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Relevant bibliographies by topics / Cryo-electron microscopy

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Academic literature on the topic 'Cryo-electron microscopy'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 January 2025

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Journal articles on the topic "Cryo-electron microscopy"

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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Nijsse, Jaap, and Adriaan C. van Aelst. "Cryo-planing for cryo-scanning electron microscopy." Scanning 21, no. 6 (December 6, 2006): 372–78. http://dx.doi.org/10.1002/sca.4950210603.

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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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Henderson, Richard, and Samar Hasnain. "`Cryo-EM': electron cryomicroscopy, cryo electron microscopy or something else?" IUCrJ 10, no. 5 (September 1, 2023): 519–20. http://dx.doi.org/10.1107/s2052252523006759.

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Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has been understood to stand for different things. We wish the wider community to engage and clarify the definition of cryoEM so that the expanding literature involving cryoEM is unified.

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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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Ye, Ke, and Lek-Heng Lim. "Cohomology of Cryo-Electron Microscopy." SIAM Journal on Applied Algebra and Geometry 1, no. 1 (January 2017): 507–35. http://dx.doi.org/10.1137/16m1070220.

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Doerr, Allison. "Single-particle cryo-electron microscopy." Nature Methods 13, no. 1 (December 30, 2015): 23. http://dx.doi.org/10.1038/nmeth.3700.

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Baker, Monya. "Cryo-electron microscopy shapes up." Nature 561, no. 7724 (September 2018): 565–67. http://dx.doi.org/10.1038/d41586-018-06791-6.

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Cossio, Pilar, and Edward Egelman. "Editorial overview: Cryo-electron microscopy." Current Opinion in Structural Biology 89 (December 2024): 102937. http://dx.doi.org/10.1016/j.sbi.2024.102937.

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Valentijn, JA, LF van Driel, AV Agronskaia, K. Knoops, RI Koning, M. Barcena, HC Gerritsen, and AJ Koster. "Novel Methods for Cryo-Fluorescence Microscopy Permitting Correlative Cryo-Electron Microscopy." Microscopy and Microanalysis 14, S2 (August 2008): 1314–15. http://dx.doi.org/10.1017/s1431927608086716.

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Dissertations / Theses on the topic "Cryo-electron microscopy"

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Briggs, John A. G. "Cryo-electron microscopy of retroviruses." Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408819.

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Toropova, Katerina. "Cryo-electron microscopy of bacteriophage MS2." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.503345.

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Grant, Timothy R. "Advances in single particle cryo electron microscopy." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.542950.

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Cheng, Kimberley. "Single-particle cryo-electron microscopy of macromolecular assemblies." Doctoral thesis, Stockholm : Skolan för teknik och hälsa, Kungliga Tekniska högskolan, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11769.

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Leong, Peter Anthony Jensen Grant J. Fraser Scott E. "Computational challenges in high-resolution cryo-electron microscopy /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-08072008-171049.

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Fiedorczuk, Karol. "Cryo-electron microscopy studies on ovine mitochondrial complex I." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/270318.

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The main objective of this work is to determine the atomic structure of mammalian respiratory complex I. Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) is one of the central enzymes in the oxidative phosphorylation pathway. It couples electron transfer between NADH and ubiquinone to proton translocation across the inner mitochondrial membrane, contributing to cellular energy production. Complex I is the largest and most elaborate protein assembly of the respiratory chain with a total mass of 970 kilodaltons. It consists of 14 conserved ‘core subunits’ and 31 mitochondria-specific ‘supernumerary subunits’. Together they form a giant, Lshaped molecule, with one arm buried in the mitochondrial membrane and another protruding into the mitochondrial matrix. Here, a novel method for the purification of ovine (Ovis aries) complex I was developed and suitable conditions for cryo-EM imaging established, after extensive screening of detergents and additives. Cryo-EM images were acquired with the recently developed direct electron detector and processed using the latest software. This allowed the solution of the nearly complete atomic model of mitochondrial complex I at 3.9 Å resolution. The membrane part of the complex contains 78 transmembrane helices, mostly contributed by conserved antiporter-like subunits responsible for proton translocation. These helices are stabilized by tightly bound lipids (including cardiolipins). The hydrophilic arm harbours flavin mononucleotide and 8 iron–sulfur clusters involved in electron transfer. Supernumerary subunits build a scaffold around the conserved core, strongly stabilizing the complex. Additionally, subunits containing cofactors (NADPH, zinc ion and phosphopantetheine) may play a regulatory role. Two distinct conformations of the complex are observed, which may describe the active and deactive states or reflect conformations occurring during the catalytic cycle of the enzyme. Currently this is the most detailed model of this molecular machine, providing insight into the mechanism, assembly and dysfunction of mitochondrial complex I. It also allows molecular analysis of numerous disease-causing mutations, and so the structure may serve as a stepping-stone for future medical developments.

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Sandin, Sara. "Cryo-electron tomography of individual protein molecules /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.

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Ekwall, Hans. "Electron microscopy of cryopreserved boar spermatozoa : with special reference to cryo-scanning electron microscopy and immunocytochemistry /." Uppsala : Dept. of Clinical Sciences, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/2007123.pdf.

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Elmlund, Dominika. "Towards unbiased 3D reconstruction : in single-particle cryo-electron microscopy." Doctoral thesis, KTH, Strukturell bioteknik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-27612.

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Cryo-electron microscopy of freestanding molecules (single-particles) plays a pivotal role in the difficult and pressing challenge of determining the structures of large macromolecular complexes. Molecular volumes are generated by aligning large sets of randomly oriented two-dimensional (2D) projection images in three dimensions (3D) before reconstruction is performed using tomographic techniques. The increasing popularity of the single-particle method is highly correlated with technical advances in instrumentation and computation. This thesis introduces new computational methods for 3D structure determination from electron microscopic projection images of single molecules. The algorithms have been developed to fill a gap in the single particle methodology – the lack of methods for ab initio 3D reconstruction of asymmetrical or low-symmetry molecules co-existing in different functional states. The proposed approach does not rely on a priori information about the structure or the character of the sample heterogeneity, which minimizes template dependence and makes the methods applicable to a wide range of single molecules. The presented algorithms constitute the basis of a new open source software package - SIMPLE (Single-particle IMage Processing Linux Engine). SIMPLE is an efficient and easy-to-use image processing system for semi-automated ab initio 3D reconstruction from challenging single-particle data sets (asymmetrical particles, significant degree of heterogeneity).
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Jarasch, Alexander. "3D modeling of ribosomal RNA using cryo-electron microscopy density maps." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-131016.

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Books on the topic "Cryo-electron microscopy"

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Appasani, Krishnarao. Cryo-Electron Microscopy in Structural Biology. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003326106.

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Strauss, Mike. Cryo-electron microscopy of membrane proteins; lipid bilayer supports and vacuum-cryo-transfer. Ottawa: National Library of Canada, 2003.

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Gutierrez-Vargas, Cristina. Single-particle cryo-electron microscopy studies of ribosomes with fragmented 28S rRNA. [New York, N.Y.?]: [publisher not identified], 2020.

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Twomey, Edward Charles. Structural Determinants of Ionotropic Glutamate Receptor Function Revealed by Cryo- electron Microscopy. [New York, N.Y.?]: [publisher not identified], 2018.

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Ho, Danny Nam. Structure Characterization of the 70S-BipA Complex Using Novel Methods of Single-Particle Cryo-Electron Microscopy. [New York, N.Y.?]: [publisher not identified], 2014.

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Jobe, Amy Beth. Cryo-electron microscopy and single particle reconstructions of the Leishmania major ribosome and of the encephalomyocarditis virus internal ribosome entry site bound to the 40S subunit. [New York, N.Y.?]: [publisher not identified], 2017.

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service), ScienceDirect (Online. Cryo-EM: Analyses, interpretation, and case studies. San Diego, Calif: Academic Press/Elsevier, 2010.

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service), ScienceDirect (Online, ed. Cryo-EM: Sample preparation and data collection. San Diego, Calif: Academic Press/Elsevier, 2010.

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Frank, Joachim. Single-Particle Cryo-Electron Microscopy. World Scientific, 2017. http://dx.doi.org/10.1142/10844.

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Cavalier, Annie. Handbook of Cryo-Preparation Methods for Electron Microscopy. CRC Press, 2008. http://dx.doi.org/10.1201/9781420006735.

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Book chapters on the topic "Cryo-electron microscopy"

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Plitzko, Jürgen, and Wolfgang P. Baumeister. "Cryo-Electron Tomography." In Springer Handbook of Microscopy, 189–228. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-00069-1_4.

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Humbel, Bruno M. "Electron Microscopy: Cryo-Preparation." In Encyclopedia of Biophysics, 596–600. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_616.

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Tsuchiya, Koji. "Cryo-transmission Electron Microscopy." In Measurement Techniques and Practices of Colloid and Interface Phenomena, 93–99. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-5931-6_14.

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Castón, José R. "Conventional Electron Microscopy, Cryo-Electron Microscopy and Cryo-Electron Tomography of Viruses." In Subcellular Biochemistry, 79–115. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-6552-8_3.

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Pilsl, Michael, and Christoph Engel. "Structural Studies of Eukaryotic RNA Polymerase I Using Cryo-Electron Microscopy." In Ribosome Biogenesis, 71–80. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_5.

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AbstractTechnical advances have pushed the resolution limit of single-particle cryo-electron microscopy (cryo-EM) throughout the past decade and made the technique accessible to a wide range of samples. Among them, multisubunit DNA-dependent RNA polymerases (Pols) are a prominent example. This review aims at briefly summarizing the architecture and structural adaptations of Pol I, highlighting the importance of cryo-electron microscopy in determining the structures of transcription complexes.

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Luque, Daniel, and José R. Castón. "Cryo-Electron Microscopy and Cryo-Electron Tomography of Viruses." In Physical Virology, 283–306. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-36815-8_12.

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Zheng, Shawn, Axel Brilot, Yifan Cheng, and David A. Agard. "Beam-Induced Motion Mechanism and Correction for Improved Cryo-Electron Microscopy and Cryo-Electron Tomography." In Cryo-Electron Tomography, 293–314. Cham: Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-51171-4_10.

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Dubochet, J., J. Bednar, P. Furrer, and A. Stasiak. "Cryo-Electron Microscopy of DNA." In Nucleic Acids and Molecular Biology, 41–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-78666-2_3.

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Frederik, P. M., M. C. A. Stuart, P. H. H. Bomans, and D. D. Lasic. "Cryo-Electron Microscopy of Liposomes." In Handbook of Nonmedical Applications of Liposomes, 309–22. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9780429291449-16.

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Bhakta, Sayan, and Marin van Heel. "Single-Particle Cryo-EM." In Cryo-Electron Microscopy in Structural Biology, 87–109. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003326106-8.

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Conference papers on the topic "Cryo-electron microscopy"

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Hye Hyun, Ji, Yanchao Dai, In Chang Choi, and Christopher H. Kang. "The Impact of TEM Analysis Temperature on Photoresist Profiles Using Cryo-FIB and Cryo-TEM." In ISTFA 2024, 221–26. ASM International, 2024. http://dx.doi.org/10.31399/asm.cp.istfa2024p0221.

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Abstract Photoresist (PR) profiles tend to have deformation and shrinkage with typical transmission electron microscopy (TEM) analysis method using a focused ion beam scanning electron microscope (FIB-SEM) and TEM. The elevated temperatures during sample preparation and TEM analysis are believed to contribute to these issues. This study evaluates the effectiveness of cryogenic workflow in mitigating PR profile shrinkage by employing cryo-focused ion beam (Cryo-FIB) and cryo-transmission electron microscopy (Cryo-TEM). Comparative experiments were conducted at room temperature and cryogenic conditions, demonstrating that full cryogenic workflow reduces the shrinkage of PR, bottom anti-reflective coating (BARC), and line critical dimension (CD). Our findings indicate that both the sample preparation and analysis temperatures influence PR profiles. This study highlights how the full cryogenic workflow significantly minimizes shrinkage, providing more accurate PR profile measurements.

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Zhang, Pengcheng, and Fei Zhou. "A novel particle picking approach for cryo-electron microscopy images." In International Conference on Cloud Computing, Performance Computing, and Deep Learning, edited by Wanyang Dai and Xiangjie Kong, 8. SPIE, 2024. http://dx.doi.org/10.1117/12.3050643.

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SINGER, AMIT. "MATHEMATICS FOR CRYO-ELECTRON MICROSCOPY." In International Congress of Mathematicians 2018. WORLD SCIENTIFIC, 2019. http://dx.doi.org/10.1142/9789813272880_0209.

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Wang, Peng. "Cryo-electron Ptychographical Phase Imaging for Biological Materials." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.365.

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Wang, Peng. "Cryo-electron Ptychographical Phase Imaging for Biological Materials." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.381.

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Bhamre, Tejal, Teng Zhang, and Amit Singer. "Orthogonal matrix retrieval in cryo-electron microscopy." In 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015). IEEE, 2015. http://dx.doi.org/10.1109/isbi.2015.7164051.

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von Ruhlnd, Christopher. "Cryo-free processing for biological light and electron microscopy." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.794.

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"Versatile Cryo-FIB Lamella Lift-out for Cryo-electron Tomography and Material Analysis." In Microscience Microscopy Congress 2023 incorporating EMAG 2023. Royal Microscopical Society, 2023. http://dx.doi.org/10.22443/rms.mmc2023.273.

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"A cryo electron microscopy facility for materials research." In Microscience Microscopy Congress 2023 incorporating EMAG 2023. Royal Microscopical Society, 2023. http://dx.doi.org/10.22443/rms.mmc2023.433.

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Müller, Heiko. "On the benefit of aberration correction in cryo electron microscopy." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.530.

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Reports on the topic "Cryo-electron microscopy"

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Kim, Doo Nam, Andrew August, Henry Kvinge, and James Evans. Structures via Reasoning - Applying AI to Cryo Electron Microscopy to Reveal Structural Variability. Office of Scientific and Technical Information (OSTI), January 2022. http://dx.doi.org/10.2172/1989048.

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Powell, Samantha, Mowei Zhou, James Evans, Grant Johnson, and Ljiljana Pasa-Tolic. Developing High-Flux Ion Soft Landing with Mass-Selection for Improved Cryo-Electron Microscopy. Office of Scientific and Technical Information (OSTI), September 2022. http://dx.doi.org/10.2172/1984695.

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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.

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Techmer, K. S., T. Heinrichs, and W. F. Kuhs. Cryo-electron microscopic studies of structures and composition of Mallik gas-hydrate-bearing samples. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 2005. http://dx.doi.org/10.4095/220810.

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