1
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Saliba N, Gagliano G, Gustavsson AK. Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559876. [PMID: 37808751 PMCID: PMC10557638 DOI: 10.1101/2023.09.27.559876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample and for efficient and automated solution exchange. By combining these innovations with PSF engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets, we demonstrate whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
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Affiliation(s)
- Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, 77005
| | - Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Applied Physics Program, Rice University, Houston, TX, 77005
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Department of BioSciences, Rice University, Houston, TX, 77005
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005
- Institute of Biosciences and Bioengineering, Rice University, Houston, TX, 77005
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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2
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Gardini L, Vignolini T, Curcio V, Pavone FS, Capitanio M. Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy. OPTICS EXPRESS 2023; 31:26208-26225. [PMID: 37710487 DOI: 10.1364/oe.492152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 09/16/2023]
Abstract
In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and of how this impacts on the image quality complicates the setting of HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the effects of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 µm). Based on this, we present a simple optical solution that exploits a rectangular slit to reduce the inclined beam thickness down to 2.6 µm while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.
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3
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Chen R, Tang X, Zhao Y, Shen Z, Zhang M, Shen Y, Li T, Chung CHY, Zhang L, Wang J, Cui B, Fei P, Guo Y, Du S, Yao S. Single-frame deep-learning super-resolution microscopy for intracellular dynamics imaging. Nat Commun 2023; 14:2854. [PMID: 37202407 DOI: 10.1038/s41467-023-38452-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) can be used to resolve subcellular structures and achieve a tenfold improvement in spatial resolution compared to that obtained by conventional fluorescence microscopy. However, the separation of single-molecule fluorescence events that requires thousands of frames dramatically increases the image acquisition time and phototoxicity, impeding the observation of instantaneous intracellular dynamics. Here we develop a deep-learning based single-frame super-resolution microscopy (SFSRM) method which utilizes a subpixel edge map and a multicomponent optimization strategy to guide the neural network to reconstruct a super-resolution image from a single frame of a diffraction-limited image. Under a tolerable signal density and an affordable signal-to-noise ratio, SFSRM enables high-fidelity live-cell imaging with spatiotemporal resolutions of 30 nm and 10 ms, allowing for prolonged monitoring of subcellular dynamics such as interplays between mitochondria and endoplasmic reticulum, the vesicle transport along microtubules, and the endosome fusion and fission. Moreover, its adaptability to different microscopes and spectra makes it a useful tool for various imaging systems.
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Affiliation(s)
- Rong Chen
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiao Tang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuxuan Zhao
- School of Optical and Electronic Information, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Zeyu Shen
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Zhang
- School of Optical and Electronic Information, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Yusheng Shen
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tiantian Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Casper Ho Yin Chung
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lijuan Zhang
- School of Pharmaceutical Sciences, Guizhou University, 550025, Guizhou, China
| | - Ji Wang
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Binbin Cui
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Yusong Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Shengwang Du
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Physics, The University of Texas at Dallas, Richardson, TX, 75080, USA.
| | - Shuhuai Yao
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
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4
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Mendonca T, Lis-Slimak K, Matheson AB, Smith MG, Anane-Adjei AB, Ashworth JC, Cavanagh R, Paterson L, Dalgarno PA, Alexander C, Tassieri M, Merry CLR, Wright AJ. OptoRheo: Simultaneous in situ micro-mechanical sensing and imaging of live 3D biological systems. Commun Biol 2023; 6:463. [PMID: 37117487 PMCID: PMC10147656 DOI: 10.1038/s42003-023-04780-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 03/30/2023] [Indexed: 04/30/2023] Open
Abstract
Biomechanical cues from the extracellular matrix (ECM) are essential for directing many cellular processes, from normal development and repair, to disease progression. To better understand cell-matrix interactions, we have developed a new instrument named 'OptoRheo' that combines light sheet fluorescence microscopy with particle tracking microrheology. OptoRheo lets us image cells in 3D as they proliferate over several days while simultaneously sensing the mechanical properties of the surrounding extracellular and pericellular matrix at a sub-cellular length scale. OptoRheo can be used in two operational modalities (with and without an optical trap) to extend the dynamic range of microrheology measurements. We corroborated this by characterising the ECM surrounding live breast cancer cells in two distinct culture systems, cell clusters in 3D hydrogels and spheroids in suspension culture. This cutting-edge instrument will transform the exploration of drug transport through complex cell culture matrices and optimise the design of the next-generation of disease models.
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Affiliation(s)
- Tania Mendonca
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Katarzyna Lis-Slimak
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Andrew B Matheson
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Matthew G Smith
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | | | - Jennifer C Ashworth
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Robert Cavanagh
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Lynn Paterson
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | - Paul A Dalgarno
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, UK
| | | | - Manlio Tassieri
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Catherine L R Merry
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Amanda J Wright
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham, UK
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5
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Understanding immune signaling using advanced imaging techniques. Biochem Soc Trans 2022; 50:853-866. [PMID: 35343569 PMCID: PMC9162467 DOI: 10.1042/bst20210479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
Abstract
Advanced imaging is key for visualizing the spatiotemporal regulation of immune signaling which is a complex process involving multiple players tightly regulated in space and time. Imaging techniques vary in their spatial resolution, spanning from nanometers to micrometers, and in their temporal resolution, ranging from microseconds to hours. In this review, we summarize state-of-the-art imaging methodologies and provide recent examples on how they helped to unravel the mysteries of immune signaling. Finally, we discuss the limitations of current technologies and share our insights on how to overcome these limitations to visualize immune signaling with unprecedented fidelity.
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6
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Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:ijms23031643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
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Affiliation(s)
| | | | | | - Juhyun Lee
- Correspondence: ; Tel.: +1-817-272-6534; Fax: +1-817-272-2251
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7
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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8
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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9
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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10
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Jannasch A, Szilagyi SA, Burmeister M, Davis QT, Hermsdorf GL, De S, Schäffer E. Fast 3D imaging of giant unilamellar vesicles using reflected light-sheet microscopy with single molecule sensitivity. J Microsc 2021; 285:40-51. [PMID: 34786705 DOI: 10.1111/jmi.13070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/29/2022]
Abstract
Observation of highly dynamic processes inside living cells at the single molecule level is key for a better understanding of biological systems. However, imaging of single molecules in living cells is usually limited by the spatial and temporal resolution, photobleaching and the signal-to-background ratio. To overcome these limitations, light-sheet microscopes with thin selective plane illumination, for example, in a reflected geometry with a high numerical aperture imaging objective, have been developed. Here, we developed a reflected light-sheet microscope with active optics for fast, high contrast, two-colour acquisition of z -stacks. We demonstrate fast volume scanning by imaging a two-colour giant unilamellar vesicle (GUV) hemisphere. In addition, the high contrast enabled the imaging and tracking of single lipids in the GUV cap. The enhanced reflected scanning light-sheet microscope enables fast 3D scanning of artificial membrane systems and potentially live cells with single-molecule sensitivity and thereby could provide quantitative and molecular insight into the operation of cells.
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Affiliation(s)
- Anita Jannasch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Sven A Szilagyi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Max Planck Institute for Solid State Physics, Heisenbergstrasse 1, Stuttgart, Germany
| | - Moritz Burmeister
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Q Tyrell Davis
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,School of Life Sciences, University of Dundee, Dow Street, Dundee, Scotland, UK
| | - Gero L Hermsdorf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
| | - Suman De
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany.,Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Broomhall, Sheffield, UK
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, Germany
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11
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Rashid FZM, Mahlandt E, van der Vaart M, Boer DEC, Varela Alvarez M, Henneman B, Brocken DJW, Voskamp P, Blok A, Shimizu T, Meijer A, Luijsterburg M, Goedhart J, Crémazy FGE, Dame R. HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic Acids Res 2021; 50:e10. [PMID: 34734265 PMCID: PMC8789088 DOI: 10.1093/nar/gkab993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023] Open
Abstract
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Eike Mahlandt
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Michiel van der Vaart
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Monica Varela Alvarez
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Bram Henneman
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Daan J W Brocken
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Anneloes J Blok
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Thomas S Shimizu
- Systems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands
| | - Annemarie H Meijer
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Joachim Goedhart
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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12
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Boka AP, Mukherjee A, Mir M. Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue and embryos. Development 2021; 148:272071. [PMID: 34490887 DOI: 10.1242/dev.199744] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
For decades, we have relied on population and time-averaged snapshots of dynamic molecular scale events to understand how genes are regulated during development and beyond. The advent of techniques to observe single-molecule kinetics in increasingly endogenous contexts, progressing from in vitro studies to living embryos, has revealed how much we have missed. Here, we provide an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), with the goal of enabling the reader to critically analyse single-molecule studies, as well as to inspire the application of SMT to their own work. We start by overviewing the basics of and motivation for SMT experiments, and the trade-offs involved when optimizing parameters. We then cover key technologies, including fluorescent labelling, excitation and detection optics, localization and tracking algorithms, and data analysis. Finally, we provide a summary of selected recent applications of SMT to study the dynamics of gene regulation.
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Affiliation(s)
- Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Sato Y, Nakao M, Kimura H. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics. Microscopy (Oxf) 2021; 70:415-422. [PMID: 34329472 PMCID: PMC8491620 DOI: 10.1093/jmicro/dfab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized by both small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind weakly to specific modifications, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformational changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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14
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Nowzari F, Wang H, Khoradmehr A, Baghban M, Baghban N, Arandian A, Muhaddesi M, Nabipour I, Zibaii MI, Najarasl M, Taheri P, Latifi H, Tamadon A. Three-Dimensional Imaging in Stem Cell-Based Researches. Front Vet Sci 2021; 8:657525. [PMID: 33937378 PMCID: PMC8079735 DOI: 10.3389/fvets.2021.657525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Stem cells have an important role in regenerative therapies, developmental biology studies and drug screening. Basic and translational research in stem cell technology needs more detailed imaging techniques. The possibility of cell-based therapeutic strategies has been validated in the stem cell field over recent years, a more detailed characterization of the properties of stem cells is needed for connectomics of large assemblies and structural analyses of these cells. The aim of stem cell imaging is the characterization of differentiation state, cellular function, purity and cell location. Recent progress in stem cell imaging field has included ultrasound-based technique to study living stem cells and florescence microscopy-based technique to investigate stem cell three-dimensional (3D) structures. Here, we summarized the fundamental characteristics of stem cells via 3D imaging methods and also discussed the emerging literatures on 3D imaging in stem cell research and the applications of both classical 2D imaging techniques and 3D methods on stem cells biology.
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Affiliation(s)
- Fariborz Nowzari
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Huimei Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mandana Baghban
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Baghban
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Alireza Arandian
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mahdi Muhaddesi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad I. Zibaii
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mostafa Najarasl
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Payam Taheri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Hamid Latifi
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
- Department of Physics, Shahid Beheshti University, Tehran, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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15
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Chen R, Zhao Y, Li M, Wang Y, Zhang L, Fei P. Efficient super-resolution volumetric imaging by radial fluctuation Bayesian analysis light-sheet microscopy. JOURNAL OF BIOPHOTONICS 2020; 13:e201960242. [PMID: 32314491 DOI: 10.1002/jbio.201960242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Various computational super-resolution methods are available based on the analysis of fluorescence fluctuation behind acquired frames. However, dilemmas often exist in the balance of fluorophore characteristics, computation cost, and achievable resolution. Here we present an approach that uses a super-resolution radial fluctuations (SRRF) image to guide the Bayesian analysis of fluorophore blinking and bleaching (3B) events, allowing greatly accelerated localization of overlapping fluorophores with high accuracy. This radial fluctuation Bayesian analysis (RFBA) approach is also extended to three dimensions for the first time and combined with light-sheet fluorescence microscopy, to achieve super-resolution volumetric imaging of thick samples densely labeled with common fluorophores. For example, a 700-nm thin Bessel plane illumination is developed to optically section the Drosophila brain, providing a high-contrast 3D image of rhythmic neurons. RFBA analyzes 30 serial volumes to reconstruct a super-resolved 3D image at 4-times higher resolutions (~70 and 170 nm), and precisely resolve the axon terminals. The computation is over 2-orders faster than conventional 3B analysis microscopy. The capability of RFBA is also verified through dual-color imaging of cell nucleus in live Drosophila brain. The spatial co-localization patterns of the nuclear envelope and DNA in a neuron deep inside the brain can be precisely extracted by our approach.
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Affiliation(s)
- Rong Chen
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Zhao
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Mengna Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yarong Wang
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Luoying Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fei
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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16
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Liu S, Huh H, Lee SH, Huang F. Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens. Annu Rev Biomed Eng 2020; 22:155-184. [PMID: 32243765 PMCID: PMC7430714 DOI: 10.1146/annurev-bioeng-060418-052203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.
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Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA;
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA
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17
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Ma H, Liu Y. Super-resolution localization microscopy: Toward high throughput, high quality, and low cost. APL PHOTONICS 2020; 5:060902. [PMID: 34350342 PMCID: PMC8330581 DOI: 10.1063/5.0011731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
After nearly 15 years since its initial debut, super-resolution localization microscopy that surpasses the diffraction-limited resolution barrier of optical microscopy has rapidly gotten out of the ivory tower and entered a new phase to address various challenging biomedical questions. Recent advances in this technology greatly increased the imaging throughput, improved the imaging quality, simplified the sample preparation, and reduced the system cost, making this technology suitable for routine biomedical research. We will provide our perspective on the recent technical advances and their implications in serving the community of biomedical research.
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Affiliation(s)
- Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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18
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Tosheva KL, Yuan Y, Matos Pereira P, Culley S, Henriques R. Between life and death: strategies to reduce phototoxicity in super-resolution microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:163001. [PMID: 33994582 PMCID: PMC8114953 DOI: 10.1088/1361-6463/ab6b95] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 05/23/2023]
Abstract
Super-resolution microscopy (SRM) enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we give an overview of new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.
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Affiliation(s)
- Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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19
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Araki S, Nakano M, Tsugane M, Sunaga F, Hattori M, Nakano M, Nagai T, Suzuki H. A simple microfluidic device for live-imaging of the vertical section of epithelial cells. Analyst 2020; 145:667-674. [PMID: 31799546 DOI: 10.1039/c9an02165e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We investigated the capability of simple microfluidic devices with trenches having vertical sidewalls for live-cell fluorescence imaging of adherent cells. An epithelial cell line that forms a two-dimensional (2D) sheet was cultured to adhere to the vertical sidewall so that its vertical section can be imaged directly using ordinal inverted-type laser-scanning microscopy. The material and the structure of the device were characterized. We show that the detailed distribution of intracellular organelles, such as microtubules and mitochondria, and of intercellular apparatus, such as claudin and zonula occludens, can be imaged with high spatio-temporal resolution with a single scan.
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Affiliation(s)
- Seigo Araki
- Precision Engineering Course, Graduate School of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
| | - Masayoshi Nakano
- Precision Engineering Course, Graduate School of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
| | - Mamiko Tsugane
- Dept. Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan and Japan Society for the Promotion of Science (JSPS), 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Fumiko Sunaga
- Dept. Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Mitsuru Hattori
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Masahiro Nakano
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Hiroaki Suzuki
- Precision Engineering Course, Graduate School of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan. and Dept. Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
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20
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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21
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Lipiec E, Ruggeri FS, Benadiba C, Borkowska AM, Kobierski JD, Miszczyk J, Wood BR, Deacon GB, Kulik A, Dietler G, Kwiatek WM. Infrared nanospectroscopic mapping of a single metaphase chromosome. Nucleic Acids Res 2019; 47:e108. [PMID: 31562528 PMCID: PMC6765102 DOI: 10.1093/nar/gkz630] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 07/07/2019] [Accepted: 07/13/2019] [Indexed: 01/27/2023] Open
Abstract
The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.
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Affiliation(s)
- Ewelina Lipiec
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Francesco S Ruggeri
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Chemistry, University of Cambridge, CB21EW, UK
| | - Carine Benadiba
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anna M Borkowska
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Jan D Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy Jagiellonian University Medical College, PL-31007 Cracow, Poland
| | - Justyna Miszczyk
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Glen B Deacon
- School of Chemistry, Faculty of Science, Monash University, 3800 Victoria, Australia
| | - Andrzej Kulik
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
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22
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Lu CH, Tang WC, Liu YT, Chang SW, Wu FCM, Chen CY, Tsai YC, Yang SM, Kuo CW, Okada Y, Hwu YK, Chen P, Chen BC. Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging. Commun Biol 2019; 2:177. [PMID: 31098410 PMCID: PMC6509110 DOI: 10.1038/s42003-019-0403-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Recent advances in super-resolution microscopy allow the localization of single molecules within individual cells but not within multiple whole cells due to weak signals from single molecules and slow acquisition process for point accumulation to reconstruct super-resolution images. Here, we report a fast, large-scale, and three-dimensional super-resolution fluorescence microscope based on single-wavelength Bessel lightsheet to selectively illuminate spontaneous blinking fluorophores tagged to the proteins of interest in space. Critical parameters such as labeling density, excitation power, and exposure time were systematically optimized resulting in a maximum imaging speed of 2.7 × 104 µm3 s-1. Fourier ring correlation analysis revealed a reconstructed image with a lateral resolution of ~75 nm through the accumulation of 250 image volumes on immobilized samples within 15 min. Hence, the designed system could open new insights into the discovery of complex biological structures and live 3D localization imaging.
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Affiliation(s)
- Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | | | - Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yun-Chi Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Chiung-Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, 565-0874 Japan
- Department of Physics, Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Yeu-Kuang Hwu
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, 30013 Taiwan
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23
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Kashekodi AB, Meinert T, Michiels R, Rohrbach A. Miniature scanning light-sheet illumination implemented in a conventional microscope. BIOMEDICAL OPTICS EXPRESS 2018; 9:4263-4274. [PMID: 30615716 PMCID: PMC6157761 DOI: 10.1364/boe.9.004263] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/02/2018] [Indexed: 05/02/2023]
Abstract
Living cells are highly dynamic systems responding to a large variety of biochemical and mechanical stimuli over minutes, which are well controlled by e.g. optical tweezers. However, live cell investigation through fluorescence microscopy is usually limited not only by the spatial and temporal imaging resolution but also by fluorophore bleaching. Therefore, we designed a miniature light-sheet illumination system that is implemented in a conventional inverted microscope equipped with optical tweezers and interferometric tracking to capture 3D images of living macrophages at reduced bleaching. The horizontal light-sheet is generated with a 0.12 mm small cantilevered mirror placed at 45° to the detection axis. The objective launched illumination beam is reflected by the micro-mirror and illuminates the sample perpendicular to the detection axis. Lateral and axial scanning of both Gaussian and Bessel beams, together with an electrically tunable lens for fast focusing, enables rapid 3D image capture without moving the sample or the objective lens. Using scanned Bessel beams and line-confocal detection, an average axial resolution of 0.8 µm together with a 10-15 fold improved image contrast is achieved.
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24
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Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
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Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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25
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Shao S, Xue B, Sun Y. Intranucleus Single-Molecule Imaging in Living Cells. Biophys J 2018; 115:181-189. [PMID: 29861035 DOI: 10.1016/j.bpj.2018.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/19/2018] [Accepted: 05/11/2018] [Indexed: 12/26/2022] Open
Abstract
Many critical processes occurring in mammalian cells are stochastic and can be directly observed at the single-molecule level within their physiological environment, which would otherwise be obscured in an ensemble measurement. There are various fundamental processes in the nucleus, such as transcription, replication, and DNA repair, the study of which can greatly benefit from intranuclear single-molecule imaging. However, the number of such studies is relatively small mainly because of lack of proper labeling and imaging methods. In the past decade, tremendous efforts have been devoted to developing tools for intranuclear imaging. Here, we mainly describe the recent methodological developments of single-molecule imaging and their emerging applications in the live nucleus. We also discuss the remaining issues and provide a perspective on future developments and applications of this field.
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Affiliation(s)
- Shipeng Shao
- State Key Laboratory of Membrane Biology, BIOPIC, School of Life Sciences, Peking University, Beijing, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, BIOPIC, School of Life Sciences, Peking University, Beijing, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, BIOPIC, School of Life Sciences, Peking University, Beijing, China.
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26
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Chakkarapani SK, Sun Y, Lee S, Fang N, Kang SH. Three-Dimensional Orientation of Anisotropic Plasmonic Aggregates at Intracellular Nuclear Indentation Sites by Integrated Light Sheet Super-Resolution Microscopy. ACS NANO 2018; 12:4156-4163. [PMID: 29578326 DOI: 10.1021/acsnano.8b00025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Three-dimensional (3D) orientations of individual anisotropic plasmonic nanoparticles in aggregates were observed in real time by integrated light sheet super-resolution microscopy ( iLSRM). Asymmetric light scattering of a gold nanorod (AuNR) was used to trigger signals based on the polarizer angle. Controlled photoswitching was achieved by turning the polarizer and obtaining a series of images at different polarization directions. 3D subdiffraction-limited super-resolution images were obtained by superlocalization of scattering signals as a function of the anisotropic optical properties of AuNRs. Varying the polarizer angle allowed resolution of the orientation of individual AuNRs. 3D images of individual nanoparticles were resolved in aggregated regions, resulting in as low as 64 nm axial resolution and 28 nm spatial resolution. The proposed imaging setup and localization approach demonstrates a convenient method for imaging under a noisy environment where the majority of scattering noise comes from cellular components. This integrated 3D iLSRM and localization technique was shown to be reliable and useful in the field of 3D nonfluorescence super-resolution imaging.
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Affiliation(s)
- Suresh Kumar Chakkarapani
- Department of Chemistry, Graduate School , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
| | - 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
| | - Ning Fang
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| | - Seong Ho Kang
- Department of Chemistry, Graduate School , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
- Department of Applied Chemistry and Institute of Natural Sciences , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
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27
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Gustavsson AK, Petrov PN, Moerner WE. Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. OPTICS EXPRESS 2018; 26:13122-13147. [PMID: 29801343 PMCID: PMC6005674 DOI: 10.1364/oe.26.013122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/30/2018] [Indexed: 05/08/2023]
Abstract
The development of imaging techniques beyond the diffraction limit has paved the way for detailed studies of nanostructures and molecular mechanisms in biological systems. Imaging thicker samples, such as mammalian cells and tissue, in all three dimensions, is challenging due to increased background and volumes to image. Light sheet illumination is a method that allows for selective irradiation of the image plane, and its inherent optical sectioning capability allows for imaging of biological samples with reduced background, photobleaching, and photodamage. In this review, we discuss the advantage of combining single-molecule imaging with light sheet illumination. We begin by describing the principles of single-molecule localization microscopy and of light sheet illumination. Finally, we present examples of designs that successfully have married single-molecule super-resolution imaging with light sheet illumination for improved precision in mammalian cells.
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28
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Park S, Kang W, Kwon YD, Shim J, Kim S, Kaang BK, Hohng S. Superresolution fluorescence microscopy for 3D reconstruction of thick samples. Mol Brain 2018; 11:17. [PMID: 29544505 PMCID: PMC5856285 DOI: 10.1186/s13041-018-0361-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/07/2018] [Indexed: 01/07/2023] Open
Abstract
Three-dimensional (3D) reconstruction of thick samples using superresolution fluorescence microscopy remains challenging due to high level of background noise and fast photobleaching of fluorescence probes. We develop superresolution fluorescence microscopy that can reconstruct 3D structures of thick samples with both high localization accuracy and no photobleaching problem. The background noise is reduced by optically sectioning the sample using line-scan confocal microscopy, and the photobleaching problem is overcome by using the DNA-PAINT (Point Accumulation for Imaging in Nanoscale Topography). As demonstrations, we take 3D superresolution images of microtubules of a whole cell, and two-color 3D images of microtubules and mitochondria. We also present superresolution images of chemical synapse of a mouse brain section at different z-positions ranging from 0 μm to 100 μm.
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Affiliation(s)
- Sangjun Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea.,Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea.,National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Wooyoung Kang
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea.,Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea.,National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Yeong-Dae Kwon
- National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jaehoon Shim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Siyong Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea. .,Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea. .,National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea.
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29
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Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE. Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10500:105000M. [PMID: 29681676 PMCID: PMC5906058 DOI: 10.1117/12.2288443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered long axial range point spread functions (PSFs) for low-background, 3D super localization of single molecules as well as 3D super-resolution imaging in thick cells. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The axial positions of the single molecules are encoded in the shape of the PSF rather than in the position or thickness of the light sheet, and the light sheet can therefore be formed using simple optics. The result is flexible and user-friendly 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSF for fiducial bead tracking and live axial drift correction. We envision TILT3D to become an important tool not only for 3D super-resolution imaging, but also for live whole-cell single-particle and single-molecule tracking.
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Affiliation(s)
- Anna-Karin Gustavsson
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Dept. of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden 17111
| | - Petar N. Petrov
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - Maurice Y. Lee
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Biophysics Program, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - Yoav Shechtman
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
| | - W. E. Moerner
- Dept. of Chemistry, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
- Biophysics Program, Stanford University, 375 North-South Axis, Stanford, CA, USA 94305-4401
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30
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Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat Commun 2018; 9:123. [PMID: 29317629 PMCID: PMC5760554 DOI: 10.1038/s41467-017-02563-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/11/2017] [Indexed: 12/24/2022] Open
Abstract
Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The result is simple and flexible 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validate TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed tetrapod PSFs for fiducial bead tracking and live axial drift correction.
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Affiliation(s)
- Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Maurice Y Lee
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.,Biomedical Engineering Department, Technion, Israel Institute of Technology, Haifa, 3200003, Israel
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA. .,Biophysics Program, Stanford University, Stanford, CA, 94305, USA.
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31
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Hedde PN, Malacrida L, Ahrar S, Siryaporn A, Gratton E. sideSPIM - selective plane illumination based on a conventional inverted microscope. BIOMEDICAL OPTICS EXPRESS 2017; 8:3918-3937. [PMID: 29026679 PMCID: PMC5611913 DOI: 10.1364/boe.8.003918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Previously described selective plane illumination microscopy techniques typically offset ease of use and sample handling for maximum imaging performance or vice versa. Also, to reduce cost and complexity while maximizing flexibility, it is highly desirable to implement light sheet microscopy such that it can be added to a standard research microscope instead of setting up a dedicated system. We devised a new approach termed sideSPIM that provides uncompromised imaging performance and easy sample handling while, at the same time, offering new applications of plane illumination towards fluidics and high throughput 3D imaging of multiple specimen. Based on an inverted epifluorescence microscope, all of the previous functionality is maintained and modifications to the existing system are kept to a minimum. At the same time, our implementation is able to take full advantage of the speed of the employed sCMOS camera and piezo stage to record data at rates of up to 5 stacks/s. Additionally, sample handling is compatible with established methods and switching magnification to change the field of view from single cells to whole organisms does not require labor intensive adjustments of the system.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Siavash Ahrar
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Albert Siryaporn
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
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32
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Oreopoulos J, Gray-Owen SD, Yip CM. High Density or Urban Sprawl: What Works Best in Biology? ACS NANO 2017; 11:1131-1135. [PMID: 28112892 DOI: 10.1021/acsnano.7b00061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
With new approaches in imaging-from new tools or reagents to processing algorithms-come unique opportunities and challenges to our understanding of biological processes, structures, and dynamics. Although innovations in super-resolution imaging are affording novel perspectives into how molecules structurally associate and localize in response to, or in order to initiate, specific signaling events in the cell, questions arise as to how to interpret these observations in the context of biological function. Just as each neighborhood in a city has its own unique vibe, culture, and indeed density, recent work has shown that membrane receptor behavior and action is governed by their localization and association state. There is tremendous potential in developing strategies for tracking how the populations of these molecular neighborhoods change dynamically.
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Affiliation(s)
- John Oreopoulos
- Institute of Biomaterials and Biomedical Engineering, University of Toronto , Toronto M5S 3G9, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto M5S 1A8, Canada
| | - Christopher M Yip
- Institute of Biomaterials and Biomedical Engineering, University of Toronto , Toronto M5S 3G9, Canada
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33
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Superresolution imaging reveals nanometer- and micrometer-scale spatial distributions of T-cell receptors in lymph nodes. Proc Natl Acad Sci U S A 2016; 113:7201-6. [PMID: 27303041 DOI: 10.1073/pnas.1512331113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
T cells become activated when T-cell receptors (TCRs) recognize agonist peptides bound to major histocompatibility complex molecules on antigen-presenting cells. T-cell activation critically relies on the spatiotemporal arrangements of TCRs on the plasma membrane. However, the molecular organizations of TCRs on lymph node-resident T cells have not yet been determined, owing to the diffraction limit of light. Here we visualized nanometer- and micrometer-scale TCR distributions in lymph nodes by light sheet direct stochastic optical reconstruction microscopy (dSTORM) and structured illumination microscopy (SIM). This dSTORM and SIM approach provides the first evidence, to our knowledge, of multiscale reorganization of TCRs during in vivo immune responses. We observed nanometer-scale plasma membrane domains, known as protein islands, on naïve T cells. These protein islands were enriched within micrometer-sized surface areas that we call territories. In vivo T-cell activation caused the TCR territories to contract, leading to the coalescence of protein islands and formation of stable TCR microclusters.
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34
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Beuzer P, La Clair JJ, Cang H. Color-Coded Super-Resolution Small-Molecule Imaging. Chembiochem 2016; 17:999-1003. [PMID: 26994590 PMCID: PMC5291120 DOI: 10.1002/cbic.201600013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 12/15/2022]
Abstract
Although the development of super-resolution microscopy dates back to 1994, its applications have been primarily focused on visualizing cellular structures and targets, including proteins, DNA and sugars. We now report on a system that allows both monitoring of the localization of exogenous small molecules in live cells at low resolution and subsequent super-resolution imaging by using stochastic optical reconstruction microscopy (STORM) on fixed cells. This represents a powerful new tool to understand the dynamics of subcellular trafficking associated with the mode and mechanism of action of exogenous small molecules.
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Affiliation(s)
- Paolo Beuzer
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James J La Clair
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1052, USA.
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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35
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Meddens MBM, Liu S, Finnegan PS, Edwards TL, James CD, Lidke KA. Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution. BIOMEDICAL OPTICS EXPRESS 2016; 7:2219-36. [PMID: 27375939 PMCID: PMC4918577 DOI: 10.1364/boe.7.002219] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/12/2016] [Accepted: 05/09/2016] [Indexed: 05/07/2023]
Abstract
We have developed a method for performing light-sheet microscopy with a single high numerical aperture lens by integrating reflective side walls into a microfluidic chip. These 45° side walls generate light-sheet illumination by reflecting a vertical light-sheet into the focal plane of the objective. Light-sheet illumination of cells loaded in the channels increases image quality in diffraction limited imaging via reduction of out-of-focus background light. Single molecule super-resolution is also improved by the decreased background resulting in better localization precision and decreased photo-bleaching, leading to more accepted localizations overall and higher quality images. Moreover, 2D and 3D single molecule super-resolution data can be acquired faster by taking advantage of the increased illumination intensities as compared to wide field, in the focused light-sheet.
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Affiliation(s)
- Marjolein B. M. Meddens
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
- Department of Pathology, University of New Mexico, 2325 Camino de Salud, Albuquerque, NM 87131,
USA
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
- Current address: Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907,
USA
| | | | - Thayne L. Edwards
- Sandia National Laboratories, 1515 Eubank SE, Albuquerque, NM 87123,
USA
| | - Conrad D. James
- Sandia National Laboratories, 1515 Eubank SE, Albuquerque, NM 87123,
USA
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, 1919 Lomas Blvd NE, Albuquerque, NM 87131,
USA
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36
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Gao J, Yang X, Djekidel MN, Wang Y, Xi P, Zhang MQ. Developing bioimaging and quantitative methods to study 3D genome. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Chen X, Wei M, Zheng MM, Zhao J, Hao H, Chang L, Xi P, Sun Y. Study of RNA Polymerase II Clustering inside Live-Cell Nuclei Using Bayesian Nanoscopy. ACS NANO 2016; 10:2447-2454. [PMID: 26855123 DOI: 10.1021/acsnano.5b07257] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nanoscale spatiotemporal clustering of RNA polymerase II (Pol II) plays an important role in transcription regulation. However, dynamics of individual Pol II clusters in live-cell nuclei has not been measured directly, prohibiting in-depth understanding of their working mechanisms. In this work, we studied the dynamics of Pol II clustering using Bayesian nanoscopy in live mammalian cell nuclei. With 50 nm spatial resolution and 4 s temporal resolution, Bayesian nanoscopy allows direct observation of the assembly and disassembly dynamics of individual Pol II clusters. The results not only provide quantifications of Pol II clusters but also shed light on the understanding of cluster formation and regulation. Our study suggests that transcription factories form on-demand and recruit Pol II molecules in their pre-elongation phase. The assembly and disassembly of individual Pol II clusters take place asynchronously. Overall, the methods developed herein are also applicable to studying a wide realm of real-time nanometer-scale nuclear processes in live cells.
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Affiliation(s)
- Xuanze Chen
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
- Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Mian Wei
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - M Mocarlo Zheng
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
- School of Physics, Peking University , Beijing 100871, China
| | - Jiaxi Zhao
- Department of Physics, Tsinghua University , Beijing 100084, China
| | - Huiwen Hao
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, 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
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
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38
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Basu S, Tan YL, Taylor EJR, Laue ED, Lee SF. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localisation Microscopy. Methods Mol Biol 2016; 1431:235-63. [PMID: 27283313 DOI: 10.1007/978-1-4939-3631-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule localisation microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal 'snapshots' of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination and protein labelling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analysing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Steven F Lee
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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39
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Komis G, Šamajová O, Ovečka M, Šamaj J. Super-resolution Microscopy in Plant Cell Imaging. TRENDS IN PLANT SCIENCE 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] [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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40
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Mazouchi A, Milstein JN. Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy. Bioinformatics 2015; 32:747-54. [PMID: 26543172 DOI: 10.1093/bioinformatics/btv630] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/24/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Single-molecule localization microscopy (SMLM) microscopy provides images of cellular structure at a resolution an order of magnitude below what can be achieved by conventional diffraction limited techniques. The concomitantly larger data sets generated by SMLM require increasingly efficient image analysis software. Density based clustering algorithms, with the most ubiquitous being DBSCAN, are commonly used to quantitatively assess sub-cellular assemblies. DBSCAN, however, is slow, scaling with the number of localizations like O(n log (n)) at best, and it's performance is highly dependent upon a subjectively selected choice of parameters. RESULTS We have developed a grid-based clustering algorithm FOCAL, which explicitly accounts for several dominant artifacts arising in SMLM image reconstructions. FOCAL is fast and efficient, scaling like O(n), and only has one set parameter. We assess DBSCAN and FOCAL on experimental dSTORM data of clusters of eukaryotic RNAP II and PALM data of the bacterial protein H-NS, then provide a detailed comparison via simulation. FOCAL performs comparable and often superior to DBSCAN while yielding a significantly faster analysis. Additionally, FOCAL provides a novel method for filtering out of focus clusters from complex SMLM images. AVAILABILITY AND IMPLEMENTATION The data and code are available at: http://www.utm.utoronto.ca/milsteinlab/resources/Software/FOCAL/ CONTACT: josh.milstein@utoronto.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A Mazouchi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - J N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada
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41
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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] [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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Galland R, Grenci G, Aravind A, Viasnoff V, Studer V, Sibarita JB. 3D high- and super-resolution imaging using single-objective SPIM. Nat Methods 2015; 12:641-4. [PMID: 25961414 DOI: 10.1038/nmeth.3402] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/12/2015] [Indexed: 11/10/2022]
Abstract
Single-objective selective-plane illumination microscopy (soSPIM) is achieved with micromirrored cavities combined with a laser beam-steering unit installed on a standard inverted microscope. The illumination and detection are done through the same objective. soSPIM can be used with standard sample preparations and features high background rejection and efficient photon collection, allowing for 3D single-molecule-based super-resolution imaging of whole cells or cell aggregates. Using larger mirrors enabled us to broaden the capabilities of our system to image Drosophila embryos.
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Affiliation(s)
- Remi Galland
- 1] Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France. [2] Centre National de la Recherche Scientifique, Bordeaux, France. [3] Mechanobiology Institute, National University of Singapore, Singapore
| | - Gianluca Grenci
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Ajay Aravind
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Virgile Viasnoff
- 1] Mechanobiology Institute, National University of Singapore, Singapore. [2] Bio Mechanics of Cellular Contacts, Centre National de la Recherche Scientifique, Singapore. [3] Department of Biological Science, National University of Singapore, Singapore
| | - Vincent Studer
- 1] Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France. [2] Centre National de la Recherche Scientifique, Bordeaux, France
| | - Jean-Baptiste Sibarita
- 1] Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France. [2] Centre National de la Recherche Scientifique, Bordeaux, France
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Truong Quang BA, Lenne PF. Superresolution measurements in vivo: imaging Drosophila embryo by photoactivated localization microscopy. Methods Cell Biol 2015; 125:119-42. [PMID: 25640427 DOI: 10.1016/bs.mcb.2014.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Visualization and quantification of supramolecular assemblies in cells are essential to understand the design principles of cells and tissues. The advent of photoactivated localization microscopy (PALM) and related techniques has offered unprecedented information on protein supramolecular assemblies in 3-D with a spatial resolution of a few tens of nanometers. Yet application of PALM microscopy for in vivo studies remains challenging. This chapter describes how to implement PALM microscopy for quantitative analysis of intercellular adhesion in the Drosophila embryo. Our protocol describes the sample preparation, the imaging setup, and the acquisition procedure. We also discuss how to proceed with quantitative analysis of data. Initially designed and implemented for Drosophila embryo imaging of intercellular adhesion, this protocol can be readily adapted to other structures than adhesions and other organisms such as Zebrafish or Caenorhabditis elegans.
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Affiliation(s)
- Binh-An Truong Quang
- Institute for Developmental Biology of Marseille (IBDM), CNRS & Aix-Marseille Université, Campus de Luminy, Marseille Cedex, France
| | - Pierre-François Lenne
- Institute for Developmental Biology of Marseille (IBDM), CNRS & Aix-Marseille Université, Campus de Luminy, Marseille Cedex, France
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Adams MW, Loftus AF, Dunn SE, Joens MS, Fitzpatrick JAJ. Light Sheet Fluorescence Microscopy (LSFM). ACTA ACUST UNITED AC 2015; 71:12.37.1-12.37.15. [PMID: 25559221 DOI: 10.1002/0471142956.cy1237s71] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development of confocal microscopy techniques introduced the ability to optically section fluorescent samples in the axial dimension, perpendicular to the image plane. These approaches, via the placement of a pinhole in the conjugate image plane, provided superior resolution in the axial (z) dimension resulting in nearly isotropic optical sections. However, increased axial resolution, via pinhole optics, comes at the cost of both speed and excitation efficiency. Light sheet fluorescent microscopy (LSFM), a century-old idea made possible with modern developments in both excitation and detection optics, provides sub-cellular resolution and optical sectioning capabilities without compromising speed or excitation efficiency. Over the past decade, several variations of LSFM have been implemented each with its own benefits and deficiencies. Here we discuss LSFM fundamentals and outline the basic principles of several major light-sheet-based imaging modalities (SPIM, inverted SPIM, multi-view SPIM, Bessel beam SPIM, and stimulated emission depletion SPIM) while considering their biological relevance in terms of intrusiveness, temporal resolution, and sample requirements.
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Affiliation(s)
- Michael W Adams
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Andrew F Loftus
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Sarah E Dunn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - Matthew S Joens
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
| | - James A J Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California
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45
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Super-resolution imaging in live cells. Dev Biol 2014; 401:175-81. [PMID: 25498481 PMCID: PMC4405210 DOI: 10.1016/j.ydbio.2014.11.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 12/26/2022]
Abstract
Over the last twenty years super-resolution fluorescence microscopy has gone from proof-of-concept experiments to commercial systems being available in many labs, improving the resolution achievable by up to a factor of 10 or more. There are three major approaches to super-resolution, stimulated emission depletion microscopy, structured illumination microscopy, and localisation microscopy, which have all produced stunning images of cellular structures. A major current challenge is optimising performance of each technique so that the same sort of data can be routinely taken in live cells. There are several major challenges, particularly phototoxicity and the speed with which images of whole cells, or groups of cells, can be acquired. In this review we discuss the various approaches which can be successfully used in live cells, the tradeoffs in resolution, speed, and ease of implementation which one must make for each approach, and the quality of results that one might expect from each technique. Super-resolution imaging of cell structures can achieve a resolution of tens of nm. There are three major techniques: STED, SIM, and localisation microscopy. Live cell super-resolution requires trading off resolution, speed, and light dose.
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46
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Winter PW, Shroff H. Faster fluorescence microscopy: advances in high speed biological imaging. Curr Opin Chem Biol 2014; 20:46-53. [PMID: 24815857 DOI: 10.1016/j.cbpa.2014.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 11/16/2022]
Abstract
The past decade has seen explosive growth in new high speed imaging methods. These can broadly be classified as either point-scanning (which offer better depth penetration) or parallelized systems (which offer higher speed). We discuss each class generally, and cover specific advances in diffraction-limited microscopes (laser-scanning confocal, spinning-disk, and light-sheet) and superresolution microscopes (single-molecule imaging, stimulated emission-depletion, and structured illumination). A theme of our review is that there is no free lunch: each technique has strengths and weaknesses, and an advance in speed usually comes at the expense of either spatial resolution or depth penetration.
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Affiliation(s)
- Peter W Winter
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892, United States.
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892, United States
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Hu YS, Zimmerley M, Li Y, Watters R, Cang H. Single-molecule super-resolution light-sheet microscopy. Chemphyschem 2014; 15:577-86. [PMID: 24615819 DOI: 10.1002/cphc.201300732] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 01/08/2014] [Indexed: 11/10/2022]
Abstract
Single-molecule super-resolution imaging is a new promising tool for investigation of sub-cellular structures. Concurrently, light-sheet microscopy, also known as selective plane illumination microscopy (SPIM), has gained rapid favor with the imaging community in developmental biology due to its fast speed, high contrast, deep penetration, and low phototoxicity. While nearly a dozen reviews thoroughly describe the development of light-sheet microscopy and its technological breakthroughs with a main focus on improving the 3D imaging speed of fish embryos, central nervous system, and other tissues, few have addressed the potential of combining light-sheet microscopy and localization-based super-resolution imaging to achieve sub-diffraction-limited resolution. Adapting light-sheet illumination for single-molecule imaging presents unique challenges for instrumentation and reconstruction algorithms. In this Minireview, we provide an overview of the recent developments that address these challenges. We compare different approaches in super-resolution and light-sheet imaging, address advantages and limitations in each approach, and outline future directions of this emerging field.
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Affiliation(s)
- Ying S Hu
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, CA 92037 (USA)
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