51
|
Abstract
Convergent advances in optical imaging and genetic engineering have fueled the development of new technologies for biological visualization. Those technologies include genetically encoded indicators based on fluorescent proteins (FPs) for imaging ions, molecules, and enzymatic activities "to spy on cells," as phrased by Roger Tsien, by sneaking into specific tissues, cell types, or subcellular compartments, and reporting on specific intracellular activities. Here we review the current range of unimolecular indicators whose working principle is the conversion of a protein conformational change into a fluorescence signal. Many of the indicators have been developed from fluorescence resonance energy transfer- and single-FP-based approaches.
Collapse
|
52
|
Ding S, Cargill AA, Das SR, Medintz IL, Claussen JC. Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes. SENSORS 2015; 15:14766-87. [PMID: 26110411 PMCID: PMC4507682 DOI: 10.3390/s150614766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 01/10/2023]
Abstract
Nanocarbon allotropes (NCAs), including zero-dimensional carbon dots (CDs), one-dimensional carbon nanotubes (CNTs) and two-dimensional graphene, exhibit exceptional material properties, such as unique electrical/thermal conductivity, biocompatibility and high quenching efficiency, that make them well suited for both electrical/electrochemical and optical sensors/biosensors alike. In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer (FRET). This review analyzes current advances in sensors and biosensors that utilize graphene, CNTs or CDs as the platform in optical sensors and biosensors. Widely utilized synthesis/fabrication techniques, intrinsic material properties and current research examples of such nanocarbon, FRET-based sensors/biosensors are illustrated. The future outlook and challenges for the research field are also detailed.
Collapse
Affiliation(s)
- Shaowei Ding
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Allison A Cargill
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Suprem R Das
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA.
| | - Jonathan C Claussen
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| |
Collapse
|
53
|
Chou KF, Dennis AM. Förster Resonance Energy Transfer between Quantum Dot Donors and Quantum Dot Acceptors. SENSORS 2015; 15:13288-325. [PMID: 26057041 PMCID: PMC4507609 DOI: 10.3390/s150613288] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023]
Abstract
Förster (or fluorescence) resonance energy transfer amongst semiconductor quantum dots (QDs) is reviewed, with particular interest in biosensing applications. The unique optical properties of QDs provide certain advantages and also specific challenges with regards to sensor design, compared to other FRET systems. The brightness and photostability of QDs make them attractive for highly sensitive sensing and long-term, repetitive imaging applications, respectively, but the overlapping donor and acceptor excitation signals that arise when QDs serve as both the donor and acceptor lead to high background signals from direct excitation of the acceptor. The fundamentals of FRET within a nominally homogeneous QD population as well as energy transfer between two distinct colors of QDs are discussed. Examples of successful sensors are highlighted, as is cascading FRET, which can be used for solar harvesting.
Collapse
Affiliation(s)
- Kenny F Chou
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Allison M Dennis
- Department of Biomedical Engineering and Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.
| |
Collapse
|
54
|
Hirai Y, Nishino E, Ohmori H. Simultaneous recording of fluorescence and electrical signals by photometric patch electrode in deep brain regions in vivo. J Neurophysiol 2015; 113:3930-42. [PMID: 25761950 DOI: 10.1152/jn.00005.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/10/2015] [Indexed: 11/22/2022] Open
Abstract
Despite its widespread use, high-resolution imaging with multiphoton microscopy to record neuronal signals in vivo is limited to the surface of brain tissue because of limited light penetration. Moreover, most imaging studies do not simultaneously record electrical neural activity, which is, however, crucial to understanding brain function. Accordingly, we developed a photometric patch electrode (PME) to overcome the depth limitation of optical measurements and also enable the simultaneous recording of neural electrical responses in deep brain regions. The PME recoding system uses a patch electrode to excite a fluorescent dye and to measure the fluorescence signal as a light guide, to record electrical signal, and to apply chemicals to the recorded cells locally. The optical signal was analyzed by either a spectrometer of high light sensitivity or a photomultiplier tube depending on the kinetics of the responses. We used the PME in Oregon Green BAPTA-1 AM-loaded avian auditory nuclei in vivo to monitor calcium signals and electrical responses. We demonstrated distinct response patterns in three different nuclei of the ascending auditory pathway. On acoustic stimulation, a robust calcium fluorescence response occurred in auditory cortex (field L) neurons that outlasted the electrical response. In the auditory midbrain (inferior colliculus), both responses were transient. In the brain-stem cochlear nucleus magnocellularis, calcium response seemed to be effectively suppressed by the activity of metabotropic glutamate receptors. In conclusion, the PME provides a powerful tool to study brain function in vivo at a tissue depth inaccessible to conventional imaging devices.
Collapse
Affiliation(s)
- Yasuharu Hirai
- Department of Neurobiology and Physiology, Faculty of Medicine, Kyoto University, Kyoto, Kyoto, Japan; and Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Kyoto, Japan
| | - Eri Nishino
- Department of Neurobiology and Physiology, Faculty of Medicine, Kyoto University, Kyoto, Kyoto, Japan; and
| | - Harunori Ohmori
- Department of Neurobiology and Physiology, Faculty of Medicine, Kyoto University, Kyoto, Kyoto, Japan; and
| |
Collapse
|
55
|
Tanimura A. Development and application of fluorescent protein-based indicators for live cell imaging. J Oral Biosci 2015. [DOI: 10.1016/j.job.2015.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
56
|
Kitamura A, Nagata K, Kinjo M. Conformational analysis of misfolded protein aggregation by FRET and live-cell imaging techniques. Int J Mol Sci 2015; 16:6076-92. [PMID: 25785563 PMCID: PMC4394520 DOI: 10.3390/ijms16036076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/11/2015] [Indexed: 12/18/2022] Open
Abstract
Cellular homeostasis is maintained by several types of protein machinery, including molecular chaperones and proteolysis systems. Dysregulation of the proteome disrupts homeostasis in cells, tissues, and the organism as a whole, and has been hypothesized to cause neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). A hallmark of neurodegenerative disorders is formation of ubiquitin-positive inclusion bodies in neurons, suggesting that the aggregation process of misfolded proteins changes during disease progression. Hence, high-throughput determination of soluble oligomers during the aggregation process, as well as the conformation of sequestered proteins in inclusion bodies, is essential for elucidation of physiological regulation mechanism and drug discovery in this field. To elucidate the interaction, accumulation, and conformation of aggregation-prone proteins, in situ spectroscopic imaging techniques, such as Förster/fluorescence resonance energy transfer (FRET), fluorescence correlation spectroscopy (FCS), and bimolecular fluorescence complementation (BiFC) have been employed. Here, we summarize recent reports in which these techniques were applied to the analysis of aggregation-prone proteins (in particular their dimerization, interactions, and conformational changes), and describe several fluorescent indicators used for real-time observation of physiological states related to proteostasis.
Collapse
Affiliation(s)
- Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
| |
Collapse
|
57
|
Abstract
Astrocytes seem to rely on relatively sluggish and spatially blurred Ca(2+) waves to communicate with fast and point-precise neural circuits. This apparent discrepancy could, however, reflect our current inability to understand the microscopic mechanisms involved. Difficulties in detecting and interpreting astrocyte Ca(2+) signals may have led to some prominent controversies in the field. Here, we argue that a deeper understanding of astrocyte physiology requires a qualitative leap in our experimental and analytical strategies.
Collapse
Affiliation(s)
- Dmitri A Rusakov
- UCL Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| |
Collapse
|
58
|
Abstract
The growing use of fluorescent biosensors to directly probe the spatiotemporal dynamics of biochemical processes in living cells has revolutionized the study of intracellular signaling. In this review, we summarize recent developments in the use of biosensors to illuminate the molecular details of G-protein-coupled receptor (GPCR) signaling pathways, which have long served as the model for our understanding of signal transduction, while also offering our perspectives on the future of this exciting field. Specifically, we highlight several ways in which biosensor-based single-cell analyses are being used to unravel many of the enduring mysteries that surround these diverse signaling pathways.
Collapse
Affiliation(s)
- Terri Clister
- From the Department of Pharmacology and Molecular Sciences and
| | - Sohum Mehta
- From the Department of Pharmacology and Molecular Sciences and
| | - Jin Zhang
- From the Department of Pharmacology and Molecular Sciences and The Solomon H. Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| |
Collapse
|
59
|
Weber-Boyvat M, Li S, Skarp KP, Olkkonen VM, Yan D, Jäntti J. Bimolecular fluorescence complementation (BiFC) technique in yeast Saccharomyces cerevisiae and mammalian cells. Methods Mol Biol 2015; 1270:277-288. [PMID: 25702124 DOI: 10.1007/978-1-4939-2309-0_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Visualization of protein-protein interactions in vivo offers a powerful tool to resolve spatial and temporal aspects of cellular functions. The bimolecular fluorescence complementation (BiFC) makes use of nonfluorescent fragments of green fluorescent protein or its variants that are added as "tags" to target proteins under study. Only upon target protein interaction is a fluorescent protein complex assembled, and the site of interaction can be monitored by microscopy. In this chapter, we describe the method and tools for the use of BiFC in the yeast Saccharomyces cerevisiae and in mammalian cells.
Collapse
Affiliation(s)
- Marion Weber-Boyvat
- Research Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
60
|
Tomida T. Visualization of the spatial and temporal dynamics of MAPK signaling using fluorescence imaging techniques. J Physiol Sci 2015; 65:37-49. [PMID: 25145828 PMCID: PMC10716987 DOI: 10.1007/s12576-014-0332-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Conserved mitogen-activated protein kinase (MAPK) signaling pathways are major mechanisms through which cells perceive and respond properly to their surrounding environment. Such homeostatic responses maintain the life of the organism. Since errors in MAPK signaling pathways can lead to cancers and to defects in immune responses, in the nervous system and metabolism, these pathways have been extensively studied as potential therapeutic targets. Although much has been studied about the roles of MAPKs in various cellular functions, less is known regarding regulation of MAPK in living organisms. This review will focus on the latest understanding of the dynamic regulation of MAPK signaling in intact cells that was revealed by using novel fluorescence imaging techniques and advanced systems-analytical methods. These techniques allowed quantitative analyses of signal transduction in situ with high spatio-temporal resolution and have revealed the nature of the molecular dynamics that determine cellular responses and fates.
Collapse
Affiliation(s)
- Taichiro Tomida
- Division of Molecular Cell Signaling, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan,
| |
Collapse
|
61
|
Tu CC, Chou YN, Hung HC, Wu J, Jiang S, Lin LY. Fluorescent porous silicon biological probes with high quantum efficiency and stability. OPTICS EXPRESS 2014; 22:29996-30003. [PMID: 25606929 DOI: 10.1364/oe.22.029996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We demonstrate porous silicon biological probes as a stable and non-toxic alternative to organic dyes or cadmium-containing quantum dots for imaging and sensing applications. The fluorescent silicon quantum dots which are embedded on the porous silicon surface are passivated with carboxyl-terminated ligands through stable Si-C covalent bonds. The porous silicon bio-probes have shown photoluminescence quantum yield around 50% under near-UV excitation, with high photochemical and thermal stability. The bio-probes can be efficiently conjugated with antibodies, which is confirmed by a standard enzyme-linked immunosorbent assay (ELISA) method.
Collapse
|
62
|
Ma L, Yang F, Zheng J. Application of fluorescence resonance energy transfer in protein studies. J Mol Struct 2014; 1077:87-100. [PMID: 25368432 DOI: 10.1016/j.molstruc.2013.12.071] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications.
Collapse
Affiliation(s)
- Linlin Ma
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Fan Yang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
| |
Collapse
|
63
|
Tartakoff AM, Wu D. The axis of progression of disease. Cancer Inform 2014; 13:7-13. [PMID: 25374458 PMCID: PMC4213200 DOI: 10.4137/cin.s17683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/05/2022] Open
Abstract
Starting with genetic or environmental perturbations, disease progression can involve a linear sequence of changes within individual cells. More often, however, a labyrinth of branching consequences emanates from the initial events. How can one repair an entity so fine and so complex that its organization and functions are only partially known? How, given the many redundancies of metabolic pathways, can interventions be effective before the last redundant element has been irreversibly damaged? Since progression ultimately proceeds beyond a point of no return, therapeutic goals must target earlier events. A key goal is therefore to identify early changes of functional importance. Moreover, when several distinct genetic or environmental causes converge on a terminal phenotype, therapeutic strategies that focus on the shared features seem unlikely to be useful - precisely because the shared events lie relatively downstream along the axis of progression. We therefore describe experimental strategies that could lead to identification of early events, both for cancer and for other diseases.
Collapse
Affiliation(s)
- Alan M Tartakoff
- Pathology Department and Cell Biology Program, Case Western Reserve University, Cleveland, OH, USA
| | - Di Wu
- Statistics Department, Harvard University, Cambridge, MA, USA
| |
Collapse
|
64
|
Devauges V, Matthews DR, Aluko J, Nedbal J, Levitt JA, Poland SP, Coban O, Weitsman G, Monypenny J, Ng T, Ameer-Beg SM. Steady-state acceptor fluorescence anisotropy imaging under evanescent excitation for visualisation of FRET at the plasma membrane. PLoS One 2014; 9:e110695. [PMID: 25360776 PMCID: PMC4215982 DOI: 10.1371/journal.pone.0110695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/15/2014] [Indexed: 11/22/2022] Open
Abstract
We present a novel imaging system combining total internal reflection fluorescence (TIRF) microscopy with measurement of steady-state acceptor fluorescence anisotropy in order to perform live cell Förster Resonance Energy Transfer (FRET) imaging at the plasma membrane. We compare directly the imaging performance of fluorescence anisotropy resolved TIRF with epifluorescence illumination. The use of high numerical aperture objective for TIRF required correction for induced depolarization factors. This arrangement enabled visualisation of conformational changes of a Raichu-Cdc42 FRET biosensor by measurement of intramolecular FRET between eGFP and mRFP1. Higher activity of the probe was found at the cell plasma membrane compared to intracellularly. Imaging fluorescence anisotropy in TIRF allowed clear differentiation of the Raichu-Cdc42 biosensor from negative control mutants. Finally, inhibition of Cdc42 was imaged dynamically in live cells, where we show temporal changes of the activity of the Raichu-Cdc42 biosensor.
Collapse
Affiliation(s)
- Viviane Devauges
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Daniel R. Matthews
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Justin Aluko
- Department of Physics, King's College London, London, United Kingdom
| | - Jakub Nedbal
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James A. Levitt
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Simon P. Poland
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Oana Coban
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Gregory Weitsman
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James Monypenny
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Tony Ng
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Simon M. Ameer-Beg
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| |
Collapse
|
65
|
Abstract
The Ras superfamily of small GTPases is composed of more than 150 members, which share a conserved structure and biochemical properties, acting as binary molecular switches turned on by binding GTP and off by hydrolyzing GTP to GDP. However, despite considerable structural and biochemical similarities, these proteins play multiple and divergent roles, being versatile and key regulators of virtually all fundamental cellular processes. Conversely, their dysfunction plays a crucial role in the pathogenesis of serious human diseases, including cancer and developmental syndromes. Fuelled by the original identification in 1982 of mutationally activated and transforming human Ras genes in human cancer cell lines, a variety of powerful experimental techniques have been intensively focused on discovering and studying structure, biochemistry, and biology of Ras and Ras-related small GTPases, leading to fundamental research breakthroughs into identification and structural and functional characterization of a huge number of Ras superfamily members, as well as of their multiple regulators and effectors. In this review we provide a general overview of the major milestones that eventually allowed to unlock the secret treasure chest of this large and important superfamily of proteins.
Collapse
|
66
|
Blackstock D, Chen W. Halo-tag mediated self-labeling of fluorescent proteins to molecular beacons for nucleic acid detection. Chem Commun (Camb) 2014; 50:13735-8. [DOI: 10.1039/c4cc07118b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
67
|
Sinha C, Arora K, Moon CS, Yarlagadda S, Woodrooffe K, Naren AP. Förster resonance energy transfer - an approach to visualize the spatiotemporal regulation of macromolecular complex formation and compartmentalized cell signaling. Biochim Biophys Acta Gen Subj 2014; 1840:3067-72. [PMID: 25086255 DOI: 10.1016/j.bbagen.2014.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND Signaling messengers and effector proteins provide an orchestrated molecular machinery to relay extracellular signals to the inside of cells and thereby facilitate distinct cellular behaviors. Formations of intracellular macromolecular complexes and segregation of signaling cascades dynamically regulate the flow of a biological process. SCOPE OF REVIEW In this review, we provide an overview of the development and application of FRET technology in monitoring cyclic nucleotide-dependent signalings and protein complexes associated with these signalings in real time and space with brief mention of other important signaling messengers and effector proteins involved in compartmentalized signaling. MAJOR CONCLUSIONS The preciseness, rapidity and specificity of cellular responses indicate restricted alterations of signaling messengers, particularly in subcellular compartments rather than globally. Not only the physical confinement and selective depletion, but also the intra- and inter-molecular interactions of signaling effectors modulate the direction of signal transduction in a compartmentalized fashion. To understand the finer details of various intracellular signaling cascades and crosstalk between proteins and other effectors, it is important to visualize these processes in live cells. Förster Resonance Energy Transfer (FRET) has been established as a useful tool to do this, even with its inherent limitations. GENERAL SIGNIFICANCE FRET technology remains as an effective tool for unraveling the complex organization and distribution of various endogenous signaling proteins, as well as the spatiotemporal dynamics of second messengers inside a single cell to distinguish the heterogeneity of cell signaling under normal physiological conditions and during pathological events.
Collapse
Affiliation(s)
- Chandrima Sinha
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA
| | - Kavisha Arora
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Chang Suk Moon
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Sunitha Yarlagadda
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Koryse Woodrooffe
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA.
| |
Collapse
|
68
|
Tateyama M, Kubo Y. [FRET analysis of the activation of GPCR]. Nihon Yakurigaku Zasshi 2014; 143:249-253. [PMID: 24813796 DOI: 10.1254/fpj.143.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
|
69
|
Hu T, Liu X, Liu S, Wang Z, Tang Z. Toward Understanding of Transfer Mechanism between Electrochemiluminescent Dyes and Luminescent Quantum Dots. Anal Chem 2014; 86:3939-46. [DOI: 10.1021/ac5004823] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Tao Hu
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Xuefeng Liu
- National Center for Nanoscience and Technology, Beijing 100090, China
| | - Shaoqin Liu
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Zhenlong Wang
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiyong Tang
- National Center for Nanoscience and Technology, Beijing 100090, China
| |
Collapse
|
70
|
Sample V, Mehta S, Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J Cell Sci 2014; 127:1151-60. [PMID: 24634506 PMCID: PMC3953811 DOI: 10.1242/jcs.099994] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/22/2013] [Indexed: 01/05/2023] Open
Abstract
In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction.
Collapse
Affiliation(s)
- Vedangi Sample
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| |
Collapse
|
71
|
Tourbin M, Al-Kattan A, Drouet C. Study on the stability of suspensions based on biomimetic apatites aimed at biomedical applications. POWDER TECHNOL 2014. [DOI: 10.1016/j.powtec.2013.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
72
|
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.
Collapse
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.
| |
Collapse
|
73
|
Castro LRV, Guiot E, Polito M, Paupardin-Tritsch D, Vincent P. Decoding spatial and temporal features of neuronal cAMP/PKA signaling with FRET biosensors. Biotechnol J 2014; 9:192-202. [PMID: 24478276 DOI: 10.1002/biot.201300202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 12/02/2013] [Accepted: 01/08/2014] [Indexed: 11/11/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) and the cyclic-AMP-dependent protein kinase (PKA) regulate a plethora of cellular functions in virtually all eukaryotic cells. In neurons, the cAMP/PKA signaling cascade controls a number of biological properties such as axonal growth, pathfinding, efficacy of synaptic transmission, regulation of excitability, or long term changes. Genetically encoded optical biosensors for cAMP or PKA are considerably improving our understanding of these processes by providing a real-time measurement in living neurons. In this review, we describe the recent progress made in the creation of biosensors for cAMP or PKA activity. These biosensors revealed profound differences in the amplitude of the cAMP signal evoked by neuromodulators between various neuronal preparations. These responses can be resolved at the level of individual neurons, also revealing differences related to the neuronal type. At the sub-cellular level, biosensors reported different signal dynamics in domains like dendrites, cell body, nucleus, and axon. Combining this imaging approach with pharmacology or genetic models points at phosphodiesterases and phosphatases as critical regulatory proteins. Biosensor imaging will certainly emerge as a forefront tool to decipher the subtle mechanics of intracellular signaling. This will certainly help us to understand the mechanism of action of current drugs and foster the development of novel molecules for neuropsychiatric diseases.
Collapse
Affiliation(s)
- Liliana R V Castro
- CNRS UMR7102, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR7102, Paris, France
| | | | | | | | | |
Collapse
|
74
|
Alouini MA, Moustoifa EF, Rubio-Albenque S, Berthelot T, Fery-Forgues S, Déléris G. Interaction of Fluorescently Labeled Triethyleneglycol and Peptide Derivatives with β-Cyclodextrin. Chemphyschem 2014; 15:444-57. [DOI: 10.1002/cphc.201301032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Indexed: 11/08/2022]
|
75
|
Fluorescent protein-based biosensors and their clinical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 113:313-48. [PMID: 23244794 DOI: 10.1016/b978-0-12-386932-6.00008-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Green fluorescent protein and its relatives have shed their light on a wide range of biological problems. To date, with a color palette consisting of fluorescent proteins with different spectra, researchers can "paint" living cells as they desire. Moreover, sophisticated biosensors engineered to contain single or multiple fluorescent proteins, including FRET-based biosensors, spatiotemporally unveil molecular mechanisms underlying physiological processes. Although such molecules have contributed considerably to basic research, their abilities to be used in applied life sciences have yet to be fully explored. Here, we review the molecular bases of fluorescent proteins and fluorescent protein-based biosensors and focus on approaches aimed at applying such proteins to the clinic.
Collapse
|
76
|
Ruggiero C, Cancino J, Giannotta M, Sallese M. Signaling initiated by the secretory compartment. Methods Enzymol 2014; 534:133-54. [PMID: 24359952 DOI: 10.1016/b978-0-12-397926-1.00008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Classical signal transduction is initiated at the plasma membrane by extracellular signals and propagates to the cytosolic face of the same membrane. Multiple studies have shown that endomembranes can act as signaling platforms for this plasma-membrane-originated signaling. Recent evidence has indicated that endomembranes can also trigger their own signaling cascades that involve some of the molecular players that are classically engaged in signal transduction at the plasma membrane. Endomembrane-initiated signaling is important for synchronization of the functioning of the secretory pathway and coordination of the activities of the secretory organelles with other cellular machineries. However, these endomembrane-initiated regulatory circuits are only partially understood to date. This novel field is slowed by a lack of specific tools and the objective difficulties in the study of signal transduction of endomembrane-localized receptors, as their accessibility is limited. For example, the ligand-binding site of the KDEL receptor (that transduces endomembrane signaling) is positioned in the lumen of the Golgi complex. Here we report some approaches that are suitable for the study of endomembrane-initiated signaling.
Collapse
Affiliation(s)
- Carmen Ruggiero
- Department of Cellular and Translational Pharmacology, Fondazione Mario Negri Sud, Unit of Genomic Approaches to Membrane Traffic, Santa Maria Imbaro (CH), Italy
| | - Jorge Cancino
- Department of Life Sciences, Institute of Protein Biochemistry, National Research Council and Telethon Institute of Genetics and Medicine, Naples, Italy
| | | | - Michele Sallese
- Department of Cellular and Translational Pharmacology, Fondazione Mario Negri Sud, Unit of Genomic Approaches to Membrane Traffic, Santa Maria Imbaro (CH), Italy.
| |
Collapse
|
77
|
Zeug A, Stawarski M, Bieganska K, Korotchenko S, Wlodarczyk J, Dityatev A, Ponimaskin E. Current microscopic methods for the neural ECM analysis. PROGRESS IN BRAIN RESEARCH 2014; 214:287-312. [PMID: 25410363 DOI: 10.1016/b978-0-444-63486-3.00013-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The extracellular matrix (ECM) occupies the space between both neurons and glial cells and thus provides a microenvironment that regulates multiple aspects of neural activities. Because of the vital role of ECM as a natural environment of cells in vivo, there is a growing interest to develop methodology allowing for the detailed structural and functional analyses of ECM. In this chapter, we provide the detailed overview of current microscopic methods used for ECM analysis and also describe general labeling strategies for ECM visualization. Since ECM remodeling involves the proteolytic cleavage of ECM, we will also describe current experimental approaches to image the proteolytic reorganization and/or degradation of ECM. The special focus of this chapter is set to the application of Förster resonance energy transfer-based approaches to monitor intracellular and extracellular matrix functions with high spatiotemporal resolution.
Collapse
Affiliation(s)
- Andre Zeug
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
| | - Michal Stawarski
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | | | - Svetlana Korotchenko
- Laboratory for Brain Extracellular Matrix Research, University of Nizhny Novgorod, Nizhny Novgorod, Russia; Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy; Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Jakub Wlodarczyk
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Alexander Dityatev
- Laboratory for Brain Extracellular Matrix Research, University of Nizhny Novgorod, Nizhny Novgorod, Russia; Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy; Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy; Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Magdeburg, Germany
| | - Evgeni Ponimaskin
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany.
| |
Collapse
|
78
|
Ast C, Draaijer A. Methods and Techniques to Measure Molecular Oxygen in Plants. LOW-OXYGEN STRESS IN PLANTS 2014. [DOI: 10.1007/978-3-7091-1254-0_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
79
|
Oliveira AF, Yasuda R. Imaging the activity of Ras superfamily GTPase proteins in small subcellular compartments in neurons. Methods Mol Biol 2014; 1071:109-28. [PMID: 24052384 DOI: 10.1007/978-1-62703-622-1_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Resolving the spatiotemporal dynamics of intracellular signaling is important for understanding the molecular mechanisms of various cellular processes induced by extracellular signals. Two-photon fluorescence lifetime imaging microscopy (2pFLIM) in combination with a fluorescence resonance energy transfer (FRET)-based signaling sensors allows one to image signaling within small subcellular compartments, such as dendritic spines of neurons, with high sensitivity and spatiotemporal resolution. In this protocol, we describe the procedures and equipment required for imaging intracellular signaling activity, with a particular focus on signaling mediated by the Ras superfamily of small GTPase proteins.
Collapse
Affiliation(s)
- Ana F Oliveira
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | | |
Collapse
|
80
|
Chong MK, Chua AJS, Tan TTT, Tan SH, Ng ML. Microscopy techniques in flavivirus research. Micron 2013; 59:33-43. [PMID: 24530363 DOI: 10.1016/j.micron.2013.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/11/2013] [Accepted: 12/11/2013] [Indexed: 11/29/2022]
Abstract
The Flavivirus genus is composed of many medically important viruses that cause high morbidity and mortality, which include Dengue and West Nile viruses. Various molecular and biochemical techniques have been developed in the endeavour to study flaviviruses. However, microscopy techniques still have irreplaceable roles in the identification of novel virus pathogens and characterization of morphological changes in virus-infected cells. Fluorescence microscopy contributes greatly in understanding the fundamental viral protein localizations and virus-host protein interactions during infection. Electron microscopy remains the gold standard for visualizing ultra-structural features of virus particles and infected cells. New imaging techniques and combinatory applications are continuously being developed to push the limit of resolution and extract more quantitative data. Currently, correlative live cell imaging and high resolution three-dimensional imaging have already been achieved through the tandem use of optical and electron microscopy in analyzing biological specimens. Microscopy techniques are also used to measure protein binding affinities and determine the mobility pattern of proteins in cells. This chapter will consolidate on the applications of various well-established microscopy techniques in flavivirus research, and discuss how recently developed microscopy techniques can potentially help advance our understanding in these membrane viruses.
Collapse
Affiliation(s)
- Mun Keat Chong
- Flavivirology Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, MD4 Level 3, Singapore 117545, Singapore
| | - Anthony Jin Shun Chua
- Flavivirology Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, MD4 Level 3, Singapore 117545, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), 28 Medical Drive, #05-01, Singapore 117456, Singapore
| | - Terence Tze Tong Tan
- Flavivirology Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, MD4 Level 3, Singapore 117545, Singapore
| | - Suat Hoon Tan
- Electron Microscopy Unit, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 12 Medical Drive, MD5, Singapore 117597, Singapore
| | - Mah Lee Ng
- Flavivirology Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, MD4 Level 3, Singapore 117545, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), 28 Medical Drive, #05-01, Singapore 117456, Singapore; Electron Microscopy Unit, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 12 Medical Drive, MD5, Singapore 117597, Singapore.
| |
Collapse
|
81
|
Miura H, Matsuda M, Aoki K. Development of a FRET biosensor with high specificity for Akt. Cell Struct Funct 2013; 39:9-20. [PMID: 24212374 DOI: 10.1247/csf.13018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The serine/threonine kinase Akt plays a critical role in cell proliferation, survival, and tumorigenesis. As a central kinase in the phosphatidylinositol 3-kinase pathway, its activation mechanism at the plasma membrane has been well characterized. However, the subcellular Akt activity in living cells is still largely unknown. Fluorescence resonance energy transfer (FRET)-based biosensors have emerged as indispensable tools to visualize the subcellular activities of signaling molecules. In this study, we developed a highly specific FRET biosensor for Akt based on the Eevee backbone, called Eevee-iAkt. Using inhibitors targeting kinases upstream and downstream of Akt, we showed that Eevee-iAkt specifically monitors Akt activity in living cells. To visualize Akt activity at different subcellular compartments, we targeted Eevee-iAkt to raft and non-raft regions of the plasma membrane, mitochondria, and nucleus in HeLa and Cos7 cells. Interestingly, we revealed substantial differences in Akt activation between HeLa and Cos7 cells upon epidermal growth factor (EGF) stimulation: Akt was transiently activated in HeLa cells with comparable levels at the plasma membrane, cytosol, and mitochondria. In contrast, sustained and spatially localized Akt activation was observed in EGF-stimulated Cos7 cells. We found high Akt activity at the plasma membrane, low activity in the cytosol, and no detectable activity at the mitochondria and nucleus in Cos7 cells. The Eevee-iAkt biosensor was shown to be a valuable tool to study the functional relationship between subcellular Akt activation and its anti-apoptotic role in living cells.
Collapse
Affiliation(s)
- Haruko Miura
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University
| | | | | |
Collapse
|
82
|
Ueda Y, Kwok S, Hayashi Y. Application of FRET probes in the analysis of neuronal plasticity. Front Neural Circuits 2013; 7:163. [PMID: 24133415 PMCID: PMC3794420 DOI: 10.3389/fncir.2013.00163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/23/2013] [Indexed: 12/12/2022] Open
Abstract
Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since green fluorescent protein (GFP) was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET), which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM) allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo.
Collapse
|
83
|
Stein F, Kress M, Reither S, Piljić A, Schultz C. FluoQ: a tool for rapid analysis of multiparameter fluorescence imaging data applied to oscillatory events. ACS Chem Biol 2013; 8:1862-8. [PMID: 23882997 DOI: 10.1021/cb4003442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The number of fluorescent sensors and their use in living cells has significantly increased in the past years. Yet, the analysis of data from single cells or cell populations usually remains a very time-consuming enterprise. Here, we introduce FluoQ, a new macro for the image analysis software ImageJ, which enables fast analysis of multiparameter time-lapse fluorescence microscopy data with minimal manual input. FluoQ provides statistical analysis of all measured parameters and delivers the results in multiple graphic and numeric displays. We demonstrate the power of FluoQ by applying the macro to data analysis in the development and optimization of novel FRET reporters for monitoring the performance of calcium/calmodulin-binding inositol trisphosphate kinases A and B (ITPKA and ITPKB) in HeLa cells. We find that conformational changes in the ITPKA-based sensor follow receptor-mediated calcium oscillations. This indicates that ITPKA contributes to the regulation of intracellular calcium transients by limiting inositol trisphosphate levels.
Collapse
Affiliation(s)
- Frank Stein
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Manuel Kress
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Sabine Reither
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Alen Piljić
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße
1, 69117 Heidelberg, Germany
| |
Collapse
|
84
|
Tsuyama T, Kishikawa JI, Han YW, Harada Y, Tsubouchi A, Noji H, Kakizuka A, Yokoyama K, Uemura T, Imamura H. In vivo fluorescent adenosine 5'-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures. Anal Chem 2013; 85:7889-96. [PMID: 23875533 DOI: 10.1021/ac4015325] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is the major energy currency of all living organisms. Despite its important functions, the spatiotemporal dynamics of ATP levels inside living multicellular organisms is unclear. In this study, we modified the genetically encoded Förster resonance energy transfer (FRET)-based ATP biosensor ATeam to optimize its affinity at low temperatures. This new biosensor, AT1.03NL, detected ATP changes inside Drosophila S2 cells more sensitively than the original biosensor did, at 25 °C. By expressing AT1.03NL in Drosophila melanogaster and Caenorhabditis elegans, we succeeded in imaging the in vivo ATP dynamics of these model animals at single-cell resolution.
Collapse
Affiliation(s)
- Taiichi Tsuyama
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
85
|
Guo-jian W, Qi Z, Hong-ping D, Da-li W, Xin-yuan Z, De-yue Y. FLUORESCENCE ENHANCEMENT OF GFP CHROMOPHORE THROUGH POLYMERIC SELF-ASSEMBLY. ACTA POLYM SIN 2013. [DOI: 10.3724/sp.j.1105.2013.12418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
86
|
Dance of the SNAREs: assembly and rearrangements detected with FRET at neuronal synapses. J Neurosci 2013; 33:5507-23. [PMID: 23536066 DOI: 10.1523/jneurosci.2337-12.2013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) mediate vesicle fusion with the plasma membrane on activation by calcium binding to synaptotagmin. In the present study, we used fluorescence resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy between fluorescently labeled SNARE proteins expressed in cultured rat hippocampal neurons to detect resting SNARE complexes, their conformational rearrangement on exocytosis, their disassembly before endocytosis of vesicular proteins, and SNARE assembly at newly docked vesicles. Assembled SNAREs are not only present in docked vesicles; unexpected residual "orphan SNARE complexes" also reside in para-active zone regions. Real-time changes in FRET between N-terminally labeled SNAP-25 and VAMP reported a reorientation of the SNARE motif upon exocytosis, SNARE disassembly in the active zone periphery, and SNARE reassembly in newly docked vesicles. With VAMP labeled C-terminally, decreased fluorescence in C-terminally labeled syntaxin (extracellular) reported trans-cis-conformational changes in SNAREs on vesicle fusion. After fusion SNAP-25 and syntaxin disperse along with VAMP, as well as the FRET signal itself, indicating diffusion of intact SNAREs after vesicle fusion but before their peripheral disassembly. Our measurements of spatiotemporal dynamics of SNARE conformational changes and movements refine models of SNARE function. Technical advances required to detect tiny changes in fluorescence in small fractions of labeled proteins in presynaptic boutons on a time scale of seconds permit the detection of rapid intermolecular interactions between small proportions of protein partners in cellular subcompartments.
Collapse
|
87
|
Tanimura A, Nezu A, Morita T. [Light microscopy techniques for live cell and animal imaging using fluorescent proteins]. Nihon Yakurigaku Zasshi 2013; 141:262-7. [PMID: 23665557 DOI: 10.1254/fpj.141.262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
88
|
Gillis J, Schipper-Krom S, Juenemann K, Gruber A, Coolen S, van den Nieuwendijk R, van Veen H, Overkleeft H, Goedhart J, Kampinga HH, Reits EA. The DNAJB6 and DNAJB8 protein chaperones prevent intracellular aggregation of polyglutamine peptides. J Biol Chem 2013; 288:17225-37. [PMID: 23612975 DOI: 10.1074/jbc.m112.421685] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fragments of proteins containing an expanded polyglutamine (polyQ) tract are thought to initiate aggregation and toxicity in at least nine neurodegenerative diseases, including Huntington's disease. Because proteasomes appear unable to digest the polyQ tract, which can initiate intracellular protein aggregation, preventing polyQ peptide aggregation by chaperones should greatly improve polyQ clearance and prevent aggregate formation. Here we expressed polyQ peptides in cells and show that their intracellular aggregation is prevented by DNAJB6 and DNAJB8, members of the DNAJ (Hsp40) chaperone family. In contrast, HSPA/Hsp70 and DNAJB1, also members of the DNAJ chaperone family, did not prevent peptide-initiated aggregation. Intriguingly, DNAJB6 and DNAJB8 also affected the soluble levels of polyQ peptides, indicating that DNAJB6 and DNAJB8 inhibit polyQ peptide aggregation directly. Together with recent data showing that purified DNAJB6 can suppress fibrillation of polyQ peptides far more efficiently than polyQ expanded protein fragments in vitro, we conclude that the mechanism of DNAJB6 and DNAJB8 is suppression of polyQ protein aggregation by directly binding the polyQ tract.
Collapse
Affiliation(s)
- Judith Gillis
- Department of Cell Biology and Histology, Academic Medical Center, Amsterdam 1105AZ, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
89
|
Nano-bio interfaces probed by advanced optical spectroscopy: From model system studies to optical biosensors. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5700-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
90
|
Aoki K, Kamioka Y, Matsuda M. Fluorescence resonance energy transfer imaging of cell signaling from in vitro to in vivo: basis of biosensor construction, live imaging, and image processing. Dev Growth Differ 2013; 55:515-22. [PMID: 23387795 DOI: 10.1111/dgd.12039] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/27/2012] [Accepted: 12/27/2012] [Indexed: 12/14/2022]
Abstract
The progress in imaging technology with fluorescent proteins has uncovered a wide range of biological processes in developmental biology. In particular, genetically-encoded biosensors based on the principle of fluorescence resonance energy transfer (FRET) have been used to visualize spatial and temporal dynamics of intracellular signaling in living cells. However, development of sensitive FRET biosensors and their application to developmental biology remain challenging tasks, which has prevented their widespread use in developmental biology. In this review, we first overview general procedures and tips of imaging with FRET biosensors. We then describe recent advances in FRET imaging - namely, the use of optimized backbones for intramolecular FRET biosensors and transposon-mediated gene transfer to generate stable cell lines and transgenic mice expressing FRET biosensors. Finally, we discuss future perspectives of FRET imaging in developmental biology.
Collapse
Affiliation(s)
- Kazuhiro Aoki
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
| | | | | |
Collapse
|
91
|
Candelario J, Chachisvilis M. Real-time detection of G protein activation using monomolecular Gγ FRET sensors. J Recept Signal Transduct Res 2013; 33:63-72. [PMID: 23336397 DOI: 10.3109/10799893.2012.759589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
G protein-coupled receptors (GPCRs) are involved in many diseases, and are the target of a large percentage of modern drugs. While only a few fluorescence resonance energy transfer (FRET) sensors have been made for real-time detection of GPCR activation, the human genome encodes roughly 950 GPCRs and a need for a broad real-time detection system is needed. In this study, we developed and characterized a new type of G protein sensor based on the Gγ subunit containing an intra-molecular FRET pair to allow detection of real-time G protein activation in multiple cell lines using time-resolved fluorescence spectroscopy. Our Gγ sensors were able to detect G protein activation to aluminum fluoride, a G protein activator, in human embryonic kidney 293 cells (HEK293). Moreover, our sensors were able to couple to the bradykinin B(2), parathyroid type 1 and adrenergic 2A GPCRs and detect G protein activation in response to the cognate ligands; bradykinin, parathyroid and noradrenaline hormones, respectively. Furthermore, our sensors also detected ligand-independent G protein activation by fluid shear stress. G protein inhibitors, pertussis toxin and guanosine 5' [β-thio] diphosphate, inhibited the FRET response to G protein stimulants indicating that the sensor response is specific to G protein activation. These findings suggest that the described Gγ sensors can be used to monitor real-time G protein activation by a variety of G protein stimulants or inhibitors.
Collapse
|
92
|
Oliveira AF, Yasuda R. An improved Ras sensor for highly sensitive and quantitative FRET-FLIM imaging. PLoS One 2013; 8:e52874. [PMID: 23349692 PMCID: PMC3544822 DOI: 10.1371/journal.pone.0052874] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/22/2012] [Indexed: 12/04/2022] Open
Abstract
Ras is a signaling protein involved in a variety of cellular processes. Hence, studying Ras signaling with high spatiotemporal resolution is crucial to understanding the roles of Ras in many important cellular functions. Previously, fluorescence lifetime imaging (FLIM) of fluorescent resonance energy transfer (FRET)-based Ras activity sensors, FRas and FRas-F, have been demonstrated to be useful for measuring the spatiotemporal dynamics of Ras signaling in subcellular micro-compartments. However the predominantly nuclear localization of the sensors' acceptor has limited its sensitivity. Here, we have overcome this limitation and developed two variants of the existing FRas sensor with different affinities: FRas2-F (Kd∼1.7 µM) and FRas2-M (Kd∼0.5 µM). We demonstrate that, under 2-photon fluorescence lifetime imaging microscopy, FRas2 sensors provide higher sensitivity compared to previous sensors in 293T cells and neurons.
Collapse
Affiliation(s)
- Ana F. Oliveira
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Doctoral Program in Biomedicine and Experimental Biology, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ryohei Yasuda
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Max-Planck Florida Institute, Jupiter, Florida, United States of America
- * E-mail:
| |
Collapse
|
93
|
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.
Collapse
Affiliation(s)
- Alec W M Simpson
- Department of Cell and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
| |
Collapse
|
94
|
Jia F, Zhang Y, Narasimhan B, Mallapragada SK. Block copolymer-quantum dot micelles for multienzyme colocalization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:17389-17395. [PMID: 23171402 DOI: 10.1021/la303115t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To mimic the structure and functionality of multienzyme complexes, which are widely present in Nature, Pluronic-based micelles were designed to colocalize multiple enzymes. To stabilize the micelles as well as to enable characterization of single enzyme immobilization and multienzyme colocalization by Förster resonance energy transfer (FRET), quantum dots (QDs) were incorporated into the micelles to form Pluronic-QD micelles using a novel microreactor. Model enzymes glucose oxidase (GOX) and horseradish peroxidase (HRP) were respectively labeled with fluorescent dyes. The results indicated that FRET occurred between the QDs and dyes that labeled each type of enzyme in single enzyme immobilization studies as well as between the dyes in colocalization studies. These observations were consistent with increases in micelle size after adsorption of dye-enzymes as verified by dynamic light scattering. In addition, the activity of single enzymes was retained after immobilization. An optimized colocalization process improved the overall conversion rate by approximately 100% compared to equivalent concentrations of free enzymes in solution. This study demonstrates a versatile platform for multienzyme colocalization and an effective strategy to characterize multienzyme immobilization and colocalization, which can be applicable to many other multienzyme systems.
Collapse
Affiliation(s)
- Feng Jia
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | | | | | | |
Collapse
|
95
|
Socher E, Imperiali B. FRET-capture: a sensitive method for the detection of dynamic protein interactions. Chembiochem 2012; 14:53-7. [PMID: 23239458 DOI: 10.1002/cbic.201200700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 01/14/2023]
Abstract
Caught in the act: The FRET-Capture approach exploits a bound solvatochromic fluorophore, 4-N,N-dimethylamino-1,8-naphthalimide, as a FRET donor in both inter- and intramolecular energy transfer. A unique feature of this method is the additional level of signal selectivity as the FRET signal is only turned on when the donor is specifically bound to the protein of interest, eliminating high background and false positive signals.
Collapse
Affiliation(s)
- Elke Socher
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | |
Collapse
|
96
|
Okamoto A, Sugizaki K, Yuki M, Yanagisawa H, Ikeda S, Sueoka T, Hayashi G, Wang DO. A nucleic acid probe labeled with desmethyl thiazole orange: a new type of hybridization-sensitive fluorescent oligonucleotide for live-cell RNA imaging. Org Biomol Chem 2012; 11:362-71. [PMID: 23172393 DOI: 10.1039/c2ob26707a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A new fluorescent nucleotide with desmethyl thiazole orange dyes, D'(505), has been developed for expansion of the function of fluorescent probes for live-cell RNA imaging. The nucleoside unit of D'(505) for DNA autosynthesis was soluble in organic solvents, which made the preparation of nucleoside units and the reactions in the cycles of DNA synthesis more efficient. The dyes of D'(505)-containing oligodeoxynucleotide were protonated below pH 7 and the oligodeoxynucleotide exhibited hybridization-sensitive fluorescence emission through the control of excitonic interactions of the dyes of D'(505). The simplified procedure and effective hybridization-sensitive fluorescence emission produced multicolored hybridization-sensitive fluorescent probes, which were useful for live-cell RNA imaging. The acceptor-bleaching method gave us information on RNA in a specific cell among many living cells.
Collapse
Affiliation(s)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
97
|
Santiago-Medina M, Myers JP, Gomez TM. Imaging adhesion and signaling dynamics in Xenopus laevis growth cones. Dev Neurobiol 2012; 72:585-99. [PMID: 21465668 DOI: 10.1002/dneu.20886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Xenopus laevis provides a robust model system to study cellular signaling and downstream processes during development both in vitro and in vivo. Intracellular signals must function within highly restricted spatial and temporal domains to activate specific downstream targets and cellular processes. Combining the versatility of developing Xenopus neurons with advances in fluorescent protein biosensors and imaging technologies has allowed many dynamic cellular processes to be visualized. This review will focus on the techniques we use to visualize and measure cell signaling, motility and adhesion by quantitative fluorescence microscopy in vitro and in vivo.
Collapse
Affiliation(s)
- Miguel Santiago-Medina
- Department of Neuroscience, Neuroscience Training Program, University of Wisconsin-Madison, WI 53706, USA
| | | | | |
Collapse
|
98
|
Yasuda R. Imaging intracellular signaling using two-photon fluorescent lifetime imaging microscopy. Cold Spring Harb Protoc 2012; 2012:1121-8. [PMID: 23118363 DOI: 10.1101/pdb.top072090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent development of Förster resonance energy transfer (FRET) sensors and FRET imaging techniques permits visualization of the dynamics of intracellular signaling events with high spatiotemporal resolution. In particular, fluorescence lifetime imaging in combination with two-photon laser-scanning microscopy (two-photon fluorescence lifetime imaging microscopy [2pFLIM]) is a powerful tool to monitor signaling events in small subcellular compartments in thick tissue. This article provides practical guidelines for quantitative imaging of intracellular signaling using 2pFLIM.
Collapse
|
99
|
Han JJ, Kiss C, Bradbury ARM, Werner JH. Time-resolved, confocal single-molecule tracking of individual organic dyes and fluorescent proteins in three dimensions. ACS NANO 2012; 6:8922-32. [PMID: 22957739 DOI: 10.1021/nn302912j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We demonstrate following individual fluorescent protein constructs and individual organic dyes as they diffuse in 3-D in solution at rates up to 1 μm(2)/s over distances of several micrometers in X, Y, and Z. Our 3-D tracking method is essentially a stage scanning confocal microscope that uses a unique spatial filter geometry and active feedback 200 times/s to follow fast 3-D motion. Here we detail simulations used to find optimal feedback parameters for following individual fluorescent proteins in 3-D and show that a wide range of parameters are capable of following individual proteins diffusing at 1 μm(2)/s rates. In addition, we experimentally show that through 3-D single-molecule tracking of a protein oligomer series (monomer, dimer, and tetramer) of the fluorescent protein Azami Green one can determine the protein oligomerization state. We also perform time-resolved spectroscopy (photon pair correlation measurements) during the measured 3-D trajectories. The photon pair correlation measurements show clear fluorescence photon antibunching, demonstrating that the trajectories are of single fluorescent molecules. We note that the rates of single-molecule diffusive motion we follow (approximately 1 μm(2)/s) are comparable to or faster than many intracellular transport processes.
Collapse
Affiliation(s)
- Jason J Han
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | | | | | | |
Collapse
|
100
|
Yasuda R. Studying signal transduction in single dendritic spines. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a005611. [PMID: 22843821 DOI: 10.1101/cshperspect.a005611] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many forms of synaptic plasticity are triggered by biochemical signaling that occurs in small postsynaptic compartments called dendritic spines, each of which typically houses the postsynaptic terminal associated with a single glutamatergic synapse. Recent advances in optical techniques allow investigators to monitor biochemical signaling in single dendritic spines and thus reveal the signaling mechanisms that link synaptic activity and the induction of synaptic plasticity. This is mostly in the study of Ca2+-dependent forms of synaptic plasticity for which many of the steps between Ca2+ influx and changes to the synapse are now known. This article introduces the new techniques used to investigate signaling in single dendritic spines and the neurobiological insights that they have produced.
Collapse
Affiliation(s)
- Ryohei Yasuda
- Neurobiology Department, Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA.
| |
Collapse
|