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https://www.readbyqxmd.com/read/28105959/expression-of-an-extracellular-ribonuclease-gene-increases-resistance-to-cucumber-mosaic-virus-in-tobacco
#1
Teppei Sugawara, Ekaterina A Trifonova, Alex V Kochetov, Yoshinori Kanayama
BACKGROUND: The apoplast plays an important role in plant defense against pathogens. Some extracellular PR-4 proteins possess ribonuclease activity and may directly inhibit the growth of pathogenic fungi. It is likely that extracellular RNases can also protect plants against some viruses with RNA genomes. However, many plant RNases are multifunctional and the direct link between their ribonucleolytic activity and antiviral defense still needs to be clarified. In this study, we evaluated the resistance of Nicotiana tabacum plants expressing a non-plant single-strand-specific extracellular RNase against Cucumber mosaic virus...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105550/stable-isotope-labeling-for-improved-comparative-analysis-of-rna-digests-by-mass-spectrometry
#2
Mellie June Paulines, Patrick A Limbach
Even with the advent of high throughput methods to detect modified ribonucleic acids (RNAs), mass spectrometry remains a reliable method to detect, characterize, and place post-transcriptional modifications within an RNA sequence. Here we have developed a stable isotope labeling comparative analysis of RNA digests (SIL-CARD) approach, which improves upon the original (18)O/(16)O labeling CARD method. Like the original, SIL-CARD allows sequence or modification information from a previously uncharacterized in vivo RNA sample to be obtained by direct comparison with a reference RNA, the sequence of which is known...
January 19, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28104774/microrna-biomarkers-and-platelet-reactivity-the-clot-thickens
#3
REVIEW
Nicholas Sunderland, Philipp Skroblin, Temo Barwari, Rachael P Huntley, Ruifang Lu, Abhishek Joshi, Ruth C Lovering, Manuel Mayr
Over the last few years, several groups have evaluated the potential of microRNAs (miRNAs) as biomarkers for cardiometabolic disease. In this review, we discuss the emerging literature on the role of miRNAs and other small noncoding RNAs in platelets and in the circulation, and the potential use of miRNAs as biomarkers for platelet activation. Platelets are a major source of miRNAs, YRNAs, and circular RNAs. By harnessing multiomics approaches, we may gain valuable insights into their potential function. Because not all miRNAs are detectable in the circulation, we also created a gene ontology annotation for circulating miRNAs using the gene ontology term extracellular space as part of blood plasma...
January 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28100693/viral-genome-packaging-terminase-cleaves-dna-using-the-canonical-ruvc-like-two-metal-catalysis-mechanism
#4
Rui-Gang Xu, Huw T Jenkins, Maria Chechik, Elena V Blagova, Anna Lopatina, Evgeny Klimuk, Leonid Minakhin, Konstantin Severinov, Sandra J Greive, Alfred A Antson
Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn(2+), Mg(2+) or Co(2+) ions for activity, but is inactive with Zn(2+) and Ca(2+) High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28093272/a-method-for-obtaining-simian-immunodeficiency-virus-rna-sequences-from-laser-capture-microdissected-and-immune-captured-cd68-and-cd163-macrophages-from-frozen-tissue-sections-of-bone-marrow-and-brain
#5
Jaclyn Mallard, Emily Papazian, Caroline Soulas, David J Nolan, Marco Salemi, Kenneth C Williams
Laser capture microdissection (LCM) is used to extract cells or tissue regions for analysis of RNA, DNA or protein. Several methods of LCM are established for different applications, but a protocol for consistently obtaining lentiviral RNA from LCM captured immune cell populations is not described. Obtaining optimal viral RNA for analysis of viral genes from immune-captured cells using immunohistochemistry (IHC) and LCM is challenging. IHC protocols have long antibody incubation times that increase risk of RNA degradation...
January 13, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28093074/insights-into-the-design-and-interpretation-of-iclip-experiments
#6
Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W Hentze, Andreas E Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R Sibley, Kathi Zarnack, Jernej Ule
BACKGROUND: Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis. This variety of approaches can create challenges for a novice user and can hamper insights from multi-study comparisons. Here, we produce data with multiple variants of CLIP and evaluate the data with various computational methods to better understand their suitability...
January 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28092684/biallelic-mutations-in-the-3-exonuclease-toe1-cause-pontocerebellar-hypoplasia-and-uncover-a-role-in-snrna-processing
#7
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen, Joseph G Gleeson
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg(2+)-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28090736/rna-protection-is-effectively-achieved-by-pullulan-film-formation
#8
Yingfu Li, Ping-Yao Hsieh, Monsur Ali, Kha Tram, Sana Jahanshahi-Anbuhi, Christine Brown, John Brennan, Carlos Filipe
RNA is a functionally versatile polymer but suffers from susceptibility to spontaneous or RNase-catalyzed degradation. This vulnerability makes it difficult to preserve RNA for extended periods of time, which limits its use in various contexts, including practical applications of functional nucleic acids. Here we present a simple method to preserve RNA by pullulan (a complex sugar produced by Aureobasidium pullulans fungus) film formation. This strategy can markedly suppress both spontaneous and RNase-promoted degradation...
January 15, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28088905/update-on-recent-developments-in-small-molecular-hiv-1-rnase-h-inhibitors-2013-2016-opportunities-and-challenges
#9
Xueshun Wang, Ping Gao, Luis Menéndez-Arias, Xinyong Liu, Peng Zhan
Combinations of antiretroviral drugs are successfully used to treat HIV-infected patients. However, drug resistance is a major problem that makes discovery of new antiretroviral drugs an ongoing priority. The ribonuclease H (RNase H) activity of the HIV-1 reverse transcriptase catalyzes the selective hydrolysis of the RNA strand of RNA:DNA heteroduplex replication intermediates, and represents an attractive unexploited target for drug development. This review reports on recent progress in the characterization of HIV-1 RNase H inhibitors from 2013 to 2016, describing their chemical structures, structure-activity relationship and binding modes...
January 13, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28088361/purification-and-characterisation-of-dsrna-using-ion-pair-reverse-phase-chromatography-and-mass-spectrometry
#10
Alison O Nwokeoji, An-Wen Kung, Peter M Kilby, David E Portwood, Mark J Dickman
RNA interference has provided valuable insight into a wide range of biological systems and is a powerful tool for the analysis of gene function. The exploitation of this pathway to block the expression of specific gene targets holds considerable promise for the development of novel RNAi-based insect management strategies. In addition, there are a wide number of future potential applications of RNAi to control agricultural insect pests as well as its use for prevention of diseases in beneficial insects. The potential to synthesise large quantities of dsRNA by in-vitro transcription or in bacterial systems for RNA interference applications has generated significant demand for the development and application of high throughput analytical tools for the rapid extraction, purification and analysis of dsRNA...
December 21, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28079937/cereal-immunity-against-powdery-mildews-targets-rnase-like-proteins-associated-with-haustoria-ralph-effectors-evolved-from-a-common-ancestral-gene
#11
https://www.readbyqxmd.com/read/28079792/amplification-of-her2-and-top2a-and-deletion-of-top2a-genes-in-a-series-of-taiwanese-breast-cancer
#12
Jim-Ray Chen, Hui-Ping Chien, Kuo-Su Chen, Cheng-Cheng Hwang, Huang-Yang Chen, Kun-Yan Yeh, Tsan-Yu Hsieh, Liang-Che Chang, Yuan-Chun Hsu, Ren-Jie Lu, Chung-Ching Hua
BACKGROUND: The prognostic relevance of topoisomerase II alpha (TOP2A) copy number change remains not well established. This study is aimed to investigate the frequency and pattern of TOP2A aberrations; to correlate TOP2A alterations with human epidermal growth factor receptor 2 (HER2) status and clinicopathological parameters, and further to explore prognostic value of TOP2A and HER2 status in breast cancer in Taiwan. METHODS: We analyzed tissue samples from 311 invasive carcinomas in tissue microarrays for TOP2A and HER2 status by fluorescent in situ hybridization...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28077645/herpes-simplex-virus-1-abrogates-cgas-sting-mediated-cytosolic-dna-sensing-pathway-via-its-virion-host-shutoff-protein-ul41
#13
Chenhe Su, Chunfu Zheng
: Cyclic GMP-AMP synthase (cGAS) is a key DNA sensor capable of detecting microbial DNA and activating the adaptor protein stimulator of interferon genes (STING), leading to interferon (IFN) production and host antiviral responses. Cells exhibited reduced type I IFN production in response to cytosolic DNA in the absence of cGAS. Although cGAS/STING-mediated DNA-sensing signal is crucial for host defense against many viruses, especial for DNA viruses, few viral components have been identified to specifically target this signaling pathway...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#14
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3' end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28076346/cryo-em-structure-of-a-human-spliceosome-activated-for-step-2-of-splicing
#15
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/28074027/a-unique-cis-encoded-small-noncoding-rna-is-regulating-legionella-pneumophila-hfq-expression-in-a-life-cycle-dependent-manner
#16
Giulia Oliva, Tobias Sahr, Monica Rolando, Maike Knoth, Carmen Buchrieser
: Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires' disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28067412/broadening-the-phenotypic-spectrum-of-pop1-skeletal-dysplasias-identification-of-pop1-mutations-in-a-mild-and-severe-skeletal-dysplasia
#17
Jimena Barraza-García, Carlos I Rivera-Pedroza, Alfonso Hisado-Oliva, Alberta Belinchón-Martínez, Lucia Sentchordi-Montané, Emma L Duncan, Graeme R Clark, Angela Del Pozo, Kristina Ibáñez-Garikano, Amaka Offiah, Pablo Prieto-Matos, Valerie Cormier-Daire, Karen E Heath
POP1 is a large protein common to the RNase-MRP and RNase-P (RMRP) endoribonucleoprotein complexes. Although its precise function is unknown, it appears to participate in the assembly or stability of both complexes. Numerous RMRP mutations have been reported in individuals with cartilage hair hypoplasia (CHH) but, to date, only three POP1 mutations have been described in two families with features similar to anauxetic dysplasia (AD). We present two further individuals, one with severe short stature and a relatively mild skeletal dysplasia and another in whom AD was suspected...
January 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28065739/r-loop-depletion-by-over-expressed-rnase-h1-in-mouse-b-cells-increases-activation-induced-deaminase-access-to-the-transcribed-strand-without-altering-frequency-of-isotype-switching
#18
Robert W Maul, Hyongi Chon, Kiran Sakhuja, Susana M Cerritelli, Lina A Gugliotti, Patricia J Gearhart, Robert J Crouch
R-loops, three-strand structures consisting of mRNA hybridized to the complementary DNA and a single-stranded DNA loop, are formed in switch regions on the heavy-chain immunoglobulin locus. To determine if R-loops have a direct effect on any of the steps involved in isotype switching, we generated a transgenic mouse that over-expressed RNase H1, an enzyme that cleaves the RNA of RNA/DNA hybrids in B cells. R-loops in the switch μ region were depleted by 70% in ex vivo activated splenic B cells. Frequencies of isotype switching to IgG1, IgG2b, IgG2c, and IgG3 were the same as C57BL/6 control cells...
January 6, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#19
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
January 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28064315/-activation-of-biosynthesis-of-guanyl-specific-ribonuclease-secreted-by-bacillus-circulans-under-salt-stress
#20
M A Kharitonova, L V Kipenskaya, O N Ilinskaya
The gene transcription of guanyl-specific ribonucleases (RNases), which provide available phosphate to cells of Bacillus, is controlled by the signal transduction system PhoP-PhoR. However, the biosynthesis of B. circulans RNase does not depend on the signal-transduction regulatory proteins of Pho regulon. It has been found that raising the salt molar concentration in culture medium increases the level of extracellular guanyl-specific ribonuclease Bci synthesized by B. circulans. Sequences homologous to the binding sites of the regulatory protein DegU were found in RNase Bci promoter...
November 2016: Molekuliarnaia Biologiia
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