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https://www.readbyqxmd.com/read/29150660/gene-expression-profile-changes-in-the-jejunum-of-weaned-piglets-after-oral-administration-of-lactobacillus-or-an-antibiotic
#1
Dongyan Zhang, Tingting Shang, Yan Huang, Sixin Wang, Hui Liu, Jing Wang, Yamin Wang, Haifeng Ji, Rijun Zhang
The small intestine plays an essential role in the health and well-being of animals. Previous studies have shown that Lactobacillus has a protective effect on intestinal morphology, intestinal epithelium integrity and appropriate maturation of gut-associated tissues. Here, gene expression in jejunum tissue of weaned piglets was investigated by RNA-seq analysis after administration of sterile saline, Lactobacillus reuteri, or an antibiotic (chlortetracycline). In total, 401 and 293 genes were significantly regulated by chlortetracycline and L...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150650/transcriptome-sequencing-and-differential-gene-expression-analysis-of-the-schistosome-transmitting-snail-oncomelania-hupensis-inhabiting-hilly-and-marshland-regions
#2
Jin-Song Zhao, An-Yun Wang, Hua-Bin Zhao, Yan-Hong Chen
The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150605/global-role-of-the-bacterial-post-transcriptional-regulator-csra-revealed-by-integrated-transcriptomics
#3
Anastasia H Potts, Christopher A Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo
CsrA is a post-transcriptional regulatory protein that is widely distributed among bacteria. This protein influences bacterial lifestyle decisions by binding to the 5' untranslated and/or early coding regions of mRNA targets, causing changes in translation initiation, RNA stability, and/or transcription elongation. Here, we assess the contribution of CsrA to gene expression in Escherichia coli on a global scale. UV crosslinking immunoprecipitation and sequencing (CLIP-seq) identify RNAs that interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA abundance, and RNA stability...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150601/decoding-critical-long-non-coding-rna-in-ovarian-cancer-epithelial-to-mesenchymal-transition
#4
Ramkrishna Mitra, Xi Chen, Evan J Greenawalt, Ujjwal Maulik, Wei Jiang, Zhongming Zhao, Christine M Eischen
Long non-coding RNA (lncRNA) are emerging as contributors to malignancies. Little is understood about the contribution of lncRNA to epithelial-to-mesenchymal transition (EMT), which correlates with metastasis. Ovarian cancer is usually diagnosed after metastasis. Here we report an integrated analysis of >700 ovarian cancer molecular profiles, including genomic data sets, from four patient cohorts identifying lncRNA DNM3OS, MEG3, and MIAT overexpression and their reproducible gene regulation in ovarian cancer EMT...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29149532/exploitation-of-micrornas-by-japanese-encephalitis-virus-in-human-microglial-cells
#5
Meghana Rastogi, Neha Srivastava, Sunit K Singh
JEV infection in CNS leads to the JE neuroinflammation. Children and old age individual have been reported to be more prone to JEV infection. MicroRNAs are endogenous, small non-coding RNAs, which regulate the gene expression. These are ∼22 nucleotide long, conserved RNA sequence that binds at the 3'UTR of a target mRNA and regulate the post-transcriptional gene expression. The role of microRNAs has been reported in several diseases like cancer, viral infection, neuro-degeneration, diabetes etc. In the present study, the human microglial cells were infected with JEV (JaOAr strain)...
November 17, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29149451/transcriptional-alterations-in-hereditary-and-sporadic-nonfunctioning-pancreatic-neuroendocrine-tumors-according-to-genotype
#6
Xavier M Keutgen, Suresh Kumar, Sudheer Gara, Myriem Boufraqech, Sunita Agarwal, Ralph H Hruban, Naris Nilubol, Martha Quezado, Richard Finney, Maggie Cam, Electron Kebebew
BACKGROUND: Nonfunctioning pancreatic neuroendocrine tumors (NFPanNETs) may be sporadic or inherited because of germline mutations associated with von Hippel-Lindau disease (VHL) or multiple endocrine neoplasia type 1 (MEN1). The clinical behavior of NFPanNETs is difficult to predict, even in tumors of the same stage and grade. The authors analyzed genotype-specific patterns of transcriptional messenger RNA (mRNA) levels of NFPanNETs to understand the molecular features that determine PanNET phenotype...
November 17, 2017: Cancer
https://www.readbyqxmd.com/read/29148410/th17-gene-expression-in-psoriatic-arthritis-synovial-fluid-and-peripheral-blood-compared-to-osteoarthritis-and-cutaneous-psoriasis
#7
Fatima Abji, Remy A Pollock, Kun Liang, Vinod Chandran, Dafna D Gladman
OBJECTIVES: The IL-23/IL-17 axis is central to the pathogenesis of psoriatic arthritis (PsA). We aimed to identify Th17 signalling genes that are dysregulated in synovial fluid of PsA compared to osteoarthritis (OA) patients and to determine if differences in peripheral blood can distinguish PsA from psoriasis patients and controls. METHODS: Synovial fluid cells (SFCs) from 14 PsA and 9 OA patients were obtained and stored in TRIzol reagent. RNA was isolated by phenol-chloroform extraction and purified with RNeasy miniprep kits...
November 9, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/29147886/peromyscus-leucopus-mouse-brain-transcriptome-response-to-powassan-virus-infection
#8
Luwanika Mlera, Kimberly Meade-White, Eric Dahlstrom, Rachel Baur, Kishore Kanakabandi, Kimmo Virtaneva, Stephen F Porcella, Marshall E Bloom
Powassan virus (POWV) is a tick-borne Flavivirus responsible for life-threatening encephalitis in North America and some regions of Russia. The ticks that have been reported to transmit the virus belong to the Ixodes species, and they feed on small-to-medium-sized mammals, such as Peromyscus leucopus mice, skunks, and woodchucks. We previously developed a P. leucopus mouse model of POWV infection, and the model is characterized by a lack of clinical signs of disease following intraperitoneal or intracranial inoculation...
November 16, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29147650/mitochondria-associated-microrna-expression-profiling-of-heart-failure
#9
Xiaoxia Wang, Chun Song, Xiao Zhou, Xiaorui Han, Jun Li, Zengwu Wang, Haibao Shang, Yuli Liu, Huiqing Cao
Heart failure (HF) is associated with mitochondrial dysfunction and energy metabolism impairment. MicroRNAs are implicated in the development of heart failure. However, the mitochondria enriched microRNA during heart failure remains elusive. Here, we generated a pressure overload-induced early and late stage heart failure model at 4 weeks and 8 weeks following transverse aortic constriction (TAC) in mice. We found that expression of mitochondrion protein COX4 was highly enriched in isolated mitochondria from cardiac tissues while GAPDH could hardly be detected...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29147069/expression-profiling-of-long-noncoding-rna-splice-variants-in-human-microvascular-endothelial-cells-lipopolysaccharide-effects-in-vitro
#10
Imran H Chowdhury, Hema P Narra, Abha Sahni, Kamil Khanipov, Casey L C Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. We report on the expression profile of long noncoding (lnc) RNAs of human microvascular endothelial cells in response to LPS...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/29146915/transcriptional-profiling-provides-new-insights-into-the-role-of-nitric-oxide-in-enhancing-ganoderma-oregonense-resistance-to-heat-stress
#11
Cheng Chen, Qiang Li, Qiangfeng Wang, Daihua Lu, Hong Zhang, Jian Wang, Rongtao Fu
Ganoderma is well known for its use in traditional Chinese medicine and is widely cultivated in China, Korea, and Japan. Increased temperatures associated with global warming are negatively influencing the growth and development of Ganoderma. Nitric oxide is reported to play an important role in alleviating fungal heat stress (HS). However, the transcriptional profiling of Ganoderma oregonense in response to HS, as well as the transcriptional response regulated by NO to cope with HS has not been reported. We used RNA-Seq technology to generate large-scale transcriptome data from G...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146111/microrna-expression-patterns-in-human-anterior-cingulate-and-motor-cortex-a-study-of-dementia-with-lewy-bodies-cases-and-controls
#12
Peter T Nelson, Wang-Xia Wang, Sarah A Janse, Katherine L Thompson
OVERVIEW: MicroRNAs (miRNAs) have been implicated in neurodegenerative diseases including Parkinson's disease and Alzheimer's disease (AD). Here, we evaluated the expression of miRNAs in anterior cingulate (AC; Brodmann area [BA] 24) and primary motor (MO; BA 4) cortical tissue from aged human brains in the University of Kentucky AD Center autopsy cohort, with a focus on dementia with Lewy bodies (DLB). METHODS: RNA was isolated from gray matter of brain samples with pathology-defined DLB, AD, AD+DLB, and low-pathology controls, with n=52 cases initially included (n=23 with DLB), all with low (<4hrs) postmortem intervals...
November 13, 2017: Brain Research
https://www.readbyqxmd.com/read/29145712/cartilage-microrna-dysregulation-during-the-onset-and-progression-of-mouse-osteoarthritis-is-independent-of-aggrecanolysis-and-overlaps-with-candidates-from-end-stage-human-disease
#13
Louise H W Kung, Varshini Ravi, Lynn Rowley, Constanza Angelucci, Amanda J Fosang, Katrina M Bell, Christopher B Little, John F Bateman
OBJECTIVE: To identify candidate microRNAs that potentially regulate the initiation and progression of osteoarthritis. METHODS: Osteoarthritis was induced in 10-12 week old male wild-type C57BL6 mice and in mice resistant to aggrecanase cleavage (Acan p.374ALGS→374NVYS) by destabilization of the medial meniscus (DMM). Osteoarthritis pathology was scored histologically. RNA from cartilage and subchondral bone were harvested in parallel by laser micro-dissection at 1 and 6 weeks post-surgery...
November 16, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29145392/conservation-of-a-microrna-cluster-in-parasitic-nematodes-and-profiling-of-mirnas-in-excretory-secretory-products-and-microvesicles-of-haemonchus-contortus
#14
Henry Y Gu, Neil D Marks, Alan D Winter, William Weir, Thomas Tzelos, Tom N McNeilly, Collette Britton, Eileen Devaney
microRNAs are small non-coding RNAs that are important regulators of gene expression in a range of animals, including nematodes. We have analysed a cluster of four miRNAs from the pathogenic nematode species Haemonchus contortus that are closely linked in the genome. We find that the cluster is conserved only in clade V parasitic nematodes and in some ascarids, but not in other clade III species nor in clade V free-living nematodes. Members of the cluster are present in parasite excretory-secretory products and can be detected in the abomasum and draining lymph nodes of infected sheep, indicating their release in vitro and in vivo...
November 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29145159/potential-link-between-m-6-a-modification-and-systemic-lupus-erythematosus
#15
REVIEW
Lian-Ju Li, Yin-Guang Fan, Rui-Xue Leng, Hai-Feng Pan, Dong-Qing Ye
The field of m(6)A modification and epitranscriptomics has recently attracted much attention. More methods allowing for precise m(6)A site profiling and location are developed and crucial players of m(6)A modification machinery are increasingly identified. Although some challenges remain, m(6)A modification is found to modulate almost all aspects of RNA metabolism, such as splicing, stability, structure, translation, and export. Thus, m(6)A modification adds a new layer of post-transcriptional gene expression regulation, and it is implicated in T cell response to HIV infection, type I interferon production, and T cell differentiation and homeostasis...
November 13, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29145027/differential-gene-expression-in-the-intestine-of-sea-cucumber-apostichopus-japonicus-under-low-and-high-salinity-conditions
#16
Libin Zhang, Qiming Feng, Lina Sun, Kui Ding, Da Huo, Yan Fang, Tao Zhang, Hongsheng Yang
Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0...
November 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29144405/genomic-analysis-of-the-asmt-gene-family-in-solanum-lycopersicum
#17
Weicheng Liu, Dake Zhao, Chunfang Zheng, Chen Chen, Xin Peng, Yuan Cheng, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29144233/a-high-resolution-mrna-expression-time-course-of-embryonic-development-in-zebrafish
#18
Richard J White, John E Collins, Ian M Sealy, Neha Wali, Christopher M Dooley, Zsofia Digby, Derek L Stemple, Daniel N Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J Enright, Elisabeth M Busch-Nentwich
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation...
November 16, 2017: ELife
https://www.readbyqxmd.com/read/29143326/lncrna-rp11-670e13-6-regulates-cell-cycle-progression-in-uvb-damaged-human-dermal-fibroblasts
#19
Mengna Li, Li Li, Xiaofeng Zhang, Yan Yan, Baoxi Wang
Long noncoding RNAs (lncRNAs) have gained extensive attention in recent years, however, their effects on ultraviolet (UV) radiation-induced skin photodamage remain to be elucidated. In this study, we performed high-throughput RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles including lncRNAs and mRNAs in UVB-irradiated primary human dermal fibroblasts (HDFs) and to explore the roles of lncRNAs in photoaging. Quantitative reverse transcription-polymerase chain reaction amplification was performed to verify the differentially expressed genes...
November 16, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/29141990/rna-sequencing-of-drosophila-melanogaster-head-tissue-on-high-sugar-and-high-fat-diets
#20
Wayne Hemphill, Osvaldo Rivera, Matthew Talbert
Obesity has been shown to increase risk for cardiovascular disease and type-2 diabetes. In addition, it has been implicated in aggravation of neurological conditions such as Alzheimer's. In the model organism Drosophila melanogaster, a physiological state mimicking diet-induced obesity can be induced by subjecting fruit flies to a solid medium disproportionately higher in sugar than protein or that has been supplemented with a rich source of saturated fat. These flies can exhibit increased circulating glucose levels, increased triglyceride content, insulin-like peptide resistance, and behavior indicative of neurological decline...
November 15, 2017: G3: Genes—Genomes—Genetics
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