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Sheng CQ, Wu SS, Cheng YK, Wu Y, Li YM. Comprehensive review of indicators and techniques for optical mapping of intracellular calcium ions. Cereb Cortex 2024; 34:bhae346. [PMID: 39191664 DOI: 10.1093/cercor/bhae346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/27/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Calcium ions (Ca2+) play crucial roles in almost every cellular process, making the detection of changes in intracellular Ca2+ essential to understanding cell function. The fluorescence indicator method has garnered widespread application due to its exceptional sensitivity, rapid analysis, cost-effectiveness, and user-friendly nature. It has successfully delineated the spatial and temporal dynamics of Ca2+ signaling across diverse cell types. However, it is vital to understand that different indicators have varying levels of accuracy, sensitivity, and stability, making choosing the right inspection method crucial. As optical detection technologies advance, they continually broaden the horizons of scientific inquiry. This primer offers a systematic synthesis of the current fluorescence indicators and optical imaging modalities utilized for the detection of intracellular Ca2+. It elucidates their practical applications and inherent limitations, serving as an essential reference for researchers seeking to identify the most suitable detection methodologies for their calcium-centric investigations.
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Affiliation(s)
- Chu-Qiao Sheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun, Jilin 130012, China
| | - Shuang-Shuang Wu
- Department of Pediatric Hematology, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yong-Kang Cheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yao Wu
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yu-Mei Li
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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Woelk LM, Kovacevic D, Husseini H, Förster F, Gerlach F, Möckl F, Altfeld M, Guse AH, Diercks BP, Werner R. DARTS: an open-source Python pipeline for Ca 2+ microdomain analysis in live cell imaging data. Front Immunol 2024; 14:1299435. [PMID: 38274810 PMCID: PMC10809147 DOI: 10.3389/fimmu.2023.1299435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Ca2+ microdomains play a key role in intracellular signaling processes. For instance, they mediate the activation of T cells and, thus, the initial adaptive immune system. They are, however, also of utmost importance for activation of other cells, and a detailed understanding of the dynamics of these spatially localized Ca2+ signals is crucial for a better understanding of the underlying signaling processes. A typical approach to analyze Ca2+ microdomain dynamics is live cell fluorescence microscopy imaging. Experiments usually involve imaging a larger number of cells of different groups (for instance, wild type and knockout cells), followed by a time consuming image and data analysis. With DARTS, we present a modular Python pipeline for efficient Ca2+ microdomain analysis in live cell imaging data. DARTS (Deconvolution, Analysis, Registration, Tracking, and Shape normalization) provides state-of-the-art image postprocessing options like deep learning-based cell detection and tracking, spatio-temporal image deconvolution, and bleaching correction. An integrated automated Ca2+ microdomain detection offers direct access to global statistics like the number of microdomains for cell groups, corresponding signal intensity levels, and the temporal evolution of the measures. With a focus on bead stimulation experiments, DARTS provides a so-called dartboard projection analysis and visualization approach. A dartboard projection covers spatio-temporal normalization of the bead contact areas and cell shape normalization onto a circular template that enables aggregation of the spatiotemporal information of the microdomain detection results for the individual cells of the cell groups of interest. The dartboard visualization allows intuitive interpretation of the spatio-temporal microdomain dynamics at the group level. The application of DARTS is illustrated by three use cases in the context of the formation of initial Ca2+ microdomains after cell stimulation. DARTS is provided as an open-source solution and will be continuously extended upon the feedback of the community. Code available at: 10.5281/zenodo.10459243.
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Affiliation(s)
- Lena-Marie Woelk
- Department of Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dejan Kovacevic
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hümeyra Husseini
- Department of Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fritz Förster
- Department of Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fynn Gerlach
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Möckl
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Altfeld
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H. Guse
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn-Philipp Diercks
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - René Werner
- Department of Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Gil Montoya DC, Ornelas-Guevara R, Diercks BP, Guse AH, Dupont G. T cell Ca 2+ microdomains through the lens of computational modeling. Front Immunol 2023; 14:1235737. [PMID: 37860008 PMCID: PMC10582754 DOI: 10.3389/fimmu.2023.1235737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Cellular Ca2+ signaling is highly organized in time and space. Locally restricted and short-lived regions of Ca2+ increase, called Ca2+ microdomains, constitute building blocks that are differentially arranged to create cellular Ca2+ signatures controlling physiological responses. Here, we focus on Ca2+ microdomains occurring in restricted cytosolic spaces between the plasma membrane and the endoplasmic reticulum, called endoplasmic reticulum-plasma membrane junctions. In T cells, these microdomains have been finely characterized. Enough quantitative data are thus available to develop detailed computational models of junctional Ca2+ dynamics. Simulations are able to predict the characteristics of Ca2+ increases at the level of single channels and in junctions of different spatial configurations, in response to various signaling molecules. Thanks to the synergy between experimental observations and computational modeling, a unified description of the molecular mechanisms that create Ca2+ microdomains in the first seconds of T cell stimulation is emerging.
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Affiliation(s)
- Diana C. Gil Montoya
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roberto Ornelas-Guevara
- Unit of Theoretical Chronobiology, Faculté des Sciences CP231, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Björn-Philipp Diercks
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H. Guse
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Geneviève Dupont
- Unit of Theoretical Chronobiology, Faculté des Sciences CP231, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Benfenati A. upU-Net Approaches for Background Emission Removal in Fluorescence Microscopy. J Imaging 2022; 8:142. [PMID: 35621906 PMCID: PMC9146274 DOI: 10.3390/jimaging8050142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Abstract
The physical process underlying microscopy imaging suffers from several issues: some of them include the blurring effect due to the Point Spread Function, the presence of Gaussian or Poisson noise, or even a mixture of these two types of perturbation. Among them, auto-fluorescence presents other artifacts in the registered image, and such fluorescence may be an important obstacle in correctly recognizing objects and organisms in the image. For example, particle tracking may suffer from the presence of this kind of perturbation. The objective of this work is to employ Deep Learning techniques, in the form of U-Nets like architectures, for background emission removal. Such fluorescence is modeled by Perlin noise, which reveals to be a suitable candidate for simulating such a phenomenon. The proposed architecture succeeds in removing the fluorescence, and at the same time, it acts as a denoiser for both Gaussian and Poisson noise. The performance of this approach is furthermore assessed on actual microscopy images and by employing the restored images for particle recognition.
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Affiliation(s)
- Alessandro Benfenati
- Environmental and Science Policy Department, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy;
- Gruppo Nazionale Calcolo Scientifico, Istituto Nazionale di Alta Matematica, P.le Aldo Moro 5, 00185 Rome, Italy
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Brock VJ, Wolf IMA, Er-Lukowiak M, Lory N, Stähler T, Woelk LM, Mittrücker HW, Müller CE, Koch-Nolte F, Rissiek B, Werner R, Guse AH, Diercks BP. P2X4 and P2X7 are essential players in basal T cell activity and Ca 2+ signaling milliseconds after T cell activation. SCIENCE ADVANCES 2022; 8:eabl9770. [PMID: 35119925 PMCID: PMC8816335 DOI: 10.1126/sciadv.abl9770] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/14/2021] [Indexed: 05/20/2023]
Abstract
Initial T cell activation is triggered by the formation of highly dynamic, spatiotemporally restricted Ca2+ microdomains. Purinergic signaling is known to be involved in Ca2+ influx in T cells at later stages compared to the initial microdomain formation. Using a high-resolution Ca2+ live-cell imaging system, we show that the two purinergic cation channels P2X4 and P2X7 not only are involved in the global Ca2+ signals but also promote initial Ca2+ microdomains tens of milliseconds after T cell stimulation. These Ca2+ microdomains were significantly decreased in T cells from P2rx4-/- and P2rx7-/- mice or by pharmacological inhibition or blocking. Furthermore, we show a pannexin-1-dependent activation of P2X4 in the absence of T cell receptor/CD3 stimulation. Subsequently, upon T cell receptor/CD3 stimulation, ATP release is increased and autocrine activation of both P2X4 and P2X7 then amplifies initial Ca2+ microdomains already in the first second of T cell activation.
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Affiliation(s)
- Valerie J. Brock
- The Ca Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Insa M. A. Wolf
- The Ca Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Marco Er-Lukowiak
- Department of Neurology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Niels Lory
- Department of Immunology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Tobias Stähler
- Department of Immunology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Lena-Marie Woelk
- Department of Computational Neuroscience, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Hans-Willi Mittrücker
- Department of Immunology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | | | - Friedrich Koch-Nolte
- Department of Immunology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Björn Rissiek
- Department of Neurology, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - René Werner
- Department of Computational Neuroscience, University Medical Centre Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Andreas H. Guse
- The Ca Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Björn-Philipp Diercks
- The Ca Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Corresponding author.
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