101
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Badura A, Sun XR, Giovannucci A, Lynch LA, Wang SSH. Fast calcium sensor proteins for monitoring neural activity. NEUROPHOTONICS 2014; 1:025008. [PMID: 25558464 PMCID: PMC4280659 DOI: 10.1117/1.nph.1.2.025008] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/12/2014] [Accepted: 09/23/2014] [Indexed: 05/18/2023]
Abstract
A major goal of the BRAIN Initiative is the development of technologies to monitor neuronal network activity during active information processing. Toward this goal, genetically encoded calcium indicator proteins have become widely used for reporting activity in preparations ranging from invertebrates to awake mammals. However, slow response times, the narrow sensitivity range of Ca2+ and in some cases, poor signal-to-noise ratio still limit their usefulness. Here, we review recent improvements in the field of neural activity-sensitive probe design with a focus on the GCaMP family of calcium indicator proteins. In this context, we present our newly developed Fast-GCaMPs, which have up to 4-fold accelerated off-responses compared with the next-fastest GCaMP, GCaMP6f. Fast-GCaMPs were designed by destabilizing the association of the hydrophobic pocket of calcium-bound calmodulin with the RS20 binding domain, an intramolecular interaction that protects the green fluorescent protein chromophore. Fast-GCaMP6f-RS06 and Fast-GCaMP6f-RS09 have rapid off-responses in stopped-flow fluorimetry, in neocortical brain slices, and in the intact cerebellum in vivo. Fast-GCaMP6f variants should be useful for tracking action potentials closely spaced in time, and for following neural activity in fast-changing compartments, such as axons and dendrites. Finally, we discuss strategies that may allow tracking of a wider range of neuronal firing rates and improve spike detection.
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Affiliation(s)
- Aleksandra Badura
- Princeton University, Princeton Neuroscience Institute and Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Xiaonan Richard Sun
- Princeton University, Princeton Neuroscience Institute and Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Andrea Giovannucci
- Princeton University, Princeton Neuroscience Institute and Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Laura A. Lynch
- Princeton University, Princeton Neuroscience Institute and Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Samuel S.-H. Wang
- Princeton University, Princeton Neuroscience Institute and Department of Molecular Biology, Princeton, New Jersey 08544, United States
- Address all correspondence to: Sam Wang, E-mail:
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102
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Li H, Wang X, Zhang N, Gottipati MK, Parpura V, Ding S. Imaging of mitochondrial Ca2+ dynamics in astrocytes using cell-specific mitochondria-targeted GCaMP5G/6s: mitochondrial Ca2+ uptake and cytosolic Ca2+ availability via the endoplasmic reticulum store. Cell Calcium 2014; 56:457-66. [PMID: 25443655 DOI: 10.1016/j.ceca.2014.09.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 11/20/2022]
Abstract
Mitochondrial Ca(2+) plays a critical physiological role in cellular energy metabolism and signaling, and its overload contributes to various pathological conditions including neuronal apoptotic death in neurological diseases. Live cell mitochondrial Ca(2+) imaging is an important approach to understand mitochondrial Ca(2+) dynamics. Recently developed GCaMP genetically-encoded Ca(2+) indicators provide unique opportunity for high sensitivity/resolution and cell type-specific mitochondrial Ca(2+) imaging. In the current study, we implemented cell-specific mitochondrial targeting of GCaMP5G/6s (mito-GCaMP5G/6s) and used two-photon microscopy to image astrocytic and neuronal mitochondrial Ca(2+) dynamics in culture, revealing Ca(2+) uptake mechanism by these organelles in response to cell stimulation. Using these mitochondrial Ca(2+) indicators, our results show that mitochondrial Ca(2+) uptake in individual mitochondria in cultured astrocytes and neurons can be seen after stimulations by ATP and glutamate, respectively. We further studied the dependence of mitochondrial Ca(2+) dynamics on cytosolic Ca(2+) changes following ATP stimulation in cultured astrocytes by simultaneously imaging mitochondrial and cytosolic Ca(2+) increase using mito-GCaMP5G and a synthetic organic Ca(2+) indicator, x-Rhod-1, respectively. Combined with molecular intervention in Ca(2+) signaling pathway, our results demonstrated that the mitochondrial Ca(2+) uptake is tightly coupled with inositol 1,4,5-trisphosphate receptor-mediated Ca(2+) release from the endoplasmic reticulum and the activation of G protein-coupled receptors. The current study provides a novel approach to image mitochondrial Ca(2+) dynamics as well as Ca(2+) interplay between the endoplasmic reticulum and mitochondria, which is relevant for neuronal and astrocytic functions in health and disease.
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Affiliation(s)
- Hailong Li
- Dalton Cardiovascular Research Center, Columbia, MO 65211, United States; Department of Bioengineering, University of Missouri, Columbia, MO 65211, United States
| | - Xiaowan Wang
- Department of Bioengineering, University of Missouri, Columbia, MO 65211, United States
| | - Nannan Zhang
- Dalton Cardiovascular Research Center, Columbia, MO 65211, United States
| | - Manoj K Gottipati
- Department of Neurobiology, University of Alabama, Birmingham, AL 35294, United States
| | - Vladimir Parpura
- Department of Neurobiology, University of Alabama, Birmingham, AL 35294, United States; Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Shinghua Ding
- Dalton Cardiovascular Research Center, Columbia, MO 65211, United States; Department of Bioengineering, University of Missouri, Columbia, MO 65211, United States.
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103
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Yao J, Li H, Xu YN, Wang QC, Qu DH. Efficient Intramolecular Energy Transfer between Two Fluorophores in a Bis-Branched [3]Rotaxane. Chem Asian J 2014; 9:3482-90. [DOI: 10.1002/asia.201402789] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 07/21/2014] [Indexed: 11/11/2022]
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104
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Jahn K, Hille C. Asante Calcium Green and Asante Calcium Red--novel calcium indicators for two-photon fluorescence lifetime imaging. PLoS One 2014; 9:e105334. [PMID: 25140519 PMCID: PMC4139374 DOI: 10.1371/journal.pone.0105334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/21/2014] [Indexed: 11/18/2022] Open
Abstract
For a comprehensive understanding of cellular processes and potential dysfunctions therein, an analysis of the ubiquitous intracellular second messenger calcium is of particular interest. This study examined the suitability of the novel Ca2+-sensitive fluorescent dyes Asante Calcium Red (ACR) and Asante Calcium Green (ACG) for two-photon (2P)-excited time-resolved fluorescence measurements. Both dyes displayed sufficient 2P fluorescence excitation in a range of 720–900 nm. In vitro, ACR and ACG exhibited a biexponential fluorescence decay behavior and the two decay time components in the ns-range could be attributed to the Ca2+-free and Ca2+-bound dye species. The amplitude-weighted average fluorescence decay time changed in a Ca2+-dependent way, unraveling in vitro dissociation constants KD of 114 nM and 15 nM for ACR and ACG, respectively. In the presence of bovine serum albumin, the absorption and steady-state fluorescence behavior of ACR was altered and its biexponential fluorescence decay showed about 5-times longer decay time components indicating dye-protein interactions. Since no ester derivative of ACG was commercially available, only ACR was evaluated for 2P-excited fluorescence lifetime imaging microscopy (2P-FLIM) in living cells of American cockroach salivary glands. In living cells, ACR also exhibited a biexponential fluorescence decay with clearly resolvable short (0.56 ns) and long (2.44 ns) decay time components attributable to the Ca2+-free and Ca2+-bound ACR species. From the amplitude-weighted average fluorescence decay times, an in situ KD of 180 nM was determined. Thus, quantitative [Ca2+]i recordings were realized, unraveling a reversible dopamine-induced [Ca2+]i elevation from 21 nM to 590 nM in salivary duct cells. It was concluded that ACR is a promising new Ca2+ indicator dye for 2P-FLIM recordings applicable in diverse biological systems.
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Affiliation(s)
- Karolina Jahn
- Department of Physical Chemistry/ALS ComBi, University of Potsdam, Potsdam, Germany
| | - Carsten Hille
- Department of Physical Chemistry/ALS ComBi, University of Potsdam, Potsdam, Germany
- * E-mail:
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105
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Cai B, Chen X, Liu F, Li J, Gu L, Liu JR, Liu J. A cell-based functional assay using a green fluorescent protein-based calcium indicator dCys-GCaMP. Assay Drug Dev Technol 2014; 12:342-51. [PMID: 25105973 DOI: 10.1089/adt.2014.584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Measurement of the changes in intracellular Ca2+ levels is an important assay for drug discovery. In this report, we describe a novel Ca2+ indicator, dCys-GCaMP, based on the green fluorescent protein and the development of a rapid and simple cell-based functional assay using this new Ca2+ indicator. We demonstrated the sensitivity and reliability of the assay by measuring the cellular responses to the agonists, antagonists, channel blockers, and modulators of the ionotropic N-methyl-D-aspartate (NMDA) subtype of glutamate receptors. HEK293 cells coexpressing the NMDA receptor and dCys-GCaMP displayed a strong increase in fluorescence intensity when stimulated with the agonist glutamate. This increase in the fluorescence signal was agonist concentration dependent and could be blocked by NMDAR antagonists and channel blockers. The pharmacological parameters measured with the dCys-GCaMP assay are in close agreement with those derived from conventional assays with synthetic dye fluo-4 and literature values. In addition, we showed that this assay could be used on G protein-coupled receptors as well, as exemplified by studies on the α1A adrenergic receptor. A limited scale evaluation of the assay performance in a 96-well compound screening format suggests that the dCys-GCaMP assay could be easily adapted to a high-throughput screening environment. The most important advantage of this new assay over the conventional fluo-4 and aequorin assays is the elimination of the dye-loading or substrate-loading process.
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Affiliation(s)
- Bin Cai
- 1 Rugen Therapeutics Ltd. , Suzhou Industrial Park, China
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106
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Lindenburg L, Merkx M. Engineering genetically encoded FRET sensors. SENSORS 2014; 14:11691-713. [PMID: 24991940 PMCID: PMC4168480 DOI: 10.3390/s140711691] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/24/2014] [Accepted: 06/26/2014] [Indexed: 01/15/2023]
Abstract
Förster Resonance Energy Transfer (FRET) between two fluorescent proteins can be exploited to create fully genetically encoded and thus subcellularly targetable sensors. FRET sensors report changes in energy transfer between a donor and an acceptor fluorescent protein that occur when an attached sensor domain undergoes a change in conformation in response to ligand binding. The design of sensitive FRET sensors remains challenging as there are few generally applicable design rules and each sensor must be optimized anew. In this review we discuss various strategies that address this shortcoming, including rational design approaches that exploit self-associating fluorescent domains and the directed evolution of FRET sensors using high-throughput screening.
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Affiliation(s)
- Laurens Lindenburg
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600MB, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600MB, The Netherlands.
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107
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Kanemaru K, Sekiya H, Xu M, Satoh K, Kitajima N, Yoshida K, Okubo Y, Sasaki T, Moritoh S, Hasuwa H, Mimura M, Horikawa K, Matsui K, Nagai T, Iino M, Tanaka KF. In vivo visualization of subtle, transient, and local activity of astrocytes using an ultrasensitive Ca(2+) indicator. Cell Rep 2014; 8:311-8. [PMID: 24981861 DOI: 10.1016/j.celrep.2014.05.056] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/16/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022] Open
Abstract
Astrocytes generate local calcium (Ca(2+)) signals that are thought to regulate their functions. Visualization of these signals in the intact brain requires an imaging method with high spatiotemporal resolution. Here, we describe such a method using transgenic mice expressing the ultrasensitive ratiometric Ca(2+) indicator yellow Cameleon-Nano 50 (YC-Nano50) in astrocytes. In these mice, we detected a unique pattern of Ca(2+) signals. These occur spontaneously, predominantly in astrocytic fine processes, but not the cell body. Upon sensory stimulation, astrocytes initially responded with Ca(2+) signals at fine processes, which then propagated to the cell body. These observations suggest that astrocytic fine processes function as a high-sensitivity detector of neuronal activities. Thus, the method provides a useful tool for studying the activity of astrocytes in brain physiology and pathology.
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Affiliation(s)
- Kazunori Kanemaru
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroshi Sekiya
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Ming Xu
- Department of Neuropsychiatry, School of Medicine, Keio University, Shinjuku, Tokyo 160-8582, Japan
| | - Kaname Satoh
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Nami Kitajima
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Keitaro Yoshida
- Department of Neuropsychiatry, School of Medicine, Keio University, Shinjuku, Tokyo 160-8582, Japan
| | - Yohei Okubo
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Takuya Sasaki
- Neurobiology Section and Center for Neural Circuits and Behavior, Division of Biological Sciences, University of California, San Diego, San Diego, CA, 92093-0357, USA
| | - Satoru Moritoh
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Hidetoshi Hasuwa
- Genome Information Research Center, Osaka University, Suita 565-0871, Japan
| | - Masaru Mimura
- Department of Neuropsychiatry, School of Medicine, Keio University, Shinjuku, Tokyo 160-8582, Japan
| | - Kazuki Horikawa
- Support Center for Advanced Medical Sciences, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Ko Matsui
- Division of Interdisciplinary Medical Science, Center for Neuroscience, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
| | - Masamitsu Iino
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
| | - Kenji F Tanaka
- Department of Neuropsychiatry, School of Medicine, Keio University, Shinjuku, Tokyo 160-8582, Japan.
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108
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Kaestner L, Scholz A, Tian Q, Ruppenthal S, Tabellion W, Wiesen K, Katus HA, Müller OJ, Kotlikoff MI, Lipp P. Genetically encoded Ca2+ indicators in cardiac myocytes. Circ Res 2014; 114:1623-39. [PMID: 24812351 DOI: 10.1161/circresaha.114.303475] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetically encoded Ca(2+) indicators constitute a powerful set of tools to investigate functional aspects of Ca(2+) signaling in isolated cardiomyocytes, cardiac tissue, and whole hearts. Here, we provide an overview of the concepts, experiences, state of the art, and ongoing developments in the use of genetically encoded Ca(2+) indicators for cardiac cells and heart tissue. This review is supplemented with in vivo viral gene transfer experiments and comparisons of available genetically encoded Ca(2+) indicators with each other and with the small molecule dye Fura-2. In the context of cardiac myocytes, we provide guidelines for selecting a genetically encoded Ca(2+) indicator. For future developments, we discuss improvements of a broad range of properties, including photophysical properties such as spectral spread and biocompatibility, as well as cellular and in vivo applications.
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Affiliation(s)
- Lars Kaestner
- From the Institute for Molecular Cell Biology and Research Center for Molecular Imaging and Screening, School of Medicine, Saarland University, Homburg-Saar, Germany (L.K., A.S., Q.T., S.R., W.T., K.W., P.L.); Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany (H.A.K., O.J.M.); DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (H.A.K., O.J.M.); and Biomedical Sciences Department, College of Veterinary Medicine, Cornell University, Ithaca, NY (M.I.K.)
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109
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Zhong S, Navaratnam D, Santos-Sacchi J. A genetically-encoded YFP sensor with enhanced chloride sensitivity, photostability and reduced ph interference demonstrates augmented transmembrane chloride movement by gerbil prestin (SLC26a5). PLoS One 2014; 9:e99095. [PMID: 24901231 PMCID: PMC4047046 DOI: 10.1371/journal.pone.0099095] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/12/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Chloride is the major anion in cells, with many diseases arising from disordered Cl- regulation. For the non-invasive investigation of Cl- flux, YFP-H148Q and its derivatives chameleon and Cl-Sensor previously were introduced as genetically encoded chloride indicators. Neither the Cl- sensitivity nor the pH-susceptibility of these modifications to YFP is optimal for precise measurements of Cl- under physiological conditions. Furthermore, the relatively poor photostability of YFP derivatives hinders their application for dynamic and quantitative Cl- measurements. Dynamic and accurate measurement of physiological concentrations of chloride would significantly affect our ability to study effects of chloride on cellular events. METHODOLOGY/PRINCIPAL FINDINGS In this study, we developed a series of YFP derivatives to remove pH interference, increase photostability and enhance chloride sensitivity. The final product, EYFP-F46L/Q69K/H148Q/I152L/V163S/S175G/S205V/A206K (monomeric Cl-YFP), has a chloride Kd of 14 mM and pKa of 5.9. The bleach time constant of 175 seconds is over 15-fold greater than wild-type EYFP. We have used the sensor fused to the transmembrane protein prestin (gerbil prestin, SLC26a5), and shown for the first time physiological (mM) chloride flux in HEK cells expressing this protein. This modified fluorescent protein will facilitate investigations of dynamics of chloride ions and their mediation of cell function. CONCLUSIONS Modifications to YFP (EYFP-F46L/Q69K/H148Q/I152L/V163S/S175G/S205V/A206K (monomeric Cl-YFP) results in a photostable fluorescent protein that allows measurement of physiological changes in chloride concentration while remaining minimally affected by changes in pH.
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Affiliation(s)
- Sheng Zhong
- Dept. of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Dhasakumar Navaratnam
- Dept. of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, Connecticut, United States of America
- Dept. of Neurobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Dept. of Neurology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Joseph Santos-Sacchi
- Dept. of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, Connecticut, United States of America
- Dept. of Neurology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Dept. of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
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110
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Santos AF, Hübener M. Chronic calcium imaging of neurons in the mouse visual cortex using a troponin C-based indicator. Cold Spring Harb Protoc 2014; 2014:2014/5/pdb.prot081737. [PMID: 24786511 DOI: 10.1101/pdb.prot081737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This protocol describes the use of the genetically encoded troponin C-based calcium indicator TN-XXL to chronically monitor the functional properties of single neocortical neurons in the mouse visual cortex. A cranial window is implanted over the brain of a mouse expressing TN-XXL in pyramidal neurons of the cerebral cortex. Several days later, the visual cortex is mapped and photographed to facilitate repeated imaging of the same region using two-photon microscopy. Initial two-photon imaging may be done ∼2 wk after the window is implanted. We show the application of this technique for long-term in vivo imaging of stimulus response properties. Beyond providing functional information, long-term imaging of TN-XXL-labeled neurons also enables the simultaneous monitoring of structural properties down to the level of single dendritic spines.
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111
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Yu X, Strub MP, Barnard TJ, Noinaj N, Piszczek G, Buchanan SK, Taraska JW. An engineered palette of metal ion quenchable fluorescent proteins. PLoS One 2014; 9:e95808. [PMID: 24752441 PMCID: PMC3994163 DOI: 10.1371/journal.pone.0095808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/31/2014] [Indexed: 12/17/2022] Open
Abstract
Many fluorescent proteins have been created to act as genetically encoded biosensors. With these sensors, changes in fluorescence report on chemical states in living cells. Transition metal ions such as copper, nickel, and zinc are crucial in many physiological and pathophysiological pathways. Here, we engineered a spectral series of optimized transition metal ion-binding fluorescent proteins that respond to metals with large changes in fluorescence intensity. These proteins can act as metal biosensors or imaging probes whose fluorescence can be tuned by metals. Each protein is uniquely modulated by four different metals (Cu2+, Ni2+, Co2+, and Zn2+). Crystallography revealed the geometry and location of metal binding to the engineered sites. When attached to the extracellular terminal of a membrane protein VAMP2, dimeric pairs of the sensors could be used in cells as ratiometric probes for transition metal ions. Thus, these engineered fluorescent proteins act as sensitive transition metal ion-responsive genetically encoded probes that span the visible spectrum.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Travis J. Barnard
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Grzegorz Piszczek
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin W. Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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112
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Brox D, Schwering M, Engelhardt J, Herten DP. Reversible Chemical Reactions for Single-Color Multiplexing Microscopy. Chemphyschem 2014; 15:2331-6. [DOI: 10.1002/cphc.201402012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 11/09/2022]
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113
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Ivannikov MV, Macleod GT. Mitochondrial free Ca²⁺ levels and their effects on energy metabolism in Drosophila motor nerve terminals. Biophys J 2014; 104:2353-61. [PMID: 23746507 DOI: 10.1016/j.bpj.2013.03.064] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/24/2013] [Accepted: 03/25/2013] [Indexed: 01/29/2023] Open
Abstract
Mitochondrial Ca²⁺ uptake exerts dual effects on mitochondria. Ca²⁺ accumulation in the mitochondrial matrix dissipates membrane potential (ΔΨm), but Ca²⁺ binding of the intramitochondrial enzymes accelerates oxidative phosphorylation, leading to mitochondrial hyperpolarization. The levels of matrix free Ca²⁺ ([Ca²⁺]m) that trigger these metabolic responses in mitochondria in nerve terminals have not been determined. Here, we estimated [Ca²⁺]m in motor neuron terminals of Drosophila larvae using two methods: the relative responses of two chemical Ca²⁺ indicators with a 20-fold difference in Ca²⁺ affinity (rhod-FF and rhod-5N), and the response of a low-affinity, genetically encoded ratiometric Ca²⁺ indicator (D4cpv) calibrated against known Ca²⁺ levels. Matrix pH (pHm) and ΔΨm were monitored using ratiometric pericam and tetramethylrhodamine ethyl ester probe, respectively, to determine when mitochondrial energy metabolism was elevated. At rest, [Ca²⁺]m was 0.22 ± 0.04 μM, but it rose to ~26 μM (24.3 ± 3.4 μM with rhod-FF/rhod-5N and 27.0 ± 2.6 μM with D4cpv) when the axon fired close to its endogenous frequency for only 2 s. This elevation in [Ca²⁺]m coincided with a rapid elevation in pHm and was followed by an after-stimulus ΔΨm hyperpolarization. However, pHm decreased and no ΔΨm hyperpolarization was observed in response to lower levels of [Ca²⁺]m, up to 13.1 μM. These data indicate that surprisingly high levels of [Ca²⁺]m are required to stimulate presynaptic mitochondrial energy metabolism.
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Affiliation(s)
- Maxim V Ivannikov
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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114
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Thestrup T, Litzlbauer J, Bartholomäus I, Mues M, Russo L, Dana H, Kovalchuk Y, Liang Y, Kalamakis G, Laukat Y, Becker S, Witte G, Geiger A, Allen T, Rome LC, Chen TW, Kim DS, Garaschuk O, Griesinger C, Griesbeck O. Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes. Nat Methods 2014; 11:175-82. [DOI: 10.1038/nmeth.2773] [Citation(s) in RCA: 253] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/29/2013] [Indexed: 01/20/2023]
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115
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Dipt S, Riemensperger T, Fiala A. Optical calcium imaging using DNA-encoded fluorescence sensors in transgenic fruit flies, Drosophila melanogaster. Methods Mol Biol 2014; 1071:195-206. [PMID: 24052390 DOI: 10.1007/978-1-62703-622-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The invention of protein-based fluorescent biosensors has paved the way to target specific cells with these probes and visualize intracellular processes not only in isolated cells or tissue cultures but also in transgenic animals. In particular, DNA-encoded fluorescence proteins sensitive to Ca(2+) ions are often used to monitor changes in intracellular Ca(2+) concentrations. This is of particular relevance in neuroscience since the dynamics of intracellular Ca(2+) concentrations represents a faithful correlate for neuronal activity, and optical Ca(2+) imaging is commonly used to monitor spatiotemporal activity across populations of neurons. In this respect Drosophila provides a favorable model organism due to the sophisticated genetic tools that facilitate the targeted expression of fluorescent Ca(2+) sensor proteins. Here we describe how optical Ca(2+) imaging of neuronal activity in the Drosophila brain can be carried out in vivo using two-photon microscopy. We exemplify this technique by describing how to monitor odor-evoked Ca(2+) dynamics in the primary olfactory center of the Drosophila brain.
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Affiliation(s)
- Shubham Dipt
- Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology and Molecular Neurobiology of Behavior, Georg-August-Universität Göttingen, Göttingen, Germany
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Hill JM, De Stefani D, Jones AWE, Ruiz A, Rizzuto R, Szabadkai G. Measuring baseline Ca(2+) levels in subcellular compartments using genetically engineered fluorescent indicators. Methods Enzymol 2014; 543:47-72. [PMID: 24924127 DOI: 10.1016/b978-0-12-801329-8.00003-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intracellular Ca(2+) signaling is involved in a series of physiological and pathological processes. In particular, an intimate crosstalk between bioenergetic metabolism and Ca(2+) homeostasis has been shown to determine cell fate in resting conditions as well as in response to stress. The endoplasmic reticulum and mitochondria represent key hubs of cellular metabolism and Ca(2+) signaling. However, it has been challenging to specifically detect highly localized Ca(2+) fluxes such as those bridging these two organelles. To circumvent this issue, various recombinant Ca(2+) indicators that can be targeted to specific subcellular compartments have been developed over the past two decades. While the use of these probes for measuring agonist-induced Ca(2+) signals in various organelles has been extensively described, the assessment of basal Ca(2+) concentrations within specific organelles is often disregarded, in spite of the fact that this parameter is vital for several metabolic functions, including the enzymatic activity of mitochondrial dehydrogenases of the Krebs cycle and protein folding in the endoplasmic reticulum. Here, we provide an overview on genetically engineered, organelle-targeted fluorescent Ca(2+) probes and outline their evolution. Moreover, we describe recently developed protocols to quantify baseline Ca(2+) concentrations in specific subcellular compartments. Among several applications, this method is suitable for assessing how changes in basal Ca(2+) levels affect the metabolic profile of cancer cells.
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Affiliation(s)
- Julia M Hill
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, United Kingdom
| | - Diego De Stefani
- Department of Biomedical Sciences, CNR Neuroscience Institute, University of Padua, Padua, Italy
| | - Aleck W E Jones
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, United Kingdom
| | - Asier Ruiz
- Department of Neurosciences, University of the Basque Country (UPV/EHU), Achúcarro Basque Center for Neuroscience-UPV/EHU, Leioa, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, (CIBERNED), Madrid, Spain
| | - Rosario Rizzuto
- Department of Biomedical Sciences, CNR Neuroscience Institute, University of Padua, Padua, Italy
| | - Gyorgy Szabadkai
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, United Kingdom; Department of Biomedical Sciences, CNR Neuroscience Institute, University of Padua, Padua, Italy.
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117
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Fluorescent biosensors: design and application to motor proteins. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:25-47. [PMID: 25095989 DOI: 10.1007/978-3-0348-0856-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reagentless biosensors are single molecular species that report the concentration of a specific target analyte, while having minimal impact on the system being studied. This chapter reviews such biosensors with emphasis on the ones that use fluorescence as readout and can be used for real-time assays of concentration changes with reasonably high time resolution and sensitivity. Reagentless biosensors can be designed with different types of recognition elements, particularly specific binding proteins and nucleic acids, including aptamers. Different ways are described in which a fluorescence signal can be used to report the target concentration. These include the use of single, environmentally sensitive fluorophores; FRET pairs, often used in genetically encoded biosensors; and pairs of identical fluorophores that undergo reversible stacking interactions to change fluorescence intensity. The applications of these biosensors in different types of real-time assays with motor proteins are described together with some specific examples. These encompass regulation and mechanism of motor proteins, using both steady-state assays and single-turnover measurements.
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118
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Wright NJD. Evolution of the techniques used in studying associative olfactory learning and memory in adult Drosophila in vivo: a historical and technical perspective. INVERTEBRATE NEUROSCIENCE 2013; 14:1-11. [PMID: 24149895 DOI: 10.1007/s10158-013-0163-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/08/2013] [Indexed: 11/25/2022]
Abstract
Drosophila melanogaster behavioral mutants have been isolated in which the ability to form associative olfactory memories has been disrupted primarily by altering cyclic adenosine monophosphate signal transduction. Unfortunately, the small size of the fruit fly and its neurons has made the application of neurobiological techniques typically used to investigate the physiology underlying these behaviors daunting. However, the realization that adult fruit flies could tolerate a window in the head capsule allowing access to the central structures thought to be involved plus the development of genetically expressed reporters of neuronal function has allowed a meteoric expansion of this field over the last decade. This review attempts to summarize the evolution of the techniques involved from the first use of a window to access these brain areas thought to be involved in associative olfactory learning and memory, the mushroom bodies and antennal lobes, to the current refinements which allow both high-resolution multiphoton imaging and patch clamping of identified neurons while applying the stimuli used in the behavioral protocols. This area of research now appears poised to reveal some very exciting mechanisms underlying behavior.
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Affiliation(s)
- Nicholas J D Wright
- Levine College of Health Sciences, Wingate University School of Pharmacy, 515 N. Main Street, Wingate, NC, 28174, USA,
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119
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Genetically encoded calcium indicator illuminates calcium dynamics in primary cilia. Nat Methods 2013; 10:1105-7. [PMID: 24056873 DOI: 10.1038/nmeth.2647] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/13/2013] [Indexed: 12/25/2022]
Abstract
Visualization of signal transduction in live primary cilia constitutes a technical challenge owing to the organelle's submicrometer dimensions and close proximity to the cell body. Using a genetically encoded calcium indicator targeted to primary cilia, we visualized calcium signaling in cilia of mouse fibroblasts and kidney cells upon chemical or mechanical stimulation with high specificity, high sensitivity and wide dynamic range.
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120
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Highlighted Ca²⁺ imaging with a genetically encoded 'caged' indicator. Sci Rep 2013; 3:1398. [PMID: 23474844 PMCID: PMC3593221 DOI: 10.1038/srep01398] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/19/2013] [Indexed: 11/08/2022] Open
Abstract
Genetically encoded fluorescent indicators for bioimaging are powerful tools for visualizing biological phenomena in specified cell types or cellular compartments. However, available gene promoters or localization sequences are not applicable for visualizing all expression events. Furthermore, a visualization technique focusing on single cells or cellular compartments is required for characterizing specific cellular properties including individuality of cells in the cell population. To address these limitations, we developed a genetically encoded caged Ca2+ indicator for which expression timing and location could be controlled. This indicator, PA-TNXL, comprises a Ca2+-binding protein and troponin between a photoactivatable FRET donor (PA-GFP) and a FRET quencher (dim variant of YFP). Ultraviolet irradiation activates the FRET Ca2+ indicator. Using this indicator, we successfully imaged Ca2+ dynamics in a given set of HeLa cells and cultured hippocampal neurons. This technology can be applied for developing other photoactivatable indicators, thereby opening a new area of biological research.
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121
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Abstract
PURPOSE OF REVIEW Tremendous advances have occurred in recent years in elucidating basic mechanisms of epilepsy at the level of ion channels and neurotransmitters. Epilepsy, however, is ultimately a disease of functionally and/or structurally aberrant connections between neurons and groups of neurons at the systems level. Recent advances in neuroimaging and electrophysiology now make it possible to investigate structural and functional connectivity of the entire brain, and these techniques are currently being used to investigate diseases that manifest as global disturbances of brain function. Epilepsy is such a disease, and our understanding of the mechanisms underlying the development of epilepsy and the generation of epileptic seizures will undoubtedly benefit from research utilizing these connectomic approaches. RECENT FINDINGS MRI using diffusion tensor imaging provides structural information, whereas functional MRI and electroencephalography provide functional information about connectivity at the whole brain level. Optogenetics, tracers, electrophysiological approaches, and calcium imaging provide connectivity information at the level of local circuits. These approaches are revealing important neuronal network disturbances underlying epileptic abnormalities. SUMMARY An understanding of the fundamental mechanisms underlying the development of epilepsy and the generation of epileptic seizures will require delineation of the aberrant functional and structural connections of the whole brain. The field of connectomics now provides approaches to accomplish this.
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122
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Bar-Shir A, Gilad AA, Chan KWY, Liu G, van Zijl PCM, Bulte JWM, McMahon MT. Metal ion sensing using ion chemical exchange saturation transfer 19F magnetic resonance imaging. J Am Chem Soc 2013; 135:12164-7. [PMID: 23905693 DOI: 10.1021/ja403542g] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although metal ions are involved in a myriad of biological processes, noninvasive detection of free metal ions in deep tissue remains a formidable challenge. We present an approach for specific sensing of the presence of Ca(2+) in which the amplification strategy of chemical exchange saturation transfer (CEST) is combined with the broad range of chemical shifts found in (19)F NMR spectroscopy to obtain magnetic resonance images of Ca(2+). We exploited the chemical shift change (Δω) of (19)F upon binding of Ca(2+) to the 5,5'-difluoro derivative of 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (5F-BAPTA) by radiofrequency labeling at the Ca(2+)-bound (19)F frequency and detection of the label transfer to the Ca(2+)-free (19)F frequency. Through the substrate binding kinetics we were able to amplify the signal of Ca(2+) onto free 5F-BAPTA and thus indirectly detect low Ca(2+) concentrations with high sensitivity.
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Affiliation(s)
- Amnon Bar-Shir
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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123
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Würth C, Grabolle M, Pauli J, Spieles M, Resch-Genger U. Relative and absolute determination of fluorescence quantum yields of transparent samples. Nat Protoc 2013; 8:1535-50. [DOI: 10.1038/nprot.2013.087] [Citation(s) in RCA: 670] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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124
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Affiliation(s)
- Z. Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724;
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington 98103;
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125
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Abstract
The small GTPase Rap1 contributes to fear learning and cortico-amygdala plasticity by inhibiting glutamate release from cortical neurons, but mechanisms of this inhibition remain unknown. Conversely, L-type calcium channels (LTCCs) become involved in glutamate release after fear learning and LTP induction. Here, we show that Rap1 deletion in mouse primary cortical neurons increases synaptic vesicle exocytosis without altering endocytosis or vesicle pool size in an LTCC-dependent manner. We identify Erk1/2 as the downstream effector of Rap1 and show that its inhibition increases plasma membrane expression of LTCCs near presynaptic terminals. We propose that the Rap1 signaling enables plasticity and fear learning by regulating LTCCs at cortico-amygdala synapses.
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126
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Samtleben S, Jaepel J, Fecher C, Andreska T, Rehberg M, Blum R. Direct imaging of ER calcium with targeted-esterase induced dye loading (TED). J Vis Exp 2013:e50317. [PMID: 23685703 PMCID: PMC3679584 DOI: 10.3791/50317] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Visualization of calcium dynamics is important to understand the role of calcium in cell physiology. To examine calcium dynamics, synthetic fluorescent Ca(2+) indictors have become popular. Here we demonstrate TED (= targeted-esterase induced dye loading), a method to improve the release of Ca(2+) indicator dyes in the ER lumen of different cell types. To date, TED was used in cell lines, glial cells, and neurons in vitro. TED bases on efficient, recombinant targeting of a high carboxylesterase activity to the ER lumen using vector-constructs that express Carboxylesterases (CES). The latest TED vectors contain a core element of CES2 fused to a red fluorescent protein, thus enabling simultaneous two-color imaging. The dynamics of free calcium in the ER are imaged in one color, while the corresponding ER structure appears in red. At the beginning of the procedure, cells are transduced with a lentivirus. Subsequently, the infected cells are seeded on coverslips to finally enable live cell imaging. Then, living cells are incubated with the acetoxymethyl ester (AM-ester) form of low-affinity Ca(2+) indicators, for instance Fluo5N-AM, Mag-Fluo4-AM, or Mag-Fura2-AM. The esterase activity in the ER cleaves off hydrophobic side chains from the AM form of the Ca(2+) indicator and a hydrophilic fluorescent dye/Ca(2+) complex is formed and trapped in the ER lumen. After dye loading, the cells are analyzed at an inverted confocal laser scanning microscope. Cells are continuously perfused with Ringer-like solutions and the ER calcium dynamics are directly visualized by time-lapse imaging. Calcium release from the ER is identified by a decrease in fluorescence intensity in regions of interest, whereas the refilling of the ER calcium store produces an increase in fluorescence intensity. Finally, the change in fluorescent intensity over time is determined by calculation of ΔF/F0.
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127
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Yawo H, Asano T, Sakai S, Ishizuka T. Optogenetic manipulation of neural and non-neural functions. Dev Growth Differ 2013; 55:474-90. [PMID: 23550617 DOI: 10.1111/dgd.12053] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 01/22/2023]
Abstract
Optogenetic manipulation of the neuronal activity enables one to analyze the neuronal network both in vivo and in vitro with precise spatio-temporal resolution. Channelrhodopsins (ChRs) are light-sensitive cation channels that depolarize the cell membrane, whereas halorhodopsins and archaerhodopsins are light-sensitive Cl(-) and H(+) transporters, respectively, that hyperpolarize it when exogenously expressed. The cause-effect relationship between a neuron and its function in the brain is thus bi-directionally investigated with evidence of necessity and sufficiency. In this review we discuss the potential of optogenetics with a focus on three major requirements for its application: (i) selection of the light-sensitive proteins optimal for optogenetic investigation, (ii) targeted expression of these selected proteins in a specific group of neurons, and (iii) targeted irradiation with high spatiotemporal resolution. We also discuss recent progress in the application of optogenetics to studies of non-neural cells such as glial cells, cardiac and skeletal myocytes. In combination with stem cell technology, optogenetics may be key to successful research using embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) derived from human patients through optical regulation of differentiation-maturation, through optical manipulation of tissue transplants and, furthermore, through facilitating survival and integration of transplants.
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Affiliation(s)
- Hiromu Yawo
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
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128
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Rossano AJ, Chouhan AK, Macleod GT. Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo. J Physiol 2013; 591:1691-706. [PMID: 23401611 PMCID: PMC3624846 DOI: 10.1113/jphysiol.2012.248377] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 01/04/2013] [Indexed: 01/27/2023] Open
Abstract
All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pH(cyto)) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pH(cyto) shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2,7-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pH(cyto). Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤ 4 s) trains of action potentials but did buffer slow (~60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca(2+) increase upon stimulation, and partial inhibition of the plasma membrane Ca(2+)-ATPase, a Ca(2+)/H(+) exchanger, attenuated pH(cyto) shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (~0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pH(cyto) shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pH(cyto) shifts cannot be dismissed as artifacts of ex vivo preparations.
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Affiliation(s)
- Adam J Rossano
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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129
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Johannssen HC, Helmchen F. Two-photon imaging of spinal cord cellular networks. Exp Neurol 2013; 242:18-26. [DOI: 10.1016/j.expneurol.2012.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 03/27/2012] [Accepted: 07/21/2012] [Indexed: 11/30/2022]
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130
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Akerboom J, Carreras Calderón N, Tian L, Wabnig S, Prigge M, Tolö J, Gordus A, Orger MB, Severi KE, Macklin JJ, Patel R, Pulver SR, Wardill TJ, Fischer E, Schüler C, Chen TW, Sarkisyan KS, Marvin JS, Bargmann CI, Kim DS, Kügler S, Lagnado L, Hegemann P, Gottschalk A, Schreiter ER, Looger LL. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci 2013; 6:2. [PMID: 23459413 PMCID: PMC3586699 DOI: 10.3389/fnmol.2013.00002] [Citation(s) in RCA: 498] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 02/11/2013] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.
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Affiliation(s)
- Jasper Akerboom
- Janelia Farm Research Campus, Howard Hughes Medical Institute Ashburn, VA, USA
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131
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Dedecker P, De Schryver FC, Hofkens J. Fluorescent Proteins: Shine on, You Crazy Diamond. J Am Chem Soc 2013; 135:2387-402. [DOI: 10.1021/ja309768d] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Peter Dedecker
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Frans C. De Schryver
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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132
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Weitz AC, Behrend MR, Lee NS, Klein RL, Chiodo VA, Hauswirth WW, Humayun MS, Weiland JD, Chow RH. Imaging the response of the retina to electrical stimulation with genetically encoded calcium indicators. J Neurophysiol 2013; 109:1979-88. [PMID: 23343890 DOI: 10.1152/jn.00852.2012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Epiretinal implants for the blind are designed to stimulate surviving retinal neurons, thus bypassing the diseased photoreceptor layer. Single-unit or multielectrode recordings from isolated animal retina are commonly used to inform the design of these implants. However, such electrical recordings provide limited information about the spatial patterns of retinal activation. Calcium imaging overcomes this limitation, as imaging enables high spatial resolution mapping of retinal ganglion cell (RGC) activity as well as simultaneous recording from hundreds of RGCs. Prior experiments in amphibian retina have demonstrated proof of principle, yet experiments in mammalian retina have been hindered by the inability to load calcium indicators into mature mammalian RGCs. Here, we report a method for labeling the majority of ganglion cells in adult rat retina with genetically encoded calcium indicators, specifically GCaMP3 and GCaMP5G. Intravitreal injection of an adeno-associated viral vector targets ∼85% of ganglion cells with high specificity. Because of the large fluorescence signals provided by the GCaMP sensors, we can now for the first time visualize the response of the retina to electrical stimulation in real-time. Imaging transduced retinas mounted on multielectrode arrays reveals how stimulus pulse shape can dramatically affect the spatial extent of RGC activation, which has clear implications in prosthetic applications. Our method can be easily adapted to work with other fluorescent indicator proteins in both wild-type and transgenic mammals.
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Affiliation(s)
- Andrew C Weitz
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
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133
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Genetically encoded Ca(2+) indicators: properties and evaluation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1787-97. [PMID: 23352808 DOI: 10.1016/j.bbamcr.2013.01.011] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/02/2013] [Accepted: 01/10/2013] [Indexed: 02/04/2023]
Abstract
Genetically encoded calcium ion (Ca(2+)) indicators have become very useful and widely used tools for Ca(2+) imaging, not only in cellular models, but also in living organisms. However, the in vivo and in situ characterization of these indicators is tedious and time consuming, and it does not provide information regarding the suitability of an indicator for particular experimental environments. Thus, initial in vitro evaluation of these tools is typically performed to determine their properties. In this review, we examined the properties of dynamic range, affinity, selectivity, and kinetics for Ca(2+) indicators. Commonly used strategies for evaluating these properties are presented. This article is part of a Special Issue entitled: 12th European Symposium on Calcium.
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134
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Sample V, Ni Q, Mehta S, Inoue T, Zhang J. Controlling enzymatic action in living cells with a kinase-inducible bimolecular switch. ACS Chem Biol 2013; 8:116-21. [PMID: 23072367 DOI: 10.1021/cb300393w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular probes designed to monitor or perturb signaling events in living cells rely on engineered molecular switches. Here, we show that a kinase-inducible bimolecular switch comprising a kinase-specific substrate and a phosphoamino acid binding domain can be used for acute regulation of cellular events. As a proof of concept, we employed a Protein Kinase A (PKA)-dependent switch and coupled it to a lipid phosphatase to manipulate the level of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) in living cells. PKA activation results in rapid degradation of PI(4,5)P(2). Conversely, when PKA is inhibited, dephosphorylation of the switch leads to the replenishment of PI(4,5)P(2). Thus, this strategy can be used for reversibly controlling enzymatic action in living cells. Furthermore, its genetic encodability and modular design should facilitate the adaptation of this approach to control different cellular activities as a function of phosphorylation-dependent input signals, thereby providing versatile tools for potentially perturbing or rewiring signaling pathways.
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Affiliation(s)
- Vedangi Sample
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Qiang Ni
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Sohum Mehta
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Takanari Inoue
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Jin Zhang
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
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135
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Ellis-Davies GCR. A chemist and biologist talk to each other about caged neurotransmitters. Beilstein J Org Chem 2013; 9:64-73. [PMID: 23399979 PMCID: PMC3566830 DOI: 10.3762/bjoc.9.8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/07/2012] [Indexed: 11/23/2022] Open
Abstract
Caged compounds are small organic molecules that can be photoactivated with brief pulses of light. They are widely used to study a great variety of biological processes by physiologists, cell biologists and neuroscientists. Initially made and invented by biologists in the late 1970s, they are now made mostly by chemists, often without any dialogue with the end users, the biologists. The idea for this review is to stimulate interaction between the two communities to further the creative development and application of these powerful optical probes.
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Affiliation(s)
- Graham CR Ellis-Davies
- Department of Neuroscience, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
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136
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Niu W, Guo J. Expanding the chemistry of fluorescent protein biosensors through genetic incorporation of unnatural amino acids. MOLECULAR BIOSYSTEMS 2013; 9:2961-70. [DOI: 10.1039/c3mb70204a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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137
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Koay MS, Janssen BMG, Merkx M. Tuning the metal binding site specificity of a fluorescent sensor protein: from copper to zinc and back. Dalton Trans 2013; 42:3230-2. [DOI: 10.1039/c2dt32082g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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138
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Abstract
There is a vast array of dyes currently available for measurement of cytosolic calcium. These encompass single and dual excitation and single and dual emission probes. The choice of particular probe depends on the experimental question and the type of equipment to be used. It is therefore extremely difficult to define a universal approach that will suit all potential investigators. Preparations under investigation are loaded with the selected organic indicator dye by incubation with ester derivatives, by micropipet injection or reverse permeabilization. Indicators can also be targeted to a range of intracellular organelles. Calibration of a fluorescent signal into Ca(2+) concentration is in theory relatively simple but the investigator needs to take great care in this process. This chapter describes the theory of these processes and some of the pitfalls users should be aware of. Precise experimental details can be found in the subsequent chapters of this volume.
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Affiliation(s)
- Alec W M Simpson
- Department of Cell and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
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139
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Depry C, Mehta S, Zhang J. Multiplexed visualization of dynamic signaling networks using genetically encoded fluorescent protein-based biosensors. Pflugers Arch 2012; 465:373-81. [PMID: 23138230 DOI: 10.1007/s00424-012-1175-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/13/2012] [Indexed: 12/25/2022]
Abstract
Cells rely on a complex, interconnected network of signaling pathways to sense and interpret changes in their extracellular environment. The development of genetically encoded fluorescent protein (FP)-based biosensors has made it possible for researchers to directly observe and characterize the spatiotemporal dynamics of these intracellular signaling pathways in living cells. However, detailed information regarding the precise temporal and spatial relationships between intersecting pathways is often lost when individual signaling events are monitored in isolation. As the development of biosensor technology continues to advance, it is becoming increasingly feasible to image multiple FP-based biosensors concurrently, permitting greater insights into the intricate coordination of intracellular signaling networks by enabling parallel monitoring of distinct signaling events within the same cell. In this review, we discuss several strategies for multiplexed imaging of FP-based biosensors, while also underscoring some of the challenges associated with these techniques and highlighting additional avenues that could lead to further improvements in parallel monitoring of intracellular signaling events.
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Affiliation(s)
- Charlene Depry
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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140
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Laine R, Stuckey DW, Manning H, Warren SC, Kennedy G, Carling D, Dunsby C, Sardini A, French PMW. Fluorescence lifetime readouts of Troponin-C-based calcium FRET sensors: a quantitative comparison of CFP and mTFP1 as donor fluorophores. PLoS One 2012; 7:e49200. [PMID: 23152874 PMCID: PMC3494685 DOI: 10.1371/journal.pone.0049200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/08/2012] [Indexed: 11/23/2022] Open
Abstract
We have compared the performance of two Troponin-C-based calcium FRET sensors using fluorescence lifetime read-outs. The first sensor, TN-L15, consists of a Troponin-C fragment inserted between CFP and Citrine while the second sensor, called mTFP-TnC-Cit, was realized by replacing CFP in TN-L15 with monomeric Teal Fluorescent Protein (mTFP1). Using cytosol preparations of transiently transfected mammalian cells, we have measured the fluorescence decay profiles of these sensors at controlled concentrations of calcium using time-correlated single photon counting. These data were fitted to discrete exponential decay models using global analysis to determine the FRET efficiency, fraction of donor molecules undergoing FRET and calcium affinity of these sensors. We have also studied the decay profiles of the donor fluorescent proteins alone and determined the sensitivity of the donor lifetime to temperature and emission wavelength. Live-cell fluorescence lifetime imaging (FLIM) of HEK293T cells expressing each of these sensors was also undertaken. We confirmed that donor fluorescence of mTFP-TnC-Cit fits well to a two-component decay model, while the TN-L15 lifetime data was best fitted to a constrained four-component model, which was supported by phasor analysis of the measured lifetime data. If the constrained global fitting is employed, the TN-L15 sensor can provide a larger dynamic range of lifetime readout than the mTFP-TnC-Cit sensor but the CFP donor is significantly more sensitive to changes in temperature and emission wavelength compared to mTFP and, while the mTFP-TnC-Cit solution phase data broadly agreed with measurements in live cells, this was not the case for the TN-L15 sensor. Our titration experiment also indicates that a similar precision in determination of calcium concentration can be achieved with both FRET biosensors when fitting a single exponential donor fluorescence decay model to the fluorescence decay profiles. We therefore suggest that mTFP-based probes are more suitable for FLIM experiments than CFP-based probes.
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Affiliation(s)
- Romain Laine
- Institute of Chemical Biology (ICB), Imperial College of Science, Technology & Medicine, Institute of Chemical Biology (ICB), London, England
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
- * E-mail:
| | - Daniel W. Stuckey
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Hugh Manning
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Sean C. Warren
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Gordon Kennedy
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - David Carling
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Chris Dunsby
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Alessandro Sardini
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Paul M. W. French
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
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141
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Yamada Y, Mikoshiba K. Quantitative comparison of novel GCaMP-type genetically encoded Ca(2+) indicators in mammalian neurons. Front Cell Neurosci 2012; 6:41. [PMID: 23060748 PMCID: PMC3465963 DOI: 10.3389/fncel.2012.00041] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 09/19/2012] [Indexed: 01/30/2023] Open
Abstract
New variants of GCaMP-type genetically encoded Ca(2+) indicators (GECIs) have been continuously developed and heavily used in many areas of biology including neuroscience. The latest subfamily called "GECOs" were developed with in vitro high-throughput screening, and shown to have novel spectral properties and/or improved fluorescent responses over their ancestor GCaMP3. The most critical parameter in evaluating performance in neurons, however, remains uncharacterized: the relationship between the GECI responses and the number of action potentials (APs). Here we analyzed the GECI responses to APs in cortical pyramidal cells of mouse acute brain slices. Unexpectedly, we found that none of the GECOs exhibited any improved performance over GCaMP3. Our results imply that careful validation is required for the accurate prediction of the actual performance of GECIs in mammalian neurons. We propose that appropriate guidelines for evaluating their efficacy should be established for the benefit of research community, given the rapidly expanding use of GECIs in neuroscience.
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Affiliation(s)
- Yoshiyuki Yamada
- Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN Wako-shi, Saitama, Japan ; Central Institute for Experimental Animals Kawasaki-shi, Kanagawa, Japan
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142
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Akerboom J, Chen TW, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, Gordus A, Orger MB, Portugues R, Engert F, Macklin JJ, Filosa A, Aggarwal A, Kerr RA, Takagi R, Kracun S, Shigetomi E, Khakh BS, Baier H, Lagnado L, Wang SSH, Bargmann CI, Kimmel BE, Jayaraman V, Svoboda K, Kim DS, Schreiter ER, Looger LL. Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci 2012; 32:13819-40. [PMID: 23035093 PMCID: PMC3482105 DOI: 10.1523/jneurosci.2601-12.2012] [Citation(s) in RCA: 887] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/25/2012] [Accepted: 08/01/2012] [Indexed: 01/14/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of "GCaMP5" sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.
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Affiliation(s)
- Jasper Akerboom
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Tsai-Wen Chen
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Trevor J. Wardill
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Lin Tian
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Jonathan S. Marvin
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Sevinç Mutlu
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Doca de Pedrouços, 1400-038 Lisboa, Portugal
| | - Nicole Carreras Calderón
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH United Kingdom
- Department of Chemistry, University of Puerto Rico–Río Piedras, San Juan, Puerto Rico 00931
| | - Federico Esposti
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH United Kingdom
| | - Bart G. Borghuis
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut 06511
| | - Xiaonan Richard Sun
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544
| | - Andrew Gordus
- Howard Hughes Medical Institute, Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065
| | - Michael B. Orger
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Doca de Pedrouços, 1400-038 Lisboa, Portugal
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - Ruben Portugues
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - Florian Engert
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138
| | - John J. Macklin
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Alessandro Filosa
- Department of Physiology, Programs in Neuroscience, Genetics, and Developmental Biology, University of California, San Francisco, San Francisco, California 94158
| | - Aman Aggarwal
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India, and
| | - Rex A. Kerr
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Ryousuke Takagi
- Department of Physiology, University of California, Los Angeles, Los Angeles, California 90095
| | - Sebastian Kracun
- Department of Physiology, University of California, Los Angeles, Los Angeles, California 90095
| | - Eiji Shigetomi
- Department of Physiology, University of California, Los Angeles, Los Angeles, California 90095
| | - Baljit S. Khakh
- Department of Physiology, University of California, Los Angeles, Los Angeles, California 90095
| | - Herwig Baier
- Department of Physiology, Programs in Neuroscience, Genetics, and Developmental Biology, University of California, San Francisco, San Francisco, California 94158
| | - Leon Lagnado
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH United Kingdom
| | - Samuel S.-H. Wang
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544
| | - Cornelia I. Bargmann
- Howard Hughes Medical Institute, Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065
| | - Bruce E. Kimmel
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Vivek Jayaraman
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Karel Svoboda
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Douglas S. Kim
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Eric R. Schreiter
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
- Department of Chemistry, University of Puerto Rico–Río Piedras, San Juan, Puerto Rico 00931
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
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143
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Mbatia HW, Burdette SC. Photochemical Tools for Studying Metal Ion Signaling and Homeostasis. Biochemistry 2012; 51:7212-24. [DOI: 10.1021/bi3001769] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hannah W. Mbatia
- University of Connecticut, 55 North Eagleville
Road, Storrs, Connecticut 06269-3060, United
States
| | - Shawn C. Burdette
- Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts
01609-2280, United States
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144
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Biocompatibility of a genetically encoded calcium indicator in a transgenic mouse model. Nat Commun 2012; 3:1031. [DOI: 10.1038/ncomms2035] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 07/31/2012] [Indexed: 11/08/2022] Open
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145
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
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Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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146
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
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147
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Devor A, Sakadžić S, Srinivasan VJ, Yaseen MA, Nizar K, Saisan PA, Tian P, Dale AM, Vinogradov SA, Franceschini MA, Boas DA. Frontiers in optical imaging of cerebral blood flow and metabolism. J Cereb Blood Flow Metab 2012; 32:1259-76. [PMID: 22252238 PMCID: PMC3390808 DOI: 10.1038/jcbfm.2011.195] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In vivo optical imaging of cerebral blood flow (CBF) and metabolism did not exist 50 years ago. While point optical fluorescence and absorption measurements of cellular metabolism and hemoglobin concentrations had already been introduced by then, point blood flow measurements appeared only 40 years ago. The advent of digital cameras has significantly advanced two-dimensional optical imaging of neuronal, metabolic, vascular, and hemodynamic signals. More recently, advanced laser sources have enabled a variety of novel three-dimensional high-spatial-resolution imaging approaches. Combined, as we discuss here, these methods are permitting a multifaceted investigation of the local regulation of CBF and metabolism with unprecedented spatial and temporal resolution. Through multimodal combination of these optical techniques with genetic methods of encoding optical reporter and actuator proteins, the future is bright for solving the mysteries of neurometabolic and neurovascular coupling and translating them to clinical utility.
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Affiliation(s)
- Anna Devor
- Department of Neurosciences, UCSD, La Jolla, CA, USA.
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148
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Tian L, Hires SA, Looger LL. Imaging neuronal activity with genetically encoded calcium indicators. Cold Spring Harb Protoc 2012; 2012:647-56. [PMID: 22661439 DOI: 10.1101/pdb.top069609] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI's performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.
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149
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Takakura H, Hattori M, Takeuchi M, Ozawa T. Visualization and quantitative analysis of G protein-coupled receptor-β-arrestin interaction in single cells and specific organs of living mice using split luciferase complementation. ACS Chem Biol 2012; 7:901-10. [PMID: 22364396 DOI: 10.1021/cb200360z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Methods used to assess the efficacy of potentially therapeutic reagents for G protein-coupled receptors (GPCRs) have been developed. Previously, we demonstrated sensitive detection of the interaction of GPCRs and β-arrestin2 (ARRB2) using 96-well microtiter plates and a bioluminescence microscope based on split click beetle luciferase complementation. Herein, using firefly luciferase emitting longer wavelength light, we demonstrate quantitative analysis of the interaction of β2-adrenergic receptor (ADRB2), a kind of GPCR, and ARRB2 in a 96-well plate assay with single-cell imaging. Additionally, we showed bioluminescence in vivo imaging of the ADRB2-ARRB2 interaction in two systems: cell implantation and hydrodynamic tail vein (HTV) methods. Specifically, in the HTV method, the luminescence signal from the liver upon stimulation of an agonist for ADRB2 was obtained in the intact systems of mice. The results demonstrate that this method enables noninvasive screening of the efficacy of chemicals at the specific organ in in vivo testing. This in vivo system can contribute to effective evaluation in pharmacokinetics and pharmacodynamics and expedite the development of new drugs for GPCRs.
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Affiliation(s)
- Hideo Takakura
- Department of Chemistry, School of
Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Mitsuru Hattori
- Department of Chemistry, School of
Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Masaki Takeuchi
- Department of Chemistry, School of
Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of
Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
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150
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Geiger A, Russo L, Gensch T, Thestrup T, Becker S, Hopfner KP, Griesinger C, Witte G, Griesbeck O. Correlating calcium binding, Förster resonance energy transfer, and conformational change in the biosensor TN-XXL. Biophys J 2012; 102:2401-10. [PMID: 22677394 PMCID: PMC3353025 DOI: 10.1016/j.bpj.2012.03.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/21/2012] [Accepted: 03/27/2012] [Indexed: 11/23/2022] Open
Abstract
Genetically encoded calcium indicators have become instrumental in imaging signaling in complex tissues and neuronal circuits in vivo. Despite their importance, structure-function relationships of these sensors often remain largely uncharacterized due to their artificial and multimodular composition. Here, we describe a combination of protein engineering and kinetic, spectroscopic, and biophysical analysis of the Förster resonance energy transfer (FRET)-based calcium biosensor TN-XXL. Using fluorescence spectroscopy of engineered tyrosines, we show that two of the four calcium binding EF-hands dominate the FRET output of TN-XXL and that local conformational changes of these hands match the kinetics of FRET change. Using small-angle x-ray scattering and NMR spectroscopy, we show that TN-XXL changes from a flexible elongated to a rigid globular shape upon binding calcium, thus resulting in FRET signal output. Furthermore, we compare calcium titrations using fluorescence lifetime spectroscopy with the ratiometric approach and investigate potential non-FRET effects that may affect the fluorophores. Thus, our data characterize the biophysics of TN-XXL in detail and may form a basis for further rational engineering of FRET-based biosensors.
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Affiliation(s)
- Anselm Geiger
- Max-Planck-Institut für Neurobiologie, Martinsried, Germany
| | - Luigi Russo
- Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | | | | | - Stefan Becker
- Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Karl-Peter Hopfner
- Genzentrum und Department Biochemie, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Gregor Witte
- Genzentrum und Department Biochemie, Ludwig-Maximilians-Universität, Munich, Germany
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