cluster of Ca²⁺ channels and Ca²⁺ channels with multiple conductance levels. The resulting software is accurate, fast, and provides detailed information usually not available through manual analysis. Options for visual inspection of the raw and processed data with key parameters are provided, in addition to a range of statistics such as the mean open probabilities, mean open times, mean close times, dwell-time distributions for different number of channels open or conductance levels, amplitude distribution of all opening events, and number of transitions between different number of open channels or conducting levels in asci format with a single click.

Myosin-II mediated traction forces evoke localized Piezo1-dependent Ca2+ flickers

Piezo channels transduce mechanical stimuli into electrical and chemical signals to powerfully influence development, tissue homeostasis, and regeneration. Studies on Piezo1 have largely focused on transduction of "outside-in" mechanical forces, and its response to internal, cell-generated forces remains poorly understood. Here, using measurements of endogenous Piezo1 activity and traction forces in native cellular conditions, we show that cellular traction forces generate spatially-restricted Piezo1-mediated Ca2+ flickers in the absence of externally-applied mechanical forces. Although Piezo1 channels diffuse readily in the plasma membrane and are widely distributed across the cell, their flicker activity is enriched near force-producing adhesions. The mechanical force that activates Piezo1 arises from Myosin II phosphorylation by Myosin Light Chain Kinase. We propose that Piezo1 Ca2+ flickers allow spatial segregation of mechanotransduction events, and that mobility allows Piezo1 channels to explore a large number of mechanical microdomains and thus respond to a greater diversity of mechanical cues.

Spatial-temporal patterning of Ca2+ signals by the subcellular distribution of IP3 and IP3 receptors

The patterning of cytosolic Ca²⁺ signals in space and time underlies their ubiquitous ability to specifically regulate numerous cellular processes. Signals mediated by liberation of Ca²⁺ sequestered in the endoplasmic reticulum (ER) through inositol trisphosphate receptor (IP₃R) channels constitute a hierarchy of events; ranging from openings of individual IP₃ channels, through the concerted openings of several clustered IP₃Rs to generate local Ca²⁺ puffs, to global Ca²⁺ waves and oscillations that engulf the entire cell. Here, we review recent progress in elucidating how this hierarchy is shaped by an interplay between the functional gating properties of IP₃Rs and their spatial distribution within the cell. We focus in particular on the subset of IP₃Rs that are organized in stationary clusters and are endowed with the ability to preferentially liberate Ca²⁺.

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.

CellSpecks: A Software for Automated Detection and Analysis of Calcium Channels in Live Cells

To couple the fidelity of patch-clamp recording with a more high-throughput screening capability, we pioneered a, to our knowledge, novel approach to single-channel recording that we named "optical patch clamp." By using highly sensitive fluorescent Ca²⁺ indicator dyes in conjunction with total internal fluorescence microscopy techniques, we monitor Ca²⁺ flux through individual Ca²⁺-permeable channels. This approach provides information about channel gating analogous to patch-clamp recording at a time resolution of ∼2 ms with the additional advantage of being massively parallel, providing simultaneous and independent recording from thousands of channels in the native environment. However, manual analysis of the data generated by this technique presents severe challenges because a video recording can include many thousands of frames. To overcome this bottleneck, we developed an image processing and analysis framework called CellSpecks capable of detecting and fully analyzing the kinetics of ion channels within a video sequence. By using randomly generated synthetic data, we tested the ability of CellSpecks to rapidly and efficiently detect and analyze the activity of thousands of ion channels, including openings for a few milliseconds. Here, we report the use of CellSpecks for the analysis of experimental data acquired by imaging muscle nicotinic acetylcholine receptors and the Alzheimer's disease-associated amyloid β pores with multiconductance levels in the plasma membrane of Xenopus laevis oocytes. We show that CellSpecks can accurately and efficiently generate location maps and create raw and processed fluorescence time traces; histograms of mean open times, mean close times, open probabilities, durations, and maximal amplitudes; and a "channel chip" showing the activity of all channels as a function of time. Although we specifically illustrate the application of CellSpecks for analyzing data from Ca²⁺ channels, it can be easily customized to analyze other spatially and temporally localized signals.

Calcium Imaging with Super-Resolution Radial Fluctuations

Calcium signals act as a ubiquitous secondary messenger in regulating many body functions. The detection of calcium microdomain signals is greatly facilitated by the existence of biomarker-targeted fluorescent probes. In this study, SRRF (super-resolution radial fluctuations) algorithm were used to compare the loci and the intensity of fluorescent probes before and after SRRF analysis. The implementation of SRRF algorithm was aimed for automatically resolving delicate and small calcium signals (to avoid the overlapped loci) on original images. For assessing the spatial accuracy of image intensity, immunofluorescence staining of retina cryostat slice for connexin 36 (Cx36) was microscopically imaged with or without the successive SRRF reconstruction. For characterizing the temporal association between SRRF and non-SRRF images, the changes of Cx36-GCaMP calcium indicator were recorded from transfected HeLa cells in response to the transient puffing of ionomycin. Image processing and analyses were conducted with Image J and Matlab. Through this study, SRRF reconstruction was found to confer an accurate measure for the identification of subcellular molecules, such as gap junctions. Compared with the conventional imaging, SRRF reconstruction generated better image resolution for the precise registration of individual signals. Temporally, the ratios of change in fluorescence intensity between SRRF and non-SRRF images were significantly correlated in the presence or absence of the subtraction of high background intensity. Quantitatively, the ratios of change in fluorescence intensity between SRRF and non-SRRF images with or without background subtraction were also significantly correlated. The merit of SRRF application on calcium live imaging was validated with the reporter gene system we worked on.

Applications of FLIKA, a Python-based image processing and analysis platform, for studying local events of cellular calcium signaling

The patterning of cytosolic Ca²⁺ signals underlies their ubiquitous ability to specifically regulate numerous cellular processes. Advances in fluorescence microscopy have made it possible to image these signals with unprecedented temporal and spatial resolution. However, this is a double-edged sword, as the resulting enormous data sets necessitate development of software to automate image processing and analysis. Here, we describe Flika, an open source, graphical user interface program written in the Python environment that contains a suite of built-in image processing tools to enable intuitive visualization of image data and analysis. We illustrate the utility and power of Flika by three applications for studying cellular Ca²⁺ signaling: a script for measuring single-cell global Ca²⁺ signals; a plugin for the detection, localization and analysis of subcellular Ca²⁺ puffs; and a script that implements a novel approach for fluctuation analysis of transient, local Ca²⁺ fluorescence signals. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.

SICT: automated detection and supervised inspection of fast Ca2+ transients

Recent advances in live Ca²⁺ imaging with increasing spatial and temporal resolution offer unprecedented opportunities, but also generate an unmet need for data processing. Here we developed SICT, a MATLAB program that automatically identifies rapid Ca²⁺ rises in time-lapse movies with low signal-to-noise ratios, using fluorescent indicators. A graphical user interface allows visual inspection of automatically detected events, reducing manual labour to less than 10% while maintaining quality control. The detection performance was tested using synthetic data with various signal-to-noise ratios. The event inspection phase was evaluated by four human observers. Reliability of the method was demonstrated in a direct comparison between manual and SICT-aided analysis. As a test case in cultured neurons, SICT detected an increase in frequency and duration of spontaneous Ca²⁺ transients in the presence of caffeine. This new method speeds up the analysis of elementary Ca²⁺ transients.

All three IP3 receptor subtypes generate Ca2+ puffs, the universal building blocks of IP3-evoked Ca2+ signals

All three subtypes of inositol 1,4,5-trisphosphate receptor (IP₃R) are intracellular Ca²⁺ channels that are co-regulated by IP₃ and Ca²⁺. This allows IP₃Rs to evoke regenerative Ca²⁺ signals, the smallest of which are Ca²⁺ puffs that reflect the coordinated opening of a few clustered IP₃Rs. We use total internal reflection microscopy (TIRF) microscopy to record Ca²⁺ signals in HEK cells expressing all three IP₃R subtypes or a single native subtype. Ca²⁺ puffs are less frequent in cells expressing one IP₃R subtype, commensurate with them expressing fewer IP₃Rs than wild-type cells. However, all three IP₃R subtypes generate broadly similar Ca²⁺ puffs with similar numbers of IP₃Rs contributing to each. This suggests that IP₃R clusters may be assembled by conserved mechanisms that generate similarly sized clusters across different IP₃R expression levels. The Ca²⁺ puffs evoked by IP₃R2 had slower kinetics and more prolonged durations, which may be due to IP₃ binding with greater affinity to IP₃R2. We conclude that Ca²⁺ puffs are the building blocks for the Ca²⁺ signals evoked by all IP₃Rs.

Summary: All IP₃ receptor subtypes can generate Ca²⁺ puffs, suggesting that these coordinated openings of clustered IP₃Rs are the building blocks of all IP₃-evoked Ca²⁺ signals.

Long-term In Vivo Calcium Imaging of Astrocytes Reveals Distinct Cellular Compartment Responses to Sensory Stimulation

Localized, heterogeneous calcium transients occur throughout astrocytes, but the characteristics and long-term stability of these signals, particularly in response to sensory stimulation, remain unknown. Here, we used a genetically encoded calcium indicator and an activity-based image analysis scheme to monitor astrocyte calcium activity in vivo. We found that different subcellular compartments (processes, somata, and endfeet) displayed distinct signaling characteristics. Closer examination of individual signals showed that sensory stimulation elevated the number of specific types of calcium peaks within astrocyte processes and somata, in a cortical layer-dependent manner, and that the signals became more synchronous upon sensory stimulation. Although mice genetically lacking astrocytic IP3R-dependent calcium signaling (Ip3r2-/-) had fewer signal peaks, the response to sensory stimulation was sustained, suggesting other calcium pathways are also involved. Long-term imaging of astrocyte populations revealed that all compartments reliably responded to stimulation over several months, but that the location of the response within processes may vary. These previously unknown characteristics of subcellular astrocyte calcium signals provide new insights into how astrocytes may encode local neuronal circuit activity.

Cortical Circuit Activity Evokes Rapid Astrocyte Calcium Signals on a Similar Timescale to Neurons

Sensory stimulation evokes intracellular calcium signals in astrocytes; however, the timing of these signals is disputed. Here, we used novel combinations of genetically encoded calcium indicators for concurrent two-photon imaging of cortical astrocytes and neurons in awake mice during whisker deflection. We identified calcium responses in both astrocyte processes and endfeet that rapidly followed neuronal events (∼120 ms after). These fast astrocyte responses were largely independent of IP₃R2-mediated signaling and known neuromodulator activity (acetylcholine, serotonin, and norepinephrine), suggesting that they are evoked by local synaptic activity. The existence of such rapid signals implies that astrocytes are fast enough to play a role in synaptic modulation and neurovascular coupling. VIDEO ABSTRACT.

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data

Local and spontaneous calcium signals play important roles in neurons and neuronal networks. Spontaneous or cell-autonomous calcium signals may be difficult to assess because they appear in an unpredictable spatiotemporal pattern and in very small neuronal loci of axons or dendrites. We developed an open source bioinformatics tool for an unbiased assessment of calcium signals in x,y-t imaging series. The tool bases its algorithm on a continuous wavelet transform-guided peak detection to identify calcium signal candidates. The highly sensitive calcium event definition is based on identification of peaks in 1D data through analysis of a 2D wavelet transform surface. For spatial analysis, the tool uses a grid to separate the x,y-image field in independently analyzed grid windows. A document containing a graphical summary of the data is automatically created and displays the loci of activity for a wide range of signal intensities. Furthermore, the number of activity events is summed up to create an estimated total activity value, which can be used to compare different experimental situations, such as calcium activity before or after an experimental treatment. All traces and data of active loci become documented. The tool can also compute the signal variance in a sliding window to visualize activity-dependent signal fluctuations. We applied the calcium signal detector to monitor activity states of cultured mouse neurons. Our data show that both the total activity value and the variance area created by a sliding window can distinguish experimental manipulations of neuronal activity states. Notably, the tool is powerful enough to compute local calcium events and ‘signal-close-to-noise’ activity in small loci of distal neurites of neurons, which remain during pharmacological blockade of neuronal activity with inhibitors such as tetrodotoxin, to block action potential firing, or inhibitors of ionotropic glutamate receptors. The tool can also offer information about local homeostatic calcium activity events in neurites.

Calcium imaging has become a standard tool to investigate local, spontaneous, or cell-autonomous calcium signals in neurons. Some of these calcium signals are fast and ‘small’, thus making it difficult to identify real signaling events due to an unavoidable signal noise. Therefore, it is difficult to assess the spatiotemporal activity footprint of individual neurons or a neuronal network. We developed this open source tool to automatically extract, count, and localize calcium signals from the whole x,y-t image series. As demonstrated here, the tool is useful for an unbiased comparison of activity states of neurons, helps to assess local calcium transients, and even visualizes local homeostatic calcium activity. The tool is powerful enough to visualize signal-close-to-noise calcium activity.

Dynamic Ca2+ imaging with a simplified lattice light-sheet microscope: A sideways view of subcellular Ca2+ puffs

We describe the construction of a simplified, inexpensive lattice light-sheet microscope, and illustrate its use for imaging subcellular Ca²⁺ puffs evoked by photoreleased i-IP₃ in cultured SH-SY5Y neuroblastoma cells loaded with the Ca²⁺ probe Cal520. The microscope provides sub-micron spatial resolution and enables recording of local Ca²⁺ transients in single-slice mode with a signal-to-noise ratio and temporal resolution (2ms) at least as good as confocal or total internal reflection microscopy. Signals arising from openings of individual IP₃R channels are clearly resolved, as are stepwise changes in fluorescence reflecting openings and closings of individual channels during puffs. Moreover, by stepping the specimen through the light-sheet, the entire volume of a cell can be scanned within a few hundred ms. The ability to directly visualize a sideways (axial) section through cells directly reveals that IP₃-evoked Ca²⁺ puffs originate at sites in very close (≤a few hundred nm) to the plasma membrane, suggesting they play a specific role in signaling to the membrane.

Endogenous signalling pathways and caged IP3 evoke Ca2+ puffs at the same abundant immobile intracellular sites

The building blocks of intracellular Ca²⁺ signals evoked by inositol 1,4,5-trisphosphate receptors (IP₃Rs) are Ca²⁺ puffs, transient focal increases in Ca²⁺ concentration that reflect the opening of small clusters of IP₃Rs. We use total internal reflection fluorescence microscopy and automated analyses to detect Ca²⁺ puffs evoked by photolysis of caged IP₃ or activation of endogenous muscarinic receptors with carbachol in human embryonic kidney 293 cells. Ca²⁺ puffs evoked by carbachol initiated at an estimated 65±7 sites/cell, and the sites remained immobile for many minutes. Photolysis of caged IP₃ evoked Ca²⁺ puffs at a similar number of sites (100±35). Increasing the carbachol concentration increased the frequency of Ca²⁺ puffs without unmasking additional Ca²⁺ release sites. By measuring responses to sequential stimulation with carbachol or photolysed caged IP₃, we established that the two stimuli evoked Ca²⁺ puffs at the same sites. We conclude that IP₃-evoked Ca²⁺ puffs initiate at numerous immobile sites and the sites become more likely to fire as the IP₃ concentration increases; there is no evidence that endogenous signalling pathways selectively deliver IP₃ to specific sites.

Summary: Ca²⁺ puffs are the building blocks for IP₃-evoked Ca²⁺ signals. Ca²⁺ puffs evoked by caged IP₃ or via endogenous signalling pathways initiate at the same fixed intracellular sites.

Lattice light sheet imaging of membrane nanotubes between human breast cancer cells in culture and in brain metastases

Membrane nanotubes are cytosolic protrusions with diameters <1 µm that extend between cells separated by tens of µm. They mediate several forms of intercellular communication and are upregulated in diverse diseases. Difficulties in visualizing and studying nanotubes within intact tissues have, however, prompted skepticism regarding their in vivo relevance, and most studies have been confined to cell culture systems. Here, we introduce lattice-light sheet imaging of MDA-MB-231 human breast cancer cells genetically engineered to brightly express membrane-targeted GFP as a promising approach to visualize membrane nanotubes in vitro and in situ. We demonstrate that cultured cells form multiple nanotubes that mediate intercellular communication of Ca²⁺ signals and actively traffic GFP-tagged membrane vesicles along their length. Furthermore, we directly visualize nanotubes in situ, interconnecting breast cancer cells in live acute brain slices from an experimental mouse model of breast cancer brain metastasis. This amenable experimental system should facilitate the transition of the study of intercellular communication by membrane nanotubes from cell culture to the whole animal.

Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels

Intracellular Local Ca releases (LCRs) from sarcoplasmic reticulum (SR) regulate cardiac pacemaker cell function by activation of electrogenic Na/Ca exchanger (NCX) during diastole. Prior studies demonstrated the existence of powerful compensatory mechanisms of LCR regulation via a complex local cross-talk of Ca pump, release and NCX. One major obstacle to study these mechanisms is that LCR exhibit complex Ca release propagation patterns (including merges and separations) that have not been characterized. Here we developed new terminology, classification, and computer algorithms for automatic detection of numerically simulated LCRs and examined LCR regulation by SR Ca pumping rate (Pup) that provides a major contribution to fight-or-flight response. In our simulations the faster SR Ca pumping accelerates action potential-induced Ca transient decay and quickly clears Ca under the cell membrane in diastole, preventing premature releases. Then the SR generates an earlier, more synchronized, and stronger diastolic LCR signal activating an earlier and larger inward NCX current. LCRs at higher Pup exhibit larger amplitudes and faster propagation with more collisions to each other. The LCRs overlap with Ca transient decay, causing an elevation of the average diastolic [Ca] nadir to ~200 nM (at Pup = 24 mM/s). Background Ca (in locations lacking LCRs) quickly decays to resting Ca levels (<100 nM) at high Pup, but remained elevated during slower decay at low Pup. Release propagation is facilitated at higher Pup by a larger LCR amplitude, whereas at low Pup by higher background Ca. While at low Pup LCRs show smaller amplitudes, their larger durations and sizes combined with longer transient decay stabilize integrals of diastolic Ca and NCX current signals. Thus, the local interplay of SR Ca pump and release channels regulates LCRs and Ca transient decay to insure fail-safe pacemaker cell operation within a wide range of rates.

Comparison of Ca2+ puffs evoked by extracellular agonists and photoreleased IP3

The inositol trisphosphate (IP3) signaling pathway evokes local Ca2+ signals (Ca2+ puffs) that arise from the concerted openings of clustered IP3 receptor/channels in the ER membrane. Physiological activation is triggered by binding of agonists to G-protein-coupled receptors (GPCRs) on the cell surface, leading to cleavage of phosphatidyl inositol bisphosphate and release of IP3 into the cytosol. Photorelease of IP3 from a caged precursor provides a convenient and widely employed means to study the final stage of IP3-mediated Ca2+ liberation, bypassing upstream signaling events to enable more precise control of the timing and relative concentration of cytosolic IP3. Here, we address whether Ca2+ puffs evoked by photoreleased IP3 fully replicate those arising from physiological agonist stimulation. We imaged puffs in individual SH-SY5Y neuroblastoma cells that were sequentially stimulated by picospritzing extracellular agonist (carbachol, CCH or bradykinin, BK) followed by photorelease of a poorly-metabolized IP3 analog, i-IP3. The centroid localizations of fluorescence signals during puffs evoked in the same cells by agonists and photorelease substantially overlapped (within ∼1μm), suggesting that IP3 from both sources accesses the same, or closely co-localized clusters of IP3Rs. Moreover, the time course and spatial spread of puffs evoked by agonists and photorelease matched closely. Because photolysis generates IP3 uniformly throughout the cytoplasm, our results imply that IP3 generated in SH-SY5Y cells by activation of receptors to CCH and BK also exerts broadly distributed actions, rather than specifically activating a subpopulation of IP3Rs that are scaffolded in close proximity to cell surface receptors to form a signaling nanodomain.

Semi-automated program for analysis of local Ca2+ spark release with application for classification of heart cell type

Local Ca²⁺ spark releases are essential to the Ca²⁺ cycling process. Thus, they play an important role in ventricular and atrial cell contraction, as well as in sinoatrial cell automaticity. Characterizing their properties in healthy cells from different regions in the heart can reveal the basic biophysical differences among these regions. We designed a semi-automatic Matlab Graphical User Interface (called Sparkalyzer) to characterize parameters of Ca²⁺ spark release from any major cardiac tissue, as recorded in line-scan mode with a confocal laser-scanning microscope. We validated the algorithm on experimental images from rabbit sinoatrial, atrial, and ventricular cells loaded with Fluo-4 AM. The program characterizes general image parameters of Ca²⁺ transients and sparks: spark duration, which indicates for how long the spark provides Ca²⁺ to the closed intracellular mechanisms (typical value: 25±1, 23±1, 26±1ms for sinoatrial, atrial, and ventricular cells, respectively); spark amplitude, which indicates the amount of Ca²⁺ released by a single spark (1.6±0.1, 1.6±0.2, 1.4±0.1F/F₀ for sinoatrial, atrial, and ventricular cells, respectively); spark length, which is the length of the Ca²⁺ wavelets fired out of a row of ryanodine receptors (5±0.1, 5±0.2, 3.4±0.3μm for sinoatrial, atrial, or ventricular cells, respectively) and number of sparks (0.14±0.02, 0.025±0.01, 0.02±0.01 for 1μm in 1s for sinoatrial, atrial, and ventricular cells, respectively). This method is reliable for Ca²⁺ spark analysis of sinoatrial, atrial, or ventricular cells. Moreover, by examining the average value of Ca²⁺ spark characteristics and their scattering around the mean, atrial, ventricular and sinoatrial cells can be differentiated.

Acetylcholine released by endothelial cells facilitates flow-mediated dilatation

KEY POINTS

The endothelium plays a pivotal role in the vascular response to chemical and mechanical stimuli. The endothelium is exquisitely sensitive to ACh, although the physiological significance of ACh-induced activation of the endothelium is unknown. In the present study, we investigated the mechanisms of flow-mediated endothelial calcium signalling. Our data establish that flow-mediated endothelial calcium responses arise from the autocrine action of non-neuronal ACh released by the endothelium.

ABSTRACT

Circulating blood generates frictional forces (shear stress) on the walls of blood vessels. These frictional forces critically regulate vascular function. The endothelium senses these frictional forces and, in response, releases various vasodilators that relax smooth muscle cells in a process termed flow-mediated dilatation. Although some elements of the signalling mechanisms have been identified, precisely how flow is sensed and transduced to cause the release of relaxing factors is poorly understood. By imaging signalling in large areas of the endothelium of intact arteries, we show that the endothelium responds to flow by releasing ACh. Once liberated, ACh acts to trigger calcium release from the internal store in endothelial cells, nitric oxide production and artery relaxation. Flow-activated release of ACh from the endothelium is non-vesicular and occurs via organic cation transporters. ACh is generated following mitochondrial production of acetylCoA. Thus, we show ACh is an autocrine signalling molecule released from endothelial cells, and identify a new role for the classical neurotransmitter in endothelial mechanotransduction.

Systematic Characterization of Dynamic Parameters of Intracellular Calcium Signals

Dynamic processes, such as intracellular calcium signaling, are hallmark of cellular biology. As real-time imaging modalities become widespread, a need for analytical tools to reliably characterize time-series data without prior knowledge of the nature of the recordings becomes more pressing. The goal of this study is to develop a signal-processing algorithm for MATLAB that autonomously computes the parameters characterizing prominent single transient responses (TR) and/or multi-peaks responses (MPR). The algorithm corrects for signal contamination and decomposes experimental recordings into contributions from drift, TRs, and MPRs. It subsequently provides numerical estimates for the following parameters: time of onset after stimulus application, activation time (time for signal to increase from 10 to 90% of peak), and amplitude of response. It also provides characterization of the (i) TRs by quantifying their area under the curve (AUC), response duration (time between 1/2 amplitude on ascent and descent of the transient), and decay constant of the exponential decay region of the deactivation phase of the response, and (ii) MPRs by quantifying the number of peaks, mean peak magnitude, mean periodicity, standard deviation of periodicity, oscillatory persistence (time between first and last discernable peak), and duty cycle (fraction of period during which system is active) for all the peaks in the signal, as well as coherent oscillations (i.e., deterministic spikes). We demonstrate that the signal detection performance of this algorithm is in agreement with user-mediated detection and that parameter estimates obtained manually and algorithmically are correlated. We then apply this algorithm to study how metabolic acidosis affects purinergic (P2) receptor-mediated calcium signaling in osteoclast precursor cells. Our results reveal that acidosis significantly attenuates the amplitude and AUC calcium responses at high ATP concentrations. Collectively, our data validated this algorithm as a general framework for comprehensively analyzing dynamic time-series.