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https://www.readbyqxmd.com/read/29352312/a-role-for-domain-i-of-the-hepatitis-c-virus-ns5a-protein-in-virus-assembly
#1
Chunhong Yin, Niluka Goonawardane, Hazel Stewart, Mark Harris
The NS5A protein of hepatitis C virus (HCV) plays roles in both virus genome replication and assembly. NS5A comprises three domains, of these domain I is believed to be involved exclusively in genome replication. In contrast, domains II and III are required for the production of infectious virus particles and are largely dispensable for genome replication. Domain I is highly conserved between HCV and related hepaciviruses, and is highly structured, exhibiting different dimeric conformations. To investigate the functions of domain I in more detail, we conducted a mutagenic study of 12 absolutely conserved and surface-exposed residues within the context of a JFH-1-derived sub-genomic replicon and infectious virus...
January 19, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29352301/crystal-structure-of-a-udp-glcnac-epimerase-for-surface-polysaccharide-biosynthesis-in-acinetobacter-baumannii
#2
Bhumika S Shah, Heather E Ashwood, Stephen J Harrop, Daniel N Farrugia, Ian T Paulsen, Bridget C Mabbutt
With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB...
2018: PloS One
https://www.readbyqxmd.com/read/29352171/a-urine-dependent-human-urothelial-organoid-offers-a-potential-alternative-to-rodent-models-of-infection
#3
Harry Horsley, Dhanuson Dharmasena, James Malone-Lee, Jennifer L Rohn
Murine models describe a defined host/pathogen interaction for urinary tract infection, but human cell studies are scant. Although recent human urothelial organoid models are promising, none demonstrate long-term tolerance to urine, the natural substrate of the tissue and of the uropathogens that live there. We developed a novel human organoid from progenitor cells which demonstrates key structural hallmarks and biomarkers of the urothelium. After three weeks of transwell culture with 100% urine at the apical interface, the organoid stratified into multiple layers...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352136/gphenovision-a-ground-mobile-system-with-multi-modal-imaging-for-field-based-high-throughput-phenotyping-of-cotton
#4
Yu Jiang, Changying Li, Jon S Robertson, Shangpeng Sun, Rui Xu, Andrew H Paterson
Imaging sensors can extend phenotyping capability, but they require a system to handle high-volume data. The overall goal of this study was to develop and evaluate a field-based high throughput phenotyping system accommodating high-resolution imagers. The system consisted of a high-clearance tractor and sensing and electrical systems. The sensing system was based on a distributed structure, integrating environmental sensors, real-time kinematic GPS, and multiple imaging sensors including RGB-D, thermal, and hyperspectral cameras...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351722/evaluation-of-matrix-effects-on-tof-sims-data-of-leu-enkephalin-and-1-2-dioleoyl-sn-glycero-3-phosphocholine-mixed-samples
#5
Shusuke Nakano, Takayuki Yamagishi, Satoka Aoyagi, André Portz, Michael Dürr, Hideo Iwai, Tomoko Kawashima
Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is one of the most powerful methods to analyze biomolecules in biological tissues and cells because it provides detailed chemical structure information and chemical images with a high spatial resolution. However, in terms of quantitative analysis, there are issues such as matrix effects that often cause secondary ion intensity changes regardless of the actual concentration in a sample. For instance, the intensity of secondary ions related to peptides is generally suppressed when lipids coexist...
January 19, 2018: Biointerphases
https://www.readbyqxmd.com/read/29351397/acute-small-intestinal-inflammation-results-in-persistent-lymphatic-alterations
#6
Sonia Rehal, Matthew Stephens, Simon Roizes, Shan Liao, Pierre-Yves von der Weid
Inflammatory bowel disease (IBD) has a complex pathophysiology with limited treatments. Structural and functional changes in the intestinal lymphatic system have been associated with the disease, with increased risk of IBD occurrence linked to a history of acute intestinal injury. To examine the potential role of the lymphatic system in inflammation recurrence, we evaluated morphological and functional changes in mouse mucosal and mesenteric lymphatic vessels, and within the mesenteric lymph nodes during acute ileitis caused by a 7-day treatment with dextran sodium sulfate (DSS)...
December 14, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/29351339/brain-functional-bold-perturbation-modelling-for-forward-fmri-and-inverse-mapping
#7
Zikuan Chen, Jennifer Robinson, Vince Calhoun
PURPOSE: To computationally separate dynamic brain functional BOLD responses from static background in a brain functional activity for forward fMRI signal analysis and inverse mapping. METHODS: A brain functional activity is represented in terms of magnetic source by a perturbation model: χ = χ0 +δχ, with δχ for BOLD magnetic perturbations and χ0 for background. A brain fMRI experiment produces a timeseries of complex-valued images (T2* images), whereby we extract the BOLD phase signals (denoted by δP) by a complex division...
2018: PloS One
https://www.readbyqxmd.com/read/29351229/joint-bearing-and-range-estimation-of-multiple-objects-from-time-frequency-analysis
#8
Jeng-Cheng Liu, Yuang-Tung Cheng, Hsien-Sen Hung
Direction-of-arrival (DOA) and range estimation is an important issue of sonar signal processing. In this paper, a novel approach using Hilbert-Huang transform (HHT) is proposed for joint bearing and range estimation of multiple targets based on a uniform linear array (ULA) of hydrophones. The structure of this ULA based on micro-electro-mechanical systems (MEMS) technology, and thus has attractive features of small size, high sensitivity and low cost, and is suitable for Autonomous Underwater Vehicle (AUV) operations...
January 19, 2018: Sensors
https://www.readbyqxmd.com/read/29350931/multiscale-and-multistep-ordering-of-flow-induced-nucleation-of-polymers
#9
Kunpeng Cui, Zhe Ma, Nan Tian, Fengmei Su, Dong Liu, Liangbin Li
Flow-induced crystallization (FIC) is a typical nonequilibrium phase transition and a core industry subject for the largest group of commercially useful polymeric materials: semicrystalline polymers. A fundamental understanding of FIC can benefit the research of nonequilibrium ordering in matter systems and help to tailor the ultimate properties of polymeric materials. Concerning the crystallization process, flow can accelerate the kinetics by orders of magnitude and induce the formation of oriented crystallites like shish-kebab, which are associated with the major influences of flow on nucleation, that is, raised nucleation density and oriented nuclei...
January 19, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29350034/probing-the-complexities-of-structural-changes-in-layered-oxide-cathode-materials-for-li-ion-batteries-during-fast-charge-discharge-cycling-and-heating
#10
Enyuan Hu, Xuelong Wang, Xiqian Yu, Xiao-Qing Yang
The rechargeable lithium-ion battery (LIB) is the most promising energy storage system to power electric vehicles with high energy density and long cycling life. However, in order to meet customers' demands for fast charging, the power performances of current LIBs need to be improved. From the cathode aspect, layer-structured cathode materials are widely used in today's market and will continue to play important roles in the near future. The high rate capability of layered cathode materials during charging and discharging is critical to the power performance of the whole cell and the thermal stability is closely related to the safety issues...
January 19, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29349451/on-the-turn-inducing-properties-of-asparagine-the-structuring-role-of-the-amide-side-chain-from-isolated-model-peptides-to-crystallized-proteins
#11
S Habka, W Y Sohn, V Vaquero-Vara, M Géléoc, B Tardivel, V Brenner, E Gloaguen, M Mons
Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations...
January 19, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29349106/the-wildland-urban-interface-raster-dataset-of-catalonia
#12
Fermín J Alcasena, Cody R Evers, Cristina Vega-Garcia
We provide the wildland urban interface (WUI) map of the autonomous community of Catalonia (Northeastern Spain). The map encompasses an area of some 3.21 million ha and is presented as a 150-m resolution raster dataset. Individual housing location, structure density and vegetation cover data were used to spatially assess in detail the interface, intermix and dispersed rural WUI communities with a geographical information system. Most WUI areas concentrate in the coastal belt where suburban sprawl has occurred nearby or within unmanaged forests...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29349103/wildfire-spread-hazard-and-exposure-metric-raster-grids-for-central-catalonia
#13
Fermín J Alcasena, Alan A Ager, Michele Salis, Michelle A Day, Cristina Vega-Garcia
We provide 40 m resolution wildfire spread, hazard and exposure metric raster grids for the 0.13 million ha fire-prone Bages County in central Catalonia (northeastern Spain) corresponding to node influence grid (NIG), crown fraction burned (CFB) and fire transmission to residential houses (TR). Fire spread and behavior data (NIG, CFB and fire perimeters) were generated with fire simulation modeling considering wildfire season extreme fire weather conditions (97th percentile). Moreover, CFB was also generated for prescribed fire (Rx) mild weather conditions...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29348580/the-epibiotic-life-of-the-cosmopolitan-diatom-fragilariopsis-doliolus-on-heterotrophic-ciliates-in-the-open-ocean
#14
Flora J Vincent, Sébastien Colin, Sarah Romac, Eleonora Scalco, Lucie Bittner, Yonara Garcia, Rubens M Lopes, John R Dolan, Adriana Zingone, Colomban de Vargas, Chris Bowler
Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate...
January 18, 2018: ISME Journal
https://www.readbyqxmd.com/read/29348528/agrocin-108-is-a-5-cytidine-nucleotide-bacteriocin-containing-a-carbocyclic-phosphoryl-ascorbate-group
#15
Christopher M Elvin, Robert E Asenstorfer, Maarten H Ryder, Scott C Donner, Graham P Jones, Max E Tate
Agrocin 108 is a 3'-O-β-D-xylopyranosyl-cytidine-5'-O-phosphodiester of an ascorbate-carbocyclic cyclopentenone analogue, with bacteriocin-like properties. This bacteriocin exhibits orders of magnitude greater than the inhibition zone diameter towards the indicator strain than either ampicillin or streptomycin. It has been isolated from cultures of Rhizobium rhizogenes strain K108. The structure of the agrocin 108 without detail, has been previously published. We now report a detailed structure elucidation, including the hitherto undetermined residual 5'-phospho-diester fragment by a combination of 1D and 2D NMR studies at various pH values in H2O/D2O, high resolution MS, pKa determination, and chemical degradation...
January 18, 2018: Journal of Antibiotics
https://www.readbyqxmd.com/read/29348526/prodigiosin-r2-a-new-prodigiosin-from-the-roseophilin-producer-streptomyces-griseoviridis-2464-s5
#16
Shoko Kimata, Takuya Matsuda, Yuta Suizu, Yoichi Hayakawa
Roseophilin (2) is a unique prodigiosin-related compound produced by Streptomyces griseoviridis 2464-S5, and is characterized by a central furan ring and a bicyclic alkyl chain. During a search for biosynthetic intermediates of 2, a new metabolite designated prodigiosin R2 (1) was isolated from the culture of the roseophilin producer. The molecular formula of 1 was established as C27H35N3O by high-resolution FAB-MS. The structure of 1 was determined by NMR spectroscopic analyses as a prodigiosin derivative with the same bicyclic alkyl chain as 2...
January 18, 2018: Journal of Antibiotics
https://www.readbyqxmd.com/read/29348327/genome-instability-as-a-consequence-of-defects-in-the-resolution-of-recombination-intermediates
#17
Stephen C West, Ying Wai Chan
The efficient processing of homologous recombination (HR) intermediates, which often contain four-way structures known as Holliday junctions (HJs), is required for proper chromosome segregation at mitosis. Eukaryotic cells possess three distinct pathways of resolution: (i) HJ dissolution mediated by BLM-topoisomerase IIIα-RMI1-RMI2 (BTR) complex, and HJ resolution catalyzed by either (ii) SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex) or (iii) GEN1. The BTR pathway acts at all times throughout the cell cycle, whereas the actions of SMX and GEN1 are restrained in S phase and become elevated late in the cell cycle to ensure the resolution of persistent recombination intermediates before mitotic division...
January 18, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29348170/crispr-rna-and-anti-crispr-protein-binding-to-the-xanthomonas-albilineans-csy1-csy2-heterodimer-in-the-type-i-f-crispr-cas-system
#18
Suji Hong, Donghyun Ka, Seo Jeong Yoon, Nayoung Suh, Migyeong Jeong, Jeong-Yong Suh, Euiyoung Bae
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against bacteriophages. In type I-F CRISPR-Cas systems, multiple Cas proteins (Csy1-4) comprise a surveillance complex (Csy complex) with CRISPR RNA (crRNA) for target recognition. Here, we report the biochemical characterization of the Csy1-Csy2 subcomplex from Xanthomonas albilineans, including the analysis of its interaction with crRNA and also AcrF2, an anti-CRISPR (Acr) protein from a phage that infects Pseudomonas aeruginosa The X...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29348167/thiosulfate-sulfurtransferase-like-domain-containing-1-protein-interacts-with-thioredoxin
#19
Marouane Libiad, Nicole Motl, David L Akey, Naoya Sakamoto, Eric R Fearon, Janet L Smith, Ruma Banerjee
Rhodanese domains are structural modules present in the sulfurtransferase superfamily. These domains can exist as single units, in tandem repeats or fused to domains with other activities. Despite their prevalence across species, the specific physiological roles of most sulfurtransferases are not known. Mammalian rhodanese and mercaptopyruvate sulfurtransferase are perhaps the best-studied members of this protein superfamily and are involved in hydrogen sulfide metabolism. The relatively unstudied human thiosulfate sulfurtransferase like domain-containing 1 (TSTD1) protein, a single-domain cytoplasmic sulfurtransferase, was also postulated to play a role in the sulfide oxidation pathway using thiosulfate to form glutathione persulfide, for subsequent processing in the mitochondrial matrix...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29348055/high-resolution-structures-of-mitochondrial-ribosomes-and-their-functional-implications
#20
REVIEW
Philipp Bieri, Basil J Greber, Nenad Ban
Mitochondrial ribosomes (mitoribosomes) almost exclusively synthesize essential components of the oxidative phosphorylation machinery. Dysfunction of mitochondrial protein biosynthesis leads to human diseases and plays an important role in the altered metabolism of cancer cells. Recent developments in cryo-electron microscopy enabled the structural characterization of complete yeast and mammalian mitoribosomes at near-atomic resolution. Despite originating from ancestral bacterial ribosomes, mitoribosomes have diverged in their composition and architecture...
January 15, 2018: Current Opinion in Structural Biology
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