1
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Okamoto K, Fujita H, Okada Y, Shinkai S, Onami S, Abe K, Fujimoto K, Sasaki K, Shioi G, Watanabe TM. Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. EMBO J 2023; 42:e112305. [PMID: 37609947 PMCID: PMC10505915 DOI: 10.15252/embj.2022112305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 08/24/2023] Open
Abstract
Nanog and Oct4 are core transcription factors that form part of a gene regulatory network to regulate hundreds of target genes for pluripotency maintenance in mouse embryonic stem cells (ESCs). To understand their function in the pluripotency maintenance, we visualised and quantified the dynamics of single molecules of Nanog and Oct4 in a mouse ESCs during pluripotency loss. Interestingly, Nanog interacted longer with its target loci upon reduced expression or at the onset of differentiation, suggesting a feedback mechanism to maintain the pluripotent state. The expression level and interaction time of Nanog and Oct4 correlate with their fluctuation and interaction frequency, respectively, which in turn depend on the ESC differentiation status. The DNA viscoelasticity near the Oct4 target locus remained flexible during differentiation, supporting its role either in chromatin opening or a preferred binding to uncondensed chromatin regions. Based on these results, we propose a new negative feedback mechanism for pluripotency maintenance via the DNA condensation state-dependent interplay of Nanog and Oct4.
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Affiliation(s)
- Kazuko Okamoto
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Amphibian Research CenterHiroshima UniversityHiroshimaJapan
| | - Hideaki Fujita
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
| | - Yasushi Okada
- Laboratory for Cell Polarity RegulationRIKEN Center for Biosystems Dynamics Research (BDR)OsakaJapan
- Department of Cell BiologyGraduate School of Medicine, The University of TokyoTokyoJapan
- Department of PhysicsUniversal Biology Institute (UBI)Graduate School of Science, The University of TokyoTokyoJapan
- International Research Center for Neurointelligence (WPI‐IRCN)Institutes for Advanced Study, The University of TokyoTokyoJapan
| | - Soya Shinkai
- Laboratory for Developmental DynamicsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD)Hiroshima UniversityHiroshimaJapan
| | - Shuichi Onami
- Laboratory for Developmental DynamicsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome DynamicsRIKEN BioResource Research Center (BRC)TsukubaJapan
| | - Kenta Fujimoto
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
| | - Kensuke Sasaki
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Go Shioi
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive BioimagingRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
- Department of Stem Cell Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHigashi‐HiroshimaJapan
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2
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Patel VR, Salinas AM, Qi D, Gupta S, Sidote DJ, Goldschen-Ohm MP. Single-molecule imaging with cell-derived nanovesicles reveals early binding dynamics at a cyclic nucleotide-gated ion channel. Nat Commun 2021; 12:6459. [PMID: 34753946 PMCID: PMC8578382 DOI: 10.1038/s41467-021-26816-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/21/2021] [Indexed: 12/05/2022] Open
Abstract
Ligand binding to membrane proteins is critical for many biological signaling processes. However, individual binding events are rarely directly observed, and their asynchronous dynamics are occluded in ensemble-averaged measures. For membrane proteins, single-molecule approaches that resolve these dynamics are challenged by dysfunction in non-native lipid environments, lack of access to intracellular sites, and costly sample preparation. Here, we introduce an approach combining cell-derived nanovesicles, microfluidics, and single-molecule fluorescence colocalization microscopy to track individual binding events at a cyclic nucleotide-gated TAX-4 ion channel critical for sensory transduction. Our observations reveal dynamics of both nucleotide binding and a subsequent conformational change likely preceding pore opening. Kinetic modeling suggests that binding of the second ligand is either independent of the first ligand or exhibits up to ~10-fold positive binding cooperativity. This approach is broadly applicable to studies of binding dynamics for proteins with extracellular or intracellular domains in native cell membrane.
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Affiliation(s)
- Vishal R Patel
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Arturo M Salinas
- Department of Physics, The University of Texas at Austin, Austin, TX, USA
| | - Darong Qi
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Shipra Gupta
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - David J Sidote
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
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3
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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4
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Frequency Shift of a SH-SAW Biosensor with Glutaraldehyde and 3-Aminopropyltriethoxysilane Functionalized Films for Detection of Epidermal Growth Factor. BIOSENSORS-BASEL 2020; 10:bios10080092. [PMID: 32764513 PMCID: PMC7459952 DOI: 10.3390/bios10080092] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/29/2023]
Abstract
The frequency shift of a shear-horizontal surface-acoustic-wave (SH-SAW) biosensor in which the concentration of biomolecule is determined by the amount of its adsorption on the sensing film was studied. Simulation results were compared with experimental results to investigate its sensitivity and to develop a model to estimate the concentration of a cancer-related biomarker antigen epidermal growth factor (EGF) in the sample, with two types of sensing films, 3-aminopropyltriethoxysilane (APTES) and glutaraldehyde. With the concentration of the targeted biomarker varying from 0.2 to 5 ng/mL, a typical exponential relationship was found between the concentration and the frequency shift of the SH-SAW sensor. Measurement results showed a clear response of this immunosensor to the mass-loading effects of the antibody–antigen. The sensitivity of the glutaraldehyde film is greater than that of the APTES film owing to the chemisorption of the antibody. In the simulation, a shift of the SH-SAW resonant frequency due to added mass occurred on applying an incremental surface mass density on the sensing film, while in real applications, the concentration of the targeted biomarker to be absorbed in the sensing film is demanded. An empirical model was proposed to calculate the frequency shift in the simulation of the SH-SAW biosensor, corresponding to the concentration of specific biomolecules absorbed on a specific film. From the semi-empirical model, the sensitivity level is found to be 0.641 and 1.709 kHz/(ng/mL) for APTES and glutaraldehyde sensing films, respectively, at a biomarker concentration of less than 1 ng/mL. The developed method is useful for quickly estimating the frequency shift with respect to the concentration of the target molecules in the simulation for SH-SAW sensors.
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5
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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6
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Li CC, Li Y, Zhang Y, Zhang CY. Single-molecule fluorescence resonance energy transfer and its biomedical applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115753] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Chien FC, Lin CY, Abrigo G. Enhancing the blinking fluorescence of single-molecule localization imaging by using a surface-plasmon-polariton-enhanced substrate. Phys Chem Chem Phys 2018; 20:27245-27255. [PMID: 30182107 DOI: 10.1039/c8cp02942c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging based on single-molecule localization microscopy combined with the surface plasmon polariton (SPP)-enhanced fluorescence of spontaneously blinking fluorophores was demonstrated to visualize the nanoscale-level positioning information of cell-adhesion-associated proteins. Glass substrates with a deposited silver layer were utilized to induce a SPP-enhanced field on the silver surface and significantly strengthen the fluorescence signals of the fluorophores by more than 300%. The illumination power density for localization imaging at a spatial resolution of 25 ± 11 nm was 31.6 W cm-2. This low illumination power density will facilitate the reduction of phototoxicity of the biospecimens for single-molecule localization imaging. The proposed strategy provides a uniform distribution of the SPP-enhanced field on the silver surface, enabling visualization of the spatial distribution of labeled proteins without interference caused by the enhanced field distribution.
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Affiliation(s)
- Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Taoyuan 32001, Taiwan.
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8
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Sato R, Kozuka J, Ueda M, Mishima R, Kumagai Y, Yoshimura A, Minoshima M, Mizukami S, Kikuchi K. Intracellular Protein-Labeling Probes for Multicolor Single-Molecule Imaging of Immune Receptor-Adaptor Molecular Dynamics. J Am Chem Soc 2017; 139:17397-17404. [PMID: 29119782 DOI: 10.1021/jacs.7b08262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared fluorescent probes for protein labeling that specifically bind to a mutant β-lactamase tag. By structural fine-tuning of cell permeability and minimized non-specific binding, SiRcB4 enabled multicolor SMI in combination with a HaloTag-based red-fluorescent probe. Upon addition of both chemical probes at sub-nanomolar concentrations, single-molecule imaging revealed the dynamics of TLR4 and its adaptor protein, TIRAP, which are involved in the innate immune system. Statistical analysis of the quantitative properties and time-lapse changes in dynamics revealed a protein-protein interaction in response to ligand stimulation.
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Affiliation(s)
- Ryota Sato
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Jun Kozuka
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Masahiro Ueda
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Reiko Mishima
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Akimasa Yoshimura
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Masafumi Minoshima
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai, Miyagi, 980-8577, Japan
| | - Kazuya Kikuchi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Chemical Imaging Techniques, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
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9
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Mandracchia B, Gennari O, Marchesano V, Paturzo M, Ferraro P. Label free imaging of cell-substrate contacts by holographic total internal reflection microscopy. JOURNAL OF BIOPHOTONICS 2017; 10:1163-1170. [PMID: 27804236 DOI: 10.1002/jbio.201600177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/31/2016] [Accepted: 10/04/2016] [Indexed: 05/25/2023]
Abstract
The study of cell adhesion contacts is pivotal to understand cell mechanics and interaction at substrates or chemical and physical stimuli. We designed and built a HoloTIR microscope for label-free quantitative phase imaging of total internal reflection. Here we show for the first time that HoloTIR is a good choice for label-free study of focal contacts and of cell/substrate interaction as its sensitivity is enhanced in comparison with standard TIR microscopy. Finally, the simplicity of implementation and relative low cost, due to the requirement of less optical components, make HoloTIR a reasonable alternative, or even an addition, to TIRF microscopy for mapping cell/substratum topography. As a proof of concept, we studied the formation of focal contacts of fibroblasts on three substrates with different levels of affinity for cell adhesion.
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Affiliation(s)
- Biagio Mandracchia
- CNR - ISASI Institute of Applied Sciences and Intelligent Systems, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale - DICMAPI, University of Naples Federico II, Piazzale Tecchio 80, 80100, Napoli, Italy
| | - Oriella Gennari
- CNR - ISASI Institute of Applied Sciences and Intelligent Systems, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy
| | - Valentina Marchesano
- CNR - ISASI Institute of Applied Sciences and Intelligent Systems, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy
| | - Melania Paturzo
- CNR - ISASI Institute of Applied Sciences and Intelligent Systems, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy
| | - Pietro Ferraro
- CNR - ISASI Institute of Applied Sciences and Intelligent Systems, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy
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10
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Martin WE, Ge N, Srijanto BR, Furnish E, Collier CP, Trinkle CA, Richards CI. Real-Time Sensing of Single-Ligand Delivery with Nanoaperture-Integrated Microfluidic Devices. ACS OMEGA 2017; 2:3858-3867. [PMID: 28782052 PMCID: PMC5537690 DOI: 10.1021/acsomega.7b00934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 05/28/2023]
Abstract
The measurement of biological events on the surface of live cells at the single-molecule level is complicated by several factors including high protein densities that are incompatible with single-molecule imaging, cellular autofluorescence, and protein mobility on the cell surface. Here, we fabricated a device composed of an array of nanoscale apertures coupled with a microfluidic delivery system to quantify single-ligand interactions with proteins on the cell surface. We cultured live cells directly on the device and isolated individual epidermal growth factor receptors (EGFRs) in the apertures while delivering fluorescently labeled epidermal growth factor. We observed single ligands binding to EGFRs, allowing us to quantify the ligand turnover in real time. These results demonstrate that this nanoaperture-coupled microfluidic device allows for the spatial isolation of individual membrane proteins while maintaining them in their cellular environment, providing the capability to monitor single-ligand binding events while maintaining receptors in their physiological environment. These methods should be applicable to a wide range of membrane proteins.
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Affiliation(s)
- W. Elliott Martin
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Ning Ge
- Department
of Mechanical Engineering, University of
Kentucky, 151 Ralph G.
Anderson Building, Lexington, Kentucky 40506, United
States
| | - Bernadeta R. Srijanto
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge Tennessee 37831, United States
| | - Emily Furnish
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - C. Patrick Collier
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge Tennessee 37831, United States
| | - Christine A. Trinkle
- Department
of Mechanical Engineering, University of
Kentucky, 151 Ralph G.
Anderson Building, Lexington, Kentucky 40506, United
States
| | - Christopher I. Richards
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
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11
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Masuda S, Yanase Y, Usukura E, Ryuzaki S, Wang P, Okamoto K, Kuboki T, Kidoaki S, Tamada K. High-resolution imaging of a cell-attached nanointerface using a gold-nanoparticle two-dimensional sheet. Sci Rep 2017. [PMID: 28623338 PMCID: PMC5473937 DOI: 10.1038/s41598-017-04000-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This paper proposes a simple, effective, non-scanning method for the visualization of a cell-attached nanointerface. The method uses localized surface plasmon resonance (LSPR) excited homogeneously on a two-dimensional (2D) self-assembled gold-nanoparticle sheet. The LSPR of the gold-nanoparticle sheet provides high-contrast interfacial images due to the confined light within a region a few tens of nanometers from the particles and the enhancement of fluorescence. Test experiments on rat basophilic leukemia (RBL-2H3) cells with fluorescence-labeled actin filaments revealed high axial and lateral resolution even under a regular epifluorescence microscope, which produced higher quality images than those captured under a total internal reflection fluorescence (TIRF) microscope. This non-scanning-type, high-resolution imaging method will be an effective tool for monitoring interfacial phenomena that exhibit relatively rapid reaction kinetics in various cellular and molecular dynamics.
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Affiliation(s)
- Shihomi Masuda
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuhki Yanase
- Graduate School of Biomedical & Health Science, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima City Hiroshima, 734-8553, Japan
| | - Eiji Usukura
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Sou Ryuzaki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Pangpang Wang
- Education Center for Global Leaders in Molecular Systems for Devices, Kyushu University, Fukuoka, 819-0395, Japan
| | - Koichi Okamoto
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Thasaneeya Kuboki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Satoru Kidoaki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kaoru Tamada
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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12
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Cai X, Bai B, Zhang R, Wang C, Chen J. Apelin receptor homodimer-oligomers revealed by single-molecule imaging and novel G protein-dependent signaling. Sci Rep 2017; 7:40335. [PMID: 28091541 PMCID: PMC5238433 DOI: 10.1038/srep40335] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/05/2016] [Indexed: 12/24/2022] Open
Abstract
The apelin receptor (APJ) belongs to family A of the G protein-coupled receptors (GPCRs) and is a potential pharmacotherapeutic target for heart failure, hypertension, and other cardiovascular diseases. There is evidence APJ heterodimerizes with other GPCRs; however, the existence of APJ homodimers and oligomers remains to be investigated. Here, we measured APJ monomer-homodimer-oligomer interconversion by monitoring APJ dynamically on cells and compared their proportions, spatial arrangement, and mobility using total internal reflection fluorescence microscopy, resonance energy transfer, and proximity biotinylation. In cells with <0.3 receptor particles/μm2, approximately 60% of APJ molecules were present as dimers or oligomers. APJ dimers were present on the cell surface in a dynamic equilibrium with constant formation and dissociation of receptor complexes. Furthermore, we applied interference peptides and MALDI-TOF mass spectrometry to confirm APJ homo-dimer and explore the dimer-interfaces. Peptides corresponding to transmembrane domain (TMD)1, 2, 3, and 4, but not TMD5, 6, and 7, disrupted APJ dimerization. APJ mutants in TMD1 and TMD2 also decreased bioluminescence resonance energy transfer of APJ dimer. APJ dimerization resulted in novel functional characteristics, such as a distinct G-protein binding profile and cell responses after agonist stimulation. Thus, dimerization may serve as a unique mechanism for fine-tuning APJ-mediated functions.
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Affiliation(s)
- Xin Cai
- Department of Physiology, School of Medicine, Shandong University, Jinan, Shandong, 250012 P.R. China.,Neurobiology Institute, Jining Medical University, Jining, Shandong, 272067 P.R. China
| | - Bo Bai
- Neurobiology Institute, Jining Medical University, Jining, Shandong, 272067 P.R. China
| | - Rumin Zhang
- Neurobiology Institute, Jining Medical University, Jining, Shandong, 272067 P.R. China
| | - Chunmei Wang
- Neurobiology Institute, Jining Medical University, Jining, Shandong, 272067 P.R. China
| | - Jing Chen
- Neurobiology Institute, Jining Medical University, Jining, Shandong, 272067 P.R. China.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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13
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Yip CM. Correlative optical and scanning probe microscopies for mapping interactions at membranes. Methods Mol Biol 2013; 950:439-56. [PMID: 23086889 DOI: 10.1007/978-1-62703-137-0_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative approaches for real-time imaging on molecular-length scales are providing researchers with powerful strategies for characterizing molecular and cellular structures and dynamics. Combinatorial techniques that integrate two or more distinct imaging modalities are particularly compelling as they provide a means for overcoming the limitations of the individual modalities and, when applied simultaneously, enable the collection of rich multi-modal datasets. Almost since its inception, scanning probe microscopy has closely associated with optical microscopy. This is particularly evident in the fields of cellular and molecular biophysics where researchers are taking full advantage of these real-time, in situ, tools to acquire three-dimensional molecular-scale topographical images with nanometer resolution, while simultaneously characterizing their structure and interactions though conventional optical microscopy. The ability to apply mechanical or optical stimuli provides an additional experimental dimension that has shown tremendous promise for examining dynamic events on sub-cellular length scales. In this chapter, we describe recent efforts in developing these integrated platforms, the methodology for, and inherent challenges in, performing coupled imaging experiments, and the potential and future opportunities of these research tools for the fields of molecular and cellular biophysics with a specific emphasis on the application of these coupled approaches for the characterization of interactions occurring at membrane interfaces.
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Affiliation(s)
- Christopher M Yip
- Department of Chemical Engineering and Applied Chemistry, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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14
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Jensen EC. Overview of Live-Cell Imaging: Requirements and Methods Used. Anat Rec (Hoboken) 2012; 296:1-8. [DOI: 10.1002/ar.22554] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/05/2012] [Accepted: 07/26/2012] [Indexed: 11/11/2022]
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15
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Lu G, Liu J, Zhang T, Li W, Hou L, Luo C, Lei F, Manfait M, Gong Q. Plasmonic near-field in the vicinity of a single gold nanoparticle investigated with fluorescence correlation spectroscopy. NANOSCALE 2012; 4:3359-3364. [PMID: 22569965 DOI: 10.1039/c2nr12137a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We proposed the estimation of the plasmonic near-field volume in the vicinity of a single gold nanoparticle, and observed experimentally the near-field variation due to a change in the polarization of the illuminating light. Under total-internal-reflection illumination, the plasmonic near-field volume is varied by tuning the polarization of the excitation light. The variation in the optical near-field around a single gold nanoparticle was simulated theoretically with a finite-difference time domain method, and was characterized experimentally employing a fluorescence correlation spectroscopy technique. The experimental results are in agreement quantitatively with the theoretical analysis. These results are highly relevant to important efforts to clarify the interaction between the emitter and the plasmonic antenna, and should be helpful in developing a plasmonic-enhanced total-internal-reflection fluorescence imaging microscope.
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Affiliation(s)
- Guowei Lu
- Department of Physics, State Key Laboratory for Mesoscopic Physics, Peking University, 100871 Beijing, China.
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16
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Brameshuber M, Schütz GJ. Detection and quantification of biomolecular association in living cells using single-molecule microscopy. Methods Enzymol 2012; 505:159-86. [PMID: 22289453 DOI: 10.1016/b978-0-12-388448-0.00017-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During their random motion, biomolecules experience a manifold of interactions that transiently conjoin their paths. It is extremely difficult to measure such binding events directly in the context of a living cell: interactions may be short lived, they may affect only a minority fraction of molecules, or they may not lead to a macroscopically observable effect. We describe here a new single-molecule imaging method that allows for detecting and quantifying associations of mobile molecules. By "thinning out clusters while conserving the stoichiometry of labeling" (TOCCSL), we can virtually dilute the probe directly in the cell, without affecting the fluorescence labeling of single clusters. Essentially, an analysis region is created within the cell by photobleaching; this region is devoid of active probe. Brownian diffusion or other transport processes lead to reentry of active probe into the analysis region. At the onset of the recovery process, single spots can be resolved as well-separated, diffraction-limited signals. Standard single-molecule microscopy then allows for characterizing the spots in terms of their composition and mobility.
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Affiliation(s)
- Mario Brameshuber
- Biophysics Institute, Johannes Kepler University Linz, Altenbergerstr., Linz, Austria
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17
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Ortega-Arroyo J, Kukura P. Interferometric scattering microscopy (iSCAT): new frontiers in ultrafast and ultrasensitive optical microscopy. Phys Chem Chem Phys 2012; 14:15625-36. [DOI: 10.1039/c2cp41013c] [Citation(s) in RCA: 205] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Brown A, Ngai TY, Barnes MA, Key JA, Cairo CW. Substituted Benzoxadiazoles as Fluorogenic Probes: A Computational Study of Absorption and Fluorescence. J Phys Chem A 2011; 116:46-54. [DOI: 10.1021/jp2079296] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alex Brown
- Department of Chemistry and ‡Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Tsz Yan Ngai
- Department of Chemistry and ‡Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Marie A. Barnes
- Department of Chemistry and ‡Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Jessie A. Key
- Department of Chemistry and ‡Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Christopher W. Cairo
- Department of Chemistry and ‡Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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19
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Esfandiari NM, Wang Y, Bass JY, Blum SA. Deconvoluting Subensemble Chemical Reaction Kinetics of Platinum–Sulfur Ligand Exchange Detected with Single-Molecule Fluorescence Microscopy. Inorg Chem 2011; 50:9201-3. [DOI: 10.1021/ic2007952] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. Melody Esfandiari
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yong Wang
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Jonathan Y. Bass
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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21
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Abstract
Observing individual molecules in a complex environment by fluorescence microscopy is becoming increasingly important in biological and medical research, for which critical reduction of observation volume is required. Here, we demonstrate the use of vertically aligned silicon dioxide nanopillars to achieve below-the-diffraction-limit observation volume in vitro and inside live cells. With a diameter much smaller than the wavelength of visible light, a transparent silicon dioxide nanopillar embedded in a nontransparent substrate restricts the propagation of light and affords evanescence wave excitation along its vertical surface. This effect creates highly confined illumination volume that selectively excites fluorescence molecules in the vicinity of the nanopillar. We show that this nanopillar illumination can be used for in vitro single-molecule detection at high fluorophore concentrations. In addition, we demonstrate that vertical nanopillars interface tightly with live cells and function as highly localized light sources inside the cell. Furthermore, specific chemical modification of the nanopillar surface makes it possible to locally recruit proteins of interest and simultaneously observe their behavior within the complex, crowded environment of the cell.
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Rurack K, Spieles M. Fluorescence quantum yields of a series of red and near-infrared dyes emitting at 600-1000 nm. Anal Chem 2011; 83:1232-42. [PMID: 21250654 DOI: 10.1021/ac101329h] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The determination of the fluorescence quantum yields (QY, Φ(f)) of a series of fluorescent dyes that span the absorption/excitation and emission ranges of 520-900 and 600-1000 nm is reported. The dyes encompass commercially available rhodamine 101 (Rh-101, Φ(f) = 0.913), cresyl violet (0.578), oxazine 170 (0.579), oxazine 1 (0.141), cryptocyanine (0.012), HITCI (0.283), IR-125 (0.132), IR-140 (0.167), and four noncommercial cyanine dyes with specific spectroscopic features, all of them in dilute ethanol solution. The QYs have been measured relative to the National Institute of Standards and Technology's standard reference material (SRM) 936a (quinine sulfate, QS) on a traceably characterized fluorometer, employing a chain of transfer standard dyes that include coumarin 102 (Φ(f) = 0.764), coumarin 153 (0.544), and DCM (0.435) as links between QS and Rh-101. The QY of Rh-101 has also been verified in direct measurements against QS using two approaches that rely only on instrument correction. In addition, the effects of temperature and the presence of oxygen on the fluorescence quantum yield of Rh-101 have been assessed.
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Affiliation(s)
- Knut Rurack
- Division 1.5 Bioanalytics, BAM Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany.
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23
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Esfandiari NM, Wang Y, McIntire TM, Blum SA. Real-Time Imaging of Platinum−Sulfur Ligand Exchange Reactions at the Single-Molecule Level via a General Chemical Technique. Organometallics 2011. [DOI: 10.1021/om100911n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- N. Melody Esfandiari
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Yong Wang
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Theresa M. McIntire
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California at Irvine, Irvine, California 92697, United States
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24
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Esfandiari NM, Wang Y, Bass JY, Cornell TP, Otte DAL, Cheng MH, Hemminger JC, McIntire TM, Mandelshtam VA, Blum SA. Single-Molecule Imaging of Platinum Ligand Exchange Reaction Reveals Reactivity Distribution. J Am Chem Soc 2010; 132:15167-9. [DOI: 10.1021/ja105517d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Yong Wang
- Department of Chemistry, University of California, Irvine, California 92697
| | - Jonathan Y. Bass
- Department of Chemistry, University of California, Irvine, California 92697
| | - Trevor P. Cornell
- Department of Chemistry, University of California, Irvine, California 92697
| | - Douglas A. L. Otte
- Department of Chemistry, University of California, Irvine, California 92697
| | - Ming H. Cheng
- Department of Chemistry, University of California, Irvine, California 92697
| | - John C. Hemminger
- Department of Chemistry, University of California, Irvine, California 92697
| | | | | | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, California 92697
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Wagner M, Weber P, Bruns T, Strauss WSL, Wittig R, Schneckenburger H. Light dose is a limiting factor to maintain cell viability in fluorescence microscopy and single molecule detection. Int J Mol Sci 2010; 11:956-966. [PMID: 20479994 PMCID: PMC2869222 DOI: 10.3390/ijms11030956] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 02/20/2010] [Accepted: 02/21/2010] [Indexed: 12/04/2022] Open
Abstract
A test system for cell viability based on colony formation has been established and applied to high resolution fluorescence microscopy and single molecule detection. Living cells were irradiated either by epi-illumination or by total internal reflection (TIR) of a laser beam, and light doses where at least 90% of irradiated cells survived were determined. These light doses were in the range of a few J/cm2 up to about 200 J/cm2 depending on the wavelength of illumination as well as on the presence or absence of a fluorescent dye (e.g., the membrane marker laurdan). In general, cells were less sensitive to TIR than to epi-illumination. However, comparably high light doses needed for repetitive excitation of single molecules limit the application of super-resolution microscopy to living cells.
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Affiliation(s)
- Michael Wagner
- Institut für Angewandte Forschung, Hochschule Aalen, Beethovenstr. 1, D-73430 Aalen, Germany; E-Mails:
(M.W.);
(P.W.);
(T.B.)
| | - Petra Weber
- Institut für Angewandte Forschung, Hochschule Aalen, Beethovenstr. 1, D-73430 Aalen, Germany; E-Mails:
(M.W.);
(P.W.);
(T.B.)
| | - Thomas Bruns
- Institut für Angewandte Forschung, Hochschule Aalen, Beethovenstr. 1, D-73430 Aalen, Germany; E-Mails:
(M.W.);
(P.W.);
(T.B.)
| | - Wolfgang S. L. Strauss
- Institut für Lasertechnologien in der Medizin und Meßtechnik an der Universität Ulm, Helmholtzstr. 12, D-89081 Ulm, Germany; E-Mails:
(W.S.L.S.);
(R.W.)
| | - Rainer Wittig
- Institut für Lasertechnologien in der Medizin und Meßtechnik an der Universität Ulm, Helmholtzstr. 12, D-89081 Ulm, Germany; E-Mails:
(W.S.L.S.);
(R.W.)
| | - Herbert Schneckenburger
- Institut für Angewandte Forschung, Hochschule Aalen, Beethovenstr. 1, D-73430 Aalen, Germany; E-Mails:
(M.W.);
(P.W.);
(T.B.)
- Institut für Lasertechnologien in der Medizin und Meßtechnik an der Universität Ulm, Helmholtzstr. 12, D-89081 Ulm, Germany; E-Mails:
(W.S.L.S.);
(R.W.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel.: +49-7361-576-3401
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Alcor D, Gouzer G, Triller A. Single-particle tracking methods for the study of membrane receptors dynamics. Eur J Neurosci 2009; 30:987-97. [PMID: 19735284 DOI: 10.1111/j.1460-9568.2009.06927.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Single-particle tracking (SPT) applications have been growing rapidly in the field of cell biology, and in particular in neurobiology, as a means of unravelling the involvement of diffusion dynamics of neurotransmitter receptors and other synaptic proteins in the regulation of neuronal activity. Suitable probes and technological improvements make SPT more accessible than it used to be and open up broad applications in cellular biology. In this technical highlight, we give an overview of the experimental approach in SPT. The concepts and results in neurobiology have already been the object of detailed reviews. Here, we focus on a qualitative description of the implementation of SPT, from molecule labelling to acquisition, data treatment and analysis of protein diffusion properties. Constraints, limitations and future developments are discussed.
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Affiliation(s)
- Damien Alcor
- Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, Paris, France
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28
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Hoover DK, Lee EJ, Yousaf MN. Total internal reflection fluorescence microscopy of cell adhesion on patterned self-assembled monolayers on gold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:2563-2566. [PMID: 19437680 DOI: 10.1021/la803927k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the use of total internal reflection fluorescence microscopy (TIRFM) to study cell adhesion on patterned self-assembled monolayers (SAMs) on gold surfaces. Microcontact printing was used to pattern hydrophobic features to which the extracellular protein fibronectin was adsorbed, while dip-pen nanolithography was used to produce electroactive nanoarrays of hydroquinone-terminated alkanethiol on gold-coated quartz substrates. The hydroquinone was electrochemically oxidized to the corresponding quinone, and an oxyamine-tethered linear Arg-Gly-Asp (RGD) peptide was chemoselectively immobilized. A prism-based method of TIRFM was used to examine adhered cells on both the microscale and nanoscale features. We also demonstrate that, following imaging with TIRFM, the substrates can be visualized using conventional fluorescence microscopy.
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Affiliation(s)
- Diana K Hoover
- Department of Chemistry, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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29
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Gregory JA, Becker EC, Pogliano K. Bacillus subtilis MinC destabilizes FtsZ-rings at new cell poles and contributes to the timing of cell division. Genes Dev 2009; 22:3475-88. [PMID: 19141479 DOI: 10.1101/gad.1732408] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Division site selection in rod-shaped bacteria depends on nucleoid occlusion, which prevents division over the chromosome and MinCD, which prevent division at the poles. MinD is thought to localize MinC to the cell poles where it prevents FtsZ assembly. Time-lapse microscopy demonstrates that in Bacillus subtilis transient polar FtsZ rings assemble adjacent to recently completed septa and that in minCD strains these persist and are used for division, producing a minicell. This suggests that MinC acts when division proteins are released from newly completed septa to prevent their immediate reassembly at new cell poles. The minCD mutant appears to uncouple FtsZ ring assembly from cell division and thus shows a variable interdivisional time and a rapid loss of cell cycle synchrony. Functional MinC-GFP expressed from the chromosome minCD locus is dynamic. It is recruited to active division sites before septal biogenesis, rotates around the septum, and moves away from completed septa. Thus high concentrations of MinC are found primarily at the septum and, more transiently, at the new cell pole. DivIVA and MinD recruit MinC to division sites, rather than mediating the stable polar localization previously thought to restrict MinC activity to the pole. Together, our results suggest that B. subtilis MinC does not inhibit FtsZ assembly at the cell poles, but rather prevents polar FtsZ rings adjacent to new cell poles from supporting cell division.
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Affiliation(s)
- James A Gregory
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA
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30
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Wieser S, Schütz GJ. Tracking single molecules in the live cell plasma membrane—Do’s and Don’t’s. Methods 2008; 46:131-40. [DOI: 10.1016/j.ymeth.2008.06.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/26/2008] [Accepted: 06/05/2008] [Indexed: 10/21/2022] Open
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Oreopoulos J, Yip CM. Combined scanning probe and total internal reflection fluorescence microscopy. Methods 2008; 46:2-10. [PMID: 18602010 DOI: 10.1016/j.ymeth.2008.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/22/2008] [Indexed: 11/19/2022] Open
Abstract
Combining scanning probe and optical microscopy represents a powerful approach for investigating structure-function relationships and dynamics of biomolecules and biomolecular assemblies, often in situ and in real-time. This platform technology allows us to obtain three-dimensional images of individual molecules with nanometer resolution, while simultaneously characterizing their structure and interactions though complementary techniques such as optical microscopy and spectroscopy. We describe herein the practical strategies for the coupling of scanning probe and total internal reflection fluorescence microscopy along with challenges and the potential applications of such platforms, with a particular focus on their application to the study of biomolecular interactions at membrane surfaces.
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Affiliation(s)
- John Oreopoulos
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ont., Canada M5S 3E1
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Mellado M, Carrasco YR. Imaging techniques: new insights into chemokine/chemokine receptor biology at the immune system. Pharmacol Ther 2008; 119:24-32. [PMID: 18573535 DOI: 10.1016/j.pharmthera.2008.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 04/28/2008] [Indexed: 11/16/2022]
Abstract
Our current knowledge of molecular and cellular responses in vivo is based mainly on event reconstruction from time-freeze observations. Conventional biochemical and genetic methods consider the cell as an individual entity and ligand/receptor pairs as isolated systems. In addition, the data refer to the average behavior of a pool of cells and/or receptors removed from their real-life context. The use of new technologies, particularly real-time imaging approaches, is showing us that biological responses are highly dynamic and extremely dependent on the context in which they take place, and therefore much more diverse than initially envisaged. This review focuses on the mechanistic insights that new imaging techniques, such as those based on resonance energy transfer and two-photon microscopy, contribute to our understanding of how receptors work within a single cell, and how cells work within a tissue. Cell movement is a complex and regulated process; it has a key role in embryogenesis, organogenesis, wound-healing and tumor invasion. Nonetheless, it is in immune system homeostasis and response that cell movement becomes essential. For this reason, immunology is being radically transformed and enriched by these new approaches. We will discuss the use of these techniques for studying chemokine/chemokine receptors and their role in the immune system function, and comment on the potential contribution to the design of therapeutic strategies.
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Affiliation(s)
- Mario Mellado
- Department of Immunology and Oncology, National Centre of Biotechnology/CSIC, Darwin 3, UAM-Campus de Cantoblanco, Madrid E-28049, Spain.
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33
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Visualizing chemical interactions in life sciences with wide-field fluorescence microscopy towards the single-molecule level. Trends Analyt Chem 2007. [DOI: 10.1016/j.trac.2007.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Vilfan ID, Kamping W, van den Hout M, Candelli A, Hage S, Dekker NH. An RNA toolbox for single-molecule force spectroscopy studies. Nucleic Acids Res 2007; 35:6625-39. [PMID: 17905817 PMCID: PMC2095808 DOI: 10.1093/nar/gkm585] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/15/2007] [Accepted: 07/17/2007] [Indexed: 01/29/2023] Open
Abstract
Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for single-molecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cation-dependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one's disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs.
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Affiliation(s)
| | | | | | | | | | - Nynke H. Dekker
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands
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Levi V, Gratton E. Exploring dynamics in living cells by tracking single particles. Cell Biochem Biophys 2007; 48:1-15. [PMID: 17703064 DOI: 10.1007/s12013-007-0010-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 12/19/2022]
Abstract
In the last years, significant advances in microscopy techniques and the introduction of a novel technology to label living cells with genetically encoded fluorescent proteins revolutionized the field of Cell Biology. Our understanding on cell dynamics built from snapshots on fixed specimens has evolved thanks to our actual capability to monitor in real time the evolution of processes in living cells. Among these new tools, single particle tracking techniques were developed to observe and follow individual particles. Hence, we are starting to unravel the mechanisms driving the motion of a wide variety of cellular components ranging from organelles to protein molecules by following their way through the cell. In this review, we introduce the single particle tracking technology to new users. We briefly describe the instrumentation and explain some of the algorithms commonly used to locate and track particles. Also, we present some common tools used to analyze trajectories and illustrate with some examples the applications of single particle tracking to study dynamics in living cells.
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Affiliation(s)
- Valeria Levi
- Laboratorio de Electrónica Cuántica, Departamento de Física, Universidad de Buenos Aires, Pabellón I Ciudad Universitaria, Buenos Aires, Argentina
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Ma X, Wang Q, Jiang Y, Xiao Z, Fang X, Chen YG. Lateral diffusion of TGF-beta type I receptor studied by single-molecule imaging. Biochem Biophys Res Commun 2007; 356:67-71. [PMID: 17346672 DOI: 10.1016/j.bbrc.2007.02.080] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 02/16/2007] [Indexed: 10/23/2022]
Abstract
In this report, we investigated the lateral diffusion of transforming growth factor beta (TGF-beta) type I receptor (TbetaRI) in living cells by imaging and tracking individual green fluorescent protein tagged TbetaRI on the cell membrane. We found that when co-expressed with TGF-beta type II receptor (TbetaRII), the mobility of TbetaRI decreased significantly after TGF-beta1 stimulation. However, in the cells that had been depleted of cholesterol with Nystatin or methyl-beta-cyclodextrin, the diffusion rate of TbetaRI was not changed by TGF-beta1 treatment. Our observations suggest that membrane lipid-rafts provide an environment that facilitates the association of TbetaRI and TbetaRII for cell signaling.
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Affiliation(s)
- Xinyong Ma
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China
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Abstract
Single-molecule spectroscopy is an important new approach for studying the intrinsically heterogeneous process of protein folding. This Review illustrates how different single-molecule fluorescence techniques have improved our understanding of mechanistic aspects in protein folding, exemplified by a series of recent experiments on a small protein.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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38
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Leutenegger M, Blom H, Widengren J, Eggeling C, Gösch M, Leitgeb RA, Lasser T. Dual-color total internal reflection fluorescence cross-correlation spectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2006; 11:040502. [PMID: 16965125 DOI: 10.1117/1.2221714] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present the development and first application of a novel dual-color total internal reflection (TIR) fluorescence system for single-molecule coincidence analysis and fluorescence cross-correlation spectroscopy (FCCS). As a performance analysis, we measured a synthetic DNA-binding assay, demonstrating this dual-color TIR-FCCS approach to be a suitable method for measuring coincidence assays such as biochemical binding, fusion, or signal transduction at solid/liquid interfaces. Due to the very high numerical aperture of the epi-illumination configuration, our setup provides a very high fluorescence collection efficiency resulting in a two- to three-fold increase in molecular brightness compared to conventional confocal FCCS. Further improvements have been achieved through global analysis of the spectroscopic data.
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Nenasheva TA, Mashanov GI. Visualization of single fluorophores in living cells. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906030110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bruns T, Strauss WSL, Sailer R, Wagner M, Schneckenburger H. Total internal reflectance fluorescence reader for selective investigations of cell membranes. JOURNAL OF BIOMEDICAL OPTICS 2006; 11:34011. [PMID: 16822061 DOI: 10.1117/1.2208617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A novel setup for fluorescence measurements of surfaces of biological samples, in particular the plasma membrane of living cells, is described. The method is based on splitting of a laser beam and multiple total internal reflections (TIR) within the bottom of a microtiter plate (cell substrate), such that up to 96 individual samples are illuminated simultaneously by an evanescent electromagnetic field. Main prerequisites are an appropriate thickness and a high transmission of the glass bottom, which is attached to the 96-well cell culture plate by a noncytotoxic adhesive. Glass rods of rectangular cross sections are optically coupled to this bottom for TIR illumination. Fluorescence arising from the plasma membrane of living cells is detected simultaneously from all samples using an integrating charge-coupled device (CCD) camera. The TIR fluorescence reader is validated using cultivated cells incubated with different fluorescent markers, as well as stably transfected cells expressing a fluorescent membrane-associating protein. In addition, particularly with regard to potential pharmaceutical applications, the kinetics of the intracellular translocation of a fluorescent protein kinase c fusion protein upon stimulation of the cells is determined.
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Affiliation(s)
- Thomas Bruns
- Hochschule Aalen, Institut für Angewandte Forschung, Germany
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Abstract
Total internal reflection fluorescence (TIRF) is the technique of choice to visualize and quantify cellular events localized at the basal plasma membrane of adherent cells. By selectively illuminating the first 200 nm above the basal membrane, it allows maximal resolution in the vertical z-axis. In this chapter, I describe a prism-based TIRF setup and the procedures to visualize the actin and microtubule cytoskeleton in migrating astrocytes. TIRF microscopy provides quantitative information on the organization of the cytoskeleton in both fixed and live migrating cells.
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Shaw JE, Oreopoulos J, Wong D, Hsu JCY, Yip CM. Coupling evanescent-wave fluorescence imaging and spectroscopy with scanning probe microscopy: challenges and insights from TIRF–AFM. SURF INTERFACE ANAL 2006. [DOI: 10.1002/sia.2444] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Uyemura T, Takagi H, Yanagida T, Sako Y. Single-molecule analysis of epidermal growth factor signaling that leads to ultrasensitive calcium response. Biophys J 2005; 88:3720-30. [PMID: 15749770 PMCID: PMC1305518 DOI: 10.1529/biophysj.104.053330] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Accepted: 02/22/2005] [Indexed: 01/22/2023] Open
Abstract
Quantitative relationships between inputs and outputs of signaling systems are fundamental information for the understanding of the mechanism of signal transduction. Here we report the correlation between the number of epidermal growth factor (EGF) bindings and the response probability of intracellular calcium elevation. Binding of EGF molecules and changes of intracellular calcium concentration were measured for identical HeLa human epithelial cells. It was found that 300 molecules of EGF were enough to induce calcium response in half of the cells. This number is quite small compared to the number of EGF receptors (EGFR) expressed on the cell surface (50,000). There was a sigmoidal correlation between the response probability and the number of EGF bindings, meaning an ultrasensitive reaction. Analysis of the cluster size distribution of EGF demonstrated that dimerization of EGFR contributes to this switch-like ultrasensitive response. Single-molecule analysis revealed that EGF bound faster to clusters of EGFR than to monomers. This property should be important for effective formation of signaling dimers of EGFR under very small numbers of EGF bindings and suggests that the expression of excess amounts of EGFR on the cell surface is required to prepare predimers of EGFR with a large association rate constant to EGF.
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Affiliation(s)
- Takeshi Uyemura
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, and Laboratories of Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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Schneckenburger H. Total internal reflection fluorescence microscopy: technical innovations and novel applications. Curr Opin Biotechnol 2005; 16:13-8. [PMID: 15722010 DOI: 10.1016/j.copbio.2004.12.004] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent years have seen the introduction of novel techniques and applications of total internal reflection fluorescence microscopy (TIRFM). Key technical achievements include miniaturization, enhanced depth resolution, reduction of detection volumes and the combination of TIRFM with other microscopic techniques. Novel applications have concentrated on single-molecule detection (e.g. of cellular receptors), imaging of exocytosis or endocytosis, measurements of adhesion foci of microtubules, and studies of the localization, activity and structural arrangement of specific ion channels. In addition to conventional fluorescent dyes, genetically engineered fluorescent proteins are increasingly being used to measure molecular conformations or intermolecular distances by fluorescence resonance energy transfer.
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Affiliation(s)
- Herbert Schneckenburger
- Hochschule Aalen, Institut für Angewandte Forschung, Beethovenstrasse 1, 73430 Aalen, Germany.
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Ohara-Imaizumi M, Nishiwaki C, Nakamichi Y, Kikuta T, Nagai S, Nagamatsu S. Correlation of syntaxin-1 and SNAP-25 clusters with docking and fusion of insulin granules analysed by total internal reflection fluorescence microscopy. Diabetologia 2004; 47:2200-7. [PMID: 15647897 DOI: 10.1007/s00125-004-1579-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 08/05/2004] [Indexed: 11/27/2022]
Abstract
AIMS/HYPOTHESIS The interaction of syntaxin-1 and SNAP-25 with insulin exocytosis was examined using the diabetic Goto-Kakizaki (GK) rat and a total internal reflection fluorescence (TIRF) imaging system. METHODS Primary rat pancreatic beta cells were immunostained with anti-syntaxin-1A, anti-SNAP-25 and anti-insulin antibodies, and then observed by TIRF microscopy. The real-time image of GFP-labelled insulin granules motion was monitored by TIRF. RESULTS The number of syntaxin-1A and SNAP-25 clusters, and the number of docked insulin granules on the plasma membrane were reduced in GK beta cells. When GK rats were treated with daily insulin injection for 2 weeks, the number of syntaxin-1 and SNAP-25 clusters was restored, along with the number of docked insulin granules. The infection of GK beta cells with Adex1CA SNAP-25 increased the number of docked insulin granules. TIRF imaging analysis demonstrated that the decreased number of fusion events from previously docked insulin granules in GK beta cells was restored when the number of docked insulin granules increased by insulin treatment or Adex1CA SNAP-25 infection. CONCLUSIONS/INTERPRETATION There was a close correlation between the number of syntaxin-1 and SNAP-25 clusters and the number of docked insulin granules, which is associated with the fusion of insulin granules.
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Affiliation(s)
- M Ohara-Imaizumi
- Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611, Japan
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Bunt G, Wouters FS. Visualization of Molecular Activities Inside Living Cells with Fluorescent Labels. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 237:205-77. [PMID: 15380669 DOI: 10.1016/s0074-7696(04)37005-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The major task of modern cell biology is to identify the function and relation of the many different gene products, discovered by genomics and proteomics approaches, in the context of the living cell. To achieve this goal, an increasing toolbox of custom-designed biosensors based on fluorescent labels is available to study the molecular activities of the cellular machinery. An overview of the current status of the young field of molecular-cellular physiology is presented that includes the application of fluorescent labels in the design of biosensors and the major detection schemes used to extract their sensing information. In particular, the use of the photophysical phenomenon of Förster resonance energy transfer (FRET) as a powerful indicator of cellular biochemical events is discussed. In addition, we will point out the challenges and directions of the field and project the short-term future for the application of fluorescence-based biosensors in biology.
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Affiliation(s)
- Gertrude Bunt
- Max-Planck-Institute for Experimental Medicine, Molecular Biology of Neuronal Signals, Göttingen, Germany
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