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Cryo electron microscopy

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https://www.readbyqxmd.com/read/28213018/pathogen-biofilm-formation-on-cantaloupe-surface-and-its-impact-on-the-antibacterial-effect-of-lauroyl-arginate-ethyl
#1
Yezhi Fu, Amanda J Deering, Arun K Bhunia, Yuan Yao
Pathogen biofilm at fruit surface may pose a particular risk to food safety. In this study, the biofilms of Listeria monocytogenes V7 and Salmonella enterica serovar Typhimurium ATCC 13311 on cantaloupe fruit surface were visualized, and the resistance of biofilms against lauroyl arginate ethyl (LAE, an antibacterial compound) was evaluated. Each bacterium was inoculated on isolated cantaloupe rind surfaces at 10(5)-10(6) CFU/cm(2) and after incubation for 2, 12, 24, and 48 h, the surfaces were imaged using cryo-scanning electron microscopy (Cryo-SEM)...
June 2017: Food Microbiology
https://www.readbyqxmd.com/read/28198180/engineering-recombinant-virus-like-nanoparticles-from-plants-for-cellular-delivery
#2
Lou Brillault, Philippe V Jutras, Noor Dashti, Eva C Thuenemann, Garry Morgan, George P Lomonossoff, Michael J Landsberg, Frank Sainsbury
Understanding capsid assembly following recombinant expression of viral structural proteins is critical to the design and modification of virus-like nanoparticles for biomedical and nanotechnology applications. Here, we use plant-based transient expression of the Bluetongue virus (BTV) structural proteins, VP3 and VP7, to obtain high yields of empty and green fluorescent protein (GFP)-encapsidating core-like particles (CLPs) from leaves. Single-particle cryo-electron microscopy of both types of particles revealed considerable differences in CLP structure compared to the crystal structure of infection-derived CLPs; in contrast, the two recombinant CLPs have an identical external structure...
February 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/28195421/protein-c-recognition-by-ion-coordinated-imprinted-monolithic-cryogels
#3
Binnaz Demirci, Nilay Bereli, Sevgi Aslıyüce, Gözde Baydemir, Adil Denizli
The protein C imprinted monolithic cryogel was synthesized using 2-hydroxyethyl methacrylate by redox cryo-polymerization method. The prepared monolithic cryogel was characterized by Fourier transform infrared spectroscopy, swelling test, surface area measurements and scanning electron microscopy. The non-imprinted cryogel was prepared as well for control. Adsorption of protein C from aqueous solutions was investigated in a continuous mode and several parameters affecting adsorption performance were optimized...
February 14, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28191458/structural-study-of-heterogeneous-biological-samples-by-cryoelectron-microscopy-and-image-processing
#4
REVIEW
H E White, A Ignatiou, D K Clare, E V Orlova
In living organisms, biological macromolecules are intrinsically flexible and naturally exist in multiple conformations. Modern electron microscopy, especially at liquid nitrogen temperatures (cryo-EM), is able to visualise biocomplexes in nearly native conditions and in multiple conformational states. The advances made during the last decade in electronic technology and software development have led to the revelation of structural variations in complexes and also improved the resolution of EM structures. Nowadays, structural studies based on single particle analysis (SPA) suggests several approaches for the separation of different conformational states and therefore disclosure of the mechanisms for functioning of complexes...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28188547/structurally-conserved-channels-in-cyanobacterial-and-plant-photosystem-ii
#5
Naoki Sakashita, Hiroshi C Watanabe, Takuya Ikeda, Hiroshi Ishikita
In the cyanobacterial photosystem II (PSII), the O4-water chain in the D1 and CP43 proteins, a chain of water molecules that are directly H-bonded to O4 of the Mn4Ca cluster, is linked with a channel that connects the protein bulk surface along with a membrane-extrinsic protein subunit, PsbU (O4-PsbU channel). The cyanobacterial PSII structure also shows that the O1 site of the Mn4Ca cluster has a chain of H-bonded water molecules, which is linked with the channel that proceeds toward the bulk surface via PsbU and PsbV (O1-PsbU/V channel)...
February 10, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28180306/the-impact-of-recent-improvements-in-cryo-electron-microscopy-technology-on-the-understanding-of-bacterial-ribosome-assembly
#6
Aida Razi, Robert A Britton, Joaquin Ortega
No abstract text is available yet for this article.
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28179369/nmd3-is-a-structural-mimic-of-eif5a-and-activates-the-cpgtpase-lsg1-during-60s-ribosome-biogenesis
#7
Andrey G Malyutin, Sharmishtha Musalgaonkar, Stephanie Patchett, Joachim Frank, Arlen W Johnson
During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position...
February 8, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28177313/strategies-for-carbohydrate-model-building-refinement-and-validation
#8
Jon Agirre
Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28164115/modeling-beta-traces-for-beta-barrels-from-cryo-em-density-maps
#9
Dong Si, Jing He
Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5-8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28159514/self-assembling-complexes-between-binary-mixtures-of-lipids-with-different-linkers-and-nucleic-acids-promote-universal-mrna-dna-and-sirna-delivery
#10
Thibault Colombani, Pauline Peuziat, Laurence Dallet, Thomas Haudebourg, Mathieu Mével, Mathieu Berchel, Olivier Lambert, Damien Habrant, Bruno Pitard
Protein expression and RNA interference require efficient delivery of DNA or mRNA and small double stranded RNA into cells, respectively. Although cationic lipids are the most commonly used synthetic delivery vectors, a clear need still exists for a better delivery of various types of nucleic acids molecules to improve their biological activity. To optimize the transfection efficiency, a molecular approach consisting in modifying the chemical structure of a given cationic lipid is usually performed, but an alternative strategy could rely on modulating the supramolecular assembly of lipidic lamellar phases sandwiching the nucleic acids molecules...
February 1, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28154417/a-global-approach-for-quantitative-super-resolution-and-electron-microscopy-on-cryo-and-epoxy-sections-using-self-labeling-protein-tags
#11
Andreas Müller, Martin Neukam, Anna Ivanova, Anke Sönmez, Carla Münster, Susanne Kretschmar, Yannis Kalaidzidis, Thomas Kurth, Jean-Marc Verbavatz, Michele Solimena
Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28151688/structural-insights-into-a-hemoglobin-albumin-cluster-in-aqueous-medium
#12
Ryuichi Shinohara, Taiga Yamada, Boris Schade, Christoph Böttcher, Takaaki Sato, Natsuhiko Sugimura, Toshimichi Shibue, Teruyuki Komatsu
A hemoglobin (Hb) wrapped covalently by three human serum albumins (HSAs) is a triangular protein cluster designed as an artificial O2-carrier and red blood cell substitute. We report the structural insights into this Hb-HSA3 cluster in aqueous medium revealed by 3D reconstruction based on cryogenic transmission electron microscopy (cryo-TEM) data and small-angle X-ray scattering (SAXS) measurements. Cryo-TEM observations showed individual particles with approximately 15 nm diameter in the vitrified ice layer...
February 6, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28138066/the-translation-elongation-cycle-capturing-multiple-states-by-cryo-electron-microscopy
#13
REVIEW
Joachim Frank
During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28138065/dynamics-of-ires-mediated-translation
#14
REVIEW
Alex G Johnson, Rosslyn Grosely, Alexey N Petrov, Joseph D Puglisi
Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of cap-binding and scanning...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28135617/translocation-of-133-cs-administered-to-cryptomeria-japonica-wood
#15
Dan Aoki, Ryutaro Asai, Rie Tomioka, Yasuyuki Matsushita, Hiroyuki Asakura, Masao Tabuchi, Kazuhiko Fukushima
To reveal the in planta behaviour of caesium (Cs), the stable isotope (133)Cs was administered into 3-year-old Cryptomeria japonica seedlings by the application of (133)CsCl aqueous solution to the bark surface. The administered (133)Cs was quantified by ICP-MS measurements, which showed transportation of (133)Cs in an ascending direction in the stem. Distribution of (133)Cs was visualized using freeze-fixed C. japonica woody stem samples and cryo-time-of-flight secondary ion mass spectrometry/scanning electron microscopy (cryo-TOF-SIMS/SEM) analysis...
January 27, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28132504/gelatin-based-nanocomplex-stabilized-pickering-emulsions-regulating-droplet-size-and-wettability-through-assembly-with-glucomannan
#16
Weiping Jin, Jieyu Zhu, Yike Jiang, Ping Shao, Bin Li, Qingrong Huang
Particle size and surface wettability play leading roles in the distribution of particles on the oil-water interface and the stability of emulsions. This work utilized nanocomplexes assembled from gelatin and tannic acid to stabilize Pickering emulsions. The sizes and surface wettability of particles were further regulated by using a polysaccharide. The sizes of nanocomplexes ranged from 205.8 to 422.2 nm and increased with the addition of polysaccharide. Their contact angles decreased from 84.1° to 59.3°, revealing their hydrophilic nature...
February 10, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28128560/mixing-block-copolymers-with-phospholipids-at-the-nanoscale-from-hybrid-polymer-lipid-wormlike-micelles-to-vesicles-presenting-lipid-nanodomains
#17
T P Tuyen Dao, A Brûlet, F Fernandes, M Er-Rafik, K Ferji, R Schweins, J-P Chapel, A Fedorov, M Schmutz, M Prieto, O Sandre, J-F Le Meins
Hybrids, i.e., intimately mixed polymer/phospholipid vesicles, can potentially marry in a single membrane the best characteristics of the two separate components. The ability of amphiphilic copolymers and phospholipids to self-assemble into hybrid membranes has been studied until now on the submicrometer scale using optical microscopy on giant hybrid unilamellar vesicles (GHUVs), but limited information is available on large hybrid unilamellar vesicles (LHUVs). In this work, copolymers based on poly(dimethylsiloxane) and poly(ethylene oxide) with different molar masses and architectures (graft, triblock) were associated with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)...
February 8, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28115689/structural-insights-into-the-functional-cycle-of-the-atpase-module-of-the-26s-proteasome
#18
Marc Wehmer, Till Rudack, Florian Beck, Antje Aufderheide, Günter Pfeifer, Jürgen M Plitzko, Friedrich Förster, Klaus Schulten, Wolfgang Baumeister, Eri Sakata
In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA(+) ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4)...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28115258/cryo-em-analysis-of-a-domain-antibody-bound-rotary-atpase-complex
#19
Roberta B Davies, Callum Smits, Andrew Sw Wong, Daniela Stock, Mary Christie, Sara Sandin, Alastair G Stewart
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7 Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins...
January 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28115257/higher-order-structures-in-purine-and-pyrimidine-metabolism
#20
REVIEW
Iva Chitrakar, Deborah M Kim-Holzapfel, Weijie Zhou, Jarrod B French
The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation in cells. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially...
January 20, 2017: Journal of Structural Biology
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