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cryo electron tomography

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https://www.readbyqxmd.com/read/29311144/differentiation-and-characterization-of-excitatory-and-inhibitory-synapses-by-cryo-electron-tomography-and-correlative-microscopy
#1
Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z Hong Zhou, Guo-Qiang Bi
As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ three-dimensional organization of synaptic organelles and macromolecules in their native state...
January 8, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29289599/a-convolutional-autoencoder-approach-for-mining-features-in-cellular-electron-cryo-tomograms-and-weakly-supervised-coarse-segmentation
#2
Xiangrui Zeng, Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai, Min Xu
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes...
December 28, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29243866/the-dual-role-of-mamb-in-magnetosome-membrane-assembly-and-magnetite-biomineralization
#3
René Uebe, Noa Keren-Khadmy, Natalie Zeytuni, Emanuel Katzmann, Yotam Navon, Geula Davidov, Ronit Bitton, Jürgen M Plitzko, Dirk Schüler, Raz Zarivach
Magnetospirillum gryphiswaldense MSR-1 synthesizes membrane-enclosed magnetite (Fe3 O4 ) nanoparticles, magnetosomes, for magnetotaxis. Formation of these organelles involves a complex process comprising key steps which are governed by specific magnetosome-associated proteins. MamB, a cation diffusion facilitator (CDF) family member has been implicated in magnetosome-directed iron transport. However, deletion mutagenesis studies revealed that MamB is essential for the formation of magnetosome membrane vesicles, but its precise role remains elusive...
December 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29235477/nucleotide-and-mal3-dependent-changes-in-fission-yeast-microtubules-suggest-a-structural-plasticity-view-of-dynamics
#4
Ottilie von Loeffelholz, Neil A Venables, Douglas Robert Drummond, Miho Katsuki, Robert Cross, Carolyn A Moores
Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29229809/proteasomes-tether-to-two-distinct-sites-at-the-nuclear-pore-complex
#5
Sahradha Albert, Miroslava Schaffer, Florian Beck, Shyamal Mosalaganti, Shoh Asano, Henry F Thomas, Jürgen M Plitzko, Martin Beck, Wolfgang Baumeister, Benjamin D Engel
The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29217280/photosome-membranes-merge-and-organize-tending-towards-rhombohedral-symmetry-when-light-is-emitted
#6
Malika Ouldali, Virginie Maury, Gisèle Nicolas, Jean Lepault
Polynoid worm elytra emit light when mechanically or electrically stimulated. Specialized cells, the photocytes, contain light emitting machineries, the photosomes. Successive stimulations induce light intensity variations and show a coupling within and between photosomes. Here, we describe, using electron tomography of cryo-substituted elytra and freeze-fracturing, the structural transition associated to light emission: undulating tubules come closer, organize and their number forming photosomes increases...
December 4, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29204884/structure-and-assembly-mechanism-of-virus-associated-pyramids
#7
REVIEW
Tessa E F Quax, Bertram Daum
Viruses have developed intricate molecular machines to infect, replicate within and escape from their host cells. Perhaps one of the most intriguing of these mechanisms is the pyramidal egress structure that has evolved in archaeal viruses, such as SIRV2 or STIV1. The structure and mechanism of these virus-associated pyramids (VAPs) has been studied by cryo-electron tomography and complementary biochemical techniques, revealing that VAPs are formed by multiple copies of a virus-encoded 10-kDa protein (PVAP) that integrate into the cell membrane and assemble into hollow, sevenfold symmetric pyramids...
December 4, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29190455/structural-features-of-the-salivary-gland-hypertrophy-virus-of-the-tsetse-fly-revealed-by-cryo-electron-microscopy-and-tomography
#8
Igor Orlov, Robert Drillien, Danièle Spehner, Max Bergoin, Adly M M Abd-Alla, Bruno P Klaholz
Glossina palipides salivary gland hypertrophy virus (GpSGHV) infects tsetse flies, which are vectors for African trypanosomosis. This virus represents a major challenge in insect mass rearing and has hampered the implementation of the sterile insect technique programs in the Member States of the International Atomic Energy Agency. GpSGHV virions consist of long rod-shaped particles over 9000Å in length, but little is known about their detailed structural organization. We show by cryo electron microscopy and cryo electron tomography that the GpSGHV virion has a unique, non-icosahedral helical structure...
November 27, 2017: Virology
https://www.readbyqxmd.com/read/29163452/the-opportunistic-pathogen-vibrio-vulnificus-produces-outer-membrane-vesicles-in-a-spatially-distinct-manner-related-to-capsular-polysaccharide
#9
Cheri M Hampton, Ricardo C Guerrero-Ferreira, Rachel E Storms, Jeannette V Taylor, Hong Yi, Paul A Gulig, Elizabeth R Wright
Vibrio vulnificus, a bacterial species that inhabits brackish waters, is an opportunistic pathogen of humans. V. vulnificus infections can cause acute gastroenteritis, invasive septicemia, tissue necrosis, and potentially death. Virulence factors associated with V. vulnificus include the capsular polysaccharide (CPS), lipopolysaccharide, flagellum, pili, and outer membrane vesicles (OMVs). The aims of this study were to characterize the morphology of V. vulnificus cells and the formation and arrangement of OMVs using cryo-electron microscopy (cryo-EM)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29149017/the-ms6-mycolyl-arabinogalactan-esterase-lysb-is-essential-for-an-efficient-mycobacteriophage-induced-lysis
#10
Adriano M Gigante, Cheri M Hampton, Rebecca S Dillard, Filipa Gil, Maria João Catalão, José Moniz-Pereira, Elizabeth R Wright, Madalena Pimentel
All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29148969/the-structure-of-the-copi-coat-determined-within-the-cell
#11
Yury S Bykov, Miroslava Schaffer, Svetlana O Dodonova, Sahradha Albert, Jürgen M Plitzko, Wolfgang Baumeister, Benjamin D Engel, John Ag Briggs
COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with in vitro reconstitution systems using purified components. In a previous paper (Dodonova et al., 2017), we determined a complete structural model of the in vitro reconstituted COPI coat. Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells...
November 17, 2017: ELife
https://www.readbyqxmd.com/read/29144446/structure-and-assembly-of-the-ebola-virus-nucleocapsid
#12
William Wan, Larissa Kolesnikova, Mairi Clarke, Alexander Koehler, Takeshi Noda, Stephan Becker, John A G Briggs
Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29113849/marker-free-method-for-accurate-alignment-between-correlated-light-cryo-light-and-electron-cryo-microscopy-data-using-sample-support-features
#13
Karen L Anderson, Christopher Page, Mark F Swift, Dorit Hanein, Niels Volkmann
Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film...
November 4, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29106371/3d-visualization-of-mitochondrial-solid-phase-calcium-stores-in-whole-cells
#14
Sharon Grayer Wolf, Yael Mutsafi, Tali Dadosh, Tal Ilani, Zipora Lansky, Ben Horowitz, Sarah Rubin, Michael Elbaum, Deborah Fass
The entry of calcium into mitochondria is central to metabolism, inter-organelle communication, and cell life/death decisions. Long-sought transporters involved in mitochondrial calcium influx and efflux have recently been identified. To obtain a unified picture of mitochondrial calcium utilization, a parallel advance in understanding the forms and quantities of mitochondrial calcium stores is needed. We present here the direct 3D visualization of mitochondrial calcium in intact mammalian cells using cryo-scanning transmission electron tomography (CSTET)...
November 6, 2017: ELife
https://www.readbyqxmd.com/read/29038566/structural-variability-and-complexity-of-the-giant-pithovirus-sibericum-particle-revealed-by-high-voltage-electron-cryo-tomography-and-energy-filtered-electron-cryo-microscopy
#15
Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe R N C Maia, Hemanth K N Reddy, Chantal Abergel, Jean-Michel Claverie, Janos Hajdu, Martin Svenda, Kazuyoshi Murata
The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28991265/a-structural-model-for-microtubule-minus-end-recognition-and-protection-by-camsap-proteins
#16
Joseph Atherton, Kai Jiang, Marcel M Stangier, Yanzhang Luo, Shasha Hua, Klaartje Houben, Jolien J E van Hooff, Agnel-Praveen Joseph, Guido Scarabelli, Barry J Grant, Anthony J Roberts, Maya Topf, Michel O Steinmetz, Marc Baldus, Carolyn A Moores, Anna Akhmanova
CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface...
November 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28973937/detection-of-isolated-protein-bound-metal-ions-by-single-particle-cryo-stem
#17
Nadav Elad, Giuliano Bellapadrona, Lothar Houben, Irit Sagi, Michael Elbaum
Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28945406/a-multiscale-description-of-biomolecular-active-matter-the-chemistry-underlying-many-life-processes
#18
Gregory A Voth
This Commentary will describe the goal of developing and implementing novel, powerful, and integrated multiscale computer simulation methodology capable of accessing the large length and long time scales inherent in the behavior of biomolecular, multiprotein "active matter" complexes within the context of cellular biology. Examples include those involved in the actin-based cytoskeleton and its mechanochemistry. The primary objective is to connect detailed molecular and chemical properties with the key mesoscopic features manifest at the scales of cellular biology through a transformative theoretical and computer simulation approach, based on real physical and chemical interactions...
March 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28938121/huntingtin-fibrils-poke-membranes
#19
COMMENT
Pedro Guedes-Dias, Erika L F Holzbaur
A hallmark of Huntington's disease is the presence of intracellular aggregates of mutant huntingtin, the pathological significance of which has long been debated. Using cryo-electron tomography, Bauerlein et al. reveal the fibrillary structure of huntingtin aggregates in situ and show that huntingtin fibrils interact with the endoplasmic reticulum, distorting its morphology and dynamics.
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28925789/motile-cilia-defects-in-diseases-other-than-primary-ciliary-dyskinesia-the-contemporary-diagnostic-and-research-role-for-transmission-electron-microscopy
#20
Hannah M Mitchison, Amelia Shoemark
Ultrastructural studies have underpinned the cell biological and clinical investigations of the varied roles of motile cilia in health and disease, with a long history since the 1950s. Recent developments from transmission electron microscopy (TEM; cryo-electron microscopy, electron tomography) have yielded higher resolution and fresh insights into the structure and function of these complex organelles. Microscopy in ciliated organisms, disease models, and in patients with ciliopathy diseases has dramatically expanded our understanding of the ubiquity, multisystem involvement, and importance of cilia in normal human development...
September 19, 2017: Ultrastructural Pathology
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