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cryo electron tomography

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https://www.readbyqxmd.com/read/29149017/the-ms6-mycolyl-arabinogalactan-esterase-lysb-is-essential-for-an-efficient-mycobacteriophage-induced-lysis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28915442/electron-cryo-tomography-captures-macromolecular-complexes-in-native-environments
#12
REVIEW
Lindsay A Baker, Michael Grange, Kay Grünewald
Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses frozen-hydrated samples, without chemical modification, to determine the structure of macromolecular complexes in their native environment. Recent developments in electron microscopes and associated technologies have greatly expanded our ability to visualize cellular features and determine the structures of macromolecular complexes in situ...
September 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28890085/in-situ-architecture-and-cellular-interactions-of-polyq-inclusions
#13
Felix J B Bäuerlein, Itika Saha, Archana Mishra, Maria Kalemanov, Antonio Martínez-Sánchez, Rüdiger Klein, Irina Dudanova, Mark S Hipp, F Ulrich Hartl, Wolfgang Baumeister, Rubén Fernández-Busnadiego
Expression of many disease-related aggregation-prone proteins results in cytotoxicity and the formation of large intracellular inclusion bodies. To gain insight into the role of inclusions in pathology and the in situ structure of protein aggregates inside cells, we employ advanced cryo-electron tomography methods to analyze the structure of inclusions formed by polyglutamine (polyQ)-expanded huntingtin exon 1 within their intact cellular context. In primary mouse neurons and immortalized human cells, polyQ inclusions consist of amyloid-like fibrils that interact with cellular endomembranes, particularly of the endoplasmic reticulum (ER)...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28883390/prophage-triggered-membrane-vesicle-formation-through-peptidoglycan-damage-in-bacillus-subtilis
#14
Masanori Toyofuku, Gerardo Cárcamo-Oyarce, Tatsuya Yamamoto, Fabian Eisenstein, Chien-Chi Hsiao, Masaharu Kurosawa, Karl Gademann, Martin Pilhofer, Nobuhiko Nomura, Leo Eberl
Bacteria release membrane vesicles (MVs) that play important roles in various biological processes. However, the mechanisms of MV formation in Gram-positive bacteria are unclear, as these cells possess a single cytoplasmic membrane that is surrounded by a thick cell wall. Here we use live cell imaging and electron cryo-tomography to describe a mechanism for MV formation in Bacillus subtilis. We show that the expression of a prophage-encoded endolysin in a sub-population of cells generates holes in the peptidoglycan cell wall...
September 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28881141/elongated-plant-virus-based-nanoparticles-for-enhanced-delivery-of-thrombolytic-therapies
#15
Andrzej S Pitek, Yunmei Wang, Sahil Gulati, Huiyun Gao, Phoebe L Stewart, Daniel I Simon, Nicole F Steinmetz
Thrombotic cardiovascular disease, including acute myocardial infarction, ischemic stroke, and venous thromboembolic disease, is the leading cause of morbidity and mortality worldwide. While reperfusion therapy with thrombolytic agents reduces mortality from acute myocardial infarction and disability from stroke, thrombolysis is generally less effective than mechanical reperfusion and is associated with fatal intracerebral hemorrhage in up to 2-5% of patients. To address these limitations, we propose the tobacco mosaic virus (TMV)-based platform technology for targeted delivery of thrombolytic therapies...
November 6, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28872144/volume-segmentation-and-analysis-of-biological-materials-using-survos-super-region-volume-segmentation-workbench
#16
Michele C Darrow, Imanol Luengo, Mark Basham, Matthew C Spink, Sarah Irvine, Andrew P French, Alun W Ashton, Elizabeth M H Duke
Segmentation is the process of isolating specific regions or objects within an imaged volume, so that further study can be undertaken on these areas of interest. When considering the analysis of complex biological systems, the segmentation of three-dimensional image data is a time consuming and labor intensive step. With the increased availability of many imaging modalities and with automated data collection schemes, this poses an increased challenge for the modern experimental biologist to move from data to knowledge...
August 23, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28861820/semiautomatic-segmentation-of-plant-golgi-stacks-in-electron-tomograms-using-3dmod
#17
Keith Ka Ki Mai, Byung-Ho Kang
Electron tomography is a powerful tool for visualizing subcellular organelles. With the advances in cryo-fixation techniques, it is now possible to reconstruct complex structures in cells preserved close to their native states in three-dimension (3D) using electron tomography. In order to better visualize these objects, 3D models are made from outlines of organelles in individual tomographic slices, which can be used to display morphological features and quantify structural parameters. While outlines of simple organelles can be drawn by hand fairly quickly, it is possible to accelerate 3D modeling of more complex organelles by means of semiautomatic segmentation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28830949/the-fusion-loops-of-the-initial-prefusion-conformation-of-herpes-simplex-virus-1-fusion-protein-point-toward-the-membrane
#18
Juan Fontana, Doina Atanasiu, Wan Ting Saw, John R Gallagher, Reagan G Cox, J Charles Whitbeck, Lauren M Brown, Roselyn J Eisenberg, Gary H Cohen
All enveloped viruses, including herpesviruses, must fuse their envelope with the host membrane to deliver their genomes into target cells, making this essential step subject to interference by antibodies and drugs. Viral fusion is mediated by a viral surface protein that transits from an initial prefusion conformation to a final postfusion conformation. Strikingly, the prefusion conformation of the herpesvirus fusion protein, gB, is poorly understood. Herpes simplex virus (HSV), a model system for herpesviruses, causes diseases ranging from mild skin lesions to serious encephalitis and neonatal infections...
August 22, 2017: MBio
https://www.readbyqxmd.com/read/28827470/visualization-of-cytosolic-ribosomes-on-the-surface-of-mitochondria-by-electron-cryo-tomography
#19
Vicki Am Gold, Piotr Chroscicki, Piotr Bragoszewski, Agnieszka Chacinska
We employed electron cryo-tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation-arrested ribosomes reveal the clustered organization of the TOM complex, corroborating earlier reports of localized translation. Ribosomes are shown to interact specifically with the TOM complex, and nascent chain binding is crucial for ribosome recruitment and stabilization. Ribosomes are bound to the membrane in discrete clusters, often in the vicinity of the crista junctions. This interaction highlights how protein synthesis may be coupled with transport...
October 2017: EMBO Reports
https://www.readbyqxmd.com/read/28811642/octahedron-iron-oxide-nanocrystals-prohibited-clostridium-difficile-spore-germination-and-attenuated-local-and-systemic-inflammation
#20
Wei-Ting Lee, Ya-Na Wu, Yi-Hsuan Chen, Shang-Rung Wu, Tsai-Miao Shih, Tsung-Ju Li, Li-Xing Yang, Chen-Sheng Yeh, Pei-Jane Tsai, Dar-Bin Shieh
Clinical management of Clostridium difficile infection is still far from satisfactory as bacterial spores are resistant to many chemical agents and physical treatments. Certain types of nanoparticles have been demonstrated to exhibit anti-microbial efficacy even in multi-drug resistance bacteria. However, most of these studies failed to show biocompatibility to the mammalian host cells and no study has revealed in vivo efficacy in C. difficile infection animal models. The spores treated with 500 µg/mL Fe3-δO4 nanoparticles for 20 minutes, 64% of the spores were inhibited from transforming into vegetative cells, which was close to the results of the sodium hypochlorite-treated positive control...
August 15, 2017: Scientific Reports
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