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https://www.readbyqxmd.com/read/28905148/building-a-pgc-lc-ms-n-glycan-retention-library-and-elution-mapping-resource
#1
Jodie L Abrahams, Matthew P Campbell, Nicolle H Packer
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS...
September 13, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28893654/strain-specific-association-of-soybean-dwarf-virus-small-subgenomic-rna-with-virus-particles
#2
Thanuja Thekke-Veetil, Nancy K McCoppin, Leslie L Domier
Soybean dwarf virus (SbDV) produces a large subgenomic RNA (LsgRNA) for expression of structural and movement proteins and a small subgenomic RNA (SsgRNA) that does not contain an open reading frame. Sucrose gradient-purified SbDV virions from soybean plants systemically infected with SbDV by aphids and Nicotiana benthamiana leaves agroinfiltrated with infectious clones of two red clover SbDV isolates encapsidated genomic RNA and were associated with SsgRNA in a strain-specific manner. The LsgRNA was protected from RNase degradation, but not packaged into virions as indicated by its presence primarily in ELISA-negative fractions near the tops of sucrose gradients even in mutants that did not express coat protein...
September 8, 2017: Virus Research
https://www.readbyqxmd.com/read/28878087/novel-stable-ebola-virus-minigenome-replicon-reveals-remarkable-stability-of-the-viral-genome
#3
Wanyin Tao, Tianyu Gan, Mingzhe Guo, Yongfen Xu, Jin Zhong
Ebola virus (EBOV) causes severe hemorrhagic fever in humans and other primates with a high case fatality rate. No approved drug or vaccine of EBOV is available, which necessitates better understanding of the virus life cycle. Studies on EBOV have been hampered because experimentations involving live virus are restricted to biosafety level 4 (BSL-4) laboratories. EBOV minigenome system has provided researchers with the opportunity to study EBOV under BSL-2 conditions. Here, we developed a novel EBOV minigenome replicon which, to our knowledge, is the first EBOV cell culture system that can stably replicate and transcribe EBOV minigenome...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28854734/amide-linkages-mimic-phosphates-in-rna-interactions-with-proteins-and-are-well-tolerated-in-the-guide-strand-of-short-interfering-rnas
#4
Daniel Mutisya, Travis Hardcastle, Samwel K Cheruiyot, Pradeep S Pallan, Scott D Kennedy, Martin Egli, Melissa L Kelley, Anja van Brabant Smith, Eriks Rozners
While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28829437/control-of-phosphorothioate-stereochemistry-substantially-increases-the-efficacy-of-antisense-oligonucleotides
#5
Naoki Iwamoto, David C D Butler, Nenad Svrzikapa, Susovan Mohapatra, Ivan Zlatev, Dinah W Y Sah, Meena, Stephany M Standley, Genliang Lu, Luciano H Apponi, Maria Frank-Kamenetsky, Jason Jingxin Zhang, Chandra Vargeese, Gregory L Verdine
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers...
September 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28827284/rhinovirus-infection-of-ormdl3-transgenic-mice-is-associated-with-reduced-rhinovirus-viral-load-and-airway-inflammation
#6
Dae Jin Song, Marina Miller, Andrew Beppu, Peter Rosenthal, Sudipta Das, Maya Karta, Christine Vuong, Amit Kumar Mehta, Michael Croft, David H Broide
Orosomucoid like 3 (ORMDL3), a gene localized to chromosome 17q21, has been linked in epidemiologic studies to childhood asthma and rhinovirus (RV) infections. As the single nucleotide polymorphisms linking ORMDL3 to asthma are associated with increased expression of ORMDL3, we have used hORMDL3(zp3-Cre) mice (which have universal increased expression of human ORMDL3) to determine whether infection of these transgenic mice with RV influences levels of airway inflammation or RV viral load. RV infection of hORMDL3(zp3-Cre) mice resulted in reduced RV viral load assessed by quantitative real-time PCR (lung and airway epithelium), as well as reduced airway inflammation (total bronchoalveolar lavage cells, neutrophils, macrophages, and lymphocytes) compared with RV-infected wild-type mice...
August 21, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28808124/rapid-rnase-l-driven-arrest-of-protein-synthesis-in-the-dsrna-response-without-degradation-of-translation-machinery
#7
Jesse Donovan, Sneha Rath, David Kolet-Mandrikov, Alexei Korennykh
Mammalian cells respond to double-stranded RNA (dsRNA) by activating a translation-inhibiting endoribonuclease, RNase L. Consensus in the field indicates that RNase L arrests protein synthesis by degrading ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). However, here we provide evidence for a different and far more efficient mechanism. By sequencing abundant RNA fragments generated by RNase L in human cells, we identify site-specific cleavage of two groups of non-coding RNAs: Y-RNAs, whose function is poorly understood, and cytosolic tRNAs, which are essential for translation...
August 14, 2017: RNA
https://www.readbyqxmd.com/read/28804020/porcine-2-5-oligoadenylate-synthetase-2-inhibits-porcine-reproductive-and-respiratory-syndrome-virus-replication-in%C3%A2-vitro
#8
Mengmeng Zhao, Bo Wan, Huawei Li, Jian He, Xinxin Chen, Linjian Wang, Yinbiao Wang, Sha Xie, Songlin Qiao, Gaiping Zhang
Porcine reproductive and respiratory syndrome virus (PRRSV) is acknowledged a fulminating infectious pathogen affecting the pig farming industry, and current vaccines and drugs could hardly inhibit this virus. The 2', 5'-oligoadenylate synthetase (OASs) have antiviral activities, but the role(s) played by porcine OAS2 in protection against PRRSV infection are unknown. Here we found that endogenous expression of the porcine OAS2 gene could be promoted by interferon (IFN)-beta or PRRSV infection in porcine alveolar macrophages...
August 10, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28800975/exopolysaccharides-from-lactobacillus-delbrueckii-oll1073r-1-modulate-innate-antiviral-immune-response-in-porcine-intestinal-epithelial-cells
#9
Paulraj Kanmani, Leonardo Albarracin, Hisakazu Kobayashi, Hikaru Iida, Ryoya Komatsu, A K M Humayun Kober, Wakako Ikeda-Ohtsubo, Yoshihito Suda, Hisashi Aso, Seiya Makino, Hiroshi Kano, Tadao Saito, Julio Villena, Haruki Kitazawa
Previous studies demonstrated that the extracellular polysaccharides (EPSs) produced by Lactobacillus delbrueckii OLL1073R-1 (LDR-1) improve antiviral immunity, especially in the systemic and respiratory compartments. However, it was not studied before whether those EPSs are able to beneficially modulate intestinal antiviral immunity. In addition, LDR-1-host interaction has been evaluated mainly with immune cells while its interaction with intestinal epithelial cells (IECs) was not addressed before. In this work, we investigated the capacity of EPSs from LDR-1 to modulate the response of porcine IECs (PIE cells) to the stimulation with the Toll-like receptor (TLR)-3 agonist poly(I:C) and the role of TLR2, TLR4, and TLR negative regulators in the immunoregulatory effect...
August 8, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28794432/tdp-43-stabilises-the-processing-intermediates-of-mitochondrial-transcripts
#10
Keiichi Izumikawa, Yuko Nobe, Harunori Yoshikawa, Hideaki Ishikawa, Yutaka Miura, Hiroshi Nakayama, Takashi Nonaka, Masato Hasegawa, Naohiro Egawa, Haruhisa Inoue, Kouki Nishikawa, Koji Yamano, Richard J Simpson, Masato Taoka, Yoshio Yamauchi, Toshiaki Isobe, Nobuhiro Takahashi
The 43-kDa trans-activating response region DNA-binding protein 43 (TDP-43) is a product of a causative gene for amyotrophic lateral sclerosis (ALS). Despite of accumulating evidence that mitochondrial dysfunction underlies the pathogenesis of TDP-43-related ALS, the roles of wild-type TDP-43 in mitochondria are unknown. Here, we show that the small TDP-43 population present in mitochondria binds directly to a subset of mitochondrial tRNAs and precursor RNA encoded in L-strand mtDNA. Upregulated expression of TDP-43 stabilised the processing intermediates of mitochondrial polycistronic transcripts and their products including the components of electron transport and 16S mt-rRNA, similar to the phenotype observed in cells deficient for mitochondrial RNase P...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28760200/rna-dependent-stabilization-of-suv39h1-at-constitutive-heterochromatin
#11
Whitney L Johnson, William T Yewdell, Jason C Bell, Shannon M McNulty, Zachary Duda, Rachel J O'Neill, Beth A Sullivan, Aaron F Straight
Heterochromatin formed by the SUV39 histone methyltransferases represses transcription from repetitive DNA sequences and ensures genomic stability. How SUV39 enzymes localize to their target genomic loci remains unclear. Here, we demonstrate that chromatin-associated RNA contributes to the stable association of SUV39H1 with constitutive heterochromatin in human cells. We find that RNA associated with mitotic chromosomes is concentrated at pericentric heterochromatin, and is encoded, in part, by repetitive α-satellite sequences, which are retained in cis at their transcription sites...
August 1, 2017: ELife
https://www.readbyqxmd.com/read/28754636/molecular-cloning-characterization-and-expression-of-duck-2-5-oligoadenylate-synthetase-like-gene
#12
Ke-Ran Bi, Kai-Kai Han, Qing-Tao Liu, Dong-Min Zhao, Xin-Mei Huang, Yu-Zhuo Liu, Jing Yang, Yin Li
2'-5'-Oligoadenylate synthetase-like protein (OASL) is an interferon-inducible antiviral protein that exerts antiviral effects through the RNase L- or retinoic acid-inducible gene I (RIG-I)-dependent signalling pathway. In this study, we identified and cloned the OASL gene (named duOASL) from healthy adult Cherry Valley ducks. Full-length duOASL cDNA (1630bp) encoded a 504-amino acid polypeptide containing three conserved domains, namely, nucleotidyltransferase domain, 2'-5'-oligoadenylate synthetase domain, and two ubiquitin-like repeats...
September 20, 2017: Gene
https://www.readbyqxmd.com/read/28743979/expression-of-rmrp-rna-is-regulated-in-chondrocyte-hypertrophy-and-determines-chondrogenic-differentiation
#13
Mandy M F Steinbusch, Marjolein M J Caron, Don A M Surtel, Franziska Friedrich, Ekkehart Lausch, Ger J M Pruijn, Wouter Verhesen, Blanche L M Schroen, Lodewijk W van Rhijn, Bernhard Zabel, Tim J M Welting
Mutations in the RMRP-gene, encoding the lncRNA component of the RNase MRP complex, are the origin of cartilage-hair hypoplasia. Cartilage-hair hypoplasia is associated with severe dwarfism caused by impaired skeletal development. However, it is not clear why mutations in RMRP RNA lead to skeletal dysplasia. Since chondrogenic differentiation of the growth plate is required for development of long bones, we hypothesized that RMRP RNA plays a pivotal role in chondrogenic differentiation. Expression of Rmrp RNA and RNase MRP protein subunits was detected in the murine growth plate and during the course of chondrogenic differentiation of ATDC5 cultures, where Rmrp RNA expression was found to be correlated with chondrocyte hypertrophy...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28740179/legionella-pneumophila-infection-activates-bystander-cells-differentially-by-bacterial-and-host-cell-vesicles
#14
Anna Lena Jung, Christina Elena Herkt, Christine Schulz, Kathrin Bolte, Kerstin Seidel, Nicoletta Scheller, Alexandra Sittka-Stark, Wilhelm Bertrams, Bernd Schmeck
Extracellular vesicles from eukaryotic cells and outer membrane vesicles (OMVs) released from gram-negative bacteria have been described as mediators of pathogen-host interaction and intercellular communication. Legionella pneumophila (L. pneumophila) is a causative agent of severe pneumonia. The differential effect of bacterial and host cell vesicles in L. pneumophila infection is unknown so far. We infected THP-1-derived or primary human macrophages with L. pneumophila and isolated supernatant vesicles by differential centrifugation...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28675355/induction-of-interferon-and-interferon-induced-antiviral-effector-genes-following-a-primary-bovine-herpesvirus-1-bhv-1-respiratory-infection
#15
Rahwa Osman, Patricia Gonzalez-Cano, Robert Brownlie, Philip J Griebel
Invitro investigations have identified a variety of mechanisms by which herpesviruses evade interferon-stimulated antiviral effector mechanisms. However, these immune evasion mechanisms have not been evaluated during a bovine herpesvirus-1 (BHV-1) infection. This study investigated the transcription and secretion of type I and II interferons (IFNs) and the transcription of IFN-stimulated genes (ISGs) during a primary BHV-1 infection of the upper respiratory tract (URT) in naïve calves. IFN-α, -β and -γ transcription in nasal turbinates and protein levels in nasal secretions increased following infection...
July 5, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28642746/virucidal-activity-of-fogged-chlorine-dioxide-and-hydrogen-peroxide-based-disinfectants-against-human-norovirus-and-its-surrogate-feline-calicivirus-on-hard-to-reach-surfaces
#16
Naim Montazeri, Clyde Manuel, Eric Moorman, Janak R Khatiwada, Leonard L Williams, Lee-Ann Jaykus
Human norovirus (NoV) is the leading cause of foodborne illnesses in the United States. Norovirus is shed in high numbers in the feces and vomitous of infected individuals. Contact surfaces contaminated with bodily fluids harboring infectious virus particles serve as vehicles for pathogen transmission. Environmental stability of NoV and its resistance to many conventional disinfectants necessitate effective inactivation strategies to control the spread of virus. We investigated the efficacy of two commercial disinfectants, hydrogen peroxide (7...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28635965/identification-genealogical-structure-and-population-genetics-of-s-alleles-in-malus-sieversii-the-wild-ancestor-of-domesticated-apple
#17
X Ma, Z Cai, W Liu, S Ge, L Tang
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris...
September 2017: Heredity
https://www.readbyqxmd.com/read/28629774/genome-instabilities-arising-from-ribonucleotides-in-dna
#18
REVIEW
Hannah L Klein
Genomic DNA is transiently contaminated with ribonucleotide residues during the process of DNA replication through misincorporation by the replicative DNA polymerases α, δ and ε, and by the normal replication process on the lagging strand, which uses RNA primers. These ribonucleotides are efficiently removed during replication by RNase H enzymes and the lagging strand synthesis machinery. However, when ribonucleotides remain in DNA they can distort the DNA helix, affect machineries for DNA replication, transcription and repair, and can stimulate genomic instabilities which are manifest as increased mutation, recombination and chromosome alterations...
August 2017: DNA Repair
https://www.readbyqxmd.com/read/28628829/ectromelia-virus-accumulates-less-double-stranded-rna-compared-to-vaccinia-virus-in-bs-c-1-cells
#19
Tiffany R Frey, Michael H Lehmann, Colton M Ryan, Marie C Pizzorno, Gerd Sutter, Adam R Hersperger
Most orthopoxviruses, including vaccinia virus (VACV), contain genes in the E3L and K3L families. The protein products of these genes have been shown to combat PKR, a host defense pathway. Interestingly, ectromelia virus (ECTV) contains an E3L ortholog but does not possess an intact K3L gene. Here, we gained insight into how ECTV can still efficiently evade PKR despite lacking K3L. Relative to VACV, we found that ECTV-infected BS-C-1 cells accumulated considerably less double-stranded (ds) RNA, which was due to lower mRNA levels and less transcriptional read-through of some genes by ECTV...
September 2017: Virology
https://www.readbyqxmd.com/read/28621789/display-of-functional-proteins-on-supramolecular-peptide-nanofibrils-using-a-split-protein-strategy
#20
John T M DiMaio, Danielle M Raymond, Bradley L Nilsson
The display of functional proteins on self-assembled peptide nanofibrils is challenging since the steric bulk of proteins attached to simple self-assembling peptides often impedes incorporation into nanofibrils. Herein is described a split-protein strategy to tether functional proteins to preassembled peptide nanofibrils. In this strategy, a short affinity motif peptide derived from a split protein system is appended to a self-assembly motif (the amphipathic Ac-(FKFE)2-NH2 peptide) to form an affinity-assembly fusion peptide...
June 27, 2017: Organic & Biomolecular Chemistry
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