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Obermair M, Hettler S, Dries M, Hugenschmidt M, Spiecker R, Gerthsen D. Carbon-film-based Zernike phase plates with smooth thickness gradient for phase-contrast transmission electron microscopy with reduced fringing artifacts. J Microsc 2022; 287:45-58. [PMID: 35438194 DOI: 10.1111/jmi.13108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022]
Abstract
Phase plates (PPs) in transmission electron microscopy (TEM) improve the contrast of weakly scattering objects under in-focus imaging conditions. A well-established PP type is the Zernike (Z)PP, which consists of a thin amorphous carbon (aC) film with a micro-scaled hole in the center. The mean inner potential of the aC film is exploited to shift the phase of the scattered electrons while the unscattered electrons in the zero-order beam propagate through the hole and remain unaffected. However, the abrupt thickness increase at the hole edge induces an abrupt change of the phase-shift distribution and leads to fringing, i.e., intensity oscillations around imaged objects, in TEM images. In this work, we have used focused-ion-beam milling to fabricate ZPPs with abrupt and graded thickness profiles around the center hole. Depending on the thickness gradient and inner hole radius, graded-ZPP-TEM images of an aC/vacuum interface and bundles of carbon nanotubes (CNTs) show strongly reduced fringing. Image simulations were performed with ZPP-phase-shift distributions derived from measured thickness profiles of graded ZPPs, which show good agreement with the experimental images. Fringing artifacts, i.e. intensity oscillations around imaged objects, are strongly reduced for Zernike phase plates with a graded thickness profile around the center hole. Focused-ion-beam milling is used to fabricate graded Zernike phase plates with specific inner hole radius and thickness gradients. The phase-shift distribution is obtained from measured thickness profiles around the center hole. Image simulations based on experimentally measured thickness/phase-shift distributions show good agreement with experimental Zernike phase-plate TEM images. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- M Obermair
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany
| | - S Hettler
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany.,Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, C/ Mariano Esquillor s/n, Zaragoza, 50018, Spain
| | - M Dries
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany
| | - M Hugenschmidt
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe Institute of Technology (KIT) Karlsruhe, Germany
| | - R Spiecker
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany.,Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, Karlsruhe, 76131, Germany
| | - D Gerthsen
- Laboratorium für Elektronenmikroskopie (LEM), Karlsruher Institut für Technologie (KIT), Engesserstraße 7, Karlsruhe, 76131, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe Institute of Technology (KIT) Karlsruhe, Germany
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OUP accepted manuscript. Microscopy (Oxf). [DOI: 10.1093/jmicro/dfac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 11/12/2022] Open
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Malac M, Hettler S, Hayashida M, Kano E, Egerton RF, Beleggia M. Phase plates in the transmission electron microscope: operating principles and applications. Microscopy (Oxf) 2020; 70:75-115. [DOI: 10.1093/jmicro/dfaa070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/30/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Abstract
In this paper, we review the current state of phase plate imaging in a transmission electron microscope. We focus especially on the hole-free phase plate design, also referred to as the Volta phase plate. We discuss the implementation, operating principles and applications of phase plate imaging. We provide an imaging theory that accounts for inelastic scattering in both the sample and in the hole-free phase plate.
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Affiliation(s)
- Marek Malac
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Simon Hettler
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia y Materiales de Aragon (INMA), Universidad de Zaragoza, Campus Río Ebro, 50018 Zaragoza, España
| | - Misa Hayashida
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Emi Kano
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Ray F Egerton
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Marco Beleggia
- DTU Nanolab, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Wang HW, Fan X. Challenges and opportunities in cryo-EM with phase plate. Curr Opin Struct Biol 2019; 58:175-182. [PMID: 31374473 DOI: 10.1016/j.sbi.2019.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Not long after the invention of transmission electron microscope (TEM), phase plate was proposed as a novel electron-optical apparatus at the back-focal plane of the objective lens to modulate the magnified specimen images with enhanced contrast, especially in cryo-electron microscopy (cryo-EM) application of biological specimens. In the past two decades, novel phase plates of different kinds were designed and fabricated for cryo-EM application. Some of them such as the Volta phase plate have already been proved very useful in single particle cryo-EM and cryo-electron tomography (cryo-ET) analysis. In this review, we discuss the current progress, challenges and opportunities of cryo-EM with phase plate.
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Affiliation(s)
- Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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Tsunoda J, Song C, Imai FL, Takagi J, Ueno H, Murata T, Iino R, Murata K. Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy. Sci Rep 2018; 8:15632. [PMID: 30353110 PMCID: PMC6199243 DOI: 10.1038/s41598-018-33977-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
EhV-ATPase is an ATP-driven Na+ pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron microscopy (cryo-EM) using Zernike phase plate. The cryo-EM map dominantly showed one of three catalytic conformations in this rotary enzyme. To further stabilize the originally heterogeneous structure caused by the ATP hydrolysis states of the V1-ATPases, a peptide epitope tag system was adopted, in which the inserted peptide epitope sequence interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. Interestingly, these two conformations identified with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V1 domain was connected to the transmembrane Vo domain through the off-axis central rotor. Furthermore, compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping.
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Affiliation(s)
- Jun Tsunoda
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Fabiana Lica Imai
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, University of Tokyo, Tokyo, 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan.,JST, PRESTO, Inage, Chiba, 263-8522, Japan
| | - Ryota Iino
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,Institute for Molecular Science, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan. .,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan.
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Reynolds MJ, Phetruen T, Fisher RL, Chen K, Pentecost BT, Gomez G, Ounjai P, Sui H. The Developmental Process of the Growing Motile Ciliary Tip Region. Sci Rep 2018; 8:7977. [PMID: 29789632 PMCID: PMC5964098 DOI: 10.1038/s41598-018-26111-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/01/2018] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic motile cilia/flagella play vital roles in various physiological processes in mammals and some protists. Defects in cilia formation underlie multiple human disorders, known as ciliopathies. The detailed processes of cilia growth and development are still far from clear despite extensive studies. In this study, we characterized the process of cilium formation (ciliogenesis) by investigating the newly developed motile cilia of deciliated protists using complementary techniques in electron microscopy and image analysis. Our results demonstrated that the distal tip region of motile cilia exhibit progressive morphological changes as cilia develop. This developmental process is time-dependent and continues after growing cilia reach their full lengths. The structural analysis of growing ciliary tips revealed that B-tubules of axonemal microtubule doublets terminate far away from the tip end, which is led by the flagellar tip complex (FTC), demonstrating that the FTC might not directly mediate the fast turnover of intraflagellar transport (IFT).
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Affiliation(s)
- Matthew J Reynolds
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
- Biology Department, University of Scranton, Scranton, PA, 18510, USA
| | - Tanaporn Phetruen
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rebecca L Fisher
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Ke Chen
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Brian T Pentecost
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - George Gomez
- Biology Department, University of Scranton, Scranton, PA, 18510, USA
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12201, USA.
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. Biophys Rep 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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