1
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Noble AJ, de Marco A. Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives. Curr Opin Struct Biol 2024; 87:102864. [PMID: 38901373 DOI: 10.1016/j.sbi.2024.102864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/22/2024]
Abstract
Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.
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Affiliation(s)
- Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA. https://twitter.com/alexjamesnoble
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA.
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2
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Exertier F, Tegg L, Taylor A, Cairney JM, Fu J, Marceau RKW. Nanoscale Analysis of Frozen Water by Atom Probe Tomography Using Graphene Encapsulation and Cryo-Workflows. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024:ozae054. [PMID: 38905154 DOI: 10.1093/mam/ozae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
There has been an increasing interest in atom probe tomography (APT) to characterize hydrated and biological materials. A major benefit of APT compared to microscopy techniques more commonly used in biology is its combination of outstanding three-dimensional (3D) spatial resolution and mass sensitivity. APT has already been successfully used to characterize biominerals, revealing key structural information at the atomic scale, however there are many challenges inherent to the analysis of soft hydrated materials. New preparation protocols, often involving specimen preparation and transfer at cryogenic temperature, enable APT analysis of hydrated materials and have the potential to enable 3D atomic scale characterization of biological materials in the near-native hydrated state. In this study, samples of pure water at the tips of tungsten needle specimens were prepared at room temperature by graphene encapsulation. A comparative study was conducted where specimens were transferred at either room temperature or cryo-temperature and analyzed by APT by varying the flight path and pulsing mode. The differences between the analysis workflows are presented along with recommendations for future studies, and the compatibility between graphene coating and cryogenic workflows is demonstrated.
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Affiliation(s)
- Florant Exertier
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Levi Tegg
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Adam Taylor
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | - Julie M Cairney
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Ross K W Marceau
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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3
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Zhan Z, Liu Y, Wang W, Du G, Cai S, Wang P. Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy. NANOSCALE HORIZONS 2024; 9:900-933. [PMID: 38512352 DOI: 10.1039/d3nh00494e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.
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Affiliation(s)
- Zhen Zhan
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Yuxin Liu
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Weizhen Wang
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Guangyu Du
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Songhua Cai
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong SAR, China.
| | - Peng Wang
- Department of Physics, University of Warwick, CV4 7AL, Coventry, UK.
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4
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Beggs KW, Kassab AJ, Colletta M, Yu Y, Kourkoutis LF, Darwish AA, Giannuzzi LA. Conjugate Multimode Heat Transfer Analysis of Cryogenic EXLO Manipulation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:66-76. [PMID: 38180779 DOI: 10.1093/micmic/ozad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
In this study, a conjugate radiation/conduction multimode heat transfer analysis of cryogenic focused ion beam (FIB) milling steps necessary for producing ex situ lift out specimens under cryogenic conditions (cryo-EXLO) is performed. Using finite volume for transient heat conduction and enclosure theory for radiation heat transfer, the analysis shows that as long as the specimen is attached or touching the FIB side wall trenches, the specimen will remain vitreous indefinitely, while actively cooled at liquid nitrogen (LN2) temperatures. To simulate the time needed to perform a transfer step to move the bulk sample containing the FIB-thinned specimen from the cryo-FIB to the cryo-EXLO cryostat, the LN2 temperature active cooling is turned off after steady-state conditions are reached and the specimen is monitored over time until the critical devitrification temperature is reached. Under these conditions, the sample will remain vitreous for >3 min, which is more than enough time needed to perform the cryo-transfer step from the FIB to the cryostat, which takes only ∼10 s. Cryo-transmission electron microscopy images of a manipulated cryo-EXLO yeast specimen prepared with cryo-FIB corroborates the heat transfer analysis.
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Affiliation(s)
- Kyle W Beggs
- Centecorp LLC, 147 Parsons Rd, Longwood, FL 32779, USA
| | | | - Michael Colletta
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Yue Yu
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Lena F Kourkoutis
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Physical Sciences Building, Cornell University, Ithaca, NY, USA
| | - Ahmed A Darwish
- EXpressLO LLC, 5483 Lee St, Unit 12, Lehigh Acres, FL 33971, USA
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5
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Vorlaufer N, Josten J, Carl S, Göbel E, Søgaard A, Taccardi N, Spiecker E, Felfer P. Preparation of atom probe tips from (nano)particles in dispersion using (di)electrophoresis and electroplating. Microsc Res Tech 2024; 87:476-483. [PMID: 37921114 DOI: 10.1002/jemt.24448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
The behavior of catalytic particles depends on their chemical structure and morphology. To reveal this information, the characterization with atom probe tomography has huge potential. Despite progresses and papers proposing various approaches towards the incorporation of particles inside atom probe tips, no single approach has been broadly applicable to date. In this paper, we introduce a workflow that allowed us to prepare atom probe specimens from Ga particles in suspension in the size range of 50 nm up to 2 μm. By combining dielectrophoresis and electrodeposition in a suitable way, we achieve a near-tip shape geometry, without a time-consuming FIB lift-out. This workflow is a simple and quick method to prepare atom probe tips and allows for a high preparation throughput. Also, not using a lift-out allowed us to use a cryo-stage, avoiding melting of the Ga particles, while ensuring a mechanical stable atom probe tip. The specimen prepared by this workflow enable a stable measurement and low fracture rates. RESEARCH HIGHLIGHTS: Enabling cryo-preparation of (nano)particles for the atom probe. Characterization of surface and bulk elemental distribution of GaPt model SCALMS.
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Affiliation(s)
- Nora Vorlaufer
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Josten
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simon Carl
- Institute of Micro- and Nanostructure Research (IMN) and Center for Nanoanalysis and Electron Microscopy (CENEM), Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erik Göbel
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Søgaard
- Institute of Chemical Reaction Engineering, Department Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- CHEC Research Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicola Taccardi
- Institute of Chemical Reaction Engineering, Department Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erdmann Spiecker
- Institute of Micro- and Nanostructure Research (IMN) and Center for Nanoanalysis and Electron Microscopy (CENEM), Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Felfer
- Institute I, Materials Science & Engineering Department, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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6
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Woods EV, Kim SH, El-Zoka AA, Stephenson LT, Gault B. Scalable substrate development for aqueous sample preparation for atom probe tomography. J Microsc 2023. [PMID: 38115688 DOI: 10.1111/jmi.13255] [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: 07/13/2023] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a 'lift-out' procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission electron microscopy (TEM) that can be used in a grid holder compatible with APT pucks. The second design is a larger, standalone self-supporting substrate called a 'crown', with several specimen positions, which self-aligns in APT pucks, prepared by electrical discharge machining (EDM). Both designs are made nanoporous, to provide strength to the liquid-substrate interface, using chemical and vacuum dealloying. Alpha brass, a simple, widely available, lower-cost alternative to previously proposed substrates, was selected for this work. The resulting designs and APT data are presented and suggestions are provided to help drive wider community adoption.
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Affiliation(s)
- Eric V Woods
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials Science and Engineering, Korea University, Seoul, Republic of Korea
| | - Ayman A El-Zoka
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - L T Stephenson
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, New South Wales, Australia
| | - B Gault
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
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7
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Schiøtz OH, Kaiser CJO, Klumpe S, Morado DR, Poege M, Schneider J, Beck F, Klebl DP, Thompson C, Plitzko JM. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods 2023:10.1038/s41592-023-02113-5. [PMID: 38110637 DOI: 10.1038/s41592-023-02113-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 12/20/2023]
Abstract
Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically <300 nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7 Å and a subregion of the 11-protofilament microtubule to 13 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
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Affiliation(s)
- Oda Helene Schiøtz
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph J O Kaiser
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Dustin R Morado
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department for Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Matthias Poege
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David P Klebl
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christopher Thompson
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Jürgen M Plitzko
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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8
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Wu Y, Qin C, Du W, Guo Z, Chen L, Guo Q. A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography. J Struct Biol 2023; 215:107971. [PMID: 37201639 DOI: 10.1016/j.jsb.2023.107971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline for preparing multicellular samples for cryo-electron tomography. The pipeline comprises sample isolation, vitrification, and lift-out-based lamella preparation using commercially available instruments. We demonstrate the efficacy of our pipeline by visualizing pancreatic β cells from mouse islets at the molecular level. This pipeline enables the determination of the properties of insulin crystals in situ for the first time, using unperturbed samples.
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Affiliation(s)
- Yichun Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Changdong Qin
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Zhenxi Guo
- School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Center for Life Sciences, College of Future Technology, Peking University, Beijing 100871, China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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9
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Klumpe S, Schioetz OH, Kaiser C, Luchner M, Brenner J, Plitzko JM. Developments in cryo-FIB Sample Preparation: Targeting in Cryo-Lift-Out Preparation of Tissues and Machine Learning Models for Fully Automated On-Grid Lamella Preparation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:511-513. [PMID: 37613116 DOI: 10.1093/micmic/ozad067.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Sven Klumpe
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Oda H Schioetz
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | | | - Marina Luchner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Johann Brenner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
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10
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Darwish AA, Dougherty TE, Heck BJ, Beggs K, Kassab AJ, Dohnalkova A, Giannuzzi LA. Cryo-Tomography of Cryo-EXLO Manipulated Yarrowia lipolytica Yeast. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1050. [PMID: 37613119 DOI: 10.1093/micmic/ozad067.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | | | | | - Kyle Beggs
- Centecorp LLC, Longwood, FL, United States
| | | | - Alice Dohnalkova
- Pacific Northwest National Laboratory, Richland, WA, United States
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11
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Douglas JO, El-Zoka A, Conroy M, Giuliani F, Gault B. Development of Site Specific Cryogenic Specimen Preparation and Transfer of Frozen Liquids for Complementary High-Resolution Analysis by Scanning Transmission Electron Microscopy and Atom Probe Tomography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1700-1701. [PMID: 37613908 DOI: 10.1093/micmic/ozad067.876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | - Ayman El-Zoka
- Department of Materials, Imperial College London, London
- Max- Planck- Institut für Eisenforschung, Düsseldorf, Germany
| | - Michele Conroy
- Department of Materials, Imperial College London, London
| | - Finn Giuliani
- Department of Materials, Imperial College London, London
| | - Baptiste Gault
- Department of Materials, Imperial College London, London
- Max- Planck- Institut für Eisenforschung, Düsseldorf, Germany
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12
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Záchej S, Pinkas D, Zánová M, Filimonenko V, Javůrek J, Váňa R. An Alternative Approach to Cryo-FIB Lift-out Using a Novel Cooled Nanomanipulator. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1046-1047. [PMID: 37613183 DOI: 10.1093/micmic/ozad067.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
| | - Dominik Pinkas
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Vlada Filimonenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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13
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Douglas JO, Conroy M, Giuliani F, Gault B. In Situ Sputtering From the Micromanipulator to Enable Cryogenic Preparation of Specimens for Atom Probe Tomography by Focused-Ion Beam. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1009-1017. [PMID: 37749683 DOI: 10.1093/micmic/ozad020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/05/2023] [Indexed: 09/27/2023]
Abstract
Workflows have been developed in the past decade to enable atom probe tomography analysis at cryogenic temperatures. The inability to control the local deposition of the metallic precursor from the gas-injection system (GIS) at cryogenic temperatures makes the preparation of site-specific specimens by using lift-out extremely challenging in the focused-ion beam. Schreiber et al. exploited redeposition to weld the lifted-out sample to a support. Here, we build on their approach to attach the region-of-interest and additionally strengthen the interface with locally sputtered metal from the micromanipulator. Following standard focused-ion beam annular milling, we demonstrate atom probe analysis of Si in both laser pulsing and voltage mode, with comparable analytical performance as a presharpened microtip coupon. Our welding approach is versatile, as various metals could be used for sputtering, and allows similar flexibility as the GIS in principle.
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Affiliation(s)
- James O Douglas
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Michele Conroy
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Finn Giuliani
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
| | - Baptiste Gault
- Department of Materials, Royal School of Mines, Imperial College London, Prince Consort Road, London SW7 2BP, UK
- Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, 40237 Düsseldorf, Germany
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14
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Wang S, Zhou H, Chen W, Jiang Y, Yan X, You H, Li X. CryoFIB milling large tissue samples for cryo-electron tomography. Sci Rep 2023; 13:5879. [PMID: 37041258 PMCID: PMC10090186 DOI: 10.1038/s41598-023-32716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Cryo-electron tomography (cryoET) is a powerful tool for exploring the molecular structure of large organisms. However, technical challenges still limit cryoET applications on large samples. In particular, localization and cutting out objects of interest from a large tissue sample are still difficult steps. In this study, we report a sample thinning strategy and workflow for tissue samples based on cryo-focused ion beam (cryoFIB) milling. This workflow provides a full solution for isolating objects of interest by starting from a millimeter-sized tissue sample and ending with hundred-nanometer-thin lamellae. The workflow involves sample fixation, pre-sectioning, a two-step milling strategy, and localization of the object of interest using cellular secondary electron imaging (CSEI). The milling strategy consists of two steps, a coarse milling step to improve the milling efficiency, followed by a fine milling step. The two-step milling creates a furrow-ridge structure with an additional conductive Pt layer to reduce the beam-induced charging issue. CSEI is highlighted in the workflow, which provides on-the-fly localization during cryoFIB milling. Tests of the complete workflow were conducted to demonstrate the high efficiency and high feasibility of the proposed method.
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Affiliation(s)
- Sihan Wang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China
| | - Heng Zhou
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China
| | - Wei Chen
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yifeng Jiang
- ZEISS Microscopy Customer Center, Beijing Laboratory, Beijing, 100088, China
| | - Xuzhen Yan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, 100050, China
| | - Hong You
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
- Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, 100050, China.
| | - Xueming Li
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing, 100084, China.
- Advanced Innovation Center for Structural Biology, Beijing, 100084, China.
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15
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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16
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Dubosq R, Woods E, Gault B, Best JP. Electron microscope loading and in situ nanoindentation of water ice at cryogenic temperatures. PLoS One 2023; 18:e0281703. [PMID: 36763688 PMCID: PMC9917277 DOI: 10.1371/journal.pone.0281703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Interest in the technique of low temperature environmental nanoindentation has gained momentum in recent years. Low temperature indentation apparatuses can, for instance, be used for systematic measurements of the mechanical properties of ice in the laboratory, in order to accurately determine the inputs for the constitutive equations describing the rheologic behaviour of natural ice (i.e., the Glen flow law). These properties are essential to predict the movement of glaciers and ice sheets over time as a response to a changing climate. Herein, we introduce a new experimental setup and protocol for electron microscope loading and in situ nanoindentation of water ice. Preliminary testing on pure water ice yield elastic modulus and hardness measurements of 4.1 GPa and 176 MPa, respectively, which fall within the range of previously published values. Our approach demonstrates the potential of low temperature, in situ, instrumented nanoindentation of ice under controlled conditions in the SEM, opening the possibility for investigating individual structural elements and systematic studies across species and concentration of impurities to refine to constitutive equations for natural ice.
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Affiliation(s)
- Renelle Dubosq
- Max-Planck-Institüt für Eisenforschung GmbH, Düsseldorf, Germany
| | - Eric Woods
- Max-Planck-Institüt für Eisenforschung GmbH, Düsseldorf, Germany
| | - Baptiste Gault
- Max-Planck-Institüt für Eisenforschung GmbH, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, United Kingdom
| | - James P. Best
- Max-Planck-Institüt für Eisenforschung GmbH, Düsseldorf, Germany
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17
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Wang C, Wojtynek M, Medalia O. Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Adv Biol Regul 2023; 87:100923. [PMID: 36280452 DOI: 10.1016/j.jbior.2022.100923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) combines a close-to-life preservation of the cell with high-resolution three-dimensional (3D) imaging. This allows to study the molecular architecture of the cellular landscape and provides unprecedented views on biological processes and structures. In this review we mainly focus on the application of cryo-ET to visualize and structurally characterize eukaryotic cells - from the periphery to the cellular interior. We discuss strategies that can be employed to investigate the structure of challenging targets in their cellular environment as well as the application of complimentary approaches in conjunction with cryo-ET.
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Affiliation(s)
- Chunyang Wang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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18
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Long DM, Singh MK, Small KA, Watt J. Cryo-FIB for TEM investigation of soft matter and beam sensitive energy materials. NANOTECHNOLOGY 2022; 33:503001. [PMID: 36121746 DOI: 10.1088/1361-6528/ac92eb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.
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Affiliation(s)
- Daniel M Long
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - Manish Kumar Singh
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Kathryn A Small
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - John Watt
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
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19
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Varsano N, Wolf SG. Electron microscopy of cellular ultrastructure in three dimensions. Curr Opin Struct Biol 2022; 76:102444. [PMID: 36041268 DOI: 10.1016/j.sbi.2022.102444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
Electron microscopy in three dimensions (3D) of cells and tissues can be essential for understanding the ultrastructural aspects of biological processes. The quest for 3D information reveals challenges at many stages of the workflow, from sample preparation, to imaging, data analysis and segmentation. Here, we outline several available methods, including volume SEM imaging, cryo-TEM and cryo-STEM tomography, each one occupying a different domain in the basic tradeoff between field-of-view and resolution. We discuss the considerations for choosing a suitable method depending on research needs and highlight recent developments that are essential for making 3D volume imaging of cells and tissues a standard tool for cellular and structural biologists.
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Affiliation(s)
- Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel
| | - Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel.
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20
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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21
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Gundlach KA, Briegel A. Zooming in on host-symbiont interactions: advances in cryo-EM sample processing methods and future application to symbiotic tissues. Symbiosis 2022. [DOI: 10.1007/s13199-022-00859-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractAnimals, plants, and fungi live in a microbe-dominated world. Investigating the interactions and processes at the host-microbe interface offers insight to how bacteria influence the development, health, and disease of the host. Optimization of existing imaging technologies and development of novel instrumentation will provide the tools needed to fully understand the dynamic relationship that occurs at the host-microbe interface throughout the lifetime of the host. In this review, we describe the current methods used in cryo-electron microscopy (cryo-EM) including cryo-fixation, sample processing, FIB-SEM, and cryotomography. Further, we highlight the new advances associated with these methods that open the cryo-EM discipline to large, complex multicellular samples, like symbiotic tissues. We describe the advantages and challenges associated with correlative imaging techniques and sample thinning methods like lift-out. By highlighting recent pioneering studies in the large-volume or symbiotic sample workflows, we provide insight into how symbiotic model systems will benefit from cryo-EM methods to provide artefact-free, near-native, macromolecular-scale resolution imaging at the host-microbe interface throughout the development and maintenance of symbiosis. Cryo-EM methods have brought a deep fundamental understanding of prokaryotic biology since its conception. We propose the application of existing and novel cryo-EM techniques to symbiotic systems is the logical next step that will bring an even greater understanding how microbes interact with their host tissues.
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22
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Schneider J, Jasnin M. Capturing actin assemblies in cells using in situ cryo-electron tomography. Eur J Cell Biol 2022; 101:151224. [PMID: 35500467 DOI: 10.1016/j.ejcb.2022.151224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Actin contributes to an exceptionally wide range of cellular processes through the assembly and disassembly of highly dynamic and ordered structures. Visualizing these structures in cells can help us understand how the molecular players of the actin machinery work together to produce force-generating systems. In recent years, cryo-electron tomography (cryo-ET) has become the method of choice for structural analysis of the cell interior at the molecular scale. Here we review advances in cryo-ET workflows that have enabled this transformation, especially the automation of sample preparation procedures, data collection, and processing. We discuss new structural analyses of dynamic actin assemblies in cryo-preserved cells, which have provided mechanistic insights into actin assembly and function at the nanoscale. Finally, we highlight the latest visual proteomics studies of actin filaments and their interactors reaching sub-nanometer resolutions in cells.
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Affiliation(s)
- Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marion Jasnin
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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23
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Molecular Dynamics Simulation and Cryo-Electron Microscopy Investigation of AOT Surfactant Structure at the Hydrated Mica Surface. MINERALS 2022. [DOI: 10.3390/min12040479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.
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24
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Hao H, Hutter T, Boyce BL, Watt J, Liu P, Mitlin D. Review of Multifunctional Separators: Stabilizing the Cathode and the Anode for Alkali (Li, Na, and K) Metal-Sulfur and Selenium Batteries. Chem Rev 2022; 122:8053-8125. [PMID: 35349271 DOI: 10.1021/acs.chemrev.1c00838] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alkali metal batteries based on lithium, sodium, and potassium anodes and sulfur-based cathodes are regarded as key for next-generation energy storage due to their high theoretical energy and potential cost effectiveness. However, metal-sulfur batteries remain challenged by several factors, including polysulfides' (PSs) dissolution, sluggish sulfur redox kinetics at the cathode, and metallic dendrite growth at the anode. Functional separators and interlayers are an innovative approach to remedying these drawbacks. Here we critically review the state-of-the-art in separators/interlayers for cathode and anode protection, covering the Li-S and the emerging Na-S and K-S systems. The approaches for improving electrochemical performance may be categorized as one or a combination of the following: Immobilization of polysulfides (cathode); catalyzing sulfur redox kinetics (cathode); introduction of protective layers to serve as an artificial solid electrolyte interphase (SEI) (anode); and combined improvement in electrolyte wetting and homogenization of ion flux (anode and cathode). It is demonstrated that while the advances in Li-S are relatively mature, less progress has been made with Na-S and K-S due to the more challenging redox chemistry at the cathode and increased electrochemical instability at the anode. Throughout these sections there is a complementary discussion of functional separators for emerging alkali metal systems based on metal-selenium and the metal-selenium sulfide. The focus then shifts to interlayers and artificial SEI/cathode electrolyte interphase (CEI) layers employed to stabilize solid-state electrolytes (SSEs) in metal-sulfur solid-state batteries (SSBs). The discussion of SSEs focuses on inorganic electrolytes based on Li- and Na-based oxides and sulfides but also touches on some hybrid systems with an inorganic matrix and a minority polymer phase. The review then moves to practical considerations for functional separators, including scaleup issues and Li-S technoeconomics. The review concludes with an outlook section, where we discuss emerging mechanics, spectroscopy, and advanced electron microscopy (e.g. cryo-transmission electron microscopy (cryo-TEM) and cryo-focused ion beam (cryo-FIB))-based approaches for analysis of functional separator structure-battery electrochemical performance interrelations. Throughout the review we identify the outstanding open scientific and technological questions while providing recommendations for future research topics.
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Affiliation(s)
- Hongchang Hao
- Materials Science and Engineering Program & Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tanya Hutter
- Materials Science and Engineering Program & Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brad L Boyce
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87110, United States
| | - John Watt
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Pengcheng Liu
- Materials Science and Engineering Program & Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David Mitlin
- Materials Science and Engineering Program & Texas Materials Institute, The University of Texas at Austin, Austin, Texas 78712, United States
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25
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Kim SH, Antonov S, Zhou X, Stephenson LT, Jung C, El-Zoka AA, Schreiber DK, Conroy M, Gault B. Atom probe analysis of electrode materials for Li-ion batteries: challenges and ways forward. JOURNAL OF MATERIALS CHEMISTRY. A 2022; 10:4926-4935. [PMID: 35341092 PMCID: PMC8887568 DOI: 10.1039/d1ta10050e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/26/2022] [Indexed: 05/24/2023]
Abstract
The worldwide development of electric vehicles as well as large-scale or grid-scale energy storage to compensate for the intermittent nature of renewable energy generation has led to a surge of interest in battery technology. Understanding the factors controlling battery capacity and, critically, their degradation mechanisms to ensure long-term, sustainable and safe operation requires detailed knowledge of their microstructure and chemistry, and their evolution under operating conditions, on the nanoscale. Atom probe tomography (APT) provides compositional mapping of materials in three dimensions with sub-nanometre resolution, and is poised to play a key role in battery research. However, APT is underpinned by an intense electric field that can drive lithium migration, and many battery materials are reactive oxides, requiring careful handling and sample transfer. Here, we report on the analysis of both anode and cathode materials and show that electric-field driven migration can be suppressed by using shielding by embedding powder particles in a metallic matrix or by using a thin conducting surface layer. We demonstrate that for a typical cathode material, cryogenic specimen preparation and transport under ultra-high vacuum leads to major delithiation of the specimen during the analysis. In contrast, the transport of specimens through air enables the analysis of the material. Finally, we discuss the possible physical underpinnings and discuss ways forward to enable shielding from the electric field, which helps address the challenges inherent to the APT analysis of battery materials.
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Affiliation(s)
- Se-Ho Kim
- Max-Planck-Institut für Eisenforschung Düsseldorf Germany
| | | | - Xuyang Zhou
- Max-Planck-Institut für Eisenforschung Düsseldorf Germany
| | | | - Chanwon Jung
- Max-Planck-Institut für Eisenforschung Düsseldorf Germany
| | | | - Daniel K Schreiber
- Energy and Environment Directorate, Pacific Northwest National Laboratory P.O. Box 999 Richland WA 99352 USA
| | - Michele Conroy
- Department of Materials, Royal School of Mines, Imperial College London London UK
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung Düsseldorf Germany
- Department of Materials, Royal School of Mines, Imperial College London London UK
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26
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Stender P, Gault B, Schwarz TM, Woods EV, Kim SH, Ott J, Stephenson LT, Schmitz G, Freysoldt C, Kästner J, El-Zoka AA. Status and Direction of Atom Probe Analysis of Frozen Liquids. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-18. [PMID: 35039105 DOI: 10.1017/s1431927621013994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging of liquids and cryogenic biological materials by electron microscopy has been recently enabled by innovative approaches for specimen preparation and the fast development of optimized instruments for cryo-enabled electron microscopy (cryo-EM). Yet, cryo-EM typically lacks advanced analytical capabilities, in particular for light elements. With the development of protocols for frozen wet specimen preparation, atom probe tomography (APT) could advantageously complement insights gained by cryo-EM. Here, we report on different approaches that have been recently proposed to enable the analysis of relatively large volumes of frozen liquids from either a flat substrate or the fractured surface of a wire. Both allowed for analyzing water ice layers which are several micrometers thick consisting of pure water, pure heavy water, and aqueous solutions. We discuss the merits of both approaches and prospects for further developments in this area. Preliminary results raise numerous questions, in part concerning the physics underpinning field evaporation. We discuss these aspects and lay out some of the challenges regarding the APT analysis of frozen liquids.
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Affiliation(s)
- Patrick Stender
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Baptiste Gault
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - Tim M Schwarz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | - Eric V Woods
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Jonas Ott
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Guido Schmitz
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
| | | | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569Stuttgart, Germany
| | - Ayman A El-Zoka
- Institute of Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstrasse 3, 70569Stuttgart, Germany
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27
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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28
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Zhang J, Zhang D, Sun L, Ji G, Huang X, Niu T, Xu J, Ma C, Zhu Y, Gao N, Xu W, Sun F. VHUT-cryo-FIB, a method to fabricate frozen hydrated lamellae from tissue specimens for in situ cryo-electron tomography. J Struct Biol 2021; 213:107763. [PMID: 34174447 DOI: 10.1016/j.jsb.2021.107763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 12/14/2022]
Abstract
Cryo-electron tomography (cryo-ET) provides a promising approach to study intact structures of macromolecules in situ, but the efficient preparation of high-quality cryosections represents a bottleneck. Although cryo-focused ion beam (cryo-FIB) milling has emerged for large and flat cryo-lamella preparation, its application to tissue specimens remains challenging. Here, we report an integrated workflow, VHUT-cryo-FIB, for efficiently preparing frozen hydrated tissue lamella that can be readily used in subsequent cryo-ET studies. The workflow includes vibratome slicing, high-pressure freezing, ultramicrotome cryo-trimming and cryo-FIB milling. Two strategies were developed for loading cryo-lamella via a side-entry cryo-holder or an FEI AutoGrid. The workflow was validated by using various tissue specimens, including rat skeletal muscle, rat liver and spinach leaf specimens, and in situ structures of ribosomes were obtained at nanometer resolution from the spinach and liver samples.
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Affiliation(s)
- Jianguo Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Danyang Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Physical Science Laboratory, Huairou National Comprehensive Science Center, No. 5 Yanqi East Second Street, Beijing 101400, China
| | - Lei Sun
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Ji
- University of Chinese Academy of Sciences, Beijing, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongxin Niu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiashu Xu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Xu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Physical Science Laboratory, Huairou National Comprehensive Science Center, No. 5 Yanqi East Second Street, Beijing 101400, China.
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Elad N, Wolf SG. Maintaining Context in Ice: Cryo-EM/ET Workflow Optimizations. Structure 2021; 28:1179-1181. [PMID: 33147474 DOI: 10.1016/j.str.2020.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Structure, breakthroughs in cryo-EM/ET research are presented. Klebl et al. (2020) demonstrate how speed in sample vitrification impacts the quality of macromolecular particles in resultant cryo-EM grids. Wu et al. (2020) combine fluorescence, ion beam milling, and tomography to unravel unique features in vitrified yeast cells.
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Affiliation(s)
- Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
| | - Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
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Cheung YWS, Nam SE, Yip CK. Recent Advances in Single-Particle Electron Microscopic Analysis of Autophagy Degradation Machinery. Int J Mol Sci 2020; 21:E8051. [PMID: 33126766 PMCID: PMC7663694 DOI: 10.3390/ijms21218051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/25/2020] [Accepted: 10/25/2020] [Indexed: 12/31/2022] Open
Abstract
Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane vesicle termed autophagosome to the delivery of the autophagosome to the lysosome or lytic vacuole for breakdown, is mediated by the core autophagy machinery composed of multiple Atg proteins, as well as the divergent sequence family of selective autophagy receptors. Single-particle electron microscopy (EM) is a molecular imaging approach that has become an increasingly important tool in the structural characterization of proteins and macromolecular complexes. This article summarizes the contributions single-particle EM have made in advancing our understanding of the core autophagy machinery and selective autophagy receptors. We also discuss current technical challenges and roadblocks, as well as look into the future of single-particle EM in autophagy research.
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Affiliation(s)
| | | | - Calvin K. Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (Y.W.S.C.); (S.-E.N.)
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31
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Hayles MF, DE Winter DAM. An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples. J Microsc 2020; 281:138-156. [PMID: 32737879 PMCID: PMC7891420 DOI: 10.1111/jmi.12951] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/31/2022]
Abstract
The introduction of cryo‐techniques to the focused ion‐beam scanning electron microscope (FIB‐SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo‐techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo‐ultramicrotomy for observation in a cryo‐transmission electron microscope (TEM). Cryo‐TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo‐fractured surfaces from bulk materials have been investigated by cryo‐SEM. Both cryo‐TEM and cryo‐SEM have provided a wealth of information, despite being 2D techniques. Cryo‐TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200–300 nm, which limits the 3D information within the context of specific structures. FIB‐milling enables imaging additional planes by creating cross‐sections (e.g. cross‐sectioning or site‐specific X‐sectioning) perpendicular to the cryo‐fracture surface, thus adding a third imaging dimension to the cryo‐SEM. This paper discusses how to produce suitable cryo‐FIB‐SEM cross‐section results from frozen, hydrated Life Science samples with emphasis on ‘common knowledge’ and reoccurring observations. Lay Description Life Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high‐vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples. Two types of electron microscopes equipped with cryo‐sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo‐FIB‐SEM, which is the basis of this paper. The electron beam images the cryo‐sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross‐sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross‐sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo‐microscopy alike.
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Affiliation(s)
- M F Hayles
- Cryo-FIB-SEM Technologist, Eindhoven, the Netherlands
| | - D A M DE Winter
- Environmental Hydrogeology, Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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32
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DE Winter DAM, Hsieh C, Marko M, Hayles MF. Cryo-FIB preparation of whole cells and tissue for cryo-TEM: use of high-pressure frozen specimens in tubes and planchets. J Microsc 2020; 281:125-137. [PMID: 32691851 PMCID: PMC7891314 DOI: 10.1111/jmi.12943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
Abstract
The desire to study macromolecular complexes within their cellular context requires the ability to produce thin samples suitable for cryo‐TEM (cryo‐transmission electron microscope) investigations. In this paper, we discuss two similar approaches, which were developed independently in Utrecht (the Netherlands) and Albany (USA). The methods are particularly suitable for both tissue samples and cell suspensions prepared by a high‐pressure freezer (HPF). The workflows are explained with particular attention to potential pitfalls, while underlying principles are highlighted (‘why to do so’). Although both workflows function with a high success rate, full execution requires considerable experience and remains demanding. In addition, throughput is low. We hope to encourage other research groups worldwide to take on the challenge of improving the HPF– cryo‐FIB‐SEM – cryo‐TEM workflow. We discuss a number of suggestions to this end. Lay Description Life is ultimately dictated by the interaction of molecules in our bodies. Highly complex equipment is being used and further developed to study these interactions. The present paper describes methods to prepare small, very thin lamellae (area of 5×5 µm2, thickness 50–300 nm) of a cell to be studied in a cryo‐transmission electron microscope (cryo‐TEM). Special care must be taken to preserve the natural state of molecules in their natural environment. In the case of cryo‐TEM, the samples must be frozen and kept frozen to be compatible with the vacuum conditions in the microscope. The frozen condition imposes technical challenges which are addressed. Two approaches to obtain the thin lamellae are described. Both make use of a focused ion beam (FIB) microscope. The FIB allows removal of material with nanometre precision by focusing a beam of ionised atoms (gallium ions) onto the sample. Careful control of the FIB allows cutting out of the required thin lamellae. In both strategies, the thin lamellae remain attached to the original sample, and the ensemble of sample with section and sample holder is transported from the FIB microscope to the TEM while being kept frozen.
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Affiliation(s)
- D A M DE Winter
- Environmental Hydrogeology, Department of Earth Sciences, Utrecht University, Princetonlaan 8a, Utrecht, the Netherlands
| | - C Hsieh
- New York State Department of Health, Wadsworth Center, Empire State Plaza, Albany, New York, U.S.A
| | - M Marko
- New York State Department of Health, Wadsworth Center, Empire State Plaza, Albany, New York, U.S.A.,College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York, U.S.A
| | - M F Hayles
- Cryo-FIB-SEM Technologist, Eindhoven, the Netherlands
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