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https://www.readbyqxmd.com/read/28918081/developmental-alcohol-exposure-impairs-synaptic-plasticity-without-overtly-altering-microglial-function-in-mouse-visual-cortex
#1
Elissa L Wong, Nina M Lutz, Victoria A Hogan, Cassandra E Lamantia, Helene R McMurray, Jason R Myers, John M Ashton, Ania K Majewska
Fetal alcohol spectrum disorder (FASD), caused by gestational ethanol (EtOH) exposure, is one of the most common causes of non-heritable and life-long mental disability worldwide, with no standard treatment or therapy available. While EtOH exposure can alter the function of both neurons and glia, it is still unclear how EtOH influences brain development to cause deficits in sensory and cognitive processing later in life. Microglia play an important role in shaping synaptic function and plasticity during neural circuit development and have been shown to mount an acute immunological response to EtOH exposure in certain brain regions...
September 13, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28917040/studying-selenoprotein-mrna-translation-using-rna-seq-and-ribosome-profiling
#2
Brian K Dalley, Lisa Baird, Michael T Howard
Deep sequencing of ribosome protected mRNA footprints, also called ribosome profiling or Ribo-Seq, is a relatively new methodology well suited to address questions regarding the mechanisms and efficiency of protein expression. Specifically, the ability of this technique to quantify ribosome abundance with codon resolution enables experiments aimed at studying many aspects of translation, including gene-specific translational efficiency, translation of regulatory upstream short open reading frames, sites of ribosome pausing, and most importantly for selenoproteins, the efficiency by which UGA codons are redefined to encode selenocysteine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28916985/whole-plastid-transcriptomes-reveal-abundant-rna-editing-sites-and-differential-editing-status-in-phalaenopsis-aphrodite-subsp-formosana
#3
Ting-Chieh Chen, Yu-Chang Liu, Xuewen Wang, Chi-Hsuan Wu, Chih-Hao Huang, Ching-Chun Chang
BACKGROUND: RNA editing is a process of post-transcriptional level of gene regulation by nucleotide modification. Previously, the chloroplast DNA of Taiwan endemic moth orchid, P. aphrodite subsp. formosana was determined, and 44 RNA editing sites were identified from 24 plastid protein-coding transcripts of leaf tissue via RT-PCR and then conventional Sanger sequencing. However, the RNA editing status of whole-plastid transcripts in leaf and other distinct tissue types in moth orchids has not been addressed...
September 16, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28916722/phosphoproteomics-reveals-that-glycogen-synthase-kinase-3-phosphorylates-multiple-splicing-factors-and-is-associated-with-alternative-splicing
#4
Mansi Y Shinde, Simone Sidoli, Katarzyna Kulej, Michael J Mallory, Caleb M Radens, Amanda Reicherter, Rebecca L Myers, Yoseph Barash, Kristen W Lynch, Benjamin A Garcia, Peter S Klein
Glycogen Synthase Kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. In vitro kinase assays and genetic and pharmacological manipulations of GSK-3 have identified more than 100 putative GSK-3 substrates in diverse cell types. Many more have been predicted on the basis of a recurrent GSK-3 consensus motif (pS/pTXXXS/T), but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. Using stable isotope labeling of amino acids in culture (SILAC) and mass spectrometry (MS) techniques to analyze the repertoire of GSK-3-dependent phosphorylation in mouse embryonic stem cells (ESCs), we found that ~2...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28916639/small-rna-seq-during-acute-maximal-exercise-reveal-rnas-involved-in-vascular-inflammation-and-cardiometabolic-health
#5
Ravi Shah, Ashish S Yeri, Avash Das, Amanda Courtright-Lim, Olivia Ziegler, Ernest Gervino, Jeffrey Ocel, Pablo Quintero Pinzon, Luke Wooster, Cole Shields Bailey, Kahraman Tanriverdi, Lea Beaulieu, Jane E Freedman, Ionita Ghiran, Gregory D Lewis, Kendall Van Keuren-Jensen, Saumya Das
OBJECTIVE: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. Approach and Results: We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry...
September 15, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28916360/trancriptome-profiles-of-amur-sturgeon-spleen-in-response-to-yersinia-ruckeri-infection
#6
Shaowu Li, Ying Zhang, Yongsheng Cao, Di Wang, Hongbai Liu, Tongyan Lu
Yersinia ruckeri (YR) is the causative agent of yersiniosis which has caused significant economic losses in fish culture worldwide, including in Amur sturgeon (Acipenser schrenckii) culture. To better understand the mechanism of the immune responses to YR in Amur sturgeon, the transcriptomic profiles of the spleens from YR-infected and non-infected groups were obtained using RNA-seq techniques. The de novo assemblies yielded totally 145 670 unigenes from the two libraries. The total numbers of transcripts in YR-infected and non-infected groups were from 110 893 to 147 336, with the mean length varying from 560 to 631 (N50: from 882 to 1083)...
September 12, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28915787/mmquant-how-to-count-multi-mapping-reads
#7
Matthias Zytnicki
BACKGROUND: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results. RESULTS: We provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene...
September 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28915238/a-high-resolution-atlas-of-gene-expression-in-the-domestic-sheep-ovis-aries
#8
Emily L Clark, Stephen J Bush, Mary E B McCulloch, Iseabail L Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C Bruce Whitelaw, Tom C Freeman, Kim M Summers, Alan L Archibald, David A Hume
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28915071/transcriptional-response-of-respiratory-epithelium-to-nontuberculous-mycobacteria
#9
Masashi Matsuyama, Andrew J Martins, Shamira Shallom, Olena Kamenyeva, Anuj Kashyap, Elizabeth P Sampaio, Juraj Kabat, Kenneth N Olivier, Adrian M Zelazny, John S Tsang, Steven M Holland
RATIONALE: The incidence of pulmonary nontuberculous mycobacterial (PNTM) disease is increasing, but host responses in respiratory epithelium infected with NTM are not fully understood. OBJECTIVE: We aimed to identify infection-relevant gene expression signatures of NTM infection of the respiratory epithelium. METHODS: We infected air-liquid interface (ALI) primary respiratory epithelial cell cultures with Mycobacterium avium subsp. avium (MAC) or Mycobacterium abscessuss subsp...
September 15, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28915060/long-non-coding-rna-lnrpt-is-regulated-by-pdgf-bb-and-modulates-proliferation-of-pulmonary-artery-smooth-muscle-cells
#10
Jidong Chen, Jiao Guo, Xiaolei Cui, Yan Dai, Zhixiong Tang, Junle Qu, J Usha Raj, Qinghua Hu, Deming Gou
Pulmonary artery hypertension (PAH) is a rare and fatal disorder with extensive remodeling of pulmonary arteries mediated by hyperproliferation of pulmonary artery smooth muscle cell (PASMC). Aberrant platelet-derived growth factor (PDGF) activity can lead to hyperproliferation of PASMC, however, little is known about the role of long noncoding RNA (lncRNA) in this process. Using RNA sequencing (RNA-seq), we identified 725 lncRNAs in rat PASMC (RPASMC), 95 of which were expressed differentially in response to PDGF-BB treatment...
September 15, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28912815/feasibility-of-metatranscriptome-analysis-from-infant-gut-microbiota-adaptation-to-solid-foods-results-in-increased-activity-of-firmicutes-at-six-months
#11
Floor Hugenholtz, Jarmo Ritari, Lotta Nylund, Mark Davids, Reetta Satokari, Willem M de Vos
Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth...
2017: International Journal of Microbiology
https://www.readbyqxmd.com/read/28912799/triportheus-albus-cope-1872-in-the-blackwater-clearwater-and-whitewater-of-the-amazon-a-case-of-phenotypic-plasticity
#12
José D A Araújo, Andrea Ghelfi, Adalberto L Val
The Amazon basin includes 1000s of bodies of water, that are sorted according to their color in three types: blackwater, clearwater, and whitewater, which significantly differ in terms of their physicochemical parameters. More than 3,000 species of fish live in the rivers of the Amazon, among them, the sardine, Triportheus albus, which is one of the few species that inhabit all three types of water. The purpose of our study was to analyze if the gene expression of T. albus is determined by the different types of water, that is, if the species presents phenotypic plasticity to live in blackwater, clearwater, and whitewater...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28912762/comparative-study-of-transcriptome-profiles-of-mouse-livers-and-skins-infected-by-fork-tailed-or-non-fork-tailed-schistosoma-japonicum
#13
Yan Yang, Jun-Jun He, Shuang Hu, Hua Chang, Xun Xiang, Jian-Fa Yang, Feng-Cai Zou
Schistosoma japonicum (S. japonicum) is a worldwide spread pathogen which penetrates host skin and then induces several diseases in infected host, such as fibrosis, formation of granulomas, hepatocirrhosis, and hepatomegaly. In present study, for the first time, transcriptomic profiles of mouse livers and skins infected by fork-tailed S. japonicum cercaria or non-fork-tailed S. japonicum cercaria were analyzed by using RNA-seq. The present findings demonstrated that transcriptomic landscapes of livers and skins infected by fork-tailed S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28912564/transcriptome-analysis-of-developing-lens-reveals-abundance-of-novel-transcripts-and-extensive-splicing-alterations
#14
Rajneesh Srivastava, Gungor Budak, Soma Dash, Salil A Lachke, Sarath Chandra Janga
Lens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. We show that the extent of novelty of expressed transcripts decreases significantly in post-natal lens compared to embryonic stages. Characterization of novel transcripts into partially novel transcripts (PNTs) and completely novel transcripts (CNTs) (novelty score ≥ 70%) revealed that the PNTs are both highly conserved across vertebrates and highly expressed across multiple stages...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912500/dynamic-changes-in-the-splenic-transcriptome-of-chickens-during-the-early-infection-and-progress-of-marek-s-disease
#15
Lu Dang, Man Teng, Hua-Wei Li, Hui-Zhen Li, Sheng-Ming Ma, Pu Zhao, Xiu-Jie Li, Rui-Guang Deng, Gai-Ping Zhang, Jun Luo
Gallid alphaherpesvirus 2 (GaHV2) is an oncogenic avian herpesvirus inducing Marek's disease (MD) and rapid-onset T-cell lymphomas. To reveal molecular events in MD pathogenesis and tumorigenesis, the dynamic splenic transcriptome of GaHV2-infected chickens during early infection and pathogenic phases has been determined utilizing RNA-seq. Based on the significant differentially expressed genes (DEGs), analysis of gene ontology, KEGG pathway and protein-protein interaction network has demonstrated that the molecular events happening during GaHV2 infection are highly relevant to the disease course...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911101/information-transduction-capacity-reduces-the-uncertainties-in-annotation-free-isoform-discovery-and-quantification
#16
Yue Deng, Feng Bao, Yang Yang, Xiangyang Ji, Mulong Du, Zhengdong Zhang, Meilin Wang, Qionghai Dai
The automated transcript discovery and quantification of high-throughput RNA sequencing (RNA-seq) data are important tasks of next-generation sequencing (NGS) research. However, these tasks are challenging due to the uncertainties that arise in the inference of complete splicing isoform variants from partially observed short reads. Here, we address this problem by explicitly reducing the inherent uncertainties in a biological system caused by missing information. In our approach, the RNA-seq procedure for transforming transcripts into short reads is considered an information transmission process...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910747/transcriptome-analysis-of-rana-chensinensis-liver-under-trichlorfon-stress
#17
Yu Ma, Bo Li, Yang Ke, Yongan Zhang, Yuhui Zhang
Trichlorfon is a selective organophosphate insecticide that is widely applied in aquaculture and agriculture for control of various parasites. However, repeated and excess applications of trichlorfon often lead to water pollution and threaten non-targeted species. Our previous studies showed that trichlorfon could cause oxidative stress, lipid peroxidation and hepatic lesions in the liver of Rana chensinensis, but the related molecular mechanisms remain unclear. To explore the interference of trichlorfon in gene transcription, the differentially expressed genes in the liver of R...
September 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28905878/detecting-splicing-patterns-in-genes-involved-in-hereditary-breast-and-ovarian-cancer
#18
Grégoire Davy, Antoine Rousselin, Nicolas Goardon, Laurent Castéra, Valentin Harter, Angelina Legros, Etienne Muller, Robin Fouillet, Baptiste Brault, Anna S Smirnova, Fréderic Lemoine, Pierre de la Grange, Marine Guillaud-Bataille, Virginie Caux-Moncoutier, Claude Houdayer, Françoise Bonnet, Cécile Blanc-Fournier, Pascaline Gaildrat, Thierry Frebourg, Alexandra Martins, Dominique Vaur, Sophie Krieger
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28905458/phosphorylation-of-ets-1-is-a-critical-event-in-dna-polymerase-iota-induced-invasion-and-metastasis-of-escc
#19
Chao He, Shuhua Wu, Aidi Gao, Ye Su, Han Min, Zeng-Fu Shang, Jinchang Wu, Li Yang, Wei-Qun Ding, Jundong Zhou
An aberrantly elevated expression of DNA polymerase ι (Pol ι) is significantly associated with poor prognosis of patients with esophageal squamous cell carcinoma (ESCC), yet the mechanisms behind remain obscure. Based on the RNA-Seq transcriptome and real-time PCR analysis, we identified ETS-1 as a candidate gene involved in Pol ι-mediated progression of ESCC. Wound-healing and transwell assay indicated that down-regulation of ETS-1 attenuates Pol ι-mediated invasiveness of ESCC. Signaling pathway analysis showed that Pol ι enhances ETS-1 phosphorylation at threonine-38 through the Erk signaling pathway in ESCC cells...
September 14, 2017: Cancer Science
https://www.readbyqxmd.com/read/28904958/transcriptomic-analysis-reveals-genes-mediating-salt-tolerance-through-calcineurin-ccha-independent-signaling-in-aspergillus-nidulans
#20
Sha Wang, Hongchang Zhou, Jun Wu, Jiangyu Han, Shasha Li, Shengwen Shao
Adaptation to changes in the environment is crucial for the viability of all organisms. Although the importance of calcineurin in the stress response has been highlighted in filamentous fungi, little is known about the involvement of ion-responsive genes and pathways in conferring salt tolerance without calcium signaling. In this study, high-throughput RNA-seq was used to investigate salt stress-induced genes in the parent, ΔcnaB, and ΔcnaBΔcchA strains of Aspergillus nidulans, which differ greatly in salt adaption...
2017: BioMed Research International
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