Purpose The present work concerns the distribution of ten heavy metals (Sb, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, and Zn) in the surrounding agricultural soils of the world largest antimony (Sb) mine in China. The objective is to explore the degree and spatial distribution of heavy metal pollution of the Sb mine-affected agricultural soils. The presented data were compared with metal concentrations in soils from mining and smelting sites in China and other countries. Materials and methods There were 29 environmental samples in all that were collected in the year 2008 for this study. Soil characteristic parameters such as pH, total organic carbon, and cation exchange capacity were determined. Metal contents were determined after digestion in a Teflon bomb with aqua regia. Cd, Cu, Ni, Pb, and Zn concentrations were determined by inductively coupled plasma-mass spectrometry. As, Sb, and Hg concentrations were determined by atomic fluorescence spectrometry (AFS-2202). Fe, Al, Cr, and Mn concentrations were determined by inductively coupled plasma-atomic emission spectrometry.Results and discussion Almost all of the ten heavy metals exhibited much higher concentrations compared with their respective natural background values, especially Sb, and they varied with sampling site. The enriched factor values show that Sb (235.8), Cd (51.8), Hg (13.8), As (3.13), Zn (2.91), Pb (2.46), and Cr (1.67) are significantly accumulated in the study area. All of the integrated pollution indexes (IPI>3) calculated from pollution indexes show that the soils are severely contaminated by investigated heavy metals.Principal component analysis, cluster analysis, and correlation analysis suggest that Cd, Cu, Pb, Zn, and Mn are derived from the sulfide mineralization paragenesis in Xikuangshan area. Cr, As, Hg, Al, and Sb are mainly due to the mining and smelting activities of this area and derived from organic matters, and Ni is mainly generated from agricultural activities. These metal concentrations in Xikuangshan agricultural topsoil are comparable or within the ranges of those in mine areas of other countries. Conclusions The heavy metal concentrations in the topsoil of Xikuangshan area are mostly higher than the background values, especially for Sb and As. Heavy metal pollution has spread in this mine area, both from mining activities and agricultural activities. Analysis of soil samples from 23 sampling locations of the area show significant spatial variation of the ten heavy metals.

Background: The central nervous system (CNS) is vulnerable to viral infection, yet few host factors in the CNS are known to defend against invasion by neurotropic viruses. Long noncoding RNAs (lncRNAs) have been revealed to play critical roles in a wide variety of biological processes and are highly abundant in the mammalian brain, but their roles in defending against invasion of pathogens into the CNS remain unclear. Results: We report here that multiple neurotropic viruses, including rabies virus, vesicular stomatitis virus, Semliki Forest virus, and herpes simplex virus 1, elicit the neuronal expression of a host-encoded lncRNA EDAL. EDAL inhibits the replication of these neurotropic viruses in neuronal cells and rabies virus infection in mouse brains. EDAL binds to the conserved histone methyltransferase enhancer of zest homolog 2 (EZH2) and specifically causes EZH2 degradation via lysosomes, reducing the cellular H3K27me3 level. The antiviral function of EDAL resides in a 56-nt antiviral substructure through which its 18-nt helix-loop intimately contacts multiple EZH2 sites surrounding T309, a known O-GlcNAcylation site. EDAL positively regulates the transcription of Pcp4l1 encoding a 10-kDa peptide, which inhibits the replication of multiple neurotropic viruses. Conclusions: Our findings show that a neuronal lncRNA can exert an effective antiviral function via blocking a specific O-GlcNAcylation that determines EZH2 lysosomal degradation, rather than the traditional interferon-dependent pathway.

Motivation The biclustering of large-scale gene expression data holds promising potential for detecting condition-specific functional gene modules (i.e. biclusters). However, existing methods do not adequately address a comprehensive detection of all significant bicluster structures and have limited power when applied to expression data generated by RNA-Sequencing (RNA-Seq), especially single-cell RNA-Seq (scRNA-Seq) data, where massive zero and low expression values are observed. Results We present a new biclustering algorithm, QUalitative BIClustering algorithm Version 2 (QUBIC2), which is empowered by: (i) a novel left-truncated mixture of Gaussian model for an accurate assessment of multimodality in zero-enriched expression data, (ii) a fast and efficient dropouts-saving expansion strategy for functional gene modules optimization using information divergency and (iii) a rigorous statistical test for the significance of all the identified biclusters in any organism, including those without substantial functional annotations. QUBIC2 demonstrated considerably improved performance in detecting biclusters compared to other five widely used algorithms on various benchmark datasets from E.coli, Human and simulated data. QUBIC2 also showcased robust and superior performance on gene expression data generated by microarray, bulk RNA-Seq and scRNA-Seq. Availability and implementation The source code of QUBIC2 is freely available at https://github.com/OSU-BMBL/QUBIC2. Contact czhang87@iu.edu or qin.ma@osumc.edu Supplementary information Supplementary data are available at Bioinformatics online.

Extreme weather conditions with negative impacts can strongly affect agricultural production. In the Danjiangkou reservoir area, citrus yields were greatly influenced by cold weather conditions and drought stress in 2011. Soil straw mulching (SM) practices have a major effect on soil water and thermal regimes. A two-year field experiment was conducted to evaluate whether the SM practices can help achieve favorable citrus fruit yields. Results showed that the annual total runoff was significantly (P<0.05) reduced with SM as compared to the control (CK). Correspondingly, mean soil water storage in the top 100 cm of the soil profile was increased in the SM as compared to the CK treatment. However, this result was significant only in the dry season (Jan to Mar), and not in the wet season (Jul to Sep) for both years. Interestingly, the SM treatment did not significantly increase citrus fruit yield in 2010 but did so in 2011, when the citrus crop was completely destroyed (zero fruit yield) in the CK treatment plot due to extremely low temperatures during the citrus overwintering stage. The mulch probably acted as an insulator, resulting in smaller fluctuations in soil temperature in the SM than in the CK treatment. The results suggested that the small effects on soil water and temperature changes created by surface mulch had limited impact on citrus fruit yield in a normal year (e.g., in 2010). However, SM practices can positively impact citrus fruit yield in extreme weather conditions.