1
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Rasaily M, Ngiimei D S, Thaosen RK, Gupta S, Deka S, Tamuli R. Methods for the detection of intracellular calcium in filamentous fungi. MethodsX 2024; 12:102570. [PMID: 38322134 PMCID: PMC10844858 DOI: 10.1016/j.mex.2024.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Calcium (Ca2+), a critical secondary messenger, is also known as the molecule of life and death. The cell responds to a minute change in Ca2+ concentration and tightly maintains Ca2+ homeostasis. Therefore, determining the cell Ca2+ level is critical to understand Ca2+ distribution in the cell and various cell processes. Many techniques have been developed to measure Ca2+ in the cell. We review here different methods used to detect and measure Ca2+ in filamentous fungi. Ca2+-sensitive fluorescent chlortetracycline hydrochloride (CTC), Ca2+-selective microelectrode, Ca2+ isotopes, aequorins, and RGECOs are commonly used to measure the Ca2+ level in filamentous fungi. The use of CTC was one of the earliest methods, developed in 1988, to measure the Ca2+ gradient in the filamentous fungus Neurospora crassa. Subsequently, Ca2+-specific microelectrodes were developed later in the 1990s to identify Ca2+ ion flux variations, and to measure Ca2+ concentration. Another method for quantifying Ca2+ is by using radio-labeled Ca2+ as a tracer. The usage of 45Ca to measure Ca2+ in Saccharomyces cerevisiae was reported previously and the same methodology was also used to detect Ca2+ in N. crassa recently. Subsequently, genetically engineered Ca2+ indicators (GECIs) like aequorins and RGECOs have been developed as Ca2+ indicators to detect and visualize Ca2+ inside the cell. In this review, we summarize various methodologies used to detect and measure Ca2+ in filamentous fungi with their advantages and limitations. •Chlortetracycline (CTC) fluorescence assay is used for visualizing Ca2+ level, whereas microelectrodes technique is used to determine Ca2+ flux in the cell.•Radioactive 45Ca is useful for quantification of Ca2+ in the cellular compartments.•Genetically modified calcium indicators (GECIs) are used to study Ca2+ dynamics in the cell.
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Affiliation(s)
- Megha Rasaily
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Serena Ngiimei D
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Rahul Kumar Thaosen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Surabhi Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Sangeeta Deka
- Centre for the Environment, Indian Institute of Technology Guwahati, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
- Centre for the Environment, Indian Institute of Technology Guwahati, India
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2
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Plaper T, Merljak E, Fink T, Satler T, Ljubetič A, Lainšček D, Jazbec V, Benčina M, Stevanoska S, Džeroski S, Jerala R. Designed allosteric protein logic. Cell Discov 2024; 10:8. [PMID: 38228615 DOI: 10.1038/s41421-023-00635-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024] Open
Abstract
The regulation of protein function by external or internal signals is one of the key features of living organisms. The ability to directly control the function of a selected protein would represent a valuable tool for regulating biological processes. Here, we present a generally applicable regulation of proteins called INSRTR, based on inserting a peptide into a loop of a target protein that retains its function. We demonstrate the versatility and robustness of coiled-coil-mediated regulation, which enables designs for either inactivation or activation of selected protein functions, and implementation of two-input logic functions with rapid response in mammalian cells. The selection of insertion positions in tested proteins was facilitated by using a predictive machine learning model. We showcase the robustness of the INSRTR strategy on proteins with diverse folds and biological functions, including enzymes, signaling mediators, DNA binders, transcriptional regulators, reporters, and antibody domains implemented as chimeric antigen receptors in T cells. Our findings highlight the potential of INSRTR as a powerful tool for precise control of protein function, advancing our understanding of biological processes and developing biotechnological and therapeutic interventions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Sintija Stevanoska
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
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3
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Zhang Y, Rózsa M, Liang Y, Bushey D, Wei Z, Zheng J, Reep D, Broussard GJ, Tsang A, Tsegaye G, Narayan S, Obara CJ, Lim JX, Patel R, Zhang R, Ahrens MB, Turner GC, Wang SSH, Korff WL, Schreiter ER, Svoboda K, Hasseman JP, Kolb I, Looger LL. Fast and sensitive GCaMP calcium indicators for imaging neural populations. Nature 2023; 615:884-891. [PMID: 36922596 PMCID: PMC10060165 DOI: 10.1038/s41586-023-05828-9] [Citation(s) in RCA: 172] [Impact Index Per Article: 172.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2023] [Indexed: 03/17/2023]
Abstract
Calcium imaging with protein-based indicators1,2 is widely used to follow neural activity in intact nervous systems, but current protein sensors report neural activity at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity and kinetics. Here we used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators3-8. The resulting 'jGCaMP8' sensors, based on the calcium-binding protein calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times of 2 ms) and the highest sensitivity for neural activity reported for a protein-based calcium sensor. jGCaMP8 sensors will allow tracking of large populations of neurons on timescales relevant to neural computation.
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Affiliation(s)
- Yan Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Márton Rózsa
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Yajie Liang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel Bushey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ziqiang Wei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jihong Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniel Reep
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Getahun Tsegaye
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | | | - Jing-Xuan Lim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Rongwei Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Glenn C Turner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Samuel S-H Wang
- Neuroscience Institute, Princeton University, Princeton, NJ, USA.
| | - Wyatt L Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Allen Institute for Neural Dynamics, Seattle, WA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jeremy P Hasseman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Ilya Kolb
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
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4
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Hu S, Yang J, Liao A, Lin Y, Liang S. Fluorescent indicators for live-cell and in vitro detection of inorganic cadmium dynamics. J Fluoresc 2022; 32:1397-1404. [PMID: 35438371 DOI: 10.1007/s10895-022-02919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/01/2022] [Indexed: 11/29/2022]
Abstract
Cadmium contamination is a severe threat to the environment and food safety. Thus, there is an urgent need to develop highly sensitive and selective cadmium detection tools. The engineered fluorescent indicator is a powerful tool for the rapid detection of inorganic cadmium in the environment. In this study, the development of yellow fluorescent indicators of cadmium chloride by inserting a fluorescent protein at different positions of the high cadmium-specific repressor and optimizing the flexible linker between the connection points is reported. These indicators provide a fast, sensitive, specific, high dynamic range, and real-time readout of cadmium ion dynamics in solution. The excitation and emission wavelength of this indicator used in this work are 420/485 and 528 nm, respectively. Fluorescent indicators N0C0/N1C1 showed a linear response to cadmium concentration within the range from 10/30 to 50/100 nM and with a detection limit of 10/33 nM under optimal condition. Escherichia coli cells containing the indicator were used to further study the response of cadmium ion concentration in living cells. E. coli N1C1 could respond to different concentrations of cadmium ions. This study provides a rapid and straightforward method for cadmium ion detection in vitro and the potential for biological imaging.
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Affiliation(s)
- Shulin Hu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Jun Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Anqi Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China. .,School of Biology and Biological Engineering, South China University of Technology, 510006, Guangzhou, People's Republic of China.
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5
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Fu Y, Colazo MG, De Buck J. Development of a blood calcium test for hypocalcemia diagnosis in dairy cows. Res Vet Sci 2022; 147:60-67. [DOI: 10.1016/j.rvsc.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
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6
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Heinrich R, Hussein W, Berlin S. Photo-transformable genetically-encoded optical probes for functional highlighting in vivo. J Neurosci Methods 2021; 355:109129. [PMID: 33711357 DOI: 10.1016/j.jneumeth.2021.109129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Studying the brain requires knowledge about both structure (i.e., connectome) and function of its constituents (neurons and glia alike). This need has prompted the development of novel tools and techniques, in particular optical techniques to examine cells remotely. Early works (1900's) led to the development of novel cell-staining techniques that, when combined with the use of a very simple light microscope, visualized individual neurons and their subcellular compartments in fixed tissues. Today, highlighting of structure and function can be performed on live cells, notably in vivo, owing to discovery of GFP and subsequent development of genetically encoded fluorescent optical tools. In this review, we focus our attention on a subset of optical biosensors, namely probes whose emission can be modified by light. We designate them photo-transformable genetically encoded probes. The family of photo-transformable probes embraces current probes that undergo photoactivation (PA), photoconversion (PC) or photoswitching (PS). We argue that these are particularly suited for studying multiple features of neurons, such as structure, connectivity and function concomitantly, for functional highlighting of neurons in vivo.
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Affiliation(s)
- Ronit Heinrich
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Wessal Hussein
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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7
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FRCaMP, a Red Fluorescent Genetically Encoded Calcium Indicator Based on Calmodulin from Schizosaccharomyces Pombe Fungus. Int J Mol Sci 2020; 22:ijms22010111. [PMID: 33374320 PMCID: PMC7794825 DOI: 10.3390/ijms22010111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Red fluorescent genetically encoded calcium indicators (GECIs) have expanded the available pallet of colors used for the visualization of neuronal calcium activity in vivo. However, their calcium-binding domain is restricted by calmodulin from metazoans. In this study, we developed red GECI, called FRCaMP, using calmodulin (CaM) from Schizosaccharomyces pombe fungus as a calcium binding domain. Compared to the R-GECO1 indicator in vitro, the purified protein FRCaMP had similar spectral characteristics, brightness, and pH stability but a 1.3-fold lower ΔF/F calcium response and 2.6-fold tighter calcium affinity with Kd of 441 nM and 2.4-6.6-fold lower photostability. In the cytosol of cultured HeLa cells, FRCaMP visualized calcium transients with a ΔF/F dynamic range of 5.6, which was similar to that of R-GECO1. FRCaMP robustly visualized the spontaneous activity of neuronal cultures and had a similar ΔF/F dynamic range of 1.7 but 2.1-fold faster decay kinetics vs. NCaMP7. On electrically stimulated cultured neurons, FRCaMP demonstrated 1.8-fold faster decay kinetics and 1.7-fold lower ΔF/F values per one action potential of 0.23 compared to the NCaMP7 indicator. The fungus-originating CaM of the FRCaMP indicator version with a deleted M13-like peptide did not interact with the cytosolic environment of the HeLa cells in contrast to the metazoa-originating CaM of the similarly truncated version of the GCaMP6s indicator with a deleted M13-like peptide. Finally, we generated a split version of the FRCaMP indicator, which allowed the simultaneous detection of calcium transients and the heterodimerization of bJun/bFos interacting proteins in the nuclei of HeLa cells with a ΔF/F dynamic range of 9.4 and a contrast of 2.3-3.5, respectively.
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8
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Tang S, Deng X, Jiang J, Kirberger M, Yang JJ. Design of Calcium-Binding Proteins to Sense Calcium. Molecules 2020; 25:molecules25092148. [PMID: 32375353 PMCID: PMC7248937 DOI: 10.3390/molecules25092148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Calcium controls numerous biological processes by interacting with different classes of calcium binding proteins (CaBP’s), with different affinities, metal selectivities, kinetics, and calcium dependent conformational changes. Due to the diverse coordination chemistry of calcium, and complexity associated with protein folding and binding cooperativity, the rational design of CaBP’s was anticipated to present multiple challenges. In this paper we will first discuss applications of statistical analysis of calcium binding sites in proteins and subsequent development of algorithms to predict and identify calcium binding proteins. Next, we report efforts to identify key determinants for calcium binding affinity, cooperativity and calcium dependent conformational changes using grafting and protein design. Finally, we report recent advances in designing protein calcium sensors to capture calcium dynamics in various cellular environments.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Jie Jiang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Michael Kirberger
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA;
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
- Correspondence: ; Tel.: +1-404-413-5520
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9
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Barykina NV, Sotskov VP, Gruzdeva AM, Wu YK, Portugues R, Subach OM, Chefanova ES, Plusnin VV, Ivashkina OI, Anokhin KV, Vlaskina AV, Korzhenevskiy DA, Nikolaeva AY, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Subach FV. FGCaMP7, an Improved Version of Fungi-Based Ratiometric Calcium Indicator for In Vivo Visualization of Neuronal Activity. Int J Mol Sci 2020; 21:ijms21083012. [PMID: 32344594 PMCID: PMC7215472 DOI: 10.3390/ijms21083012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) have become a widespread tool for the visualization of neuronal activity. As compared to popular GCaMP GECIs, the FGCaMP indicator benefits from calmodulin and M13-peptide from the fungi Aspergillus niger and Aspergillus fumigatus, which prevent its interaction with the intracellular environment. However, FGCaMP exhibits a two-phase fluorescence behavior with the variation of calcium ion concentration, has moderate sensitivity in neurons (as compared to the GCaMP6s indicator), and has not been fully characterized in vitro and in vivo. To address these limitations, we developed an enhanced version of FGCaMP, called FGCaMP7. FGCaMP7 preserves the ratiometric phenotype of FGCaMP, with a 3.1-fold larger ratiometric dynamic range in vitro. FGCaMP7 demonstrates 2.7- and 8.7-fold greater photostability compared to mEGFP and mTagBFP2 fluorescent proteins in vitro, respectively. The ratiometric response of FGCaMP7 is 1.6- and 1.4-fold higher, compared to the intensiometric response of GCaMP6s, in non-stimulated and stimulated neuronal cultures, respectively. We reveal the inertness of FGCaMP7 to the intracellular environment of HeLa cells using its truncated version with a deleted M13-like peptide; in contrast to the similarly truncated variant of GCaMP6s. We characterize the crystal structure of the parental FGCaMP indicator. Finally, we test the in vivo performance of FGCaMP7 in mouse brain using a two-photon microscope and an NVista miniscope; and in zebrafish using two-color ratiometric confocal imaging.
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Affiliation(s)
- Natalia V. Barykina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna M. Gruzdeva
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - You Kure Wu
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
| | - Ruben Portugues
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; (Y.K.W.); (R.P.)
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Elizaveta S. Chefanova
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Viktor V. Plusnin
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Department of NBIC-technologies, Moscow Institute of Physics and Technology, 123182 Moscow, Russia;
| | - Olga I. Ivashkina
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia; (N.V.B.); (O.I.I.); (K.V.A.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; (V.P.S.); (A.M.G.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tatiana V. Rakitina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna M. Varizhuk
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Galina E. Pozmogova
- Department of Biophysics, Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.M.V.); (G.E.P.)
- Department of Biophysics, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119435 Moscow, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (V.V.P.); (A.V.V.); (D.A.K.); (A.Y.N.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196-7100-3389
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10
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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11
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Penzkofer A, Silapetere A, Hegemann P. Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 20:E4086. [PMID: 31438573 PMCID: PMC6747118 DOI: 10.3390/ijms20174086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
QuasAr1 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense by directed evolution. Here we report absorption and emission spectroscopic studies of QuasAr1 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of QuasAr1 was studied by long-time attenuation coefficient measurements at room temperature (23 ± 2 °C) and at 2.5 ± 0.5 °C. The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 65 ± 3 °C). In the protein melting process the originally present protonated retinal Schiff base (PRSB) with absorption maximum at 580 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Long-time storage of QuasAr1 at temperatures around 2.5 °C and around 23 °C caused gradual protonated retinal Schiff base isomer changes to other isomer conformations, de-protonation to retinal Schiff base isomers, and apoprotein structure changes showing up in ultraviolet absorption increase. Reaction coordinate schemes are presented for the thermal protonated retinal Schiff base isomerizations and deprotonations in parallel with the dynamic apoprotein restructurings.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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12
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Subach OM, Barykina NV, Anokhin KV, Piatkevich KD, Subach FV. Near-Infrared Genetically Encoded Positive Calcium Indicator Based on GAF-FP Bacterial Phytochrome. Int J Mol Sci 2019; 20:ijms20143488. [PMID: 31315229 PMCID: PMC6678319 DOI: 10.3390/ijms20143488] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 02/01/2023] Open
Abstract
A variety of genetically encoded calcium indicators are currently available for visualization of calcium dynamics in cultured cells and in vivo. Only one of them, called NIR-GECO1, exhibits fluorescence in the near-infrared region of the spectrum. NIR-GECO1 is engineered based on the near-infrared fluorescent protein mIFP derived from bacterial phytochromes. However, NIR-GECO1 has an inverted response to calcium ions and its excitation spectrum is not optimal for the commonly used 640 nm lasers. Using small near-infrared bacterial phytochrome GAF-FP and calmodulin/M13-peptide pair, we developed a near-infrared calcium indicator called GAF-CaMP2. In vitro, GAF-CaMP2 showed a positive response of 78% and high affinity (Kd of 466 nM) to the calcium ions. It had excitation and emission maxima at 642 and 674 nm, respectively. GAF-CaMP2 had a 2.0-fold lower brightness, 5.5-fold faster maturation and lower pH stability compared to GAF-FP in vitro. GAF-CaMP2 showed 2.9-fold higher photostability than smURFP protein. The GAF-CaMP2 fusion with sfGFP demonstrated a ratiometric response with a dynamic range of 169% when expressed in the cytosol of mammalian cells in culture. Finally, we successfully applied the ratiometric version of GAF-CaMP2 for the simultaneous visualization of calcium transients in three organelles of mammalian cells using four-color fluorescence microscopy.
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Affiliation(s)
- Oksana M Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | | | - Konstantin V Anokhin
- P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia
- Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Fedor V Subach
- National Research Center "Kurchatov Institute", Moscow 123182, Russia.
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Abstract
The global population is ageing at an accelerating speed. The ability to perform working memory tasks together with rapid processing becomes increasingly difficult with increases in age. With increasing national average life spans and a rise in the prevalence of age-related disease, it is pertinent to discuss the unique perspectives that can be gained from imaging the aged brain. Differences in structure, function, blood flow, and neurovascular coupling are present in both healthy aged brains and in diseased brains and have not yet been explored to their full depth in contemporary imaging studies. Imaging methods ranging from optical imaging to magnetic resonance imaging (MRI) to newer technologies such as photoacoustic tomography each offer unique advantages and challenges in imaging the aged brain. This paper will summarize first the importance and challenges of imaging the aged brain and then offer analysis of potential imaging modalities and their representative applications. The potential breakthroughs in brain imaging are also envisioned.
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Affiliation(s)
- Hannah Humayun
- Photoacoustic Imaging Laboratory, Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Junjie Yao
- Photoacoustic Imaging Laboratory, Department of Biomedical Engineering, Duke University, Durham, NC, USA
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14
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Advances in Engineering and Application of Optogenetic Indicators for Neuroscience. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9030562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Our ability to investigate the brain is limited by available technologies that can record biological processes in vivo with suitable spatiotemporal resolution. Advances in optogenetics now enable optical recording and perturbation of central physiological processes within the intact brains of model organisms. By monitoring key signaling molecules noninvasively, we can better appreciate how information is processed and integrated within intact circuits. In this review, we describe recent efforts engineering genetically-encoded fluorescence indicators to monitor neuronal activity. We summarize recent advances of sensors for calcium, potassium, voltage, and select neurotransmitters, focusing on their molecular design, properties, and current limitations. We also highlight impressive applications of these sensors in neuroscience research. We adopt the view that advances in sensor engineering will yield enduring insights on systems neuroscience. Neuroscientists are eager to adopt suitable tools for imaging neural activity in vivo, making this a golden age for engineering optogenetic indicators.
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15
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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16
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Singh M, Lujan B, Renden R. Presynaptic GCaMP expression decreases vesicle release probability at the calyx of Held. Synapse 2018; 72:e22040. [PMID: 29935099 PMCID: PMC6186185 DOI: 10.1002/syn.22040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
Synaptic vesicle (SV) exocytosis is intimately dependent on free local Ca2+ near active zones. Genetically encoded calcium indicators (GECIs) have become an indispensable tool to monitor calcium dynamics during physiological responses, and they are widely used as a proxy to monitor activity in neuronal ensembles and at synaptic terminals. However, GECIs’ ability to bind Ca2+ at physiologically relevant concentration makes them strong candidates to affect calcium homeostasis and alter synaptic transmission by exogenously increasing Ca2+ buffering. In the present study, we show that genetically expressed GCaMP6m modulates SV release probability at the mouse calyx of Held synapse. GCaMP6m expression for approximately three weeks decreased initial SV release for both low‐frequency stimulation and high‐frequency stimulation trains, and slowed presynaptic short‐term depression. However, GCaMP6m does not affect quantal events during spontaneous activity at this synapse. This study emphasizes the careful use of GECIs as monitors of neuronal activity and inspects the role of these transgenic indicators which may alter calcium‐dependent physiological responses.
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Affiliation(s)
- Mahendra Singh
- Department of Physiology and Cell Biology, University of Nevada, Reno, Nevada, 89557
| | - Brendan Lujan
- Department of Physiology and Cell Biology, University of Nevada, Reno, Nevada, 89557.,Currently at Vollum Institute, Oregon Health and Science University, Portland, Oregon
| | - Robert Renden
- Department of Physiology and Cell Biology, University of Nevada, Reno, Nevada, 89557
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17
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Doronin DA, Barykina NV, Subach OM, Sotskov VP, Plusnin VV, Ivleva OA, Isaakova EA, Varizhuk AM, Pozmogova GE, Malyshev AY, Smirnov IV, Piatkevich KD, Anokhin KV, Enikolopov GN, Subach FV. Genetically encoded calcium indicator with NTnC-like design and enhanced fluorescence contrast and kinetics. BMC Biotechnol 2018; 18:10. [PMID: 29439686 PMCID: PMC5812234 DOI: 10.1186/s12896-018-0417-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Background The recently developed genetically encoded calcium indicator (GECI), called NTnC, has a novel design with reduced size due to utilization of the troponin C (TnC) as a Ca2+-binding moiety inserted into the mNeonGreen fluorescent protein. NTnC binds two times less Ca2+ ions while maintaining a higher fluorescence brightness at the basal level of Ca2+ in neurons as compared with the calmodulin-based GECIs, such as GCaMPs. In spite of NTnC’s high brightness, pH-stability, and high sensitivity to single action potentials, it has a limited fluorescence contrast (F-Ca2+/F+Ca2+) and slow Ca2+ dissociation kinetics. Results Herein, we developed a new NTnC-like GECI with enhanced fluorescence contrast and kinetics by replacing the mNeonGreen fluorescent subunit of the NTnC indicator with EYFP. Similar to NTnC, the developed indicator, named iYTnC2, has an inverted fluorescence response to Ca2+ (i.e. becoming dimmer with an increase of Ca2+ concentration). In the presence of Mg2+ ions, iYTnC2 demonstrated a 2.8-fold improved fluorescence contrast in vitro as compared with NTnC. The iYTnC2 indicator has lower brightness and pH-stability, but similar photostability as compared with NTnC in vitro. Stopped-flow fluorimetry studies revealed that iYTnC2 has 5-fold faster Ca2+ dissociation kinetics than NTnC. When compared with GCaMP6f GECI, iYTnC2 has up to 5.6-fold faster Ca2+ association kinetics and 1.7-fold slower dissociation kinetics. During calcium transients in cultured mammalian cells, iYTnC2 demonstrated a 2.7-fold higher fluorescence contrast as compared with that for the NTnC. iYTnC2 demonstrated a 4-fold larger response to Ca2+ transients in neuronal cultures than responses of NTnC. iYTnC2 response in neurons was additionally characterized using whole-cell patch clamp. Finally, we demonstrated that iYTnC2 can visualize neuronal activity in vivo in the hippocampus of freely moving mice using a nVista miniscope. Conclusions We demonstrate that expanding the family of NTnC-like calcium indicators is a promising strategy for the development of the next generation of GECIs with smaller molecule size and lower Ca2+ ions buffering capacity as compared with commonly used GECIs. Electronic supplementary material The online version of this article (10.1186/s12896-018-0417-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D A Doronin
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia
| | - N V Barykina
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia.,P.K. Anokhin Institute of Normal Physiology, Moscow, 125315, Russia
| | - O M Subach
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia.,National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - V P Sotskov
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia
| | - V V Plusnin
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia
| | - O A Ivleva
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia.,Lomonosov Moscow State University, Moscow, 119991, Russia
| | - E A Isaakova
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - A M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.,Engelhardt Institute of Molecular Biology RAS, Moscow, 119991, Russia
| | - G E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - A Y Malyshev
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, 117485, Russia
| | - I V Smirnov
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, 117485, Russia
| | - K D Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K V Anokhin
- P.K. Anokhin Institute of Normal Physiology, Moscow, 125315, Russia.,National Research Center "Kurchatov Institute", Moscow, 123182, Russia.,Lomonosov Moscow State University, Moscow, 119991, Russia
| | - G N Enikolopov
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia. .,Department of Anesthesiology, Stony Brook University Medical Center, Stony Brook, NY, 11794, USA. .,Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - F V Subach
- Moscow Institute of Physics and Technology, Moscow, 123182, Russia. .,National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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18
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Komis G, Novák D, Ovečka M, Šamajová O, Šamaj J. Advances in Imaging Plant Cell Dynamics. PLANT PHYSIOLOGY 2018; 176:80-93. [PMID: 29167354 PMCID: PMC5761809 DOI: 10.1104/pp.17.00962] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/20/2017] [Indexed: 05/20/2023]
Abstract
Advanced bioimaging uncovers insights into subcellular structures of plants.
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Affiliation(s)
- George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
| | - Dominik Novák
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, 783 71 Olomouc, Czech Republic
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