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https://www.readbyqxmd.com/read/29341394/hydrolysis-by-catalytic-iggs-of-microrna-specific-for-patients-with-schizophrenia
#1
Evgeny A Ermakov, Svetlana A Ivanova, Valentina N Buneva, Georgy A Nevinsky
Significant importance of autoimmune changes in the pathogenesis of schizophrenia (SCZ) is not established. Here, we present the first evidence that autoantibodies of 100% SCZ patients possess RNase activity: сCMP > poly(C) > poly(A) > yeast RNA. In addition, we have got an unexpected result: there was revealed site-specific hydrolysis of four known SCZ specific microRNAs (miR-137, miR-9-5p, miR-219-2-3p, and miR-219a-5p) playing an important role in the regulation of several genes functioning...
January 17, 2018: IUBMB Life
https://www.readbyqxmd.com/read/29340026/evaluating-the-bias-of-circrna-predictions-from-total-rna-seq-data
#2
Jinzeng Wang, Kang Liu, Ya Liu, Qi Lv, Fan Zhang, Haiyun Wang
CircRNAs are a group of endogenous noncoding RNAs. The quickly developing high throughput RNA sequencing technologies along with novel bioinformatics approaches have enabled researchers to systematically identify circRNAs and their biological functions in cells. Deep sequencing of rRNA-depleted RNAs treated with RNase R, which digests linear RNAs and leaves circRNAs enriched, is an efficient way to identify circRNAs. However, very few of RNase R treated data are at hand but a large amount of total RNA-Seq data with no sequencing costs is available, for circRNA predictions...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339148/biochemical-characterization-of-campylobacter-jejuni-pnpase-an-exoribonuclease-important-for-bacterial-pathogenicity
#3
Jorge Casinhas, Rute G Matos, Nabila Haddad, Cecília M Arraiano
Bacteria need to promptly respond to environmental changes. Ribonucleases (RNases) are key factors in the adaptation to new environments by enabling a rapid adjustment in RNA levels. The exoribonuclease polynucleotide phosphorylase (PNPase) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization in C. jejuni. However, the mechanism of action of this ribonuclease is not yet known...
January 12, 2018: Biochimie
https://www.readbyqxmd.com/read/29332592/construction-of-an-m1gs-ribozyme-for-targeted-and-rapid-mrna-cleavage-application-on-the-ets-2-oncogene
#4
Chrisavgi Toumpeki, Dimitrios Anastasakis, Ioannis Panagoulias, Vassiliki Stamatopoulou, Tassos Georgakopoulos, Sofia Kallia-Raftopoulos, Athanasia Mouzaki, Denis Drainas
Background RNase P-mediated cleavage of target RNAs has been proposed as a promising tool for gene silencing. Ets-2 proto-oncogene controls the expression of a wide variety of genes involved in cancer and immunity. Objective Construction of a functional RNase P-based ribozyme (M1GS303) that targets Ets-2 mRNA Method The accessible sites for targeting of Ets-2 mRNA were identified by footprinting analysis. M1GS303 ribozyme was constructed by cloning. The activity of the ribozyme in the presence or absence of spiramysin in E...
January 11, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29329887/determination-of-n-glycans-by-high-performance-liquid-chromatography-using-6-aminoquinolyl-n-hydroxysuccinimidyl-carbamate-as-the-glycosylamine-labeling-reagent
#5
Yike Wu, Qiuyue Sha, Juan Du, Chang Wang, Liang Zhang, Bi-Feng Liu, Yawei Lin, Xin Liu
Robust, efficient identification and accurate quantification of N-glycans are of great significance in N-glycomics analysis. Here, a simple and rapid derivatization method, based on the combination of microwave-assisted deglycosylation and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) labeling, was developed for the analysis of N-glycan by high performance liquid chromatography with fluorescence detection (HPLC-FLD). After optimizing various parameters affecting deglycosylation and derivatization by RNase B, the time for N-glycan labeling was shortened to 50 min with ∼10-fold enhancement in detection sensitivity comparing to conventional 2-aminobenzoic acid (2-AA) labeling method...
January 8, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29329457/a-novel-application-of-rnase-h2-dependent-quantitative-pcr-for-detection-and-quantification-of-grosmannia-clavigera-a-mountain-pine-beetle-fungal-symbiont-in-environmental-samples
#6
Chandra H McAllister, Colleen E Fortier, Kate R St Onge, Bianca M Sacchi, Meaghan J Nawrot, Troy Locke, Janice E K Cooke
Mountain pine beetle (Dendroctonus ponderosae Hopkins; MPB) is an economically and ecologically important pest of pine species in western North America. Mountain pine beetles form complex multipartite relationships with microbial partners, including the ophiostomoid fungi Grosmannia clavigera (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield, Ophiostoma montium (Rumbold) von Arx, Grosmannia aurea (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield, Leptographium longiclavatum (Lee, Kim, and Breuil) and Leptographium terebrantis (Barras and Perry)...
January 10, 2018: Tree Physiology
https://www.readbyqxmd.com/read/29322447/characterization-of-circular-rna-concatemers
#7
Thomas B Hansen
Circular RNAs (circRNAs) constitute a novel subset in the fascinating world of noncoding RNA, and they are found in practically all eukaryotes. Most of them exhibit low expression levels but some are extremely abundant. Typically, circRNAs are studied by RT-PCR-based assays, but for certain types of analyses this technique is not suitable. Circular RNA with repetitive exons (circular concatemers) has been observed by us and others when transiently expressing circRNAs in cells, however techniques and assays to study these species have not been established...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29322445/northern-blot-analysis-of-circular-rnas
#8
Tim Schneider, Silke Schreiner, Christian Preußer, Albrecht Bindereif, Oliver Rossbach
Northern blotting enables the specific detection and characterization of RNA molecules. Recently, circular RNAs (circRNAs) were described as a new class of cell type-specific noncoding RNAs. With the discovery of many novel circRNAs on the basis of high-throughput sequencing and bioinformatics, a solid biochemical approach is required to directly detect and validate specific circRNA species. Here we give a detailed overview of how different Northern blot methods can be employed to validate specific circRNAs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321565/characterization-of-novel-endo-%C3%AE-n-acetylglucosaminidases-from-sphingobacterium-species-beauveria-bassiana-and-cordyceps-militaris-that-specifically-hydrolyze-fucose-containing-oligosaccharides-and-human-igg
#9
Yibo Huang, Yujiro Higuchi, Takashi Kinoshita, Ai Mitani, Yasunari Eshima, Kaoru Takegawa
Endo-β-N-acetylglucosaminidase (ENGase) catalyzes hydrolysis of N-linked oligosaccharides. Although many ENGases have been characterized from various organisms, so far no fucose-containing oligosaccharides-specific ENGase has been identified in any organism. Here, we screened soil samples, using dansyl chloride (Dns)-labeled sialylglycan (Dns-SG) as a substrate, and discovered a strain that exhibits ENGase activity in the culture supernatant; this strain, named here as strain HMA12, was identified as a Sphingobacterium species by 16S ribosomal RNA gene analysis...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29315962/multiple-dicer1-related-tumors-in-a-child-with-a-large-interstitial-14q32-deletion
#10
Leanne de Kock, Dominique Geoffrion, Barbara Rivera, Rabea Wagener, Nelly Sabbaghian, Susanne Bens, Benjamin Ellezam, Dorothée Bouron-Dal Soglio, Jessica Ordóñez, Stephanie Sacharow, Jose Fernando Polo Nieto, R Paul Guillerman, Gordan M Vujanic, John R Priest, Reiner Siebert, William D Foulkes
Germ-line interstitial deletions involving the 14q32 chromosomal region, resulting in 14q32 deletion syndrome, are rare. DICER1 is a recently described cancer-predisposition gene located at 14q32.13. We report the case of a male child with an approximately 5.8 Mbp 14q32.13q32.2 germ-line deletion, which included the full DICER1 locus. We reviewed available clinical and pathological material, and conducted genetic analyses. In addition to having congenital dysmorphic features, the child developed multiple DICER1 syndrome-related tumors before age 5 years: a pediatric cystic nephroma (pCN), a ciliary body medulloepithelioma (CBME), and a small lung cyst (consistent with occult pleuropulmonary blastoma Type I/Ir cysts seen in DICER1 mutation carriers)...
January 9, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29314657/molecular-and-genetic-interactions-of-the-rna-degradation-machineries-in-firmicute-bacteria
#11
REVIEW
Peter Redder
Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane-associated endoribonuclease RNase E, and is stable enough to be purified without falling apart...
January 5, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29313337/improved-reversible-cross-linking-based-solid-phase-rna-extraction-for-pathogen-diagnostics
#12
Fei Zhao, Eun Yeong Lee, Yong Shin
In this study, we developed an amine-functionalized, diatomaceous earth-based, dimethyl suberimidate assisted (ADD) system as a novel binding strategy to improve solid-phase extraction method for rapid and simple purification of RNA from biological samples including human cells and pathogenic bacteria. This ADD system is based on reversible cross-linking reactions between RNA and the silica matrix. The formation of robust covalent bonds protects RNA from both the sufferance of washing steps and isolation with ribonuclease (RNase)-rich samples, leading to the extraction of higher quality RNA...
January 9, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29311560/a-central-role-for-pi3k-akt-signaling-pathway-in-linking-samhd1-deficiency-to-the-type-i-interferon-signature
#13
Changhoon Oh, Jeongmin Ryoo, Kiwon Park, Baek Kim, Michele B Daly, DongYeon Cho, Kwangseog Ahn
The autoimmune disorder Aicardi-Goutières syndrome (AGS) is characterized by a constitutive type I interferon response. SAMHD1 possesses both dNTPase and RNase activities and mutations in SAMHD1 cause AGS; however, how SAMHD1-deficiency causes the type I interferon response in patients with AGS remains unknown. Here, we show that endogenous RNA substrates accumulated in the absence of SAMHD1 act as a major immunogenic source for the type I interferon response. Reconstitution of SAMHD1-negative human cells with wild-type but not RNase-defective SAMHD1 abolishes spontaneous type I interferon induction...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311133/dual-ire1-rnase-functions-dictate-glioblastoma-development
#14
Stéphanie Lhomond, Tony Avril, Nicolas Dejeans, Konstantinos Voutetakis, Dimitrios Doultsinos, Mari McMahon, Raphaël Pineau, Joanna Obacz, Olga Papadodima, Florence Jouan, Heloise Bourien, Marianthi Logotheti, Gwénaële Jégou, Néstor Pallares-Lupon, Kathleen Schmit, Pierre-Jean Le Reste, Amandine Etcheverry, Jean Mosser, Kim Barroso, Elodie Vauléon, Marion Maurel, Afshin Samali, John B Patterson, Olivier Pluquet, Claudio Hetz, Véronique Quillien, Aristotelis Chatziioannou, Eric Chevet
Proteostasis imbalance is emerging as a major hallmark of cancer, driving tumor aggressiveness. Evidence suggests that the endoplasmic reticulum (ER), a major site for protein folding and quality control, plays a critical role in cancer development. This concept is valid in glioblastoma multiform (GBM), the most lethal primary brain cancer with no effective treatment. We previously demonstrated that the ER stress sensor IRE1α (referred to as IRE1) contributes to GBM progression, through XBP1 mRNA splicing and regulated IRE1-dependent decay (RIDD) of RNA Here, we first demonstrated IRE1 signaling significance to human GBM and defined specific IRE1-dependent gene expression signatures that were confronted to human GBM transcriptomes...
January 8, 2018: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29306413/relative-quantitation-of-neutral-and-sialylated-n-glycans-using-stable-isotopic-labeled-d0-d5-benzoyl-chloride-by-maldi-ms
#15
Chang Wang, Yike Wu, Liang Zhang, Bi-Feng Liu, Yawei Lin, Xin Liu
Quantitative analysis of glycans is an emerging field in glycomic research. Herein we present a rapid and effective dual-labeling strategy, in the combination of isotopic derivatization of N-glycosylamine-based glycans by d0/d5-benzoyl chloride and methylamidation of sialic acids, to relatively quantify both neutral and sialylated N-glycans simultaneously by MALDI-MS. The derivatization efficiencies were increased by microwave-accelerated deglycosylation which not only largely reduce the time of glycoprotein deglycosylation but also inhibit the hydrolysis of intermediate glycosylamines produced by PNGase F digestion...
March 9, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29304825/bacterial-ribonuclease-binase-exerts-an-intra-cellular-anti-viral-mode-of-action-targeting-viral-rnas-in-influenza-a-virus-infected-mdck-ii-cells
#16
Raihan Shah Mahmud, Ahmed Mostafa, Christin Müller, Pumaree Kanrai, Vera Ulyanova, Yulia Sokurenko, Julia Dzieciolowski, Irina Kuznetsova, Olga Ilinskaya, Stephan Pleschka
BACKGROUND: Influenza is a severe contagious disease especially in children, elderly and immunocompromised patients. Beside vaccination, the discovery of new anti-viral agents represents an important strategy to encounter seasonal and pandemic influenza A virus (IAV) strains. The bacterial extra-cellular ribonuclease binase is a well-studied RNase from Bacillus pumilus. Treatment with binase was shown to improve survival of laboratory animals infected with different RNA viruses. Although binase reduced IAV titer in vitro and in vivo, the mode of action (MOA) of binase against IAV at the molecular level has yet not been studied in depth and remains elusive...
January 5, 2018: Virology Journal
https://www.readbyqxmd.com/read/29297728/chronic-fatigue-and-immune-deficiency-syndrome-cfids-cellular-metabolism-and-ionizing-radiation-a-review-of-contemporary-scientific-literature-and-suggested-directions-for-future-research
#17
Andrej Rusin, Colin Seymour, Carmel Mothersill
PURPOSE: To investigate biochemical pathways known to be involved in radiation response and in CFIDS to determine if there might be common underlying mechanisms leading to symptoms experienced by those accidentally or deliberately exposed to radiation and those suffering from CFIDS. If such a link were established, to suggest testable hypotheses to investigate the mechanisms with the aim of identifying new therapeutic targets. CONCLUSIONS: Evidence for involvement of the alpha-synuclein, cytochrome c oxidiase, αB-crystallin, RNase L, and lactate dehydrogenase/STAT1 pathways is strong and suggests a common underlying mechanism involving mitochondrial dysfunction mediated by ROS and disruption of ATP production...
January 3, 2018: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/29297355/identification-of-streptococcal-small-rnas-that-are-putative-targets-of-rnase-iii-through-bioinformatics-analysis-of-rna-sequencing-data
#18
Ethan C Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
BACKGROUND: Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29295939/structure-of-hiv-1-reverse-transcriptase-cleaving-rna-in-an-rna-dna-hybrid
#19
Lan Tian, Min-Sung Kim, Hongzhi Li, Jimin Wang, Wei Yang
HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA hybrid. A preferred substrate sequence is absolutely required to enable the RNA/DNA hybrid to adopt the distorted conformation needed to interact properly with the RNase H active site in RT. Substituting two nucleotides 4 bp upstream from the cleavage site results in scissile-phosphate displacement by 4 Å...
January 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29295617/mno2-nanosheet-powered-janus-protection-dna-nanomachines-supporting-robust-rna-imaging
#20
Feng Chen, Min Bai, Yue Zhao, Ke Cao, Xiaowen Cao, Yongxi Zhao
Both biomarker and probe degradations cause serious false assay results. Yet, protecting target or target/probe simultane-ously has rarely been explored. Herein, MnO2 nanosheet-powered target/probe Janus protection DNA nanomachines are reported. It is formed by RNA-responsive assembly of chemically modified two DNA partzymes and one substrate probe in living cells. MnO2 nanosheets are used to facilitate cellular uptake of DNA reagents and generate Mn2+ as indispensable DNAzyme cofactors for efficient catalytic cleavage...
January 3, 2018: Analytical Chemistry
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