Read by QxMD icon Read

Structure resolution

Martin Hampl, David Kachlik, Katerina Kikalova, Roxane Riemer, Matej Halaj, Vlastimil Novak, Premysl Stejskal, Miroslav Vaverka, Lumir Hrabalek, David Krahulik, Ondrej Nanka
BACKGROUND: Mastoid emissary vein is especially important from the neurosurgical point of view, because it is located in variable number in the area of the occipitomastoid suture and it can become a source of significant bleeding in surgical approaches through the mastoid process, especially in retrosigmoid craniotomy, which is used for approaches to pathologies localized in the cerebellopontine angle. Ideal imaging method for diagnosis of these neglected structures when planning a surgical approach is high-resolution computed tomography...
May 20, 2018: Acta Neurochirurgica
Joshua Pan, Robin M Meyers, Brittany C Michel, Nazar Mashtalir, Ann E Sizemore, Jonathan N Wells, Seth H Cassel, Francisca Vazquez, Barbara A Weir, William C Hahn, Joseph A Marsh, Aviad Tsherniak, Cigall Kadoch
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex...
May 14, 2018: Cell Systems
Miada F Abdelwahab, Mostafa A Fouad, Mohamed S Kamel, Ferhat Can Özkaya, Rainer Kalscheuer, Werner E G Müller, Wenhan Lin, Zhen Liu, Weaam Ebrahim, Georgios Daletos, Peter Proksch
Chemical investigation of a freshwater sediment-derived fungus, Penicillium sp. (S1a1), led to the isolation of three new tanzawaic acid derivatives, including penitanzchroman (1), tanzawaic acids Y (2) and Z (3), along with six known tanzawaic acid analogues (4-9), three known isochromans (10-12) and two known benzoquinones (13 and 14). The structures of the new compounds were established based on high-resolution mass spectrometry, and detailed analysis of one- and two-dimensional NMR spectroscopy. The relative configuration of the new compounds was assigned on the basis of NMR spectroscopic data including ROESY spectra...
May 17, 2018: Fitoterapia
Xiao-Yue Huang, Lan Ling, Wei-Xian Zhang
Solid phase reactions of Cr(VI) with Fe(0) were investigated with spherical-aberration-corrected scanning transmission electron microscopy (Cs-STEM) integrated with X-ray energy-dispersive spectroscopy (XEDS). Near-atomic resolution elemental mappings of Cr(VI)-Fe(0) reactions were acquired. Experimental results show that rate and extent of Cr(VI) encapsulation are strongly dependent on the initial concentration of Cr(VI) in solution. Low Cr loading in nZVI (<1.0wt%) promotes the electrochemical oxidation and continuous corrosion of nZVI while high Cr loading (>1...
May 2018: Journal of Environmental Sciences (China)
Alex F Rosenthal, James S Griffin, Michael Wagner, Aaron I Packman, Oluwaseyi Balogun, George F Wells
Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging due to imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activity. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid...
May 19, 2018: Biotechnology and Bioengineering
Sergey Artyukhin, Dmitry Fishman, Clément Faugeras, Marek Potemski, Alexandre Revcolevschi, Maxim Mostovoy, Paul H M van Loosdrecht
We study the absorption spectra of the yellow excitons in Cu2 O in high magnetic fields using polarization-resolved optical absorption measurements with a high frequency resolution. We show that the symmetry of the yellow exciton results in unusual selection rules for the optical absorption of polarized light and that the mixing of ortho- and para- excitons in magnetic field is important. The calculation of the energies of the yellow exciton series in strong and weak magnetic field limits suggests that a broad n = 2 line is comprized by two closely overlapping lines, gives a good fit to experimental data and allows to interpret the complex structure of excitonic levels...
May 18, 2018: Scientific Reports
Reimar H Leike, Torsten A Enßlin
Most simulation schemes for partial differential equations (PDEs) focus on minimizing a simple error norm of a discretized version of a field. This paper takes a fundamentally different approach; the discretized field is interpreted as data providing information about a real physical field that is unknown. This information is sought to be conserved by the scheme as the field evolves in time. Such an information theoretic approach to simulation was pursued before by information field dynamics (IFD). In this paper we work out the theory of IFD for nonlinear PDEs in a noiseless Gaussian approximation...
March 2018: Physical Review. E
Matthew Burg, Claire Rosebrough, Lauren M Drouin, Antonette Bennett, Mario Mietzsch, Paul Chipman, Robert McKenna, Duncan Sousa, Mark Potter, Barry Byrne, R Jude Samulski, Mavis Agbandje-McKenna
AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2...
May 15, 2018: Journal of Structural Biology
Xiang Wang, Zeyuan Guan, Zhou Gong, Junjie Yan, Guangsheng Yang, Yao-Guang Liu, Ping Yin
Plant cytoplasmic male sterility (CMS) is an important phenomenon and is widely utilized in hybrid crop breeding. The Wild Abortive CMS (CMS-WA), a well-known CMS type, has been successfully applied in the commercial production of hybrid rice seeds for more than 40 years. The CMS-WA causal gene WA352 encodes a novel transmenbrane protein and the interacts with the mitochondrial copper chaperone COX11, triggering reactive oxygen species production and resulting in male sterility in CMS-WA lines. However, the structure of WA352 is currently unknown, and the structural mechanism whereby WA352 perturbs COX11 function to cause CMS remains largely unknown...
May 15, 2018: Biochemical and Biophysical Research Communications
Jiansen Jiang, Yaqiang Wang, Lukas Sušac, Henry Chan, Ritwika Basu, Z Hong Zhou, Juli Feigon
Telomerase is an RNA-protein complex (RNP) that extends telomeric DNA at the 3' ends of chromosomes using its telomerase reverse transcriptase (TERT) and integral template-containing telomerase RNA (TER). Its activity is a critical determinant of human health, affecting aging, cancer, and stem cell renewal. Lack of atomic models of telomerase, particularly one with DNA bound, has limited our mechanistic understanding of telomeric DNA repeat synthesis. We report the 4.8 Å resolution cryoelectron microscopy structure of active Tetrahymena telomerase bound to telomeric DNA...
May 17, 2018: Cell
Dan Li, Cong Liu
A new solid-state NMR study determines the high-resolution hetero-amyloid structure of the RIPK1-RIPK3 signaling complex that is involved in mediating necroptosis. The structure demonstrates specific formation of hetero-amyloids over homo-amyloids and the structural basis for a functional amyloid to act as a platform to recruit and activate downstream partners in intracellular signaling.
May 17, 2018: Cell
Jagannath Mondal, Navjeet Ahalawat, Subhendu Pandit, Lewis E Kay, Pramodh Vallurupalli
Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive...
May 18, 2018: PLoS Computational Biology
Chunyang Wang, Kui Du, Kepeng Song, Xinglong Ye, Lu Qi, Suyun He, Daiming Tang, Ning Lu, Haijun Jin, Feng Li, Hengqiang Ye
Low-angle grain boundaries generally exist in the form of dislocation arrays, while high-angle grain boundaries (misorientation angle >15°) exist in the form of structural units in bulk metals. Here, through in situ atomic resolution aberration corrected electron microscopy observations, we report size-dependent grain-boundary structures improving both stabilities of electrical conductivity and mechanical properties in sub-10-nm-sized gold crystals. With the diameter of a nanocrystal decreasing below 10 nm, the high-angle grain boundary in the crystal exists as an array of dislocations...
May 4, 2018: Physical Review Letters
Nicholas J Porter, Florence F Wagner, David W Christianson
Among the metal-dependent histone deacetylases, the class IIb isozyme HDAC6 is remarkable because of its role in the regulation of microtubule dynamics in the cytosol. Selective inhibition of HDAC6 results in microtubule hyperacetylation, leading to cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy and the treatment of other disorders. HDAC6 inhibitors generally consist of a Zn2+ -binding group such as a hydroxamate, a linker, and a capping group; the capping group is a critical determinant of isozyme selectivity...
May 18, 2018: Biochemistry
Chengjian Wang, Yu Lu, Jianli Han, Wanjun Jin, Lingmei Li, Ying Zhang, Xuezheng Song, Linjuan Huang, Zhongfu Wang
Most glycoproteins and biological protein samples undergo both O- and N-glycosylation, making characterization of their structures very complicated and time-consuming. Nevertheless, to fully understand the biological functions of glycosylation, both the glycosylation forms need to be analyzed. Herein we report a versatile, convenient one-pot method in which O- and N-glycans are simultaneously released from glycoproteins and chromogenically labelled in situ and thus available for further characterization. In this procedure, glycoproteins are incubated with 1-phenyl-3-methyl-5-pyrazolone (PMP) in aqueous ammonium hydroxide, making O-glycans released from protein backbones by beta-elimination and N-glycans liberated by alkaline hydrolysis...
May 18, 2018: Journal of Proteome Research
Sheikh M F Rabbi, Matthew K Tighe, Richard J Flavel, Brent N Kaiser, Chris N Guppy, Xiaoxian Zhang, Iain M Young
The mechanisms controlling the genesis of rhizosheaths are not well understood, despite their importance in controlling the flux of nutrients and water from soil to root. Here, we examine the development of rhizosheaths from drought-tolerant and drought-sensitive chickpea varieties; focusing on the three-dimensional characterization of the pore volume (> 16 μm voxel spatial resolution) obtained from X-ray microtomography, along with the characterization of mucilage and root hairs, and water sorption. We observe that drought-tolerant plants generate a larger diameter root, and a greater and more porous mass of rhizosheath, which also has a significantly increased water sorptivity, as compared with bulk soil...
May 18, 2018: New Phytologist
Seulgi Noh, Hyosun Choi, Ji Soo Kim, Il-Hwan Kim, Ji Young Mun
There is a global trend of increase in the demand for three-dimensional electron microscopy with high resolution. The ultrastructural change and related functional studies are necessary to investigate biological phenomena. In this study, currently available 3D reconstruction techniques of electron microscopes (serial block-face scanning electron microscopy and focused ion beam-scanning electron microscopy) were used to investigate hyperpigmentary disorders in human skin. In the basal layer of the epidermis in the human skin, there are melanocytes that produce melanin and keratinocytes that act as a barrier against environmental damage...
May 18, 2018: Microscopy Research and Technique
Zhaoye Zhou, Gengyan Zhao, Richard Kijowski, Fang Liu
PURPOSE: To describe and evaluate a new segmentation method using deep convolutional neural network (CNN), 3D fully connected conditional random field (CRF), and 3D simplex deformable modeling to improve the efficiency and accuracy of knee joint tissue segmentation. METHODS: A segmentation pipeline was built by combining a semantic segmentation CNN, 3D fully connected CRF, and 3D simplex deformable modeling. A convolutional encoder-decoder network was designed as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification for 12 different joint structures...
May 17, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Kareem Soliman, Fabian Göttfert, Hendrik Rosewich, Sven Thoms, Jutta Gärtner
Peroxisomes are ubiquitous cell organelles involved in many metabolic and signaling functions. Their assembly requires peroxins, encoded by PEX genes. Mutations in PEX genes are the cause of Zellweger Syndrome spectrum (ZSS), a heterogeneous group of peroxisomal biogenesis disorders (PBD). The size and morphological features of peroxisomes are below the diffraction limit of light, which makes them attractive for super-resolution imaging. We applied Stimulated Emission Depletion (STED) microscopy to study the morphology of human peroxisomes and peroxisomal protein localization in human controls and ZSS patients...
May 17, 2018: Scientific Reports
Krishnashish Bose, Christopher J Lech, Brahim Heddi, Anh Tuân Phan
We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4 T2 G4 ] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface...
May 17, 2018: Nature Communications
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"