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Grosjean M, Grichine A, Pezet M, Destaing O, Delon A, Wang I. Shaping an evanescent focus of light for high spatial resolution optogenetic activations in live cells. OPTICS EXPRESS 2024; 32:19480-19494. [PMID: 38859082 DOI: 10.1364/oe.522639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 06/12/2024]
Abstract
Confining light illumination in the three dimensions of space is a challenge for various applications. Among these, optogenetic methods developed for live experiments in cell biology would benefit from such a localized illumination as it would improve the spatial resolution of diffusive photosensitive proteins leading to spatially constrained biological responses in specific subcellular organelles. Here, we describe a method to create and move a focused evanescent spot, at the interface between a glass substrate and an aqueous sample, across the field of view of a high numerical aperture microscope objective, using a digital micro-mirror device (DMD). We show that, after correcting the optical aberrations, light is confined within a spot of sub-micron lateral size and ∼100 nm axial depth above the coverslip, resulting in a volume of illumination drastically smaller than the one generated by a standard propagative focus. This evanescent focus is sufficient to induce a more intense and localized recruitment compared to a propagative focus on the optogenetic system CRY2-CIBN, improving the resolution of its pattern of activation.
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2
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Wessel AK, Yoshii Y, Reder A, Boudjemaa R, Szczesna M, Betton JM, Bernal-Bayard J, Beloin C, Lopez D, Völker U, Ghigo JM. Escherichia coli SPFH Membrane Microdomain Proteins HflKC Contribute to Aminoglycoside and Oxidative Stress Tolerance. Microbiol Spectr 2023; 11:e0176723. [PMID: 37347165 PMCID: PMC10434171 DOI: 10.1128/spectrum.01767-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Many eukaryotic membrane-dependent functions are often spatially and temporally regulated by membrane microdomains (FMMs), also known as lipid rafts. These domains are enriched in polyisoprenoid lipids and scaffolding proteins belonging to the stomatin, prohibitin, flotillin, and HflK/C (SPFH) protein superfamily that was also identified in Gram-positive bacteria. In contrast, little is still known about FMMs in Gram-negative bacteria. In Escherichia coli K-12, 4 SPFH proteins, YqiK, QmcA, HflK, and HflC, were shown to localize in discrete polar or lateral inner membrane locations, raising the possibility that E. coli SPFH proteins could contribute to the assembly of inner membrane FMMs and the regulation of cellular processes. Here, we studied the determinant of the localization of QmcA and HflC and showed that FMM-associated cardiolipin lipid biosynthesis is required for their native localization pattern. Using Biolog phenotypic arrays, we showed that a mutant lacking all SPFH genes displayed increased sensitivity to aminoglycosides and oxidative stress that is due to the absence of HflKC. Our study therefore provides further insights into the contribution of SPFH proteins to stress tolerance in E. coli. IMPORTANCE Eukaryotic cells often segregate physiological processes in cholesterol-rich functional membrane microdomains. These domains are also called lipid rafts and contain proteins of the stomatin, prohibitin, flotillin, and HflK/C (SPFH) superfamily, which are also present in prokaryotes but have been mostly studied in Gram-positive bacteria. Here, we showed that the cell localization of the SPFH proteins QmcA and HflKC in the Gram-negative bacterium E. coli is altered in the absence of cardiolipin lipid synthesis. This suggests that cardiolipins contribute to E. coli membrane microdomain assembly. Using a broad phenotypic analysis, we also showed that HflKC contribute to E. coli tolerance to aminoglycosides and oxidative stress. Our study, therefore, provides new insights into the cellular processes associated with SPFH proteins in E. coli.
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Affiliation(s)
- Aimee K. Wessel
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Alexander Reder
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | - Magdalena Szczesna
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
- Centre for Bacteriology Resistance Biology, Imperial College London, London, United Kingdom
| | - Jean-Michel Betton
- Institut Pasteur, Université de Paris-Cité, UMR UMR6047, Stress adaptation and metabolism in enterobacteria, Paris, France
| | - Joaquin Bernal-Bayard
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Christophe Beloin
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Daniel Lopez
- Universidad Autonoma de Madrid, Centro Nacional de Biotecnologia, Madrid, Spain
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
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3
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Hung ST, Llobet Rosell A, Jurriens D, Siemons M, Soloviev O, Kapitein LC, Grußmayer K, Neukomm LJ, Verhaegen M, Smith C. Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult Drosophila brains. Front Neurosci 2022; 16:954949. [PMID: 36278016 PMCID: PMC9583434 DOI: 10.3389/fnins.2022.954949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) enables the high-resolution visualization of organelle structures and the precise localization of individual proteins. However, the expected resolution is not achieved in tissue as the imaging conditions deteriorate. Sample-induced aberrations distort the point spread function (PSF), and high background fluorescence decreases the localization precision. Here, we synergistically combine sensorless adaptive optics (AO), in-situ 3D-PSF calibration, and a single-objective lens inclined light sheet microscope (SOLEIL), termed (AO-SOLEIL), to mitigate deep tissue-induced deteriorations. We apply AO-SOLEIL on several dSTORM samples including brains of adult Drosophila. We observed a 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction while we used synergistic solution. AO-SOLEIL enhances the overall imaging resolution and further facilitates the visualization of sub-cellular structures in tissue.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Arnau Llobet Rosell
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Lukas J. Neukomm
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Michel Verhaegen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Carlas Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
- *Correspondence: Carlas Smith
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4
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Siemons ME, Kapitein LC, Stallinga S. Axial accuracy in localization microscopy with 3D point spread function engineering. OPTICS EXPRESS 2022; 30:28290-28300. [PMID: 36299028 DOI: 10.1364/oe.461750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/09/2022] [Indexed: 06/16/2023]
Abstract
Single-molecule localization microscopy has developed into a widely used technique to overcome the diffraction limit and enables 3D localization of single-emitters with nanometer precision. A widely used method to enable 3D encoding is to use a cylindrical lens or a phase mask to engineer the point spread function (PSF). The performance of these PSFs is often assessed by comparing the precision they achieve, ignoring accuracy. Nonetheless, accurate localization is required in many applications, such as multi-plane imaging, measuring and modelling of physical processes based on volumetric data, and 3D particle averaging. However, there are PSF model mismatches in the localization schemes due to how reference PSFs are obtained, look-up-tables are created, or spots are fitted. Currently there is little insight in how these model mismatches give rise to systematic axial localization errors, how large these errors are, and how to mitigate them. In this theoretical and simulation work we use a vector PSF model, which incorporates super-critical angle fluorescence (SAF) and the appropriate aplanatic correction factor, to analyze the errors in z-localization. We introduce theory for defining the focal plane in SAF conditions and analyze the predicted axial errors for an astigmatic PSF, double-helix PSF, and saddle-point PSF. These simulations indicate that the absolute axial biases can be as large as 140 nm, 250 nm, and 120 nm for the astigmatic, saddle-point, and double-helix PSF respectively, with relative errors of more than 50%. Finally, we discuss potential experimental methods to verify these findings and propose a workflow to mitigate these effects.
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5
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Wang J, Zhang Y. Adaptive optics in super-resolution microscopy. BIOPHYSICS REPORTS 2021; 7:267-279. [PMID: 37287764 PMCID: PMC10233472 DOI: 10.52601/bpr.2021.210015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 06/09/2023] Open
Abstract
Fluorescence microscopy has become a routine tool in biology for interrogating life activities with minimal perturbation. While the resolution of fluorescence microscopy is in theory governed only by the diffraction of light, the resolution obtainable in practice is also constrained by the presence of optical aberrations. The past two decades have witnessed the advent of super-resolution microscopy that overcomes the diffraction barrier, enabling numerous biological investigations at the nanoscale. Adaptive optics, a technique borrowed from astronomical imaging, has been applied to correct for optical aberrations in essentially every microscopy modality, especially in super-resolution microscopy in the last decade, to restore optimal image quality and resolution. In this review, we briefly introduce the fundamental concepts of adaptive optics and the operating principles of the major super-resolution imaging techniques. We highlight some recent implementations and advances in adaptive optics for active and dynamic aberration correction in super-resolution microscopy.
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Affiliation(s)
- Jingyu Wang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK
| | - Yongdeng Zhang
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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6
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Sun Y, Lee S, Kang SH. Cubic spline-based depth-dependent localization of mitochondria-endoplasmic reticulum contacts by three-dimensional light-sheet super-resolution microscopy. Analyst 2021; 146:4781-4788. [PMID: 34231561 DOI: 10.1039/d1an00852h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The contact distance between mitochondria (Mito) and endoplasmic reticulum (ER) has received considerable attention owing to their crucial function in maintaining lipid and calcium homeostasis. Herein, cubic spline algorithm-based depth-dependent fluorescence-free three-dimensional light-sheet super-resolution microscopy (3D LSRM) with dual-wavelength illumination sources was investigated to study the distance of Mito-ER contacts in various live cells. To detect wavelength-dependent scattering, 12 nm gold nanoparticles (AuNPs) and 20 nm silver nanoparticles (AgNPs) as fluorescence-free nanoprobes were conjugated with Mito and ER. The cubic spline algorithm-based method showed improved localization precision in lateral and axial directions compared with that for previously used least squares and least cubic algorithms. The cubic spline-based depth-dependent localization was applied to the spatial localization of nanoprobes in super-resolution images, in which the average distance of Mito and ER was 22.4 nm in HeLa cells, 22.2 nm in RAW264.7 macrophage cells, 21.9 nm in AGS cells, 21.4 nm in HT29 cells, and 21.3 nm in HEK293 cells. The distances were ∼12% larger than those previously determined by electron microscopy, which demonstrated that this method was accessible and reliable for studying the intracellular structures of various live cells at the subdiffraction limit resolution.
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Affiliation(s)
- Yucheng Sun
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea and Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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7
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Mau A, Friedl K, Leterrier C, Bourg N, Lévêque-Fort S. Fast widefield scan provides tunable and uniform illumination optimizing super-resolution microscopy on large fields. Nat Commun 2021; 12:3077. [PMID: 34031402 PMCID: PMC8144377 DOI: 10.1038/s41467-021-23405-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Non-uniform illumination limits quantitative analyses of fluorescence imaging techniques. In particular, single molecule localization microscopy (SMLM) relies on high irradiances, but conventional Gaussian-shaped laser illumination restricts the usable field of view to around 40 µm × 40 µm. We present Adaptable Scanning for Tunable Excitation Regions (ASTER), a versatile illumination technique that generates uniform and adaptable illumination. ASTER is also highly compatible with optical sectioning techniques such as total internal reflection fluorescence (TIRF). For SMLM, ASTER delivers homogeneous blinking kinetics at reasonable laser power over fields-of-view up to 200 µm × 200 µm. We demonstrate that ASTER improves clustering analysis and nanoscopic size measurements by imaging nanorulers, microtubules and clathrin-coated pits in COS-7 cells, and β2-spectrin in neurons. ASTER's sharp and quantitative illumination paves the way for high-throughput quantification of biological structures and processes in classical and super-resolution fluorescence microscopies.
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Affiliation(s)
- Adrien Mau
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, Orsay, France
- Abbelight, Cachan, France
| | - Karoline Friedl
- Abbelight, Cachan, France
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | | | | | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, Orsay, France.
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8
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Vickers NA, Andersson SB. Feedforward Control for Single Particle Tracking Synthetic Motion. IFAC-PAPERSONLINE 2021; 53:8878-8883. [PMID: 34027521 PMCID: PMC8135106 DOI: 10.1016/j.ifacol.2020.12.1407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single particle tracking (SPT) is a method to study the transport of biomolecules with nanometer resolution. Unfortunately, recent reports show that systematic errors in position localization and uncertainty in model parameter estimates limits the utility of these techniques in studying biological processes. There is a need for an experimental method with a known ground-truth that tests the total SPT system (sample, microscope, algorithm) on both localization and estimation of model parameters. Synthetic motion is a known ground-truth method that moves a particle along a trajectory. This trajectory is a realization of a Markovian stochastic process that represents models of biomolecular transport. Here we describe a platform for creating synthetic motion using common equipment and well-known, simple methods that can be easily adopted by the biophysics community. In this paper we describe the synthetic motion system and calibration to achieve nanometer accuracy and precision. Steady state input-output characteristics are analyzed with both line scans and grid scans. The resulting relationship is described by an affine transformation, which is inverted and used as a prefilter. Model inverse feed forward control is used to increase the system bandwidth. The system model was identified from frequency response function measurements using an integrated stepped-sine with coherent demodulation built into the FPGA controller. Zero magnitude error tracking controller method was used to invert non-minimum phase zeros to achieve a stable discrete time feed forward filter.
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Affiliation(s)
- Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA 02155 USA
- Division of Systems Engineering, Boston University, Boston, MA 02155 USA
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9
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Zelger P, Bodner L, Offterdinger M, Velas L, Schütz GJ, Jesacher A. Three-dimensional single molecule localization close to the coverslip: a comparison of methods exploiting supercritical angle fluorescence. BIOMEDICAL OPTICS EXPRESS 2021; 12:802-822. [PMID: 33680543 PMCID: PMC7901312 DOI: 10.1364/boe.413018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The precise spatial localization of single molecules in three dimensions is an important basis for single molecule localization microscopy (SMLM) and tracking. At distances up to a few hundred nanometers from the coverslip, evanescent wave coupling into the glass, also known as supercritical angle fluorescence (SAF), can strongly improve the axial precision, thus facilitating almost isotropic localization performance. Specific detection systems, introduced as Supercritical angle localization microscopy (SALM) or Direct optical nanoscopy with axially localized detection (DONALD), have been developed to exploit SAF in modified two-channel imaging schemes. Recently, our group has shown that off-focus microscopy, i.e., imaging at an intentional slight defocus, can perform equally well, but uses only a single detection arm. Here we compare SALM, off-focus imaging and the most commonly used 3D SMLM techniques, namely cylindrical lens and biplane imaging, regarding 3D localization in close proximity to the coverslip. We show that all methods gain from SAF, which leaves a high detection NA as the only major key requirement to unlock the SAF benefit. We find parameter settings for cylindrical lens and biplane imaging for highest z-precision. Further, we compare the methods in view of robustness to aberrations, fixed dipole emission and double-emitter events. We show that biplane imaging provides the best overall performance and support our findings by DNA-PAINT experiments on DNA-nanoruler samples. Our study sheds light on the effects of SAF for SMLM and is helpful for researchers who plan to employ localization-based 3D nanoscopy close to the coverslip.
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Affiliation(s)
- Philipp Zelger
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Lisa Bodner
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Martin Offterdinger
- Division of Neurobiochemistry, Biooptics, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Lukas Velas
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Gerhard J. Schütz
- Institute of Applied Physics, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alexander Jesacher
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
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10
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 285] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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11
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Petrov PN, Moerner WE. Addressing systematic errors in axial distance measurements in single-emitter localization microscopy. OPTICS EXPRESS 2020; 28:18616-18632. [PMID: 32672159 PMCID: PMC7340385 DOI: 10.1364/oe.391496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Nanoscale localization of point emitters is critical to several methods in optical fluorescence microscopy, including single-molecule super-resolution imaging and tracking. While the precision of the localization procedure has been the topic of extensive study, localization accuracy has been less emphasized, in part due to the challenge of producing an experimental sample containing unperturbed point emitters at known three-dimensional positions in a relevant geometry. We report a new experimental system which reproduces a widely-adopted geometry in high-numerical aperture localization microscopy, in which molecules are situated in an aqueous medium above a glass coverslip imaged with an oil-immersion objective. We demonstrate a calibration procedure that enables measurement of the depth-dependent point spread function (PSF) for open aperture imaging as well as imaging with engineered PSFs with index mismatch. We reveal the complicated, depth-varying behavior of the focal plane position in this system and discuss the axial localization biases incurred by common approximations of this behavior. We compare our results to theoretical calculations.
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Affiliation(s)
- Petar N. Petrov
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305, USA
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12
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Tröger J, Hoischen C, Perner B, Monajembashi S, Barbotin A, Löschberger A, Eggeling C, Kessels MM, Qualmann B, Hemmerich P. Comparison of Multiscale Imaging Methods for Brain Research. Cells 2020; 9:E1377. [PMID: 32492970 PMCID: PMC7349602 DOI: 10.3390/cells9061377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
A major challenge in neuroscience is how to study structural alterations in the brain. Even small changes in synaptic composition could have severe outcomes for body functions. Many neuropathological diseases are attributable to disorganization of particular synaptic proteins. Yet, to detect and comprehensively describe and evaluate such often rather subtle deviations from the normal physiological status in a detailed and quantitative manner is very challenging. Here, we have compared side-by-side several commercially available light microscopes for their suitability in visualizing synaptic components in larger parts of the brain at low resolution, at extended resolution as well as at super-resolution. Microscopic technologies included stereo, widefield, deconvolution, confocal, and super-resolution set-ups. We also analyzed the impact of adaptive optics, a motorized objective correction collar and CUDA graphics card technology on imaging quality and acquisition speed. Our observations evaluate a basic set of techniques, which allow for multi-color brain imaging from centimeter to nanometer scales. The comparative multi-modal strategy we established can be used as a guide for researchers to select the most appropriate light microscopy method in addressing specific questions in brain research, and we also give insights into recent developments such as optical aberration corrections.
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Affiliation(s)
- Jessica Tröger
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Christian Hoischen
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Birgit Perner
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
- Molecular Genetics Lab, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Shamci Monajembashi
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
| | - Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX13PJ, UK;
| | - Anna Löschberger
- Advanced Development Light Microscopy, Carl Zeiss Microscopy GmbH, Carl-Zeiss-Promenade 10, 07745 Jena, Germany;
| | - Christian Eggeling
- MRC Human Immunology Unit & Wolfson Imaging Center Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX39DS, UK;
- Dep. Biophysical Imaging, Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, and Institute for Applied Optics and Biophysics, Faculty of Physics and Astronomy, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Michael M. Kessels
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital—Friedrich Schiller University Jena, Nonnenplan 2-4, 07743 Jena, Germany;
| | - Peter Hemmerich
- Core Facility Imaging, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (C.H.); (B.P.); (S.M.)
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13
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Xu F, Ma D, MacPherson KP, Liu S, Bu Y, Wang Y, Tang Y, Bi C, Kwok T, Chubykin AA, Yin P, Calve S, Landreth GE, Huang F. Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval. Nat Methods 2020; 17:531-540. [PMID: 32371980 PMCID: PMC7289454 DOI: 10.1038/s41592-020-0816-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades resolution with increasing depth. We propose a method that enables the construction of an in situ 3D response of single emitters directly from single-molecule blinking datasets, and therefore allows their locations to be pinpointed with precision that achieves the Cramér-Rao lower bound and uncompromised fidelity. We demonstrate this method, named in situ PSF retrieval (INSPR), across a range of cellular and tissue architectures, from mitochondrial networks and nuclear pores in mammalian cells to amyloid-β plaques and dendrites in brain tissues and elastic fibers in developing cartilage of mice. This advancement expands the routine applicability of super-resolution microscopy from selected cellular targets near coverslips to intra- and extracellular targets deep inside tissues.
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Affiliation(s)
- Fan Xu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Kathryn P MacPherson
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Ye Bu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yu Tang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tim Kwok
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Gary E Landreth
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA. .,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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14
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Innovative particle standards and long-lived imaging for 2D and 3D dSTORM. Sci Rep 2019; 9:17967. [PMID: 31784555 PMCID: PMC6884466 DOI: 10.1038/s41598-019-53528-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Direct stochastic optical reconstruction microscopy (dSTORM), developed in the last decade, has revolutionised optical microscopy by enabling scientists to visualise objects beyond the resolution provided by conventional microscopy (200 nm). We developed an innovative method based on blinking particle standards and conditions for long-lived imaging over several weeks. Stable localisation precisions within the 10 nm-range were achieved for single virions and in cellulo 2D imaging of centrosomes, as well as their reliable reconstruction in 3D dSTORM.
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15
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Belkahla H, Boudjemaa R, Caorsi V, Pineau D, Curcio A, Lomas JS, Decorse P, Chevillot-Biraud A, Azaïs T, Wilhelm C, Randriamahazaka H, Hémadi M. Carbon dots, a powerful non-toxic support for bioimaging by fluorescence nanoscopy and eradication of bacteria by photothermia. NANOSCALE ADVANCES 2019; 1:2571-2579. [PMID: 36132715 PMCID: PMC9418816 DOI: 10.1039/c9na00140a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/17/2019] [Indexed: 05/02/2023]
Abstract
Carbon Dots (CDs) are innovative materials which have potential applications in many fields, including nanomedicine, energy and catalysis. Here CDs were produced by the alkali-assisted ultrasonic route and characterized by several techniques to determine their composition and properties. Fluorescence nanoscopy using single-molecule localization microscopy shows that they have very good photophysical properties and a remarkable blinking behaviour at 405 nm. Moreover, these CDs are a safe material, non-toxic towards different cell lines (cancer and non-cancer cells) even at very high concentration, reflecting an excellent biocompatibility. Photothermia, i.e. their heating capacity under laser irradiation, was evaluated at two wavelengths and at several power densities. The resulting temperature increment was high (5 < ΔT < 45 °C) and appropriate for biomedical applications. Bioimaging and photothermia were then performed on E. coli, a Gram(-) bacterium, incubated with CDs. Remarkably, by photothermia at 680 nm (0.3, 1 and 1.9 W cm-2) or 808 nm (1.9 W cm-2), CDs are able to eradicate bacteria in their exponential and stationary phases. Images obtained by 3D super-resolution microscopy clearly show the different CD distributions in surviving bacteria after mild photothermal treatment. These results confirm that CDs are multifunctional materials with a wide range of biomedical applications.
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Affiliation(s)
- H Belkahla
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - R Boudjemaa
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - V Caorsi
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - D Pineau
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Curcio
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - J S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - P Decorse
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Chevillot-Biraud
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - T Azaïs
- Laboratoire de Chimie de la Matière Condensée de Paris, Sorbonne Université, CNRS-UMR 7574, Collège de France 4 place Jussieu 75005 Paris France
| | - C Wilhelm
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - H Randriamahazaka
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - M Hémadi
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
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16
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Li Y, Wu YL, Hoess P, Mund M, Ries J. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. BIOMEDICAL OPTICS EXPRESS 2019; 10:2708-2718. [PMID: 31259045 PMCID: PMC6583355 DOI: 10.1364/boe.10.002708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 05/22/2023]
Abstract
Three-dimensional single molecule localization microscopy relies on the fitting of the individual molecules with a point spread function (PSF) model. The reconstructed images often show local squeezing or expansion in z. A common cause is depth-induced aberrations in conjunction with an imperfect PSF model calibrated from beads on a coverslip, resulting in a mismatch between measured PSF and real PSF. Here, we developed a strategy for accurate z-localization in which we use the imperfect PSF model for fitting, determine the fitting errors and correct for them in a post-processing step. We present an open-source software tool and a simple experimental calibration procedure that allow retrieving accurate z-positions in any PSF engineering approach or fitting modality, even at large imaging depths.
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Affiliation(s)
- Yiming Li
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Yu-Le Wu
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Philipp Hoess
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Markus Mund
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Current affiliation: Department of Biochemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
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17
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Lin R, Clowsley AH, Lutz T, Baddeley D, Soeller C. 3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples. Methods 2019; 174:56-71. [PMID: 31129290 DOI: 10.1016/j.ymeth.2019.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 12/29/2022] Open
Abstract
Assessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time- and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.
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Affiliation(s)
- Ruisheng Lin
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Alexander H Clowsley
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - Tobias Lutz
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom
| | - David Baddeley
- Department of Cell Biology, Yale University, USA; Bioengineering Institute, University of Auckland, New Zealand
| | - Christian Soeller
- Living Systems Institute and Biomedical Physics, University of Exeter, United Kingdom.
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18
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Combining 3D single molecule localization strategies for reproducible bioimaging. Nat Commun 2019; 10:1980. [PMID: 31040275 PMCID: PMC6491430 DOI: 10.1038/s41467-019-09901-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
Here, we present a 3D localization-based super-resolution technique providing a slowly varying localization precision over a 1 μm range with precisions down to 15 nm. The axial localization is performed through a combination of point spread function (PSF) shaping and supercritical angle fluorescence (SAF), which yields absolute axial information. Using a dual-view scheme, the axial detection is decoupled from the lateral detection and optimized independently to provide a weakly anisotropic 3D resolution over the imaging range. This method can be readily implemented on most homemade PSF shaping setups and provides drift-free, tilt-insensitive and achromatic results. Its insensitivity to these unavoidable experimental biases is especially adapted for multicolor 3D super-resolution microscopy, as we demonstrate by imaging cell cytoskeleton, living bacteria membranes and axon periodic submembrane scaffolds. We further illustrate the interest of the technique for biological multicolor imaging over a several-μm range by direct merging of multiple acquisitions at different depths. 3D single molecule localization microscopy suffers from several experimental biases that degrade the resolution or localization precision. Here the authors present a dual-view detection scheme combining supercritical angle fluorescence and astigmatic imaging to obtain precise and unbiased 3D super resolution images.
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19
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Kim T, Moon S, Xu K. Information-rich localization microscopy through machine learning. Nat Commun 2019; 10:1996. [PMID: 31040287 PMCID: PMC6491467 DOI: 10.1038/s41467-019-10036-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Recent years have witnessed the development of single-molecule localization microscopy as a generic tool for sampling diverse biologically relevant information at the super-resolution level. While current approaches often rely on the target-specific alteration of the point spread function to encode the multidimensional contents of single fluorophores, the details of the point spread function in an unmodified microscope already contain rich information. Here we introduce a data-driven approach in which artificial neural networks are trained to make a direct link between an experimental point spread function image and its underlying, multidimensional parameters, and compare results with alternative approaches based on maximum likelihood estimation. To demonstrate this concept in real systems, we decipher in fixed cells both the colors and the axial positions of single molecules in regular localization microscopy data.
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Affiliation(s)
- Taehwan Kim
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Seonah Moon
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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20
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Capmany A, Yoshimura A, Kerdous R, Caorsi V, Lescure A, Nery ED, Coudrier E, Goud B, Schauer K. MYO1C stabilizes actin and facilitates arrival of transport carriers at the Golgi apparatus. J Cell Sci 2019; 132:jcs.225029. [DOI: 10.1242/jcs.225029] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/01/2019] [Indexed: 12/22/2022] Open
Abstract
We aim to identify the myosin motor proteins that control trafficking at the Golgi apparatus. In addition to the known Golgi-associated myosins MYO6, MYO18A and MYH9 (myosin IIA), we identify MYO1C as a novel player at the Golgi. We demonstrate that depletion of MYO1C induces Golgi apparatus fragmentation and decompaction. MYO1C accumulates at dynamic structures around the Golgi apparatus that colocalize with Golgi-associated actin dots. MYO1C depletion leads to loss of cellular F-actin, and Golgi apparatus decompaction is also observed after the inhibition or loss of the Arp2/3 complex. We show that the functional consequences of MYO1C depletion is a delay in the arrival of incoming transport carriers, both from the anterograde and retrograde routes. We propose that MYO1C stabilizes actin at the Golgi apparatus facilitating the arrival of incoming transport carriers at the Golgi.
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Affiliation(s)
- Anahi Capmany
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Azumi Yoshimura
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Rachid Kerdous
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | | | - Aurianne Lescure
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Department of Translational Research, BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Department of Translational Research, BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Evelyne Coudrier
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Bruno Goud
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Kristine Schauer
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
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21
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Heil HS, Schreiber B, Götz R, Emmerling M, Dabauvalle MC, Krohne G, Höfling S, Kamp M, Sauer M, Heinze KG. Sharpening emitter localization in front of a tuned mirror. LIGHT, SCIENCE & APPLICATIONS 2018; 7:99. [PMID: 30534368 PMCID: PMC6279778 DOI: 10.1038/s41377-018-0104-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 05/23/2023]
Abstract
Single-molecule localization microscopy (SMLM) aims for maximized precision and a high signal-to-noise ratio1. Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2-4. Here, we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two. The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength, as experimentally demonstrated for dual-color SMLM in cells.
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Affiliation(s)
- Hannah S. Heil
- Rudolf Virchow Center, Research Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str.2, 97080 Würzburg, Germany
| | - Benjamin Schreiber
- Rudolf Virchow Center, Research Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str.2, 97080 Würzburg, Germany
| | - Ralph Götz
- Department of Biotechnology and Biophysics, Biozentrum, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Monika Emmerling
- Technische Physik, Physikalisches Institut and Wilhelm Conrad Röntgen-Center for Complex Material Systems, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Marie-Christine Dabauvalle
- Division of Electron Microscopy, Biozentrum, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Georg Krohne
- Division of Electron Microscopy, Biozentrum, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sven Höfling
- Technische Physik, Physikalisches Institut and Wilhelm Conrad Röntgen-Center for Complex Material Systems, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, KY16 9SS UK
| | - Martin Kamp
- Technische Physik, Physikalisches Institut and Wilhelm Conrad Röntgen-Center for Complex Material Systems, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biozentrum, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Katrin G. Heinze
- Rudolf Virchow Center, Research Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str.2, 97080 Würzburg, Germany
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22
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Nanometer-scale Multiplexed Super-Resolution Imaging with an Economic 3D-DNA-PAINT Microscope. Chemphyschem 2018; 19:3024-3034. [DOI: 10.1002/cphc.201800630] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Indexed: 01/08/2023]
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23
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Niederauer C, Blumhardt P, Mücksch J, Heymann M, Lambacher A, Schwille P. Direct characterization of the evanescent field in objective-type total internal reflection fluorescence microscopy. OPTICS EXPRESS 2018; 26:20492-20506. [PMID: 30119359 DOI: 10.1364/oe.26.020492] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/08/2018] [Indexed: 05/22/2023]
Abstract
Total internal reflection fluorescence (TIRF) microscopy is a commonly used method for studying fluorescently labeled molecules in close proximity to a surface. Usually, the TIRF axial excitation profile is assumed to be single-exponential with a characteristic penetration depth, governed by the incident angle of the excitation laser beam towards the optical axis. However, in practice, the excitation profile does not only comprise the theoretically predicted single-exponential evanescent field, but also an additional non-evanescent contribution, supposedly caused by scattering within the optical path or optical aberrations. We developed a calibration slide to directly characterize the TIRF excitation field. Our slide features ten height steps ranging from 25 to 550 nanometers, fabricated from a polymer with a refractive index matching that of water. Fluorophores in aqueous solution above the polymer step layers sample the excitation profile at different heights. The obtained excitation profiles confirm the theoretically predicted exponential decay over increasing step heights as well as the presence of a non-evanescent contribution.
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