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RNA metabolism

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https://www.readbyqxmd.com/read/28636618/de-novo-transcriptome-of-the-mayfly-cloeon-viridulum-and-transcriptional-signatures-of-prometabola
#1
Qin Si, Juan-Yan Luo, Ze Hu, Wei Zhang, Chang-Fa Zhou
Mayflies (Ephemeroptera) display many primitive characters and a unique type of metamorphosis (Prometabola). However, information on the genomes and transcriptomes of this insect group is limited. The RNA sequencing study presented here generated the first de novo transcriptome assembly of Cloeon viridulum (Ephemeroptera: Baetidae), and compared gene expression signatures among the young larva (YL), mature larva (ML), subimago (SI), and imago (IM) stages of this mayfly. The transcriptome, based on 88 Gb of sequence data, comprised a set of 81,185 high quality transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28636533/microrna-149-suppresses-hepatic-inflammatory-response-through-antagonizing-stat3-signaling-pathway
#2
Qiqi Zhang, Jia Su, Ziwei Wang, Hui Qi, Zeyong Ge, Zhijun Li, Wei-Dong Chen, Yan-Dong Wang
Chronic inflammation is increasingly recognized as an important component of tumorigenesis and metabolic diseases. The roles of microRNA149* (miRNA149*) in inflammation remain poorly understood. Here, we demonstrate that miR-149* is a suppressor of STAT3-mediated inflammation. MiR-149*-/- mice were generated with CRISPR/CAS9 technique. In a lipopolysaccharide (LPS)-induced inflammation model, miR-149*-/- mice show more severe liver injury and inflammation, compared with wild-type (WT) mice. MiR-149*-/- mice also displayed elevated messenger RNA (mRNA) levels of interleukin (IL)-6, inducible nitric oxide synthase (iNOS), complement C3 (C3) and IL-4 in response to LPS...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28635589/regulation-of-escherichia-coli-pathogenesis-by-alternative-sigma-factor-n
#3
James T Riordan, Avishek Mitra
σ(N) (also σ(54)) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σ(N) is encoded as the first gene of a five-gene operon including rpoN (σ(N)), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σ(N) has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors...
June 2017: EcoSal Plus
https://www.readbyqxmd.com/read/28632173/gene-expression-profiling-reveals-potential-players-of-left-right-asymmetry-in-female-chicken-gonads
#4
Zhiyi Wan, Yanan Lu, Lei Rui, Xiaoxue Yu, Fang Yang, Chengfang Tu, Zandong Li
Most female birds develop only a left ovary, whereas males develop bilateral testes. The mechanism underlying this process is still not completely understood. Here, we provide a comprehensive transcriptional analysis of female chicken gonads and identify novel candidate side-biased genes. RNA-Seq analysis was carried out on total RNA harvested from the left and right gonads on embryonic day 6 (E6), E12, and post-hatching day 1 (D1). By comparing the gene expression profiles between the left and right gonads, 347 differentially expressed genes (DEGs) were obtained on E6, 3730 were obtained on E12, and 2787 were obtained on D1...
June 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28630030/alzheimer-s-brains-show-inter-related-changes-in-rna-and-lipid-metabolism
#5
Shahar Barbash, Benjamin P Garfinkel, Rotem Maoz, Alon Simchovitz, Bettina Nadorp, Alessandro Guffanti, Estelle R Bennett, Courtney Nadeau, Andreas Türk, Lukas Paul, Torsten Reda, Yan Li, Aron S Buchman, David S Greenberg, Alexander Seitz, David A Bennett, Patrick Giavalisco, Hermona Soreq
Alzheimer's disease (AD) involves changes in both lipid and RNA metabolism, but it remained unknown if these differences associate with AD's cognition and/or post-mortem neuropathology indices. Here, we report RNA-sequencing evidence of inter-related associations between lipid processing, cognition level, and AD neuropathology. In two unrelated cohorts, we identified pathway-enriched facilitation of lipid processing and alternative splicing genes, including the neuronal-enriched NOVA1 and hnRNPA1. Specifically, this association emerged in temporal lobe tissue samples from donors where postmortem evidence demonstrated AD neuropathology, but who presented normal cognition proximate to death...
June 16, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28629776/unveiling-the-non-repair-face-of-the-base-excision-repair-pathway-in-rna-processing-a-missing-link-between-dna-repair-and-gene-expression
#6
REVIEW
Giulia Antoniali, Matilde Clarissa Malfatti, Gianluca Tell
The Base Excision Repair (BER) pathway, initially studied as a mere DNA repair pathway, has been later found to be implicated in the expression of cancer related genes in human. For several years, this intricate involvement in apparently different processes represented a mystery, which we now are starting to unveil. The BER handles simple alkylation and oxidative lesions arising from both endogenous and exogenous sources, including cancer therapy agents. Surprisingly, BER pathway involvement in transcriptional regulation, immunoglobulin variability and switch recombination, RNA metabolism and nucleolar function is astonishingly consolidating...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28629321/the-biocontrol-agent-pseudomonas-chlororaphis-pa23-primes-brassica-napus-defenses-through-distinct-gene-networks
#7
Kelly A Duke, Michael G Becker, Ian J Girard, Jenna L Millar, W G Dilantha Fernando, Mark F Belmonte, Teresa R de Kievit
BACKGROUND: The biological control agent Pseudomonas chlororaphis PA23 is capable of protecting Brassica napus (canola) from the necrotrophic fungus Sclerotinia sclerotiorum via direct antagonism. While we have elucidated bacterial genes and gene products responsible biocontrol, little is known about how the host plant responds to bacterial priming on the leaf surface, including global changes in gene activity in the presence and absence of S. sclerotiorum. RESULTS: Application of PA23 to the aerial surfaces of canola plants reduced the number of S...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28629193/telomere-biology-insights-into-an-intriguing-phenomenon
#8
REVIEW
Shriram Venkatesan, Aik Kia Khaw, Manoor Prakash Hande
Bacteria and viruses possess circular DNA, whereas eukaryotes with typically very large DNA molecules have had to evolve into linear chromosomes to circumvent the problem of supercoiling circular DNA of that size. Consequently, such organisms possess telomeres to cap chromosome ends. Telomeres are essentially tandem repeats of any DNA sequence that are present at the ends of chromosomes. Their biology has been an enigmatic one, involving various molecules interacting dynamically in an evolutionarily well-trimmed fashion...
June 19, 2017: Cells
https://www.readbyqxmd.com/read/28628858/unravelling-the-structural-interactions-between-pkr-kinase-domain-and-its-small-molecule-inhibitors-using-computational-approaches
#9
Sagar Barage, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The RNA-dependent protein kinase (PKR), an eIF2α kinase plays an important role in anti-viral response, apoptosis and cell survival. It is also implicated to play a role in several cancers, metabolic and neurodegenerative disorders. A few ATP competitive inhibitors of the PKR have been reported in the literature with promising results in vitro and in vivo. The aim of this study was to unravel the structural interactions between these inhibitors and the PKR kinase domain using molecular simulations and docking...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628672/low-dose-exposure-to-bisphenols-a-f-and-s-of-human-primary-adipocyte-impacts-coding-and-non-coding-rna-profiles
#10
Marie Verbanck, Mickaël Canouil, Audrey Leloire, Véronique Dhennin, Xavier Coumoul, Loïc Yengo, Philippe Froguel, Odile Poulain-Godefroy
Bisphenol A (BPA) exposure has been suspected to be associated with deleterious effects on health including obesity and metabolically-linked diseases. Although bisphenols F (BPF) and S (BPS) are BPA structural analogs commonly used in many marketed products as a replacement for BPA, only sparse toxicological data are available yet. Our objective was to comprehensively characterize bisphenols gene targets in a human primary adipocyte model, in order to determine whether they may induce cellular dysfunction, using chronic exposure at two concentrations: a "low-dose" similar to the dose usually encountered in human biological fluids and a higher dose...
2017: PloS One
https://www.readbyqxmd.com/read/28628240/comparative-transcriptome-analysis-of-nodules-of-two-mesorhizobium-chickpea-associations-with-differential-symbiotic-efficiency-under-phosphate-deficiency
#11
Maryam Nasr Esfahani, Komaki Inoue, Ha Duc Chu, Kien Huu Nguyen, Chien Van Ha, Yasuko Watanabe, David J Burritt, Luis Herrera-Estrella, Keiichi Mochida, Lam-Son Phan Tran
Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M...
June 19, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28627816/spectrophotometric-determination-of-selenium-through-triiodide-anion
#12
Otilia Bizerea-Spiridon, Radu Nartita, Alexandru F Rogobete, Adina Negrea, Ramona Stroescu, Teofana O Bizerea, Constantin Ilie, Otilia Marginean
BACKGROUND: Selenium is a chemical element found in the human body that plays a crucial role in its regulation. Depending on the concentration, it may have beneficial or have toxic effects. Selenium is incorporated as selenocysteine amino acid residue in selenoproteins which play an important role in many biological functions: anti-oxidant defense, regulation of the immune function and of the inflammatory response, metabolism of thyroid hormones, functioning of the central nervous system, biosynthesis of DNA and RNA, fertility, and reproduction...
May 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28627653/mir-543-functions-as-a-tumor-suppressor-in-glioma-in-vitro-and-in-vivo
#13
Liang Xu, Ju Yu, Zhongyong Wang, Qing Zhu, Wenjie Wang, Qing Lan
Gliomas are the most common primary central nervous system tumors and account for approximately 80% of malignant brain tumors. MicroRNAs (miRNAs) are a class of small non-coding, regulatory RNA molecules that mediate the expression levels of specific proteins. As a member of the miRNA family, miR-543 plays a tumor suppressive or an oncogenic role in different types of tumors. However, the expression and role of miR-543 in glioma remain unknown. In the present study, the expression level of miR-543 in glioma cell lines and tissues was investigated...
June 12, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28626890/transcriptomic-analysis-of-rice-aleurone-cells-identified-a-novel-abscisic-acid-response-element
#14
Kenneth A Watanabe, Arielle Homayouni, Lingkun Gu, Kuan-Ying Huang, Tuan-Hua David Ho, Qingxi J Shen
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signaling. However, its consensus sequence, (ACGTG(G/T)C), is present in the promoters of only about 40% of ABA induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA-sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements and particle bombardment-mediated transient expression studies were performed to verify the function...
June 18, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28626467/mutation-in-hvcbp20-cap-binding-protein-20-adapts-barley-to-drought-stress-at-phenotypic-and-transcriptomic-levels
#15
Agata Daszkowska-Golec, Anna Skubacz, Marek Marzec, Michal Slota, Marzena Kurowska, Monika Gajecka, Patrycja Gajewska, Tomasz Płociniczak, Krzysztof Sitko, Andrzej Pacak, Zofia Szweykowska-Kulinska, Iwona Szarejko
CBP20 (Cap-Binding Protein 20) encodes a small subunit of the cap-binding complex (CBC), which is involved in the conserved cell processes related to RNA metabolism in plants and, simultaneously, engaged in the signaling network of drought response, which is dependent on ABA. Here, we report the enhanced tolerance to drought stress of barley mutant in the HvCBP20 gene manifested at the morphological, physiological, and transcriptomic levels. Physiological analyses revealed differences between the hvcbp20.ab mutant and its WT in response to a water deficiency...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28626026/protein-kinase-c%C3%AE-activates-fat-mass-and-obesity-associated-protein-by-influencing-its-ubiquitin-proteasome-degradation
#16
Haoran Tai, Xiaobo Wang, Jiao Zhou, Xiaojuan Han, Tingting Fang, Hui Gong, Ning Huang, Honghan Chen, Jianqiong Qin, Ming Yang, Xiawei Wei, Li Yang, Hengyi Xiao
PKCβ is a serine-threonine kinase associated with obesity and diabetic complications; its activation contributes to weight gain, and deletion of its gene results in resistance to genetic- and diet-induced obesity. Fat mass and obesity-associated (FTO) protein is a recently identified RNA demethylase, and its overexpression in mice leads to increased body weight as well as fat mass. Although sharing some features in anabolism regulation, PKCβ and FTO have not been investigated together; therefore, their relationship has not been established...
June 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28625786/drug-induces-depression-like-phenotypes-and-alters-gene-expression-profiles-in-drosophila
#17
Ming-Di Jiang, Ya Zheng, Jia-Lin Wang, Yu-Feng Wang
BACKGROUND: Major depressive disorder (MDD) is a severe mental illness that affects more than 350 million people worldwide. However, the molecular mechanisms of depression are currently unclear. Studies suggest that Drosophila and humans have similar depression-like symptoms under pressure. In this research, we choose Drosophila melanogaster as the animal model to explore the molecular mechanisms that trigger depression. RESULTS: We found that feeding D. melanogaster with the medium containing Levodopa or Chlorpromazine could induce depression-like phenotypes in both behavioral and biochemical biomarkers, including significantly decreased food intake, mating frequency, serotonin (5-HT) concentration, and increased malondialdehyde (MDA) concentration as well as reduced activity of superoxide dismutase (SOD)...
June 15, 2017: Brain Research Bulletin
https://www.readbyqxmd.com/read/28625740/comparative-proteomic-analysis-of-two-transgenic-low-gliadin-wheat-lines-and-non-transgenic-wheat-control
#18
María Dolores García-Molina, Vera Muccilli, Rosaria Saletti, Salvatore Foti, Stefania Masci, Francisco Barro
Gluten proteins are major determinants of the bread making quality of wheat, but also of important wheat-related disorders, including coeliac disease (CD), and allergies. We carried out a proteomic study using the total grain proteins from two low-gliadin wheat lines, obtained by RNAi, and the untransformed wild type as reference. The impact of silencing on both target and on non-target proteins was evaluated. Because of the great protein complexity, we performed separate analyses of four kernel protein fractions: gliadins and glutenin subunits, and metabolic and CM-like proteins, by using a classical 2D electrophoresis gel based approach followed by RP-HPLC/nESI-MS/MS...
June 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28625541/plant-derived-antifungal-compounds-trigger-a-common-transcriptional-response
#19
Zhe Wang
Understanding the mechanism of action of antifungal drugs is vital for better control of mycosis, which kills >1.3 million lives every year thus remains a major health problem worldwide. In this study, we investigate the activities of three different categories of plant-derived antifungal compounds (resveratrol, honokiol and osthole) via transcriptomics and bioinformatics analysis, with the goal of discovering the common Mode-of-Action (MoA) at molecular level. The result shows that a common transcriptional response (72 gene are up-regulated while 10 genes are down-regulated, commonly) are triggered by above representative antifungal compounds in Schizosaccharomyces pombe (S...
June 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28625352/rna-seq-and-metabolic-flux-analysis-of-tetraselmis-sp-m8-during-nitrogen-starvation-reveals-a-two-stage-lipid-accumulation-mechanism
#20
David K Y Lim, Holger Schuhmann, Skye R Thomas-Hall, Kenneth C K Chan, Taylor J Wass, Felipe Aguilera, T Catalina Adarme-Vega, Cristiana G O Dal'Molin, Glen J Thorpe, Jacqueline Batley, David Edwards, Peer M Schenk
To map out key lipid-related pathways that lead to rapid triacylglyceride accumulation in oleaginous microalgae, RNA-Seq was performed with Tetraselmis sp. M8 at 24h after exhaustion of exogenous nitrogen to reveal molecular changes during early stationary phase. Further gene expression profiling by quantitative real-time PCR at 16-72h revealed a distinct shift in expression of the fatty acid/triacylglyceride biosynthesis and β-oxidation pathways, when cells transitioned from log-phase into early-stationary and stationary phase...
June 6, 2017: Bioresource Technology
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