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https://www.readbyqxmd.com/read/28081470/inhibition-viral-rnp-and-anti-inflammatory-activity-of-coumarins-against-influenza-virus
#1
YuTao Wang, Wen Yan, QiaoLian Chen, WanYi Huang, Zifeng Yang, Xiong Li, XinHua Wang
Influenza viruses pose a severe threat to human health and a significant increase in antiviral drug-resistant among influenza viruses worldwide has been observed. Therefore, there is an urgent need to develop the new antiviral drugs, specifically from the natural products. In this study, the anti-viral and anti-inflammatory activities of coumarins against influenza A virus in vitro were investigated. One of the derivatives eleutheroside B1 showed a wide spectrum of anti- human influenza virus effect with the IC50 value of 64-125μg/ml in vitro, but it showed no effects against avian influenza virus...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28076346/cryo-em-structure-of-a-human-spliceosome-activated-for-step-2-of-splicing
#2
Karl Bertram, Dmitry E Agafonov, Wen-Ti Liu, Olexandr Dybkov, Cindy L Will, Klaus Hartmuth, Henning Urlaub, Berthold Kastner, Holger Stark, Reinhard Lu Hrmann
Spliceosome rearrangements facilitated by RNA helicase Prp16 before catalytic step 2 of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after Prp16 action (C*). The architecture of the catalytic U2-U6 RNP core of the human C* spliceosome is highly similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated (by ~20 Å) from the catalytic centre, and its position close to the U6 snRNA ACAGA box is stabilised by interactions with the Prp8 RNase H-like and Prp17 WD40 domains...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28062037/single-molecule-insight-into-target-recognition-by-crispr-cas-complexes
#3
M Rutkauskas, A Krivoy, M D Szczelkun, C Rouillon, R Seidel
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28052104/insertional-mutagenesis-by-crispr-cas9-ribonucleoprotein-gene-editing-in-cells-targeted-for-point-mutation-repair-directed-by-short-single-stranded-dna-oligonucleotides
#4
Natalia Rivera-Torres, Kelly Banas, Pawel Bialk, Kevin M Bloh, Eric B Kmiec
CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells...
2017: PloS One
https://www.readbyqxmd.com/read/28041848/spatiotemporal-control-of-intracellular-phase-transitions-using-light-activated-optodroplets
#5
Yongdae Shin, Joel Berry, Nicole Pannucci, Mikko P Haataja, Jared E Toettcher, Clifford P Brangwynne
Phase transitions driven by intrinsically disordered protein regions (IDRs) have emerged as a ubiquitous mechanism for assembling liquid-like RNA/protein (RNP) bodies and other membrane-less organelles. However, a lack of tools to control intracellular phase transitions limits our ability to understand their role in cell physiology and disease. Here, we introduce an optogenetic platform that uses light to activate IDR-mediated phase transitions in living cells. We use this "optoDroplet" system to study condensed phases driven by the IDRs of various RNP body proteins, including FUS, DDX4, and HNRNPA1...
January 12, 2017: Cell
https://www.readbyqxmd.com/read/28032591/the-pre-existing-population-of-5s-rrna-effects-p53-stabilization-during-ribosome-biogenesis-inhibition
#6
Carmine Onofrillo, Alice Galbiati, Lorenzo Montanaro, Massimo Derenzini
Pre-ribosomal complex RPL5/RPL11/5S rRNA (5S RNP) is considered the central MDM2 inhibitory complex that control p53 stabilization during ribosome biogenesis inhibition. Despite its role is well defined, the dynamic of 5S RNP assembly still requires further characterization. In the present work, we report that MDM2 inhibition is dependent by a pre-existing population of 5S rRNA.
December 9, 2016: Oncotarget
https://www.readbyqxmd.com/read/28027957/site-directed-chemical-probing-to-map-transient-rna-protein-interactions
#7
Mélodie Duval, Alessandra Marenna, Clément Chevalier, Stefano Marzi
RNA-protein interactions are at the bases of many biological processes, forming either tight and stable functional ribonucleoprotein (RNP) complexes (i.e. the ribosome) or transitory ones, such as the complexes involving RNA chaperone proteins. To localize the sites where a protein interacts on an RNA molecule, a common simple and inexpensive biochemical method is the footprinting technique. The protein leaves its footprint on the RNA acting as a shield to protect the regions of interaction from chemical modification or cleavages obtained with chemical or enzymatic nucleases...
December 24, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28008714/bioinformatic-tools-for-analysis-of-clip-ribonucleoprotein-data
#8
REVIEW
Supriyo De, Myriam Gorospe
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28007449/structural-studies-of-influenza-virus-rnps-by-electron-microscopy-indicate-molecular-contortions-within-np-supra-structures
#9
John R Gallagher, Udana Torian, Dustin M McCraw, Audray K Harris
Ribonucleoprotein (RNP) complexes of influenza viruses are composed of multiple copies of the viral nucleoprotein (NP) that can form filamentous supra-structures. RNPs package distinct viral genomic RNA segments of different lengths into pleomorphic influenza virions. RNPs also function in viral RNA transcription and replication. Different RNP segments have varying lengths, but all must be incorporated into virions during assembly and then released during viral entry for productive infection cycles. RNP structures serve varied functions in the viral replication cycle, therefore understanding their molecular organization and flexibility is essential to understanding these functions...
December 19, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27999116/revisiting-gnra-and-uncg-folds-u-turns-versus-z-turns-in-rna-hairpin-loops
#10
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion occurs for loops with UNCG sequences, for instance within tRNA anticodon loops...
December 20, 2016: RNA
https://www.readbyqxmd.com/read/27988434/anti-ro-ssa-and-anti-la-ssb-antibodies-association-with-mild-lupus-manifestations-in-645-childhood-onset-systemic-lupus-erythematosus
#11
REVIEW
Glaucia V Novak, Mariana Marques, Verena Balbi, Natali W S Gormezano, Kátia Kozu, Ana P Sakamoto, Rosa M R Pereira, Maria T Terreri, Claudia S Magalhães, Andressa Guariento, Adriana M E Sallum, Roberto Marini, Virginia Paes Leme Ferriani, Cássia Maria Barbosa, Tânia Caroline Monteiro de Castro, Valéria C Ramos, Eloisa Bonfá, Clovis A Silva
BACKGROUND: To our knowledge there are no studies assessing anti-Ro/SSA and anti-La/SSB autoantibodies in a large population of childhood-systemic lupus erythematosus(cSLE) patients. METHODS: This was a retrospective multicenter cohort study performed in 10 Pediatric Rheumatology services, São Paulo state, Brazil. Anti-Ro/SSA and anti-La/SSB antibodies were measured by enzyme linked immunosorbent assay(ELISA) in 645 cSLE patients. RESULTS: Anti-Ro/SSA and anti-La/SSB antibodies were evidenced in 209/645(32%) and 102/645(16%) of cSLE patients, respectively...
December 14, 2016: Autoimmunity Reviews
https://www.readbyqxmd.com/read/27975019/usefulness-of-the-clavien-dindo-classification-in-understanding-the-limitations-and-indications-of-larynx-preserving-esophageal-reconstruction
#12
Hiroki Umezawa, Junichi Nakao, Takeshi Matsutani, Hiroaki Kuwahara, Marie Taga, Rei Ogawa
BACKGROUND: The Clavien-Dindo (CD) classification is used to evaluate the severity of surgical complications. However, its usefulness in esophageal reconstruction has not been reported. To address this, this case series study used the CD classification to evaluate the complications after cervical esophageal reconstruction with free jejunum transfer or supercharged pedicled intestinal transfer. METHODS: All consecutive patients who underwent esophageal cancer surgery with larynx-preserving free jejunum or pedicled ileocolic transfer in June 2012-December 2015 were identified...
November 2016: Plastic and Reconstructive Surgery. Global Open
https://www.readbyqxmd.com/read/27940596/predicting-cardiopulmonary-involvement-in-patients-with-systemic-sclerosis-complementary-value-of-nailfold-videocapillaroscopy-patterns-and-disease-specific-autoantibodies
#13
Iris M Markusse, Jessica Meijs, Berber de Boer, Jaap A Bakker, H Pascal C Schippers, Anne A Schouffoer, Nina Ajmone Marsan, Lucia J M Kroft, Maarten K Ninaber, Tom W J Huizinga, Jeska K de Vries-Bouwstra
OBJECTIVE: To evaluate the prevalence of anti-extractable nuclear antigen (anti-ENA) antibodies in Dutch SSc patients and the predictive power of the combination of specific anti-ENA antibodies and nailfold videocapillaroscopy (NVC) patterns to improve identification of patients with high risk for cardiopulmonary involvement. METHODS: A total of 287 patients (79%) from the Leiden SSc-Cohort had data available on NVC-pattern (no SSc-specific, early, active, late) and anti-ENA antibodies...
December 10, 2016: Rheumatology
https://www.readbyqxmd.com/read/27935277/structural-roles-of-noncoding-rnas-in-the-heart-of-enzymatic-complexes
#14
William J Martin, Nicholas J Reiter
Over billions of years of evolution, nature has embraced proteins as the major workhorse molecules of the cell. However, nearly every aspect of metabolism is dependent upon how structured RNAs interact with proteins, ligands, and other nucleic acids. Key processes, including telomere maintenance, RNA processing, and protein synthesis, require large RNAs that assemble into elaborate three-dimensional shapes. These RNAs can (i) act as flexible scaffolds for protein subunits, (ii) participate directly in substrate recognition, and (iii) serve as catalytic components...
December 29, 2016: Biochemistry
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#15
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27929729/fyco1-and-autophagy-control-the-integrity-of-the-haploid-male-germ-cell-specific-rnp-granules
#16
Matteo Da Ros, Tiina Lehtiniemi, Opeyemi Olotu, Daniel Fischer, Fu-Ping Zhang, Helena Vihinen, Eija Jokitalo, Anu Sironen, Jorma Toppari, Noora Kotaja
Ribonucleoprotein (RNP) granules play a major role in compartmentalizing cytoplasmic RNA regulation. Haploid round spermatids that have exceptionally diverse transcriptomes are characterized by a unique germ cell-specific RNP granule, the chromatoid body (CB). The CB shares many characteristics with somatic RNP granules but also has germline-specific features. The CB appears to be a central structure in PIWI-interacting RNA (piRNA)-targeted RNA regulation. Here, we identified a novel CB component, FYCO1, which is involved in the intracellular transport of autophagic vesicles in somatic cells...
December 8, 2016: Autophagy
https://www.readbyqxmd.com/read/27923990/regulation-of-prp43-mediated-disassembly-of-spliceosomes-by-its-cofactors-ntr1-and-ntr2
#17
Jean-Baptiste Fourmann, Marcel J Tauchert, Ralf Ficner, Patrizia Fabrizio, Reinhard Lührmann
The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assembled/wild-type spliceosomes remains unclear. First, we show that Ntr1's G-patch motif (Ntr1GP) can be replaced by the GP motif of Pfa1/Sqs1, a Prp43's cofactor in ribosome biogenesis, demonstrating that the specific function of Ntr1GP is to activate Prp43 for spliceosome disassembly and not to guide Prp43 to its binding site in the spliceosome...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902801/achieving-plant-crispr-targeting-that-limits-off-target-effects
#18
Jeffrey D Wolt, Kan Wang, Dipali Sashital, Carolyn J Lawrence-Dill
The CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein) has been used to generate targeted changes for direct modification of endogenous genes in an increasing number of plant species; but development of plant genome editing has not yet fully considered potential off-target mismatches that may lead to unintended changes within the genome. Assessing the specificity of CRISPR-Cas9 for increasing editing efficiency as well as the potential for unanticipated downstream effects from off-target mutations is an important regulatory consideration for agricultural applications...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27892924/the-pattern-recognition-receptor-core-of-solanaceae-detects-bacterial-cold-shock-protein
#19
Lei Wang, Markus Albert, Elias Einig, Ursula Fürst, Damaris Krust, Georg Felix
Plants and animals recognize microbial invaders by detecting microbe-associated molecular patterns (MAMPs) by cell surface receptors. Many plant species of the Solanaceae family detect the highly conserved nucleic acid binding motif RNP-1 of bacterial cold-shock proteins (CSPs), represented by the peptide csp22, as a MAMP. Here, we exploited the natural variation in csp22 perception observed between cultivated tomato (Solanum lycopersicum) and Solanum pennellii to map and identify the leucine-rich repeat (LRR) receptor kinase CORE (cold shock protein receptor) of tomato as the specific, high-affinity receptor site for csp22...
November 28, 2016: Nature Plants
https://www.readbyqxmd.com/read/27882870/large-scale-remodeling-of-a-repressed-exon-ribonucleoprotein-to-an-exon-definition-complex-active-for-splicing
#20
Somsakul Pop Wongpalee, Ajay Vashisht, Shalini Sharma, Darryl Chui, James A Wohlschlegel, Douglas L Black
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition...
November 24, 2016: ELife
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