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1,542 results for “Calcium”
Quasi-free-standing AA-stacked bilayer graphene induced by calcium intercalation of the graphene-silicon carbide interface
<p>APRES datasets and LEED images for "Quasi-free-standing AA-stacked bilayer graphene induced by calcium intercalation of<br>the graphene-silicon carbide interface" publication.</p>
Data from: A mechanism of lysosomal calcium entry
<p>Lysosomal calcium (Ca2+) release is critical to cell signaling and is mediated by well-known lysosomal Ca2+ channels. Yet, how lysosomes refill their Ca2+ remains hitherto undescribed. Here, from an RNAi screen in C. elegans we identify an evolutionarily conserved gene, lci-1, that facilitates lysosomal Ca2+ entry in C. elegans and mammalian cells. We found that its human homolog TMEM165, previously designated as a Ca2+/H+ exchanger (CAX), imports Ca2+ pH-dependently into lysosomes. Using two-ion mapping and electrophysiology we show that TMEM165, hereafter referred to as human LCI, acts as a proton-activated, lysosomal Ca2+ importer. Defects in lysosomal Ca2+ channels cause several neurodegenerative diseases, and knowledge of lysosomal Ca2+ importers may provide new avenues to explore the physiology of Ca2+ channels.</p>
Calcium dynamics upon heating in murine neonatal cardiomyocytes transduced with truncated human TRPV1(−109 a.a.) and the localization of TRPV1 in these cells
<h3>Abstract</h3> <p>The expression of truncated human TRPV1(−109 a.a.) in cardiomyocytes allowed us to induce action potentials (APs) by pulse irradiation with an infrared (IR) diode laser. We studied the calcium dynamics in these cells (Ca_TRPV.zip image set). Murine cardiomyocytes were transducted by AAV-based vectors bearing construction of TRPV1(−109 a.a.) with mRuby (for expression detection) and vectors bearing GCaMP6s calcium sensor. Cardiomyocytes were heated by IR laser with a repetition rate of 2 Hz and 30 ms pulse width in a calcium-free medium.<br>To explain the observed calcium dynamics, we also studied the subcellular localization of human TRPV1 in Murine cardiomyocytes ER_a-flag_100x_param1_Z-stack002.nd2</p> <h3>Primary cell production and transformation</h3> <p>Experiments were carried out using C57Bl/6J mice (The Jackson Laboratory, #000664, RRID: IMSR_JAX:000664). The mixed mouse primary neonatal cardiomyocyte cell culture was obtained using a neonatal heart dissociation kit (Miltenyi Biotec, 130-098-373) according to the manufacturer’s instructions. The cells were cultured in DMEM/F12, 1:1 mixture (BioloT, 1.3.7.2.) supplemented with 10% FBS, penicillin 100 U/ml /streptomycin 100 mg/ml, and L-glutamine 0.365 g/l. The culture was seeded on 10mm coverslips coated with 10 mg/ml gelatin diluted in PBS and maintained at 37℃ in 5% CO2. For transient expression of the hTRPV1 channel, a reporter protein, and a fluorescent Ca2+ sensor GCaMP6s, we used AAV-based vectors with the encoded genes above. We used the AAV-DJ serotype at a MOI of 12,000 VG/cells for cTnT_hTRPV1(sh)_P2A_mRuby based viruses, and a MOI of 2,500 VG/cells for cTnT_GCaMP6s ones. The cells were infected on the next day after plating, and the transgene expression peak was observed on the third day after the infection.</p> <h3>Distant heating system</h3> <p>The system was equipped with a fiber coupled laser diode (LD) 4PN-117 (SemiNex) as a powerful heating laser, providing radiation at a wavelength of 1375 nm with an average power of up to 4.3 W through a multimode fiber with a core diameter of 105 μm and 0.22NA. The LD was mounted onto a TEC-controlled plate “264 TEC HP LaserMount” (A.I.), which was operated by TEC driver TECSource 5305 (A.I.); current stabilization and control for LD were performed with LD driver LaserSource 4320 (A.I.). The laser was controlled via the TTL output from the HEKA EPC-10 amplifier. Different laser intensities and pulse widths were used. Laser power, P, can be computed from trigger voltage, U, by an equation: P [W] = -0.28 + 1.42 * U [V].</p> <p>Intracellular calcium recordings of single cardiac cells<br>Neonatal cardiomyocyte cells transduced with GCaMP6s sensor were viewed and acquired under a water immersion Olympus LUMPLFLN40×W objective with 40X magnification. Data acquisition was performed at 20 fps using a Scientifica SliceScopePro 2000 microscope (Scientifica, UK) equipped with a Hamamatsu Orca Flash 4.0 CMOS monochrome digital camera (Hamamatsu Photonics) connected to a PC running the free software uManager. A CoolLED pE-300ultra was used as a light source. It was synchronized with the laser heating system via BNC-TTL output from the Heka Elektronik EPC 10 USB Patch Clamp Amplifier. To synchronize the pacing and the GCamp6s signal registration, the light source was switched off for one acquisition cycle at the beginning of the pacing. The GCamp6s signal was analyzed using Fiji software.</p> <h3><br>TRPV1 channel localization</h3> <p>To understand the localization of the expressed TRPV1 channels in neonatal mice cardiomyocytes, we utilized cells infected with AAV-PHP.S serotype viruses with pAAV_cTnT_hTRPV1_P2A_FLAG-tag at a MOI of 2500 VG/cells. To visualize endoplasmic reticulum, we stained the live cells with ER-Tracker™ Red (BODIPY™ TR Glibenclamide, Thermo Fisher Scientific, E34250) according to the manufacturer’s instructions. After the staining with ER-tracker, cardiomyocytes were fixed with 4% paraformaldehyde (Sigma-Aldrich, 158127-100G) for 5 minutes at room temperature and washed trice with 0.3% Tween 20 (Sigma-Aldrich, P1379-250ML) diluted in PBS (5 minutes each). The fixed cells then were blocked with PBS containing 0.12% tween 20, 1% bovine serum albumin (BSA, PanEko, 68100.10г), and 10% goat serum (Thermo Fisher Scientific, 16210072) for 40 minutes at room temperature. After the buffer removal, the cardiomyocytes were labeled with of DYKDDDDK Tag Recombinant Rabbit Monoclonal Antibody (8H8L17, Invitrogen, MA1-142-A488) at 1:500 dilution in 1% BSA, 10% goat serum, and 89% PBS for 2 hours at room temperature. The samples were washed three times with PBS after the incubations. Then, the cells were stained with Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody Alexa Fluor™ 488 (Invitrogen, A-11008) at dilution 1:500 for 1 hour at room temperature. The removal of non-conjugated antibodies was performed in parallel with cell nuclei staining. The cells were incubated with PBS supplemented with 2 μg/ml DAPI (Miltenyi Biotec, 130-111-570) for 15 minutes at room temperature. For further experiments, glasses with the labeled cells were placed onto the Superfrost Plus adhesion slides (Epredia, EPBRSF41296SP) in 20 µl VECTASHIELD Vibrance Antifade Mounting Media (Vector Laboratories, H-1700-2) and stored at +4℃ in the dark.<br>The samples were analyzed using an inverted Nikon A1 confocal microscope and visualized using Nikon NIS-Elements software. We pictured the sample in each channel individually exciting DAPI, DYKDDDDK Tag-Alexa Fluor 488, and ER-tracker by laser lines 405 nm, 488 nm and 561 nm, respectively. Colocolization analysis was performed using ImageJ software.</p>
Dissolved calcium and pH raster layers for freshwater environments in Canada and the USA
<p>Calcium concentration and pH are key parameters that are linked to multiple chemical and biological processes in freshwater environments. This dataset presents high-resolution (10 x 10 km) interpolated raster layers for these two variables across Canada and the continental USA. These layers were generated via spatial interpolation (Kriging with a fixed zero nugget) after comparison of multiple interpolation methods, using water quality data for lakes and rivers compiled from multiple sources. This is the first time that such data have been made available at this scale and resolution, providing a valuable resource for research, including projects evaluating risks from environmental change, pollution, and invasive species. </p>
TRPV1 calcium imaging assay data from testing of capsaicinoids
<p>irTRPV1 calcium imaging assay data collected in HTS format included legend to files, raw data, feature files with description, aligned data and final GraphPad file. Correspoinding paper's DOI will be added once generated.</p>
Examination of 6 and 12 Month Follow-up of Calcium Hydroxide and Calcium Silicate Materials Used in Direct and Indirect Pulp Capping
<p>This dataset includes data evaluating the clinical and radiographic 6 and 12-month treatment success of calcium hydroxide and calcium silicate materials in indirect pulp therapy (IPT) and direct pulp capping (DPC) applications in teeth with deep dentin caries.</p>
Mouse CA1 Calcium Imaging and Behavioural Dataset in 3x3 Geometric Morph Paradigm
<p>The following dataset was collected by Dr. J. Quinn Lee, Dr. Alexandra T. Keinath, and Erica Cianfarano in the laboratory of Dr. Mark P. Brandon. All methods and details are described in the original research article reporting these data published in <em>Neuron</em>: Lee, Keinath, Cianfarano, and Brandon (2025) Identifying representational structure in CA1 to benchmark theoretical models of cognitive mapping. Any use of the following dataset must cite the original publication in Neuron. The code base to reproduce all analyses and figures can be found at: <a href="https://github.com/jquinnlee/georepca1">https://github.com/jquinnlee/georepca1</a></p> <p dir="auto">The dataset (Python joblib files or MATLAB .mat files in the zipped "data" folder) are given names of animal IDs from the original study that can be downloaded from Zenodo and contain the following fields in each file:</p> <p dir="auto">SFPs: spatial footprints (also known as ROI) for every registered cell, centered over each cell. Shape - Dimx, dimy, number of SFPs (ROIs), number of days. If cell is not registered it will be nan along dimx and dimy for a given day.</p> <p dir="auto">blocked: location of blocked (occluded) partitions in 3x3 design of environment. Location of partitions are shown in paper, but are organized in the following way – [[0, 1, 2], [3, 4, 5], [6, 7, 8]]. If no partitions are blocked, value is -1.</p> <p dir="auto">centroids: centroid of spatial footprint. Shape – number of cells, x-y location, number of days.</p> <p dir="auto">envs: environment shape identified with string name</p> <p dir="auto">maps: three types of maps generated from the dataset. “sampling” is the occupancy of animal in each spatial bin, shape – xbins, ybins, number of days. “smoothed” is the event rate map smoothed with 2.5 cm gaussian kernel, shape – xbins, ybins, number of cells, number of days. “unsmoothed” is the same event rate map data without smoothing.</p> <p dir="auto">position: x-y position data for all days. List shape number of days, with shape on each day indicating x-y position in first dimension, and number of temporal bins / frames in second dimension.</p> <p dir="auto">trace: rise-extracted calcium traces, where “1” indicates a significant event. See paper for details on processing pipeline. If cell is not registered on given day, will appear as nan the same shape.</p> <p dir="auto">Precomputed results can also be downloaded in the zipped "results" folder to avoid recomputing main results from scratch using the Github code base linked above.</p>
Mapping the interaction surface between CaVβ and actin and its role in calcium channel clearance
<p><strong>HADDOCK protein-protein docking data for the Ca<sub>V</sub>β/F-actin complex models reported in "Mapping the interaction surface between Ca<sub>V</sub>β and actin and its role in calcium channel clearance".</strong></p> <p> </p> <p>The dataset is divided in four different folders:</p> <ol> <li><strong>Cavbeta2:</strong> data for the docking between dimeric actin (PDB 5OOE) and Ca<sub>V</sub>β<sub>2</sub> (PDB 5V2P) using XL-MS-derived distance restraints </li> <li><strong>Cavbeta4:</strong> data for the docking between dimeric actin (PDB 5OOE) and Ca<sub>V</sub>β<sub>4</sub> (PDB 1VYV) using XL-MS-derived distance restraints </li> <li><strong>Monomer:</strong> data for the control docking between <em>monomeric</em> actin (PDB 5OOE) and Ca<sub>V</sub>β<sub>2</sub> (PDB 5V2P) using XL-MS-derived distance restraints </li> <li><strong>Ab_initio:</strong> data for the control dockings between dimeric actin (PDB 5OOE) and Ca<sub>V</sub>β<sub>2</sub> (PDB 5V2P) <em>without</em> XL-MS-derived distance restraints and using the <em>ab initio</em> options available in HADDOCK 2.4</li> </ol> <p> </p> <p>Each of the <strong>Cavbeta</strong> folders (1-2) and the <strong>Monomer</strong> folder (3) contain:</p> <p>- Inputs: </p> <ul> <li>HADDOCK run parameter file (job_params.json)</li> <li>XL/MS-derived unambiguous distance restraints (unambig.tbl)</li> <li>Bioinformatics-derived (CPORT and NACCESS) ambiguous distance restraints (ambig.tbl)</li> </ul> <p>- Outputs:</p> <ul> <li>Top 4 models of the selected HADDOCK cluster (cluster1_1.pdb, ..., cluster1_4.pdb)</li> <li>Source data for the docking analyses presented in the Supplementary Information (Supplementary Figures 4, 6, 9, 13 and 14 and Supplementary Table 4)</li> </ul> <p> </p> <p>The <strong>Ab_initio</strong> folder (4) contains:</p> <p>- Input: </p> <ul> <li>HADDOCK run parameter files for each of the six control simulations presented in Supplementary Table 6 (job_params.json)</li> </ul> <p>- Outputs:</p> <ul> <li>Source data for the docking analyses presented in Supplementary Table 6</li> <li>Model from control simulation 1 shown in Supplementary Figure 5</li> </ul> <p> </p>
Simultaneous two-photon voltage or calcium imaging and multi-channel LFP recordings in barrel cortex of awake and anesthetized mice
<p>Neuronal population activity, both spontaneous and sensory-evoked, generates propagating waves in cortex. However, high spatiotemporal-resolution mapping of these waves is difficult as calcium imaging, the work horse of current imaging, does not reveal subthreshold activity.</p> <p>Here, we present a platform combining voltage or calcium two-photon imaging with multi-channel local field potential (LFP) recordings in different layers of the barrel cortex from anesthetized and awake head-restrained mice. A chronic cranial window with access port allows injecting a viral vector expressing GCaMP6f or the voltage-sensitive dye (VSD) ANNINE-6plus, as well as entering the brain with a multi-channel neural probe. We present both average spontaneous activity and average evoked signals in response to multi-whisker air-puff stimulations.</p> <p>Time domain analysis shows the dependence of the evoked responses on the cortical layer and on the state of the animal, here separated into anesthetized, awake but resting, and running. The simultaneous data acquisition allows to compare the average membrane depolarization measured with ANNINE-6plus with the amplitude and shape of the LFP recordings. The calcium imaging data connects these data sets to the large existing database of this important second messenger. Interestingly, in the calcium imaging data, we found a few cells which showed a decrease in calcium concentration in response to vibrissa stimulation in awake mice.</p> <p>This system offers a multimodal technique to study the spatiotemporal dynamics of neuronal signals through a 3D architecture in vivo. It will provide novel insights on sensory coding, closing the gap between electrical and optical recordings.</p>
CeA Psilocin fiber photometry study: Data and custom code from experiments looking at changes in calcium dynamics in response to an air puff events
<p>Psilocybin, and its active metabolite psilocin, have been shown to elicit rapid and long-lasting symptom improvements in a variety of affective psychiatric illnesses. However, the specific mechanisms behind these therapeutic effects remain relatively unknown. The central amygdala (CeA) is a primary output region within the extended amygdala that is heavily dysregulated in affective psychiatric disorders. Here, we utilized fiber photometry to measure changes in CeA reactivity to an aversive air puff stimulus after psilocin administration, both acutely and at varying prolonged time points. We found that administration of psilocin increased reactivity acutely in females, but not males. Additionally, we show that one dose of psilocin produced decreases in reactivity in males, but not females, 28-days post administration, with decreases seen as early as 2-days post administration. We further report stimulus-specific changes in CeA reactivity after psilocin with differential responsivity to an aversive air puff stimulus and an auditory stimulus. We also measured changes in behavioral response to the air puff stimulus and report sex differences in exploratory behavior but not threat responding or general locomotion. This study provides evidence that a single dose of psilocin can elicit sex-specific, dynamic, and enduring changes in CeA reactivity to an aversive stimulus. These data are an important step towards dissecting circuit-based mechanisms underlying the effects of psychedelics.</p>
Additional movies for a manuscript titled 'Leaf epidermal cells respond to application and removal of mechanical force by distinct cytosolic calcium waves'
<p>This repository provides 21 additional videos that highlight the spectrum of mechanically stimulated calcium responses observed in the leaf epidermis of <em>Arabidopsis t</em>. expressing the genetically encoded calcium indicator R-GECO1. These movies correspond to figures in a manuscript entitled 'Leaf epidermal cells respond to application and removal of mechanical force by distinct cytosolic calcium waves'. In each movie, a cantilever exerts approximately 5 mN force to the epidermis (where the cantilever looks like a shadow in the movies). Each movie contains a scale bar and the relative time (hr:min:sec). Placement of the cantilever generally occurs after approximately 1 minute.</p>
Cytosolic peptides encoding CaV1 C-termini downregulate the calcium channel activity-neuritogenesis coupling
<p><span>L-type Ca<sup>2+</sup> (Ca<sub>V</sub>1) channels transduce channel activities into nuclear signals critical to neuritogenesis. Also, standalone peptides encoded by </span><span><span>Ca<sub>V</sub>1</span> DCT (distal carboxyl-terminus) act as nuclear transcription factors reportedly promoting neuritogenesis. Here, by focusing on exemplary </span><span><span>Ca<sub>V</sub>1</span>.3 and cortical neurons under basal conditions, we discover that cytosolic DCT peptides downregulate neurite outgrowth by the interactions with </span><span><span>Ca<sub>V</sub>1</span>'s apo-calmodulin binding motif. Distinct from nuclear DCT, various cytosolic peptides exert a gradient of inhibitory effects on </span><span>Ca<sup>2+</sup></span><span> influx via CaV1 channels and neurite extension and arborization, and also the intermediate events including CREB activation and c-Fos expression. The inhibition efficacies of DCT are quantitatively correlated with its binding affinities. Meanwhile, c</span><span>ytosolic inhibition tends to facilitate neuritogenesis indirectly by favoring </span><span>Ca<sup>2+</sup>-sensitive nuclear retention of DCT. In summary, DCT peptides as a class of </span><span><span>Ca<sub>V</sub>1</span> inhibitors specifically regulate the channel activity-neuritogenesis coupling in a variant-, affinity-, and localization-dependent manner.</span></p>
Code used in exporting calcium imaging data from raw traces for Veit et al. 2022
<p>This contains scripts and functions used in extracting stimulus responses from raw calcium imaging traces stored in HDF5 format. Note the current version does not contain the HDF5 files with raw traces.</p>
Ascaris intestine calcium fluorescence dataset showing synergism of levamisole and Cry5B
<p><span>A novel class of biocidal compounds are the Crystal 3D (Cry) and Cytolytic (Cyt) proteins produced by <em>Bacillus thuringiensis </em>(Bt). Some Bt Cry proteins have a selective nematocidal activity, with Cry5B being the most studied. Cry5B kills nematode parasites by binding selectively to membrane glycosphingolipids, then forming pores in the cell membranes of the intestine leading to damage. Cry5B selectively targets multiple species of nematodes from different clades and has no effect against mammalian hosts. Levamisole is a cholinomimetic anthelmintic that acts by selectively opening L-subtype nicotinic acetylcholine receptor ion-channels (L-AChRs) that have been found on muscles of nematodes. A synergistic nematocidal interaction between levamisole and Cry5B has been described previously on whole worms, but the location, mechanism and time-course of this synergism is not known. In this study we follow the timeline of the effects of levamisole and Cry5B on the Ca<sup>2+</sup> levels of enterocyte cells of the intestine of <em>Ascaris suum</em> using fluorescence imaging. </span><span> The peak <span>Ca<sup>2+</sup> responses</span> to <span>levamisole were observed after approximately 10 minutes and the peak responses to activated Cry5B were seen after approximately 80 minutes. </span>When levamisole and Cry5B were applied simultaneously, we observed that the responses to Cry5B were bigger and occurred sooner than when it was applied by itself. It is proposed that there is an irreversible cytoplasmic Ca<sup>2+</sup> overload that leads to cell-death in the enterocyte that is induced by levamisole opening Ca<sup>2+</sup> permeable L-subtype nAChRs and the development of Ca<sup>2+</sup> permeable Cry5B toxin pores in enterocyte plasma membranes. The effects of levamisole potentiate and speed the actions of Cry5B. </span></p>
Virus – calcium carbonate composites: Possible mechanisms of bacteriophage-induced vaterite formation - Dataset
<p>Raw data (optical microscopy, electron microscopy, X-ray diffraction) from carbonate precipitation experiments in the presence of bacterial viruses.</p>
Data from: Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor
<p>Calcium-sensing receptor (CaSR) is a class C G protein-coupled receptor (GPCR) that plays an important role in calcium homeostasis and parathyroid hormone secretion. Here, we present multiple cryo-electron microscopy structures of full-length CaSR in distinct ligand-bound states. Ligands (Ca<sup>2+</sup> and l-tryptophan) bind to the extracellular domain of CaSR and induce large-scale conformational changes, leading to the closure of two heptahelical transmembrane domains (7TMDs) for activation. The positive modulator (evocalcet) and the negative allosteric modulator (NPS-2143) occupy the similar binding pocket in 7TMD. The binding of NPS-2143 causes a considerable rearrangement of two 7TMDs, forming an inactivated TM6/TM6 interface. Moreover, a total of 305 disease-causing missense mutations of CaSR have been mapped to the structure in the active state, creating hotspot maps of five clinical endocrine disorders. Our results provide a structural framework for understanding the activation, allosteric modulation mechanism, and disease therapy for class C GPCRs.</p>
The intracellular C-terminus confers compartment-specific targeting of voltage-gated calcium channels
<p>This table contains all tabulated data for:</p> <p>Chin and Kaeser, 2024. "The intracellular C-terminus confers compartment-specific targeting of voltage-gated calcium channels."</p> <p>Detailed methods are provided in the paper. </p>
Supplementary Figure 1 - Debulking surgery after muscular paraffin oil injections: Effects on calcium homeostasis and patient satisfaction
<p><strong><span>Figure legend</span></strong><span>: A-B: Plot for serum concentration of 1,25 dihydroxyvitamin D from baseline, and 1, 3, 6, and 12 months after surgery. Plot A is for normocalcemic men, while plot B is for hypercalcemic men.</span></p>
Coral resistance to ocean acidification linked to increased calcium at the site of calcification
<p>This file contains all the data and code for "Coral resistance to ocean acidification linked to increased calcium at the site of calcification" by DeCarlo et al. in Proceedings of the Royal Society B. Run the file, "run.R" in R to reproduce the analysis and create all the figures.</p> <p>Please see the published paper for methods and details: http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2018.0564</p>
Preliminary data and analysis from ultrafast calcium or voltage imaging recordings at 8-bits resolution using a Kinetix camera
<p><span>This dataset was obtained from brain slices of the mouse. Data are from transversal hippocampal slices from </span><span>30-40 postnatal days old C57Bl6 mice (of both genders), stained with the Ca<sup>2+</sup> indicator Fluo-4 AM; or from layer-5 pyramidal neurons loaded intracellularly either with the Ca<sup>2+</sup> indicator Oregon Green BAPTA-5N or with the voltage sensitive dye JPW1114. <span> </span>Details are in the Read_me file. This dataset cannot be used for publications without permission of the contact person.</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.