551
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Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:16172-16176. [PMID: 27804198 PMCID: PMC5215487 DOI: 10.1002/anie.201608284] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/20/2016] [Indexed: 01/29/2023]
Abstract
Super‐resolution microscopy (SRM) greatly benefits from the ability to install small photostable fluorescent labels into proteins. Genetic code expansion (GCE) technology addresses this demand, allowing the introduction of small labeling sites, in the form of uniquely reactive noncanonical amino acids (ncAAs), at any residue in a target protein. However, low incorporation efficiency of ncAAs and high background fluorescence limit its current SRM applications. Redirecting the subcellular localization of the pyrrolysine‐based GCE system for click chemistry, combined with DNA‐PAINT microscopy, enables the visualization of even low‐abundance proteins inside mammalian cells. This approach links a versatile, biocompatible, and potentially unbleachable labeling method with residue‐specific precision. Moreover, our reengineered GCE system eliminates untargeted background fluorescence and substantially boosts the expression yield, which is of general interest for enhanced protein engineering in eukaryotes using GCE.
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Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Present address: Werner Reichardt Centre for Integrative, Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Nataliia V Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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552
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Agostinho A, Höög C. REC8 density along chromosomes prevents illegitimate synapsis. Cell Cycle 2016; 15:2543-2544. [PMID: 27359070 DOI: 10.1080/15384101.2016.1204853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Ana Agostinho
- a Department of Cell and Molecular Biology , Karolinska Institutet , Stockholm , Sweden
| | - Christer Höög
- a Department of Cell and Molecular Biology , Karolinska Institutet , Stockholm , Sweden
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553
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Compans B, Choquet D, Hosy E. Review on the role of AMPA receptor nano-organization and dynamic in the properties of synaptic transmission. Neurophotonics 2016; 3:041811. [PMID: 27981061 PMCID: PMC5109202 DOI: 10.1117/1.nph.3.4.041811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Receptor trafficking and its regulation have appeared in the last two decades to be a major controller of basal synaptic transmission and its activity-dependent plasticity. More recently, considerable advances in super-resolution microscopy have begun deciphering the subdiffraction organization of synaptic elements and their functional roles. In particular, the dynamic nanoscale organization of neurotransmitter receptors in the postsynaptic membrane has recently been suggested to play a major role in various aspects of synapstic function. We here review the recent advances in our understanding of alpha-amino-3-hydroxy-5-méthyl-4-isoxazolepropionic acid subtype glutamate receptors subsynaptic organization and their role in short- and long-term synaptic plasticity.
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Affiliation(s)
- Benjamin Compans
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
- University of Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, France
| | - Eric Hosy
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
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554
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Markert SM, Britz S, Proppert S, Lang M, Witvliet D, Mulcahy B, Sauer M, Zhen M, Bessereau JL, Stigloher C. Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome. Neurophotonics 2016; 3:041802. [PMID: 27175373 PMCID: PMC4855082 DOI: 10.1117/1.nph.3.4.041802] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/08/2016] [Indexed: 06/02/2023]
Abstract
Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.
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Affiliation(s)
| | - Sebastian Britz
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Sven Proppert
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
- University of Würzburg, Department of Neurophysiology, Institute of Physiology, Röntgenring 9, Würzburg 97070, Germany
| | - Marietta Lang
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Jean-Louis Bessereau
- Institut NeuroMyoGene, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, 16 rue R. Dubois, Villeurbanne Cedex F-69622, France
| | - Christian Stigloher
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
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555
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Zhang J, Carver CM, Choveau FS, Shapiro MS. Clustering and Functional Coupling of Diverse Ion Channels and Signaling Proteins Revealed by Super-resolution STORM Microscopy in Neurons. Neuron 2016; 92:461-478. [PMID: 27693258 DOI: 10.1016/j.neuron.2016.09.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/24/2016] [Accepted: 08/26/2016] [Indexed: 11/25/2022]
Abstract
The fidelity of neuronal signaling requires organization of signaling molecules into macromolecular complexes, whose components are in intimate proximity. The intrinsic diffraction limit of light makes visualization of individual signaling complexes using visible light extremely difficult. However, using super-resolution stochastic optical reconstruction microscopy (STORM), we observed intimate association of individual molecules within signaling complexes containing ion channels (M-type K+, L-type Ca2+, or TRPV1 channels) and G protein-coupled receptors coupled by the scaffolding protein A-kinase-anchoring protein (AKAP)79/150. Some channels assembled as multi-channel supercomplexes. Surprisingly, we identified novel layers of interplay within macromolecular complexes containing diverse channel types at the single-complex level in sensory neurons, dependent on AKAP79/150. Electrophysiological studies revealed that such ion channels are functionally coupled as well. Our findings illustrate the novel role of AKAP79/150 as a molecular coupler of different channels that conveys crosstalk between channel activities within single microdomains in tuning the physiological response of neurons.
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Affiliation(s)
- Jie Zhang
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Chase M Carver
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Frank S Choveau
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mark S Shapiro
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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556
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Hanne J, Göttfert F, Schimer J, Anders-Össwein M, Konvalinka J, Engelhardt J, Müller B, Hell SW, Kräusslich HG. Stimulated Emission Depletion Nanoscopy Reveals Time-Course of Human Immunodeficiency Virus Proteolytic Maturation. ACS Nano 2016; 10:8215-8222. [PMID: 27517329 DOI: 10.1021/acsnano.6b03850] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Concomitant with human immunodeficiency virus type 1 (HIV-1) budding from a host cell, cleavage of the structural Gag polyproteins by the viral protease (PR) triggers complete remodeling of virion architecture. This maturation process is essential for virus infectivity. Electron tomography provided structures of immature and mature HIV-1 with a diameter of 120-140 nm, but information about the sequence and dynamics of structural rearrangements is lacking. Here, we employed super-resolution STED (stimulated emission depletion) fluorescence nanoscopy of HIV-1 carrying labeled Gag to visualize the virion architecture. The incomplete Gag lattice of immature virions was clearly distinguishable from the condensed distribution of mature protein subunits. Synchronized activation of PR within purified particles by photocleavage of a caged PR inhibitor enabled time-resolved in situ observation of the induction of proteolysis and maturation by super-resolution microscopy. This study shows the rearrangement of subviral structures in a super-resolution light microscope over time, outwitting phototoxicity and fluorophore bleaching through synchronization of a biological process by an optical switch.
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Affiliation(s)
- Janina Hanne
- Department of Infectious Diseases, Virology, Heidelberg University , Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fabian Göttfert
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Jiří Schimer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n.2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
| | - Maria Anders-Össwein
- Department of Infectious Diseases, Virology, Heidelberg University , Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n.2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova 8, 12843 Prague 2, Czech Republic
| | - Johann Engelhardt
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Heidelberg University , Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
- Molecular Medicine Partnership Unit , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stefan W Hell
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University , Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
- Molecular Medicine Partnership Unit , Meyerhofstrasse 1, 69117 Heidelberg, Germany
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557
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Abstract
In recent years, single-molecule fluorescence imaging has been reconciling a fundamental mismatch between optical microscopy and subcellular biophysics. However, the next step in nanoscale imaging in living cells can be accessed only by optical excitation confinement geometries. Here, we review three methods of confinement that can enable nanoscale imaging in living cells: excitation confinement by laser illumination with beam shaping; physical confinement by micron-scale geometries in bacterial cells; and nanoscale confinement by nanophotonics.
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Affiliation(s)
- Stephen A Lee
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Aleks Ponjavic
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Chanrith Siv
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Steven F Lee
- Department of Chemistry, Cambridge University , Cambridge CB2 1EW, United Kingdom
| | - Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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558
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Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J. Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope. eLife 2016; 5. [PMID: 27630123 PMCID: PMC5065316 DOI: 10.7554/elife.19071] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/13/2016] [Indexed: 01/01/2023] Open
Abstract
The nuclear pore complex (NPC) mediates nucleocytoplasmic transport through the nuclear envelope. How the NPC assembles into this double membrane boundary has remained enigmatic. Here, we captured temporally staged assembly intermediates by correlating live cell imaging with high-resolution electron tomography and super-resolution microscopy. Intermediates were dome-shaped evaginations of the inner nuclear membrane (INM), that grew in diameter and depth until they fused with the flat outer nuclear membrane. Live and super-resolved fluorescence microscopy revealed the molecular maturation of the intermediates, which initially contained the nuclear and cytoplasmic ring component Nup107, and only later the cytoplasmic filament component Nup358. EM particle averaging showed that the evagination base was surrounded by an 8-fold rotationally symmetric ring structure from the beginning and that a growing mushroom-shaped density was continuously associated with the deforming membrane. Quantitative structural analysis revealed that interphase NPC assembly proceeds by an asymmetric inside-out extrusion of the INM.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Khanh Huy Bui
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail Eltsov
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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559
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Xie W, Chojnowski A, Boudier T, Lim JS, Ahmed S, Ser Z, Stewart C, Burke B. A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations. Curr Biol 2016; 26:2651-8. [PMID: 27641764 DOI: 10.1016/j.cub.2016.07.049] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 11/22/2022]
Abstract
The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution.
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560
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MacGillavry HD, Blanpied TA. Single-Molecule Tracking Photoactivated Localization Microscopy to Map Nano-Scale Structure and Dynamics in Living Spines. ACTA ACUST UNITED AC 2016; 65:2.20.1-2.20.19. [PMID: 25429311 DOI: 10.1002/0471142301.ns0220s65] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Super-resolution microscopy has rapidly become an indispensable tool in cell biology and neuroscience by enabling measurement in live cells of structures smaller than the classical limit imposed by diffraction. The most widely applied super-resolution method currently is localization microscopy, which takes advantage of the ability to determine the position of individual fluorescent molecules with nanometer accuracy even in cells. By iteratively measuring sparse subsets of photoactivatable fluorescent proteins, protein distribution in macromolecular structures can be accurately reconstructed. Moreover, the motion trajectories of individual molecules within cells can be measured, providing unique ability to measure transport kinetics, exchange rates, and binding affinities of even small subsets of molecules with high temporal resolution and great spatial specificity. This unit describes protocols to measure and quantify the distribution of scaffold proteins within single synapses of cultured hippocampal neurons, and to track and measure the diffusion of intracellular constituents of the neuronal plasma membrane.
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Affiliation(s)
- Harold D MacGillavry
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Thomas A Blanpied
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
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561
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Hanne J, Zila V, Heilemann M, Müller B, Kräusslich HG. Super-resolved insights into human immunodeficiency virus biology. FEBS Lett 2016; 590:1858-76. [PMID: 27117435 DOI: 10.1002/1873-3468.12186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 11/06/2022]
Abstract
The recent development of fluorescence microscopy approaches overcoming the diffraction limit of light microscopy opened possibilities for studying small-scale cellular processes. The spatial resolution achieved by these novel techniques, together with the possibility to perform live-cell and multicolor imaging, make them ideally suited for visualization of native viruses and subviral structures within the complex environment of a host cell or organ, thus providing fundamentally new possibilities for investigating virus-cell interactions. Here, we review the use of super-resolution microscopy approaches to study virus-cell interactions, and discuss recent insights into human immunodeficiency virus biology obtained by exploiting these novel techniques.
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Affiliation(s)
- Janina Hanne
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany.,Optical Nanoscopy Division, German Cancer Research Center, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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562
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Coumans JVF, Palanisamy SKA, McFarlane J, Moens PDJ. Proteomic and Microscopic Strategies towards the Analysis of the Cytoskeletal Networks in Major Neuropsychiatric Disorders. Int J Mol Sci 2016; 17:E581. [PMID: 27104521 PMCID: PMC4849037 DOI: 10.3390/ijms17040581] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Mental health disorders have become worldwide health priorities. It is estimated that in the next 20 years they will account for a 16 trillion United State dollars (US$) loss. Up to now, the underlying pathophysiology of psychiatric disorders remains elusive. Altered cytoskeleton proteins expression that may influence the assembly, organization and maintenance of cytoskeletal integrity has been reported in major depressive disorders, schizophrenia and to some extent bipolar disorders. The use of quantitative proteomics, dynamic microscopy and super-resolution microscopy to investigate disease-specific protein signatures holds great promise to improve our understanding of these disorders. In this review, we present the currently available quantitative proteomic approaches use in neurology, gel-based, stable isotope-labelling and label-free methodologies and evaluate their strengths and limitations. We also reported on enrichment/subfractionation methods that target the cytoskeleton associated proteins and discuss the need of alternative methods for further characterization of the neurocytoskeletal proteome. Finally, we present live cell imaging approaches and emerging dynamic microscopy technology that will provide the tools necessary to investigate protein interactions and their dynamics in the whole cells. While these areas of research are still in their infancy, they offer huge potential towards the understanding of the neuronal network stability and its modification across neuropsychiatric disorders.
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Affiliation(s)
- Joëlle V F Coumans
- School of Rural Medicine, University of New England, Armidale, NSW 2351, Australia.
| | - Suresh K A Palanisamy
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
| | - Jim McFarlane
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
| | - Pierre D J Moens
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
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563
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Nirschl JJ, Magiera MM, Lazarus JE, Janke C, Holzbaur ELF. α-Tubulin Tyrosination and CLIP-170 Phosphorylation Regulate the Initiation of Dynein-Driven Transport in Neurons. Cell Rep 2016; 14:2637-52. [PMID: 26972003 PMCID: PMC4819336 DOI: 10.1016/j.celrep.2016.02.046] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/08/2016] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
Motor-cargo recruitment to microtubules is often the rate-limiting step of intracellular transport, and defects in this recruitment can cause neurodegenerative disease. Here, we use in vitro reconstitution assays with single-molecule resolution, live-cell transport assays in primary neurons, computational image analysis, and computer simulations to investigate the factors regulating retrograde transport initiation in the distal axon. We find that phosphorylation of the cytoskeletal-organelle linker protein CLIP-170 and post-translational modifications of the microtubule track combine to precisely control the initiation of retrograde transport. Computer simulations of organelle dynamics in the distal axon indicate that while CLIP-170 primarily regulates the time to microtubule encounter, the tyrosination state of the microtubule lattice regulates the likelihood of binding. These mechanisms interact to control transport initiation in the axon in a manner sensitive to the specialized cytoskeletal architecture of the neuron.
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Affiliation(s)
- Jeffrey J Nirschl
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria M Magiera
- Institut Curie, PSL Research University, CNRS UMR3348, 91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, 91405 Orsay, France
| | - Jacob E Lazarus
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carsten Janke
- Institut Curie, PSL Research University, CNRS UMR3348, 91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, 91405 Orsay, France
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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564
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Schoen M, Reichel JM, Demestre M, Putz S, Deshpande D, Proepper C, Liebau S, Schmeisser MJ, Ludolph AC, Michaelis J, Boeckers TM. Super-Resolution Microscopy Reveals Presynaptic Localization of the ALS/FTD Related Protein FUS in Hippocampal Neurons. Front Cell Neurosci 2016; 9:496. [PMID: 26834559 PMCID: PMC4709451 DOI: 10.3389/fncel.2015.00496] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/09/2015] [Indexed: 12/12/2022] Open
Abstract
Fused in Sarcoma (FUS) is a multifunctional RNA-/DNA-binding protein, which is involved in the pathogenesis of the neurodegenerative disorders amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A common hallmark of these disorders is the abnormal accumulation of mutated FUS protein in the cytoplasm. Under normal conditions FUS is confined to the nuclear compartment, in neurons, however, additional somatodendritic localization can be observed. In this study, we carefully analyzed the subcellular localization of endogenous FUS at synaptic sites of hippocampal neurons which are among the most affected cell types in FTD with FUS pathology. We could confirm a strong nuclear localization of FUS as well as its prominent and widespread neuronal expression throughout the adult and developing rat brain, particularly in the hippocampus, the cerebellum and the outer layers of the cortex. Intriguingly, FUS was also consistently observed at synaptic sites as detected by neuronal subcellular fractionation as well as by immunolabeling. To define a pre- and/or postsynaptic localization of FUS, we employed super-resolution fluorescence localization microscopy. FUS was found to be localized within the axon terminal in close proximity to the presynaptic vesicle protein Synaptophysin1 and adjacent to the active zone protein Bassoon, but well separated from the postsynaptic protein PSD-95. Having shown the presynaptic localization of FUS in the nervous system, a novel extranuclear role of FUS at neuronal contact sites has to be considered. Since there is growing evidence that local presynaptic translation might also be an important mechanism for plasticity, FUS - like the fragile X mental retardation protein FMRP - might act as one of the presynaptic RNA-binding proteins regulating this machinery. Our observation of presynaptic FUS should foster further investigations to determine its role in neurodegenerative diseases such as ALS and FTD.
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Affiliation(s)
- Michael Schoen
- Institute for Anatomy and Cell Biology, Ulm University Ulm, Germany
| | | | - Maria Demestre
- Institute for Anatomy and Cell Biology, Ulm University Ulm, Germany
| | - Stefan Putz
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany; Department of Neurology, Ulm UniversityUlm, Germany
| | | | | | - Stefan Liebau
- Institute of Neuroanatomy, Eberhard Karls University Tübingen Tübingen, Germany
| | - Michael J Schmeisser
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany; Department of Neurology, Ulm UniversityUlm, Germany
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565
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Lehmann M, Lichtner G, Klenz H, Schmoranzer J. Novel organic dyes for multicolor localization-based super-resolution microscopy. J Biophotonics 2016; 9:161-70. [PMID: 25973835 DOI: 10.1002/jbio.201500119] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 05/07/2023]
Abstract
Precise multicolor single molecule localization-based microscopy (SMLM) requires bright probes with compatible photo-chemical and spectral properties to resolve distinct molecular species at the nanoscale. The accuracy of multicolor SMLM is further challenged by color channel crosstalk and chromatic alignment errors. These constrains limit the applicability of known reversibly switchable organic dyes for optimized multicolor SMLM. Here, we tested 28 commercially available dyes for their suitability to super-resolve a known cellular nanostructure. We identified eight novel dyes in different spectral regimes that enable high quality dSTORM imaging. Among those, the spectrally close dyes CF647 and CF680 comprise an optimal dye pair for spectral demixing-based, registration free multicolor dSTORM with low crosstalk. Combining this dye pair with the separately excited CF568 we performed 3-color dSTORM to image the relative nanoscale distribution of components of the endocytic machinery and the cytoskeleton.
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Affiliation(s)
- Martin Lehmann
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Gregor Lichtner
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Haider Klenz
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Jan Schmoranzer
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany.
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566
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Abstract
We observed the formation of chromatin ring structures at centromeres of somatic rye and Arabidopsis chromosomes. To test whether this behavior is present also in other plant species and tissues we analyzed Arabidopsis, rye, wheat, Aegilops and barley centromeres during cell divisions and in interphase nuclei by immunostaining and FISH. Furthermore, structured illumination microscopy (super-resolution) was applied to investigate the ultrastructure of centromere chromatin beyond the classical refraction limit of light. It became obvious, that a ring formation at centromeres may appear during mitosis, meiosis and in interphase nuclei in all species analyzed. However, varying centromere structures, as ring formations or globular organized chromatin fibers, were identified in different tissues of one and the same species. In addition, we found that a chromatin ring formation may also be caused by subtelomeric repeats in barley. Thus, we conclude that the formation of chromatin rings may appear in different plant species and tissues, but that it is not specific for centromere function. Based on our findings we established a model describing the ultrastructure of plant centromeres and discuss it in comparison to previous models proposed for animals and plants.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
- *Correspondence: Veit Schubert
| | - Alevtina Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural AcademyMoscow, Russia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenStadt Seeland, Germany
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567
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Abstract
There is an emerging interest in brain-mapping projects in countries across the world, including the USA, Europe, Australia and China. In 2014, Japan started a brain-mapping project called Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS). Brain/MINDS aims to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain, and takes advantage of a unique non-human primate animal model, the common marmoset (Callithrix jacchus). In Brain/MINDS, the RIKEN Brain Science Institute acts as a central institute. The objectives of Brain/MINDS can be categorized into the following three major subject areas: (i) structure and functional mapping of a non-human primate brain (the marmoset brain); (ii) development of innovative neurotechnologies for brain mapping; and (iii) human brain mapping; and clinical research. Brain/MINDS researchers are highly motivated to identify the neuronal circuits responsible for the phenotype of neurological and psychiatric disorders, and to understand the development of these devastating disorders through the integration of these three subject areas.
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Affiliation(s)
- Hideyuki Okano
- Laboratory for Marmoset Neural Architecture, Brain Science Institute RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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568
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Johnson JL, He J, Ramadass M, Pestonjamasp K, Kiosses WB, Zhang J, Catz SD. Munc13-4 Is a Rab11-binding Protein That Regulates Rab11-positive Vesicle Trafficking and Docking at the Plasma Membrane. J Biol Chem 2015; 291:3423-38. [PMID: 26637356 DOI: 10.1074/jbc.m115.705871] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 11/06/2022] Open
Abstract
The small GTPase Rab11 and its effectors control trafficking of recycling endosomes, receptor replenishment and the up-regulation of adhesion and adaptor molecules at the plasma membrane. Despite recent advances in the understanding of Rab11-regulated mechanisms, the final steps mediating docking and fusion of Rab11-positive vesicles at the plasma membrane are not fully understood. Munc13-4 is a docking factor proposed to regulate fusion through interactions with SNAREs. In hematopoietic cells, including neutrophils, Munc13-4 regulates exocytosis in a Rab27a-dependent manner, but its possible regulation of other GTPases has not been explored in detail. Here, we show that Munc13-4 binds to Rab11 and regulates the trafficking of Rab11-containing vesicles. Using a novel Time-resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay, we demonstrate that Munc13-4 binds to Rab11a but not to dominant negative Rab11a. Immunoprecipitation analysis confirmed the specificity of the interaction between Munc13-4 and Rab11, and super-resolution microscopy studies support the interaction of endogenous Munc13-4 with Rab11 at the single molecule level in neutrophils. Vesicular dynamic analysis shows the common spatio-temporal distribution of Munc13-4 and Rab11, while expression of a calcium binding-deficient mutant of Munc13-4 significantly affected Rab11 trafficking. Munc13-4-deficient neutrophils showed normal endocytosis, but the trafficking, up-regulation, and retention of Rab11-positive vesicles at the plasma membrane was significantly impaired. This correlated with deficient NADPH oxidase activation at the plasma membrane in response to Rab11 interference. Our data demonstrate that Munc13-4 is a Rab11-binding partner that regulates the final steps of Rab11-positive vesicle docking at the plasma membrane.
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Affiliation(s)
| | - Jing He
- From the Department of Molecular and Experimental Medicine and
| | | | - Kersi Pestonjamasp
- Cancer Center Microscopy Shared Resource, University of California San Diego, La Jolla, California 92093
| | - William B Kiosses
- Light Microscopy Core Facility, The Scripps Research Institute, La Jolla, California 92037 and
| | - Jinzhong Zhang
- From the Department of Molecular and Experimental Medicine and
| | - Sergio D Catz
- From the Department of Molecular and Experimental Medicine and
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569
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Komis G, Šamajová O, Ovečka M, Šamaj J. Super-resolution Microscopy in Plant Cell Imaging. Trends Plant Sci 2015; 20:834-843. [PMID: 26482957 DOI: 10.1016/j.tplants.2015.08.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/20/2015] [Accepted: 08/26/2015] [Indexed: 05/20/2023]
Abstract
Although the development of super-resolution microscopy methods dates back to 1994, relevant applications in plant cell imaging only started to emerge in 2010. Since then, the principal super-resolution methods, including structured-illumination microscopy (SIM), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), and stimulated emission depletion microscopy (STED), have been implemented in plant cell research. However, progress has been limited due to the challenging properties of plant material. Here we summarize the basic principles of existing super-resolution methods and provide examples of applications in plant science. The limitations imposed by the nature of plant material are reviewed and the potential for future applications in plant cell imaging is highlighted.
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Affiliation(s)
- George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Faculty of Science, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Faculty of Science, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Faculty of Science, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Faculty of Science, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
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570
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Vreja IC, Nikić I, Göttfert F, Bates M, Kröhnert K, Outeiro TF, Hell SW, Lemke EA, Rizzoli SO. Super-resolution Microscopy of Clickable Amino Acids Reveals the Effects of Fluorescent Protein Tagging on Protein Assemblies. ACS Nano 2015; 9:11034-11041. [PMID: 26498474 DOI: 10.1021/acsnano.5b04434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The advent of super-resolution microscopy (nanoscopy) has set high standards for fluorescence tagging. Fluorescent proteins (FPs) are convenient tags in conventional imaging, but their use in nanoscopy has been questioned due to their relatively large size and propensity to form multimers. Here, we compared the nanoscale organization of proteins with or without FP tags by introducing the unnatural amino acid propargyl-L-lysine (PRK) in 26 proteins known to form multimolecular arrangements and into their FP-tagged variants. We revealed the proteins by coupling synthetic fluorophores to PRK via click chemistry and visualized them using ground-state depletion microscopy followed by individual molecule return, as well as stimulated emission depletion microscopy. The arrangements formed by the FP-tagged and nontagged proteins were similar. Mild, but statistically significant differences were observed for only six proteins (23% of all proteins tested). This suggests that FP-based nanoscopy is generally reliable. Unnatural amino acids should be a reliable alternative for the few proteins that are sensitive to FP tagging.
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Affiliation(s)
- Ingrid C Vreja
- International Max Planck Research School for Molecular Biology , Göttingen, Germany
| | - Ivana Nikić
- Structural and Computational Biology Unit, EMBL , 69117 Heidelberg, Germany
| | - Fabian Göttfert
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Mark Bates
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | | | | | - Stefan W Hell
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, EMBL , 69117 Heidelberg, Germany
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571
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Liao Y, Schroeder JW, Gao B, Simmons LA, Biteen JS. Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair. Proc Natl Acad Sci U S A 2015; 112:E6898-906. [PMID: 26575623 DOI: 10.1073/pnas.1507386112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MutS is responsible for initiating the correction of DNA replication errors. To understand how MutS searches for and identifies rare base-pair mismatches, we characterized the dynamic movement of MutS and the replisome in real time using superresolution microscopy and single-molecule tracking in living cells. We report that MutS dynamics are heterogeneous in cells, with one MutS population exploring the nucleoid rapidly, while another MutS population moves to and transiently dwells at the replisome region, even in the absence of appreciable mismatch formation. Analysis of MutS motion shows that the speed of MutS is correlated with its separation distance from the replisome and that MutS motion slows when it enters the replisome region. We also show that mismatch detection increases MutS speed, supporting the model for MutS sliding clamp formation after mismatch recognition. Using variants of MutS and the replication processivity clamp to impair mismatch repair, we find that MutS dynamically moves to and from the replisome before mismatch binding to scan for errors. Furthermore, a block to DNA synthesis shows that MutS is only capable of binding mismatches near the replisome. It is well-established that MutS engages in an ATPase cycle, which is necessary for signaling downstream events. We show that a variant of MutS with a nucleotide binding defect is no longer capable of dynamic movement to and from the replisome, showing that proper nucleotide binding is critical for MutS to localize to the replisome in vivo. Our results provide mechanistic insight into the trafficking and movement of MutS in live cells as it searches for mismatches.
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572
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Ishitsuka Y, Savage N, Li Y, Bergs A, Grün N, Kohler D, Donnelly R, Nienhaus GU, Fischer R, Takeshita N. Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growth. Sci Adv 2015; 1:e1500947. [PMID: 26665168 PMCID: PMC4673053 DOI: 10.1126/sciadv.1500947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/14/2015] [Indexed: 05/02/2023]
Abstract
Polar (directional) cell growth, a key cellular mechanism shared among a wide range of species, relies on targeted insertion of new material at specific locations of the plasma membrane. How these cell polarity sites are stably maintained during massive membrane insertion has remained elusive. Conventional live-cell optical microscopy fails to visualize polarity site formation in the crowded cell membrane environment because of its limited resolution. We have used advanced live-cell imaging techniques to directly observe the localization, assembly, and disassembly processes of cell polarity sites with high spatiotemporal resolution in a rapidly growing filamentous fungus, Aspergillus nidulans. We show that the membrane-associated polarity site marker TeaR is transported on microtubules along with secretory vesicles and forms a protein cluster at that point of the apical membrane where the plus end of the microtubule touches. There, a small patch of membrane is added through exocytosis, and the TeaR cluster gets quickly dispersed over the membrane. There is an incessant disassembly and reassembly of polarity sites at the growth zone, and each new polarity site locus is slightly offset from preceding ones. On the basis of our imaging results and computational modeling, we propose a transient polarity model that explains how cell polarity is stably maintained during highly active directional growth.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Natasha Savage
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yiming Li
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Anna Bergs
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Nathalie Grün
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Daria Kohler
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Rebecca Donnelly
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute of Nanotechnology, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
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573
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Fabre PJ, Benke A, Joye E, Nguyen Huynh TH, Manley S, Duboule D. Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states. Proc Natl Acad Sci U S A 2015; 112:13964-9. [PMID: 26504220 DOI: 10.1073/pnas.1517972112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around the HoxD gene cluster. This reorganization follows a global transition from one set of regulatory contacts to another, between two topologically associating domains (TADs) located on either side of the HoxD locus. Here, we use 3D DNA FISH to assess the spatial organization of chromatin at and around the HoxD gene cluster and report that although the two TADs are tightly associated, they appear as spatially distinct units. We measured the relative position of genes within the cluster and found that they segregate over long distances, suggesting that a physical elongation of the HoxD cluster can occur. We analyzed this possibility by super-resolution imaging (STORM) and found that tissues with distinct transcriptional activity exhibit differing degrees of elongation. We also observed that the morphological change of the HoxD cluster in developing digits is associated with its position at the boundary between the two TADs. Such variations in the fine-scale architecture of the gene cluster suggest causal links among its spatial configuration, transcriptional activation, and the flanking chromatin context.
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574
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Scheible MB, Ong LL, Woehrstein JB, Jungmann R, Yin P, Simmel FC. A Compact DNA Cube with Side Length 10 nm. Small 2015; 11:5200-5. [PMID: 26294348 PMCID: PMC4707664 DOI: 10.1002/smll.201501370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/09/2015] [Indexed: 05/09/2023]
Abstract
A small and compact DNA cube with zeptoliter volume is constructed by means of a generalized DNA brick concept using short synthetic oligonucleotides with varying lengths. By mimicking design principles from the DNA origami technique, the DNA cube offers higher stability and assembly yields compared to other approaches. Its potential application as nanoscale fluorescent probe is demonstrated using super-resolution imaging.
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Affiliation(s)
- Max B. Scheible
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Friedrich C. Simmel
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
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575
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Booth M, Andrade D, Burke D, Patton B, Zurauskas M. Aberrations and adaptive optics in super-resolution microscopy. Microscopy (Oxf) 2015; 64:251-61. [PMID: 26124194 PMCID: PMC4711293 DOI: 10.1093/jmicro/dfv033] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/29/2015] [Indexed: 12/05/2022] Open
Abstract
As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy - or rather nanoscopy - to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem.
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Affiliation(s)
- Martin Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Débora Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Daniel Burke
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Brian Patton
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Mantas Zurauskas
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
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576
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Jacak J, Schaller S, Borgmann D, Winkler SM. Characterization of the Distance Relationship Between Localized Serotonin Receptors and Glia Cells on Fluorescence Microscopy Images of Brain Tissue. Microsc Microanal 2015; 21:826-836. [PMID: 26173412 DOI: 10.1017/s1431927615013513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We here present two new methods for the characterization of fluorescent localization microscopy images obtained from immunostained brain tissue sections. Direct stochastic optical reconstruction microscopy images of 5-HT1A serotonin receptors and glial fibrillary acidic proteins in healthy cryopreserved brain tissues are analyzed. In detail, we here present two image processing methods for characterizing differences in receptor distribution on glial cells and their distribution on neural cells: One variant relies on skeleton extraction and adaptive thresholding, the other on k-means based discrete layer segmentation. Experimental results show that both methods can be applied for distinguishing classes of images with respect to serotonin receptor distribution. Quantification of nanoscopic changes in relative protein expression on particular cell types can be used to analyze degeneration in tissues caused by diseases or medical treatment.
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Affiliation(s)
- Jaroslaw Jacak
- 1Department of Medical Engineering,University of Applied Sciences Upper Austria,Garnisonstraße 21,4020 Linz,Austria
| | - Susanne Schaller
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Daniela Borgmann
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
| | - Stephan M Winkler
- 3Bioinformatics Research Group,University of Applied Sciences Upper Austria,Softwarepark 11,4232 Hagenberg,Austria
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577
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Ziomkiewicz I, Sporring J, Pomorski TG, Schulz A. Novel approach to measure the size of plasma-membrane nanodomains in single molecule localization microscopy. Cytometry A 2015; 87:868-77. [PMID: 26109552 DOI: 10.1002/cyto.a.22708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/14/2015] [Accepted: 05/26/2015] [Indexed: 01/20/2023]
Abstract
Many membrane proteins are not evenly distributed over the plasma membrane, but gathered in domains assumed to have a particular lipid composition. Using single molecule localization microscopy (SMLM) we have immunolocalized a glycosylphosphatidylinositol (GPI)-anchor protein that labels nanodomains in a specialized plant cell type, and compared the suitability of three methods to estimate their size. As conventional methods full width at half maximum (FWHM) and the full diameter (FWMin) of domains were used. A boundary detection method of the domain area (DA) was performed in order to take irregular shapes into account. In order to compare the influence of the chosen measurement methods, we have developed a MatLab program that allows for automated analysis of domain sizes from multiple SMLM images and provides the statistics of three key features of domains: FWHM and FWMin along their long and short axes as well as the DA, derived from the molecular density. Domains formed by the GPI-anchor protein are approximating elliptical shapes. Direct and indirect immunolabeling resulted in a statistically significant difference in apparent domain size, reflecting the fact that the secondary antibody molecules extend the uncertainty along the nanodomain border. FWMin values along the long and short axis give good estimates of regular, geometrically centred domain shapes, while the DA value matches regular as well as irregular shapes best, as derived from computer-generated, irregular point clusters.
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Affiliation(s)
- Iwona Ziomkiewicz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Jon Sporring
- Department of Computer Science, University of Copenhagen, Denmark
| | | | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
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578
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Cattoni DI, Valeri A, Le Gall A, Nollmann M. A matter of scale: how emerging technologies are redefining our view of chromosome architecture. Trends Genet 2015; 31:454-64. [PMID: 26113398 DOI: 10.1016/j.tig.2015.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 11/25/2022]
Abstract
The 3D folding of the genome and its relation to fundamental processes such as gene regulation, replication, and segregation remains one of the most puzzling and exciting questions in genetics. In this review, we describe how the use of new technologies is starting to revolutionize the field of chromosome organization, and to shed light on the mechanisms of transcription, replication, and repair. In particular, we concentrate on recent studies using genome-wide methods, single-molecule technologies, and super-resolution microscopy (SRM). We summarize some of the main concerns when employing these techniques, and discuss potential new and exciting perspectives that illuminate the connection between 3D genomic organization and gene regulation.
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Affiliation(s)
- Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Alessandro Valeri
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
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579
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Shechtman Y, Weiss L, Backer AS, Sahl SJ, Moerner WE. Precise Three-Dimensional Scan-Free Multiple-Particle Tracking over Large Axial Ranges with Tetrapod Point Spread Functions. Nano Lett 2015; 15:4194-9. [PMID: 25939423 PMCID: PMC4462996 DOI: 10.1021/acs.nanolett.5b01396] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We employ a novel framework for information-optimal microscopy to design a family of point spread functions (PSFs), the Tetrapod PSFs, which enable high-precision localization of nanoscale emitters in three dimensions over customizable axial (z) ranges of up to 20 μm with a high numerical aperture objective lens. To illustrate, we perform flow profiling in a microfluidic channel and show scan-free tracking of single quantum-dot-labeled phospholipid molecules on the surface of living, thick mammalian cells.
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Affiliation(s)
- Yoav Shechtman
- Department
of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, United States
| | - Lucien
E. Weiss
- Department
of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, United States
| | - Adam S. Backer
- Institute
for Computational and Mathematical Engineering, 475 Via Ortega, Stanford, California 94305, United States
| | - Steffen J. Sahl
- Department
of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, 375 North-South Mall, Stanford, California 94305, United States
- E-mail:
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580
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Lemgruber L, Sant'Anna C, Griffths C, Abud Y, Mhlanga M, Wallich R, Frischknecht F. Nanoscopic Localization of Surface-Exposed Antigens of Borrelia burgdorferi. Microsc Microanal 2015; 21:680-688. [PMID: 25739645 DOI: 10.1017/s1431927615000318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, is transmitted to humans through the bite of infected Ixodes spp. ticks. Successful infection of vertebrate hosts necessitates sophisticated means of the pathogen to escape the vertebrates' immune system. One strategy employed by Lyme disease spirochetes to evade adaptive immunity involves a highly coordinated regulation of the expression of outer surface proteins that is vital for infection, dissemination, and persistence. Here we characterized the expression pattern of bacterial surface antigens using different microscopy techniques, from fluorescent wide field to super-resolution and immunogold-scanning electron microscopy. A fluorescent strain of B. burgdorferi spirochetes was labeled with monoclonal antibodies directed against various bacterial surface antigens. Our results indicate that OspA is more evenly distributed over the surface than OspB and OspC that were present as punctate areas.
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Affiliation(s)
- Leandro Lemgruber
- 1Department of Infectious Diseases - Parasitology,Im Neuenheimer Feld 324,University of Heidelberg Medical School,69120, Heidelberg,Germany
| | - Celso Sant'Anna
- 2Laboratory of Microscopy for Life Sciences,Diretoria de Metrologia Aplicada às Ciências da Vida - Dimav,Instituto Nacional de Metrologia,Qualidade e Tecnologia - Inmetro,25250-020,Duque de Caxias,Rio de Janeiro,Brazil
| | - Caron Griffths
- 4Gene Expression and Biophysics Group,Synthetic Biology Emerging Research Area,Council for Scientific and Industrial Research,Box 395,Pretoria 0001S,South Africa
| | - Yuri Abud
- 2Laboratory of Microscopy for Life Sciences,Diretoria de Metrologia Aplicada às Ciências da Vida - Dimav,Instituto Nacional de Metrologia,Qualidade e Tecnologia - Inmetro,25250-020,Duque de Caxias,Rio de Janeiro,Brazil
| | - Musa Mhlanga
- 4Gene Expression and Biophysics Group,Synthetic Biology Emerging Research Area,Council for Scientific and Industrial Research,Box 395,Pretoria 0001S,South Africa
| | - Reinhard Wallich
- 5Institute for Immunology,Im Neuenheimer Feld 305,University of Heidelberg Medical School,69120,Heidelberg,Germany
| | - Friedrich Frischknecht
- 1Department of Infectious Diseases - Parasitology,Im Neuenheimer Feld 324,University of Heidelberg Medical School,69120, Heidelberg,Germany
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581
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Reid DA, Keegan S, Leo-Macias A, Watanabe G, Strande NT, Chang HH, Oksuz BA, Fenyo D, Lieber MR, Ramsden DA, Rothenberg E. Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair. Proc Natl Acad Sci U S A 2015; 112:E2575-84. [PMID: 25941401 DOI: 10.1073/pnas.1420115112] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nonhomologous end-joining (NHEJ) is a major repair pathway for DNA double-strand breaks (DSBs), involving synapsis and ligation of the broken strands. We describe the use of in vivo and in vitro single-molecule methods to define the organization and interaction of NHEJ repair proteins at DSB ends. Super-resolution fluorescence microscopy allowed the precise visualization of XRCC4, XLF, and DNA ligase IV filaments adjacent to DSBs, which bridge the broken chromosome and direct rejoining. We show, by single-molecule FRET analysis of the Ku/XRCC4/XLF/DNA ligase IV NHEJ ligation complex, that end-to-end synapsis involves a dynamic positioning of the two ends relative to one another. Our observations form the basis of a new model for NHEJ that describes the mechanism whereby filament-forming proteins bridge DNA DSBs in vivo. In this scheme, the filaments at either end of the DSB interact dynamically to achieve optimal configuration and end-to-end positioning and ligation.
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582
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Gorris HH. Special issue: single molecule techniques. Molecules 2015; 20:7772-4. [PMID: 26007165 DOI: 10.3390/molecules20057772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 12/04/2022] Open
Abstract
Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of “Single Molecule Techniques”. Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy.
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583
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Lee S, Noda K, Hirata S, Vacha M. Position-Dependent Three-Dimensional Diffusion in Nematic Liquid Crystal Monitored by Single-Particle Fluorescence Localization and Tracking. J Phys Chem Lett 2015; 6:1403-1407. [PMID: 26263142 DOI: 10.1021/acs.jpclett.5b00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Anisotropic mass diffusion in liquid crystals (LCs) is important from the point of both basic LC physics and their applications in optoelectronic devices. We use super-resolution fluorescence microscopy with astigmatic imaging to track 3D diffusion of quantum dots (QDs) in an ordered nematic LC. The method allowed us to evaluate the diffusion coefficients independently along the three spatial axes as well as to determine the absolute position of the QD with respect to the cell wall. We found variations of the diffusion coefficient along the different directions across the cell thickness and explained these as being due to changes of a tilt angle of the LC director. Close to the surface, the diffusion is slowed down due to the confinement effect of the cell wall. Overall, the QD diffusion is much slower than expected for a corresponding particle size. This phenomenon is suggested to originate from reorientation of the LC director in the vicinity of the particle.
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Affiliation(s)
- Seonik Lee
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo, Japan
| | - Koushi Noda
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo, Japan
| | - Shuzo Hirata
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo, Japan
| | - Martin Vacha
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo, Japan
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584
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Abstract
We demonstrate multicolor three-dimensional super-resolution imaging with quantum dots (QSTORM). By combining quantum dot asynchronous spectral blueing with stochastic optical reconstruction microscopy and adaptive optics, we achieve three-dimensional imaging with 24 nm lateral and 37 nm axial resolution. By pairing two short-pass filters with two appropriate quantum dots, we are able to image single blueing quantum dots on two channels simultaneously, enabling multicolor imaging with high photon counts.
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Affiliation(s)
- Jianquan Xu
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Kayvan F Tehrani
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Peter Kner
- College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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585
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Zhang X, Chen X, Zeng Z, Zhang M, Sun Y, Xi P, Peng J, Xu P. Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI). ACS Nano 2015; 9:2659-67. [PMID: 25695314 DOI: 10.1021/nn5064387] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Reversibly switchable fluorescent proteins (RSFPs) can be effectively used for super-resolution optical fluctuation imaging (SOFI) based on the switching and fluctuation of single molecules. Several properties of RSFPs strongly influence the quality of SOFI images. These properties include (i) the averaged fluorescence intensity in the fluctuation state, (ii) the on/off contrast ratio, (iii) the photostability, and (iv) the oligomerization tendency. The first three properties determine the fluctuation range of the imaged pixels and the SOFI signal, which are of essential importance to the spatial resolution, and the last may lead to artificial aggregation of target proteins. The RSFPs that are currently used for SOFI are low in averaged fluorescence intensity in the fluctuation state, photostability, and on/off contrast ratio, thereby limiting the range of application of SOFI in biological super-resolution imaging. In this study, we developed a novel monomeric green RSFP termed Skylan-S, which features very high photostability, contrast ratio, and averaged fluorescence intensity in the fluctuation state. Taking advantage of the excellent optical properties of Skylan-S, a 4-fold improvement in the fluctuation range of the imaged pixels and higher SOFI resolution can be obtained compared with Dronpa. Furthermore, super-resolution imaging of the actin or tubulin structures and clathrin-coated pits (CCPs) in living U2OS cells labeled with Skylan-S was demonstrated using the SOFI technique. Overall, Skylan-S developed with outstanding photochemical properties is promising for long-time SOFI imaging with high spatial-temporal resolution.
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Affiliation(s)
- Xi Zhang
- †Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanze Chen
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
- ∥State Key Laboratory of Biomembrane and Membrane Biotechnology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Zeng
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Mingshu Zhang
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yujie Sun
- ∥State Key Laboratory of Biomembrane and Membrane Biotechnology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Peng Xi
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Jianxin Peng
- †Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Pingyong Xu
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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586
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Park H, Hoang DT, Paeng K, Kaufman LJ. Localizing exciton recombination sites in conformationally distinct single conjugated polymers by super-resolution fluorescence imaging. ACS Nano 2015; 9:3151-3158. [PMID: 25743935 DOI: 10.1021/acsnano.5b00086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To thoroughly elucidate how molecular conformation and photophysical properties of conjugated polymers (CPs) are related requires simultaneous probing of both. Previous efforts used fluorescence imaging with one nanometer accuracy (FIONA) to image CPs, which allowed simultaneous estimation of molecular conformation and probing of fluorescence intensity decay. We show that calculating the molecular radius of gyration for putative folded and unfolded poly(2-methoxy-5-(2'-ethylhexyloxy)1,4-phenylenevinylene) (MEH-PPV) molecules using FIONA underestimates molecular extension by averaging over emitters during localization. In contrast, employing algorithms based on single molecule high resolution imaging with photobleaching (SHRImP), including an approach we term all-frames SHRImP, allows localization of individual emitters. SHRImP processing corroborates that compact MEH-PPV molecules have distinct photophysical properties from extended ones. Estimated radii of gyration for isolated 168 kDa MEH-PPV molecules immobilized in polystyrene and exhibiting either stepwise or continuous intensity decays are found to be 12.6 and 25.3 nm, respectively, while the distance between exciton recombination sites is estimated to be ∼10 nm independent of molecular conformation.
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Affiliation(s)
- Heungman Park
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dat Tien Hoang
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Keewook Paeng
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
- ‡Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Laura J Kaufman
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
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587
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Abstract
Memory formation in the brain is thought to rely on the remodeling of synaptic connections which eventually results in neural network rewiring. This remodeling is likely to involve ultrathin astroglial protrusions which often occur in the immediate vicinity of excitatory synapses. The phenomenology, cellular mechanisms, and causal relationships of such astroglial restructuring remain, however, poorly understood. This is in large part because monitoring and probing of the underpinning molecular machinery on the scale of nanoscopic astroglial compartments remains a challenge. Here we briefly summarize the current knowledge regarding the cellular organisation of astroglia in the synaptic microenvironment and discuss molecular mechanisms potentially involved in use-dependent astroglial morphogenesis. We also discuss recent observations concerning morphological astroglial plasticity, the respective monitoring methods, and some of the newly emerging techniques that might help with conceptual advances in the area.
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Affiliation(s)
- Janosch P Heller
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, Queen Square, London, United Kingdom
| | - Dmitri A Rusakov
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, Queen Square, London, United Kingdom
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588
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Tian Y, Merdasa A, Peter M, Abdellah M, Zheng K, Ponseca CS, Pullerits T, Yartsev A, Sundström V, Scheblykin IG. Giant photoluminescence blinking of perovskite nanocrystals reveals single-trap control of luminescence. Nano Lett 2015; 15:1603-8. [PMID: 25706329 DOI: 10.1021/nl5041397] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fluorescence super-resolution microscopy showed correlated fluctuations of photoluminescence intensity and spatial localization of individual perovskite (CH3NH3PbI3) nanocrystals of size ∼200 × 30 × 30 nm(3). The photoluminescence blinking amplitude caused by a single quencher was a hundred thousand times larger than that of a typical dye molecule at the same excitation power density. The quencher is proposed to be a chemical or structural defect that traps free charges leading to nonradiative recombination. These trapping sites can be activated and deactivated by light.
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Affiliation(s)
- Yuxi Tian
- Chemical Physics, Lund University , Box 124, SE-22100, Lund, Sweden
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589
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Lowe AR, Tang JH, Yassif J, Graf M, Huang WYC, Groves JT, Weis K, Liphardt JT. Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner. eLife 2015; 4. [PMID: 25748139 PMCID: PMC4375889 DOI: 10.7554/elife.04052] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/27/2015] [Indexed: 11/13/2022] Open
Abstract
Soluble karyopherins of the importin-β (impβ) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impβ or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impβ at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impβ, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impβ is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impβ or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impβ•Nup153 complexes but not those of TRN1•Nup153. We propose that impβ and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability. DOI:http://dx.doi.org/10.7554/eLife.04052.001 In our cells, genetic material is contained within the nucleus, which is separated from the rest of the cell by a double-layered membrane called the nuclear envelope. Within this membrane there are pores that allow proteins and other molecules to enter and exit the nucleus. Small molecules can pass through these pores unaided, which is known as ‘passive’ transport. However, larger cargos need help from transport receptor proteins in a process called ‘active’ transport. Large cargos bind to transport receptors, such as importin-β, in the cytoplasm and are then guided through the pore. Once the cargo and importin-β are inside the nucleus, a protein called RanGTP binds to importin-β to release the cargo. It is thought that importin-β and RanGTP are only important for the active transport of cargo. Here, Lowe et al. studied how importin-β interacts with the pore. The experiments show that in the absence of RanGTP, importin-β accumulates inside the pore and binds to a protein called Nup153, which is part of the complex of proteins that makes up the pore. However, when RanGTP is present, some of the importin-β is displaced from Nup153 and leaves the pore, which makes it easier for cargo to pass through. Further experiments show that when Nup153 and importin-β are mixed, they associate into a gel-like material that can be ‘melted’ by RanGTP. Lowe et al. propose a model for how RanGTP may control the flow of cargo through the nuclear pore by affecting the binding of importin-β to Nup153. Lowe et al.'s findings suggest that passive and active transport of cargo across the nuclear pore are fundamentally connected and suggest that RanGTP provides the cell with an additional layer of control over nucleocytoplasmic transport. DOI:http://dx.doi.org/10.7554/eLife.04052.002
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Affiliation(s)
- Alan R Lowe
- Institute for Structural and Molecular Biology, University College London and Birkbeck College, London, United Kingdom
| | - Jeffrey H Tang
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jaime Yassif
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Michael Graf
- Section of Life Sciences and Technologies, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - William Y C Huang
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jay T Groves
- QB3, University of California, Berkeley, Berkeley, United States
| | - Karsten Weis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jan T Liphardt
- Department of Physics, University of California, Berkeley, Berkeley, United States
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590
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Abstract
The complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction-unlimited fluorescence microscopy to resolve them. Because of the vast range of different processes that can be studied, sub-diffraction imaging should work efficiently under many different conditions. Photochromic stochastic optical fluctuation imaging (pcSOFI) is a recent addition to the field of diffraction-unlimited fluorescence microscopy. This robust and versatile method employs a statistical analysis of random fluctuations in the emission of single labels, in this case reversibly switchable fluorescent proteins (RSFPs), to retrieve super-resolution information. Added to the resolution enhancement, pcSOFI also offers contrast enhancement and background reduction in a practical and convenient way. Here, we describe the necessary steps to obtain diffraction-unlimited images, including multicolor and three-dimensional imaging, and highlight the advantages of pcSOFI together with the circumstances under which pcSOFI can be favorably applied.
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Affiliation(s)
- Sam Duwé
- Department of Chemistry, University of Leuven, Heverlee, Belgium
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591
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Liesche J, Marek M, Günther-Pomorski T. Cell wall staining with Trypan blue enables quantitative analysis of morphological changes in yeast cells. Front Microbiol 2015; 6:107. [PMID: 25717323 PMCID: PMC4324143 DOI: 10.3389/fmicb.2015.00107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/27/2015] [Indexed: 11/13/2022] Open
Abstract
Yeast cells are protected by a cell wall that plays an important role in the exchange of substances with the environment. The cell wall structure is dynamic and can adapt to different physiological states or environmental conditions. For the investigation of morphological changes, selective staining with fluorescent dyes is a valuable tool. Furthermore, cell wall staining is used to facilitate sub-cellular localization experiments with fluorescently-labeled proteins and the detection of yeast cells in non-fungal host tissues. Here, we report staining of Saccharomyces cerevisiae cell wall with Trypan Blue, which emits strong red fluorescence upon binding to chitin and yeast glucan; thereby, it facilitates cell wall analysis by confocal and super-resolution microscopy. The staining pattern of Trypan Blue was similar to that of the widely used UV-excitable, blue fluorescent cell wall stain Calcofluor White. Trypan Blue staining facilitated quantification of cell size and cell wall volume when utilizing the optical sectioning capacity of a confocal microscope. This enabled the quantification of morphological changes during growth under anaerobic conditions and in the presence of chemicals, demonstrating the potential of this approach for morphological investigations or screening assays.
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Affiliation(s)
- Johannes Liesche
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
| | - Magdalena Marek
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
| | - Thomas Günther-Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark
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592
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Abstract
Brain function relies on accurate information transfer at chemical synapses. At the presynaptic active zone (AZ) a variety of specialized proteins are assembled to complex architectures, which set the basis for speed, precision and plasticity of synaptic transmission. Calcium channels are pivotal for the initiation of excitation-secretion coupling and, correspondingly, capture a central position at the AZ. Combining quantitative functional studies with modeling approaches has provided predictions of channel properties, numbers and even positions on the nanometer scale. However, elucidating the nanoscopic organization of the surrounding protein network requires direct ultrastructural access. Without this information, knowledge of molecular synaptic structure-function relationships remains incomplete. Recently, super-resolution microscopy (SRM) techniques have begun to enter the neurosciences. These approaches combine high spatial resolution with the molecular specificity of fluorescence microscopy. Here, we discuss how SRM can be used to obtain information on the organization of AZ proteins.
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Affiliation(s)
- Nadine Ehmann
- Department of Neurophysiology, Institute of Physiology, University of Würzburg Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg Würzburg, Germany
| | - Robert J Kittel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg Würzburg, Germany
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593
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Das S, Yin T, Yang Q, Zhang J, Wu YI, Yu J. Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling. Proc Natl Acad Sci U S A 2015; 112:E267-76. [PMID: 25561548 DOI: 10.1073/pnas.1409667112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polarized Rac1 signaling is a hallmark of many cellular functions, including cell adhesion, motility, and cell division. The two steps of Rac1 activation are its translocation to the plasma membrane and the exchange of nucleotide from GDP to GTP. It is, however, unclear whether these two processes are regulated independent of each other and what their respective roles are in polarization of Rac1 signaling. We designed a single-particle tracking (SPT) method to quantitatively analyze the kinetics of Rac1 membrane translocation in living cells. We found that the rate of Rac1 translocation was significantly elevated in protrusions during cell spreading on collagen. Furthermore, combining FRET sensor imaging with SPT measurements in the same cell, the recruitment of Rac1 was found to be polarized to an extent similar to that of the nucleotide exchange process. Statistical analysis of single-molecule trajectories and optogenetic manipulation of membrane lipids revealed that Rac1 membrane translocation precedes nucleotide exchange, and is governed primarily by interactions with phospholipids, particularly PI(3,4,5)P3, instead of protein factors. Overall, the study highlights the significance of membrane translocation in spatial Rac1 signaling, which is in addition to the traditional view focusing primarily on GEF distribution and exchange reaction.
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594
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Jayasinghe ID, Clowsley AH, Munro M, Hou Y, Crossman DJ, Soeller C. Revealing T-Tubules in Striated Muscle with New Optical Super-Resolution Microscopy Techniquess. Eur J Transl Myol 2014; 25:4747. [PMID: 26913143 PMCID: PMC4748971 DOI: 10.4081/ejtm.2015.4747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/18/2014] [Indexed: 01/03/2023] Open
Abstract
The t-tubular system plays a central role in the synchronisation of calcium signalling and excitation-contraction coupling in most striated muscle cells. Light microscopy has been used for imaging t-tubules for well over 100 years and together with electron microscopy (EM), has revealed the three-dimensional complexities of the t-system topology within cardiomyocytes and skeletal muscle fibres from a range of species. The emerging super-resolution single molecule localisation microscopy (SMLM) techniques are offering a near 10-fold improvement over the resolution of conventional fluorescence light microscopy methods, with the ability to spectrally resolve nanometre scale distributions of multiple molecular targets. In conjunction with the next generation of electron microscopy, SMLM has allowed the visualisation and quantification of intricate t-tubule morphologies within large areas of muscle cells at an unprecedented level of detail. In this paper, we review recent advancements in the t-tubule structural biology with the utility of various microscopy techniques. We outline the technical considerations in adapting SMLM to study t-tubules and its potential to further our understanding of the molecular processes that underlie the sub-micron scale structural alterations observed in a range of muscle pathologies.
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Affiliation(s)
| | | | - Michelle Munro
- Department of Physiology, The University of Auckland , New Zealand
| | - Yufeng Hou
- Department of Physiology, The University of Auckland , New Zealand
| | - David J Crossman
- Department of Physiology, The University of Auckland , New Zealand
| | - Christian Soeller
- Biomedical Physics, University of Exeter, UK, New Zealand; Biomedical Physics, University of Exeter, UK, New Zealand
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595
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Abstract
Cell-specific information on the quantity and localization of key mRNAs at single copy sensitivity in single cells is critical for evaluating basic cellular process, disease risk, and efficacy of therapy. Quantification of overexpressed mRNAs beyond the diffraction limit is constrained by the optical property of the probes and microscopy techniques. In this report, nanosized barium titanium oxide (BaTiO3, BTO) crystals were utilized as probes for mRNA quantification by a second harmonic super-resolution microscopy (SHaSM). The SHaSM was able to detect a single copy of the human epidermal growth factor receptor 2 (Her2) mRNA at a resolution of 55.6 nm with the ability to resolve multiple mRNA copies in a diffraction-limited spot. Her2 mRNA per cell was counted in SK-BR-3, MCF-7, and HeLa cell lines as 595±79.1, 38.9±8.26, and 1.5±2.8, respectively. Our single-cell quantification results were validated with the fluorescence in situ hybridization studies and quantitative PCR, showing better specificity and selectivity over current single-molecule approaches for transcript detection. The SHaSM is expected to have an upper limit of resolving ∼10(4) transcripts in a single cell with the ability to monitor intracellular transcriptional dynamics at video rate. The developed approach has strong potential in clinical research and in the early diagnosis of life-threatening diseases such as cancer.
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596
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Merdasa A, Jiménez ÁJ, Camacho R, Meyer M, Würthner F, Scheblykin IG. Single Lévy states-disorder induced energy funnels in molecular aggregates. Nano Lett 2014; 14:6774-6781. [PMID: 25349900 DOI: 10.1021/nl5021188] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Using fluorescence super-resolution microscopy we studied simultaneous spectral, spatial localization, and blinking behavior of individual 1D J-aggregates. Excitons migrating 100 nm are funneled to a trap appearing as an additional red-shifted blinking fluorescence band. We propose that the trap is a Frenkel exciton state formed much below the main exciton band edge due to an environmentally induced heavy-tailed Lévy disorder. This points to disorder engineering as a new avenue in controlling light-harvesting in molecular ensembles.
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Affiliation(s)
- Aboma Merdasa
- Chemical Physics, Lund University , P.O. Box 124, 22100 Lund, Sweden
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597
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Adrian M, Kusters R, Wierenga CJ, Storm C, Hoogenraad CC, Kapitein LC. Barriers in the brain: resolving dendritic spine morphology and compartmentalization. Front Neuroanat 2014; 8:142. [PMID: 25538570 PMCID: PMC4255500 DOI: 10.3389/fnana.2014.00142] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/13/2014] [Indexed: 11/23/2022] Open
Abstract
Dendritic spines are micron-sized protrusions that harbor the majority of excitatory synapses in the central nervous system. The head of the spine is connected to the dendritic shaft by a 50-400 nm thin membrane tube, called the spine neck, which has been hypothesized to confine biochemical and electric signals within the spine compartment. Such compartmentalization could minimize interspinal crosstalk and thereby support spine-specific synapse plasticity. However, to what extent compartmentalization is governed by spine morphology, and in particular the diameter of the spine neck, has remained unresolved. Here, we review recent advances in tool development - both experimental and theoretical - that facilitate studying the role of the spine neck in compartmentalization. Special emphasis is given to recent advances in microscopy methods and quantitative modeling applications as we discuss compartmentalization of biochemical signals, membrane receptors and electrical signals in spines. Multidisciplinary approaches should help to answer how dendritic spine architecture affects the cellular and molecular processes required for synapse maintenance and modulation.
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Affiliation(s)
- Max Adrian
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Remy Kusters
- Department of Applied Physics, Eindhoven University of TechnologyEindhoven, Netherlands
| | - Corette J. Wierenga
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of TechnologyEindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of TechnologyEindhoven, Netherlands
| | - Casper C. Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
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598
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Monaghan P, Green D, Pallister J, Klein R, White J, Williams C, McMillan P, Tilley L, Lampe M, Hawes P, Wang LF. Detailed morphological characterisation of Hendra virus infection of different cell types using super-resolution and conventional imaging. Virol J 2014; 11:200. [PMID: 25428656 PMCID: PMC4254186 DOI: 10.1186/s12985-014-0200-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/07/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Hendra virus (HeV) is a pleomorphic virus belonging to the Paramyxovirus family. Our long-term aim is to understand the process of assembly of HeV virions. As a first step, we sought to determine the most appropriate cell culture system with which to study this process, and then to use this model to define the morphology of the virus and identify the site of assembly by imaging key virus encoded proteins in infected cells. METHODS A range of primary cells and immortalised cell lines were infected with HeV, fixed at various time points post-infection, labelled for HeV proteins and imaged by confocal, super-resolution and transmission electron microscopy. RESULTS Significant differences were noted in viral protein distribution depending on the infected cell type. At 8 hpi HeV G protein was detected in the endoplasmic reticulum and M protein was seen predominantly in the nucleus in all cells tested. At 18 hpi, HeV-infected Vero cells showed M and G proteins throughout the cell and in transmission electron microscope (TEM) sections, in pleomorphic virus-like structures. In HeV infected MDBK, A549 and HeLa cells, HeV M protein was seen predominantly in the nucleus with G protein at the membrane. In HeV-infected primary bovine and porcine aortic endothelial cells and two bat-derived cell lines, HeV M protein was not seen at such high levels in the nucleus at any time point tested (8,12, 18, 24, 48 hpi) but was observed predominantly at the cell surface in a punctate pattern co-localised with G protein. These HeV M and G positive structures were confirmed as round HeV virions by TEM and super-resolution (SR) microscopy. SR imaging demonstrated for the first time sub-virion imaging of paramyxovirus proteins and the respective localisation of HeV G, M and N proteins within virions. CONCLUSION These findings provide novel insights into the structure of HeV and show that for HeV imaging studies the choice of tissue culture cells may affect the experimental results. The results also indicate that HeV should be considered a predominantly round virus with a mean diameter of approximately 280 nm by TEM and 310 nm by SR imaging.
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Affiliation(s)
- Paul Monaghan
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Diane Green
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Jackie Pallister
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Reuben Klein
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - John White
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Catherine Williams
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Paul McMillan
- Department of Biochemistry and Molecular Biology, Melbourne, Australia.
- ARC Centre of Excellence for Coherent X-ray Science, Melbourne, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3010, Australia.
- Current Address: Biological Optical Microscopy Platform, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, Melbourne, Australia.
- ARC Centre of Excellence for Coherent X-ray Science, Melbourne, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3010, Australia.
- Current Address: Biological Optical Microscopy Platform, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Marko Lampe
- Leica Microsystems, CMS GmbH, Ernst-Leitz Strasse 17-37, Wetzlar, Germany.
- Current Address: European Molecular Biology Laboratory, Meyerhofstr 1, D-69117, Heidelberg, Germany.
- Current Address: Translational Lung Research Center (TLRC), Department Translational Pulmonology, University of Heidelberg, Im Neuenheimer Feld 350, D-69120, Heidelberg, Germany.
| | - Pippa Hawes
- Pirbright Institute, Pirbright, Woking, Surrey, GU240NF, UK.
| | - Lin-Fa Wang
- CSIRO Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
- Duke-NUS Graduate Medical School, Singapore, Singapore.
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599
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Lew M, Moerner WE. Azimuthal polarization filtering for accurate, precise, and robust single-molecule localization microscopy. Nano Lett 2014; 14:6407-13. [PMID: 25272093 PMCID: PMC4245985 DOI: 10.1021/nl502914k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/26/2014] [Indexed: 05/08/2023]
Abstract
Many single nanoemitters such as fluorescent molecules produce dipole radiation that leads to systematic position errors in both particle tracking and super-resolution microscopy. Via vectorial diffraction equations and simulations, we show that imaging only azimuthally polarized light in the microscope naturally avoids emission from the z-component of the transition dipole moment, resulting in negligible localization errors for all emitter orientations and degrees of objective lens misfocus. Furthermore, localization accuracy is maintained even in the presence of aberrations resulting from imaging in mismatched media.
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Affiliation(s)
- Matthew
D. Lew
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
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600
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Schnell SJ, Ma J, Yang W. Three-Dimensional Mapping of mRNA Export through the Nuclear Pore Complex. Genes (Basel) 2014; 5:1032-49. [PMID: 25393401 PMCID: PMC4276925 DOI: 10.3390/genes5041032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/02/2014] [Accepted: 10/20/2014] [Indexed: 11/30/2022] Open
Abstract
The locations of transcription and translation of mRNA in eukaryotic cells are spatially separated by the nuclear envelope (NE). Plenty of nuclear pore complexes (NPCs) embedded in the NE function as the major gateway for the export of transcribed mRNAs from the nucleus to the cytoplasm. Whereas the NPC, perhaps one of the largest protein complexes, provides a relatively large channel for macromolecules to selectively pass through it in inherently three-dimensional (3D) movements, this channel is nonetheless below the diffraction limit of conventional light microscopy. A full understanding of the mRNA export mechanism urgently requires real-time mapping of the 3D dynamics of mRNA in the NPC of live cells with innovative imaging techniques breaking the diffraction limit of conventional light microscopy. Recently, super-resolution fluorescence microscopy and single-particle tracking (SPT) techniques have been applied to the study of nuclear export of mRNA in live cells. In this review, we emphasize the necessity of 3D mapping techniques in the study of mRNA export, briefly summarize the feasibility of current 3D imaging approaches, and highlight the new features of mRNA nuclear export elucidated with a newly developed 3D imaging approach combining SPT-based super-resolution imaging and 2D-to-3D deconvolution algorithms.
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Affiliation(s)
- Steven J Schnell
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.
| | - Jiong Ma
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.
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