ResearchPad - omics https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis]]> https://www.researchpad.co/article/elastic_article_10897 Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.

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<![CDATA[Cell Atlas technologies and insights into tissue architecture]]> https://www.researchpad.co/article/elastic_article_9194 Since Robert Hooke first described the existence of ‘cells’ in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function has expanded greatly; our understanding of cell types and states at the molecular level, and how these function within tissue architecture, is still limited. A greater understanding of our cells could revolutionise basic biology and medicine. Atlasing initiatives like the Human Cell Atlas aim to identify all cell types at the molecular level, including their physical locations, and to make this reference data openly available to the scientific community. This is made possible by a recent technology revolution: both in single-cell molecular profiling, particularly single-cell RNA sequencing, and in spatially resolved methods for assessing gene and protein expression. Here, we review available and upcoming atlasing technologies, the biological insights gained to date and the promise of this field for the future.

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<![CDATA[Proteome of a Moraxella catarrhalis Strain under Iron-Restricted Conditions]]> https://www.researchpad.co/article/N6abcacc8-f132-44f7-a1d6-521478c8be18

Moraxella catarrhalis is a leading cause of otitis media and exacerbations of chronic obstructive pulmonary disease; however, its response to iron starvation during infection is not completely understood. Here, we announce a sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) data set describing the differential expression of the M. catarrhalis CCRI-195ME proteome under iron-restricted versus iron-replete conditions.

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<![CDATA[Analysis of the Microbiome of Rainbow Trout (Oncorhynchus mykiss) Exposed to the Pathogen Flavobacterium psychrophilum 10094]]> https://www.researchpad.co/article/N0c1d2def-daba-4efc-a2f9-260efc945fdc

Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.

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<![CDATA[Language deficits in specific language impairment, attention deficit/hyperactivity disorder, and autism spectrum disorder: An analysis of polygenic risk]]> https://www.researchpad.co/article/Ndf794d63-119a-4d3e-a23d-87d735b77a15

Language is one of the cognitive domains often impaired across many neurodevelopmental disorders. While for some disorders the linguistic deficit is the primary impairment (e.g., specific language impairment, SLI), for others it may accompany broader behavioral problems (e.g., autism). The precise nature of this phenotypic overlap has been the subject of debate. Moreover, several studies have found genetic overlaps across neurodevelopmental disorders. This raises the question of whether these genetic overlaps may correlate with phenotypic overlaps and, if so, in what manner. Here, we apply a genome‐wide approach to the study of the linguistic deficit in SLI, autism spectrum disorder (ASD), and attention deficit/hyperactivity disorder (ADHD). Using a discovery genome‐wide association study of SLI, we generate polygenic risk scores (PRS) in an independent sample which includes children with language impairment, SLI, ASD or ADHD and age‐matched controls and perform regression analyses across groups. The SLI‐trained PRS significantly predicted risk in the SLI case–control group (adjusted R 2 = 6.24%; P = 0.024) but not in the ASD or ADHD case‐control groups (adjusted R 2 = 0.0004%, 0.01%; P = 0.984, 0.889, respectively) nor for height, used as a negative control (R 2 = 0.2%; P = 0.452). Additionally, there was a significant difference in the normalized PRS between children with SLI and children with ASD (common language effect size = 0.66; P = 0.044). Our study suggests no additive common‐variant genetic overlap between SLI and ASD and ADHD. This is discussed in the context of phenotypic studies of SLI and related disorders. Autism Res 2020, 13: 369–381. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc.

Lay Summary

Language deficits are characteristic of specific language impairment (SLI), but may also be found in other neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Many studies examined the overlaps and differences across the language deficits in these disorders, but few studies have examined the genetic aspect thereof. In this study, we use a genome‐wide approach to evaluate whether common genetic variants increasing risk of SLI may also be associated with ASD and ADHD in the same manner. Our results suggest that this is not the case, and we discuss this finding in the context of theories concerning the etiologies of these disorders.

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<![CDATA[Metagenomic Sequences of Three Drinking Water and Two Shower Hose Biofilm Samples Treated with or without Copper-Silver Ionization]]> https://www.researchpad.co/article/Nbdb25338-f9f5-46a2-9e81-1cbbfbd4ad92

We announce five shotgun metagenomics data sets from two Norwegian premise plumbing systems. The samples were shotgun sequenced on two lanes of an Illumina HiSeq 3000 instrument (THRUplex chemistry, 151 bp, paired-end reads), providing an extensive resource for sequence analyses of tap water and biofilm microbial communities.

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<![CDATA[Identification of exosomal miR-455-5p and miR-1255a as therapeutic targets for breast cancer]]> https://www.researchpad.co/article/N88906e9c-1e83-4778-bba4-98e21aacfc94

Abstract

Accumulated evidence has demonstrated exosomes of cancer cells carry microRNAs (miRNAs) to non-malignant cells to induce metastasis. The present study aimed to identify crucial exosomal miRNAs for breast cancer (BC) using microarray data (GSE83669 and GSE50429) from Gene Expression Omnibus database, including exosomal samples from human BC cells (MCF7, MDA-MB-231) and normal mammary epithelial cell line (MCF10, MCF-10A), as well as original cell samples. Differentially expressed miRNAs (DEMs) were identified using EdgeR package, and mRNA targets were predicted using miRWalk2 database. The target genes were overlapped with BC genes from Comparative Toxicogenomics Database (CTD) to construct BC-related interaction network. Potential functions were analyzed by DAVID. The expression of crucial miRNAs and target genes were confirmed in other microarray datasets or TCGA sequencing data. Their associations with survival and other clinical characteristics were validated by Kaplan–Meier plotter and LinkedOmics database. As a result, 9 and 8 DEMs were identified to be shared in two datasets for exosomal and original cells, respectively. Further comparison showed that miR-455-5p was specifically differentially expressed in exosomes, and miR-1255a was commonly expressed in exosomal and original cells samples. miR-455-5p could interact with CDKN1B to influence cell cycle process and miR-1255a could regulate SMAD4 to participate in TGF-β signaling pathway. High expressed miR-455-5p (basal-like) and miR-1255a (overall) were associated with poor overall survival, while the high expression of their target genes was associated with excellent overall, recurrence-free or distant metastasis-free survival. In conclusion, the present study preliminarily indicates that exosomal miR-455-5p and miR-1255a may be novel therapeutic targets for BC.

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<![CDATA[Fecal Metagenome Sequences from Lactating Dairy Cows Shedding Escherichia coli O157:H7]]> https://www.researchpad.co/article/5c16cf34d5eed0c48452d172

Cattle are primary reservoirs of Escherichia coli O157:H7, a causative agent of severe human infections. To facilitate analyses of the communities in which this pathogen is found, we sequenced the fecal metagenomes of 10 dairy cows shedding E. coli O157:H7 and added them to the public domain.

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<![CDATA[A Divergent Strain of Culex pipiens-Associated Tunisia Virus in the Malaria Vector Anopheles epiroticus]]> https://www.researchpad.co/article/5c16cf87d5eed0c48452e54d

Here, we report the draft genome sequence of a divergent strain of Culex pipiens-associated Tunisia virus (CpATV) identified in the malaria vector Anopheles epiroticus (CpATV-AnE). CpATV-AnE expands the reference virus sequence, introducing an extended replicase with novel virga-like domains.

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<![CDATA[Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle]]> https://www.researchpad.co/article/5c16cf28d5eed0c48452ceb1

Here, we present a comprehensive transcriptomics data set of Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host. This study samples from 16 stages across the entire B. malayi life cycle, including stage 1 through 4 larvae, adult males and females, embryos, immature microfilariae, and mature microfilariae.

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<![CDATA[Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico “Dead Zone”]]> https://www.researchpad.co/article/5c16cf21d5eed0c48452ccc3

Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist.

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