Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.

With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics.

Innovative Insights into Single-Cell Technologies and Multi-Omics Integration in Livestock and Poultry.

In recent years, single-cell RNA sequencing (scRNA-seq) has marked significant strides in livestock and poultry research, especially when integrated with multi-omics approaches. These advancements provide a nuanced view into complex regulatory networks and cellular dynamics. This review outlines the application of scRNA-seq in key species, including poultry, swine, and ruminants, with a focus on outcomes related to cellular heterogeneity, developmental biology, and reproductive mechanisms.

Toxicological effects and molecular metabolic of polystyrene nanoplastics on soybean (Glycine max L.): Strengthening defense ability by enhancing secondary metabolisms.

Nanoplastics, as emerging pollutants, have attracted worldwide concern for their possible environmental dangers. The ingestion and accumulation of nanoplastics in crops can contaminate the food chain and have unintended consequences for human health. In this study, we revealed the effects of polystyrene nanoplastics (PS-NPs; 80 nm) at different concentrations (0, 10, 100 mg L) on soybean (Glycine max L.

Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.

With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle.

Nucleic Acid-Based Biological Nanopore Sensing Strategies for Tumor Marker Detection.

Cancer, which is characterized by high mortality rates, poses a significant threat to global human health. Early diagnosis is of paramount importance in managing cancer, and tumor markers have emerged as crucial indicators for achieving this goal. The advent of precision medicine has further emphasized the need for the effective detection of these markers.

Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants.

The economic significance of ruminants in agriculture underscores the need for advanced research methodologies to enhance their traits. This review aims to elucidate the transformative role of pan-omics technologies in ruminant research, focusing on their application in uncovering the genetic mechanisms underlying complex traits such as growth, reproduction, production performance, and rumen function. Pan-omics analysis not only helps in identifying key genes and their regulatory networks associated with important economic traits but also reveals the impact of environmental factors on trait expression.

Application of GWAS and mGWAS in Livestock and Poultry Breeding.

In recent years, genome-wide association studies (GWAS) and metabolome genome-wide association studies (mGWAS) have emerged as crucial methods for investigating complex traits in animals and plants. These have played pivotal roles in research on livestock and poultry breeding, facilitating a deeper understanding of genetic diversity, the relationship between genes, and genetic bases in livestock and poultry. This article provides a review of the applications of GWAS and mGWAS in animal genetic breeding, aiming to offer reference and inspiration for relevant researchers, promote innovation in animal genetic improvement and breeding methods, and contribute to the sustainable development of animal husbandry.

Exploring the additive effect of Ampelopsis grossedentata flavonoids and Tween 80 on feeding Nubian goats.

Introduction: The ban on antibiotics in animal husbandry underscores the crucial need for safe, natural feed additives. This study investigates the effects of Ampelopsis grossedentata flavonoids (AGF) and Tween 80 on the growth performance, blood indexes, and rumen microbiota of Nubian goats, evaluating their potential as alternative feed additives in livestock management.

Methods: Thirty-two goats were randomly divided into four groups.

Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.

Beef is a major global source of protein, playing an essential role in the human diet. The worldwide production and consumption of beef continue to rise, reflecting a significant trend. However, despite the critical importance of beef cattle resources in agriculture, the diversity of cattle breeds faces severe challenges, with many breeds at risk of extinction.

A multifunctional nanoplatform for chemotherapy and nanocatalytic synergistic cancer therapy achieved by amplified lipid peroxidation.

Traditional cancer chemotherapy suffers from low efficacy and severe side effects, limiting its use as a first-line treatment. To address this issue, we investigated a novel way to induce lipid peroxidation (LPO), which plays an essential role in ferroptosis and may be useful against cancer cells and tumors. In this study, a pH-responsive synergistic cancer therapy nanoplatform was prepared using CaCO co-loaded with oleanolic acid (OA) and lipoxygenase (LOX), resulting in the formation OLCaP NP.

Transcriptomic annotation of the Chungtien schizothoracin (Ptychobarbus chungtienensis) using Iso-seq and RNA-seq data.

The Chungtien schizothoracin (Ptychobarbus chungtienensis), an endangered fish species endemic to the Zhongdian Plateau, remains underexplored in terms of transcriptomic sequencing. This investigation used tissues from five distinct organs (heart, liver, spleen, kidney, and brain) of the Chungtien schizothoracin for PacBio Iso-seq and RNA-seq analyses, yielding a repertoire of 16,598 full-length transcripts spanning lengths from 363 bp to 7,157 bp. Gene family clustering and phylogenetic analysis encompassed a comprehensive set of 13 fish species, all of which were cyprinids, including the zebrafish and the examined species Ptychobarbus chungtienensis.

Calcium-sensing receptor-mediated macrophage polarization improves myocardial remodeling in spontaneously hypertensive rats.

Chronic inflammation is a key element in the progression of essential hypertension (EH). Calcium plays a key role in inflammation, so its receptor, the calcium-sensing receptor (CaSR), is an essential mediator of the inflammatory process. Compelling evidence suggests that CaSR mediates inflammation in tissues and immune cells, where it mediates their activity and chemotaxis.

Pan-Omics in Sheep: Unveiling Genetic Landscapes.

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies.

Multiple omics analysis reveals the regulation of SIRT5 on mitochondrial function and lipid metabolism during the differentiation of bovine preadipocytes.

Preadipocyte differentiation represents a critical stage in adipogenesis, with mitochondria playing an undeniable pivotal role. Given the intricate interplay between transcription and metabolic signaling during adipogenesis, the regulation of sirtuin 5 (SIRT5) on mitochondrial function and lipid metabolism was revealed via multiple omics analysis. The findings suggest that SIRT5 plays a crucial role in promoting mitochondrial biosynthesis and maintaining mitochondrial function during preadipocyte differentiation.

Two High-Quality Genome Assemblies Reveal Genomic Variations Associated with Plumage Color.

As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The genus features two species, and , that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive.

Comparative Analysis of Gene Indel Polymorphism and Expression among Zhongdian Yellow Cattle, Zhongdian Yak, and Their Hybrids.

Bovine spongiform encephalopathy (BSE) is a fatal disease in cattle caused by misfolded prion proteins and linked to indel polymorphisms in the promoter and intron 1 of the gene. The aim of this study was to determine the allele, genotype, and haplotype frequencies of indel polymorphisms and to investigate the effect of gene expressions of 23 bp and 12 bp indels via polymerase chain reaction (PCR) in Zhongdian Yak () (YK), Zhongdian Yellow cattle () (YC), and Zhongdian Yakow ( × ) (PK). Resultant high allelic frequencies were found in 23- and 12+, while haplotype frequencies were very low in 23+/12 in YK, YC, and PK.

Molecular Cloning and Functional Characterization of the 5' Regulatory Region of the Gene from Yaks.

The solute transport protein family 11 A1 (), also recognized as natural resistance-associated macrophage protein 1 (), represents a transmembrane protein encoded by the gene. A variety of prior investigations have illuminated its involvement in conferring resistance or susceptibility to bacterial agents, positioning it as a promising candidate gene for breeding disease-resistant animals. Yaks (), renowned inhabitants of the Qinghai-Tibet Plateau in China, stand as robust ruminants distinguished by their adaptability and formidable disease resistance.

Exploring the Impact of Ampelopsis Grossedentata Flavonoids on Growth Performance, Ruminal Microbiota, and Plasma Physiology and Biochemistry of Kids.

This study was conducted to evaluate the influences of supplementing Ampelopsis grossedentata flavonoids (AGF) on the rumen bacterial microbiome, plasma physiology and biochemistry, and growth performance of goats. Twenty-four Nubian kids were randomly allocated to three dietary treatments: the control (CON, basal diet), the 1.0 g/kg AGF treatment (AGF), and the 12.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption.

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A/C DNA motif for programmable biosensing and information encryption.

Murine Cytomegalovirus Infection Induced miR-1929-3p Down-Regulation Promotes the Proliferation and Apoptosis of Vascular Smooth Muscle Cells in Mice by Targeting Endothelin A Receptor and Downstream NLRP3 Activation Pathway.

Our previous study demonstrated in vivo that mouse cytomegalovirus (MCMV) infection promoted vascular remodeling after downregulation of miR-1929-3p. This study aimed to investigate the role of miR-1929-3p/ETAR/NLRP3 pathway in mouse vascular smooth muscle cells (MOVAS) after MCMV infection. First, PCR was used to detect the success of the infection.

Low expression of miR-1929-3p mediates murine cytomegalovirus-induced fibrosis in cardiac fibroblasts via targeting endothelin a receptor/NLRP3 inflammasome pathway.

MicroRNAs are crucial in the development of myocardial remodeling in hypertension. Low miR-1929-3p expression induced by murine cytomegalovirus (MCMV) infection is closely related to hypertensive myocardial remodeling. This study investigated the molecular mechanism of miR-1929-3p-induced myocardial remodeling after MCMV infection.

Fluorescent detection of brown spot of tobacco caused by based on lambda exonuclease-induced DNAzyme amplification.

A rapid, simple, and sensitive fluorescent detection method for brown spot of tobacco is established by lambda exonuclease-induced Mg-dependent DNAzyme amplification. It contains hybridization of the genome and HP1, digestion of the 5'-phosphorylated strand of the hybrid dsDNA by lambda exonuclease, acquisition of complete Mg-dependent DNAzyme, cleavage of the substrate modified with FAM and BHQ-1, and fluorescent detection. The proposed assay exhibits good sensitivity (10 pg L), selectivity and reproducibility.

Detection of Tobacco Bacterial Wilt Caused by by Combining Polymerase Chain Reaction with an α-Hemolysin Nanopore.

Tobacco bacterial wilt is a serious disease caused by the soil-borne bacterium (). Herein, a rapid and purification-free α-hemolysin (α-HL) nanopore-sensing strategy based on polymerase chain reaction (PCR) and lambda exonuclease digestion was established to detect . A 198-nucleotide-long single-stranded DNA was obtained via asymmetric PCR or the lambda exonuclease-mediated digestion of the PCR product.