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https://www.readbyqxmd.com/read/29793215/in-silico-insight-into-voltage-gated-sodium-channel-1-7-inhibition-for-anti-pain-drug-discovery
#1
Mingxing Wang, Wei Li, Ying Wang, Yongbo Song, Jian Wang, Maosheng Cheng
Studies on human genetics have implicated the voltage-gated sodium channel Nav1.7 as an appealing target for the treatment of pain. In this study, we put forward a ligand-based pharmacophore for the first time, which was generated by a set of multiple chemical scaffolds including sulfonamide and non-sulfonamide derivatives and consisted of four chemical features: an aromatic ring, a hydrophobic group and two hydrogen acceptors. The active cavity was divided into three regions according to the properties of the amino acids surrounded and was used for the docking of 16 known active inhibitors...
May 18, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29793193/a-validation-study-of-the-1-2-indandione-reagent-for-operational-use-in-the-uk-part-2-optimization-of-processing-conditions
#2
Niko Nicolasora, Rory Downham, Rachel-May Dyer, Laura Hussey, Aoife Luscombe, Vaughn Sears
This paper contains details of work carried out to identify the most effective processing conditions for the optimized 1,2-indandione/zn formulation developed for use under UK conditions. Using direct measurements of fluorescence taken from test spots of amino acids and eccrine sweat during oven processing, complemented with experiments on real fingermarks, it was established that processing temperatures above 120°C in the oven were detrimental to the fluorescence of the developed mark. Alternative methods of development to oven processing were found to be effective, but less controllable...
May 2, 2018: Forensic Science International
https://www.readbyqxmd.com/read/29793047/transcript-profiling-of-salt-tolerant-tobacco-mutants-generated-via-mutation-breeding
#3
Özge Çelik, Aybüke Ekşioğlu, Enes Yağız Akdaş
The main aim of the study is to identify the genes differentially, predominantly or specifically expressed in salt tolerant tobacco mutants, improved from Akhisar 97 and İzmir Özbaş varieties via mutation breeding, with respect to unstressed control plants. Seven tobacco mutants which have different salt tolerance capacities were evaluated by Gene Fishing analysis. Under stress conditions differentially expressed 100 reproducible bands were identified (74 of up-regulated and 20 of down-regulated while 6 were unknown)...
May 21, 2018: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/29793033/expression-of-anabaena-sensory-rhodopsin-is-influenced-by-different-codons-of-seven-residues-at-the-n-terminal-region
#4
Otgontuya Tsogbadrakh, Ah Reum Choi, Kwang-Hwan Jung
Microbial rhodopsins are well-known seven-transmembrane proteins that have been extensively studied for their structure and function. These retinal-binding proteins can be divided into two types. Type I is microbial rhodopsin, and type II (visual pigment) is expressed mostly in mammalian eyes. The two primary functions of type I rhodopsin are ion pumping activity and sensory transduction. Anabaena sensory rhodopsin (ASR) is a microbial rhodopsin with a specific function of photosensory transduction. ASR is expressed at moderate levels in Escherichia coli, but its expression level is lower compared to the general green light absorbing proteorhodopsin (GPR)...
May 21, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29792951/an-analysis-of-variability-in-genome-organisation-of-intracellular-calcium-release-channels-across-insect-orders
#5
Bartlomiej J Troczka, Ewan Richardson, Rafael Homem, T G Emyr Davies
Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated Ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP3 R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP3 Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792932/cystine-glutamate-transporter-system-x-c-is-involved-in-nitric-oxide-production-in-mouse-peritoneal-macrophages
#6
Sho Kobayashi, Shinji Hamashima, Takujiro Homma, Mami Sato, Ryosuke Kusumi, Shiro Bannai, Junich Fujii, Hideyo Sato
The amino acid transport system xc - is important for maintaining intracellular glutathione levels and extracellular redox balance. The main component of system xc - , xCT, is strongly induced by various stimuli, including oxidative stress and bacterial lipopolysaccharides (LPS) in macrophages. In the present study, we investigated the production of nitric oxide by LPS-stimulated mouse peritoneal macrophages isolated from both xCT-deficient and wild-type mice. After culturing macrophages in the presence of LPS for 24-48 h, nitrite levels in the medium of xCT-deficient macrophages were significantly decreased compared to that of wild-type cells...
May 21, 2018: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/29792906/four-novel-antibacterial-sesquiterpene-%C3%AE-amino-acid-quaternary-ammonium-hybrids-from-the-mycelium-of-mushroom-stereum-hirsutum
#7
Yuan-Chang Duan, Jun Feng, Na Bai, Guo-Hong Li, Ke-Qin Zhang, Pei-Ji Zhao
The mushroom Stereum hirsutum is parasitized by Tremella aurantia to form a heterogeneous basidiocarp Jin'er, which has been used as food and folk medicine in Chinese society. In present work, the S. hirsutum was fermented in YMG broth, and four novel mixed terpenes, stereumamides A-D (1-4), which are sesquiterpenes combined with α-amino acids to form quaternary ammonium hybrids, were isolated from the Stereum hirsutum FP-91666 and their structures were elucidated by spectroscopic data analysis. Stereumamides A and D showed antibacterial activity against Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium, with the minimum inhibitory concentration (MIC) values of 12...
May 21, 2018: Fitoterapia
https://www.readbyqxmd.com/read/29792880/molecular-alterations-during-larval-development-of-haemonchus-contortus-in-vitro-are-under-tight-post-transcriptional-control
#8
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29792841/decarboxylation-of-ang-1-7-to-ala-1-ang-1-7-leads-to-significant-changes-in-pharmacodynamics
#9
Anja Tetzner, Maura Naughton, Kinga Gebolys, Jenny Eichhorst, Esther Sala, Óscar Villacañas, Thomas Walther
The heptapeptide angiotensin (Ang)-(1-7) is part of the beneficial arm of the renin-angiotensin system. Ang-(1-7) has cardiovascular protective effects, stimulates regeneration, and opposes the often detrimental effects of Ang II. We recently identified the G protein-coupled receptors Mas and MrgD as receptors for the heptapeptide. Ala1 -Ang-(1-7) (Alamandine), a decarboxylated form of Ang-(1-7), has similar vasorelaxant effects, but has been described to only stimulate MrgD. Therefore, this study aimed to characterise the consequences of the lack of the carboxyl group in amino acid 1 on intracellular signalling and to identify the receptor fingerprint for Ala1 -Ang-(1-7)...
May 21, 2018: European Journal of Pharmacology
https://www.readbyqxmd.com/read/29792801/developing-a-novel-sulfoxide-containing-ms-cleavable-homobifunctional-cysteine-reactive-cross-linker-for-studying-protein-protein-interactions
#10
Craig B Gutierrez, Sarah A Block, Clinton Yu, Stephanie M Soohoo, Alexander S Huszagh, Scott D Rychnovsky, Lan Huang
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the mostly widely used cross-linking reagents are targeting lysines. While such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792709/glycofunctionalization-of-poly-lactic-co-glycolic-acid-polymers-building-blocks-for-the-generation-of-defined-sugar-coated-nanoparticles
#11
Alessandro Palmioli, Barbara La Ferla
A set of poly(lactic- co-glycolic acid) polymers functionalized with different monosaccharides as well as glycodendrimers and surface-decorated nanoparticles (NPs) were synthesized and characterized. The functionalization of the polymer was carried out through amide bond formation with amino-modified sugar monomers and through a biocompatible chemoselective method exploiting the reducing end of a free sugar. The assemblage of the NPs adopting a nanoprecipitation method was straightforward and allowed the preparation of sugars/sugar dendrimer coated NPs...
May 24, 2018: Organic Letters
https://www.readbyqxmd.com/read/29792664/tricolor-white-light-emitting-carbon-dots-with-multiple-cores-shell-structure-for-wled-application
#12
Tianyi Zhang, Feifei Zhao, Li Li, Bin Qi, Dongxia Zhu, Jianhua Lü, Changli Lü
The past few years have witnessed the rapid development of carbon dots (CDs) due to their outstanding optical properties and a wide range of applications. However, the design and control of CDs with long-wavelength and multicolor emission are still huge challenges to be addressed for their practical use in different fields. Here, novel nitrogen doped multiple-cores@shell structured CDs with tricolor emissions of red, green and blue were constructed via one pot hydrothermal method from citric acid (CA) and 5-amino-1,10-phenanthroline (Aphen) as reactants and the growth process of CDs was monitored with the reaction time in the synthetic system...
May 24, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29792573/inherent-resistance-to-14%C3%AE-demethylation-inhibitor-fungicides-in-colletotrichum-truncatum-is-likely-linked-to-cyp51a-and-or-cyp51b-gene-variants
#13
Shuning Chen, Yunyun Wang, Guido Schnabel, Congyue Annie Peng, Satyanarayana Lagishetty, Kerry Smith, Chao-Xi Luo, Huizhu Yuan
Anthracnose disease, caused by Colletotrichum truncatum, affects marketable yield during preharvest production and postharvest storage of fruits and vegetables worldwide. Demethylation inhibitor fungicides (DMIs) are among the very few chemical classes of single-site mode of action fungicides that are effective in controlling anthracnose disease. However, some species are inherently resistant to DMIs and more information is needed to understand this phenomenon. Isolates of C. truncatum were collected from the USA and China from peach, soybean, citrus, and begonia and sensitivity to six DMIs (difenoconazole, propiconazole, metconazole, tebuconazole, flutriafol and fenbuconazole) was determined...
May 24, 2018: Phytopathology
https://www.readbyqxmd.com/read/29792428/structures-and-activities-of-tiahuramides-a-c-cyclic-depsipeptides-from-a-tahitian-collection-of-the-marine-cyanobacterium-lyngbya-majuscula
#14
Annabel Levert, Rebeca Alvariño, Louis Bornancin, Eliane Abou Mansour, Adam M Burja, Anne-Marie Genevière, Isabelle Bonnard, Eva Alonso, Luis Botana, Bernard Banaigs
The structures of three new cyclic depsipeptides, tiahuramides A (1), B (2), and C (3), from a French Polynesian collection of the marine cyanobacterium Lyngbya majuscula are described. The planar structures of these compounds were established by a combination of mass spectrometry and 1D and 2D NMR experiments. Absolute configurations of natural and nonproteinogenic amino acids were determined through a combination of acid hydrolysis, derivitization with Marfey's reagent, and HPLC. The absolute configuration of hydroxy acids was confirmed by Mosher's method...
May 24, 2018: Journal of Natural Products
https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#15
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29792315/genomic-variation-among-and-within-six-juglans-species
#16
Kristian A Stevens, Keith Woeste, Sandeep Chakraborty, Marc W Crepeau, Charles A Leslie, Pedro J Martínez-García, Daniela Puiu, Jeanne Romero-Severson, Mark Coggeshall, Abhaya M Dandekar, Daniel Kluepfel, David B Neale, Steven L Salzberg, Charles H Langley
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia : Juglans sigillata (also from section Dioscaryon ), Juglans nigra , Juglans microcarpa, Juglans hindsii (from section Rhysocaryon ) , Juglans cathayensis (from section Cardiocaryon ), and the closely related Pterocarya stenoptera. While these are 'draft' genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding...
May 23, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29792261/structure-based-analysis-of-cysz-mediated-cellular-uptake-of-sulfate
#17
Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher-Dufrisne, Pattama Wiriyasermkul, M Hunter Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, James Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R Rajashankar, Burkhard Rost, Diomedes Logothetis, Matthias Quick, Wayne A Hendrickson, Filippo Mancia
Sulfur, most abundantly found in the environment as sulfate (SO4 2- ), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO4 2- at the molecular level is limited. CysZ has been described as a SO4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO4 2- across membranes...
May 24, 2018: ELife
https://www.readbyqxmd.com/read/29792237/according-to-mitochondrial-dna-evidence-parascaris-equorum-and-parascaris-univalens-may-represent-the-same-species
#18
J F Gao, X X Zhang, X X Wang, Q Li, Y Li, W W Xu, Y Gao, C R Wang
Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates...
May 24, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29792177/investigation-of-the-thermophilic-mechanism-in-the-genus-porphyrobacter-by-comparative-genomic-analysis
#19
Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu, Xue-Wei Xu
BACKGROUND: Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792119/maple-2-3-0-an-improved-system-for-evaluating-the-functionomes-of-genomes-and-metagenomes
#20
Wataru Arai, Takeaki Taniguchi, Susumu Goto, Yuki Moriya, Hideya Uehara, Kazuhiro Takemoto, Hiroyuki Ogata, Hideto Takami
MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.
May 24, 2018: Bioscience, Biotechnology, and Biochemistry
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