Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Association between diminished miRNA expression and acquired alterations of ABO antigen expression in leukemia patients

Supplementary Table S1. The clinical significance of miRNAs in acute leukemia.

opencc-by-4.0Feb 2020View details →

Research on the Relationship of Ions Content with TNF-α and TGF-β Expression in BALF of Silica-induced Rats

All data of this article.

Spillover of an alien parasite reduces expression of costly behaviour in native host species

We used a natural experiment of populations of native red squirrels (Sciurus vulgaris) that were colonised by the alien grey squirrel (Sciurus carolinensis), comparing repeated measurements of red squirrel parasite infection and personality with those taken in sites where only the native species occurred. Using data from 323 arena tests across three experimental (native species and IAS) and three control sites (only native species), we found negative correlations between native species’ activity and infection with Strongyloides robustus in the sites invaded by the alien species. Activity was also negatively correlated with infection by its native helminth (Trypanoxyuris sciuri) but only when grey squirrels were present, while in the red-only sites there was no relationship of T. sciuri infection with any of the personality traits. Moreover, individuals that acquired S. robustus during the study reduced their activity after infection, while this was not the case for animals that remained uninfected.

Dataset related to article "Costimulatory Molecules and Immune Checkpoints Are Differentially Expressed on Different Subsets of Dendritic Cells."

Dendritic cells (DCs) play a crucial role in initiating and shaping immune responses. The effects of DCs on adaptive immune responses depend partly on functional specialization of distinct DC subsets, and partly on the activation state of DCs, which is largely dictated by environmental signals. Fully activated immunostimulatory DCs express high levels of costimulatory molecules, produce pro-inflammatory cytokines, and stimulate T cell proliferation, whereas tolerogenic DCs express low levels of costimulatory molecules, produce immunomodulatory cytokines and impair T cell proliferation. Relevant to the increasing use of immune checkpoint blockade in cancer treatment, signals generated from inhibitory checkpoint molecules on DC surface may also contribute to the inhibitory properties of tolerogenic DCs. Yet, our knowledge on the expression of inhibitory molecules on human DC subsets is fragmentary. Therefore, in this study, we investigated the expression of three immune checkpoints on peripheral blood DC subsets, in basal conditions and upon exposure to pro-inflammatory and anti-inflammatory stimuli, by using a flow cytometric panel that allows a direct comparison of the activatory/inhibitory phenotype of DC-lineage and inflammatory DC subsets. We demonstrated that functionally distinct DC subsets are characterized by differential expression of activatory and inhibitory molecules, and that cDC1s in particular are endowed with a unique immune checkpoint repertoire characterized by high TIM-3 expression, scarce PD-L1 expression and lack of ILT2. Notably, this unique cDC1 repertoire was subverted in a group of patients with myelodysplastic syndromes included in the study. Applied to the characterization of DCs in the tumor microenvironment, this panel has the potential to provide valuable information to be used for investigating the role of DC subsets in cancer, guiding DC-targeting treatments, and possibly identifying predictive biomarkers for clinical response to cancer immunotherapy.

Table S1. List of relevant studies of gene expression with available eQTL data.

Supplementary Table S1. List of relevant studies of gene expression with available eQTL data. The table contains information of gene expression eQTL data used in the current study: source name (CEDAR, GTEx, blood eQTL by Westra et al.), tissue name and corresponding article DOI. Part of the article: Williams FMK et al. "Sequence variation at 8q24.21 and risk of back pain"

opencc-by-4.0Jul 2019View details →

Parvalbumin expression in oligodendrocyte-like CG4 cells causes a reduction in mitochondrial volume, attenuation in reactive oxygen species production and a decrease in cell processes' length and branching

Forebrain glial cells - ependymal cells and astrocytes -acquire upon injury- a “reactive” phenotype associated with parvalbumin (PV) upregulation. Since free radicals, e.g. reactive oxygen species (ROS) play a role in the pathogenesis of multiple sclerosis, and that PV-upregulation in glial cells is inversely correlated with the level of oxidative stress, we hypothesized that PV-upregulation might also protect oligodendrocytes by decreasing ROS production. Lentiviral transduction techniques allowed for PV overexpression in CG4 oligodendrocyte progenitor cells (OPCs). Depending on the growth medium CG4 cells can be maintained in an OPC-like state, or induced to differentiate into an oligodendrocyte (OLG)-like phenotype. While increased levels of PV had no effect on cell proliferation and invasiveness in vitro, PV decreased the mitochondria volume in CG4 cell bodies, as well as the mitochondrial density in CG4 processes in both OPC-like and OLG-like states. In line with the PV-induced global decrease in mitochondrial volume, elevated PV levels reduced transcript levels of mitochondrial transcription factors involved in mitochondria biogenesis. In differentiated PV-overexpressing CG4 cells with a decreased mitochondrial volume, UV-induced ROS production was lower than in control CG4 cells hinting towards a possible role of PV in counteracting oxidative stress. Unexpectedly, PV also decreased the length of processes in undifferentiated CG4 cells and moreover diminished branching of differentiated CG4 cell processes, strongly correlated with the decreased density of mitochondria in CG4 cell processes. Thus besides conferring a protective role against oxidative stress, PV in a cell autonomous fashion additionally affects process’ growth and branching in CG4 cells.

opencc-by-4.0Apr 2020View details →

Figure S1: β-catenin expression is controls and T-ALL patients.

β-catenin expression is controls and T-ALL patients.

opencc-by-4.0May 2020View details →

Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS

Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS data for the Applied Medical Science MSci Research Project.

opencc-zeroJun 2020View details →

Data from: Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens

Many diapausing insects undergo a nutrient storage period prior to their entry into diapause. Bumble bee queens diapause as adults in the winter preceding their spring nest initiation period. Before diapause, they sequester glycogen and lipids, which they metabolize during the overwintering period. We used RNA sequencing to examine how age and nectar diet (specifically, the concentration of sucrose in nectar) impact gene expression in the pre-overwintering bumble bee queen fat body, the "liver-like" organ in insects with broad functions related to nutrient storage and metabolism. We found that diet on its own, and in combination with age, impacts the expression of genes involved in detoxification. Age was also a strong driver of gene expression, especially at earlier ages (up to 3 days). In addition to these molecular correlates of diet and age, we also found a putative molecular signature of diapause entry or preparation in adult queens in the oldest age group (12 days) fed the most sucrose-rich diet, based on comparisons between our data set and another transcriptome data set from bumble bee queens. This transcriptomic pattern suggests that preparation for (or entry into) diapause might be in part mediated by nutritional state in bumble bee queens. Collectively, these findings show that there are molecular processes in the fat body that are responsive to sucrose levels in the diet and/or associated with age-related maturational changes. A better understanding of these processes may shed light on important aspects of bumble bee biology, such as queen responses to nutritional and other forms of stress, and the factors that regulate their entrance into diapause.

opencc-by-4.0Jul 2020View details →

Volcano plot of Sigma B-dependent differential gene expression of Clostridioides difficile

A customized whole-genome DNA microarray of Clostridioides difficile 630∆erm was used (8x15K format, Agilent). Quadruplicate samples were analysed for the DNA microarray. Using the ULS fluorescent labelling kit for Agilent arrays (Kreatech), 1 µg of total RNA was used for labelling with either Cy3 (Ptet-sigB) or Cy5 (Ptet-sLucopt). After pooling and fragmentation, 300 ng of labelled RNA per sample was hybridized according to the two-color microarray protocol from Agilent. DNA microarrays were scanned with an Agilent C scanner and analysed. CDS_ID=GenBank identifier, gene_name=annotated gene name (when available), locus_tag= locus tag, protein=annotation of protein function (when available), log2FC= log 2 of the fold change (sigB overproduction/control), adj_Pvalue = adjusted P-value, significance = -10log(adj_Pvalue).

opencc-zeroJul 2020View details →

Data from: Chronic traffic noise increases food intake and alters gene expression associated with metabolism and disease in bats

<ol> <li>Anthropogenic noise exposure has deleterious effects on the foraging ecology of many animals. However, the effects of chronic anthropogenic noise on food intake and health condition in wildlife remain largely unknown.</li> <li>We tested whether traffic noise exposure over multiple days would change food intake and would have effects on the health of Asian particoloured bats. We broadcast traffic noise to the bats of two noise-exposure groups (group A, 5 bats; group C, 6 bats) and broadcast silence files to the bats of two control groups (group B, 5 bats; group D, 6 bats) for 12 days. We measured the changes in food intake, body weight, and concentration of faecal triiodothyronine (T3) and thyroxine (T4) in groups A and B. We compared the transcriptional profiles in brain, kidney and liver tissues between bats in groups C and D.</li> <li>The bats exposed to traffic noise had a significantly higher daily food intake and a significantly greater body weight than bats in control group during the period of playback. Faecal T3 and T4 were higher in the noise-exposure group after playback had been on for more than one day.</li> <li>We found a total of 169 differentially expressed genes (DEGs) between noise-exposure and control groups. Some DEGs related to stress response were up-regulated in the bats exposed to noise. The 169 DEGs were mainly enriched in Gene Ontology (GO) terms associated with metabolism, fundamental cellular processes, stress response and immune response. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways affected by noise exposure were linked with metabolism, disease, apoptosis, autophagy, phagosome and ribosome.</li> </ol> Synthesis and applications. Our results suggest that bats exposed to chronic traffic noise while roosting may need more energetic intake and have a greater motivation to forage than others not exposed to noise, probably as a result of a stress response. Furthermore, chronic traffic noise may increase the risk of metabolic dysregulation, immune disorders, and other diseases. Management measures for reducing noise disturbance, for example, implementing sound barriers, are essential.

opencc-zeroJul 2020View details →

Arsenic (+3 oxidation state) methyltransferase gene polymorphisms and expression on bladder cancer

Inorganic arsenic (iAs) is a recognized environment-related factor for bladder cancer (BCa). Arsenic (+3 oxidation state) methyltransferase (AS3MT) gene might influence BCa by regulating iAs metabolism. The objectives of the present study were to systematically review eligible case-control studies about AS3MT polymorphisms and BCa and to further compare the genotype distribution and allele distribution between BCa patients and controls by meta-analysis for humans. Besides, to clarify the effects of AS3MT expression on BCa clinical outcomes and survival time, we also conducted a series of analyses based on The Cancer Genome Atlas (TCGA) dataset. Databases were systematically retrieved and we applied Stata software to perform meta-analysis. The registration of this study protocol is at PROSPERO and ID is CRD42019133947. Five articles were recruited and pooled results demonstrated that rs3740393 and rs11191438 polymorphisms were related to BCa risk in overall population (P<0.05) in the overall population. In addition, GG and GC genotypes in rs3740393 and GG genotype in rs11191438 might be the susceptibility genotypes for BCa. Results based on 168 BCa samples from TGCA indicated that patients with higher expression of AS3MT had poor overall survival time and AS3MT expression is an independent indicator for BCa survival. This study identified that AS3MT polymorphisms could affect BCa risk and AS3MT expression was pivotal in prognosis of BCa.

opencc-zeroDec 2008View details →

Data from: A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs

The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence. Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression. Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease. Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes - Data

This file contains the data that was used in the paper titled "A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes", which is submitted for review. The preprint is available at <a href="https://www.biorxiv.org/content/10.1101/2020.03.30.016675v1.abstract">https://www.biorxiv.org/content/10.1101/2020.03.30.016675v1.abstract</a>

opencc-by-4.0Aug 2020View details →

Plasmid Design for Tunable Two‐Enzyme Co‐Expression Promotes Whole‐Cell Production of Cellobiose

We provide underlying data for the publication "Plasmid design for tunable two-enzyme co-expression promotes whole-cell production of cellobiose". Please find the abstract below. Catalyst development for biochemical cascade reactions often follows a “whole cell approach” in which a single microbial cell is made to express all of the required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux from substrate to product necessitates precise balancing between the individual activities. Here, we show effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors enabling tunable two‐enzyme co‐expression in E. coli , for the purpose of whole‐cell production of cellobiose. Flux efficiency in the transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co‐expression cope with large differences in the specific activity of cellobiose phosphorylase (14 U mg−1) and sucrose phosphorylase (122 U mg−1). Comparing mono‐ and bicistronic co‐expression strategies, we analyze genetic elements controlling transcription, transcription‐translation coupling or plasmid replication for effect on activity, and also stable producibility, of the whole cell catalyst. We discover a key role of the bom (basis of mobility) site for plasmid stability dependent on the origin of replication and demonstrate the importance of RBS (ribosome binding site) strength for balanced bicistronic co‐expression. Whole cell catalysts show high specific rates (460 μmol cellobiose min−1 g−1 dry cells) and performance metrics (30 g L−1; &sim;82% yield; 3.8 g L−1 h−1 overall productivity) promising for cellobiose production.

opencc-zeroAug 2020View details →

Species-specific effects of thermal stress on the expression of genetic variation across a diverse group of plant and animal taxa under experimental conditions

Assessing the genetic adaptive potential of populations and species is essential for better understanding evolutionary processes. However, the expression of genetic variation may depend on environmental conditions, which may speed up or slow down evolutionary responses. Thus, the same selection pressure may lead to different responses. Against this background, we here investigate the effects of thermal stress on genetic variation, mainly under controlled laboratory conditions. We estimated additive genetic variance (VA), narrow-sense heritability (h2), and the coefficient of genetic variation (CVA) under both benign control and stressful thermal conditions. We included six species spanning a diverse range of plant and animal taxa and a total of 25 morphological and life-history traits. Our results show that (1) thermal stress reduced fitness components, (2) the majority of traits showed significant genetic variation, and that (3) thermal stress affected the expression of genetic variation (VA, h2 or CVA) in only one third of the cases (25 of 75 analyses, mostly in one clonal species). Moreover, effects were highly species-specific, with genetic variation increasing in 11 and decreasing in 14 cases under stress. Our results hence indicate that thermal stress does not generally affect the expression of genetic variation under laboratory conditions but, nevertheless, increases or decreases genetic variation in specific cases. Consequently, predicting the rate of genetic adaptation might not be generally complicated by environmental variation, but requires a careful case-by-case consideration.

opencc-zeroAug 2020View details →

Negative mood affects the expression of negative but not positive emotions in mice

Whether, and to what extent animals experience emotions is crucial for understanding their decisions and behaviour, and underpins a range of scientific fields, including animal behaviour, neuroscience, evolutionary biology and animal welfare science. However, research has predominantly focussed on alleviating negative emotions in animals, with the expression of positive emotions left largely unexplored. Therefore, little is known about positive emotions in animals and how their expression is mediated. We used tail handling to induce negative mood in laboratory mice and found that whilst being more anxious and depressed increased their expression of a discrete negative emotion ('disappointment') meaning that they were less resilient to negative events, their capacity to express a discrete positive emotion ('elation') was unaffected relative to control mice. Therefore, we show not only that mice have discrete positive emotions, but that they do so regardless of their current mood state. Our findings are the first to suggest that the expression of discrete positive and negative emotions in animals are not equally affected by long-term mood state. Our results also demonstrate that repeated negative events can have a cumulative effect to reduce resilience in laboratory animals, which has significant implications for animal welfare.