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https://www.readbyqxmd.com/read/28806763/genome-wide-regulation-of-electro-acupuncture-on-the-neural-stat5-loss-induced-obese-mice
#1
Shu-Ping Fu, Hao Hong, Sheng-Feng Lu, Chen-Jun Hu, Hou-Xi Xu, Qian Li, Mei-Ling Yu, Chen Ou, Jian-Zhong Meng, Tian-Lin Wang, Lothar Hennighausen, Bing-Mei Zhu
Acupuncture is reported to be effective in treating obesity related illnesses, but its mechanism is still unclear. To investigate this mechanism we applied electro-acupuncture (EA) in a mouse model of obesity and used RNA-seq to identify molecular consequences. Deletion of the transcription factor STAT5 from neurons (Stat5NKO) led to obesity. Acupuncture, in turn, reduced body weight and the ratio of epididymal white adipose tissue (Epi-WAT) to body weight, and it also decreased plasma concentrations of glucose, triglyceride, and cholesterol...
2017: PloS One
https://www.readbyqxmd.com/read/28806730/a-systems-approach-reveals-distinct-metabolic-strategies-among-the-nci-60-cancer-cell-lines
#2
Maike K Aurich, Ronan M T Fleming, Ines Thiele
The metabolic phenotype of cancer cells is reflected by the metabolites they consume and by the byproducts they release. Here, we use quantitative, extracellular metabolomic data of the NCI-60 panel and a novel computational method to generate 120 condition-specific cancer cell line metabolic models. These condition-specific cancer models used distinct metabolic strategies to generate energy and cofactors. The analysis of the models' capability to deal with environmental perturbations revealed three oxotypes, differing in the range of allowable oxygen uptake rates...
August 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28806688/concentration-dependent-transcriptome-responses-of-zebrafish-embryos-after-exposure-to-cadmium-cobalt-and-copper
#3
Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Schäfers, Martina Fenske
Environmental metals are known to cause harmful effects to fish of which many molecular mechanisms still require elucidation. Particularly concentration dependence of gene expression effects is unclear. Focusing on this matter, zebrafish embryo toxicity tests were used in combination with transcriptomics. Embryos were exposed to three concentrations of copper (CuSO4), cadmium (CdCl2) and cobalt (CoSO4) from just after fertilization until the end of the 48hpf pre- and 96hpf post-hatch stage. The RNA was then analyzed on Agilent's Zebrafish (V3, 4×44K) arrays...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28805544/rna-silencing-in-plant-symbiotic-bacteria-insights-from-a-protein-centric-view
#4
José I Jiménez-Zurdo, Marta Robledo
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28803234/rna-sequencing-and-bioinformatics-analysis-implicate-the-regulatory-role-of-a-long-noncoding-rna-mrna-network-in-hepatic-stellate-cell-activation
#5
Can-Jie Guo, Xiao Xiao, Li Sheng, Lili Chen, Wei Zhong, Hai Li, Jing Hua, Xiong Ma
BACKGROUND/AIMS: To analyze the long noncoding (lncRNA)-mRNA expression network and potential roles in rat hepatic stellate cells (HSCs) during activation. METHODS: LncRNA expression was analyzed in quiescent and culture-activated HSCs by RNA sequencing, and differentially expressed lncRNAs verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) were subjected to bioinformatics analysis. In vivo analyses of differential lncRNA-mRNA expression were performed on a rat model of liver fibrosis...
August 11, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28802227/anti-inflammatory-effects-of-shufengjiedu-capsule-for-upper-respiratory-infection-via-the-erk-pathway
#6
Yanmei Li, Nianwei Chang, Yanqi Han, Mengge Zhou, Jie Gao, Yuanyuan Hou, Min Jiang, Tiejun Zhang, Gang Bai
BACKGROUND: Shufengjiedu Capsule (SFJD) is a type of Chinese traditional medicine compound for the treatment of acute upper respiratory tract infection. The present work aims to decipher the mechanism of SFJD. METHODS: In this study, we used target prediction and RNA sequence (RNA-Seq) based on transcriptome analysis to clarify the inflammation-eliminating mechanism of SFJD. Firstly, Pseudomonas aeruginosa (PAK) was used to induce acute lung injury in KM mice. After being treated by SFJD, the differently expressed genes were analyzed by RNA-Seq...
August 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28800319/mir-503-3p-induces-apoptosis-of-lung-cancer-cells-by-regulating-p21-and-cdk4-expression
#7
Yi Sun, Li Li, Shigang Xing, Yinghua Pan, Yunxiang Shi, Linghua Zhang, Qiang Shen
Studies have shown that microRNAs (miRNAs) can promote or suppress tumor growth and therefore act as targets for cancer therapy. Hsa-miR-503-5p, a mature miRNA derived from 5' ends of pre-miR-503, has been proved to regulate cell proliferation, transformation, migration and invasion. However, the biological function of miR-503-3p derived from 3' ends of pre-miR-503 has never been reported. In current study, we found that miR-503-3p inhibits lung cancer cell viability and induces cell apoptosis. To better understand the molecular mechanism underlying the miR-503-3p participating in this process, PCR array and RNA-sequencing (RNA-seq) were performed and some differential expression genes were discovered between NC and miR-503-3p treated groups...
July 28, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28799693/the-small-rna-real-a-novel-regulatory-element-embedded-in-the-pseudomonas-aeruginosa-quorum-sensing-networks
#8
Sara Carloni, Raffaella Macchi, Sara Sattin, Silvia Ferrara, Giovanni Bertoni
The small RNA ReaL of the opportunistic pathogen Pseudomonas aeruginosa has been characterized. Our results indicate that ReaL contributes to P. aeruginosa virulence. In the Galleria mellonella infection model, reaL gene deletion resulted in decreased virulence, while ReaL overexpression resulted in a hyper-virulent phenotype. We also demonstrate that ReaL is embedded in the P. aeruginosa quorum sensing (QS) with the role of linking las to pqs systems. We show that ReaL is negatively regulated by the las regulator LasR and impacts positively the synthesis of the pqs quinolone signal PQS by a positive post-transcriptional effect on the pqsC gene...
August 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28798764/root-transcriptomic-analysis-revealing-the-importance-of-energy-metabolism-to-the-development-of-deep-roots-in-rice-oryza-sativa-l
#9
Qiaojun Lou, Liang Chen, Hanwei Mei, Kai Xu, Haibin Wei, Fangjun Feng, Tiemei Li, Xiaomeng Pang, Caiping Shi, Lijun Luo, Yang Zhong
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28798667/the-foxp2-driven-network-in-developmental-disorders-and-neurodegeneration
#10
Franz Oswald, Patricia Klöble, André Ruland, David Rosenkranz, Bastian Hinz, Falk Butter, Sanja Ramljak, Ulrich Zechner, Holger Herlyn
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28798471/identification-of-competing-endogenous-rnas-of-the-tumor-suppressor-gene-pten-a-probabilistic-approach
#11
Kourosh Zarringhalam, Yvonne Tay, Prajna Kulkarni, Assaf C Bester, Pier Paolo Pandolfi, Rahul V Kulkarni
Regulation by microRNAs (miRNAs) and modulation of miRNA activity are critical components of diverse cellular processes. Recent research has shown that miRNA-based regulation of the tumor suppressor gene PTEN can be modulated by the expression of other miRNA targets acting as competing endogenous RNAs (ceRNAs). However, the key sequence-based features enabling a transcript to act as an effective ceRNA are not well understood and a quantitative model associating statistical significance to such features is currently lacking...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796489/rational-modular-rna-engineering-based-on-in-vivo-profiling-of-structural-accessibility
#12
Abigail N Leistra, Paul Amador, Aishwarya Buvanendiran, Alex Moon-Walker, Lydia M Contreras
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28795788/new-molecular-insights-into-an-archaeal-rnase-j-reveal-a-conserved-processive-exoribonucleolysis-mechanism-of-the-rnase-j-family
#13
Xin Zheng, Na Feng, Defeng Li, Xiuzhu Dong, Jie Li
RNase J, a prokaryotic 5'-3' exo/endoribonuclease, contributes to mRNA decay, rRNA maturation, and post-transcriptional regulation. Yet the processive-exoribonucleolysis mechanism remains obscure. Here, we solved the first RNA-free and RNA-bound structures of an archaeal RNase J, and through intensive biochemical studies provided detailed mechanistic insights into the catalysis and processivity. Distinct dimerization/tetramerization patterns were observed for archaeal and bacterial RNase Js, and unique archaeal Loops I and II were found involved in RNA interaction...
August 10, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28795686/hdl-and-atherosclerotic-cardiovascular-disease-genetic-insights-into-complex-biology
#14
REVIEW
Robert S Rosenson, H Bryan Brewer, Philip J Barter, Johan L M Björkegren, M John Chapman, Daniel Gaudet, Daniel Seung Kim, Eric Niesor, Kerry-Anne Rye, Frank M Sacks, Jean-Claude Tardif, Robert A Hegele
Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants...
August 10, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28794999/modulation-of-the-p53-family-network-by-rna-binding-proteins
#15
Chris Lucchesi, Jin Zhang, Xinbin Chen
Since its discovery more than three decades ago, tumor suppressor p53 has been shown to play pivotal roles in both maintaining genomic integrity and tumor suppression. p53 functions as a transcription factor responding to a multitude of cellular stressors, regulating the transcription of many genes involved in cell-cycle arrest, senescence, autophagy, and apoptosis. Extensive work has revealed that p53 is one of the most commonly mutated tumor suppressor genes. The last three decades have demonstrated that p53 activity is controlled through transcriptional regulation and posttranslational modifications...
December 2016: Translational Cancer Research
https://www.readbyqxmd.com/read/28794184/post-transcriptional-regulation-of-mouse-neurogenesis-by-pumilio-proteins
#16
Meng Zhang, Dong Chen, Jing Xia, Wenqi Han, Xiekui Cui, Nils Neuenkirchen, Gretchen Hermes, Nenad Sestan, Haifan Lin
Despite extensive studies on mammalian neurogenesis, its post-transcriptional regulation remains under-explored. Here we report that neural-specific inactivation of two murine post-transcriptional regulators, Pumilio 1 (Pum1) and Pum2, severely reduced the number of neural stem cells (NSCs) in the postnatal dentate gyrus (DG), drastically increased perinatal apoptosis, altered DG cell composition, and impaired learning and memory. Consistently, the mutant DG neurospheres generated fewer NSCs with defects in proliferation, survival, and differentiation, supporting a major role of Pum1 and Pum2 in hippocampal neurogenesis and function...
August 9, 2017: Genes & Development
https://www.readbyqxmd.com/read/28793261/the-conserved-disease-associated-rna-binding-protein-dnab2-interacts-with-the-fragile-x-protein-ortholog-in-drosophila-neurons
#17
Rick S Bienkowski, Ayan Banerjee, J Christopher Rounds, Jennifer Rha, Omotola F Omotade, Christina Gross, Kevin J Morris, Sara W Leung, ChangHui Pak, Stephanie K Jones, Michael R Santoro, Stephen T Warren, James Q Zheng, Gary J Bassell, Anita H Corbett, Kenneth H Moberg
The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A) RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28793054/revealing-potential-long-non-coding-rna-biomarkers-in-lung-adenocarcinoma-using-long-non-coding-rna-mediated-competitive-endogenous-rna-network
#18
T-G Zhu, X Xiao, Q Wei, M Yue, L-X Zhang
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value >0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure...
August 7, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28792517/comparison-of-alternative-approaches-for-analysing-multi-level-rna-seq-data
#19
Irina Mohorianu, Amanda Bretman, Damian T Smith, Emily K Fowler, Tamas Dalmay, Tracey Chapman
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D...
2017: PloS One
https://www.readbyqxmd.com/read/28792098/identification-of-expression-quantitative-trait-loci-eqtls-in-human-peripheral-blood-mononuclear-cells-pbmcs-and-shared-with-liver-and-brain
#20
Pei He, Wei Xia, Lan Wang, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Peng-Fei Bing, Fang-Fei Xie, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei, Fei-Yan Deng
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified...
August 9, 2017: Journal of Cellular Biochemistry
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