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Janicot R, Garcia-Marcos M. Get Ready to Sharpen Your Tools: A Short Guide to Heterotrimeric G Protein Activity Biosensors. Mol Pharmacol 2024; 106:129-144. [PMID: 38991745 PMCID: PMC11331509 DOI: 10.1124/molpharm.124.000949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of transmembrane receptors encoded in the human genome, and they initiate cellular responses triggered by a plethora of extracellular stimuli ranging from neurotransmitters and hormones to photons. Upon stimulation, GPCRs activate heterotrimeric G proteins (Gαβγ) in the cytoplasm, which then convey signals to their effectors to elicit cellular responses. Given the broad biological and biomedical relevance of GPCRs and G proteins in physiology and disease, there is great interest in developing and optimizing approaches to measure their signaling activity with high accuracy and across experimental systems pertinent to their functions in cellular communication. This review provides a historical perspective on approaches to measure GPCR-G protein signaling, from quantification of second messengers and other indirect readouts of activity to biosensors that directly detect the activity of G proteins. The latter is the focus of a more detailed overview of the evolution of design principles for various optical biosensors of G protein activity with different experimental capabilities. We will highlight advantages and limitations of biosensors that detect different G protein activation hallmarks, like dissociation of Gα and Gβγ or nucleotide exchange on Gα, as well as their suitability to detect signaling mediated by endogenous versus exogenous signaling components or in physiologically relevant systems like primary cells. Overall, this review intends to provide an assessment of the state-of-the-art for biosensors that directly measure G protein activity to allow readers to make informed decisions on the selection and implementation of currently available tools. SIGNIFICANCE STATEMENT: G protein activity biosensors have become essential and widespread tools to assess GPCR signaling and pharmacology. Yet, investigators face the challenge of choosing from a growing list of G protein activity biosensors. This review provides an overview of the features and capabilities of different optical biosensor designs for the direct detection of G protein activity in cells, with the aim of facilitating the rational selection of systems that align with the specific scientific questions and needs of investigators.
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Affiliation(s)
- Remi Janicot
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine (R.J., M.G.-M.) and Department of Biology, College of Arts & Sciences (M.G.-M.), Boston University, Boston, Massachusetts
| | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine (R.J., M.G.-M.) and Department of Biology, College of Arts & Sciences (M.G.-M.), Boston University, Boston, Massachusetts
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2
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Andreeva VD, Regeni I, Yang T, Elmanova A, Presselt M, Dietzek-Ivanšić B, Bonnet S. Red-to-Blue Triplet-Triplet Annihilation Upconversion for Calcium Sensing. J Phys Chem Lett 2024; 15:7430-7435. [PMID: 39007727 DOI: 10.1021/acs.jpclett.4c01528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Triplet-triplet annihilation upconversion is a bimolecular process converting low-energy photons into high-energy photons. Here, we report a calcium-sensing system working via triplet-triplet annihilation (TTA) upconverted emission. The probe itself was obtained by covalent conjugation of a blue emitter, perylene, with a calcium-chelating moiety, and it was sensitized by the red-light-absorbing photosensitizer palladium(II) tetraphenyltetrabenzoporphyrin (PdTPTBP). Sensing was selective for Ca2+ and occurred in the micromolar domain. In deoxygenated conditions, the TTA upconverted luminescence gradually appeared upon adding an increasing concentration of calcium ions, to reach a maximum upconversion quantum yield of 0.0020.
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Affiliation(s)
- Valeriia D Andreeva
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Irene Regeni
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Tingxiang Yang
- School of BiosciencesUniversity of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, United Kingdom
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Anna Elmanova
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- SciClus GmbH & Co. KG, Moritz-von-Rohr-Straße 1a, 07745 Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Philosophenweg 7a, 07743 Jena, Germany
| | - Martin Presselt
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- SciClus GmbH & Co. KG, Moritz-von-Rohr-Straße 1a, 07745 Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Philosophenweg 7a, 07743 Jena, Germany
| | - Benjamin Dietzek-Ivanšić
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
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3
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Boto T, Tomchik SM. Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila. Cold Spring Harb Protoc 2024; 2024:pdb.top107799. [PMID: 37197830 DOI: 10.1101/pdb.top107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Learning and memory allow animals to adjust their behavior based on the predictive value of their past experiences. Memories often exist in complex representations, spread across numerous cells and synapses in the brain. Studying relatively simple forms of memory provides insights into the fundamental processes that underlie multiple forms of memory. Associative learning occurs when an animal learns the relationship between two previously unrelated sensory stimuli, such as when a hungry animal learns that a particular odor is followed by a tasty reward. Drosophila is a particularly powerful model to study how this type of memory works. The fundamental principles are widely shared among animals, and there is a wide range of genetic tools available to study circuit function in flies. In addition, the olfactory structures that mediate associative learning in flies, such as the mushroom body and its associated neurons, are anatomically organized, relatively well-characterized, and readily accessible to imaging. Here, we review the olfactory anatomy and physiology of the olfactory system, describe how plasticity in the olfactory pathway mediates learning and memory, and explain the general principles underlying calcium imaging approaches.
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Affiliation(s)
- Tamara Boto
- Department of Physiology, Trinity College Dublin, Dublin 2, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Seth M Tomchik
- Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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4
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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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5
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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6
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Xu S, Xiao X, Manshaii F, Chen J. Injectable Fluorescent Neural Interfaces for Cell-Specific Stimulating and Imaging. NANO LETTERS 2024. [PMID: 38606614 DOI: 10.1021/acs.nanolett.4c00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Building on current explorations in chronic optical neural interfaces, it is essential to address the risk of photothermal damage in traditional optogenetics. By focusing on calcium fluorescence for imaging rather than stimulation, injectable fluorescent neural interfaces significantly minimize photothermal damage and improve the accuracy of neuronal imaging. Key advancements including the use of injectable microelectronics for targeted electrical stimulation and their integration with cell-specific genetically encoded calcium indicators have been discussed. These injectable electronics that allow for post-treatment retrieval offer a minimally invasive solution, enhancing both usability and reliability. Furthermore, the integration of genetically encoded fluorescent calcium indicators with injectable bioelectronics enables precise neuronal recording and imaging of individual neurons. This shift not only minimizes risks such as photothermal conversion but also boosts safety, specificity, and effectiveness of neural imaging. Embracing these advancements represents a significant leap forward in biomedical engineering and neuroscience, paving the way for advanced brain-machine interfaces.
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Affiliation(s)
- Shumao Xu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Xiao Xiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Farid Manshaii
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jun Chen
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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7
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Pang B, Wu X, Chen H, Yan Y, Du Z, Yu Z, Yang X, Wang W, Lu K. Exploring the memory: existing activity-dependent tools to tag and manipulate engram cells. Front Cell Neurosci 2024; 17:1279032. [PMID: 38259503 PMCID: PMC10800721 DOI: 10.3389/fncel.2023.1279032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/17/2023] [Indexed: 01/24/2024] Open
Abstract
The theory of engrams, proposed several years ago, is highly crucial to understanding the progress of memory. Although it significantly contributes to identifying new treatments for cognitive disorders, it is limited by a lack of technology. Several scientists have attempted to validate this theory but failed. With the increasing availability of activity-dependent tools, several researchers have found traces of engram cells. Activity-dependent tools are based on the mechanisms underlying neuronal activity and use a combination of emerging molecular biological and genetic technology. Scientists have used these tools to tag and manipulate engram neurons and identified numerous internal connections between engram neurons and memory. In this review, we provide the background, principles, and selected examples of applications of existing activity-dependent tools. Using a combination of traditional definitions and concepts of engram cells, we discuss the applications and limitations of these tools and propose certain developmental directions to further explore the functions of engram cells.
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Affiliation(s)
- Bo Pang
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Xiaoyan Wu
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Hailun Chen
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Yiwen Yan
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Zibo Du
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zihan Yu
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Xiai Yang
- Department of Neurology, Ankang Central Hospital, Ankang, China
| | - Wanshan Wang
- Laboratory Animal Management Center, Southern Medical University, Guangzhou, China
- Guangzhou Southern Medical Laboratory Animal Sci. and Tech. Co., Ltd., Guangzhou, China
| | - Kangrong Lu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Southern Medical University, Guangzhou, China
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8
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Roelle S, Kamath ND, Matreyek KA. Mammalian Genomic Manipulation with Orthogonal Bxb1 DNA Recombinase Sites for the Functional Characterization of Protein Variants. ACS Synth Biol 2023; 12:3352-3365. [PMID: 37922210 PMCID: PMC10661055 DOI: 10.1021/acssynbio.3c00355] [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: 06/10/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 11/05/2023]
Abstract
The Bxb1 bacteriophage serine DNA recombinase is an efficient tool for engineering recombinant DNA into the genomes of cultured cells. Generally, a single engineered "landing pad" site is introduced into the cell genome, permitting the integration of transgenic circuits or libraries of transgene variants. While sufficient for many studies, the extent of genetic manipulation possible with a single recombinase site is limiting and insufficient for more complex cell-based assays. Here, we harnessed two orthogonal Bxb1 recombinase sites to enable alternative avenues for using mammalian synthetic biology to characterize transgenic protein variants. By designing plasmids flanked by a second pair of auxiliary recombination sites, we demonstrate that we can avoid the genomic integration of undesirable bacterial DNA elements using the same starting cells engineered for whole-plasmid integration. We also created "double landing pad" cells simultaneously harboring two orthogonal Bxb1 recombinase sites at separate genomic loci, allowing complex cell-based genetic assays. Integration of a genetically encoded calcium indicator allowed for the real-time monitoring of intracellular calcium signaling dynamics, including kinetic perturbations that occur upon overexpression of the wild-type or variant version of the calcium signaling relay protein STIM1. A panel of missense mutants of the HIV-1 accessory protein Vif was paired with various paralogs within the human Apobec3 innate immune protein family to identify combinations capable or incapable of interacting within cells. These cells allow transgenic protein variant libraries to be readily paired with assay-specific protein partners or biosensors, enabling new functional readouts for large-scale genetic assays for protein function.
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Affiliation(s)
- Sarah
M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Nisha D. Kamath
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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9
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Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
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Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
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10
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Valiente-Gabioud AA, Fabritius A, Griesbeck O. Probing the interstitial calcium compartment. J Physiol 2023; 601:4217-4226. [PMID: 36073135 DOI: 10.1113/jp279510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Calcium in interstitial fluids is a crucial ion pool for entry into cells through a plethora of calcium-permeable channels. It is also sensed actively by dedicated receptors. While the mechanisms of global calcium homeostasis and regulation in body fluids appear well understood, more efforts and new technology are needed to elucidate local calcium handling in the small and relatively isolated interstitial spaces between cells. Here we review current methodology for monitoring interstitial calcium and highlight the potential of new approaches for its study. In particular, new generations of high-performance low-affinity genetically encoded calcium indicators could allow imaging of calcium in relatively inaccessible intercellular structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
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11
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Sridhar S, Khamaj A, Asthana MK. Cognitive neuroscience perspective on memory: overview and summary. Front Hum Neurosci 2023; 17:1217093. [PMID: 37565054 PMCID: PMC10410470 DOI: 10.3389/fnhum.2023.1217093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
This paper explores memory from a cognitive neuroscience perspective and examines associated neural mechanisms. It examines the different types of memory: working, declarative, and non-declarative, and the brain regions involved in each type. The paper highlights the role of different brain regions, such as the prefrontal cortex in working memory and the hippocampus in declarative memory. The paper also examines the mechanisms that underlie the formation and consolidation of memory, including the importance of sleep in the consolidation of memory and the role of the hippocampus in linking new memories to existing cognitive schemata. The paper highlights two types of memory consolidation processes: cellular consolidation and system consolidation. Cellular consolidation is the process of stabilizing information by strengthening synaptic connections. System consolidation models suggest that memories are initially stored in the hippocampus and are gradually consolidated into the neocortex over time. The consolidation process involves a hippocampal-neocortical binding process incorporating newly acquired information into existing cognitive schemata. The paper highlights the role of the medial temporal lobe and its involvement in autobiographical memory. Further, the paper discusses the relationship between episodic and semantic memory and the role of the hippocampus. Finally, the paper underscores the need for further research into the neurobiological mechanisms underlying non-declarative memory, particularly conditioning. Overall, the paper provides a comprehensive overview from a cognitive neuroscience perspective of the different processes involved in memory consolidation of different types of memory.
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Affiliation(s)
- Sruthi Sridhar
- Department of Psychology, Mount Allison University, Sackville, NB, Canada
| | - Abdulrahman Khamaj
- Department of Industrial Engineering, College of Engineering, Jazan University, Jazan, Saudi Arabia
| | - Manish Kumar Asthana
- Department of Humanities and Social Sciences, Indian Institute of Technology Roorkee, Roorkee, India
- Department of Design, Indian Institute of Technology Roorkee, Roorkee, India
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12
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Hasani H, Sun J, Zhu SI, Rong Q, Willomitzer F, Amor R, McConnell G, Cossairt O, Goodhill GJ. Whole-brain imaging of freely-moving zebrafish. Front Neurosci 2023; 17:1127574. [PMID: 37139528 PMCID: PMC10150962 DOI: 10.3389/fnins.2023.1127574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
One of the holy grails of neuroscience is to record the activity of every neuron in the brain while an animal moves freely and performs complex behavioral tasks. While important steps forward have been taken recently in large-scale neural recording in rodent models, single neuron resolution across the entire mammalian brain remains elusive. In contrast the larval zebrafish offers great promise in this regard. Zebrafish are a vertebrate model with substantial homology to the mammalian brain, but their transparency allows whole-brain recordings of genetically-encoded fluorescent indicators at single-neuron resolution using optical microscopy techniques. Furthermore zebrafish begin to show a complex repertoire of natural behavior from an early age, including hunting small, fast-moving prey using visual cues. Until recently work to address the neural bases of these behaviors mostly relied on assays where the fish was immobilized under the microscope objective, and stimuli such as prey were presented virtually. However significant progress has recently been made in developing brain imaging techniques for zebrafish which are not immobilized. Here we discuss recent advances, focusing particularly on techniques based on light-field microscopy. We also draw attention to several important outstanding issues which remain to be addressed to increase the ecological validity of the results obtained.
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Affiliation(s)
- Hamid Hasani
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, United States
| | - Jipeng Sun
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Qiangzhou Rong
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Florian Willomitzer
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, United States
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Oliver Cossairt
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Geoffrey J. Goodhill
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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13
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Pan YK, Perry SF. The control of breathing in fishes - historical perspectives and the path ahead. J Exp Biol 2023; 226:307288. [PMID: 37097020 DOI: 10.1242/jeb.245529] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The study of breathing in fishes has featured prominently in Journal of Experimental Biology (JEB), particularly during the latter half of the past century. Indeed, many of the seminal discoveries in this important sub-field of comparative respiratory physiology were reported first in JEB. The period spanning 1960-1990 (the 'golden age of comparative respiratory physiology') witnessed intense innovation in the development of methods to study the control of breathing. Many of the guiding principles of piscine ventilatory control originated during this period, including our understanding of the dominance of O2 as the driver of ventilation in fish. However, a critical issue - the identity of the peripheral O2 chemoreceptors - remained unanswered until methods for cell isolation, culture and patch-clamp recording established that gill neuroepithelial cells (NECs) respond to hypoxia in vitro. Yet, the role of the NECs and other putative peripheral or central chemoreceptors in the control of ventilation in vivo remains poorly understood. Further progress will be driven by the implementation of genetic tools, most of which can be used in zebrafish (Danio rerio). These tools include CRISPR/Cas9 for selective gene knockout, and Tol2 systems for transgenesis, the latter of which enables optogenetic stimulation of cellular pathways, cellular ablation and in vivo cell-specific biosensing. Using these methods, the next period of discovery will see the identification of the peripheral sensory pathways that initiate ventilatory responses, and will elucidate the nature of their integration within the central nervous system and their link to the efferent motor neurons that control breathing.
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Affiliation(s)
- Yihang Kevin Pan
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
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14
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Krueger TD, Tang L, Fang C. Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing. BIOSENSORS 2023; 13:bios13020218. [PMID: 36831983 PMCID: PMC9954042 DOI: 10.3390/bios13020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 05/14/2023]
Abstract
Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca2+) concentrations in vivo with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca2+-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca2+-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities.
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15
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Day-Cooney J, Dalangin R, Zhong H, Mao T. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. J Neurochem 2023; 164:284-308. [PMID: 35285522 PMCID: PMC11322610 DOI: 10.1111/jnc.15608] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The brain relies on many forms of dynamic activities in individual neurons, from synaptic transmission to electrical activity and intracellular signaling events. Monitoring these neuronal activities with high spatiotemporal resolution in the context of animal behavior is a necessary step to achieve a mechanistic understanding of brain function. With the rapid development and dissemination of highly optimized genetically encoded fluorescent sensors, a growing number of brain activities can now be visualized in vivo. To date, cellular calcium imaging, which has been largely used as a proxy for electrical activity, has become a mainstay in systems neuroscience. While challenges remain, voltage imaging of neural populations is now possible. In addition, it is becoming increasingly practical to image over half a dozen neurotransmitters, as well as certain intracellular signaling and metabolic activities. These new capabilities enable neuroscientists to test previously unattainable hypotheses and questions. This review summarizes recent progress in the development and delivery of genetically encoded fluorescent sensors, and highlights example applications in the context of in vivo imaging.
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Affiliation(s)
- Julian Day-Cooney
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rochelin Dalangin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
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16
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Teal LB, Ingram SM, Bubser M, McClure E, Jones CK. The Evolving Role of Animal Models in the Discovery and Development of Novel Treatments for Psychiatric Disorders. ADVANCES IN NEUROBIOLOGY 2023; 30:37-99. [PMID: 36928846 DOI: 10.1007/978-3-031-21054-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Historically, animal models have been routinely used in the characterization of novel chemical entities (NCEs) for various psychiatric disorders. Animal models have been essential in the in vivo validation of novel drug targets, establishment of lead compound pharmacokinetic to pharmacodynamic relationships, optimization of lead compounds through preclinical candidate selection, and development of translational measures of target occupancy and functional target engagement. Yet, with decades of multiple NCE failures in Phase II and III efficacy trials for different psychiatric disorders, the utility and value of animal models in the drug discovery process have come under intense scrutiny along with the widespread withdrawal of the pharmaceutical industry from psychiatric drug discovery. More recently, the development and utilization of animal models for the discovery of psychiatric NCEs has undergone a dynamic evolution with the application of the Research Domain Criteria (RDoC) framework for better design of preclinical to clinical translational studies combined with innovative genetic, neural circuitry-based, and automated testing technologies. In this chapter, the authors will discuss this evolving role of animal models for improving the different stages of the discovery and development in the identification of next generation treatments for psychiatric disorders.
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Affiliation(s)
- Laura B Teal
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN, USA
| | - Shalonda M Ingram
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN, USA
| | - Michael Bubser
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN, USA
| | - Elliott McClure
- College of Pharmacy and Health Sciences, Lipscomb University, Nashville, TN, USA
| | - Carrie K Jones
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN, USA.
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17
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Romero G, Park J, Koehler F, Pralle A, Anikeeva P. Modulating cell signalling in vivo with magnetic nanotransducers. NATURE REVIEWS. METHODS PRIMERS 2022; 2:92. [PMID: 38111858 PMCID: PMC10727510 DOI: 10.1038/s43586-022-00170-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 12/20/2023]
Abstract
Weak magnetic fields offer nearly lossless transmission of signals within biological tissue. Magnetic nanomaterials are capable of transducing magnetic fields into a range of biologically relevant signals in vitro and in vivo. These nanotransducers have recently enabled magnetic control of cellular processes, from neuronal firing and gene expression to programmed apoptosis. Effective implementation of magnetically controlled cellular signalling relies on careful tailoring of magnetic nanotransducers and magnetic fields to the responses of the intended molecular targets. This primer discusses the versatility of magnetic modulation modalities and offers practical guidelines for selection of appropriate materials and field parameters, with a particular focus on applications in neuroscience. With recent developments in magnetic instrumentation and nanoparticle chemistries, including those that are commercially available, magnetic approaches promise to empower research aimed at connecting molecular and cellular signalling to physiology and behaviour in untethered moving subjects.
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Affiliation(s)
- Gabriela Romero
- Department of Biomedical Engineering and Chemical Engineering, University of Texas at San Antonio, San Antonio, TX, USA
| | - Jimin Park
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Florian Koehler
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arnd Pralle
- Department of Physics, University at Buffalo, the State University of New York, Buffalo, NY, USA
| | - Polina Anikeeva
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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18
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Kulakova MV, Karginov AV, Alexandrov AI, Agaphonov MO. The GEM-GECO Calcium Indicator Is Useable in Ogataea parapolymorpha Yeast, but Aggravates Effects of Increased Cytosolic Calcium Levels. Int J Mol Sci 2022; 23:ijms231710004. [PMID: 36077401 PMCID: PMC9456557 DOI: 10.3390/ijms231710004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Ca2+ is a ubiquitous second messenger, which allows eukaryotic cells to respond to external stimuli. The use of genetically encoded Ca2+ indicators allows real-time monitoring of cytosolic Ca2+ levels to study such responses. Here we explored the possibility of using the ratiometric Ca2+ indicator GEM-GECO for monitoring cytosolic Ca2+ concentration ([Ca2+]cyt) in the yeast Ogataea parapolymorpha. High-level production of GEM-GECO led to a severe growth defect in cells lacking the vacuolar Ca2+ ATPase Pmc1, which is involved in [Ca2+]cyt control, and prompted a phenotype resembling that of Pmc1 deficiency, in a strain with wild-type PMC1. This was likely due to the presence of the calmodulin domain in GEM-GECO. In contrast to previous studies of genetically-encoded calcium indicators in neuronal cells, our results suggest that physiological effects of GEM-GECO expression in yeast cells are due not to Ca2+ depletion, but to excessive Ca2+ signaling. Despite these drawbacks, study of fluorescence in individual cells revealed switching of GEM-GECO from the Ca2+-free to Ca2+-bound state minutes after external addition of CaCl2. This was followed by gradual return of GEM-GECO to a Ca2+-free-state that was impaired in the pmc1-Δ mutant. These results demonstrate GEM-GECO usability for [Ca2+]cyt monitoring in budding yeast.
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19
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Grienberger C, Giovannucci A, Zeiger W, Portera-Cailliau C. Two-photon calcium imaging of neuronal activity. NATURE REVIEWS. METHODS PRIMERS 2022; 2:67. [PMID: 38124998 PMCID: PMC10732251 DOI: 10.1038/s43586-022-00147-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/07/2022] [Indexed: 12/23/2023]
Abstract
In vivo two-photon calcium imaging (2PCI) is a technique used for recording neuronal activity in the intact brain. It is based on the principle that, when neurons fire action potentials, intracellular calcium levels rise, which can be detected using fluorescent molecules that bind to calcium. This Primer is designed for scientists who are considering embarking on experiments with 2PCI. We provide the reader with a background on the basic concepts behind calcium imaging and on the reasons why 2PCI is an increasingly powerful and versatile technique in neuroscience. The Primer explains the different steps involved in experiments with 2PCI, provides examples of what ideal preparations should look like and explains how data are analysed. We also discuss some of the current limitations of the technique, and the types of solutions to circumvent them. Finally, we conclude by anticipating what the future of 2PCI might look like, emphasizing some of the analysis pipelines that are being developed and international efforts for data sharing.
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Affiliation(s)
- Christine Grienberger
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, USA
| | - Andrea Giovannucci
- Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Zeiger
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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20
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Mustapha F, Sengupta K, Puech PH. May the force be with your (immune) cells: an introduction to traction force microscopy in Immunology. Front Immunol 2022; 13:898558. [PMID: 35990636 PMCID: PMC9389945 DOI: 10.3389/fimmu.2022.898558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/28/2022] [Indexed: 11/21/2022] Open
Abstract
For more than a couple of decades now, "force" has been recognized as an important physical parameter that cells employ to adapt to their microenvironment. Whether it is externally applied, or internally generated, cells use force to modulate their various actions, from adhesion and migration to differentiation and immune function. T lymphocytes use such mechano-sensitivity to decipher signals when recognizing cognate antigens presented on the surface of antigen presenting cells (APCs), a critical process in the adaptive immune response. As such, many techniques have been developed and used to measure the forces felt/exerted by these small, solitary and extremely reactive cells to decipher their influence on diverse T cell functions, primarily activation. Here, we focus on traction force microscopy (TFM), in which a deformable substrate, coated with the appropriate molecules, acts as a force sensor on the cellular scale. This technique has recently become a center of interest for many groups in the "ImmunoBiophysics" community and, as a consequence, has been subjected to refinements for its application to immune cells. Here, we present an overview of TFM, the precautions and pitfalls, and the most recent developments in the context of T cell immunology.
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Affiliation(s)
- Farah Mustapha
- Laboratory Adhesion Inflammation (LAI), INSERM, CNRS, Aix Marseille University, Marseille, France
- Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), CNRS, Aix Marseille University, Marseille, France
- Turing Center for Living Systems (CENTURI), Marseille, France
| | - Kheya Sengupta
- Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), CNRS, Aix Marseille University, Marseille, France
- Turing Center for Living Systems (CENTURI), Marseille, France
| | - Pierre-Henri Puech
- Laboratory Adhesion Inflammation (LAI), INSERM, CNRS, Aix Marseille University, Marseille, France
- Turing Center for Living Systems (CENTURI), Marseille, France
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21
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Kempmann A, Gensch T, Offenhäusser A, Tihaa I, Maybeck V, Balfanz S, Baumann A. The Functional Characterization of GCaMP3.0 Variants Specifically Targeted to Subcellular Domains. Int J Mol Sci 2022; 23:ijms23126593. [PMID: 35743038 PMCID: PMC9223625 DOI: 10.3390/ijms23126593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Calcium (Ca2+) ions play a pivotal role in physiology and cellular signaling. The intracellular Ca2+ concentration ([Ca2+]i) is about three orders of magnitude lower than the extracellular concentration, resulting in a steep transmembrane concentration gradient. Thus, the spatial and the temporal dynamics of [Ca2+]i are ideally suited to modulate Ca2+-mediated cellular responses to external signals. A variety of highly sophisticated methods have been developed to gain insight into cellular Ca2+ dynamics. In addition to electrophysiological measurements and the application of synthetic dyes that change their fluorescent properties upon interaction with Ca2+, the introduction and the ongoing development of genetically encoded Ca2+ indicators (GECI) opened a new era to study Ca2+-driven processes in living cells and organisms. Here, we have focused on one well-established GECI, i.e., GCaMP3.0. We have systematically modified the protein with sequence motifs, allowing localization of the sensor in the nucleus, in the mitochondrial matrix, at the mitochondrial outer membrane, and at the plasma membrane. The individual variants and a cytosolic version of GCaMP3.0 were overexpressed and purified from E. coli cells to study their biophysical properties in solution. All versions were examined to monitor Ca2+ signaling in stably transfected cell lines and in primary cortical neurons transduced with recombinant Adeno-associated viruses (rAAV). In this comparative study, we provide evidence for a robust approach to reliably trace Ca2+ signals at the (sub)-cellular level with pronounced temporal resolution.
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Affiliation(s)
- Annika Kempmann
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Andreas Offenhäusser
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Irina Tihaa
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Vanessa Maybeck
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Sabine Balfanz
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Arnd Baumann
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
- Correspondence: ; Tel.: +49-2461-614014
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22
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Charles AS, Cermak N, Affan RO, Scott BB, Schiller J, Mishne G. GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2022; 31:3509-3524. [PMID: 35533160 PMCID: PMC9278524 DOI: 10.1109/tip.2022.3171414] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Optical imaging of calcium signals in the brain has enabled researchers to observe the activity of hundreds-to-thousands of individual neurons simultaneously. Current methods predominantly use morphological information, typically focusing on expected shapes of cell bodies, to better identify neurons in the field-of-view. The explicit shape constraints limit the applicability of automated cell identification to other important imaging scales with more complex morphologies, e.g., dendritic or widefield imaging. Specifically, fluorescing components may be broken up, incompletely found, or merged in ways that do not accurately describe the underlying neural activity. Here we present Graph Filtered Temporal Dictionary (GraFT), a new approach that frames the problem of isolating independent fluorescing components as a dictionary learning problem. Specifically, we focus on the time-traces-the main quantity used in scientific discovery-and learn a time trace dictionary with the spatial maps acting as the presence coefficients encoding which pixels the time-traces are active in. Furthermore, we present a novel graph filtering model which redefines connectivity between pixels in terms of their shared temporal activity, rather than spatial proximity. This model greatly eases the ability of our method to handle data with complex non-local spatial structure. We demonstrate important properties of our method, such as robustness to morphology, simultaneously detecting different neuronal types, and implicitly inferring number of neurons, on both synthetic data and real data examples. Specifically, we demonstrate applications of our method to calcium imaging both at the dendritic, somatic, and widefield scales.
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23
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Donaldson PD, Swisher SL. Transparent, Low-Impedance Inkjet-Printed PEDOT:PSS Microelectrodes for Multi-modal Neuroscience. PHYSICA STATUS SOLIDI. A, APPLICATIONS AND MATERIALS SCIENCE : PSS 2022; 219:2100683. [PMID: 37641661 PMCID: PMC10461862 DOI: 10.1002/pssa.202100683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 08/31/2023]
Abstract
Transparent microelectrodes that facilitate simultaneous optical and electrophysiological interfacing are desirable tools for neuroscience. Electrodes made from transparent conductors such as graphene and indium tin oxide (ITO) show promise but are often limited by poor interfacial charge-transfer properties. Here, microelectrodes are demonstrated that take advantage of the transparency and volumetric capacitance of the mixed ion-electron conductor Poly(3,4- ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS). Ring-shaped microelectrodes are fabricated by inkjet-printing PEDOT:PSS, encapsulating with Parylene-C, and then exposing a contact site that is much smaller than the microelectrode outer diameter. This unique structure allows the encapsulated portion of the microelectrode volume surrounding the contact site to participate in signal transduction, which reduces impedance and enhances charge storage capacity. While using the same 100 μm diameter contact site, increasing the outer diameter of the encapsulated electrode from 300 to 550 μm reduces the impedance from 294±21 to 98±2 kΩ, respectively, at 1 Hz. Similarly, the charge storage capacity is enhanced from 6 to 21 mC cm-2. The PEDOT:PSS microelectrodes provide a low-haze, high-transmittance optical interface, demonstrating their suitability for optical neuroscience applications. They remain functional after a million 1 V stimulation cycles, up to 600 μA of stimulation current, and more than 1000 mechanical bending cycles.
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Affiliation(s)
- Preston D Donaldson
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah L Swisher
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Ortega-de San Luis C, Ryan TJ. Understanding the physical basis of memory: Molecular mechanisms of the engram. J Biol Chem 2022; 298:101866. [PMID: 35346687 PMCID: PMC9065729 DOI: 10.1016/j.jbc.2022.101866] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/18/2022] Open
Abstract
Memory, defined as the storage and use of learned information in the brain, is necessary to modulate behavior and critical for animals to adapt to their environments and survive. Despite being a cornerstone of brain function, questions surrounding the molecular and cellular mechanisms of how information is encoded, stored, and recalled remain largely unanswered. One widely held theory is that an engram is formed by a group of neurons that are active during learning, which undergoes biochemical and physical changes to store information in a stable state, and that are later reactivated during recall of the memory. In the past decade, the development of engram labeling methodologies has proven useful to investigate the biology of memory at the molecular and cellular levels. Engram technology allows the study of individual memories associated with particular experiences and their evolution over time, with enough experimental resolution to discriminate between different memory processes: learning (encoding), consolidation (the passage from short-term to long-term memories), and storage (the maintenance of memory in the brain). Here, we review the current understanding of memory formation at a molecular and cellular level by focusing on insights provided using engram technology.
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Affiliation(s)
- Clara Ortega-de San Luis
- School of Biochemistry and Immunology and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland.
| | - Tomás J Ryan
- School of Biochemistry and Immunology and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland; Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, Victoria, Australia; Child & Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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25
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Wu SY, Shen Y, Shkolnikov I, Campbell RE. Fluorescent Indicators For Biological Imaging of Monatomic Ions. Front Cell Dev Biol 2022; 10:885440. [PMID: 35573682 PMCID: PMC9093666 DOI: 10.3389/fcell.2022.885440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Monatomic ions play critical biological roles including maintaining the cellular osmotic pressure, transmitting signals, and catalyzing redox reactions as cofactors in enzymes. The ability to visualize monatomic ion concentration, and dynamic changes in the concentration, is essential to understanding their many biological functions. A growing number of genetically encodable and synthetic indicators enable the visualization and detection of monatomic ions in biological systems. With this review, we aim to provide a survey of the current landscape of reported indicators. We hope this review will be a useful guide to researchers who are interested in using indicators for biological applications and to tool developers seeking opportunities to create new and improved indicators.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Irene Shkolnikov
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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26
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Guo J, He J, Dehesh K, Cui X, Yang Z. CamelliA-based simultaneous imaging of Ca2+ dynamics in subcellular compartments. PLANT PHYSIOLOGY 2022; 188:2253-2271. [PMID: 35218352 PMCID: PMC8968278 DOI: 10.1093/plphys/kiac020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
As a universal second messenger, calcium (Ca2+) transmits specific cellular signals via a spatiotemporal signature generated from its extracellular source and internal stores. Our knowledge of the mechanisms underlying the generation of a Ca2+ signature is hampered by limited tools for simultaneously monitoring dynamic Ca2+ levels in multiple subcellular compartments. To overcome the limitation and to further improve spatiotemporal resolutions, we have assembled a molecular toolset (CamelliA lines) in Arabidopsis (Arabidopsis thaliana) that enables simultaneous and high-resolution monitoring of Ca2+ dynamics in multiple subcellular compartments through imaging different single-colored genetically encoded calcium indicators. We uncovered several Ca2+ signatures in three types of Arabidopsis cells in response to internal and external cues, including rapid oscillations of cytosolic Ca2+ and apical plasma membrane Ca2+ influx in fast-growing Arabidopsis pollen tubes, the spatiotemporal relationship of Ca2+ dynamics in four subcellular compartments of root epidermal cells challenged with salt, and a shockwave-like Ca2+ wave propagating in laser-wounded leaf epidermis. These observations serve as a testimony to the wide applicability of the CamelliA lines for elucidating the subcellular sources contributing to the Ca2+ signatures in plants.
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Affiliation(s)
- Jingzhe Guo
- Institute for Integrative Genome Biology, University of California, Riverside, 92521 California, USA
- Department of Botany and Plant Sciences, University of California, Riverside, 92521 California, USA
| | - Jiangman He
- Institute for Integrative Genome Biology, University of California, Riverside, 92521 California, USA
- Department of Botany and Plant Sciences, University of California, Riverside, 92521 California, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology, University of California, Riverside, 92521 California, USA
- Department of Botany and Plant Sciences, University of California, Riverside, 92521 California, USA
| | - Xinping Cui
- Institute for Integrative Genome Biology, University of California, Riverside, 92521 California, USA
- Department of Statistics, University of California, Riverside, 92521 California, USA
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27
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Zhao H, Zastrow ML. Transition Metals Induce Quenching of Monomeric Near-Infrared Fluorescent Proteins. Biochemistry 2022; 61:494-504. [PMID: 35289592 DOI: 10.1021/acs.biochem.1c00705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition metals such as zinc and copper are essential in numerous life processes, and both deficiency and toxic overload of these metals are associated with various diseases. Fluorescent metal sensors are powerful tools for studying the roles of metal ions in the physiology and pathology of biological systems. Green fluorescent protein (GFP) and its derivatives are highly utilized for protein-based sensor design, but application to anaerobic systems is limited because these proteins require oxygen to become fluorescent. Bacteriophytochrome-based monomeric near-infrared fluorescent proteins (miRFPs) covalently bind a bilin cofactor, which can be added exogenously for anaerobic cells. miRFPs can also have emission wavelengths extending to >700 nm, which is valuable for imaging applications. Here, we evaluated the suitability of miRFP670 and miRFP709 as platforms for single fluorescent protein metal ion sensors. We found that divalent metal ions like Zn2+, Co2+, Ni2+, and Cu2+ can quench from ∼6-20% (Zn2+, Co2+, and Ni2+) and up to nearly 90% (Cu2+) of the fluorescence intensity of pure miRFPs and have similar impacts in live Escherichia coli cells expressing miRFPs. The presence of a 6× histidine tag for purification influences metal quenching, but significant Cu2+-induced quenching and a picomolar binding affinity are retained in the absence of the His6 tag in both cuvettes and live bacterial cells. By comparing the Cu2+ and Cu+-induced quenching results for miRFP670 and miRFP709 and through examining absorption spectra and previously reported crystal structures, we propose a surface metal binding site near the biliverdin IXα chromophore.
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Affiliation(s)
- Haowen Zhao
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Penzkofer A, Silapetere A, Hegemann P. Photocycle dynamics of the Archaerhodopsin 3 based fluorescent voltage sensor Archon2. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 225:112331. [PMID: 34688164 DOI: 10.1016/j.jphotobiol.2021.112331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022]
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor Archon2 in pH 8 Tris buffer was studied. Archon2 is a mutant of Archaerhodopsin 3 (Arch) from Halorubrum sodomense obtained by a robotic multidimensional directed evolution approach (Archon2 = Arch T56P-P60S-T80P-D95H-T99S-T116I-F161V-T183I-L197I-A225C). The samples were photo-excited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_586 (absorption maximum at λmax = 586 nm, excitation wavelengths λexc = 590 nm and 632.8 nm). The photocycle dynamics were studied by recording absorption spectra during light exposure and after light exposure. Ret_586 photoisomerized to Ret_535 (main component) and Ret_485 (minor component). Ret_535 backward photoisomerized to Ret_586 in light-adapted state (named Ret_586la) and partly deprotonated to neutral retinal Schiff base (RSB) Ret_372 in light adapted state (named Ret_372la, same isomer form as Ret_535). After excitation light switch-off Ret_372la recovered to Ret_372 in dark-adapted state (Ret_372da) which slowly re-protonated to Ret_535, and Ret_535 slowly isomerized back to Ret_586 in dark-adapted state (Ret_586da). Photocycle schemes and reaction coordinate diagrams are developed and photocycle parameters are determined.
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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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Miyata Y, Fuse H, Tokumoto S, Hiki Y, Deviatiiarov R, Yoshida Y, Yamada TG, Cornette R, Gusev O, Shagimardanova E, Funahashi A, Kikawada T. Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells. Sci Rep 2021; 11:19698. [PMID: 34611198 PMCID: PMC8492635 DOI: 10.1038/s41598-021-98905-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/16/2021] [Indexed: 01/01/2023] Open
Abstract
Pv11 is an insect cell line established from the midge Polypedilum vanderplanki, whose larval form exhibits an extreme desiccation tolerance known as anhydrobiosis. Pv11 itself is also capable of anhydrobiosis, which is induced by trehalose treatment. Here we report the successful construction of a genome editing system for Pv11 cells and its application to the identification of signaling pathways involved in anhydrobiosis. Using the Cas9-mediated gene knock-in system, we established Pv11 cells that stably expressed GCaMP3 to monitor intracellular Ca2+ mobilization. Intriguingly, trehalose treatment evoked a transient increase in cytosolic Ca2+ concentration, and further experiments revealed that the calmodulin-calcineurin-NFAT pathway contributes to tolerance of trehalose treatment as well as desiccation tolerance, while the calmodulin-calmodulin kinase-CREB pathway conferred only desiccation tolerance on Pv11 cells. Thus, our results show a critical contribution of the trehalose-induced Ca2+ surge to anhydrobiosis and demonstrate temporally different roles for each signaling pathway.
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Affiliation(s)
- Yugo Miyata
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroto Fuse
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yusuke Hiki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Ruslan Deviatiiarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Richard Cornette
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Takahiro Kikawada
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
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High rates of calcium-free diffusion in the cytosol of living cells. Biophys J 2021; 120:3960-3972. [PMID: 34454909 DOI: 10.1016/j.bpj.2021.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/07/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Calcium (Ca2+) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca2+ concentration spread in space and time is key for the versatility of the signals. Ca2+ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca2+ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca2+-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.
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Miranda C, Howell MR, Lusk JF, Marschall E, Eshima J, Anderson T, Smith BS. Automated microscope-independent fluorescence-guided micropipette. BIOMEDICAL OPTICS EXPRESS 2021; 12:4689-4699. [PMID: 34513218 PMCID: PMC8407805 DOI: 10.1364/boe.431372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Glass micropipette electrodes are commonly used to provide high resolution recordings of neurons. Although it is the gold standard for single cell recordings, it is highly dependent on the skill of the electrophysiologist. Here, we demonstrate a method of guiding micropipette electrodes to neurons by collecting fluorescence at the aperture, using an intra-electrode tapered optical fiber. The use of a tapered fiber for excitation and collection of fluorescence at the micropipette tip couples the feedback mechanism directly to the distance between the target and electrode. In this study, intra-electrode tapered optical fibers provide a targeted robotic approach to labeled neurons that is independent of microscopy.
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Affiliation(s)
- Christopher Miranda
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Madeleine R. Howell
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Joel F. Lusk
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Ethan Marschall
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Jarrett Eshima
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Trent Anderson
- University of Arizona, College of Medicine – Phoenix, Phoenix, AZ 85004, USA
| | - Barbara S. Smith
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
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Lohr C, Beiersdorfer A, Fischer T, Hirnet D, Rotermund N, Sauer J, Schulz K, Gee CE. Using Genetically Encoded Calcium Indicators to Study Astrocyte Physiology: A Field Guide. Front Cell Neurosci 2021; 15:690147. [PMID: 34177468 PMCID: PMC8226001 DOI: 10.3389/fncel.2021.690147] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/06/2021] [Indexed: 01/14/2023] Open
Abstract
Ca2+ imaging is the most frequently used technique to study glial cell physiology. While chemical Ca2+ indicators served to visualize and measure changes in glial cell cytosolic Ca2+ concentration for several decades, genetically encoded Ca2+ indicators (GECIs) have become state of the art in recent years. Great improvements have been made since the development of the first GECI and a large number of GECIs with different physical properties exist, rendering it difficult to select the optimal Ca2+ indicator. This review discusses some of the most frequently used GECIs and their suitability for glial cell research.
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Affiliation(s)
- Christian Lohr
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | | | - Timo Fischer
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | - Daniela Hirnet
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | - Natalie Rotermund
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | - Jessica Sauer
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | - Kristina Schulz
- Division of Neurophysiology, University of Hamburg, Hamburg, Germany
| | - Christine E Gee
- Institute of Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Medium-throughput zebrafish optogenetic platform identifies deficits in subsequent neural activity following brief early exposure to cannabidiol and Δ 9-tetrahydrocannabinol. Sci Rep 2021; 11:11515. [PMID: 34075141 PMCID: PMC8169761 DOI: 10.1038/s41598-021-90902-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 01/20/2023] Open
Abstract
In light of legislative changes and the widespread use of cannabis as a recreational and medicinal drug, delayed effects of cannabis upon brief exposure during embryonic development are of high interest as early pregnancies often go undetected. Here, zebrafish embryos were exposed to cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC) until the end of gastrulation (1-10 h post-fertilization) and analyzed later in development (4-5 days post-fertilization). In order to measure neural activity, we implemented Calcium-Modulated Photoactivatable Ratiometric Integrator (CaMPARI) and optimized the protocol for a 96-well format complemented by locomotor analysis. Our results revealed that neural activity was decreased by CBD more than THC. At higher doses, both cannabinoids could dramatically reduce neural activity and locomotor activity. Interestingly, the decrease was more pronounced when CBD and THC were combined. At the receptor level, CBD-mediated reduction of locomotor activity was partially prevented using cannabinoid type 1 and 2 receptor inhibitors. Overall, we report that CBD toxicity occurs via two cannabinoid receptors and is synergistically enhanced by THC exposure to negatively impact neural activity late in larval development. Future studies are warranted to reveal other cannabinoids and their receptors to understand the implications of cannabis consumption on fetal development.
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Tang L, Zhang S, Zhao Y, Rozanov ND, Zhu L, Wu J, Campbell RE, Fang C. Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca 2+ Biosensor. Int J Mol Sci 2021; 22:E445. [PMID: 33466257 PMCID: PMC7794744 DOI: 10.3390/ijms22010445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/25/2023] Open
Abstract
Ratiometric indicators with long emission wavelengths are highly preferred in modern bioimaging and life sciences. Herein, we elucidated the working mechanism of a standalone red fluorescent protein (FP)-based Ca2+ biosensor, REX-GECO1, using a series of spectroscopic and computational methods. Upon 480 nm photoexcitation, the Ca2+-free biosensor chromophore becomes trapped in an excited dark state. Binding with Ca2+ switches the route to ultrafast excited-state proton transfer through a short hydrogen bond to an adjacent Glu80 residue, which is key for the biosensor's functionality. Inspired by the 2D-fluorescence map, REX-GECO1 for Ca2+ imaging in the ionomycin-treated human HeLa cells was achieved for the first time with a red/green emission ratio change (ΔR/R0) of ~300%, outperforming many FRET- and single FP-based indicators. These spectroscopy-driven discoveries enable targeted design for the next-generation biosensors with larger dynamic range and longer emission wavelengths.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Shuce Zhang
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Yufeng Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Nikita D. Rozanov
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Jiahui Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
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35
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Potekhina ES, Bass DY, Kelmanson IV, Fetisova ES, Ivanenko AV, Belousov VV, Bilan DS. Drug Screening with Genetically Encoded Fluorescent Sensors: Today and Tomorrow. Int J Mol Sci 2020; 22:E148. [PMID: 33375682 PMCID: PMC7794770 DOI: 10.3390/ijms22010148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Genetically-encoded fluorescent sensors have been actively developed over the last few decades and used in live imaging and drug screening. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically-encoded fluorescent sensors in drug screening. In combination with high-throughput screening (HTS), some genetically-encoded fluorescent sensors may provide high reproducibility and robustness to assays. We provide a brief overview of successful, perspective, and hopeful attempts at using genetically encoded fluorescent sensors in HTS of modulators of ion channels, Ca2+ homeostasis, GPCR activity, and for screening cytotoxic, anticancer, and anti-parasitic compounds. We discuss the advantages of sensors in whole organism drug screening models and the perspectives of the combination of human disease modeling by CRISPR techniques with genetically encoded fluorescent sensors for drug screening.
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Affiliation(s)
- Ekaterina S. Potekhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dina Y. Bass
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ilya V. Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena S. Fetisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
| | - Alexander V. Ivanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, 117997 Moscow, Russia
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.Y.B.); (I.V.K.); (E.S.F.); (A.V.I.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Nguyen LP, Nguyen HT, Yong HJ, Reyes-Alcaraz A, Lee YN, Park HK, Na YH, Lee CS, Ham BJ, Seong JY, Hwang JI. Establishment of a NanoBiT-Based Cytosolic Ca 2+ Sensor by Optimizing Calmodulin-Binding Motif and Protein Expression Levels. Mol Cells 2020; 43:909-920. [PMID: 33162399 PMCID: PMC7700839 DOI: 10.14348/molcells.2020.0144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Cytosolic Ca2+ levels ([Ca2+]c) change dynamically in response to inducers, repressors, and physiological conditions, and aberrant [Ca2+]c concentration regulation is associated with cancer, heart failure, and diabetes. Therefore, [Ca2+]c is considered as a good indicator of physiological and pathological cellular responses, and is a crucial biomarker for drug discovery. A genetically encoded calcium indicator (GECI) was recently developed to measure [Ca2+]c in single cells and animal models. GECI have some advantages over chemically synthesized indicators, although they also have some drawbacks such as poor signal-to-noise ratio (SNR), low positive signal, delayed response, artifactual responses due to protein overexpression, and expensive detection equipment. Here, we developed an indicator based on interactions between Ca2+-loaded calmodulin and target proteins, and generated an innovative GECI sensor using split nano-luciferase (Nluc) fragments to detect changes in [Ca2+]c. Stimulation-dependent luciferase activities were optimized by combining large and small subunits of Nluc binary technology (NanoBiT, LgBiT:SmBiT) fusion proteins and regulating the receptor expression levels. We constructed the binary [Ca2+]c sensors using a multicistronic expression system in a single vector linked via the internal ribosome entry site (IRES), and examined the detection efficiencies. Promoter optimization studies indicated that promoter-dependent protein expression levels were crucial to optimize SNR and sensitivity. This novel [Ca2+]c assay has high SNR and sensitivity, is easy to use, suitable for high-throughput assays, and may be useful to detect [Ca2+]c in single cells and animal models.
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Affiliation(s)
- Lan Phuong Nguyen
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Huong Thi Nguyen
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hyo Jeong Yong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | | | - Yoo-Na Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hee-Kyung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Yun Hee Na
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Cheol Soon Lee
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University College of Medicine, Seoul 02841, Korea
| | - Jae Young Seong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Jong-Ik Hwang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
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Krasitskaya VV, Bashmakova EE, Frank LA. Coelenterazine-Dependent Luciferases as a Powerful Analytical Tool for Research and Biomedical Applications. Int J Mol Sci 2020; 21:E7465. [PMID: 33050422 PMCID: PMC7590018 DOI: 10.3390/ijms21207465] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
: The functioning of bioluminescent systems in most of the known marine organisms is based on the oxidation reaction of the same substrate-coelenterazine (CTZ), catalyzed by luciferase. Despite the diversity in structures and the functioning mechanisms, these enzymes can be united into a common group called CTZ-dependent luciferases. Among these, there are two sharply different types of the system organization-Ca2+-regulated photoproteins and luciferases themselves that function in accordance with the classical enzyme-substrate kinetics. Along with deep and comprehensive fundamental research on these systems, approaches and methods of their practical use as highly sensitive reporters in analytics have been developed. The research aiming at the creation of artificial luciferases and synthetic CTZ analogues with new unique properties has led to the development of new experimental analytical methods based on them. The commercial availability of many ready-to-use assay systems based on CTZ-dependent luciferases is also important when choosing them by first-time-users. The development of analytical methods based on these bioluminescent systems is currently booming. The bioluminescent systems under consideration were successfully applied in various biological research areas, which confirms them to be a powerful analytical tool. In this review, we consider the main directions, results, and achievements in research involving these luciferases.
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Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Eugenia E. Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
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Patient-Derived Induced Pluripotent Stem Cell-Based Models in Parkinson's Disease for Drug Identification. Int J Mol Sci 2020; 21:ijms21197113. [PMID: 32993172 PMCID: PMC7582359 DOI: 10.3390/ijms21197113] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a common progressive neurodegenerative disorder characterized by loss of striatal-projecting dopaminergic neurons of the ventral forebrain, resulting in motor and cognitive deficits. Despite extensive efforts in understanding PD pathogenesis, no disease-modifying drugs exist. Recent advances in cell reprogramming technologies have facilitated the generation of patient-derived models for sporadic or familial PD and the identification of early, potentially triggering, pathological phenotypes while they provide amenable systems for drug discovery. Emerging developments highlight the enhanced potential of using more sophisticated cellular systems, including neuronal and glial co-cultures as well as three-dimensional systems that better simulate the human pathophysiology. In combination with high-throughput high-content screening technologies, these approaches open new perspectives for the identification of disease-modifying compounds. In this review, we discuss current advances and the challenges ahead in the use of patient-derived induced pluripotent stem cells for drug discovery in PD. We address new concepts implicating non-neuronal cells in disease pathogenesis and highlight the necessity for functional assays, such as calcium imaging and multi-electrode array recordings, to predict drug efficacy. Finally, we argue that artificial intelligence technologies will be pivotal for analysis of the large and complex data sets obtained, becoming game-changers in the process of drug discovery.
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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 Archon2. Int J Mol Sci 2020; 21:ijms21186576. [PMID: 32911811 PMCID: PMC7555599 DOI: 10.3390/ijms21186576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023] Open
Abstract
Archon2 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense using robotic multidimensional directed evolution approach. Here we report absorption and emission spectroscopic studies of Archon2 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 Archon2 was studied by long-time attenuation coefficient measurements at room temperature (21 ± 1 °C) and at refrigerator temperature (3 ± 1 °C). The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 63 ± 3 °C). In the protein melting process protonated retinal Schiff base (PRSB) with absorption maximum at 586 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Storage of Archon2 at room temperature and refrigerator temperature caused absorption coefficient decrease because of partial protein clustering to aggregates at condensation nuclei and sedimentation. At room temperature an onset of light scattering was observed after two days because of the beginning of protein unfolding. During the period of observation (18 days at 21 °C, 22 days at 3 °C) no change of retinal isomer composition was observed indicating a high potential energy barrier of S0 ground-state isomerization.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
- Correspondence: ; Tel.: +49-941-943-2107
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
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40
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Williams PDE, Verma S, Robertson AP, Martin RJ. Adapting techniques for calcium imaging in muscles of adult Brugia malayi. INVERTEBRATE NEUROSCIENCE 2020; 20:12. [PMID: 32803437 DOI: 10.1007/s10158-020-00247-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Brugia malayi is a human filarial nematode parasite that causes lymphatic filariasis or 'elephantiasis' a disfiguring neglected tropical disease. This parasite is a more tractable nematode parasite for the experimental study of anthelmintic drugs and has been studied with patch-clamp and RNAi techniques. Unlike in C. elegans however, calcium signaling in B. malayi or other nematode parasites has not been achieved, limiting the studies of the mode of action of anthelmintic drugs. We describe here the development of calcium imaging methods that allow us to characterize changes in cellular calcium in the muscles of B. malayi. This is a powerful technique that can help in elucidating the mode of action of selected anthelmintics. We developed two approaches that allow the recording of calcium signals in the muscles of adult B. malayi: (a) soaking the muscles with Fluo-3AM, promoting large-scale imaging of multiple cells simultaneously and, (b) direct insertion of Fluo-3 using microinjection, providing the possibility of performing dual calcium and electrophysiological recordings. Here, we describe the techniques used to optimize dye entry into the muscle cells and demonstrate that detectable increases in Fluo-3 fluorescence to elevated calcium concentrations can be achieved in B. malayi using both techniques.
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Affiliation(s)
- Paul D E Williams
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50011, USA
| | - Saurabh Verma
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50011, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50011, USA
| | - Richard J Martin
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Dr, Ames, IA, 50011, USA.
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41
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Zarowny L, Aggarwal A, Rutten VMS, Kolb I, Patel R, Huang HY, Chang YF, Phan T, Kanyo R, Ahrens MB, Allison WT, Podgorski K, Campbell RE. Bright and High-Performance Genetically Encoded Ca 2+ Indicator Based on mNeonGreen Fluorescent Protein. ACS Sens 2020; 5:1959-1968. [PMID: 32571014 DOI: 10.1021/acssensors.0c00279] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetically encodable calcium ion (Ca2+) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost 2 decades of steady improvements in the Aequorea victoria GFP-based GCaMP series of GECIs, the performance of the most recent generation (i.e., jGCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression toward ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60% brighter than GCaMP6s in vitro and provides comparable performance as demonstrated by imaging Ca2+ dynamics in cultured cells, primary neurons, and in vivo in larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.
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Affiliation(s)
- Landon Zarowny
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Abhi Aggarwal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - Virginia M. S. Rutten
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
- Gatsby Computational Neuroscience Unit, UCL, London WC1E 6BT, U.K
| | - Ilya Kolb
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - Ronak Patel
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - Hsin-Yi Huang
- LumiSTAR Biotechnology, Inc., National Biotechnology Research Park, Taipei City 115, Taiwan
| | - Yu-Fen Chang
- LumiSTAR Biotechnology, Inc., National Biotechnology Research Park, Taipei City 115, Taiwan
| | - Tiffany Phan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Richard Kanyo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Misha B. Ahrens
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - W. Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Kaspar Podgorski
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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42
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Okkelman IA, McGarrigle R, O’Carroll S, Berrio DC, Schenke-Layland K, Hynes J, Dmitriev RI. Extracellular Ca2+-Sensing Fluorescent Protein Biosensor Based on a Collagen-Binding Domain. ACS APPLIED BIO MATERIALS 2020; 3:5310-5321. [DOI: 10.1021/acsabm.0c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Irina A. Okkelman
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Ryan McGarrigle
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Shane O’Carroll
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Daniel Carvajal Berrio
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
| | - Katja Schenke-Layland
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen 72770, Germany
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles 90095, California, United States
| | - James Hynes
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Ruslan I. Dmitriev
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
- I.M. Sechenov First Moscow State University, Institute for Regenerative Medicine, Moscow 119992, Russian Federation
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
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43
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Harding EK, Fung SW, Bonin RP. Insights Into Spinal Dorsal Horn Circuit Function and Dysfunction Using Optical Approaches. Front Neural Circuits 2020; 14:31. [PMID: 32595458 PMCID: PMC7303281 DOI: 10.3389/fncir.2020.00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022] Open
Abstract
Somatosensation encompasses a variety of essential modalities including touch, pressure, proprioception, temperature, pain, and itch. These peripheral sensations are crucial for all types of behaviors, ranging from social interaction to danger avoidance. Somatosensory information is transmitted from primary afferent fibers in the periphery into the central nervous system via the dorsal horn of the spinal cord. The dorsal horn functions as an intermediary processing center for this information, comprising a complex network of excitatory and inhibitory interneurons as well as projection neurons that transmit the processed somatosensory information from the spinal cord to the brain. It is now known that there can be dysfunction within this spinal cord circuitry in pathological pain conditions and that these perturbations contribute to the development and maintenance of pathological pain. However, the complex and heterogeneous network of the spinal dorsal horn has hampered efforts to further elucidate its role in somatosensory processing. Emerging optical techniques promise to illuminate the underlying organization and function of the dorsal horn and provide insights into the role of spinal cord sensory processing in shaping the behavioral response to somatosensory input that we ultimately observe. This review article will focus on recent advances in optogenetics and fluorescence imaging techniques in the spinal cord, encompassing findings from both in vivo and in vitro preparations. We will also discuss the current limitations and difficulties of employing these techniques to interrogate the spinal cord and current practices and approaches to overcome these challenges.
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Affiliation(s)
- Erika K Harding
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Wanchi Fung
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Robert P Bonin
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,University of Toronto Centre for the Study of Pain, University of Toronto, Toronto, ON, Canada
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44
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Sensing Senses: Optical Biosensors to Study Gustation. SENSORS 2020; 20:s20071811. [PMID: 32218129 PMCID: PMC7180777 DOI: 10.3390/s20071811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/11/2022]
Abstract
The five basic taste modalities, sweet, bitter, umami, salty and sour induce changes of Ca2+ levels, pH and/or membrane potential in taste cells of the tongue and/or in neurons that convey and decode gustatory signals to the brain. Optical biosensors, which can be either synthetic dyes or genetically encoded proteins whose fluorescence spectra depend on levels of Ca2+, pH or membrane potential, have been used in primary cells/tissues or in recombinant systems to study taste-related intra- and intercellular signaling mechanisms or to discover new ligands. Taste-evoked responses were measured by microscopy achieving high spatial and temporal resolution, while plate readers were employed for higher throughput screening. Here, these approaches making use of fluorescent optical biosensors to investigate specific taste-related questions or to screen new agonists/antagonists for the different taste modalities were reviewed systematically. Furthermore, in the context of recent developments in genetically encoded sensors, 3D cultures and imaging technologies, we propose new feasible approaches for studying taste physiology and for compound screening.
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45
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O'Banion CP, Yasuda R. Fluorescent sensors for neuronal signaling. Curr Opin Neurobiol 2020; 63:31-41. [PMID: 32203701 DOI: 10.1016/j.conb.2020.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/30/2020] [Accepted: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Dissecting neuronal structure and function in relation to behavior is an immense undertaking. Researchers require imaging tools to study neuronal activity and biochemical signaling in situ in order to study the roles of neuronal and biochemical activity in information processing. A large number of genetically encoded fluorescent biosensors have been reported in the literature over the past few years as there is a push to develop new technology in neuroscience. Here, we review the classes and characteristics of fluorescent biosensors and highlight some considerations that investigators should keep in mind when choosing their tool. In addition, we discuss recent advances in biosensor development.
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Affiliation(s)
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, United States.
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46
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Choi JE, Kim J, Kim J. Capturing activated neurons and synapses. Neurosci Res 2020; 152:25-34. [DOI: 10.1016/j.neures.2019.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/12/2022]
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47
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Zou W, Le K, Zastrow ML. Live‐Cell Copper‐Induced Fluorescence Quenching of the Flavin‐Binding Fluorescent Protein CreiLOV. Chembiochem 2020; 21:1356-1363. [DOI: 10.1002/cbic.201900669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Wenping Zou
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Khoa Le
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
| | - Melissa L. Zastrow
- Department of ChemistryUniversity of Houston 3585 Cullen Boulevard Houston TX 77204 USA
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48
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Penzkofer A, Silapetere A, Hegemann P. Photocycle Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 21:ijms21010160. [PMID: 31881701 PMCID: PMC6982170 DOI: 10.3390/ijms21010160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor QuasAr1 (Archaerhodopsin 3 P60S-T80S-D95H-D106H-F161V mutant from Halorubrum sodomense) in pH 8 Tris buffer was studied. The samples were photoexcited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_580 (absorption maximum at λmax ≈ 580 nm), and the retinal Schiff base photoisomerization and protonation state changes were followed by absorption spectra recordings during light exposure and after light exposure. Ret_580 turned out to be composed of two protonated retinal Schiff base isomers, namely Ret_580I and Ret_580II. Photoexcitation of Ret_580I resulted in barrier-involved isomerization to Ret_540 (quantum yield ≈ 0.056) and subsequent retinal proton release leading to Ret_410 deprotonated retinal Schiff base (RSB). In the dark, Ret_410 partially recovered to Ret_580I and partially stabilized to irreversible Ret_400 due to apoprotein restructuring (Ret_410 lifetime ≈ 2 h). Photoexcitation of Ret_580II resulted in barrier-involved isomerization to Ret_640 (quantum yield ≈ 0.00135) and subsequent deprotonation to Ret_370 (RSB). In the dark, Ret_370 partially recovered to Ret_580II and partially stabilized to irreversible Ret_350 due to apoprotein restructuring (Ret_370 lifetime ≈ 10 h). Photocycle schemes and reaction coordinate diagrams for Ret_580I and Ret_580II were developed and photocyle parameters were determined.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
- Correspondence: ; Tel.: +49-941-943-2107
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
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49
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Surana S, Villarroel‐Campos D, Lazo OM, Moretto E, Tosolini AP, Rhymes ER, Richter S, Sleigh JN, Schiavo G. The evolution of the axonal transport toolkit. Traffic 2019; 21:13-33. [DOI: 10.1111/tra.12710] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sunaina Surana
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
| | - David Villarroel‐Campos
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
| | - Oscar M. Lazo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
- UK Dementia Research InstituteUniversity College London London UK
| | - Edoardo Moretto
- UK Dementia Research InstituteUniversity College London London UK
| | - Andrew P. Tosolini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
| | - Elena R. Rhymes
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
| | - Sandy Richter
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
| | - James N. Sleigh
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
- UK Dementia Research InstituteUniversity College London London UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of NeurologyUniversity College London London UK
- UK Dementia Research InstituteUniversity College London London UK
- Discoveries Centre for Regenerative and Precision MedicineUniversity College London London UK
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50
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Roelse M, Wehrens R, Henquet MG, Witkamp RF, Hall RD, Jongsma MA. The Effect of Calcium Buffering and Calcium Sensor Type on the Sensitivity of an Array-Based Bitter Receptor Screening Assay. Chem Senses 2019; 44:497-505. [PMID: 31278864 PMCID: PMC7357244 DOI: 10.1093/chemse/bjz044] [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] [Indexed: 11/14/2022] Open
Abstract
The genetically encoded calcium sensor protein Cameleon YC3.6 has previously been applied for functional G protein-coupled receptor screening using receptor cell arrays. However, different types of sensors are available, with a wide range in [Ca2+] sensitivity, Hill coefficients, calcium binding domains, and fluorophores, which could potentially improve the performance of the assay. Here, we compared the responses of 3 structurally different calcium sensor proteins (Cameleon YC3.6, Nano140, and Twitch2B) simultaneously, on a single chip, at different cytosolic expression levels and in combination with 2 different bitter receptors, TAS2R8 and TAS2R14. Sensor concentrations were modified by varying the amount of calcium sensor DNA that was printed on the DNA arrays prior to reverse transfection. We found that ~2-fold lower concentrations of calcium sensor protein, by transfecting 4 times less sensor-coding DNA, resulted in more sensitive bitter responses. The best results were obtained with Twitch2B, where, relative to YC3.6 at the default DNA concentration, a 4-fold lower DNA concentration increased sensitivity 60-fold and signal strength 5- to 10-fold. Next, we compared the performance of YC3.6 and Twitch2B against an array with 11 different bitter taste receptors. We observed a 2- to 8-fold increase in sensitivity using Twitch2B compared with YC3.6. The bitter receptor arrays contained 300 spots and could be exposed to a series of 18 injections within 1 h resulting in 5400 measurements. These optimized sensor conditions provide a basis for enhancing receptomics calcium assays for receptors with poor Ca2+ signaling and will benefit future high-throughput receptomics experiments.
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Affiliation(s)
- Margriet Roelse
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen, The Netherlands.,Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen.,Nutritional Biology and Health, Wageningen University and Research, Stippeneng, WE Wageningen, The Netherlandsand
| | - Ron Wehrens
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen, The Netherlands.,BU Biometris, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen
| | - Maurice Gl Henquet
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Renger F Witkamp
- Nutritional Biology and Health, Wageningen University and Research, Stippeneng, WE Wageningen, The Netherlandsand
| | - Robert D Hall
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen, The Netherlands.,Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen
| | - Maarten A Jongsma
- BU Bioscience, Wageningen University and Research, Droevendaalsesteeg, PB Wageningen, The Netherlands
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