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Single particle electron microscopy

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https://www.readbyqxmd.com/read/29149555/mapping-the-reactions-in-a-single-zero-valent-iron-nanoparticle
#1
Lan Ling, Xiao-Yue Huang, Meirong Li, Wei-Xian Zhang
Nanoscale zero-valent iron (nZVI) posseses unique functionalities for metal-metalloid removal and sequestration. So far, direct evidence on the heavy metal-iron reactions in the solid phase is still limited due to low concentration of heavy metals and small size of nanoparticles. In this work, angstrom-resolution spectral mappings on the reactions of nZVI with chromate, arsenate, nickel, silver, cesium, and zinc ions are presented. This work was achieved with spherical aberration-corrected scanning transmission electron microscopy integrated with high-sensitivity X-ray energy-dispersive spectroscopy scanning transmission electron microscopy (XEDS-STEM)...
November 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29138260/chloroplast-division-protein-arc3-acts-on-ftsz2-by-preventing-filament-bundling-and-enhancing-gtpase-activity
#2
Rahamthulla S Shaik, Min Woo Sung, Stanislav Vitha, Andreas Holzenburg
Chloroplasts evolved from cyanobacterial endosymbiotic ancestors and their division is a complex process initiated by assembly of cytoskeletal FtsZ proteins into a ring structure at the division site (Z-ring). The cyanobacterial Z-ring positioning system (MinCDE proteins) is also conserved in chloroplasts except that MinC was lost and replaced by the eukaryotic ARC3. Both MinC and ARC3 act as negative regulators of FtsZ assembly, but ARC3 bears little sequence similarity with MinC. Here, light scattering assays, co-sedimentation, GTPase assay and transmission electron microscopy (TEM) in conjunction with single particle analysis have been used to elucidate the structure of ARC3 and its effect on its main target in chloroplast division: FtsZ2...
November 14, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29132296/a-fragment-based-method-for-modeling-of-protein-segments-into-cryo-em-density-maps
#3
Jochen Ismer, Alexander S Rose, Johanna K S Tiemann, Peter W Hildebrand
BACKGROUND: Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. RESULTS: Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit)...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29129967/single-particle-analyzer-of-mass-a-charge-detection-mass-spectrometer-with-a-multi-detector-electrostatic-ion-trap
#4
Andrew G Elliott, Samuel I Merenbloom, Satrajit Chakrabarty, Evan R Williams
A new charge detection mass spectrometer that combines array detection and electrostatic ion trapping to repeatedly measure the masses of single ions is described. This instrument has four detector tubes inside an electrostatic ion trap with conical electrodes (cone trap) to provide multiple measurements of an ion on each pass through the trap resulting in a signal gain over a conventional trap with a single detection tube. Simulations of a cone trap and a dual ion mirror trap design indicate that more passes through the trap per unit time are possible with the latter...
March 2017: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29126032/human-myeloma-igg4-reveals-relatively-rigid-asymmetric-y-like-structure-with-different-conformational-stability-of-ch2-domains
#5
Vladimir M Tischenko, Zav'yalov Vladimir P, Sergey N Ryazantsev
Human IgG4 (hIgG4) has weak pro-inflammatory activity. The structural basis for this is still unclear. Here a 3D model of myeloma hIgG4 was created at ∼3nm resolution using electron microscopy (EM) with negative staining and single-particle 3D reconstruction. The hIgG4 model reveals relatively rigid asymmetric Y-like structure. The model shows that one Fab subunit is closer to the upper portion of the Fc subunit (CH2 domain) than the other Fab. This is in agreement with X-ray crystallography and X-ray/neutron scattering, recently published by others...
November 7, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29123676/merging-single-shot-xfel-diffraction-data-from-inorganic-nanoparticles-a-new-approach-to-size-and-orientation-determination
#6
Xuanxuan Li, John C H Spence, Brenda G Hogue, Haiguang Liu
X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29119721/integrated-transmission-electron-and-single-molecule-fluorescence-microscopy-correlates-reactivity-with-ultrastructure-in-a-single-catalyst-particle
#7
Bert Marc Weckhuysen, Hans Gerritsen, Sajjad Mohammadian, Sam Kalirai, Pieter Bruijnincx, Florian Meirer, Eelco Vogt, Zoran Ristanovic, Frank Hendriks
Establishing structure-activity relationships in complex, hierarchically structured nanomaterials, such as fluid catalytic cracking (FCC) catalysts, requires characterization with complementary, correlated analysis techniques. An integrated setup has been developed to perform transmission electron microscopy (TEM) and single molecule fluorescence (SMF) microscopy on such nanostructured samples. Correlated structure-reactivity information was obtained for 100 nm thin, microtomed sections of a single FCC catalyst particle using this novel SMF-TEM high-resolution combination...
November 9, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29118099/the-potential-of-cryo-electron-microscopy-for-structure-based-drug-design
#8
REVIEW
Andreas Boland, Leifu Chang, David Barford
Structure-based drug design plays a central role in therapeutic development. Until recently, protein crystallography and NMR have dominated experimental approaches to obtain structural information of biological molecules. However, in recent years rapid technical developments in single particle cryo-electron microscopy (cryo-EM) have enabled the determination to near-atomic resolution of macromolecules ranging from large multi-subunit molecular machines to proteins as small as 64 kDa. These advances have revolutionized structural biology by hugely expanding both the range of macromolecules whose structures can be determined, and by providing a description of macromolecular dynamics...
November 8, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/29118098/x-ray-free-electron-laser-opportunities-for-drug-discovery
#9
REVIEW
Robert K Y Cheng, Rafael Abela, Michael Hennig
Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization...
November 8, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/29114027/an-alphavirus-e2-membrane-proximal-domain-promotes-envelope-protein-lateral-interactions-and-virus-budding
#10
Emily A Byrd, Margaret Kielian
Alphaviruses are members of a group of small enveloped RNA viruses that includes important human pathogens such as Chikungunya virus and the equine encephalitis viruses. The virus membrane is covered by a lattice composed of 80 spikes, each a trimer of heterodimers of the E2 and E1 transmembrane proteins. During virus endocytic entry, the E1 glycoprotein mediates the low-pH-dependent fusion of the virus membrane with the endosome membrane, thus initiating virus infection. While much is known about E1 structural rearrangements during membrane fusion, it is unclear how the E1/E2 dimer dissociates, a step required for the fusion reaction...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29109807/ultrasonic-spray-pyrolysis-deposited-copper-sulphide-thin-films-for-solar-cell-applications
#11
Y E Firat, H Yildirim, K Erturk, A Peksoz
Polycrystalline copper sulphide (Cu x S) thin films were grown by ultrasonic spray pyrolysis method using aqueous solutions of copper chloride and thiourea without any complexing agent at various substrate temperatures of 240, 280, and 320°C. The films were characterized for their structural, optical, and electrical properties by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive analysis of X-rays (EDAX), atomic force microscopy (AFM), contact angle (CA), optical absorption, and current-voltage (I-V) measurements...
2017: Scanning
https://www.readbyqxmd.com/read/29102060/multifunctionalized-mesoporous-silica-as-an-efficient-reversed-phase-anion-exchange-mixed-mode-sorbent-for-solid-phase-extraction-of-four-acidic-nonsteroidal-anti-inflammatory-drugs-in-environmental-water-samples
#12
Yun Li, Chaonan Huang, Jiajia Yang, Junyu Peng, Jing Jin, Huilian Ma, Jiping Chen
A mesoporous silica Santa Barbara Amorphous-15 (SBA-15) has been first functionalized with 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (a silane with three amines) and then reacted with an excess of phenyl glycidyl ether to generate a mixed-mode anion-exchanger containing both anion-exchange (three amines) and reversed-phase (multiple ether-linked phenyls) functionalities in a single branched ligand. The resulting material has been characterized by scanning electron microscopy, transmission electron microscopy, nitrogen adsorption-desorption measurements, Fourier-transform infrared spectroscopy, and elemental analysis...
October 23, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29100109/big-data-in-cryoem-automated-collection-processing-and-accessibility-of-em-data
#13
REVIEW
Philip R Baldwin, Yong Zi Tan, Edward T Eng, William J Rice, Alex J Noble, Carl J Negro, Michael A Cianfrocco, Clinton S Potter, Bridget Carragher
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing...
October 31, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29084163/atomic-resolution-structure-of-the-oncolytic-parvovirus-luiii-by-electron-microscopy-and-3d-image-reconstruction
#14
Nikéa Pittman, Adam Misseldine, Lorena Geilen, Sujata Halder, J Kennon Smith, Justin Kurian, Paul Chipman, Mandy Janssen, Robert Mckenna, Timothy S Baker, Anthony D'Abramo, Susan Cotmore, Peter Tattersall, Mavis Agbandje-McKenna
LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3...
October 30, 2017: Viruses
https://www.readbyqxmd.com/read/29081898/mahalanobis-distance-for-class-averaging-of-cryo-em-images
#15
Tejal Bhamre, Zhizhen Zhao, Amit Singer
Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing directions. One of the main challenges in cryo-EM is the typically low signal to noise ratio (SNR) of the acquired images. 2D classification of images, followed by class averaging, improves the SNR of the resulting averages, and is used for selecting particles from micrographs and for inspecting the particle images...
April 2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
https://www.readbyqxmd.com/read/29080674/rapid-increase-of-near-atomic-resolution-virus-capsid-structures-determined-by-cryo-electron-microscopy
#16
Phuong T Ho, Vijay S Reddy
The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010...
October 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29076722/size-distribution-of-nanoparticles-in-solution-characterized-by-combining-resonance-light-scattering-correlation-spectroscopy-with-the-maximum-entropy-method
#17
Bocheng Zhang, Heng Liu, Xiangyi Huang, Chaoqing Dong, Jicun Ren
A single-nanoparticle detection method is reported for characterizing the size distribution of noble metal nanoparticles in solution by combining resonance light scattering correlation spectroscopy (RLSCS) with the maximum entropy method (MEM). The principle of RLSCS is based on the autocorrelation analysis of the resonance light scattering (RLS) fluctuations due to Brownian motion of a single nanoparticle in a highly focused detection volume (less than 1.0 fL), which resembles fluorescence correlation spectroscopy (FCS)...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29075413/the-effect-of-photodynamic-therapy-and-polymer-solution-containing-nano-particles-of-ag-zno-on-push-out-bond-strength-of-the-sealers-ah-plus-and-mta-fillapex
#18
Hamidreza Yavari, Negin Ghasemi, Baharak Divband, Yashar Rezaei, Golchin Jabbari, Salar Payahoo
BACKGROUND: The aim of this in vitrostudy was to examine and compare the effect of photodynamic therapy and solution containing nano particles Ag/ZnO on adhesion of endodontic sealers to dentinal walls of human root canal. MATERIAL AND METHODS: Ninty single-rooted human teeth were selected and their clinical crown was cut from the cemento-enamel junction zone. Canals were prepared by RaCe rotary system and the smear layer was removed using 17% EDTA and 5.25% NaOCl...
September 2017: Journal of Clinical and Experimental Dentistry
https://www.readbyqxmd.com/read/29075100/biodegradable-rifampicin-releasing-coating-of-surgical-meshes-for-the-prevention-of-bacterial-infections
#19
Jochen Reinbold, Teresa Hierlemann, Lukas Urich, Ann-Kristin Uhde, Ingrid Müller, Tobias Weindl, Ulrich Vogel, Christian Schlensak, Hans Peter Wendel, Stefanie Krajewski
Polypropylene mesh implants are routinely used to repair abdominal wall defects or incisional hernia. However, complications associated with mesh implantation, such as mesh-related infections, can cause serious problems and may require complete surgical removal. Hence, the aim of the present study was the development of a safe and efficient coating to reduce postoperative mesh infections. Biodegradable poly(lactide-co-glycolide acid) microspheres loaded with rifampicin as an antibacterial agent were prepared through single emulsion evaporation method...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/29072451/chemical-imaging-of-nanoscale-interfacial-inhomogeneity-in-lifepo4-composite-electrodes-from-a-cycled-large-format-battery
#20
Jigang Zhou, Jian Wang, Yongfeng Hu, Mi Lu
The nanoscale interfacial inhomogeneity in a cycled large-format LiFePO4 (LFP) composite electrode has been studied by X-ray photoemission electron microscopy at single particle spatial resolution with a probe depth of ∼5 nm. The loss of active lithium in cycled LFP causes the coexsitence of fully delithiated LFP (FePO4) and partially delithiated LFP (Li0.6FePO4 or Li0.8FePO4) as a function of the extent of lithium loss. The distribution of various lithium loss phases along with local agglomeration of LFP and degradation of binder and carbon black are correlatively visualized...
November 2, 2017: ACS Applied Materials & Interfaces
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