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Journal articles on the topic 'Cryo-electron microscopy and tomography'

Author: Grafiati

Published: 29 March 2025

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1

Stewart, Phoebe L. "Cryo-electron microscopy and cryo-electron tomography of nanoparticles." Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 9, no. 2 (June 23, 2016): e1417. http://dx.doi.org/10.1002/wnan.1417.

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2

Lyu, Cheng-An, Yao Shen, and Peijun Zhang. "Zooming in and out: Exploring RNA Viral Infections with Multiscale Microscopic Methods." Viruses 16, no. 9 (September 23, 2024): 1504. http://dx.doi.org/10.3390/v16091504.

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RNA viruses, being submicroscopic organisms, have intriguing biological makeups and substantially impact human health. Microscopic methods have been utilized for studying RNA viruses at a variety of scales. In order of observation scale from large to small, fluorescence microscopy, cryo-soft X-ray tomography (cryo-SXT), serial cryo-focused ion beam/scanning electron microscopy (cryo-FIB/SEM) volume imaging, cryo-electron tomography (cryo-ET), and cryo-electron microscopy (cryo-EM) single-particle analysis (SPA) have been employed, enabling researchers to explore the intricate world of RNA viruses, their ultrastructure, dynamics, and interactions with host cells. These methods evolve to be combined to achieve a wide resolution range from atomic to sub-nano resolutions, making correlative microscopy an emerging trend. The developments in microscopic methods provide multi-fold and spatial information, advancing our understanding of viral infections and providing critical tools for developing novel antiviral strategies and rapid responses to emerging viral threats.

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Carlson, David B., Jeff Gelb, Vadim Palshin, and James E. Evans. "Laboratory-Based Cryogenic Soft X-Ray Tomography with Correlative Cryo-Light and Electron Microscopy." Microscopy and Microanalysis 19, no. 1 (January 18, 2013): 22–29. http://dx.doi.org/10.1017/s1431927612013827.

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AbstractHere we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal subcellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm half-pitch spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 μm thick. Structures as small as 90 nm can be detected in tomographic reconstructions following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft X-ray microscopy, and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft X-ray microscope will enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.

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Weis, Felix, and Wim J. H. Hagen. "Combining high throughput and high quality for cryo-electron microscopy data collection." Acta Crystallographica Section D Structural Biology 76, no. 8 (July 27, 2020): 724–28. http://dx.doi.org/10.1107/s2059798320008347.

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Cryo-electron microscopy (cryo-EM) can be used to elucidate the 3D structure of macromolecular complexes. Driven by technological breakthroughs in electron-microscope and electron-detector development, coupled with improved image-processing procedures, it is now possible to reach high resolution both in single-particle analysis and in cryo-electron tomography and subtomogram-averaging approaches. As a consequence, the way in which cryo-EM data are collected has changed and new challenges have arisen in terms of microscope alignment, aberration correction and imaging parameters. This review describes how high-end data collection is performed at the EMBL Heidelberg cryo-EM platform, presenting recent microscope implementations that allow an increase in throughput while maintaining aberration-free imaging and the optimization of acquisition parameters to collect high-resolution data.

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Cyrklaff, M., M. Kudryashev, N. Kilian, P. Henrich, F. Frischknecht, and M. Lanzer. "Cryo-Electron Tomography of Malaria Parasites." Microscopy and Microanalysis 15, S2 (July 2009): 864–65. http://dx.doi.org/10.1017/s1431927609099267.

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6

Apkarian, Robert P. "Comments on Cryo High Resolution Scanning Electron Microscopy." Microscopy Today 12, no. 1 (January 2004): 45. http://dx.doi.org/10.1017/s1551929500051841.

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Stephen Carmichael wrote about Cryoelectron Tomography in the May 2003 issue of Microscopy Today. Citing new preparation methods, small cells can be vitrified, observed frozen in the TEM and a series of digital images captured while the specimen is being rotated around the axis perpendicular to the electron beam producing a 3-D tomogram. Gina Sosinski and Maryann Martone wrote about imaging big and messy biological structures using cryo-electron Tomography in the July issue of Microscopy Today. Cryo-HRSEM now also seeks to provide 3-D information approaching the molecular level from frozen hydrated cell and molecular systems. Vitrification procedures for small specimens such as platelets and biomolecules on grids are accomplished by plunge freezing in liquefied etiiane as is done with cryo-TEM procedures. Bulk specimens such as organic hydrogels and tissues are routinely high pressure frozen (HPF) in 3mm gold planchets. Employing an in-lens cryostage, identical to those used in cryo-TEM, cryo-HRSEM provides 3-D high-resolution images because secondary electrons are efficiently collected above the lens in a single scan thus minimizing specimen irradiation.

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7

Marko, M., C. Hsieh, A. Leith, and C. Mannella. "Requirements for Phase-Plate Cryo-Electron Tomography." Microscopy and Microanalysis 16, S2 (July 2010): 546–47. http://dx.doi.org/10.1017/s1431927610054048.

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8

Voorhout, W., F. De Haas, P. Frederik, R. Schoenmakers, W. Busing, and D. Hubert. "An Optimized Solution for Cryo Electron Tomography." Microscopy and Microanalysis 12, S02 (July 31, 2006): 1110–11. http://dx.doi.org/10.1017/s1431927606065822.

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9

Ziese, U., D. Typke, R. Hegerl, and W. Baumeister. "Cryo Electron Microscopy of SSV1 phage particles." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 842–43. http://dx.doi.org/10.1017/s0424820100140580.

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SSVl phages are lemon-shaped particles, normally about 90 nm x 40 nm in size, with short tail fibres attached to one pole, produced by the thermophilic archaeon Sulfolobus shibate, isolate B12. They are made of 3 different proteins and DNA (15.5 kbp). Two proteins, together with host lipid, form the envelope, the third protein is associated with the DNA. Interestingly, this virus produces particles of varying size and shape. We have investigated the mass of the virions by STEM mass determination, the inner structure by cryo-electron microscopy, and the shape variability by electron tomography. Automatic electron tomography (AET) has been shown to be a useful technique for collecting 3D structural data of individual biological particles under low dose conditions, in negative stain as well as in frozen-hydrated preparations.Taking electron micrographs of vitrified samples we obtained images revealing some details of the inner structure and, on some particles, a periodic structure of the envelope. (Fig. 1a-b) The inner structure has periodicities of about 2.5 nm, which is in agreement with that found by Lepault et al on vitrified samples of the phages lambda and T4.

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10

Young, Lindsey N., and Elizabeth Villa. "Bringing Structure to Cell Biology with Cryo-Electron Tomography." Annual Review of Biophysics 52, no. 1 (May 9, 2023): 573–95. http://dx.doi.org/10.1146/annurev-biophys-111622-091327.

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Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure–function relationships in their native environment and becoming a tool for discovering new biology.

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11

Chen, Xin. "Applications of Cryogenic Electron Microscopy in Characterizing Electrochemical Materials and Interfaces." Highlights in Science, Engineering and Technology 96 (May 5, 2024): 14–20. http://dx.doi.org/10.54097/7csg5b12.

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Cryogenic electron microscopy (cryo-EM) has emerged as a pivotal technology in materials science, particularly in characterizing electrochemical materials and interfaces. This paper delves into the recent advancements and applications of cryo-EM, underscoring its significance in understanding the intricate structures and mechanisms of materials sensitive to air and electron beams, such as lithium-ion battery electrodes. Cryo-EM's ability to capture materials in a near-natural state using vitreous ice and its compatibility with advanced imaging techniques like cryo-electron energy loss spectroscopy (cryo-EELS), cryo-electron tomography (cryo-ET), and cryo-focused ion beam (cryo-FIB) enhances our understanding of quantum and energy materials. This research will discuss the revolutionary impact of cryo-EM in areas like energy conservation and conversion, highlighting its role in visualizing sensitive materials and electrochemical reaction processes. This research addresses the need for comprehensive discussions on the characterization of quantum and energy materials through cryo-EM and related techniques, offering a thorough overview of recent advancements in this rapidly evolving field.

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Chang, Yi-Wei, Songye Chen, Elitza I. Tocheva, Anke Treuner-Lange, Stephanie Löbach, Lotte Søgaard-Andersen, and Grant J. Jensen. "Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography." Nature Methods 11, no. 7 (May 11, 2014): 737–39. http://dx.doi.org/10.1038/nmeth.2961.

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13

Zhang, Peijun. "Correlative cryo-electron tomography and optical microscopy of cells." Current Opinion in Structural Biology 23, no. 5 (October 2013): 763–70. http://dx.doi.org/10.1016/j.sbi.2013.07.017.

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14

Agard, D. A., M. B. Braunfeld, Hans Chen, Rebecca McQuitty, and John Sedat. "Approaches for High Resolution Cryo-Electron Tomography of Biological Specimens." Microscopy and Microanalysis 3, S2 (August 1997): 1111–12. http://dx.doi.org/10.1017/s1431927600012447.

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Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. Use of intermediate voltage electron microscopes extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety cellular organelles and assemblies such as centrosomes (Moritz et al.,1995a,b), kinetochores (McEwen, 1993) and chromatin (Woodcock, 1994), have clearly demonstrated the power of this method for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significant new insights into biological function.Although the information that tomography provides is unique, its use as a general tool in the biological community has been limited due to the complexities involved in data collection and processing.We are simultaneously trying to make this approach accessible through automation as well as trying to extend the resolution and accuracy of the reconstructions. Significant, has been the use of low-dose cryo-electron microscopic automated data collection methods.

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15

Henderson, Richard. "Realizing the potential of electron cryo-microscopy." Quarterly Reviews of Biophysics 37, no. 1 (February 2004): 3–13. http://dx.doi.org/10.1017/s0033583504003920.

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1. Introduction 32. Background 53. 2D crystals 74. 1D crystals (helical arrays) 85. Icosahedral single particles 86. Single particles with lower symmetry 97. Cellular and subcellular electron tomography 108. Conclusion and future prospects 109. References 11Structural analysis by electron microscopy of biological macromolecules or macromolecular assemblies embedded in rapidly frozen, vitreous ice has made great advances during the last few years. Electron cryo-microscopy, or cryo-EM, can now be used to analyse the structures of molecules arranged in the form of two-dimensional crystals, helical arrays or as single particles with or without symmetry. Although it has been possible, using crystalline or helical specimens, to reach a resolution adequate to build atomic models (4 Å), there is every hope this will soon also be possible with single particles. Small and large single particles present different obstacles to progress.

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Nithyanandham Masilamani and Dhanraj Ganapathy. "Awareness of Cryo Electro-Tomography among Dental Students." International Journal of Research in Pharmaceutical Sciences 11, SPL3 (October 7, 2020): 1050–53. http://dx.doi.org/10.26452/ijrps.v11ispl3.3333.

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CryoElectronomography (CryoET) is indeed an imaging method used to create high resolution (~1-4 nm) three-dimensional viewpoints of specimen, usually physiological macromolecules as well as cell lines. CryoET is really a highly specialized implementation of scanning electron microscopy cryomicroscopy whereby the specimen are scanned since they are tilted, triggering a series of Image data which can be processed to create a 3d image, analogous to 3D images, similar to a CT scan of the human body. This survey was done for assessing the awareness of Cryo electro tomography amongst dental students. This was a questionnaire oriented cross-sectional type of survey comprising 100 dental college students in Chennai. A self-designed questionnaire comprising ten questions based on the knowledge and awareness aboutCryo-electron tomography amongst dental college students. Questionnaires were circulated through an online website survey planet. The questions explored the awareness of using Cryo-electron tomography as a tool to study various biological applications. After the responses were received from 100 participants, data was collected and analyzed .7% are aware about Cryo Electro-tomography. 3% are aware of the mechanism of action of Cryo Electro-tomography. 5% are aware of the diagnostic applications of Cryo Electro-tomography. 3% are aware of the limitations Cryo Electro-tomography.91% are willing to learn about Cryo Electro-tomography. This study concluded that dental students showed less knowledge and awareness toward Cryo Electro-tomography. There are large gaps in the knowledge and attitudes requiring strong remedial measures.

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17

Ognjenović, Jana, Reinhard Grisshammer, and Sriram Subramaniam. "Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies." Annual Review of Biomedical Engineering 21, no. 1 (June 4, 2019): 395–415. http://dx.doi.org/10.1146/annurev-bioeng-060418-052453.

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In recent years, cryo electron microscopy (cryo-EM) technology has been transformed with the development of better instrumentation, direct electron detectors, improved methods for specimen preparation, and improved software for data analysis. Analyses using single-particle cryo-EM methods have enabled determination of structures of proteins with sizes smaller than 100 kDa and resolutions of ∼2 Å in some cases. The use of electron tomography combined with subvolume averaging is beginning to allow the visualization of macromolecular complexes in their native environment in unprecedented detail. As a result of these advances, solutions to many intractable challenges in structural and cell biology, such as analysis of highly dynamic soluble and membrane-embedded protein complexes or partially ordered protein aggregates, are now within reach. Recent reports of structural studies of G protein–coupled receptors, spliceosomes, and fibrillar specimens illustrate the progress that has been made using cryo-EM methods, and are the main focus of this review.

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Kochovski, Zdravko, Guosong Chen, Jiayin Yuan, and Yan Lu. "Cryo-Electron microscopy for the study of self-assembled poly(ionic liquid) nanoparticles and protein supramolecular structures." Colloid and Polymer Science 298, no. 7 (May 23, 2020): 707–17. http://dx.doi.org/10.1007/s00396-020-04657-w.

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Abstract Cryo-electron microscopy (cryo-EM) is a powerful structure determination technique that is well-suited to the study of protein and polymer self-assembly in solution. In contrast to conventional transmission electron microscopy (TEM) sample preparation, which often times involves drying and staining, the frozen-hydrated sample preparation allows the specimens to be kept and imaged in a state closest to their native one. Here, we give a short overview of the basic principles of Cryo-EM and review our results on applying it to the study of different protein and polymer self-assembled nanostructures. More specifically, we show how we have applied cryo-electron tomography (cryo-ET) to visualize the internal morphology of self-assembled poly(ionic liquid) nanoparticles and cryo-EM single particle analysis (SPA) to determine the three-dimensional (3D) structures of artificial protein microtubules.

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19

Renken, C. "Signal to Noise Ratio Mapping for Cryo-Electron Tomography." Microscopy and Microanalysis 15, S2 (July 2009): 568–69. http://dx.doi.org/10.1017/s1431927609098237.

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20

Nicastro, D. "Cryo-Electron Tomography: New Views of Cells and Organelles." Microscopy and Microanalysis 16, S2 (July 2010): 834–35. http://dx.doi.org/10.1017/s1431927610057430.

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21

Schwartz, CL, SC Dawson, and A. Hoenger. "Cryo-Electron Tomography of Isolated Cytoskeletons of Giardia intestinalis." Microscopy and Microanalysis 14, S2 (August 2008): 1304–5. http://dx.doi.org/10.1017/s1431927608085462.

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22

Wright, ER, JS Poindexter, P. Viollier, and GJ Jensen. "Electron Cryo-Tomography of Viral Infection Within Caulobacter crescentus." Microscopy and Microanalysis 14, S2 (August 2008): 1576–77. http://dx.doi.org/10.1017/s1431927608085632.

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23

Danev, Radostin, Hirofumi Iijima, Mizuki Matsuzaki, and Sohei Motoki. "Fast and accurate defocus modulation for improved tunability of cryo-EM experiments." IUCrJ 7, no. 3 (April 25, 2020): 566–74. http://dx.doi.org/10.1107/s205225252000408x.

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Current data collection strategies in electron cryo-microscopy (cryo-EM) record multiframe movies with static optical settings. This limits the number of adjustable parameters that can be used to optimize the experiment. Here, a method for fast and accurate defocus (FADE) modulation during movie acquisition is proposed. It uses the objective lens aperture as an electrostatic pole that locally modifies the electron beam potential. The beam potential variation is converted to defocus change by the typically undesired chromatic aberration of the objective lens. The simplicity, electrostatic principle and low electrical impedance of the device allow fast switching speeds that will enable per-frame defocus modulation of cryo-EM movies. Researchers will be able to define custom defocus `recipes' and tailor the experiment for optimal information extraction from the sample. The FADE method could help to convert the microscope into a more dynamic and flexible optical platform that delivers better performance in cryo-EM single-particle analysis and electron cryo-tomography.

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Engel, Leeya, Claudia Vasquez, Elizabeth Montabana, Belle Sow, Marcin Walkiewicz, William Weis, and Alexander Dunn. "Micropatterning of electron microscopy grids for improved cellular cryo-electron tomography throughput." Microscopy and Microanalysis 27, S1 (July 30, 2021): 2570–73. http://dx.doi.org/10.1017/s1431927621009132.

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Liu, Yun-Tao, and Chang-Lu Tao. "Digitalizing neuronal synapses with cryo-electron tomography and correlative microscopy." Current Opinion in Neurobiology 76 (October 2022): 102595. http://dx.doi.org/10.1016/j.conb.2022.102595.

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Frischknecht, F., S. Munter, M. Kudryashev, S. Lepper, S. Hegge, W. Baumeister, R. Wallich, U. Schwarz, and M. Cyrklaff. "Imaging Motile Pathogens by Light microscopy and Cryo-electron Tomography." Microscopy and Microanalysis 15, S2 (July 2009): 80–81. http://dx.doi.org/10.1017/s1431927609099371.

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27

Thomas, Connon I., Nicolai T. Urban, Ye Sun, Lesley A. Colgan, Xun Tu, Ryohei Yasuda, and Naomi Kamasawa. "Cryo-Confocal Imaging for CLEM Mapping in Brain Tissues." Microscopy Today 29, no. 5 (September 2021): 34–39. http://dx.doi.org/10.1017/s1551929521001073.

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Abstract:In correlative light and electron microscopy (CLEM) workflows, identifying the same sub-cellular features in tissue by both light (LM) and electron microscopy (EM) remains a challenge. Furthermore, use of cryo-fixation for EM is desirable to capture rapid biological phenomena. Here, we describe a workflow that incorporates cryo-confocal laser scanning microscopy into the CLEM process, mapping cells in brain slices to re-image them with serial section scanning electron microscopy (ssSEM) array tomography. The addition of Airyscan detection increased the signal-to-noise ratio (SNR), allowing individual spines in thick frozen tissue to be visualized at a sufficient spatial resolution, providing a new tool for a CLEM approach to capture biological dynamics.

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Plitzko, Jürgen M., Alexander Rigort, and Andrew Leis. "Correlative cryo-light microscopy and cryo-electron tomography: from cellular territories to molecular landscapes." Current Opinion in Biotechnology 20, no. 1 (February 2009): 83–89. http://dx.doi.org/10.1016/j.copbio.2009.03.008.

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Saibil, Helen R., Kay Grünewald, and David I. Stuart. "A national facility for biological cryo-electron microscopy." Acta Crystallographica Section D Biological Crystallography 71, no. 1 (January 1, 2015): 127–35. http://dx.doi.org/10.1107/s1399004714025280.

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Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

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Bert, Wim, Dieter Slos, Olivier Leroux, and Myriam Claeys. "Cryo-fixation and associated developments in transmission electron microscopy: a cool future for nematology." Nematology 18, no. 1 (2016): 1–14. http://dx.doi.org/10.1163/15685411-00002943.

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At present, the importance of sample preparation equipment for electron microscopy represents the driving force behind major breakthroughs in microscopy and cell biology. In this paper we present an introduction to the most commonly used cryo-fixation techniques, with special attention paid towards high-pressure freezing followed by freeze substitution. Techniques associated with cryo-fixation, such as immunolocalisation, cryo-sectioning, and correlative light and electron microscopy, are also highlighted. For studies that do not require high resolution, high quality results, or the immediate arrest of certain processes, conventional methods will provide answers to many questions. For some applications, such as immunocytochemistry, three-dimensional reconstruction of serial sections or electron tomography, improved preservation of the ultrastructure is required. This review of nematode cryo-fixation highlights that cryo-fixation not only results in a superior preservation of fine structural details, but also underlines the fact that some observations based on results solely obtained through conventional fixation approaches were either incorrect, or otherwise had severe limitations. Although the use of cryo-fixation has hitherto been largely restricted to model organisms, the advantages of cryo-fixation are sufficiently self-evident that we must conclude that the cryo-fixation method is highly likely to become the standard for nematode fixation in the near future.

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Sartori, Anna, Rudolf Gatz, Florian Beck, Alexander Rigort, Wolfgang Baumeister, and Juergen M. Plitzko. "Correlative microscopy: Bridging the gap between fluorescence light microscopy and cryo-electron tomography." Journal of Structural Biology 160, no. 2 (November 2007): 135–45. http://dx.doi.org/10.1016/j.jsb.2007.07.011.

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Nicastro, D., T. Heuser, J. Lin, and C. F. Barber. "Cryo-Electron Tomography Reveals Novel Features of Cilia and Flagella." Microscopy and Microanalysis 18, S2 (July 2012): 554–55. http://dx.doi.org/10.1017/s143192761200462x.

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Rigort, A., F. Bäuerlein, T. Laugks, M. Hayles, C. Mathisen, B. Lich, R. Morrison, A. Leis, W. Baumeister, and J. Plitzko. "A 360º Rotatable Cryo-FIB Stage for Micromachining Frozen-Hydrated Specimens for Cryo-Electron Tomography." Microscopy and Microanalysis 16, S2 (July 2010): 220–21. http://dx.doi.org/10.1017/s1431927610058186.

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Hu, Guo-Bin. "Whole Cell Cryo-Electron Tomography Suggests Mitochondria Divide by Budding." Microscopy and Microanalysis 20, no. 4 (May 28, 2014): 1180–87. http://dx.doi.org/10.1017/s1431927614001317.

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AbstractEukaryotes rely on mitochondrial division to guarantee that each new generation of cells acquires an adequate number of mitochondria. Mitochondrial division has long been thought to occur by binary fission and, more recently, evidence has supported the idea that binary fission is mediated by dynamin-related protein (Drp1) and the endoplasmic reticulum. However, studies to date have depended on fluorescence microscopy and conventional electron microscopy. Here, we utilize whole cell cryo-electron tomography to visualize mitochondrial division in frozen hydrated intact HeLa cells. We observe a large number of relatively small mitochondria protruding from and connected to large mitochondria or mitochondrial networks. Therefore, this study provides evidence that mitochondria divide by budding.

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Kiss, Gabriella, Xuemin Chen, Melinda A. Brindley, Patricia Campbell, Claudio L. Afonso, Zunlong Ke, Jens M. Holl, et al. "Capturing Enveloped Viruses on Affinity Grids for Downstream Cryo-Electron Microscopy Applications." Microscopy and Microanalysis 20, no. 1 (November 26, 2013): 164–74. http://dx.doi.org/10.1017/s1431927613013937.

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AbstractElectron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.

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Sorrentino, Andrea, Josep Nicolás, Ricardo Valcárcel, Francisco Javier Chichón, Marc Rosanes, Jose Avila, Andrei Tkachuk, Jeff Irwin, Salvador Ferrer, and Eva Pereiro. "MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging." Journal of Synchrotron Radiation 22, no. 4 (June 25, 2015): 1112–17. http://dx.doi.org/10.1107/s1600577515008632.

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The performance of MISTRAL is reported, the soft X-ray transmission microscopy beamline at the ALBA light source (Barcelona, Spain) which is primarily dedicated to cryo soft X-ray tomography (cryo-SXT) for three-dimensional visualization of whole unstained cells at spatial resolutions down to 30 nm (half pitch). Short acquisition times allowing for high-throughput and correlative microscopy studies have promoted cryo-SXT as an emerging cellular imaging tool for structural cell biologists bridging the gap between optical and electron microscopy. In addition, the beamline offers the possibility of imaging magnetic domains in thin magnetic films that are illustrated here with an example.

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Engel, Leeya, Claudia G. Vasquez, Elizabeth A. Montabana, Belle M. Sow, Marcin P. Walkiewicz, William I. Weis, and Alexander R. Dunn. "Lattice Micropatterning of Electron Microscopy Grids for Improved Cellular Cryo-Electron Tomography Throughput." Biophysical Journal 120, no. 3 (February 2021): 173a. http://dx.doi.org/10.1016/j.bpj.2020.11.1218.

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Lau, Katherine, Caspar Jonker, Jingyue Liu, and Marit Smeets. "The Undesirable Effects and Impacts of Ice Contamination Experienced in the Cryo-Electron Tomography Workflow and Available Solutions." Microscopy Today 30, no. 3 (May 2022): 30–35. http://dx.doi.org/10.1017/s1551929522000621.

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Abstract:Cryo-electron tomography (cryo-ET) is a powerful technique that can provide unprecedented insight into protein-protein interactions and molecular machinery in a near-native state. The adoption of cryo-ET by life science research groups is hampered by the challenges associated with cryo-ET sample preparation. The current sample preparation process has many steps at which ice contamination may occur to negatively affect the final sample and data quality. A survey was conducted to better understand the effects and impact of ice contamination to the cryo-ET outcome. Over 80 cryo-electron microscopy users worldwide participated in our survey. The results are presented in this article. We furthermore discussed the currently available solutions that can alleviate the ice contamination problems to increase the sample yield and cryo-ET data output.

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Marko, M., C. Hsieh, D. Vetter, NJ Salmon, and C. Mannella. "Cryo-FIB Preparation for Cryo-TEM Tomography." Microscopy and Microanalysis 16, S2 (July 2010): 178–79. http://dx.doi.org/10.1017/s1431927610054036.

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Schorb, Martin, Leander Gaechter, Ori Avinoam, Frank Sieckmann, Mairi Clarke, Cecilia Bebeacua, Yury S. Bykov, Andreas F. P. Sonnen, Reinhard Lihl, and John A. G. Briggs. "New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography." Journal of Structural Biology 197, no. 2 (February 2017): 83–93. http://dx.doi.org/10.1016/j.jsb.2016.06.020.

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Kumar, Ishika, Anju Paudyal, Anna Kádková, Michelle Stewart, Jakob Balslev Sørensen, and Julika Radecke. "An Improved Method for Growing Primary Neurons on Electron Microscopy Grids Co-Cultured with Astrocytes." International Journal of Molecular Sciences 24, no. 20 (October 14, 2023): 15191. http://dx.doi.org/10.3390/ijms242015191.

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With the increasing popularity of cryo-electron tomography (cryo-ET) in recent years, the quest to establish a method for growing primary neurons directly on electron microscopy grids (EM grids) has been ongoing. Here we describe a straightforward way to establish a mature neuronal network on EM grids, which includes formation of synaptic contacts. These synapses were thin enough to allow for direct visualization of small filaments such as SNARE proteins tethering the synaptic vesicle (SV) to the active zone plasma membrane on a Titan Krios without prior focused ion-beam milling.

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Carroll, Brittany L., and Jun Liu. "Structural Conservation and Adaptation of the Bacterial Flagella Motor." Biomolecules 10, no. 11 (October 29, 2020): 1492. http://dx.doi.org/10.3390/biom10111492.

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Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.

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Frank, J., C. A. Mannella, and C. Rieder. "An Integrated Biological Imaging Facility: Capabilities of the Biological Microscopy and Image Reconstruction Resource." Microscopy and Microanalysis 3, S2 (August 1997): 271–72. http://dx.doi.org/10.1017/s1431927600008242.

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The Biological Microscopy and Image Reconstruction Resource (BMIRR) is operated by the Wadsworth Center as a national biotechnology resource, with funding through the NIH Center for Research Resources and from NSF. This biological imaging resource has evolved continuously over the past two decades. Early development focussed on correlative, same-cell light and electron microscopic techniques, combining the capabilities of video-enhanced light microscopy and high-voltage electron microscopy. A current area of development is electron microscopic tomography, whereby the full 3D capabilities of higher voltage (400-1200 KV) electron microscopy is brought to bear on biological problems. In particular, the recent development of techniques for merging projection data from two mutually perpendicular tilt series has permitted significantly improved resolution, reducing the missing wedge of information to a missing pyramid. Attention is now turning to optimization of conditions for applying tomography to frozen-hydrated specimens, using automated data collection on our cryo-IVEM. Combined with parallel advances in same-cell manipulation and viewing, the BMIRR provides biologists with a unique combination of imaging and computational tools for research into the 3D structure and dynamics that underly cellular processes (see figures and refs. 2-4).

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Assaiya, Anshul, Ananth Prasad Burada, Surbhi Dhingra, and Janesh Kumar. "An overview of the recent advances in cryo-electron microscopy for life sciences." Emerging Topics in Life Sciences 5, no. 1 (March 24, 2021): 151–68. http://dx.doi.org/10.1042/etls20200295.

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Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.

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Keller, P., O. Ben-Nun Shaul, B. Heymann, D. Winkler, A. Oppenheim, and AC Steven. "Analysis of Simian Virus 40 Chromatin Structure by Cryo-Electron Tomography." Microscopy and Microanalysis 15, S2 (July 2009): 644–45. http://dx.doi.org/10.1017/s1431927609096196.

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Nicastro, D. "Plastic Section and Cryo-Electron Tomography Using the IMOD Software Package." Microscopy and Microanalysis 15, S2 (July 2009): 1532–33. http://dx.doi.org/10.1017/s1431927609097207.

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Holl, J., R. Guerrero-Ferreira, G. Williams, M. Brindley, R. Plemper, and E. Wright. "In situ Structural Studies of Paramyxovirus Glycoproteins by Cryo-Electron Tomography." Microscopy and Microanalysis 16, S2 (July 2010): 1092–93. http://dx.doi.org/10.1017/s1431927610062252.

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Zhao, X., J. Pitzer, M. Motaleb, S. Norris, and J. Liu. "Molecular Architecture of Bacterial Flagellar Stator Revealed by Cryo-Electron Tomography." Microscopy and Microanalysis 17, S2 (July 2011): 110–11. http://dx.doi.org/10.1017/s1431927611001425.

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Kuebel, C., and S. Dieckhoff. "TEM Analysis of Aluminum Anodization Layers – Cryo-EFTEM and Electron Tomography." Microscopy and Microanalysis 12, S02 (July 31, 2006): 1580–81. http://dx.doi.org/10.1017/s1431927606068371.

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Parrell, Daniel, Joseph Olson, Rachelle A. Lemke, Timothy J. Donohue, and Elizabeth R. Wright. "Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy." Biomolecules 14, no. 8 (August 14, 2024): 1006. http://dx.doi.org/10.3390/biom14081006.

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Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

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