1
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Liu Q, Fong B, Yoo S, Unruh JR, Guo F, Yu Z, Chen J, Si K, Li R, Zhou C. Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface. Proc Natl Acad Sci U S A 2023; 120:e2300475120. [PMID: 37494397 PMCID: PMC10401023 DOI: 10.1073/pnas.2300475120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Eukaryotes organize cellular contents into membrane-bound organelles and membrane-less condensates, for example, protein aggregates. An unsolved question is why the ubiquitously distributed proteins throughout the cytosol give rise to spatially localized protein aggregates on the organellar surface, like mitochondria. We report that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in budding yeast and human cells. This is because misfolded cytosolic proteins do not autonomously aggregate in vivo; instead, they are recruited to the condensation sites initiated by Tom70's substrates (nascent mitochondrial proteins) on the organellar membrane using multivalent hydrophobic interactions. Knocking out Tom70 partially impairs, while overexpressing Tom70 increases the formation and association between cytosolic protein aggregates and mitochondria. In addition, ectopic targeting Tom70 and its substrates to the vacuole surface is able to redirect the localized aggregation from mitochondria to the vacuolar surface. Although other redundant mechanisms may exist, this nascent mitochondrial proteins-based initiation of protein aggregation likely explains the localized condensation of otherwise ubiquitously distributed molecules on the mitochondria. Disrupting the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on Aging, Novato, CA94945
| | - Benjamin Fong
- Buck Institute for Research on Aging, Novato, CA94945
| | - Seungmin Yoo
- Buck Institute for Research on Aging, Novato, CA94945
| | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Jingjing Chen
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, MO64110
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS66160
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD21218
- Mechanobiology Institute and Department of Biological Science, National University of Singapore, Singapore117411, Singapore
| | - Chuankai Zhou
- Buck Institute for Research on Aging, Novato, CA94945
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2
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Vyunisheva SA, Myslivets SA, Davletshin NN, Eremeeva EV, Vysotski ES, Pavlov IN, Vyunishev AM. Intracavity enhancement of GFP fluorescence induced by femtosecond laser pulses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122885. [PMID: 37247552 DOI: 10.1016/j.saa.2023.122885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023]
Abstract
The phenomenon of fluorescence is widely used in molecular biology for studying the interaction of light with biological objects. In this article, we present an experimental investigation of the enhancement of laser-induced fluorescence of Clytia gregaria green fluorescent protein. The laser-induced fluorescence method applied in our work combines the advantages of femtosecond laser pulses and a photonic crystal cavity, with the time dependence of the fluorescence signal studied. It is shown that a green fluorescent protein solution placed in a microcavity and excited by femtosecond laser pulses leads to an increase in fluorescence on the microcavity modes, which can be estimated by two orders of magnitude. The dependences of fluorescence signal saturation on the average integrated optical pump power are demonstrated and analyzed. The results obtained are of interest for the development of potential applications of biophotonics and extension of convenient methods of laser-induced fluorescence.
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Affiliation(s)
- Sofiya A Vyunisheva
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 38, Krasnoyarsk, 660036, Russia; Sukachev Institute of Forest, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 28, Krasnoyarsk, 660036, Russia.
| | - Sergey A Myslivets
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 38, Krasnoyarsk, 660036, Russia; Institute of Engineering Physics and Radio Electronics, Siberian Federal University, Academician Kirensky Str. 26, Krasnoyarsk, 660074, Russia.
| | - Nikolay N Davletshin
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 38, Krasnoyarsk, 660036, Russia; Institute of Engineering Physics and Radio Electronics, Siberian Federal University, Academician Kirensky Str. 26, Krasnoyarsk, 660074, Russia.
| | - Elena V Eremeeva
- Institute of Biophysics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 50, Krasnoyarsk, 660036, Russia.
| | - Eugene S Vysotski
- Institute of Biophysics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 50, Krasnoyarsk, 660036, Russia.
| | - Igor N Pavlov
- Sukachev Institute of Forest, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 28, Krasnoyarsk, 660036, Russia; Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Mira Ave. 82, Krasnoyarsk, 660049, Russia.
| | - Andrey M Vyunishev
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 38, Krasnoyarsk, 660036, Russia; Institute of Engineering Physics and Radio Electronics, Siberian Federal University, Academician Kirensky Str. 26, Krasnoyarsk, 660074, Russia.
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3
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Heckert A, Dahal L, Tjian R, Darzacq X. Recovering mixtures of fast-diffusing states from short single-particle trajectories. eLife 2022; 11:e70169. [PMID: 36066004 PMCID: PMC9451534 DOI: 10.7554/elife.70169] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.
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Affiliation(s)
- Alec Heckert
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Liza Dahal
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
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4
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Manton JD. Answering some questions about structured illumination microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210109. [PMID: 35152757 PMCID: PMC8841787 DOI: 10.1098/rsta.2021.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/02/2021] [Indexed: 05/05/2023]
Abstract
Structured illumination microscopy (SIM) provides images of fluorescent objects at an enhanced resolution greater than that of conventional epifluorescence wide-field microscopy. Initially demonstrated in 1999 to enhance the lateral resolution twofold, it has since been extended to enhance axial resolution twofold (2008), applied to live-cell imaging (2009) and combined with myriad other techniques, including interferometric detection (2008), confocal microscopy (2010) and light sheet illumination (2012). Despite these impressive developments, SIM remains, perhaps, the most poorly understood 'super-resolution' method. In this article, we provide answers to the 13 questions regarding SIM proposed by Prakash et al. along with answers to a further three questions. After providing a general overview of the technique and its developments, we explain why SIM as normally used is still diffraction-limited. We then highlight the necessity for a non-polynomial, and not just nonlinear, response to the illuminating light in order to make SIM a true, diffraction-unlimited, super-resolution technique. In addition, we present a derivation of a real-space SIM reconstruction approach that can be used to process conventional SIM and image scanning microscopy (ISM) data and extended to process data with quasi-arbitrary illumination patterns. Finally, we provide a simple bibliometric analysis of SIM development over the past two decades and provide a short outlook on potential future work. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- James D. Manton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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5
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Liu Q, Chang CE, Wooldredge AC, Fong B, Kennedy BK, Zhou C. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging. eLife 2022; 11:e75658. [PMID: 35234609 PMCID: PMC8926401 DOI: 10.7554/elife.75658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here, we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on AgingNovatoUnited States
| | | | | | - Benjamin Fong
- Buck Institute for Research on AgingNovatoUnited States
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoUnited States
- Healthy Longevity Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
- Singapore Institute of Clinical Sciences, A(∗)STARSingaporeSingapore
| | - Chuankai Zhou
- Buck Institute for Research on AgingNovatoUnited States
- USC Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
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6
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Huebinger J, Grecco H, Masip ME, Christmann J, Fuhr GR, Bastiaens PIH. Ultrarapid cryo-arrest of living cells on a microscope enables multiscale imaging of out-of-equilibrium molecular patterns. SCIENCE ADVANCES 2021; 7:eabk0882. [PMID: 34890224 PMCID: PMC8664253 DOI: 10.1126/sciadv.abk0882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Imaging molecular patterns in cells by fluorescence micro- or nanoscopy has the potential to relate collective molecular behavior to cellular function. However, spatial and spectroscopic resolution is fundamentally limited by motional blur caused by finite photon fluxes and photobleaching. At physiological temperatures, photochemical reactivity does not only limit imaging at multiple scales but is also toxic to biochemical reactions that maintain cellular organization. Here, we present cryoprotectant-free ultrarapid cryo-arrest directly on a multimodal fluorescence microscope that preserves the out-of-equilibrium molecular organization of living cells. This allows the imaging of dynamic processes before cryo-arrest in combination with precise molecular pattern determination at multiple scales within the same cells under cryo-arrest. We both experimentally and theoretically show that ultrarapid cryo-arrest overcomes the fundamental resolution barrier imposed by motional blur and photochemical reactivity, enabling observation of native molecular distributions and reaction patterns that are not resolvable at physiological temperatures.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Hernan Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires, Argentina
| | - Martín E. Masip
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Jens Christmann
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Günter R. Fuhr
- Fraunhofer Institute for Biomedical Engineering, Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Philippe I. H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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7
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Minner-Meinen R, Weber JN, Albrecht A, Matis R, Behnecke M, Tietge C, Frank S, Schulze J, Buschmann H, Walla PJ, Mendel RR, Hänsch R, Kaufholdt D. Split-HaloTag imaging assay for sophisticated microscopy of protein-protein interactions in planta. PLANT COMMUNICATIONS 2021; 2:100212. [PMID: 34746759 PMCID: PMC8555439 DOI: 10.1016/j.xplc.2021.100212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 05/04/2023]
Abstract
An ever-increasing number of intracellular multi-protein networks have been identified in plant cells. Split-GFP-based protein-protein interaction assays combine the advantages of in vivo interaction studies in a native environment with additional visualization of protein complex localization. Because of their simple protocols, they have become some of the most frequently used methods. However, standard fluorescent proteins present several drawbacks for sophisticated microscopy. With the HaloTag system, these drawbacks can be overcome, as this reporter forms covalent irreversible bonds with synthetic photostable fluorescent ligands. Dyes can be used in adjustable concentrations and are suitable for advanced microscopy methods. Therefore, we have established the Split-HaloTag imaging assay in plants, which is based on the reconstitution of a functional HaloTag protein upon protein-protein interaction and the subsequent covalent binding of an added fluorescent ligand. Its suitability and robustness were demonstrated using a well-characterized interaction as an example of protein-protein interaction at cellular structures: the anchoring of the molybdenum cofactor biosynthesis complex to filamentous actin. In addition, a specific interaction was visualized in a more distinctive manner with subdiffractional polarization microscopy, Airyscan, and structured illumination microscopy to provide examples of sophisticated imaging. Split-GFP and Split-HaloTag can complement one another, as Split-HaloTag represents an alternative option and an addition to the large toolbox of in vivo methods. Therefore, this promising new Split-HaloTag imaging assay provides a unique and sensitive approach for more detailed characterization of protein-protein interactions using specific microscopy techniques, such as 3D imaging, single-molecule tracking, and super-resolution microscopy.
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Affiliation(s)
- Rieke Minner-Meinen
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Jan-Niklas Weber
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Andreas Albrecht
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Rainer Matis
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Maria Behnecke
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Cindy Tietge
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Stefan Frank
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Jutta Schulze
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Henrik Buschmann
- Botany Department, Universität Osnabrück, Barbara Strasse 11, 49076 Osnabrück, Germany
| | - Peter Jomo Walla
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Ralf-R. Mendel
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Robert Hänsch
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Tiansheng Road No. 2, Beibei District, 400715 Chongqing, P.R. China
- Corresponding author
| | - David Kaufholdt
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
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8
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Miriklis EL, Rozario AM, Rothenberg E, Bell TDM, Whelan DR. Understanding DNA organization, damage, and repair with super-resolution fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 33765677 DOI: 10.1088/2050-6120/abf239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/25/2021] [Indexed: 11/12/2022]
Abstract
Super-resolution microscopy (SRM) comprises a suite of techniques well-suited to probing the nanoscale landscape of genomic function and dysfunction. Offering the specificity and sensitivity that has made conventional fluorescence microscopy a cornerstone technique of biological research, SRM allows for spatial resolutions as good as 10 nanometers. Moreover, single molecule localization microscopies (SMLMs) enable examination of individual molecular targets and nanofoci allowing for the characterization of subpopulations within a single cell. This review describes how key advances in both SRM techniques and sample preparation have enabled unprecedented insights into DNA structure and function, and highlights many of these new discoveries. Ongoing development and application of these novel, highly interdisciplinary SRM assays will continue to expand the toolbox available for research into the nanoscale genomic landscape.
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Affiliation(s)
| | | | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States of America
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Donna R Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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9
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Wang W, Ma Y, Bonaccorsi S, Cong VT, Pandžić E, Yang Z, Goyette J, Lisi F, Tilley RD, Gaus K, Gooding JJ. Investigating Spatial Heterogeneity of Nanoparticles Movement in Live Cells with Pair-Correlation Microscopy and Phasor Analysis. Anal Chem 2021; 93:3803-3812. [PMID: 33590750 DOI: 10.1021/acs.analchem.0c04285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How nanoparticles distribute in living cells and overcome cellular barriers are important criteria in the design of drug carriers. Pair-correlation microscopy is a correlation analysis of fluctuation in the fluorescence intensity obtained by a confocal line scan that can quantify the dynamic properties of nanoparticle diffusion including the number of mobile nanoparticles, diffusion coefficient, and transit time across a spatial distance. Due to the potential heterogeneities in nanoparticle properties and the complexity within the cellular environment, quantification of averaged auto- and pair-correlation profiles may obscure important insights into the ability of nanoparticles to deliver drugs. To overcome this issue, we used phasor analysis to develop a data standardizing method, which can segment the scanned line into several subregions according to diffusion and address the spatial heterogeneity of nanoparticles moving inside cells. The phasor analysis is a fit-free method that represents autocorrelation profiles for each pixel relative to free diffusion on the so-called phasor plots. Phasor plots can then be used to select subpopulations for which the auto- and pair-correlation analysis can be performed separately. We demonstrate the phasor analysis for pair-correlation microscopy for investigating 16 nm, Cy5-labeled silica nanoparticles diffusing across the plasma membrane and green fluorescent proteins (GFP) diffusing across nuclear envelope in MCF-7 cells.
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Affiliation(s)
- Wenqian Wang
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Yuanqing Ma
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Simone Bonaccorsi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Vu Thanh Cong
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Elvis Pandžić
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Zhengmin Yang
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Jesse Goyette
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Fabio Lisi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Richard D Tilley
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
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10
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Optogenetic Imaging of Protein Activity Using Two-Photon Fluorescence Lifetime Imaging Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:295-308. [PMID: 33398821 DOI: 10.1007/978-981-15-8763-4_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Spatiotemporal dynamics of cellular proteins, including protein-protein interactions and conformational changes, is essential for understanding cellular functions such as synaptic plasticity, cell motility, and cell division. One of the best ways to understand the mechanisms of signal transduction is to visualize protein activity with high spatiotemporal resolution in living cells within tissues. Optogenetic probes such as fluorescent proteins, in combination with Förster Resonance Energy Transfer (FRET) techniques, enable the measurement of protein-protein interactions and conformational changes in response to signaling events in living cells. Of the various FRET detection systems, two-photon fluorescence lifetime imaging microscopy (2pFLIM) is one of the methods best suited to monitoring FRET in subcellular compartments of living cells located deep within tissues, such as brain slices. This review will introduce the principle of 2pFLIM-FRET and the use of chromoproteins for imaging intracellular protein activities and protein-protein interactions. Also, we will discuss two examples of 2pFLIM-FRET application: imaging actin polymerization in synapses of hippocampal neurons in brain sections and detecting small GTPase Cdc42 activity in astrocytes.
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11
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Li Y, Yi J, Liu W, Liu Y, Liu J. Gaining insight into cellular cardiac physiology using single particle tracking. J Mol Cell Cardiol 2020; 148:63-77. [PMID: 32871158 DOI: 10.1016/j.yjmcc.2020.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022]
Abstract
Single particle tracking (SPT) is a robust technique to monitor single-molecule behaviors in living cells directly. By this approach, we can uncover the potential biological significance of particle dynamics by statistically characterizing individual molecular behaviors. SPT provides valuable information at the single-molecule level, that could be obscured by simple averaging that is inherent to conventional ensemble measurements. Here, we give a brief introduction to SPT including the commonly used optical implementations, fluorescence labeling strategies, and data analysis methods. We then focus on how SPT has been harnessed to decipher myocardial function. In this context, SPT has provided novel insight into the lateral diffusion of signal receptors and ion channels, the dynamic organization of cardiac nanodomains, subunit composition and stoichiometry of cardiac ion channels, myosin movement along actin filaments, the kinetic features of transcription factors involved in cardiac remodeling, and the intercellular communication by nanotubes. Finally, we speculate on the prospects and challenges of applying SPT to future questions regarding cellular cardiac physiology using SPT.
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Affiliation(s)
- Ying Li
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Jing Yi
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Wenjuan Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Yun Liu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Guangdong Province, China.
| | - Jie Liu
- School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
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12
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Shen Z, Cui S, Dogariu A. Polarization-encoded field measurement in subwavelength scattering. OPTICS LETTERS 2019; 44:3446-3449. [PMID: 31305544 DOI: 10.1364/ol.44.003446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
We demonstrate that polarization encoding provides a convenient way to realize a robust common-path interferometer for measuring both the phase and the amplitude of scattered optical fields. Moreover, for a given detector array, the design allows maximizing the interferometric visibility and, therefore, permits reaching the sensitivity limit for the field measurement. The approach is of particular interest for inefficient scattering scenarios such as subwavelength scattering.
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13
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Otero C, Carreño A, Polanco R, Llancalahuen FM, Arratia-Pérez R, Gacitúa M, Fuentes JA. Rhenium (I) Complexes as Probes for Prokaryotic and Fungal Cells by Fluorescence Microscopy: Do Ligands Matter? Front Chem 2019; 7:454. [PMID: 31297366 PMCID: PMC6606945 DOI: 10.3389/fchem.2019.00454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/07/2019] [Indexed: 12/22/2022] Open
Abstract
Re(I) complexes have exposed highly suitable properties for cellular imaging (especially for fluorescent microscopy) such as low cytotoxicity, good cellular uptake, and differential staining. These features can be modulated or tuned by modifying the ligands surrounding the metal core. However, most of Re(I)-based complexes have been tested for non-walled cells, such as epithelial cells. In this context, it has been proposed that Re(I) complexes are inefficient to stain walled cells (i.e., cells protected by a rigid cell wall, such as bacteria and fungi), presumably due to this physical barrier hampering cellular uptake. More recently, a series of studies have been published showing that a suitable combination of ligands is useful for obtaining Re(I)-based complexes able to stain walled cells. This review summarizes the main characteristics of different fluorophores used in bioimage, remarking the advantages of d6-based complexes, and focusing on Re(I) complexes. In addition, we explored different structural features of these complexes that allow for obtaining fluorophores especially designed for walled cells (bacteria and fungi), with especial emphasis on the ligand choice. Since many pathogens correspond to bacteria and fungi (yeasts and molds), and considering that these organisms have been increasingly used in several biotechnological applications, development of new tools for their study, such as the design of new fluorophores, is fundamental and attractive.
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Affiliation(s)
- Carolina Otero
- Facultad de Medicina, Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Alexander Carreño
- Center for Applied Nanosciences (CANS), Universidad Andres Bello, Santiago, Chile
| | - Rubén Polanco
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago, Chile
| | - Felipe M Llancalahuen
- Facultad de Medicina, Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Ramiro Arratia-Pérez
- Center for Applied Nanosciences (CANS), Universidad Andres Bello, Santiago, Chile
| | - Manuel Gacitúa
- Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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14
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Aaron J, Wait E, DeSantis M, Chew TL. Practical Considerations in Particle and Object Tracking and Analysis. ACTA ACUST UNITED AC 2019; 83:e88. [PMID: 31050869 DOI: 10.1002/cpcb.88] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rapid advancement of live-cell imaging technologies has enabled biologists to generate high-dimensional data to follow biological movement at the microscopic level. Yet, the "perceived" ease of use of modern microscopes has led to challenges whereby sub-optimal data are commonly generated that cannot support quantitative tracking and analysis as a result of various ill-advised decisions made during image acquisition. Even optimally acquired images often require further optimization through digital processing before they can be analyzed. In writing this article, we presume our target audience to be biologists with a foundational understanding of digital image acquisition and processing, who are seeking to understand the essential steps for particle/object tracking experiments. It is with this targeted readership in mind that we review the basic principles of image-processing techniques as well as analysis strategies commonly used for tracking experiments. We conclude this technical survey with a discussion of how movement behavior can be mathematically modeled and described. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jesse Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Eric Wait
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Michael DeSantis
- Light Microscopy Facility, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.,Light Microscopy Facility, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
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15
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Abstract
Interferometric scattering microscopy (iSCAT) is an extremely sensitive imaging method based on the efficient detection of light scattered by nanoscopic objects. The ability to, at least in principle, maintain high imaging contrast independent of the exposure time or the scattering cross section of the object allows for unique applications in single-particle tracking, label-free imaging of nanoscopic (dis)assembly, and quantitative single-molecule characterization. We illustrate these capabilities in areas as diverse as mechanistic studies of motor protein function, viral capsid assembly, and single-molecule mass measurement in solution. We anticipate that iSCAT will become a widely used approach to unravel previously hidden details of biomolecular dynamics and interactions.
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Affiliation(s)
- Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom; ,
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom; ,
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16
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Ando J, Nakamura A, Visootsat A, Yamamoto M, Song C, Murata K, Iino R. Single-Nanoparticle Tracking with Angstrom Localization Precision and Microsecond Time Resolution. Biophys J 2018; 115:2413-2427. [PMID: 30527446 PMCID: PMC6302141 DOI: 10.1016/j.bpj.2018.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 11/16/2022] Open
Abstract
Gold nanoparticles (AuNPs) have been used as a contrast agent for optical imaging of various single biomolecules. Because AuNPs have high scattering efficiency without photobleaching, biomolecular dynamics have been observed with nanometer localization precision and sub-millisecond time resolution. To understand the working principle of biomolecular motors in greater detail, further improvement of the localization precision and time resolution is necessary. Here, we investigated the lower limit of localization precision achievable with AuNPs and the fundamental law, which determines the localization precision. We first used objective-lens-type total internal reflection dark-field microscopy to obtain a scattering signal from an isolated AuNP. The localization precision was inversely proportional to the square root of the photon number, which is consistent with theoretical estimation. The lower limit of precision for a 40 nm AuNP was ∼0.3 nm with 1 ms time resolution and was restricted by detector saturation. To achieve higher localization precision, we designed and constructed an annular illumination total internal reflection dark-field microscopy system with an axicon lens, which can illuminate the AuNPs at high laser intensity without damaging the objective lens. In addition, we used high image magnification to avoid detector saturation. Consequently, we achieved 1.3 Å localization precision for 40 nm AuNPs and 1.9 Å localization precision for 30 nm AuNPs at 1 ms time resolution. Furthermore, even at 33 μs time resolution, localization precisions at 5.4 Å for 40 nm AuNPs and at 1.7 nm for 30 nm AuNPs were achieved. We then observed motion of head of kinesin-1 labeled with AuNP at microsecond time resolution. Transition cycles of bound/unbound states and tethered diffusion of unbound head during stepping motion on microtubule were clearly captured with higher time resolution or smaller AuNP than those used in previous studies, indicating applicability to single-molecule imaging of biomolecular motors.
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Affiliation(s)
- Jun Ando
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Akasit Visootsat
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Mayuko Yamamoto
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
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17
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Cui Y, Yu M, Yao X, Xing J, Lin J, Li X. Single-Particle Tracking for the Quantification of Membrane Protein Dynamics in Living Plant Cells. MOLECULAR PLANT 2018; 11:1315-1327. [PMID: 30296600 DOI: 10.1016/j.molp.2018.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 05/25/2023]
Abstract
The plasma membrane is a sophisticated, organized, and highly heterogeneous structure that compartmentalizes cellular processes. To decipher the biological processes involving membrane proteins, it is necessary to analyze their spatiotemporal dynamics. However, it is difficult to directly assess the dynamics and interactions of biomolecules in living cells using traditional biochemical methods. Single-particle tracking (SPT) methods for imaging and tracking single particles conjugated with fluorescent probes offer an ideal approach to acquire valuable and complementary information about dynamic intracellular processes. SPT can be used to quantitatively monitor the diverse motions of individual particles in living cells. SPT also provides super-spatiotemporal resolution that allows early-stage or rapid response information to be obtained for a better understanding of molecular basis of associated signal transduction processes. More importantly, SPT can be used to detect the motion paths of individual biomolecules in vivo and in situ, thus unveiling the dynamic behavior of the biomolecules that support developmental processes in living cells. In this review, we give an overview of SPT methods, from image acquisition to the detection of single particles, as well as tracking and data analysis. We also discuss recent applications of SPT methods in the field of plant biology to reveal the complex biological functions of membrane proteins.
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Affiliation(s)
- Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaomin Yao
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jingjing Xing
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Jinming Street, Kaifeng 475001, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083, China.
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18
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He K, Huang X, Wang X, Yoo S, Ruiz P, Gdor I, Ferrier NJ, Scherer N, Hereld M, Katsaggelos AK, Cossairt O. Design and simulation of a snapshot multi-focal interferometric microscope. OPTICS EXPRESS 2018; 26:27381-27402. [PMID: 30469808 DOI: 10.1364/oe.26.027381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/19/2018] [Indexed: 05/25/2023]
Abstract
Realizing both high temporal and spatial resolution across a large volume is a key challenge for 3D fluorescent imaging. Towards achieving this objective, we introduce an interferometric multifocus microscopy (iMFM) system, a combination of multifocus microscopy (MFM) with two opposing objective lenses. We show that the proposed iMFM is capable of simultaneously producing multiple focal plane interferometry that provides axial super-resolution and hence isotropic 3D resolution with a single exposure. We design and simulate the iMFM microscope by employing two special diffractive optical elements. The point spread function of this new iMFM microscope is simulated and the image formation model is given. For reconstruction, we use the Richardson-Lucy deconvolution algorithm with total variation regularization for 3D extended object recovery, and a maximum likelihood estimator (MLE) for single molecule tracking. A method for determining an initial axial position of the molecule is also proposed to improve the convergence of the MLE. We demonstrate both theoretically and numerically that isotropic 3D nanoscopic localization accuracy is achievable with an axial imaging range of 2um when tracking a fluorescent molecule in three dimensions and that the diffraction limited axial resolution can be improved by 3-4 times in the single shot wide-field 3D extended object recovery. We believe that iMFM will be a useful tool in 3D dynamic event imaging that requires both high temporal and spatial resolution.
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19
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Basu S, Needham LM, Lando D, Taylor EJR, Wohlfahrt KJ, Shah D, Boucher W, Tan YL, Bates LE, Tkachenko O, Cramard J, Lagerholm BC, Eggeling C, Hendrich B, Klenerman D, Lee SF, Laue ED. FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells. Nat Commun 2018; 9:2520. [PMID: 29955052 PMCID: PMC6023872 DOI: 10.1038/s41467-018-04486-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
A major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods of time in the dense environments found in living cells. Here, we introduce the concept of using FRET to enhance the photophysical properties of photo-modulatable (PM) fluorophores commonly used in such studies. By developing novel single-molecule FRET pairs, consisting of a PM donor fluorophore (either mEos3.2 or PA-JF549) next to a photostable acceptor dye JF646, we demonstrate that FRET competes with normal photobleaching kinetic pathways to increase the photostability of both donor fluorophores. This effect was further enhanced using a triplet-state quencher. Our approach allows us to significantly improve single-molecule tracking of chromatin-binding proteins in live mammalian cells. In addition, it provides a novel way to track the localization and dynamics of protein complexes by labeling one protein with the PM donor and its interaction partner with the acceptor dye.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa-Maria Needham
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Kai J Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Devina Shah
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lawrence E Bates
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Olga Tkachenko
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Julie Cramard
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - B Christoffer Lagerholm
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Brian Hendrich
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Dave Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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20
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PhotoGate microscopy to track single molecules in crowded environments. Nat Commun 2017; 8:13978. [PMID: 28071667 PMCID: PMC5234080 DOI: 10.1038/ncomms13978] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/17/2016] [Indexed: 01/26/2023] Open
Abstract
Tracking single molecules inside cells reveals the dynamics of biological processes, including receptor trafficking, signalling and cargo transport. However, individual molecules often cannot be resolved inside cells due to their high density. Here we develop the PhotoGate technique that controls the number of fluorescent particles in a region of interest by repeatedly photobleaching its boundary. PhotoGate bypasses the requirement of photoactivation to track single particles at surface densities two orders of magnitude greater than the single-molecule detection limit. Using this method, we observe ligand-induced dimerization of a receptor tyrosine kinase at the cell surface and directly measure binding and dissociation of signalling molecules from early endosomes in a dense cytoplasm with single-molecule resolution. We additionally develop a numerical simulation suite for rapid quantitative optimization of Photogate experimental conditions. PhotoGate yields longer tracking times and more accurate measurements of complex stoichiometry than existing single-molecule imaging methods.
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21
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Hansen SR, Rodgers ML, Hoskins AA. Fluorescent Labeling of Proteins in Whole Cell Extracts for Single-Molecule Imaging. Methods Enzymol 2016; 581:83-104. [PMID: 27793294 DOI: 10.1016/bs.mie.2016.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cellular machines such as the spliceosome and ribosome can be composed of dozens of individual proteins and nucleic acids. Given this complexity, it is not surprising that many cellular activities have not yet been biochemically reconstituted. Such processes are often studied in vitro in whole cell or fractionated lysates. This presents a challenge for obtaining detailed biochemical information when the components being investigated may be only a minor component of the extract and unrelated processes may interfere with the assay. Single-molecule fluorescence microscopy methods allow particular biomolecules to be analyzed even in the complex milieu of a cell extract. This is due to the use of bright fluorophores that emit light at wavelengths at which few cellular components fluoresce, and the development of chemical biology tools for attaching these fluorophores to specific cellular proteins. Here, we describe a protocol for fluorescent labeling of endogenous, SNAP-tagged yeast proteins in whole cell extract. This method allows biochemical reactions to be followed in cell lysates in real time using colocalization single-molecule fluorescence microscopy. Labeled complexes can also be isolated from extract and characterized by SNAP tag single-molecule pull-down (SNAP-SiMPull). These approaches have proven useful for studying complex biological machines such as the spliceosome that cannot yet be reconstituted from purified components.
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Affiliation(s)
- S R Hansen
- University of Wisconsin-Madison, Madison, WI, United States
| | - M L Rodgers
- University of Wisconsin-Madison, Madison, WI, United States
| | - A A Hoskins
- University of Wisconsin-Madison, Madison, WI, United States.
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22
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Mangeol P, Peterman EJG. High-resolution real-time dual-view imaging with multiple point of view microscopy. BIOMEDICAL OPTICS EXPRESS 2016; 7:3631-3642. [PMID: 27699125 PMCID: PMC5030037 DOI: 10.1364/boe.7.003631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/22/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Most methods to observe three-dimensional processes in living samples are based on imaging a single plane that is sequentially scanned through the sample. Sequential scanning is inherently slow, which can make it difficult to capture objects moving quickly in three dimensions. Here we present a novel method, multiple point-of-view microscopy (MPoVM), that allows simultaneous capturing of the front and side views of a sample with high resolution. MPoVM can be implemented in most fluorescence microscopes, offering new opportunities in the study of dynamic biological processes in three dimensions.
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Affiliation(s)
- Pierre Mangeol
- Department of Physics and Astronomy & LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Erwin J. G. Peterman
- Department of Physics and Astronomy & LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
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23
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Ostromohov N, Bercovici M, Kaigala GV. Delivery of minimally dispersed liquid interfaces for sequential surface chemistry. LAB ON A CHIP 2016; 16:3015-23. [PMID: 27354032 DOI: 10.1039/c6lc00473c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present a method for sequential delivery of reagents to a reaction site with minimal dispersion of their interfaces. Using segmented flow to encapsulate the reagents as droplets, the dispersion between reagent plugs remains confined in a limited volume, while being transmitted to the reaction surface. In close proximity to the target surface, we use a passive array of microstructures for removal of the oil phase such that the original reagent sequence is reconstructed, and only the aqueous phase reaches the reaction surface. We provide a detailed analysis of the conditions under which the method can be applied and demonstrate maintaining a transition time of 560 ms between reagents transported to a reaction site over a distance of 60 cm. We implemented the method using a vertical microfluidic probe on an open surface, allowing contact-free interaction with biological samples, and demonstrated two examples of assays implemented using the method: measurements of receptor-ligand reaction kinetics and of the fluorescence response of immobilized GFP to local variations in pH. We believe that the method can be useful for studying the dynamic response of cells and proteins to various stimuli, as well as for highly automated multi-step assays.
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Affiliation(s)
- N Ostromohov
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel. and IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
| | - M Bercovici
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
| | - G V Kaigala
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
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24
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Johnson CK, Harms GS. Tracking and localization of calmodulin in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2017-26. [DOI: 10.1016/j.bbamcr.2016.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023]
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25
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Chao J, Ram S, Ward ES, Ober RJ. Investigating the usage of point spread functions in point source and microsphere localization. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2016; 9713:97131M. [PMID: 27141148 PMCID: PMC4851249 DOI: 10.1117/12.2208631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Using a point spread function (PSF) to localize a point-like object, such as a fluorescent molecule or microsphere, represents a common task in single molecule microscopy image data analysis. The localization may differ in purpose depending on the application or experiment, but a unifying theme is the importance of being able to closely recover the true location of the point-like object with high accuracy. We present two simulation studies, both relating to the performance of object localization via the maximum likelihood fitting of a PSF to the object's image. In the first study, we investigate the integration of the PSF over an image pixel, which represents a critical part of the localization algorithm. Specifically, we explore how the fineness of the integration affects how well a point source can be localized, and find the use of too coarse a step size to produce location estimates that are far from the true location, especially when the images are acquired at relatively low magnifications. We also propose a method for selecting an appropriate step size. In the second study, we investigate the suitability of the common practice of using a PSF to localize a microsphere, despite the mismatch between the microsphere's image and the fitted PSF. Using criteria based on the standard errors of the mean and variance, we find the method suitable for microspheres up to 1 μm and 100 nm in diameter, when the localization is performed, respectively, with and without the simultaneous estimation of the width of the PSF.
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Affiliation(s)
- Jerry Chao
- Dept. of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA; Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Sripad Ram
- Dept. of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - E Sally Ward
- Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA; Dept. of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Raimund J Ober
- Dept. of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA; Dept. of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
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26
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Yu B, Yu J, Li W, Cao B, Li H, Chen D, Niu H. Nanoscale three-dimensional single particle tracking by light-sheet-based double-helix point spread function microscopy. APPLIED OPTICS 2016; 55:449-53. [PMID: 26835916 DOI: 10.1364/ao.55.000449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The double-helix point spread function (DH-PSF) microscopy has become an essential tool for nanoscale three-dimensional (3D) localization and tracking of single molecules in living cells. However, its localization precision is limited by fluorescent contrast in thick samples because the signal-to-noise ratio of the system is low due to the inherent low transfer function efficiency and background fluorescence. Here we combine DH-PSF microscopy with light-sheet illumination to eliminate out-of-focus background fluorescence for high-precision 3D single particle tracking. To demonstrate the capability of the method, we obtain the single fluorescent bead image with light-sheet illumination, with three-dimensional localization accuracy better than that of epi-illumination. We also show that the single fluorescent beads in agarose solution can be tracked, which demonstrates the possibility of our method for the study of dynamic processes in complex biological specimens.
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27
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Rose M, Hirmiz N, Moran-Mirabal JM, Fradin C. Lipid Diffusion in Supported Lipid Bilayers: A Comparison between Line-Scanning Fluorescence Correlation Spectroscopy and Single-Particle Tracking. MEMBRANES 2015; 5:702-21. [PMID: 26610279 PMCID: PMC4704007 DOI: 10.3390/membranes5040702] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 11/06/2015] [Indexed: 11/16/2022]
Abstract
Diffusion in lipid membranes is an essential component of many cellular process and fluorescence a method of choice to study membrane dynamics. The goal of this work was to directly compare two common fluorescence methods, line-scanning fluorescence correlation spectroscopy and single-particle tracking, to observe the diffusion of a fluorescent lipophilic dye, DiD, in a complex five-component mitochondria-like solid-supported lipid bilayer. We measured diffusion coefficients of DFCS ~ 3 um2 * s-1 and DSPT ~ 2 um2 * s-1, respectively. These comparable, yet statistically different values are used to highlight the main message of the paper, namely that the two considered methods give access to distinctly different dynamic ranges: D sup or approximatively 1um2 * s-1 for FCS and D inf or approximatively 5 um2 s-1 for SPT (with standard imaging conditions). In the context of membrane diffusion, this means that FCS allows studying lipid diffusion in fluid membranes, as well as the diffusion of loosely-bound proteins hovering above the membrane. SPT, on the other hand, is ideal to study the motions of membrane-inserted proteins, especially those presenting different conformations, but only allows studying lipid diffusion in relatively viscous membranes, such as supported lipid bilayers and cell membranes.
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Affiliation(s)
- Markus Rose
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
| | - Nehad Hirmiz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
| | - Jose M Moran-Mirabal
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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28
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Chao J, Ram S, Lee T, Ward ES, Ober RJ. Investigation of the numerics of point spread function integration in single molecule localization. OPTICS EXPRESS 2015; 23:16866-16883. [PMID: 26191698 PMCID: PMC4523554 DOI: 10.1364/oe.23.016866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/18/2015] [Accepted: 05/28/2015] [Indexed: 05/29/2023]
Abstract
The computation of point spread functions, which are typically used to model the image profile of a single molecule, represents a central task in the analysis of single molecule microscopy data. To determine how the accuracy of the computation affects how well a single molecule can be localized, we investigate how the fineness with which the point spread function is integrated over an image pixel impacts the performance of the maximum likelihood location estimator. We consider both the Airy and the two-dimensional Gaussian point spread functions. Our results show that the point spread function needs to be adequately integrated over a pixel to ensure that the estimator closely recovers the true location of the single molecule with an accuracy that is comparable to the best possible accuracy as determined using the Fisher information formalism. Importantly, if integration with an insufficiently fine step size is carried out, the resulting estimates can be significantly different from the true location, particularly when the image data is acquired at relatively low magnifications. We also present a methodology for determining an adequate step size for integrating the point spread function.
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Affiliation(s)
- Jerry Chao
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843,
USA
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843,
USA
| | - Sripad Ram
- Department of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080,
USA
| | - Taiyoon Lee
- Department of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080,
USA
| | - E. Sally Ward
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843,
USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX 77843,
USA
| | - Raimund J. Ober
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843,
USA
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843,
USA
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29
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Rodgers ML, Paulson J, Hoskins AA. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull. RNA (NEW YORK, N.Y.) 2015; 21:1031-41. [PMID: 25805862 PMCID: PMC4408783 DOI: 10.1261/rna.047845.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/03/2015] [Indexed: 05/08/2023]
Abstract
Large macromolecular complexes such as the spliceosomal small nuclear ribonucleoproteins (snRNPs) play a variety of roles within the cell. Despite their biological importance, biochemical studies of snRNPs and other machines are often thwarted by practical difficulties in the isolation of sufficient amounts of material. Studies of the snRNPs as well as other macromolecular machines would be greatly facilitated by new approaches that enable their isolation and biochemical characterization. One such approach is single-molecule pull-down (SiMPull) that combines in situ immunopurification of complexes from cell lysates with subsequent single-molecule fluorescence microscopy experiments. We report the development of a new method, called SNAP-SiMPull, that can readily be applied to studies of splicing factors and snRNPs isolated from whole-cell lysates. SNAP-SiMPull overcomes many of the limitations imposed by conventional SiMPull strategies that rely on fluorescent proteins. We have used SNAP-SiMPull to study the yeast branchpoint bridging protein (BBP) as well as the U1 and U6 snRNPs. SNAP-SiMPull will likely find broad use for rapidly isolating complex cellular machines for single-molecule fluorescence colocalization experiments.
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Affiliation(s)
- Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua Paulson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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30
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Lauer FM, Kaemmerer E, Meckel T. Single molecule microscopy in 3D cell cultures and tissues. Adv Drug Deliv Rev 2014; 79-80:79-94. [PMID: 25453259 DOI: 10.1016/j.addr.2014.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/20/2014] [Accepted: 10/03/2014] [Indexed: 12/19/2022]
Abstract
From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.
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Affiliation(s)
- Florian M Lauer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany
| | - Elke Kaemmerer
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany; Institute of Health and Biomedical Innovation, Science and Engineering Faculty, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, 4059 QLD, Brisbane, Australia
| | - Tobias Meckel
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287 Darmstadt, Germany.
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31
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Rezgui R, Lestini R, Kühn J, Fave X, McLeod L, Myllykallio H, Alexandrou A, Bouzigues C. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging. PLoS One 2014; 9:e113493. [PMID: 25412080 PMCID: PMC4239081 DOI: 10.1371/journal.pone.0113493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022] Open
Abstract
As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab) on 5′ and 3′-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5′ or 3′ extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.
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Affiliation(s)
- Rachid Rezgui
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Joëlle Kühn
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Xenia Fave
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Lauren McLeod
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Antigoni Alexandrou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Cedric Bouzigues
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
- * E-mail:
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32
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Imaging live cells at the nanometer-scale with single-molecule microscopy: obstacles and achievements in experiment optimization for microbiology. Molecules 2014; 19:12116-49. [PMID: 25123183 PMCID: PMC4346097 DOI: 10.3390/molecules190812116] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/01/2014] [Accepted: 08/01/2014] [Indexed: 12/19/2022] Open
Abstract
Single-molecule fluorescence microscopy enables biological investigations inside living cells to achieve millisecond- and nanometer-scale resolution. Although single-molecule-based methods are becoming increasingly accessible to non-experts, optimizing new single-molecule experiments can be challenging, in particular when super-resolution imaging and tracking are applied to live cells. In this review, we summarize common obstacles to live-cell single-molecule microscopy and describe the methods we have developed and applied to overcome these challenges in live bacteria. We examine the choice of fluorophore and labeling scheme, approaches to achieving single-molecule levels of fluorescence, considerations for maintaining cell viability, and strategies for detecting single-molecule signals in the presence of noise and sample drift. We also discuss methods for analyzing single-molecule trajectories and the challenges presented by the finite size of a bacterial cell and the curvature of the bacterial membrane.
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33
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Ichimura T, Jin T, Fujita H, Higuchi H, Watanabe TM. Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles. Front Physiol 2014; 5:273. [PMID: 25120488 PMCID: PMC4114191 DOI: 10.3389/fphys.2014.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/05/2014] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies.
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Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan
| | - Takashi Jin
- Laboratory for Nano-Bio Probes, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideo Higuchi
- Department of Physics, School of Science, The University of Tokyo Bunkyo, Tokyo, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
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34
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In cellulo evaluation of phototransformation quantum yields in fluorescent proteins used as markers for single-molecule localization microscopy. PLoS One 2014; 9:e98362. [PMID: 24915511 PMCID: PMC4051587 DOI: 10.1371/journal.pone.0098362] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule localization microscopy of biological samples requires a precise knowledge of the employed fluorescent labels. Photoactivation, photoblinking and photobleaching of phototransformable fluorescent proteins influence the data acquisition and data processing strategies to be used in (Fluorescence) Photoactivation Localization Microscopy ((F)-PALM), notably for reliable molecular counting. As these parameters might depend on the local environment, they should be measured in cellulo in biologically relevant experimental conditions. Here, we measured phototransformation quantum yields for Dendra2 fused to actin in fixed mammalian cells in typical (F)-PALM experiments. To this aim, we developed a data processing strategy based on the clustering optimization procedure proposed by Lee et al (PNAS 109, 17436–17441, 2012). Using simulations, we estimated the range of experimental parameters (molecular density, molecular orientation, background level, laser power, frametime) adequate for an accurate determination of the phototransformation yields. Under illumination at 561 nm in PBS buffer at pH 7.4, the photobleaching yield of Dendra2 fused to actin was measured to be (2.5±0.4)×10−5, whereas the blinking-off yield and thermally-activated blinking-on rate were measured to be (2.3±0.2)×10−5 and 11.7±0.5 s−1, respectively. These phototransformation yields differed from those measured in poly-vinyl alcohol (PVA) and were strongly affected by addition of the antifading agent 1,4-diazabicyclo[2.2.2]octane (DABCO). In the presence of DABCO, the photobleaching yield was reduced 2-fold, the blinking-off yield was decreased more than 3-fold, and the blinking-on rate was increased 2-fold. Therefore, DABCO largely improved Dendra2 photostability in fixed mammalian cells. These findings are consistent with redox-based bleaching and blinking mechanisms under (F)-PALM experimental conditions. Finally, the green-to-red photoconversion quantum yield of Dendra2 was estimated to be (1.4±0.6)×10−5in cellulo under 405 nm illumination.
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35
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Lanzanò L, Gratton E. Orbital Single Particle Tracking on a commercial confocal microscope using piezoelectric stage feedback. Methods Appl Fluoresc 2014; 2. [PMID: 25419461 DOI: 10.1088/2050-6120/2/2/024010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Single Particle Tracking (SPT) is a technique used to locate fluorescent particles with nanometer precision. In the orbital tracking method the position of a particle is obtained analyzing the distribution of intensity along a circular orbit scanned around the particle. In combination with an active feedback this method allows tracking of particles in 2D and 3D with millisecond temporal resolution. Here we describe a SPT setup based on a feedback approach implemented with minimal modification of a commercially available confocal laser scanning microscope, the Zeiss LSM 510, in combination with an external piezoelectric stage scanner. The commercial microscope offers the advantage of a user-friendly software interface and pre-calibrated hardware components. The use of an external piezo-scanner allows the addition of feedback into the system but also represents a limitation in terms of its mechanical response. We describe in detail this implementation of the orbital tracking method and discuss advantages and limitations. As an example of application to live cell experiments we perform the 3D tracking of acidic vesicles in live polarized epithelial cells.
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Affiliation(s)
- Luca Lanzanò
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States
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36
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Kurz V, Nelson EM, Perry N, Timp W, Timp G. Epigenetic memory emerging from integrated transcription bursts. Biophys J 2014; 105:1526-32. [PMID: 24048004 DOI: 10.1016/j.bpj.2013.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
Some autonomous bacteria coordinate their actions using quorum-sensing (QS) signals to affect gene expression. However, noise in the gene environment can compromise the cellular response. By exercising precise control over a cell's genes and its microenvironment, we have studied the key positive autoregulation element by which the lux QS system integrates noisy signals into an epigenetic memory. We observed transcriptional bursting of the lux receptor in cells stimulated by near-threshold levels of QS ligand. The bursts are integrated over time into an epigenetic memory that confers enhanced sensitivity to the ligand. An emergent property of the system is manifested in pattern formation among phenotypes within a chemical gradient.
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Affiliation(s)
- Volker Kurz
- University of Notre Dame, Notre Dame, Indiana
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37
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Sibarita JB. High-density single-particle tracking: quantifying molecule organization and dynamics at the nanoscale. Histochem Cell Biol 2014; 141:587-95. [PMID: 24671496 DOI: 10.1007/s00418-014-1214-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Abstract
The organization and dynamics of proteins are fundamental parameters for cellular function. Their study, at the single-molecule level, provides precise information on molecular interactions. Over the last 30 years, the single-particle tracking imaging technique has proven its capability to efficiently quantify such parameters in many biological systems, with nanometric accuracy and millisecond temporal resolutions. Nevertheless, the low concentration of labeling required for single-molecule imaging usually prevents the extraction of large statistics. The advent of high-density single-molecule-based super-resolution techniques has revolutionized the field, allowing monitoring of thousands of biomolecules in the minute timescale and providing unprecedented insight into the molecular organization and dynamics of cellular compounds. In this issue, I will review the main principles of single-particle tracking, a highly interdisciplinary technique at the interface between microscopy, image analysis and labeling strategies. I will point out the advantages brought by high-density single-particle tracking which will be illustrated with a few recent biological results.
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Affiliation(s)
- Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, University of Bordeaux, 33000, Bordeaux, France,
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38
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A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment. Histochem Cell Biol 2014; 141:629-38. [DOI: 10.1007/s00418-014-1192-3] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2014] [Indexed: 11/27/2022]
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39
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Sengupta P, van Engelenburg SB, Lippincott-Schwartz J. Superresolution imaging of biological systems using photoactivated localization microscopy. Chem Rev 2014; 114:3189-202. [PMID: 24417572 DOI: 10.1021/cr400614m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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40
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Jung G, Wiehler J, Steipe B, Bräuchle C, Zumbusch A. Single-molecule microscopy of the green fluorescent protein using simultaneous two-color excitation. Chemphyschem 2014; 2:392-6. [PMID: 23686962 DOI: 10.1002/1439-7641(20010618)2:6<392::aid-cphc392>3.0.co;2-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2000] [Indexed: 11/05/2022]
Abstract
In vivo microscopy of the Green Fluorescent Protein (GFP), the most important label in cell biology, with single-molecule sensitivity is hampered by an insufficient signal-to-noise ratio. A significant improvement is obtained with a novel two-color excitation technique. The picture clearly shows the increased brightness of GFP in in vitro single-molecule assays and in live-cell microscopy under two-color illumination (upper cell) as compared to normal illumination (lower cell).
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Affiliation(s)
- G Jung
- Department Chemie, Lehrstuhl Physikalische Chemie I, Ludwig-Maximilians Universität München, München, Germany
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41
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Wang S, Jing B, Zhu Y. Molecule motion at polymer brush interfaces from single-molecule experimental perspectives. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/polb.23414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shengqin Wang
- Institute of Materials Research and Engineering; A*STAR (Agency for Science, Technology and Research); 3 Research Link Singapore 117602 Singapore
| | - Benxin Jing
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
| | - Yingxi Zhu
- Department of Chemical and Biomolecular Engineering; University of Notre Dame; Notre Dame Indiana 46556
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42
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Friaa O, Furukawa M, Shamas-Din A, Leber B, Andrews DW, Fradin C. Optimizing the acquisition and analysis of confocal images for quantitative single-mobile-particle detection. Chemphyschem 2013; 14:2476-90. [PMID: 23824691 DOI: 10.1002/cphc.201201047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/18/2013] [Indexed: 11/06/2022]
Abstract
Quantification of the fluorescence properties of diffusing particles in solution is an invaluable source of information for characterizing the interactions, stoichiometry, or conformation of molecules directly in their native environment. In the case of heterogeneous populations, single-particle detection should be the method of choice and it can, in principle, be achieved by using confocal imaging. However, the detection of single mobile particles in confocal images presents specific challenges. In particular, it requires an adapted set of imaging parameters for capturing the confocal images and an adapted event-detection scheme for analyzing the image. Herein, we report a theoretical framework that allows a prediction of the properties of a homogenous particle population. This model assumes that the particles have linear trajectories with reference to the confocal volume, which holds true for particles with moderate mobility. We compare the predictions of our model to the results as obtained by analyzing the confocal images of solutions of fluorescently labeled liposomes. Based on this comparison, we propose improvements to the simple line-by-line thresholding event-detection scheme, which is commonly used for single-mobile-particle detection. We show that an optimal combination of imaging and analysis parameters allows the reliable detection of fluorescent liposomes for concentrations between 1 and 100 pM. This result confirms the importance of confocal single-particle detection as a complementary technique to ensemble fluorescence-correlation techniques for the studies of mobile particle.
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Affiliation(s)
- Ouided Friaa
- Department of Physics & Astronomy, McMaster University, Hamilton, ON, Canada
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43
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Chen Z, Cornish VW, Min W. Chemical tags: inspiration for advanced imaging techniques. Curr Opin Chem Biol 2013; 17:637-43. [PMID: 23769339 DOI: 10.1016/j.cbpa.2013.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/06/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
This review summarizes recent applications of chemical tags in conjunction with advanced bio-imaging techniques including single-molecule fluorescence, spatiotemporally resolved ensemble microscopy techniques, and imaging modalities beyond fluorescence. We aim to illustrate the unique advantages of chemical tags in facilitating contemporary microscopy to address biological problems that are difficult or near impossible to approach otherwise. We hope our review will inspire more innovative applications enabled by the mingling of these two growing fields.
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Affiliation(s)
- Zhixing Chen
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Chang JC, Rosenthal SJ. Quantum dot-based single-molecule microscopy for the study of protein dynamics. Methods Mol Biol 2013; 1026:71-84. [PMID: 23749570 DOI: 10.1007/978-1-62703-468-5_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Real-time microscopic visualization of single molecules in living cells provides a molecular perspective of cellular dynamics, which is difficult to be observed by conventional ensemble techniques. Among various classes of fluorescent tags used in single-molecule tracking, quantum dots are particularly useful due to their unique photophysical properties. This chapter provides an overview of single quantum dot tracking for protein dynamic studies. First, we review the fundamental diffraction limit of conventional optical systems and recent developments in single-molecule detection beyond the diffraction barrier. Second, we describe methods to prepare water-soluble quantum dots for biological labeling and single-molecule microscopy experimental design. Third, we provide detailed methods to perform quantum dot-based single-molecule microscopy. This technical section covers three protocols including (1) imaging system calibration using spin-coated single quantum dots, (2) single quantum dot labeling in living cells, and (3) tracking algorithms for single-molecule analysis.
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Affiliation(s)
- Jerry C Chang
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
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Abstract
Direct visualization of biological processes at single-molecule level provides a detailed perspective which conventional bulk measurements are hard to achieve. Among various classes of fluorescent tags used in single-molecule tracking, quantum dots are particularly useful due to their unique photophysical properties. In this chapter, we describe the principles, methodologies, and experimental protocols for qdot-based single-molecule imaging. The first half provides an overview of fluorescent microscopy and advances in single-molecule tracking using quantum dots. The remainder of this chapter describes methods to carry out qdot-based single-molecule experiments. Detailed protocols including qdot labeling, microscopy setup, and single-molecule analysis using appropriate computational programs are given.
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Affiliation(s)
- Jerry C Chang
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
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Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging. Proc Natl Acad Sci U S A 2012; 109:17052-7. [PMID: 23035245 DOI: 10.1073/pnas.1204589109] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Simultaneous tracking of many thousands of individual particles in live cells is possible now with the advent of high-density superresolution imaging methods. We present an approach to extract local biophysical properties of cell-particle interaction from such newly acquired large collection of data. Because classical methods do not keep the spatial localization of individual trajectories, it is not possible to access localized biophysical parameters. In contrast, by combining the high-density superresolution imaging data with the present analysis, we determine the local properties of protein dynamics. We specifically focus on AMPA receptor (AMPAR) trafficking and estimate the strength of their molecular interaction at the subdiffraction level in hippocampal dendrites. These interactions correspond to attracting potential wells of large size, showing that the high density of AMPARs is generated by physical interactions with an ensemble of cooperative membrane surface binding sites, rather than molecular crowding or aggregation, which is the case for the membrane viral glycoprotein VSVG. We further show that AMPARs can either be pushed in or out of dendritic spines. Finally, we characterize the recurrent step of influenza trajectories. To conclude, the present analysis allows the identification of the molecular organization responsible for the heterogeneities of random trajectories in cells.
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48
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Sengupta P, Lippincott-Schwartz J. Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair-correlation analysis. Bioessays 2012; 34:396-405. [PMID: 22447653 PMCID: PMC3659788 DOI: 10.1002/bies.201200022] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pointillistic based super-resolution techniques, such as photoactivated localization microscopy (PALM), involve multiple cycles of sequential activation, imaging, and precise localization of single fluorescent molecules. A super-resolution image, having nanoscopic structural information, is then constructed by compiling all the image sequences. Because the final image resolution is determined by the localization precision of detected single molecules and their density, accurate image reconstruction requires imaging of biological structures labeled with fluorescent molecules at high density. In such image datasets, stochastic variations in photon emission and intervening dark states lead to uncertainties in identification of single molecules. This, in turn, prevents the proper utilization of the wealth of information on molecular distribution and quantity. A recent strategy for overcoming this problem is pair-correlation analysis applied to PALM. Using rigorous statistical algorithms to estimate the number of detected proteins, this approach allows the spatial organization of molecules to be quantitatively described.
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Affiliation(s)
- Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MA, USA.
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Goedhart J, von Stetten D, Noirclerc-Savoye M, Lelimousin M, Joosen L, Hink MA, van Weeren L, Gadella TWJ, Royant A. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%. Nat Commun 2012; 3:751. [PMID: 22434194 PMCID: PMC3316892 DOI: 10.1038/ncomms1738] [Citation(s) in RCA: 506] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 02/08/2012] [Indexed: 11/09/2022] Open
Abstract
Cyan variants of green fluorescent protein are widely used as donors in Förster resonance energy transfer experiments. The popular, but modestly bright, Enhanced Cyan Fluorescent Protein (ECFP) was sequentially improved into the brighter variants Super Cyan Fluorescent Protein 3A (SCFP3A) and mTurquoise, the latter exhibiting a high-fluorescence quantum yield and a long mono-exponential fluorescence lifetime. Here we combine X-ray crystallography and excited-state calculations to rationalize these stepwise improvements. The enhancement originates from stabilization of the seventh β-strand and the strengthening of the sole chromophore-stabilizing hydrogen bond. The structural analysis highlighted one suboptimal internal residue, which was subjected to saturation mutagenesis combined with fluorescence lifetime-based screening. This resulted in mTurquoise2, a brighter variant with faster maturation, high photostability, longer mono-exponential lifetime and the highest quantum yield measured for a monomeric fluorescent protein. Together, these properties make mTurquoise2 the preferable cyan variant of green fluorescent protein for long-term imaging and as donor for Förster resonance energy transfer to a yellow fluorescent protein.
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Affiliation(s)
- Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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Abstract
RNA transport granules deliver translationally repressed mRNAs to synaptic sites in dendrites, where synaptic activity promotes their localized translation. Although the identity of many proteins that make up the neuronal granules is known, the stoichiometry of their core component, the mRNA, is poorly understood. By imaging nine different dendritically localized mRNA species with single-molecule sensitivity and subdiffraction-limit resolution in cultured hippocampal neurons, we show that two molecules of the same or different mRNA species do not assemble in common structures. Even mRNA species with a common dendritic localization element, the sequence that is believed to mediate the incorporation of these mRNAs into common complexes, do not colocalize. These results suggest that mRNA molecules traffic to the distal reaches of dendrites singly and independently of others, a model that permits a finer control of mRNA content within a synapse for synaptic plasticity.
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