Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.

Recent advances in phyto-combined remediation of heavy metal pollution in soil.

The global industrialization and modernization have witnessed a rapid progress made in agricultural production, along with the issue of soil heavy metal (HM) pollution, which has posed severe threats to soil quality, crop yield, and human health. Phytoremediation, as an alternative to physical and chemical methods, offers a more cost-effective, eco-friendly, and aesthetically appealing means for in-situ remediation. Despite its advantages, traditional phytoremediation faces challenges, including variable soil physicochemical properties, the bioavailability of HMs, and the slow growth and limited biomass of plants used for remediation. This study presents a critical overview of the predominant plant-based HM remediation strategies. It expounds upon the mechanisms of plant absorption, translocation, accumulation, and detoxification of HMs. Moreover, the advancements and practical applications of phyto-combined remediation strategies, such as the addition of exogenous substances, genetic modification of plants, enhancement by rhizosphere microorganisms, and intensification of agricultural technologies, are synthesized. In addition, this paper also emphasizes the economic and practical feasibility of some strategies, proposing solutions to extant challenges in traditional phytoremediation. It advocates for the development of cost-effective, minimally polluting, and biocompatible exogenous substances, along with the careful selection and application of hyperaccumulating plants. We further delineate specific future research avenues, such as refining genetic engineering techniques to avoid adverse impacts on plant growth and the ecosystem, and tailoring phyto-combined strategies to diverse soil types and HM pollutants. These proposed directions aim to enhance the practical application of phytoremediation and its integration into a broader remediation framework, thereby addressing the urgent need for sustainable soil decontamination and protection of ecological and human health.

Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population.

Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.

Relation extraction: advancements through deep learning and entity-related features.

Capturing semantics and structure surrounding the target entity pair is crucial for relation extraction. The task is challenging due to the limited semantic elements and structural features of the target entity pair within a sentence. To tackle this problem, this paper introduces an approach that fuses entity-related features under convolutional neural networks and graph convolution neural networks. Our approach combines the unit features of the target entity pair to generate corresponding fusion features and applies the deep learning framework to extract high-order abstract features for relation extraction. Experimental results from three public datasets (ACE05 English, ACE05 Chinese, and SanWen) indicate that the proposed approach achieves F1-scores of 77.70%, 90.12%, and 68.84%, respectively, highlighting its effectiveness and robustness. This paper provides a comprehensive description of the approach and experimental results.

The inhibitory effect of Isoliquiritigenin on the proliferation of human arterial smooth muscle cell.

BACKGROUND: Isoliquiritigenin (ISL) has various biological activities including as antioxidant and an inhibitor of PI3K/AKT signaling pathway. However, both oxidative stress and activated PI3K/AKT signaling contribute to the aberrant proliferation of vascular smooth muscle cells (VSMCs). This study is aimed to explore the effect of ISL on the proliferation of human arterial smooth muscle cells (HASMCs) and to investigate the underlying mechanisms. METHODS: BrdU incorporation, cell cycle and reactive oxygen species (ROS) in normal or ISL treated HASMCs were analyzed by flow cytometry. Cell viablity was measured by CCK-8. Protein expression levels were examined by Western blot, and superoxide dismutase (SOD) activity was detected by using commercial kit. RESULTS: We observed that ISL could inhibit the proliferation of HASMCs in a dose and time dependent manner. Cell cycle of ISL treated HASMCs arrested mainly in G1/S phase and accompanied with elevated expression of p27 and decreased expression of CyclinD1 and CyclinE. In addition, ISL could down-regulated the expression of p-PI3K and p-AKT, alleviated oxidative stress and enhanced the SOD activity in HASMCs. Furthermore, H2O2 treatment partly improved cell viability and up regulated p-PI3K and p-AKT in HASMCs. CONCLUSIONS: Therefore, we concluded that ISL inhibited the proliferation of HASMCs via attenuating oxidative stress and suppressing PI3K/AKT signaling pathway. The inhibitory effect of ISL on PI3K/AKT signaling pathway, at least partly, was mediated by ROS.