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RNA metabolism

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https://www.readbyqxmd.com/read/28937776/4-c-methoxy-2-deoxy-2-fluoro-modified-ribonucleotides-improve-metabolic-stability-and-elicit-efficient-rnai-mediated-gene-silencing
#1
Elise Malek-Adamian, Dale Guenther, Shigeo Matsuda, Saúl Martínez-Montero, Ivan Zlatev, Joel Harp, Mihai Burai Patrascu, Donald J Foster, Johans J Fakhoury, Lydia Perkins, Nicolas Moitessier, Rajar Manoharan, Nate Taneja, Anna Bisbe, Klaus Charisse, Martin A Maier, Kallanthottathil G Rajeev, Martin Egli, Muthiah Manoharan, Masad J Damha
We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a non-stereoselective approach starting from 2'-F U. (1)H-NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias towards the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects...
September 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28937658/extracellular-vesicle-associated-rna-as-a-carrier-of-epigenetic-information
#2
REVIEW
Carlo Maria Di Liegro, Gabriella Schiera, Italia Di Liegro
Post-transcriptional regulation of messenger RNA (mRNA) metabolism and subcellular localization is of the utmost importance both during development and in cell differentiation. Besides carrying genetic information, mRNAs contain cis-acting signals (zip codes), usually present in their 5'- and 3'-untranslated regions (UTRs). By binding to these signals, trans-acting factors, such as RNA-binding proteins (RBPs), and/or non-coding RNAs (ncRNAs), control mRNA localization, translation and stability. RBPs can also form complexes with non-coding RNAs of different sizes...
September 22, 2017: Genes
https://www.readbyqxmd.com/read/28936677/prokaryotic-assemblages-in-the-maritime-antarctic-lake-limnopolar-byers-peninsula-south-shetland-islands
#3
M Papale, C Rizzo, J A Villescusa, C Rochera, A Camacho, L Michaud, A Lo Giudice
The potentially metabolically active components within the prokaryotic assemblages inhabiting the Antarctic Lake Limnopolar (Byers Peninsula, Maritime Antarctica) were investigated by a polyphasic approach which included culture-dependent and culture-independent methods (based on RNA molecules). Results support previous observations on the Proteobacteria and Bacteroidetes dominance, followed by Actinobacteria, in Antarctic lakes. In particular, Alpha-, Betaproteobacteria and Bacteroidetes were mainly detected by CARD-FISH and cDNA cloning, whereas Gammaproteobacteria and Actinobacteria dominated within the cultivable fraction...
September 21, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28936208/cas9-nickase-assisted-rna-repression-enables-stable-and-efficient-manipulation-of-essential-metabolic-genes-in-clostridium-cellulolyticum
#4
Tao Xu, Yongchao Li, Zhili He, Joy D Van Nostrand, Jizhong Zhou
Essential gene functions remain largely underexplored in bacteria. Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing; however, its genetic manipulation to reduce the formation of less-valuable acetate is technically challenging due to the essentiality of acetate-producing genes. Here we developed a Cas9 nickase-assisted chromosome-based RNA repression to stably manipulate essential genes in C. cellulolyticum. Our plasmid-based expression of antisense RNA (asRNA) molecules targeting the phosphotransacetylase (pta) gene successfully reduced the enzymatic activity by 35% in cellobiose-grown cells, metabolically decreased the acetate titer by 15 and 52% in wildtype transformants on cellulose and xylan, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28935979/intergrative-metabolomic-and-transcriptomic-analyses-unveil-nutrient-remobilization-events-in-leaf-senescence-of-tobacco
#5
Wei Li, Hailiang Zhang, Xiaoxu Li, Fengxia Zhang, Cheng Liu, Yongmei Du, Xiaoming Gao, Zenglin Zhang, Xiaobing Zhang, Zhihui Hou, Hui Zhou, Xiaofei Sheng, Guodong Wang, Yongfeng Guo
Leaf senescence in plants is a coordinated process that involves remobilization of nutrients from senescing leaves to sink tissues. The molecular events associated with nutrient remobilization are however not well understood. In this study the tobacco system with a source-sink relationship between different leaf positions was used in analyzing the spatiotemporal changes of 76 metabolites from leaves at 3 different stalk positions and 8 developmental stages. The metabolomic data was then compared with RNA-seq data from the same samples to analyze the activities of the metabolic pathways that are important for nutrient remobilization...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935950/transcriptome-analyses-suggest-a-novel-hypothesis-for-whitefly-adaptation-to-tobacco
#6
Wen-Qiang Xia, Xin-Ru Wang, Yan Liang, Shu-Sheng Liu, Xiao-Wei Wang
The adaptation of herbivorous insects to various host plants facilitates the spread and outbreak of many important invasive pests, however, the molecular mechanisms that underneath this process are poorly understood. In the past three decades, two species of the whitefly Bemisia tabaci complex, Middle East-Asia Minor 1 and Mediterranean, have invaded many countries. Their rapid and widespread invasions are partially due to their ability to infest a wide range of host plants. In this study, we determined the transcriptome and phenotypic changes of one Mediterranean whitefly population during its adaptation to tobacco, an unsuitable host plant...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935841/light-and-plastid-signals-regulate-different-sets-of-genes-in-the-albino-mutant-pap7-1
#7
Björn Grübler, Livia Merendino, Sven O Twardziok, Morgane Mininno, Guillaume Allorent, Fabien Chevalier, Monique Liebers, Robert Blanvillain, Klaus Mayer, Silva Lerbs-Mache, Stephane Ravanel, Thomas Pfannschmidt
Plants possessing dysfunctional plastids due to defects in pigment biosynthesis or translation are known to repress photosynthesis-associated nuclear genes (PhANGs) via retrograde signals from the disturbed organelles towards the nucleus. These signals are thought to be essential for proper biogenesis and function of the plastid. Mutants lacking plastid-encoded RNA polymerase-associated proteins (PAPs) display a genetic arrest in eoplast-chloroplast transition leading to an albino phenotype in the light. Retrograde signaling in these mutants, thus, could be expected to be similar as under conditions inducing plastid dysfunction...
September 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28935149/molecular-aspects-of-cancer-chemopreventive-and-therapeutic-efficacies-of-tea-and-tea-polyphenols
#8
REVIEW
Subhayan Sur, Chinmay Kumar Panda
The natural dietary product tea (Camellia sinensis) and its bioactive polyphenols such as epigallocatechin gallate (EGCG) and theaflavin (TF) demonstrated potential anticancer effects in different preclinical and clinical studies. The aim of the present review was to understand the molecular mechanisms of the tea and tea polyphenol-mediated cancer prevention and therapy. In the setting of in vivo cancer prevention studies, administration of the tea and tea polyphenols at preinitiation stages only showed partial prevention, whereas continuous administration showed potential effect in restriction of carcinogenesis in the body's multiple organs at early premalignant stages throughout the experiment...
November 2017: Nutrition
https://www.readbyqxmd.com/read/28934490/number-of-inadvertent-rna-targets-for-morpholino-knockdown-in-danio-rerio-is-largely-underestimated-evidence-from-the-study-of-ser-arg-rich-splicing-factors
#9
Marine Joris, Marie Schloesser, Denis Baurain, Marc Hanikenne, Marc Muller, Patrick Motte
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934375/into-the-wild-parallel-transcriptomics-of-the-tsetse-wigglesworthia-mutualism-within-kenyan-populations
#10
Miguel Medina Munoz, Adam R Pollio, Hunter L White, Rita V M Rio
Tsetse flies (Diptera: Glossinidae) have medical significance as the obligate vectors of African trypanosomes. In addition, tsetse harbor a simple gut microbiota. A predominant gut microbiota member, the Gammaproteobacterium Wigglesworthia spp., has coevolved with tsetse for a significant portion of Glossina radiation proving critical to tsetse fitness. Although multiple roles have been described for Wigglesworthia within colony flies, little research has been dedicated towards functional characterization within wild tsetse...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#11
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28934090/adipogenic-effects-and-gene-expression-profiling-of-firemaster%C3%A2-550-components-in-human-primary-preadipocytes
#12
Emily W Y Tung, Vian Peshdary, Remi Gagné, Andrea Rowan-Carroll, Carole L Yauk, Adéle Boudreau, Ella Atlas
BACKGROUND: Exposure to flame retardants has been associated with negative health outcomes including metabolic effects. As polybrominated diphenyl ether flame retardants were pulled from commerce, human exposure to new flame retardants such as Firemaster® 550 (FM550) has increased. Although previous studies in murine systems have shown that FM550 and its main components increase adipogenesis, the effects of FM550 in human models have not been elucidated. OBJECTIVES: The objectives of this study were to determine if FM550 and its components are active in human preadipocytes, and to further investigate their mode of action...
September 14, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28934014/nucleoplasmic-nup98-controls-gene-expression-by-regulating-a-dexh-d-box-protein
#13
Juliana S Capitanio, Ben Montpetit, Richard W Wozniak
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, (1-3) but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. (4-6) Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity...
September 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28933412/genetic-substrate-reduction-therapy-a-promising-approach-for-lysosomal-storage-disorders
#14
REVIEW
Maria Francisca Coutinho, Juliana Inês Santos, Liliana Matos, Sandra Alves
Lysosomal storage diseases are a group of rare genetic disorders characterized by the accumulation of storage molecules in late endosomes/lysosomes. Most of them result from mutations in genes encoding for the catabolic enzymes that ensure intralysosomal digestion. Conventional therapeutic options include enzyme replacement therapy, an approach targeting the functional loss of the enzyme by injection of a recombinant one. Even though this is successful for some diseases, it is mostly effective for peripheral manifestations and has no impact on neuropathology...
November 9, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28933110/-effect-of-lanthanum-on-accumulation-of-active-constituent-and-key-enzymes-expression-of-salvia-miltiorrhiza-hairy-root
#15
Li-Hua Bian, Lin Zou, Bing-Qian Zhou, Wei Liu, Jie Zhou, Xiao Wang
The effect of Lanthanum on the accumulation of active constituent and key enzymes expression of Salvia miltiorrhiza hairy root were studied and furthermore signaling molecules mediating the synthesis of secondary metabolism was also defined in order to provide references for the reveal of synthesis mechanism of active constituent of S. miltiorrhiza hairy root inducing by Lanthanum. The content of active constituents were detected by HPLC. RNA was extracted with RNA prep Pure RNA purification kit (Tiangen). The results shows that LaCl3 processing promoted the accumulation of tanshinones and phenolic acids in S...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932910/a-histone-deacetylase-gene-slhda3-acts-as-a-negative-regulator-of-fruit-ripening-and-carotenoid-accumulation
#16
Jun-E Guo, Zongli Hu, Xiaohui Yu, Anzhou Li, Fenfen Li, Yunshu Wang, Shibing Tian, Guoping Chen
SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone acetyltransferases and deacetylases, which play crucial roles in the regulation of transcription activation. There is an increasing research focus on histone deacetylation in crops, but the role of histone deacetylase genes (HDACs) in tomato has not been elucidated...
September 20, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28932082/effects-and-mechanism-of-adenovirus-mediated-phosphatase-and-tension-homologue-deleted-on-chromosome-ten-gene-on-collagen-deposition-in-rat-liver-fibrosis
#17
Shu-Rui Xie, Jun-Yan An, Li-Bo Zheng, Xiao-Xia Huo, Jian Guo, David Shih, Xiao-Lan Zhang
AIM: To evaluate the effects of phosphatase and tension homologue deleted on chromosome ten (PTEN) gene on collagen metabolism in hepatic fibrosis and the underlying mechanisms. METHODS: Rat primary hepatic stellate cells (HSCs) and human LX-2 cells were transfected with adenovirus containing cDNA constructs encoding wild-type PTEN (Ad-PTEN), PTEN mutant G129E gene (Ad-G129E), and RNA interference constructs targeting the PTEN sequence PTEN short hairpin RNA to up-regulate and down-regulate the expression of PTEN...
August 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28931848/integrated-analysis-of-microrna-and-mrna-expression-profiles-during-the-sex-differentiation-sensitive-period-in-oriental-river-prawn-macrobrachium-nipponense
#18
Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu
Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931802/hepatitis-c-virus-infection-increases-c-jun-n-terminal-kinase-jnk-phosphorylation-and-accentuates-hepatocyte-lipoapoptosis
#19
Hiroko Takaki, Yuko Akazawa, Youko Kido, Mami Morishita, Takuya Honda, Hidetaka Shibata, Satoshi Miuma, Hisamitsu Miyaaki, Naota Taura, Hisayoshi Kondo, Kazuhiko Nakao
BACKGROUND Hepatitis C virus (HCV) infection and metabolic diseases including nonalcoholic steatohepatitis (NASH) exhibit a complex interplay. Although free fatty acid-mediated apoptosis is a prominent feature of NASH, the impact of HCV infection on hepatocyte lipotoxicity has remained largely unexplored. The study aimed at identifying whether infection by HCV affected the apoptotic pathway in hepatocytes during fatty acid assault. MATERIAL AND METHODS OR6 cells, which are derived from human hepatocellular carcinoma Huh-7 cells and harbor a full-length HCV RNA genome replication system, were treated with palmitate...
September 21, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28930607/transcriptomics-in-amyotrophic-lateral-sclerosis
#20
Marios G Krokidis, Panagiotis Vlamos
Amyotrophic lateral sclerosis (ALS) is an adult-onset, incurable neurodegenerative disease characterized by the selective death of upper and lowers motor neurons in the spinal cord, brainstem and motor cortex, which ultimately leads to paralysis and death within 2-3 years of onset. ALS is poorly understood, although multiple studies have been proposed to explain the pathophysiological mechanisms of the disorder. The development of microarray technology, for simultaneous analysis of the transcriptional expression of thousands of genes, has provided new possibilities to get better insights into the pathogenesis of ALS, and most important, potential new candidate targets for novel treatments...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
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