mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction

Sarcopenia is an age-associated loss of skeletal muscle mass and strength that increases the risk of disability. Calorie restriction (CR), the consumption of fewer calories while maintaining adequate nutrition, mitigates sarcopenia and many other age-related diseases. To identify potential mechanisms by which CR preserves skeletal muscle integrity during aging, we used mRNA-Seq for deep characterization of gene regulation and mRNA abundance in skeletal muscle of old mice compared with old mice subjected to CR. mRNA-Seq revealed complex CR-associated changes in expression of mRNA isoforms, many of which occur without a change in total message abundance and thus would not be detected by methods other than mRNA-Seq. Functional annotation of differentially expressed genes reveals CR-associated upregulation of pathways involved in energy metabolism and lipid biosynthesis, and downregulation of pathways mediating protein breakdown and oxidative stress, consistent with earlier microarray-based studies. CR-associated changes not noted in previous studies involved downregulation of genes controlling actin cytoskeletal structures and muscle development. These CR-associated changes reflect generally healthier muscle, consistent with CR's mitigation of sarcopenia. mRNA-Seq generates a rich picture of the changes in gene expression associated with CR, and may facilitate identification of genes that are primary mediators of CR's effects.     

A proposed framework for determining the environmental impact of replacing agricultural grassland with Miscanthus in Ireland

Energy crops offer an opportunity to substantially increase bioenergy resources which can replace rapidly depleting fossil fuel reserves and mitigate the effect of climate change. Energy crops are typically established within traditional agricultural systems such as tillage land or grassland. Associated land use conversion has environmental implications. The aim of this paper is to propose a framework to examine how such environmental implications can be assessed, based on (a) a Strategic Environmental Assessment (SEA) approach which considers potential impacts at different stages of a plan across a wide range of environmental receptors and (b) a literature review. The example we used was that of Miscanthus replacing grassland farming. This scenario is particularly relevant to Ireland, where over 90% of the agricultural land is permanent pasture, but is also applicable to grassland conversion throughout Europe and the United States. Two consecutive phases of land‐use change were identified for assessment, each with a distinct set of environmental impacts. The first was a transition phase, lasting from initial livestock clearance and grassland ploughing until the Miscanthus crop became established (2–3 years). The second phase was the mature crop phase, lasting up to 25 years. Miscanthus cultivation was more likely to impact negatively on the environment during the transition phase than the mature phase, primarily due to abrupt disturbance and the time required for a new equilibrium to establish. However, a literature review of the impact on the environmental receptors revealed that replacing Irish agricultural grassland with Miscanthus had the potential to improve biodiversity, water, air and soil quality, and climatic factors once the crop became established and reached maturity. In order to confirm these findings an appropriate monitoring programme involving objectives and indicators associated with each environmental receptor would need to be developed.     

Single-cell transcriptomics analysis reveals intratumoral heterogeneity and identifies a gene signature associated with prognosis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) tumors exhibit high heterogeneity. However, current understanding of tumor cell heterogeneity of HCC and the association with prognosis remains very limited. In the present study, we collected and examined tumor tissue from one HCC patient by single-cell RNA sequencing (scRNA-seq). We identified 5753 cells and 16 clusters including hepatocytes/cancer cells, T cells, macrophages, endothelial cells, fibroblasts, NK cells, neutrophils, and B cells. In six tumor cell subclusters, we identified a cluster of proliferative tumor cells associated with poor prognosis. We downloaded scRNA-seq data of {"type":"entrez-geo","attrs":{"text":"GSE125449","term_id":"125449"}}GSE125449 from the NCBI-GEO as validation dataset, and found that a cluster of hepatocytes exhibited high proliferation activity in HCC. Furthermore, we identified a gene signature related to the proliferation of HCC cells. This gene signature is efficient to classify HCC patients into two groups with distinct prognosis in both TCGA and ICGC database cohorts. Our results reveal the intratumoral heterogeneity of HCC at single cell level and identify a gene signature associated with HCC prognosis.     

N2O emission associated with shifts of bacterial communities in riparian wetland during the spring thawing periods

Soil freeze–thaw processes lead to high nitrous oxide (N₂O) emissions and exacerbate the greenhouse effect. The wetlands of the Inner Mongolia Plateau are in the pronounced seasonal freeze–thaw zone, but the effect of spring thaw on N₂O emissions and related microbial mechanisms is still unclear. We investigated the effects of different periods (freeze, freeze–thaw, and thaw) on soil bacterial community diversity and composition and greenhouse gas emissions during the spring freeze–thaw in the XiLin River riparian wetlands in China by amplicon sequencing and static dark box methods. The results showed that the freeze–thaw periods predominantly impact on the diversity and composition of the bacterial communities. The phyla composition of the soil bacteria communities of the three periods is similar in level, with Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria dominating the microbial communities. The alpha‐diversity of bacterial communities in different periods varies that the freezing period is higher than that of the freeze–thaw period (p < .05). Soil total carbon, soil water content, and microbial biomass carbon were the primary factors regulating the abundance and compositions of the bacterial communities during spring thawing periods. Based on functional predictions, the relative abundance of nitrification and denitrification genes was higher in the freezing period than in the thawing period, while the abundance was lowest in the freeze–thawing period. The correlation results found that N₂O emissions were significantly correlated with amoA and amoB in nitrification genes, indicating that nitrification may be the main process of N₂O production during spring thaw. This study reveals potential microbial mechanisms of N₂O emission during spring thaw and provides data support and theoretical basis for further insight into the mechanism of N₂O emission during spring thaw.     

Transcriptional analysis of gasoline engine exhaust particulate matter 2.5-exposed human umbilical vein endothelial cells reveals the different gene expression patterns related to the cardiovascular diseases

Particulate matter (PM) causes several diseases, including cardiovascular diseases (CVDs). Previous studies compared the gene expression patterns in airway epithelial cells and keratinocytes exposed to PM. However, analysis of differentially expressed gene (DEGs) in endothelial cells exposed to PM2.5 (diameter less than 2.5 μm) from fossil fuel combustion has been limited. Here, we exposed human umbilical vein endothelial cells (HUVECs) to PM2.5 from combustion of gasoline, performed RNA-seq analysis, and identified DEGs. Exposure to the IC50 concentrations of gasoline engine exhaust PM2.5 (GPM) for 24 h yielded 1081 (up-regulation: 446, down-regulation: 635) DEGs. The most highly up-regulated gene is NGFR followed by ADM2 and NUPR1. The most highly down-regulated gene is TNFSF10 followed by GDF3 and EDN1. Gene Ontology enrichment analysis revealed that GPM regulated genes involved in cardiovascular system development, tube development and circulatory system development. Kyoto Encyclopedia of Genes and Genomes and Reactome pathway analyses showed that genes related to cytokine–cytokine receptor interactions and cytokine signaling in the immune system were significantly affected by GPM. We confirmed the RNA-seq data of some highly altered genes by qRT-PCR and showed the induction of NGFR, ADM2 and IL-11 at a protein level, indicating that the observed gene expression patterns were reliable. Given the adverse effects of PM2.5 on CVDs, our findings provide new insight into the importance of several DEGs and pathways in GPM-induced CVDs.     

ST6Gal1 is up‐regulated and associated with aberrant IgA1 glycosylation in IgA nephropathy: An integrated analysis of the transcriptome

Galactose‐deficient IgA1 (Gd‐IgA1) plays a crucial role in the development of Immunoglobulin A nephropathy (IgAN), however, the underlying pathogenic mechanisms driving Gd‐IgA1 production in B cells are not well understood. In this study, RNA‐seq analysis identified 337 down‐regulated and 405 up‐regulated genes in B cells from 17 patients with IgAN and 6 healthy controls. Among them, ST6Gal1, which was associated with IgAN in a previous genome‐wide association study (GWAS), was up‐regulated in IgAN and significantly positive correlated with elevated Gd‐IgA1. In addition, we identified increased plasma ST6Gal1 levels in 100 patients with IgAN, which were associated with higher levels of proteinuria, plasma IgA, Gd‐IgA1 levels, greater degrees of systemic complement activation including C3a, Bb, C4d, MAC and a lower proportion classified as C2 grade (crescent proportion ≥25%). Interesting, in vitro, recombinant ST6Gal1 (rST6Gal1) exposure reduced the production of Gd‐IgA1 in cultured peripheral blood mononuclear cells from IgAN patients. rST6Gal1 stimuli also increased expression of C1GALT1, which were well‐known proportional to the decrease in galactose deficiency of IgA1. In conclusions, we identified increased plasma ST6Gal1 levels and the association of ST6Gal1 with disease severity of IgAN. Additionally, rST6Gal1 administration in vitro increased expression of C1GALT1 and reduced the production of Gd‐IgA1.