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Fuentes LA, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. J Cell Biol 2023; 222:e202301112. [PMID: 37516910 PMCID: PMC10373298 DOI: 10.1083/jcb.202301112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/31/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023] Open
Abstract
The endoplasmic reticulum's (ER's) structure is directly linked to the many functions of the ER, but its formation is not fully understood. We investigate how the ER-membrane curving protein reticulon 4 (Rtn4) localizes to and organizes in the membrane and how that affects the local ER structure. We show a strong correlation between the local Rtn4 density and the local ER membrane curvature. Our data further reveal that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis. Rtn4 oligomers are linear shaped, contain about five copies of the protein, and preferentially orient parallel to the tubule axis. Our observations support a mechanism in which oligomerization leads to an increase of the local Rtn4 concentration with each molecule, increasing membrane curvature through a hairpin wedging mechanism. This quantitative analysis of Rtn4 and its effects on the ER membrane result in a new model of tubule shape as it relates to Rtn4.
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Affiliation(s)
- Lukas A. Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
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2
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Fuentes LA, Marin Z, Tyson J, Baddeley D, Bewersdorf J. The nanoscale organization of reticulon 4 shapes local endoplasmic reticulum structure in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525608. [PMID: 36747764 PMCID: PMC9900957 DOI: 10.1101/2023.01.26.525608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
UNLABELLED The endoplasmic reticulum’s (ER) structure is directly linked to the many functions of the ER but its formation is not fully understood. We investigate how the ER-membrane curving protein reticulon 4 (Rtn4) localizes to and organizes in the membrane and how that affects local ER structure. We show a strong correlation between the local Rtn4 density and the local ER membrane curvature. Our data further reveal that the typical ER tubule possesses an elliptical cross-section with Rtn4 enriched at either end of the major axis. Rtn4 oligomers are linear-shaped, contain about five copies of the protein, and preferentially orient parallel to the tubule axis. Our observations support a mechanism in which oligomerization leads to an increase of the local Rtn4 concentration with each molecule increasing membrane curvature through a hairpin wedging mechanism. This quantitative analysis of Rtn4 and its effects on the ER membrane result in a new model of tubule shape as it relates to Rtn4. SUMMARY Rtn4 forms linear-shaped oligomers that contain an average of five Rtn4 proteins, localize to the sides of elliptical tubules, prefer orientations near parallel to the tubule axis, and increase local curvature of the ER membrane by increasing local Rtn4 density.
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Affiliation(s)
- Lukas A. Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jonathan Tyson
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
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3
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Learning and evaluating the overlapping roles of physics and physiology in perceiving contrast and resolution in microscopy. SN APPLIED SCIENCES 2023. [DOI: 10.1007/s42452-022-05223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AbstractSimple compound microscopy is widely used across the globe. However, contrast and resolution fascinate students and are difficult to learn due to their limited practical experience. Although the laws of physics have been derived thoroughly, their real implementation in the human body is uncertain. This study quantifies contrast and resolution through human perception and technological tools and assesses the degree of overlap between physics and physiology. Thus, an opaque repository for a compound microscope with a mobile holder is devised to capture the images of Leishman-stained smears and USAF targets. Another receptacle is fabricated to hold coloured filters against a light bulb, which projects on the microscope mirror through a connecting pipe. The images with a different sequence of filters are subjected to analysis by volunteers and using digital image processing techniques. The perception of contrast and resolution through the human eye and digital processing shows an overlap of 82.57% for contrast and 76.40% for resolution. Also, participants opt for contrast (81.66%) against the resolution (75.51%). The preferred sequence of light for contrast and resolution is white > green > blue > red and white > blue > green > red, respectively. Green > blue > red is preceded by white when both contrast and resolution are examined concurrently. Thus, the integrated role of the two disciplines in learning contrast and resolution has been studied and evaluated practically beyond the limits of the textbook on a hands-on basis. Simultaneously, the subjective selection of resolution or contrast using low-cost colour filters is an affordable approach to upgrade a microscope.
Graphical abstract
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4
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Wang Y, Soto Rodriguez PED, Woythe L, Sánchez S, Samitier J, Zijlstra P, Albertazzi L. Multicolor Super-Resolution Microscopy of Protein Corona on Single Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:37345-37355. [PMID: 35961006 PMCID: PMC9412947 DOI: 10.1021/acsami.2c06975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Nanoparticles represent a promising class of material for nanomedicine and molecular biosensing. The formation of a protein corona due to nonspecific particle-protein interactions is a determining factor for the biological fate of nanoparticles in vivo and strongly impacts the performance of nanoparticles when used as biosensors. Nonspecific interactions are usually highly heterogeneous, yet little is known about the heterogeneity of the protein corona that may lead to inter- and intraparticle differences in composition and protein distribution. Here, we present a super-resolution microscopic approach to study the protein corona on single silica nanoparticles and subsequent cellular interactions using multicolor stimulated emission depletion (STED) microscopy. We demonstrate that STED resolves structural features of protein corona on single particles including the distribution on the particle surface and the degree of protein internalization in porous particles. Using multicolor measurements of multiple labeled protein species, we determine the composition of the protein corona at the single-particle level. We quantify particle-to-particle differences in the composition and find that the composition is considerably influenced by the particle geometry. In a subsequent cellular uptake measurement, we demonstrate multicolor STED of protein corona on single particles internalized by cells. Our study shows that STED microscopy opens the window toward mechanistic understanding of protein coronas and aids in the rational design of nanoparticles as nanomedicines and biosensors.
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Affiliation(s)
- Yuyang Wang
- Department
of Applied Physics and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Paul E. D. Soto Rodriguez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Laura Woythe
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Samuel Sánchez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeige Lluís Companys 23, 08010 Barcelona, Spain
| | - Josep Samitier
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department
of Electronics and Biomedical Engineering, University of Barcelona (UB), 08028 Barcelona, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Peter Zijlstra
- Department
of Applied Physics and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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5
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Super-Resolution Microscopy and Their Applications in Food Materials: Beyond the Resolution Limits of Fluorescence Microscopy. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-022-02883-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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6
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Siegmund R, Werner F, Jakobs S, Geisler C, Egner A. isoSTED microscopy with water-immersion lenses and background reduction. Biophys J 2021; 120:3303-3314. [PMID: 34246627 PMCID: PMC8392127 DOI: 10.1016/j.bpj.2021.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 01/17/2023] Open
Abstract
Fluorescence microscopy is an excellent tool to gain knowledge on cellular structures and biochemical processes. Stimulated emission depletion (STED) microscopy provides a resolution in the range of a few 10 nm at relatively fast data acquisition. As cellular structures can be oriented in any direction, it is of great benefit if the microscope exhibits an isotropic resolution. Here, we present an isoSTED microscope that utilizes water-immersion objective lenses and enables imaging of cellular structures with an isotropic resolution of better than 60 nm in living samples at room temperature and without CO2 supply or another pH control. This corresponds to a reduction of the focal volume by far more than two orders of magnitude as compared to confocal microscopy. The imaging speed is in the range of 0.8 s/μm3. Because fluorescence signal can only be detected from a diffraction-limited volume, a background signal is inevitably observed at resolutions well beyond the diffraction limit. Therefore, we additionally present a method that allows us to identify this unspecific background signal and to remove it from the image.
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Affiliation(s)
- René Siegmund
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany
| | - Frank Werner
- Institute of Mathematics, University of Würzburg, Würzburg, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany
| | - Alexander Egner
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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7
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Hao X, Allgeyer ES, Lee DR, Antonello J, Watters K, Gerdes JA, Schroeder LK, Bottanelli F, Zhao J, Kidd P, Lessard MD, Rothman JE, Cooley L, Biederer T, Booth MJ, Bewersdorf J. Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution. Nat Methods 2021; 18:688-693. [PMID: 34059828 PMCID: PMC7610943 DOI: 10.1038/s41592-021-01149-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/08/2021] [Indexed: 02/02/2023]
Abstract
Understanding cellular organization demands the best possible spatial resolution in all three dimensions. In fluorescence microscopy, this is achieved by 4Pi nanoscopy methods that combine the concepts of using two opposing objectives for optimal diffraction-limited 3D resolution with switching fluorescent molecules between bright and dark states to break the diffraction limit. However, optical aberrations have limited these nanoscopes to thin samples and prevented their application in thick specimens. Here we have developed an improved iso-stimulated emission depletion nanoscope, which uses an advanced adaptive optics strategy to achieve sub-50-nm isotropic resolution of structures such as neuronal synapses and ring canals previously inaccessible in tissue. The adaptive optics scheme presented in this work is generally applicable to any microscope with a similar beam path geometry involving two opposing objectives to optimize resolution when imaging deep in aberrating specimens.
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Affiliation(s)
- Xiang Hao
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Technology, Zhejiang University, Hangzhou, China
| | - Edward S Allgeyer
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Dong-Ryoung Lee
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Jacopo Antonello
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Katherine Watters
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Lena K Schroeder
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Cellular Imaging Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Francesca Bottanelli
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Jiaxi Zhao
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Mark D Lessard
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Lynn Cooley
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Martin J Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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8
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Olevsko I, Szederkenyi K, Corridon J, Au A, Delhomme B, Bastien T, Fernandes J, Yip C, Oheim M, Salomon A. A simple, inexpensive and multi-scale 3-D fluorescent test sample for optical sectioning microscopies. Microsc Res Tech 2021; 84:2625-2635. [PMID: 34008289 DOI: 10.1002/jemt.23813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/05/2021] [Accepted: 04/27/2021] [Indexed: 11/11/2022]
Abstract
Fluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities can expect a homogenous and time-invariant illumination and an uniform detection sensitivity, which are prerequisites for imaging analysis, tracking or fluorimetric pH or Ca2+ -concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning microscopes calls for a regular calibration with a standardized point source. The test samples required for such measurements are typically different ones, they are often expensive and they depend much on the very microscope technique used. Similarly, the ever-increasing choice among microscope techniques and geometries increases the demand for comparison across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: commercial tissue paper labeled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-μm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.
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Affiliation(s)
- Ilya Olevsko
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel
| | - Kaitlin Szederkenyi
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Jennifer Corridon
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Aaron Au
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Brigitte Delhomme
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Thierry Bastien
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Plateforme de Prototypage, Paris, France
| | - Julien Fernandes
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Christopher Yip
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Martin Oheim
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Adi Salomon
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel.,Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
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9
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Velasco MGM, Zhang M, Antonello J, Yuan P, Allgeyer ES, May D, M’Saad O, Kidd P, Barentine AES, Greco V, Grutzendler J, Booth MJ, Bewersdorf J. 3D super-resolution deep-tissue imaging in living mice. OPTICA 2021; 8:442-450. [PMID: 34239948 PMCID: PMC8243577 DOI: 10.1364/optica.416841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 05/08/2023]
Abstract
Stimulated emission depletion (STED) microscopy enables the three-dimensional (3D) visualization of dynamic nanoscale structures in living cells, offering unique insights into their organization. However, 3D-STED imaging deep inside biological tissue is obstructed by optical aberrations and light scattering. We present a STED system that overcomes these challenges. Through the combination of two-photon excitation, adaptive optics, red-emitting organic dyes, and a long-working-distance water-immersion objective lens, our system achieves aberration-corrected 3D super-resolution imaging, which we demonstrate 164 µm deep in fixed mouse brain tissue and 76 µm deep in the brain of a living mouse.
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Affiliation(s)
- Mary Grace M. Velasco
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Mengyang Zhang
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jacopo Antonello
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Peng Yuan
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: Department of Biology, Stanford University, Stanford, California 94304, USA
| | - Edward S. Allgeyer
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Current Address: The Gurdon Institute, University of Cambridge, Cambridge CB21QN, UK
| | - Dennis May
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ons M’Saad
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Andrew E. S. Barentine
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Valentina Greco
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jaime Grutzendler
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Joerg Bewersdorf
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Corresponding author:
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10
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Roy D, Steinkühler J, Zhao Z, Lipowsky R, Dimova R. Mechanical Tension of Biomembranes Can Be Measured by Super Resolution (STED) Microscopy of Force-Induced Nanotubes. NANO LETTERS 2020; 20:3185-3191. [PMID: 32320255 PMCID: PMC7304919 DOI: 10.1021/acs.nanolett.9b05232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Indexed: 05/26/2023]
Abstract
Membrane tension modulates the morphology of plasma-membrane tubular protrusions in cells but is difficult to measure. Here, we propose to use microscopy imaging to assess the membrane tension. We report direct measurement of membrane nanotube diameters with unprecedented resolution using stimulated emission depletion (STED) microscopy. For this purpose, we integrated an optical tweezers setup in a commercial microscope equipped for STED imaging and established micropipette aspiration of giant vesicles. Membrane nanotubes were pulled from the vesicles at specific membrane tension imposed by the aspiration pipet. Tube diameters calculated from the applied tension using the membrane curvature elasticity model are in excellent agreement with data measured directly with STED. Our approach can be extended to cellular membranes and will then allow us to estimate the mechanical membrane tension within the force-induced nanotubes.
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11
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Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS NANO 2020; 14:394-405. [PMID: 31841303 DOI: 10.1021/acsnano.9b05891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In stimulated emission depletion (STED) nanoscopy, the major origin of decreased signal-to-noise ratio within images can be attributed to sample photobleaching and strong optical aberrations. This is due to STED utilizing a high-power depletion laser (increasing the risk of photodamage), while the depletion beam is very sensitive to sample-induced aberrations. Here, we demonstrate a custom-built STED microscope with automated aberration correction that is capable of 3D super-resolution imaging through thick, highly aberrating tissue. We introduce and investigate a state of the art image denoising method by block-matching and collaborative 3D filtering (BM3D) to numerically enhance fine object details otherwise mixed with noise and further enhance the image quality. Numerical denoising provides an increase in the final effective resolution of the STED imaging of 31% using the well established Fourier ring correlation metric. Results achieved through the combination of aberration correction and tailored image processing are experimentally validated through super-resolved 3D imaging of axons in differentiated induced pluripotent stem cells growing under an 80 μm thick layer of tissue with lateral and axial resolution of 204 and 310 nm, respectively.
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Affiliation(s)
- Piotr Zdańkowski
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - Maciej Trusiak
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - David McGloin
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- School of Electrical and Data Engineering , University of Technology Sydney , Ultimo , New South Wales 2007 , Australia
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
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12
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A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae. Proc Natl Acad Sci U S A 2019; 116:15817-15822. [PMID: 31337683 DOI: 10.1073/pnas.1905924116] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Stimulation emission depletion (STED) microscopy enables ultrastructural imaging of organelle dynamics with a high spatiotemporal resolution in living cells. For the visualization of the mitochondrial membrane dynamics in STED microscopy, rationally designed mitochondrial fluorescent markers with enhanced photostability are required. Herein, we report the development of a superphotostable fluorescent labeling reagent with long fluorescence lifetime, whose design is based on a structurally reinforced naphthophosphole fluorophore that is conjugated with an electron-donating diphenylamino group. The combination of long-lived fluorescence and superphotostable features of the fluorophore allowed us to selectively capture the ultrastructures of the mitochondrial cristae with a resolution of ∼60 nm when depleted at 660 nm. This chemical tool provides morphological information of the cristae, which has so far only been observed in fixed cells using electron microscopy. Moreover, this method gives information about the dynamic ultrastructures such as the intermembrane fusion in different mitochondria as well as the intercristae mergence in a single mitochondrion during the apoptosis-like mitochondrial swelling process.
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Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nat Commun 2019; 10:3103. [PMID: 31308370 PMCID: PMC6629685 DOI: 10.1038/s41467-019-11024-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/05/2019] [Indexed: 11/30/2022] Open
Abstract
Fourier ring correlation (FRC) has recently gained popularity among fluorescence microscopists as a straightforward and objective method to measure the effective image resolution. While the knowledge of the numeric resolution value is helpful in e.g., interpreting imaging results, much more practical use can be made of FRC analysis—in this article we propose blind image restoration methods enabled by it. We apply FRC to perform image de-noising by frequency domain filtering. We propose novel blind linear and non-linear image deconvolution methods that use FRC to estimate the effective point-spread-function, directly from the images. We show how FRC can be used as a powerful metric to observe the progress of iterative deconvolution. We also address two important limitations in FRC that may be of more general interest: how to make FRC work with single images (within certain practical limits) and with three-dimensional images with highly anisotropic resolution. Fourier ring correlation (FRC) analysis is commonly used in fluorescence microscopy to measure effective image resolution. Here, the authors demonstrate that FRC can also be leveraged in blind image restoration methods, such as image deconvolution.
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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Schroeder LK, Barentine AES, Merta H, Schweighofer S, Zhang Y, Baddeley D, Bewersdorf J, Bahmanyar S. Dynamic nanoscale morphology of the ER surveyed by STED microscopy. J Cell Biol 2019; 218:83-96. [PMID: 30442642 PMCID: PMC6314542 DOI: 10.1083/jcb.201809107] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 01/21/2023] Open
Abstract
The endoplasmic reticulum (ER) is composed of interconnected membrane sheets and tubules. Superresolution microscopy recently revealed densely packed, rapidly moving ER tubules mistaken for sheets by conventional light microscopy, highlighting the importance of revisiting classical views of ER structure with high spatiotemporal resolution in living cells. In this study, we use live-cell stimulated emission depletion (STED) microscopy to survey the architecture of the ER at 50-nm resolution. We determine the nanoscale dimensions of ER tubules and sheets for the first time in living cells. We demonstrate that ER sheets contain highly dynamic, subdiffraction-sized holes, which we call nanoholes, that coexist with uniform sheet regions. Reticulon family members localize to curved edges of holes within sheets and are required for their formation. The luminal tether Climp63 and microtubule cytoskeleton modulate their nanoscale dynamics and organization. Thus, by providing the first quantitative analysis of ER membrane structure and dynamics at the nanoscale, our work reveals that the ER in living cells is not limited to uniform sheets and tubules; instead, we suggest the ER contains a continuum of membrane structures that includes dynamic nanoholes in sheets as well as clustered tubules.
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Affiliation(s)
- Lena K Schroeder
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT
| | - Andrew E S Barentine
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT.,Department of Biomedical Engineering, Yale University, New Haven, CT
| | - Holly Merta
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT
| | - Sarah Schweighofer
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT
| | - Yongdeng Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT
| | - David Baddeley
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT.,Nanobiology Institute, Yale University, West Haven, CT.,Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT .,Department of Biomedical Engineering, Yale University, New Haven, CT.,Nanobiology Institute, Yale University, West Haven, CT
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT
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