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Zhang CJ, Mou H, Yuan J, Wang YH, Sun SN, Wang W, Xu ZH, Yu SJ, Jin K, Jin ZB. Effects of fluorescent protein tdTomato on mouse retina. Exp Eye Res 2024; 243:109910. [PMID: 38663720 DOI: 10.1016/j.exer.2024.109910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 02/26/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Fluorescent proteins (FPs) have been widely used to investigate cellular and molecular interactions and trace biological events in many applications. Some of the FPs have been demonstrated to cause undesirable cellular damage by light-induced ROS production in vivo or in vitro. However, it remains unknown if one of the most popular FPs, tdTomato, has similar effects in neuronal cells. In this study, we discovered that tdTomato expression led to unexpected retinal dysfunction and ultrastructural defects in the transgenic mouse retina. The retinal dysfunction mainly manifested in the reduced photopic electroretinogram (ERG) responses and decreased contrast sensitivity in visual acuity, caused by mitochondrial damages characterized with cellular redistribution, morphological modifications and molecular profiling alterations. Taken together, our findings for the first time demonstrated the retinal dysfunction and ultrastructural defects in the retinas of tdTomato-transgenic mice, calling for a more careful design and interpretation of experiments involved in FPs.
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Affiliation(s)
- Chang-Jun Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Hao Mou
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Jing Yuan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Ya-Han Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Shu-Ning Sun
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Wen Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Ze-Hua Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Si-Jian Yu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China.
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China.
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2
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Day-Cooney J, Dalangin R, Zhong H, Mao T. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. J Neurochem 2023; 164:284-308. [PMID: 35285522 PMCID: PMC11322610 DOI: 10.1111/jnc.15608] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The brain relies on many forms of dynamic activities in individual neurons, from synaptic transmission to electrical activity and intracellular signaling events. Monitoring these neuronal activities with high spatiotemporal resolution in the context of animal behavior is a necessary step to achieve a mechanistic understanding of brain function. With the rapid development and dissemination of highly optimized genetically encoded fluorescent sensors, a growing number of brain activities can now be visualized in vivo. To date, cellular calcium imaging, which has been largely used as a proxy for electrical activity, has become a mainstay in systems neuroscience. While challenges remain, voltage imaging of neural populations is now possible. In addition, it is becoming increasingly practical to image over half a dozen neurotransmitters, as well as certain intracellular signaling and metabolic activities. These new capabilities enable neuroscientists to test previously unattainable hypotheses and questions. This review summarizes recent progress in the development and delivery of genetically encoded fluorescent sensors, and highlights example applications in the context of in vivo imaging.
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Affiliation(s)
- Julian Day-Cooney
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rochelin Dalangin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
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3
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Stellon D, Talbot J, Hewitt AW, King AE, Cook AL. Seeing Neurodegeneration in a New Light Using Genetically Encoded Fluorescent Biosensors and iPSCs. Int J Mol Sci 2023; 24:1766. [PMID: 36675282 PMCID: PMC9861453 DOI: 10.3390/ijms24021766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Neurodegenerative diseases present a progressive loss of neuronal structure and function, leading to cell death and irrecoverable brain atrophy. Most have disease-modifying therapies, in part because the mechanisms of neurodegeneration are yet to be defined, preventing the development of targeted therapies. To overcome this, there is a need for tools that enable a quantitative assessment of how cellular mechanisms and diverse environmental conditions contribute to disease. One such tool is genetically encodable fluorescent biosensors (GEFBs), engineered constructs encoding proteins with novel functions capable of sensing spatiotemporal changes in specific pathways, enzyme functions, or metabolite levels. GEFB technology therefore presents a plethora of unique sensing capabilities that, when coupled with induced pluripotent stem cells (iPSCs), present a powerful tool for exploring disease mechanisms and identifying novel therapeutics. In this review, we discuss different GEFBs relevant to neurodegenerative disease and how they can be used with iPSCs to illuminate unresolved questions about causes and risks for neurodegenerative disease.
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Affiliation(s)
- David Stellon
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
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4
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Wen Y, Xie D, Liu Z. Advances in protein analysis in single live cells: principle, instrumentation and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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5
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Kierzek M, Deal PE, Miller EW, Mukherjee S, Wachten D, Baumann A, Kaupp UB, Strünker T, Brenker C. Simultaneous recording of multiple cellular signaling events by frequency- and spectrally-tuned multiplexing of fluorescent probes. eLife 2021; 10:e63129. [PMID: 34859780 PMCID: PMC8700268 DOI: 10.7554/elife.63129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Fluorescent probes that change their spectral properties upon binding to small biomolecules, ions, or changes in the membrane potential (Vm) are invaluable tools to study cellular signaling pathways. Here, we introduce a novel technique for simultaneous recording of multiple probes at millisecond time resolution: frequency- and spectrally-tuned multiplexing (FASTM). Different from present multiplexing approaches, FASTM uses phase-sensitive signal detection, which renders various combinations of common probes for Vm and ions accessible for multiplexing. Using kinetic stopped-flow fluorimetry, we show that FASTM allows simultaneous recording of rapid changes in Ca2+, pH, Na+, and Vm with high sensitivity and minimal crosstalk. FASTM is also suited for multiplexing using single-cell microscopy and genetically encoded FRET biosensors. Moreover, FASTM is compatible with optochemical tools to study signaling using light. Finally, we show that the exceptional time resolution of FASTM also allows resolving rapid chemical reactions. Altogether, FASTM opens new opportunities for interrogating cellular signaling.
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Affiliation(s)
- Michelina Kierzek
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- CiM-IMPRS Graduate School, University of MünsterMünsterGermany
| | - Parker E Deal
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Evan W Miller
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular & Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States
| | - Shatanik Mukherjee
- Molecular Sensory Systems, Center of Advanced European Studies and ResearchBonnGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Department of Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Arnd Baumann
- Institute of Biological Information Processing (IBI-1), Research Center JülichJülichGermany
| | - U Benjamin Kaupp
- Life & Medical Sciences Institute (LIMES), University of BonnBonnGermany
| | - Timo Strünker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
- Cells in Motion Interfaculty Centre, University of MünsterMünsterGermany
| | - Christoph Brenker
- Centre of Reproductive Medicine and Andrology, University of MünsterMünsterGermany
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6
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Secilmis M, Altun HY, Pilic J, Erdogan YC, Cokluk Z, Ata BN, Sevimli G, Zaki AG, Yigit EN, Öztürk G, Malli R, Eroglu E. A Co-Culture-Based Multiparametric Imaging Technique to Dissect Local H 2O 2 Signals with Targeted HyPer7. BIOSENSORS 2021; 11:338. [PMID: 34562927 PMCID: PMC8466187 DOI: 10.3390/bios11090338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/19/2023]
Abstract
Multispectral live-cell imaging is an informative approach that permits detecting biological processes simultaneously in the spatial and temporal domain by exploiting spectrally distinct biosensors. However, the combination of fluorescent biosensors with distinct spectral properties such as different sensitivities, and dynamic ranges can undermine accurate co-imaging of the same analyte in different subcellular locales. We advanced a single-color multiparametric imaging method, which allows simultaneous detection of hydrogen peroxide (H2O2) in multiple cell locales (nucleus, cytosol, mitochondria) using the H2O2 biosensor HyPer7. Co-culturing of endothelial cells stably expressing differentially targeted HyPer7 biosensors paved the way for co-imaging compartmentalized H2O2 signals simultaneously in neighboring cells in a single experimental setup. We termed this approach COMPARE IT, which is an acronym for co-culture-based multiparametric imaging technique. Employing this approach, we detected lower H2O2 levels in mitochondria of endothelial cells compared to the cell nucleus and cytosol under basal conditions. Upon administering exogenous H2O2, the cytosolic and nuclear-targeted probes displayed similarly slow and moderate HyPer7 responses, whereas the mitochondria-targeted HyPer7 signal plateaued faster and reached higher amplitudes. Our results indicate striking differences in mitochondrial H2O2 accumulation of endothelial cells. Here, we present the method's potential as a practicable and informative multiparametric live-cell imaging technique.
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Affiliation(s)
- Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Hamza Yusuf Altun
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Johannes Pilic
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Yusuf Ceyhun Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Busra Nur Ata
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
| | - Esra Nur Yigit
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Department of Biotechnology, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Physiology Department, International School of Medicine, Istanbul Medipol University, 34810 Istanbul, Turkey
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956 Istanbul, Turkey; (M.S.); (H.Y.A.); (Y.C.E.); (Z.C.); (B.N.A.); (G.S.); (A.G.Z.)
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria;
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey; (E.N.Y.); (G.Ö.)
- Nanotechnology Research and Application Center, Sabanci University, 34956 Istanbul, Turkey
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7
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Simultaneous readout of multiple FRET pairs using photochromism. Nat Commun 2021; 12:2005. [PMID: 33790271 PMCID: PMC8012603 DOI: 10.1038/s41467-021-22043-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/17/2021] [Indexed: 01/11/2023] Open
Abstract
Förster resonant energy transfer (FRET) is a powerful mechanism to probe associations in situ. Simultaneously performing more than one FRET measurement can be challenging due to the spectral bandwidth required for the donor and acceptor fluorophores. We present an approach to distinguish overlapping FRET pairs based on the photochromism of the donor fluorophores, even if the involved fluorophores display essentially identical absorption and emission spectra. We develop the theory underlying this method and validate our approach using numerical simulations. To apply our system, we develop rsAKARev, a photochromic biosensor for cAMP-dependent protein kinase (PKA), and combine it with the spectrally-identical biosensor EKARev, a reporter for extracellular signal-regulated kinase (ERK) activity, to deliver simultaneous readout of both activities in the same cell. We further perform multiplexed PKA, ERK, and calcium measurements by including a third, spectrally-shifted biosensor. Our work demonstrates that exploiting donor photochromism in FRET can be a powerful approach to simultaneously read out multiple associations within living cells. Performing multiple FRET measurements at once can be challenging. Here the authors report a method to discriminate between overlapping FRET pairs, even if the fluorophores display almost identical absorption and emission spectra, based on the photochromism of the donor fluorophores.
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8
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Sensing Extracellular Calcium - An Insight into the Structure and Function of the Calcium-Sensing Receptor (CaSR). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:1031-1063. [PMID: 31646544 DOI: 10.1007/978-3-030-12457-1_41] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The calcium-sensing receptor (CaSR) is a G protein-coupled receptor that plays a key role in calcium homeostasis, by sensing free calcium levels in blood and regulating parathyroid hormone secretion in response. The CaSR is highly expressed in parathyroid gland and kidney where its role is well characterised, but also in other tissues where its function remains to be determined. The CaSR can be activated by a variety of endogenous ligands, as well as by synthetic modulators such as Cinacalcet, used in the clinic to treat secondary hyperparathyroidism in patients with chronic kidney disease. The CaSR couples to multiple G proteins, in a tissue-specific manner, activating several signalling pathways and thus regulating diverse intracellular events. The multifaceted nature of this receptor makes it a valuable therapeutic target for calciotropic and non-calciotropic diseases. It is therefore essential to understand the complexity behind the pharmacology, trafficking, and signalling characteristics of this receptor. This review provides an overview of the latest knowledge about the CaSR and discusses future hot topics in this field.
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9
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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10
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Patejdl R, Noack T. Calcium movement in smooth muscle and evaluation of graded functional intercellular coupling. CHAOS (WOODBURY, N.Y.) 2018; 28:106311. [PMID: 30384639 DOI: 10.1063/1.5035168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
Spontaneous activity of vascular smooth muscle is present in small arteries and some venous tissues like the hepatic portal vein. Whereas the ability to generate rhythmic membrane potential changes is expressed in a high number of primary oscillators, the generation of physiological tone and phasic activity requires synchronization of specialized pacemaker activity (Interstitial Cajal-like cells) by intercellular propagation and regeneration of excitation or a strong coupling mechanism of smooth muscle cells. The aim of this study was to deduce oscillator coupling by analyzing the spatiotemporal homogeneity of calcium oscillations within a native tissue preparation. Portal vein tissue was loaded with a calcium-sensitive dye (Fluo-3). By combining confocal microscopy and computation of spatial auto- and cross-correlation of the calcium signals, temporal and spatial coupling between cells was characterized. Spontaneous oscillations of calcium signals were measured at different predefined regions of interest. Cross-correlation analysis of these signals revealed that their damping was very similar in all directions of the investigated z-plane. In single experiments, improved cell-to-cell coupling was seen when noradrenaline (1-10 μM) was added to the bath-solution. With the chosen parameters of frame refresh, the velocity of signal propagation was faster than the maximum detectable velocity, but it could be estimated to exceed 0.1 mm/s. Correlative Network Analysis is a new and very useful tool to determine the functional coupling parameters of quasi-homogenous biological networks and their temporal changes. The action and significance of pharmacological modulators can be well studied on cellular and functional aspects with this newly introduced technique in biological sciences.
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Affiliation(s)
- R Patejdl
- Department of Physiology, University of Rostock, Universitätsmedizin, Oscar-Langendorff Institut für Physiologie, Gertrudenstr. 9, D-18057 Rostock, Germany
| | - T Noack
- Department of Physiology, University of Rostock, Universitätsmedizin, Oscar-Langendorff Institut für Physiologie, Gertrudenstr. 9, D-18057 Rostock, Germany
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11
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Mehta S, Zhang Y, Roth RH, Zhang JF, Mo A, Tenner B, Huganir RL, Zhang J. Single-fluorophore biosensors for sensitive and multiplexed detection of signalling activities. Nat Cell Biol 2018; 20:1215-1225. [PMID: 30250062 PMCID: PMC6258557 DOI: 10.1038/s41556-018-0200-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/20/2018] [Indexed: 01/07/2023]
Abstract
Unraveling the dynamic molecular interplay behind complex physiological processes such as neuronal plasticity requires the ability to both detect minute changes in biochemical states in response to physiological signals and track multiple signaling activities simultaneously. Fluorescent protein-based biosensors have enabled the real-time monitoring of dynamic signaling processes within the native context of living cells, yet most commonly used biosensors exhibit poor sensitivity (e.g., dynamic range) and are limited to imaging signaling activities in isolation. Here, we address this challenge by developing a suite of excitation ratiometric kinase activity biosensors that offer the highest reported dynamic range and enable the detection of subtle changes in signaling activity that could not be reliably detected previously, as well as a suite of single-fluorophore biosensors that enable the simultaneous tracking of as many as six distinct signaling activities in single living cells.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
| | - Yong Zhang
- Department of Neurobiology, School of Basic Medical Sciences and Neuroscience Research Institute; Key Lab for Neuroscience, Ministry of Education of China and National Health Commission of the P.R. China; IDG/McGovern Institute for Brain Research at PKU, Peking University, Beijing, China
| | - Richard H Roth
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Albert Mo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard L Huganir
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,The Kavli Neuroscience Discovery Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA. .,Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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High-Resolution Imaging of STIM/Orai Subcellular Localization Using Array Confocal Laser Scanning Microscopy. Methods Mol Biol 2018. [PMID: 30203287 DOI: 10.1007/978-1-4939-8704-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The expression of chimeras that consist of a fluorescent protein (FP) conjugated with a protein of interest provides the ability to visualize, track, and quantify the subcellular localization and dynamics of specific proteins in biological samples. Array confocal laser scanning microscopy is an eminently suitable technique for live-cell imaging of FP-tagged fusion proteins. Here, we describe real-time monitoring of the subcellular dynamics of the stromal-interacting molecule 1 (STIM1) and Orai1, the key protagonists of store-operated Ca2+ entry (SOCE) under resting conditions, and upon Ca2+ mobilization from the endoplasmic reticulum (ER).
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13
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Ross BL, Tenner B, Markwardt ML, Zviman A, Shi G, Kerr JP, Snell NE, McFarland JJ, Mauban JR, Ward CW, Rizzo MA, Zhang J. Single-color, ratiometric biosensors for detecting signaling activities in live cells. eLife 2018; 7:e35458. [PMID: 29968564 PMCID: PMC6037473 DOI: 10.7554/elife.35458] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 11/22/2022] Open
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of signal transduction by enabling the real-time tracking of signaling activities in live cells. Investigating the interaction between signaling networks has become increasingly important to understanding complex cellular phenomena, necessitating an update of the biosensor toolkit to allow monitoring and perturbing multiple activities simultaneously in the same cell. We therefore developed a new class of fluorescent biosensors based on homo-FRET, deemed FLuorescence Anisotropy REporters (FLAREs), which combine the multiplexing ability of single-color sensors with a quantitative, ratiometric readout. Using an array of color variants, we were able to demonstrate multiplexed imaging of three activity reporters simultaneously in the same cell. We further demonstrate the compatibility of FLAREs for use with optogenetic tools as well as intravital two-photon imaging.
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Affiliation(s)
- Brian L Ross
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreUnited States
| | - Brian Tenner
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Michele L Markwardt
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Adam Zviman
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Guoli Shi
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jaclyn P Kerr
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Nicole E Snell
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | | | - Joseph R Mauban
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Christopher W Ward
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Megan A Rizzo
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jin Zhang
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of Pharmacology and Molecular SciencesJohns Hopkins University School of MedicineBaltimoreUnited States
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14
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Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring. Proc Natl Acad Sci U S A 2017; 114:E1866-E1874. [PMID: 28223521 DOI: 10.1073/pnas.1615375114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Here, we report a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 d through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with >95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual contents within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activity such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to understand dynamic cell behavior, including processes such as induced pluripotency and differentiation.
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15
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A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo. Nat Biotechnol 2016; 34:760-7. [PMID: 27240196 PMCID: PMC4942401 DOI: 10.1038/nbt.3550] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/22/2016] [Indexed: 02/02/2023]
Abstract
Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.
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16
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Marinović M, Šoštar M, Filić V, Antolović V, Weber I. Quantitative imaging of Rac1 activity in Dictyostelium cells with a fluorescently labelled GTPase-binding domain from DPAKa kinase. Histochem Cell Biol 2016; 146:267-79. [DOI: 10.1007/s00418-016-1440-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2016] [Indexed: 02/06/2023]
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17
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Doucette J, Zhao Z, Geyer RJ, Barra MM, Balunas MJ, Zweifach A. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening. ACTA ACUST UNITED AC 2016; 21:535-47. [DOI: 10.1177/1087057116634007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/31/2016] [Indexed: 11/16/2022]
Abstract
Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)–activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.
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Affiliation(s)
- Jaimee Doucette
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Ziyan Zhao
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Rory J. Geyer
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Melanie M. Barra
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut at Storrs, Storrs, CT
| | - Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT
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18
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Venkatachalam V, Cohen AE. Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J 2015; 107:1554-63. [PMID: 25296307 DOI: 10.1016/j.bpj.2014.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/02/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
To study the impact of neural activity on cellular physiology, one would like to combine precise control of firing patterns with highly sensitive probes of cellular physiology. Light-gated ion channels, e.g., Channelrhodopsin-2, enable precise control of firing patterns; green fluorescent protein-based reporters, e.g., the GCaMP6f Ca(2+) reporter, enable highly sensitive probing of cellular physiology. However, for most actuator-reporter combinations, spectral overlap prevents straightforward combination within a single cell. Here we explore multiwavelength control of channelrhodopsins to circumvent this limitation. The "stoplight" technique described in this article uses channelrhodopsin variants that are opened by blue light and closed by orange light. Cells are illuminated with constant blue light to excite fluorescence of a green fluorescent protein-based reporter. Modulated illumination with orange light negatively regulates activation of the channelrhodopsin. We performed detailed photophysical characterization and kinetic modeling of four candidate stoplight channelrhodopsins. The variant with the highest contrast, sdChR(C138S,E154A), enabled all-optical measurements of activity-induced calcium transients in cultured rat hippocampal neurons, although cell-to-cell variation in expression levels presents a challenge for quantification.
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Affiliation(s)
- Veena Venkatachalam
- Biophysics Program, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland.
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19
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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20
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Tamura T, Hamachi I. Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 2014; 9:2708-17. [PMID: 25317665 DOI: 10.1021/cb500661v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based fluorescent biosensors have emerged as key bioanalytical tools to visualize and quantify a wide range of biological substances and events in vitro, in cells, and even in vivo. On the basis of the construction method, the protein-based fluorescent biosensors can be principally classified into two classes: (1) genetically encoded fluorescent biosensors harnessing fluorescent proteins (FPs) and (2) semisynthetic biosensors comprised of protein scaffolds and synthetic fluorophores. Recent advances in protein engineering and chemical biology not only allowed the further optimization of conventional biosensors but also facilitated the creation of novel biosensors based on unique strategies. In this review, we survey the recent studies in the development and improvement of protein-based fluorescent biosensors and highlight the successful applications to live cell and in vivo imaging. Furthermore, we provide perspectives on possible future directions of the technique.
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Affiliation(s)
- Tomonori Tamura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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21
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Hou JH, Kralj JM, Douglass AD, Engert F, Cohen AE. Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents. Front Physiol 2014; 5:344. [PMID: 25309445 PMCID: PMC4161048 DOI: 10.3389/fphys.2014.00344] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/22/2014] [Indexed: 01/31/2023] Open
Abstract
The cardiac action potential (AP) and the consequent cytosolic Ca2+ transient are key indicators of cardiac function. Natural developmental processes, as well as many drugs and pathologies change the waveform, propagation, or variability (between cells or over time) of these parameters. Here we apply a genetically encoded dual-function calcium and voltage reporter (CaViar) to study the development of the zebrafish heart in vivo between 1.5 and 4 days post fertilization (dpf). We developed a high-sensitivity spinning disk confocal microscope and associated software for simultaneous three-dimensional optical mapping of voltage and calcium. We produced a transgenic zebrafish line expressing CaViar under control of the heart-specific cmlc2 promoter, and applied ion channel blockers at a series of developmental stages to map the maturation of the action potential in vivo. Early in development, the AP initiated via a calcium current through L-type calcium channels. Between 90 and 102 h post fertilization (hpf), the ventricular AP switched to a sodium-driven upswing, while the atrial AP remained calcium driven. In the adult zebrafish heart, a sodium current drives the AP in both the atrium and ventricle. Simultaneous voltage and calcium imaging with genetically encoded reporters provides a new approach for monitoring cardiac development, and the effects of drugs on cardiac function.
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Affiliation(s)
- Jennifer H Hou
- Department of Physics, Harvard University Cambridge, MA, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University Cambridge, MA, USA
| | - Adam D Douglass
- Department of Molecular and Cellular Biology, Harvard University Cambridge, MA, USA
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University Cambridge, MA, USA
| | - Adam E Cohen
- Department of Physics, Harvard University Cambridge, MA, USA ; Department of Chemistry and Chemical Biology, Harvard University Cambridge, MA, USA ; Howard Hughes Medical Institute Chevy Chase, MD, USA
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22
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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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23
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Jara JH, Genç B, Klessner JL, Ozdinler PH. Retrograde labeling, transduction, and genetic targeting allow cellular analysis of corticospinal motor neurons: implications in health and disease. Front Neuroanat 2014; 8:16. [PMID: 24723858 PMCID: PMC3972458 DOI: 10.3389/fnana.2014.00016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/10/2014] [Indexed: 12/11/2022] Open
Abstract
Corticospinal motor neurons (CSMN) have a unique ability to receive, integrate, translate, and transmit the cerebral cortex's input toward spinal cord targets and therefore act as a “spokesperson” for the initiation and modulation of voluntary movements that require cortical input. CSMN degeneration has an immense impact on motor neuron circuitry and is one of the underlying causes of numerous neurodegenerative diseases, such as primary lateral sclerosis (PLS), hereditary spastic paraplegia (HSP), and amyotrophic lateral sclerosis (ALS). In addition, CSMN death results in long-term paralysis in spinal cord injury patients. Detailed cellular analyses are crucial to gain a better understanding of the pathologies underlying CSMN degeneration. However, visualizing and identifying these vulnerable neuron populations in the complex and heterogeneous environment of the cerebral cortex have proved challenging. Here, we will review recent developments and current applications of novel strategies that reveal the cellular and molecular basis of CSMN health and vulnerability. Such studies hold promise for building long-term effective treatment solutions in the near future.
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Affiliation(s)
- Javier H Jara
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
| | - Barış Genç
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
| | - Jodi L Klessner
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
| | - P Hande Ozdinler
- Davee Department of Neurology and Clinical Neurological Sciences, Feinberg School of Medicine, Northwestern University Chicago, IL, USA ; Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University Chicago, IL, USA ; Cognitive Neurology and Alzheimer's Disease Center, Feinberg School of Medicine, Northwestern University Chicago IL, USA
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24
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Roukos DH. Cancer heterogeneity and signaling network-based drug target. Pharmacogenomics 2014; 14:1243-6. [PMID: 23930670 DOI: 10.2217/pgs.13.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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25
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Roukos DH. Genome network medicine: innovation to overcome huge challenges in cancer therapy. WIRES SYSTEMS BIOLOGY AND MEDICINE 2014; 6:201-208. [DOI: 10.1002/wsbm.1254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Dimitrios H. Roukos
- Centre for Biosystems & Genomic Network Medicine Ioannina University Ioannina Greece
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26
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Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
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27
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Hertel F, Zhang J. Monitoring of post-translational modification dynamics with genetically encoded fluorescent reporters. Biopolymers 2014; 101:180-7. [PMID: 23576192 PMCID: PMC3883948 DOI: 10.1002/bip.22254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/01/2013] [Indexed: 11/06/2022]
Abstract
Post-translational modifications (PTMs) of proteins are essential mechanisms for virtually all dynamic processes within cellular signaling networks. Genetically encoded reporters based on fluorescent proteins (FPs) are powerful tools for spatiotemporal visualization of cellular parameters. Consequently, commonly used modular biosensor designs have been adapted to generate several protein-based indicators for monitoring various PTMs or the activity of corresponding enzymes in living cells, providing new biological insights into dynamics and regulatory functions of individual PTMs. In this review, we describe the application of general design strategies focusing on PTMs and discuss important considerations for engineering feasible indicators depending on the purpose. Moreover, we present developments and enhancements of PTM biosensors from selected studies and give an outlook on future perspectives of this versatile approach.
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Affiliation(s)
- Fabian Hertel
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
| | - Jin Zhang
- The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, Baltimore, MD 21205, USA
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28
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Oldach L, Zhang J. Genetically encoded fluorescent biosensors for live-cell visualization of protein phosphorylation. ACTA ACUST UNITED AC 2014; 21:186-97. [PMID: 24485761 DOI: 10.1016/j.chembiol.2013.12.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Abstract
Fluorescence-based, genetically encodable biosensors are widely used tools for real-time analysis of biological processes. Over the last few decades, the number of available genetically encodable biosensors and the types of processes they can monitor have increased rapidly. Here, we aim to introduce the reader to general principles and practices in biosensor development and highlight ways in which biosensors can be used to illuminate outstanding questions of biological function. Specifically, we focus on sensors developed for monitoring kinase activity and use them to illustrate some common considerations for biosensor design. We describe several uses to which kinase and second-messenger biosensors have been put, and conclude with considerations for the use of biosensors once they are developed. Overall, as fluorescence-based biosensors continue to diversify and improve, we expect them to continue to be widely used as reliable and fruitful tools for gaining deeper insights into cellular and organismal function.
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Affiliation(s)
- Laurel Oldach
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Department of Oncology, The Johns Hopkins University School of Medicine, 307 Hunterian Building, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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29
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Tewson PH, Quinn AM, Hughes TE. A multiplexed fluorescent assay for independent second-messenger systems: decoding GPCR activation in living cells. JOURNAL OF BIOMOLECULAR SCREENING 2013; 18:797-806. [PMID: 23580666 PMCID: PMC4242713 DOI: 10.1177/1087057113485427] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is a growing need in drug discovery and basic research to measure multiple second-messenger components of cell signaling pathways in real time and in relevant tissues and cell types. Many G-protein-coupled receptors activate the heterotrimeric protein, Gq, which in turn activates phospholipase C (PLC). PLC cleaves phosphatidylinositol 4,5-bisphosphate (PIP2) to produce two second messengers: diacylglycerol (DAG), which remains in the plasma membrane, and inositol triphosphate (IP3), which diffuses through the cytosol to release stores of intracellular calcium ions (Ca(2+)). Our goal was to create a series of multiplex sensors that would make it possible to simultaneously measure two different components of the Gq pathway in living cells. Here we describe new fluorescent sensors for DAG and PIP2 that produce robust changes in green or red fluorescence and can be combined with one another, or with existing Ca(2+) sensors, in a live-cell assay. These assays can detect multiple components of Gq signaling, simultaneously in real time, on standard fluorescent plate readers or live-cell imaging systems.
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30
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Zhang C, Wei ZH, Ye BC. Quantitative monitoring of 2-oxoglutarate in Escherichia coli cells by a fluorescence resonance energy transfer-based biosensor. Appl Microbiol Biotechnol 2013; 97:8307-16. [PMID: 23893310 DOI: 10.1007/s00253-013-5121-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/07/2013] [Accepted: 07/10/2013] [Indexed: 11/25/2022]
Abstract
2-Oxoglutarate (2OG) is a metabolite from the highly conserved Krebs cycle and not only plays a critical role in metabolism but also acts as a signaling molecule in a variety of organisms. Environmental inorganic nitrogen is reduced to ammonium by microorganisms, whose metabolic pathways involve the conversion of 2OG to glutamate and glutamine. Tracking of 2OG in real time would be useful for studies on cell metabolism and signal transduction. Here, we developed a genetically encoded 2OG biosensor based on fluorescent resonance energy transfer by inserting the functional 2OG-binding domain GAF of the NifA protein between the fluorescence resonance energy transfer (FRET) pair YFP/CFP. The dynamic range of the sensors is 100 μM to 10 mM, which appeared identical to the physiological range observed in E. coli. We optimized the peptide lengths of the binding domain to obtain a sensor with a maximal ratio change of 0.95 upon 2OG binding and demonstrated the feasibility of this sensor for the visualization of metabolites both in vitro and in vivo.
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Affiliation(s)
- Chang Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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31
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Batti L, Mukhtarov M, Audero E, Ivanov A, Paolicelli RC, Zurborg S, Gross C, Bregestovski P, Heppenstall PA. Transgenic mouse lines for non-invasive ratiometric monitoring of intracellular chloride. Front Mol Neurosci 2013; 6:11. [PMID: 23734096 PMCID: PMC3659292 DOI: 10.3389/fnmol.2013.00011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/26/2013] [Indexed: 11/13/2022] Open
Abstract
Chloride is the most abundant physiological anion and participates in a variety of cellular processes including trans-epithelial transport, cell volume regulation, and regulation of electrical excitability. The development of tools to monitor intracellular chloride concentration ([Cli]) is therefore important for the evaluation of cellular function in normal and pathological conditions. Recently, several Cl-sensitive genetically encoded probes have been described which allow for non-invasive monitoring of [Cli]. Here we describe two mouse lines expressing a CFP-YFP-based Cl probe called Cl-Sensor. First, we generated transgenic mice expressing Cl-Sensor under the control of the mouse Thy1 mini promoter. Cl-Sensor exhibited good expression from postnatal day two (P2) in neurons of the hippocampus and cortex, and its level increased strongly during development. Using simultaneous whole-cell monitoring of ionic currents and Cl-dependent fluorescence, we determined that the apparent EC 50 for Cli was 46 mM, indicating that this line is appropriate for measuring neuronal [Cli] in postnatal mice. We also describe a transgenic mouse reporter line for Cre-dependent conditional expression of Cl-Sensor, which was targeted to the Rosa26 locus and by incorporating a strong exogenous promoter induced robust expression upon Cre-mediated recombination. We demonstrate high levels of tissue-specific expression in two different Cre-driver lines targeting cells of the myeloid lineage and peripheral sensory neurons. Using these mice the apparent EC 50 for Cli was estimated to be 61 and 54 mM in macrophages and DRG, respectively. Our data suggest that these mouse lines will be useful models for ratiometric monitoring of Cli in specific cell types in vivo.
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Affiliation(s)
- Laura Batti
- Mouse Biology Unit, European Molecular Biology Laboratory Monterotondo, Italy
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