Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

<div><p>Abstract Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.</p></div

Additional file 1: Table S1. of Reduced Kidney Function, Albuminuria, and Risks for All-cause and Cardiovascular Mortality in China: A Population-based Cohort Study

and S2.Hazard ratios for all-cause and cardiovascular mortality by indicators of chronic kidney disease among participants aged less than 65 years old, as well as among those aged more than 65 years old. (DOCX 17 kb

Comparative Study of the Structure of Hydroproducts Derived from Loblolly Pine and Straw Grass

The structural characteristics of products derived from the hydrothermal carbonization (HTC) of loblolly pine (LP) and straw grass (SG) were investigated via solid-state cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS ¹³C NMR), heteronuclear single-quantum correlation nuclear magnetic resonance (HSQC-NMR), and solution ¹³C NMR and ³¹P NMR techniques. Results revealed that after HTC, hydrochars from both LP and SG mainly consisted of a combination of lignin, furfural, and condensed polyaromatic structures with a high level of fixed carbon content and higher heating value (HHV). Hydrochar from LP exhibited a higher aryl to furan ratio, and those from SG contained more aliphatic functional groups. Solution ¹³C NMR and HSQC revealed that both liquid chemicals were condensed polyphenolic structures with aliphatic groups that exist mainly in the form of side chains. Although the LP products exhibited a higher proportion of aromatic structures, the types of polyphenol and aliphatic C–H were more diverse in the SG products. Results also indicated that reactions such as chain scission and condensation occurred during hydrothermal carbonization processes. Overall, HTC was found to be an effective refinery treatment for converting different waste biomass into valuable energy materials and chemicals

Pathological molecular mechanism of symptomatic late-onset Fuchs endothelial corneal dystrophy by bioinformatic analysis

<div><p>Fuchs endothelial corneal dystrophy (FECD) is a degenerative disease characterized by corneal endothelial decompensation. FECD causes corneal stromal and epithelial edema and progressively develops into bullous keratopathy, which can eventually lead to blindness. However, the exact pathogenesis is unknown. In this study, we performed an in-depth bioinformatic analysis of the dataset GSE74123 to determine the differentially expressed genes (DEGs) of symptomatic late-onset FECD compared with a normal control. Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were used to analyze the pathological molecular mechanism of FECD. We found that cell senescence, reactive oxygen species (ROS), the extracellular matrix (ECM), epithelial-mesenchymal transition (EMT) and immune response-related genes play an important role in the pathological development of symptomatic late-onset FECD. In addition, we revealed that down-regulated IL-6, enhanced NF-κB activity and a suite of orchestrated chemokine responses induce fibrocyte differentiation from monocyte to dendritic cell maturation. PI3K plays a key role in the molecular mechanism of symptomatic late-onset FECD. This study enhances our understanding of the molecular mechanism of FECD pathogenesis and will improve the diagnostics and therapy of FECD patients in the future.</p></div

The biological process (BP) in GO enrichment of DEGs.

<p>(A) The top 25 significantly up-regulated BP GO terms in FECD group. (B) The top 25 significantly down-regulated BP GO terms in FECD group.</p

Heatmaps of four major types of genes.

<p>(A) Senescence, (B) ECM, (C) EMT, (D) visual perception and (E) immune response related DEGs were picked and normalized by Z-score. Red represents up-regulated expression. Blue represents up-regulated expression.</p

The summary of the dataset GSE74123.

<p>(A) The cluster heatmap of GSE74123. (B) The PCA of GSE74123 showed that significant differences between the two groups of samples. (C) Pearson heatmap showed the correlation between the two groups of samples. There was a high correlation within each group of samples. (D) The volcano plot showed the distribution of all genes by fold change and P value. The expression of FECD group was compared with control group. Genes with |log2 (fold change) | > 1 and P value < 0.05 were selected as the DEGs.</p

Signaling pathway analysis in symptomatic late-onset FECD.

<p>(A) Top 25 significantly different pathways were selected according to DEGs in FECD. (B) PPI of genes which appeared more than 10 times in significantly different pathways. Some important pathways in this study were labeled on it. (C) Signaling pathway network was plotted according to KEGG database.</p

The schematic diagram of possible pathological and molecular mechanisms of symptomatic late-onset FECD.

<p>In the symptomatic late-onset of FECD, corneal stroma is cloudy. DM becomes thick. Corneal guttae appear. The density of CECs is decreased. CECs lose their hexagonal shape. The reason for these phenomena is that the expression of cell senescence, EMT, ECM and immune response related genes changes.</p

The prevalence of three levels of physical activity in Jiangxi province of China by age-sex, 2007 and 2010.

a<p>Due to the limited participants in these age groups, we combined them with age group 65–69 and the same prevalence values were utilized.</p><p>The prevalence of three levels of physical activity in Jiangxi province of China by age-sex, 2007 and 2010.</p