Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle.

Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of alternative polyadenylation (APA) in intramuscular fat deposition remains unclear. We compared APA events in muscle samples from high and low intramuscular fat (IMF) cattle, based on RNA-seq data.

Unlocking the role of novel primary/di-amine oxidases in crop improvement: Tissue specificity leads to specific roles connected to abiotic stress, hormone responses and sensing nitrogen.

Genetic improvements of solanaceous crops for quality and stress responsive traits are needed because of the central role vegetables and fruits have in providing nutrients to human diets. Copper amine oxidase (CuAO) encoding genes involved in metabolism of primary/di-amine nitrogenous compounds, play a role in balancing internal nitrogen (N) pools especially when external N supply fluctuates during growth, development and environmental stresses. In the present study, we investigated the occurrence, molecular evolution and possible role(s) of these unknown genes in tomato crops.

Integrative analysis of whole genome bisulfite and transcriptome sequencing reveals the effect of sodium butyrate on DNA methylation in the differentiation of bovine skeletal muscle satellite cells.

Butyric acid as a short-chain fatty acid (SCFA) is one of the key microbial metabolites of ruminants. Numerous studies indicate that butyrate is crucial in muscle growth and development, and plays an important molecular regulatory role mainly by inhibiting histone deacetylation. DNA methylation, a major epigenetic modification, is involved in cell differentiation.

Increasing nitrogen use efficiency in agronomically important plants: An insight into gene characteristics on a genome-wide scale in barley.

Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare).

Sodium Butyrate Induces Mitophagy and Apoptosis of Bovine Skeletal Muscle Satellite Cells through the Mammalian Target of Rapamycin Signaling Pathway.

Sodium butyrate (NaB) is one of the short-chain fatty acids and is notably produced in large amounts from dietary fiber in the gut. Recent evidence suggests that NaB induces cell proliferation and apoptosis. Skeletal muscle is rich in plenty of mitochondrial.

The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle.

Objectives: This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells (PBMCs) with a large-scale GWAS of 45 complex traits in Chinese Holstein cattle. Lipopolysaccharide (LPS) is a crucial mediator of chronic inflammation to modulate immune responses. PBMCs include primary T and B cells, natural killer (NK) cells, monocytes (Mono), and dendritic cells (DC).

Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure.

Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and development, this study characterized genome-wide H3K27ac modification changes and super-enhancer profiles in rumen epithelial primary cells (REPC) induced with butyrate by ChIP-seq, and analyzed its effects on gene expression and functional pathways by integrating RNA-seq data. The results showed that genome-wide acetylation modification was observed in the REPC with 94,675 and 48,688 peaks in the butyrate treatment and control group, respectively.

Improving modeling of low-altitude particulate matter emission and dispersion: A cotton gin case study.

Monitoring and modeling of airborne particulate matter (PM) from low-altitude sources is becoming an important regulatory target as the adverse health consequences of PM become better understood. However, application of models not specifically designed for simulation of PM from low-altitude emissions may bias predictions. To address this problem, we describe the modification and validation of an air dispersion model for the simulation of low-altitude PM dispersion from a typical cotton ginning facility.

Effectiveness and diurnal variations of vegetative environmental buffers (VEBs) for mitigating NH and PM emissions from poultry houses.

Air pollutants from poultry production, such as ammonia (NH) and particulate matter (PM), have raised concerns due to their potential negative impacts on human health and the environment. Vegetative environmental buffers (VEBs), consisting of trees and/or grasses planted around poultry houses, have been investigated as a mitigation strategy for these emissions. Although previous research demonstrated that VEBs can reduce NH and PM emissions, these studies used a limited number of samplers and did not examine concentration profiles.

Genomic sequencing of fourteen bacillus thuringiensis isolates: insights into geographic variation and phylogenetic implications.

Objective: This work was performed in support of a separate study investigating the activity of pesticidal proteins produced by Bacillus thuringiensis against the Asian citrus psyllid, Diaphorina citri. The fourteen Bacillus isolates chosen were selected from a large, geographically diverse collection that was characterized only by biochemical phenotype and morphology of the parasporal crystal, hence, for each isolate it was desired to determine the specific pesticidal proteins produced, assign each to a Bacillus cereus multilocus sequence type (ST), and predict their placement within the classical Bt serotyping system. In addition, phylogenetic distances between the isolates and Bacillus thuringiensis serovar type strains were determined by calculating digital DNA-DNA hybridization (dDDH) values among the isolates.

Harnessing male germline epigenomics for the genetic improvement in cattle.

Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.

Trophobiosis between a new species of (Hymenoptera, Formicidae) and new (Hemiptera, Xenococcidae) from Peru, and establishment of the species-group.

We describe a new pair of trophobiotic partners from the ant genus and the root mealybug genus . A recent field study on ants and associated root mealybugs, conducted in the Peruvian Amazon, led to the discovery of LaPolla & Schneider, and its root mealybug symbiont Schneider & LaPolla, The new root mealybug belongs to the family Xenococcidae, whose members are all obligate associates of ants. Providing joint descriptions of new mutualist partners in the same article is a novel approach for this system, and it offers benefits to the ongoing study of mutualism and patterns of association among these symbiotic ants and scales.

Temporal changes of genes associated with intestinal homeostasis in broiler chickens following a single infection with Eimeria acervulina.

Infection with the protozoan parasite Eimeria can cause the economically devastating disease coccidiosis, which is characterized by gross tissue damage and inflammation resulting in blunted villi and altered intestinal homeostasis. Male broiler chickens at 21 d of age were given a single challenge with Eimeria acervulina. Temporal changes in intestinal morphology and gene expression were investigated at 0, 3, 5, 7, 10, and 14 d postinfection (dpi).

A Neotropical complex of species (Hemiptera, Coccomorpha, Rhizoecidae) collected from the nests of ants (Hymenoptera, Formicidae).

We describe five new Neotropical species of living in association with ants: , , , , and We also redescribe and based on type specimens and other collections. Together, these seven species form a morphologically similar group that we informally refer to as the -complex of . All members of the -complex are confirmed or are speculated to be mutualists of ants.

The conservation of human functional variants and their effects across livestock species.

Despite the clear potential of livestock models of human functional variants to provide important insights into the biological mechanisms driving human diseases and traits, their use to date has been limited. Generating such models via genome editing is costly and time consuming, and it is unclear which variants will have conserved effects across species. In this study we address these issues by studying naturally occurring livestock models of human functional variants.

Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2.

Recessive alleles represent genetic risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and validation of these genetic defects, including haplotype-based detection, variant selection from sequence data, and validation using knockout embryos. Holstein haplotype 2 (HH2), which causes embryonic death, was used to demonstrate the approach.

Unraveling the genetics of polyamine metabolism in barley for senescence-related crop improvement.

We explored the polyamine (PA) metabolic pathway genes in barley (Hv) to understand plant development and stress adaptation in Gramineae crops with emphasis on leaf senescence. Bioinformatics and functional genomics tools were utilized for genome-wide identification, comprehensive gene features, evolution, development and stress effects on the expression of the polyamine metabolic pathway gene families (PMGs). Three S-adenosylmethionine decarboxylases (HvSAMDCs), two ornithine decarboxylases (HvODCs), one arginine decarboxylase (HvADC), one spermidine synthase (HvSPDS), two spermine synthases (HvSPMSs), five copper amine oxidases (HvCuAOs) and seven polyamine oxidases (HvPAOs) members of PMGs were identified and characterized in barley.