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Relevant bibliographies by topics / Cryo-electron tomography, cryo-ultramicrotomy, cryo-planing / Journal articles

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Journal articles on the topic 'Cryo-electron tomography, cryo-ultramicrotomy, cryo-planing'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Wagenknecht, Terence, Chyongere Hsieh, and Michael Marko. "Skeletal muscle triad junction ultrastructure by Focused-Ion-Beam milling of muscle and Cryo-Electron Tomography." European Journal of Translational Myology 25, no. 1 (2015): 49. http://dx.doi.org/10.4081/ejtm.2015.4823.

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Cryo-electron tomography (cryo-ET) has emerged as perhaps the only practical technique for revealing nanometer-level three-dimensional structural details of subcellular macromolecular complexes in their native context, inside the cell. As currently practiced, the specimen should be 0.1- 0.2 microns in thickness to achieve optimal resolution. Thus, application of cryo-ET to intact frozen (vitreous) tissues, such as skeletal muscle, requires that they be sectioned. Cryo-ultramicrotomy is notoriously difficult and artifact-prone when applied to frozen cells and tissue, but a new technique, focuse

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2

Harris, Matthew. "Cryo Electron Tomography." Imaging & Microscopy 9, no. 4 (2007): 31–32. http://dx.doi.org/10.1002/imic.200790206.

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3

Doerr, Allison. "Cryo-electron tomography." Nature Methods 14, no. 1 (2017): 34. http://dx.doi.org/10.1038/nmeth.4115.

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4

Moreno-Serrano, José A., and Tulio F. Solano Castillo. "Crio-Tomografía de rayos X (Cryo-XT) de fábricas virales en células infectadas con virus vaccinia." Revista de Investigaciones Altoandinas -Journal of High Andean Research 20, no. 4 (2018): 409–18. http://dx.doi.org/10.18271/ria.2018.418.

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5

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

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6

Pierson, Jason, and Peter J. Peters. "Successful Cryo Electron Tomography of Vitreous Cryo Sections." Microscopy and Microanalysis 23, S1 (2017): 2310–11. http://dx.doi.org/10.1017/s1431927617012211.

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7

Pierson, J., M. Vos, J. R. McIntosh, and P. J. Peters. "Perspectives on electron cryo-tomography of vitreous cryo-sections." Microscopy 60, suppl 1 (2011): S93—S100. http://dx.doi.org/10.1093/jmicro/dfr014.

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8

Nithyanandham Masilamani and Dhanraj Ganapathy. "Awareness of Cryo Electro-Tomography among Dental Students." International Journal of Research in Pharmaceutical Sciences 11, SPL3 (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

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9

YANAGISAWA, Haruaki, and Masahide KIKKAWA. "Introduction to Cryo-Electron Tomography." Nihon Kessho Gakkaishi 63, no. 3 (2021): 184–88. http://dx.doi.org/10.5940/jcrsj.63.184.

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10

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

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11

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 (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 des

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12

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 (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 nan

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13

McEwen, B. F., M. Marko, C.-E. Hsieh, and J. Frank. "The Potential of Cryo-Electron Tomography as Assessed by Reconstruction of Sea Urchin Axonemes." Microscopy and Microanalysis 5, S2 (1999): 410–11. http://dx.doi.org/10.1017/s1431927600015373.

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Recent improvements in digital image acquisition, and automated TEM, have lowered the electron dose requirement for collecting a tomographic tilt series to the point where cryo-electron tomography is now feasible. Theoretical calculations indicate that resolution values of 2-5 nm can be obtained for fully hydrated specimens 100-500 nm thick. This resolution is sufficient for identifying individual macromolecules, and macromolecular assemblies, within-organelles and small cells. However, initial applications to cells and organelles fell short of theoretical resolution limits, indicating further

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14

Mahamid, Julia, Jan Arnold, and Jurgen M. Plitzko. "Site Specific Cryo-FIB Preparations Aimed at in situ Cryo-Electron Tomography." Microscopy and Microanalysis 23, S1 (2017): 250–51. http://dx.doi.org/10.1017/s1431927617001933.

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15

Pyle, Euan, and Giulia Zanetti. "Current data processing strategies for cryo-electron tomography and subtomogram averaging." Biochemical Journal 478, no. 10 (2021): 1827–45. http://dx.doi.org/10.1042/bcj20200715.

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Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from tomograms, aligned, and averaged in a process called subtomogram averaging (STA). STA overcomes the low signal to noise ratio within the individual subtomograms to generate structures of the particle(s) of interest. In recent years, cryo-ET with STA has increasingly been capable of reac

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16

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

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17

Norlen, Lars. "Molecular Cryo-Electron Tomography of Skin." Open Dermatology Journal 4, no. 1 (2010): 46–47. http://dx.doi.org/10.2174/1874372201004010046.

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18

Danev, Radostin, Shuji Kanamaru, Michael Marko, and Kuniaki Nagayama. "Zernike phase contrast cryo-electron tomography." Journal of Structural Biology 171, no. 2 (2010): 174–81. http://dx.doi.org/10.1016/j.jsb.2010.03.013.

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19

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

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20

Guerrero-Ferreira, Ricardo C., and Elizabeth R. Wright. "Cryo-electron tomography of bacterial viruses." Virology 435, no. 1 (2013): 179–86. http://dx.doi.org/10.1016/j.virol.2012.08.022.

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21

Cyrklaff, M., C. Risco, J. J. Fernandez, et al. "Cryo-electron tomography of vaccinia virus." Proceedings of the National Academy of Sciences 102, no. 8 (2005): 2772–77. http://dx.doi.org/10.1073/pnas.0409825102.

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22

Leis, A. P., M. Beck, M. Gruska, et al. "Cryo-electron tomography of biological specimens." IEEE Signal Processing Magazine 23, no. 3 (2006): 95–103. http://dx.doi.org/10.1109/msp.2006.1628882.

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23

Baumeister, Wolfgang. "The power of cryo-electron tomography." Acta Crystallographica Section A Foundations and Advances 73, a1 (2017): a415. http://dx.doi.org/10.1107/s0108767317095952.

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24

Cyrklaff, Marek, Petr Chlanda, Anna Sartori, and Simone Lepper. "Cryo-electron Tomography of Whole Cells." Imaging & Microscopy 9, no. 3 (2007): 50–53. http://dx.doi.org/10.1002/imic.200790182.

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25

Battisti, A. J., J. D. Yoder, P. Plevka, et al. "Cryo-Electron Tomography of Rubella Virus." Journal of Virology 86, no. 20 (2012): 11078–85. http://dx.doi.org/10.1128/jvi.01390-12.

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26

Nicastro, Daniela, Achilleas S. Frangakis, Dieter Typke, and Wolfgang Baumeister. "Cryo-electron Tomography of Neurospora Mitochondria." Journal of Structural Biology 129, no. 1 (2000): 48–56. http://dx.doi.org/10.1006/jsbi.1999.4204.

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27

Bai, Haobo, Yong Guan, Liang Chen, Gang Liu, and Yangchao Tian. "The Precise Alignment and Auto-fusion of Correlative Cryo-SXT and Cryo-FM." Microscopy and Microanalysis 24, S2 (2018): 142–43. http://dx.doi.org/10.1017/s1431927618013090.

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Abstract:Cell's sub-cellular architecture and function can be revealed by Cryo soft X-ray tomography (Cryo-SXT) and Cryo-fluorescence microscopy (Cryo-FM) respectively. To understand the connection between cells' structure and function, correlative Cryo-SXT and Cryo-FM has been applied. Here we introduce a semiautomatic precise alignment and fusion technology of Cryo-SXT and Cryo-fluorescence microscopy.

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28

Dunstone, Michelle A., and Alex de Marco. "Cryo-electron tomography: an ideal method to study membrane-associated proteins." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1726 (2017): 20160210. http://dx.doi.org/10.1098/rstb.2016.0210.

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Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-a

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29

Apkarian, Robert P. "Comments on Cryo High Resolution Scanning Electron Microscopy." Microscopy Today 12, no. 1 (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 hyd

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30

Carroll, Brittany L., and Jun Liu. "Structural Conservation and Adaptation of the Bacterial Flagella Motor." Biomolecules 10, no. 11 (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 ins

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31

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 (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 princ

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32

Plitzko, Jürgen, Philipp Erdmann, and Sven Klumpe. "Deposition-free Cryo-FIB Lift-out Transfer for Cryo-Electron Tomography Specimen Preparation." Microscopy and Microanalysis 27, S1 (2021): 3032–34. http://dx.doi.org/10.1017/s1431927621010527.

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33

Plevka, Pavel, Anthony J. Battisti, Dennis C. Winkler, et al. "Sample Preparation Induced Artifacts in Cryo-Electron Tomographs." Microscopy and Microanalysis 18, no. 5 (2012): 1043–48. http://dx.doi.org/10.1017/s1431927612001298.

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AbstractWe investigated the effects of sample preparation and of the exposure to an electron beam on particles in cryo-electron tomographs. Various virus particles with icosahedral symmetry were examined, allowing a comparison of symmetrically related components that should be identical in structure but might be affected differently by these imaging artifacts. Comparison of tomographic reconstructions with previously determined structures established by an independent method showed that neither freezing nor electron beam exposure produced a significant amount of shrinkage along the z axis (thi

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34

Parvate, Amar, Evan P. Williams, Mariah K. Taylor, et al. "Diverse Morphology and Structural Features of Old and New World Hantaviruses." Viruses 11, no. 9 (2019): 862. http://dx.doi.org/10.3390/v11090862.

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To further understanding of the structure and morphology of the Orthohantavirus, family Hantaviridae, we have employed cryo-electron microscopy (cryo-EM) for three New World hantaviruses: Andes (ANDV), Sin Nombre (SNV), and Black Creek Canal (BCCV). Building upon our prior cryo-EM and cryo-tomography study of the Old World hantavirus, Hantaan virus (HTNV), we have expanded our studies to examine the entire virion population present in cell culture supernatant. Hence, in contrast to the prior cryo-EM/ET studies in which we used a polyethylene precipitation, a sucrose gradient, and a sucrose cus

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35

Burbaum, Laura, Miroslava Schaffer, Benjamin D. Engel, et al. "Charting Molecular Landscapes Using Cryo-Electron Tomography." Microscopy Today 25, no. 3 (2017): 26–31. http://dx.doi.org/10.1017/s1551929517000384.

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36

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

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37

Kamyshinsky, R. A., Y. M. Chesnokov, and A. S. Orekhov. "Cryo-Electron Tomography Studies of Cell Systems." Crystallography Reports 65, no. 5 (2020): 744–48. http://dx.doi.org/10.1134/s1063774520050090.

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38

Turoňová, Beata, Lukas Marsalek, and Philipp Slusallek. "On geometric artifacts in cryo electron tomography." Ultramicroscopy 163 (April 2016): 48–61. http://dx.doi.org/10.1016/j.ultramic.2016.01.002.

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39

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 (2006): 1110–11. http://dx.doi.org/10.1017/s1431927606065822.

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40

Guichard, Paul, Denis Chrétien, Sergio Marco, and Anne-Marie Tassin. "Procentriole assembly revealed by cryo-electron tomography." EMBO Journal 29, no. 9 (2010): 1565–72. http://dx.doi.org/10.1038/emboj.2010.45.

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41

Bongini, L., D. Fanelli, F. Piazza, P. De Los Rios, S. Sandin, and U. Skoglund. "Dynamics of antibodies from cryo-electron tomography." Biophysical Chemistry 115, no. 2-3 (2005): 235–40. http://dx.doi.org/10.1016/j.bpc.2004.12.037.

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42

Koning, Roman I., and Abraham J. Koster. "Cryo-electron tomography in biology and medicine." Annals of Anatomy - Anatomischer Anzeiger 191, no. 5 (2009): 427–45. http://dx.doi.org/10.1016/j.aanat.2009.04.003.

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43

Hylton, Ryan K., and Matthew T. Swulius. "Challenges and triumphs in cryo-electron tomography." iScience 24, no. 9 (2021): 102959. http://dx.doi.org/10.1016/j.isci.2021.102959.

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44

Kiss, Gabriella, Xuemin Chen, Melinda A. Brindley, et al. "Capturing Enveloped Viruses on Affinity Grids for Downstream Cryo-Electron Microscopy Applications." Microscopy and Microanalysis 20, no. 1 (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

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45

Ognjenović, Jana, Reinhard Grisshammer, and Sriram Subramaniam. "Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies." Annual Review of Biomedical Engineering 21, no. 1 (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.

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46

Wang, Ke, Korrinn Strunk, Gongpu Zhao, Jennifer L. Gray, and Peijun Zhang. "3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography." Journal of Structural Biology 180, no. 2 (2012): 318–26. http://dx.doi.org/10.1016/j.jsb.2012.07.003.

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47

Schaffer, Miroslava. "Cryo-FIB: Overcoming the Hurdle of Sample Preparation for In Situ Cryo-Electron Tomography." Microscopy and Microanalysis 24, S1 (2018): 2326–27. http://dx.doi.org/10.1017/s1431927618012114.

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48

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 (2009): 83–89. http://dx.doi.org/10.1016/j.copbio.2009.03.008.

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49

Nicolas, William, Florian Fäßler, Elliot Meyerowitz, and Grant Jensen. "Peaking into the plant cell wall using cryo-FIB milling and electron cryo-tomography." Microscopy and Microanalysis 27, S1 (2021): 3024–26. http://dx.doi.org/10.1017/s1431927621010503.

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50

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 (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

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