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RNA metabolism

Siroon Bekkering, Inge van den Munckhof, Tim Nielen, Evert Lamfers, Charles Dinarello, Joost Rutten, Jacqueline de Graaf, Leo A B Joosten, Mihai G Netea, Marc E R Gomes, Niels P Riksen
BACKGROUND AND AIMS: We have recently reported that monocytes can undergo functional and transcriptional reprogramming towards a long-term pro-inflammatory phenotype after brief in vitro exposure to atherogenic stimuli such as oxidized LDL. This process is termed 'trained immunity', and is mediated by epigenetic remodeling and a metabolic switch towards increased aerobic glycolysis. We hypothesize that trained immunity contributes to atherogenesis. Therefore, we investigated the inflammatory phenotype and epigenetic remodeling of monocytes from patients with and without established atherosclerosis...
October 12, 2016: Atherosclerosis
Luis Figueroa-Yañez, Alejandro Pereira-Santana, Ana Arroyo-Herrera, Ulises Rodriguez-Corona, Felipe Sanchez-Teyer, Jorge Espadas-Alcocer, Francisco Espadas-Gil, Felipe Barredo-Pool, Enrique Castaño, Luis Carlos Rodriguez-Zapata
Plants respond to stress through metabolic and morphological changes that increase their ability to survive and grow. To this end, several transcription factor families are responsible for transmitting the signals that are required for these changes. Here, we studied the transcription factor superfamily AP2/ERF, particularly, RAP2.4 from Carica papaya cv. Maradol. We isolated four genes (CpRap2.4a, CpRAap2.4b, CpRap2.1 and CpRap2.10), and an in silico analysis showed that the four genes encode proteins that contain a conserved APETALA2 (AP2) domain located within group I and II transcription factors of the AP2/ERF superfamily...
2016: PloS One
Jun Li, Wei Zhen, Dengkai Long, Ling Ding, Anhui Gong, Chenghong Xiao, Weike Jiang, Xiaoqing Liu, Tao Zhou, Luqi Huang
Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P...
2016: PloS One
Ru-Yue Xiao, Junjun Hao, Yi-Hong Ding, Yan-Yun Che, Xiao-Ju Zou, Bin Liang
Due to misbalanced energy surplus and expenditure, obesity has become a common chronic disorder that is highly associated with many metabolic diseases. Pu-erh tea, a traditional Chinese beverage, has been believed to have numerous health benefits, such as anti-obesity. However, the underlying mechanisms of its anti-obesity effect are yet to be understood. Here, we take the advantages of transcriptional profile by RNA sequencing (RNA-Seq) to view the global gene expression of Pu-erh tea. The model organism Caenorhabditis elegans was treated with different concentrations of Pu-erh tea water extract (PTE, 0 g/mL, 0...
October 17, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Carmela Nardelli, Ilaria Granata, Laura Iaffaldano, Valeria D'Argenio, Valentina Del Monaco, Giuseppe Maria Maruotti, Daniela Omodei, Luigi Del Vecchio, Pasquale Martinelli, Francesco Salvatore, Mario Rosario Guarracino, Lucia Sacchetti, Lucio Pastore
Clinical findings and data obtained in animal models indicate that nutrient uptake and exposure to environmental agents during pregnancy may affect fetal/newborn gestational programming thereby resulting in obesity and/or obesity-related disorders in offspring. Human amniotic mesenchymal stem cells (hA-MSCs) differentiate into adipocytes, and are thus a suitable model to investigate adipocyte functions in obesity. The aim of this study was to elucidate the miRNome of hA-MSCs and its contribution to obesity in pregnancy...
October 20, 2016: Stem Cells and Development
Xiangrui Li, Fangmei Zhang, Brad Coates, Yunhui Zhang, Xuguo Zhou, Dengfa Cheng
MicroRNAs (miRNAs) are short single-stranded non-coding RNAs that regulate gene expression, particularly during development. In this study, 345 miRNAs were identified from the English green aphid, Sitobion avenae (F.), of which 168 were conserved and 177 were S. avenae-specific. Quantitative comparison of miRNA expression levels indicated that 16 and 12 miRNAs were significantly up-regulated in winged and wingless S. avenae small RNA libraries, respectively. Differential expression of these miRNAs was confirmed by real-time quantitative RT-PCR validation...
October 20, 2016: Scientific Reports
Aharon Nachshon, Hanifa J Abu-Toamih Atamni, Yael Steuerman, Roa'a Sheikh-Hamed, Alexandra Dorman, Richard Mott, Juliane C Dohm, Hans Lehrach, Marc Sultan, Ron Shamir, Sascha Sauer, Heinz Himmelbauer, Fuad A Iraqi, Irit Gat-Viks
A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions...
2016: Frontiers in Genetics
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
Szu Yuan Li, Katalin Susztak
An increasing amount of evidence suggests that metabolic alterations play a key role in chronic kidney disease (CKD) pathogenesis. In this issue of the JCI, Long et al. report that the long noncoding RNA (lncRNA) taurine-upregulated 1 (Tug1) contributes to CKD development. The authors show that Tug1 regulates mitochondrial function in podocytes by epigenetic targeting of expression of the transcription factor PPARγ coactivator 1α (PGC-1α, encoded by Ppargc1a). Transgenic overexpression of Tug1 specifically in podocytes ameliorated diabetes-induced CKD in mice...
October 17, 2016: Journal of Clinical Investigation
Antonino Baez, Joseph Shiloach
The damaging effect of high oxygen concentration on growth of Escherichia coli is well established. Over-oxygenation increases the intracellular concentration of reactive oxygen species (ROS), causing the destruction of the [4Fe-4S] cluster of dehydratases and limiting the biosynthesis of both branched-chain amino acids and nicotinamide adenine dinucleotide. A key enzyme that reduces the damaging effect of superoxide is superoxide dismutase (SOD). Its transcriptional regulation is controlled by global transcription regulators that respond to changes in oxygen and iron concentrations and pH...
October 18, 2016: Antonie Van Leeuwenhoek
Rongfang Guo, Zhongkai Huang, Yanping Deng, Xiaodong Chen, Xu XuHan, Zhongxiong Lai
Brassica sprouts contain abundant phytochemicals, especially glucosinolates (GSs). Various methods have been used to enhance GS content in sprouts. However, the molecular basis of GS metabolism in sprouts remains an open question. Here we employed RNA-seq analysis to compare the transcriptomes of high-GS (JL-08) and low-GS (JL-09) Brassica alboglabra sprouts. Paired-end Illumina RNA-seq reads were generated and mapped to the Brassica oleracea reference genome. The differentially expressed genes were analyzed between JL-08 and JL-09...
2016: Frontiers in Plant Science
Lindsey J Anstine, Chris Bobba, Samir Ghadiali, Joy Lincoln
Risk factors of heart valve disease are well defined and prolonged exposure throughout life leads to degeneration and dysfunction in up to 33% of the population. While aortic valve replacement remains the most common need for cardiovascular surgery particularly in those aged over 65, the underlying mechanisms of progressive deterioration are unknown. In other cardiovascular systems, a decline in endothelial cell integrity and function play a major role in promoting pathological changes, and while similar mechanisms have been speculated in the valves, studies to support this are lacking...
October 15, 2016: Journal of Molecular and Cellular Cardiology
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Ji-Young Choi, Ye Jin Kim, Ri Ryu, Su-Jung Cho, Eun-Young Kwon, Myung-Sook Choi
Green tea (GT) has various health effects, including anti-obesity properties. However, the multiple molecular mechanisms of the effects have not been fully determined. The aim of this study was to elucidate the anti-obesity effects of GT via the analysis of its metabolic and transcriptional responses based on RNA-seq profiles. C57BL/6J mice were fed a normal, high-fat (60% energy as fat), or high-fat + 0.25% (w/w) GT diet for 12 weeks. The GT extract ameliorated obesity, hepatic steatosis, dyslipidemia, and insulin resistance in diet-induced obesity (DIO) mice...
October 14, 2016: Nutrients
Zhongyang Lu, Yanchun Li, Colleen W Brinson, Keith L Kirkwood, Maria F Lopes-Virella, Yan Huang
BACKGROUND: We reported that high-fat diet (HFD)-induced metabolic syndrome (MetS) exacerbates lipopolysaccharide (LPS)-stimulated periodontitis and palmitate, the major saturated fatty acid in the HFD, amplified LPS-stimulated gene expression in vitro. Since CD36 is a major receptor for fatty acids, we investigated periodontal CD36 expression in mice with periodontitis and MetS, and the role of CD36 in inflammatory genes in macrophages stimulated by palmitate. METHODS: MetS and periodontitis were induced in mice by HFD and periodontal injection of LPS, respectively...
October 18, 2016: Oral Diseases
Stefan Holdenrieder
Liquid profiling is a traditional concept in laboratory diagnostics using patterns of blood-derived biochemical molecules for disease detection and characterization. Beyond protein and cellular parameters, molecular biomarkers at the DNA, RNA and miRNA level have been developed as promising diagnostic tools in metabolic and malignant diseases as new technologies for ultrasensitive profiling of nucleic acids in blood and body fluids became available. In cancer disease, they are successfully applied for the stratification of patients for individually tailored therapies, treatment monitoring and the sensitive detection of minimal residual disease...
2016: Advances in Experimental Medicine and Biology
Guoyun Zhang, Aiguo Duan, Jianguo Zhang, Caiyun He
Long non-coding RNAs (lncRNAs), which are >200nt longer transcripts, potentially play important roles in almost all biological processes in plants and mammals. However, the functions and profiles of lncRNAs in fruit is less understood. Therefore, it is urgent and necessary to identify and analyze the functions of lncRNAs in sea buckthorns. Using RNA-sequencing, we synthetically identified lncRNAs in mature fruit from the red and yellow sea buckthorn. We obtained 567,778,938 clean reads from six samples and identified 3428 lncRNAs in mature fruit, including 2498 intergenic lncRNAs, 593 anti-sense lncRNAs, and 337 intronic lncRNAs...
October 14, 2016: Gene
Hye Yeon Koh, Hyun Park, Jun Hyuck Lee, Se Jong Han, Young Chang Sohn, Sung Gu Lee
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ 2 fold, p <0...
October 17, 2016: Environmental Microbiology
Matthias Gimpel, Sabine Brantl
Dual-function sRNAs are a subgroup of small regulatory RNAs that act on the one hand as base-pairing sRNAs to inhibit or activate target gene expression and on the other hand as peptide-encoding mRNAs that function either in the same or in another metabolic pathway. Here, we review and compare the five currently known and intensively characterized dual-function sRNAs with regard to their two functions, their biological role, their evolutionary conservation and their requirements for RNA chaperones. Furthermore, we summarize the data available on five potential dual-function sRNAs, whose base-pairing function is well established whereas the role of their encoded peptides has not yet been elucidated...
October 17, 2016: Molecular Microbiology
Jian Huang, Lei Zhao, Ping Yang, Zhen Chen, Ni Tang, Xiong Z Ruan, Yaxi Chen
Hepatitis B virus (HBV) is a hepatocyte-specific DNA virus whose gene expression and replication are closely associated with hepatic metabolic processes. Thus, a potential anti-viral strategy is to target the host metabolic factors necessary for HBV gene expression and replication. Recent studies revealed that fatty acid translocase CD36 is involved in the replication, assembly, storage, and secretion of certain viruses, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV). However, the relationship between CD36 and the HBV life cycle remains unclear...
2016: PloS One
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