Search Results (2,924)

Temperature has always been an important environmental factor, and changes in water temperature are closely related to the entire life process of fish. Investigating the impact of thermal stress on fish physiology is critical for optimizing aquaculture. This study employed transcriptomic and metabolomic approaches to investigate temperature-induced variations in the gene expression and metabolic profiles of turbot. The results showed that thermal stress could induce abnormal genes transcription, and functional annotation demonstrated predominant associations of these genes with key pathways including PI3K-Akt signaling, PPAR regulation, steroid biosynthesis, fatty acid metabolism, and FoxO signaling cascade. Metabolomic analysis revealed that amino acid metabolism was dysregulated, such as valine, leucine, and isoleucine. Joint analysis revealed significant positive associations between CDH1, Col9a1, and ECT2 genes and leucine/isoleucine metabolism. The expression levels of Plch2 and Col9a1 genes exhibited significant regulatory effects on valine metabolism. Moreover, the gene cluster comprising DNAJB6, Gcnt1 and trim71 was significantly involved in the metabolic regulation of galactonic acid. Collectively, these findings demonstrate that thermal stress induces significant alterations in gene expression, metabolic profiles, and signaling pathways in turbot, offering new perspectives for thermal stress mitigation strategies. Full article

The high operational velocities of high-speed trains present constraints on their onboard track intrusion detection systems for real-time capture and analysis, encompassing limited computational resources and motion image blurring. This emphasizes the critical necessity of track perimeter intrusion monitoring systems. Consequently, an intelligent monitoring system employing trackside cameras is constructed, integrating weakly supervised video anomaly detection and unsupervised foreground segmentation, which offers a solution for monitoring foreign objects on high-speed train tracks. To address the challenges of complex dataset annotation and unidentified target detection, weakly supervised learning detection is proposed to track foreign object intrusions based on video. The pretraining of Xception3D and the integration of multiple attention mechanisms have markedly enhanced the feature extraction capabilities. The Top-K sample selection alongside the amplitude score/feature loss function effectively discriminates abnormal from normal samples, incorporating time-smoothing constraints to ensure detection consistency across consecutive frames. Once abnormal video frames are identified, a multiscale variational autoencoder is proposed for the positioning of foreign objects. A downsampling/upsampling module is optimized to increase feature extraction efficiency. The pixel-level background weight distribution loss function is engineered to jointly balance background authenticity and noise resistance. Ultimately, the experimental results indicate that the video anomaly detection model achieved an AUC of 0.99 on the track anomaly detection dataset and processes 2 s video segments in 0.41 s. The proposed foreground segmentation algorithm achieved an F1 score of 0.9030 in the track anomaly dataset and 0.8375 on CDnet2014, with 91 Frames per Second, confirming its efficacy. Full article

Didelphis aurita is a widely distributed neotropical marsupial frequently found in peri-urban environments and known to harbor various pathogens, including hemoparasites of the genus Hepatozoon. However, the systemic physiological responses of naturally infected individuals remain poorly understood. This study aimed to characterize the serum proteomic profile of Didelphis aurita naturally infected with Hepatozoon sp., providing insights into host–parasite interactions and potential biomarkers of infection. Serum samples were analyzed using liquid chromatography–tandem mass spectrometry (LC-MS/MS), followed by functional annotation based on Gene Ontology and KEGG pathway enrichment. A total of 67 proteins were identified, 33 of which were exclusive to infected animals. The most abundant proteins included albumin, hemoglobin subunits, and venom metalloproteinase inhibitors (DM43 and DM64). Functional enrichment revealed significant involvement in complement and coagulation cascades, protease inhibition, antioxidant defense, and extracellular vesicle localization. Key proteins such as fibrinogen, plasminogen, antithrombin, SERPIN family members, vitronectin, and fibronectin suggest an integrated host response involving hemostasis, inflammation control, and tissue remodeling. This is the first report of the serum proteome of Didelphis aurita naturally infected with Hepatozoon sp. Despite the absence of protein validation, the findings provide novel insights into marsupial immunophysiology and offer a foundation for future biomarker research and ecoimmunological surveillance in synanthropic species. Full article

Background/Objectives: Morphological defects such as limb malformations, cranial asymmetries, loin deviations, jaw misalignments, and navel irregularities are associated with early culling and reduced productivity in beef cattle. In Bos taurus indicus such as Nellore, the genetic basis of these traits remains poorly characterized. This study aimed to investigate the genetic architecture of six morphological defects in Nellore cattle, namely feet and legs malformation, chamfer asymmetry, fallen hump, loin deviation, jaw misalignment, and navel irregularities, via a genome-wide association study (GWAS) approach tailored for binary traits. Methods: Depending on the trait, the number of genotyped animals analyzed ranged from 3369 to 23,206, using 385,079 SNPs (after quality control). Analyses were conducted using a linear mixed model framework adapted for binary outcomes. Results: Significant associations were identified for four traits: feet and legs, chamfer, hump, and loin. No significant markers were detected for jaw or navel defects, likely due to lower sample sizes and trait incidence. Gene annotation revealed 49 candidate genes related to feet and legs, 4 for chamfer, 4 for hump, and 6 for loin. Conclusions: Candidate genes were enriched for biological functions, including bone remodeling, muscle development, lipid metabolism, and epithelial organization. Overlaps with QTL related to conformation, feed intake, reproductive traits, and carcass quality were also observed. These findings provide novel insights into the genetic control of morphological defects in Nellore cattle and may inform breeding strategies aimed at improving structural soundness. Full article

Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host–microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including Prevotella, Fibrobacter, and Ruminococcus, correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production. Full article

Studies have shown that the iron concentration in the peritoneal fluid of women is associated with the severity of endometriosis. Therefore, investigation of iron metabolism-related genes (IM-RGs) in endometriosis holds significant implications for both prevention and therapeutic strategies in affected patients. Differentially expressed IM-RGs (DEIM-RGs) were identified by intersecting IM-RGs with differentially expressed genes derived from GSE86534. Mendelian randomization analysis was employed to determine DEIM-RGs causally associated with endometriosis, with subsequent verification through sensitivity analyses and the Steiger test. Biomarkers associated with IM-RGs in endometriosis were validated using expression data from GSE86534 and GSE105764. Functional annotation, regulatory network construction, and immunological profiling were conducted for these biomarkers. Single-cell RNA sequencing (scRNA-seq) (GSE213216) was utilized to identify distinctively expressed cellular subsets between endometriosis and controls. Experimental validation of biomarker expression was performed via reverse transcription–quantitative polymerase chain reaction (RT-qPCR). BMP6 and SLC48A1, biomarkers indicative of cellular BMP response, were influenced by a medicus variant mutation that inactivated PINK1 in complex I, concurrently enriched by both biomarkers. The lncRNA NEAT1 regulated BMP6 through hsa-mir-22-3p and hsa-mir-124-3p, while SLC48A1 was modulated by hsa-mir-423-5p, hsa-mir-19a-3p, and hsa-mir-19b-3p. Immune profiling revealed a negative correlation between BMP6 and monocytes, whereas SLC48A1 displayed a positive correlation with activated natural killer cells. scRNA-seq analysis identified macrophages and stromal stem cells as pivotal cellular components in endometriosis, exhibiting altered self-communication networks. RT-qPCR confirmed elevated expression of BMP6 and SLC48A1 in endometriosis samples relative to controls. Both BMP6 and SLC48A1 were consistently overexpressed in endometriosis, reinforcing their potential as biomarkers. Moreover, macrophages and stromal stem cells were delineated as key contributors. These findings provide novel insights into therapeutic and preventive approaches for patients with endometriosis. Full article

In this study, we conducted a whole-genome analysis of the Lacticaseibacillus paracasei subsp. paracasei 2LB isolated from Kazakh traditional fermented milk (koumiss) to identify genes associated with the safety and probiotic potential of the strain. A comparative genomic analysis of the core and pan-genome of L. paracasei 2LB was performed. Functional annotation revealed the presence of genes putatively involved in metabolism, genetic information processing, and cellular processes. In terms of safety parameters, the stability of its genetic material, the absence of the ability to synthesize virulence factors, and genes responsible for antibiotic resistance were characterized. Also, in vitro studies of the L. paracasei 2LB strain showed resistance to stress factors and antimicrobial activity, and the presence of coding sequences encoding adhesion factors, bacteriocins, bile salts, pH, cold and heat shock, and osmotic stress was observed through genomic analysis. These results indicate that the L. paracasei 2LB strain is a potential probiotic candidate and demonstrate that whole-genome analysis is a useful method for assessing the quality and safety of probiotics. Full article

Nitrous oxide (N₂O), a potent greenhouse gas, is an important environmental concern associated with biological nitrogen removal in wastewater treatment plants. Anaerobic ammonium oxidation (anammox), recognized as an advanced carbon-neutral nitrogen removal technology, requires a continuous supply of nitrite, which also serves as a key precursor for N₂O generation. However, the regulation of the carbon-to-nitrogen (C/N) ratio to minimize N₂O emission in mainstream anammox systems remains insufficiently understood. In this study, we evaluated the long-term nitrogen removal performance and N₂O emission potential of an oxygen-limited anammox biofilm reactor treating synthetic municipal wastewater with a typical C/N range of 4.0–6.0. Experimental results demonstrated that the highest nitrogen removal efficiency (95.3%), achieved through coupled anammox and denitrification, and the lowest N₂O emission factor (0.73%) occurred at a C/N ratio of 5.0. As the C/N ratio increased from 4.0 to 5.0, N₂O emissions decreased progressively, but rose slightly when the ratio was further increased to 6.0. High-throughput sequencing revealed that microbial community composition and the abundance of key functional taxa were significantly influenced by the C/N ratio. At a C/N ratio of 5.0, proliferation of anammox bacteria and the disappearance of Acinetobacter populations appeared to contribute to the significant reduction in N₂O emission. Furthermore, gene annotation analysis indicated higher abundances of anammox-associated genes (hzs, hdh) and N₂O reductase gene (nosZ) at this ratio compared with others. Overall, this study identifies a C/N-dependent strategy for mitigating N₂O emissions in mainstream anammox systems and provides new insights into advancing carbon-neutral wastewater treatment. Full article

This study proposes a behavioral monitoring framework for newborn piglets based on SPMF-YOLO object detection and ByteTrack multi-object tracking, which enables precise quantification of early postnatal activity levels and health assessment. The method enhances small-object detection performance by incorporating the SPDConv module, the MFM module, and the NWD loss function into YOLOv11. When combined with the ByteTrack algorithm, it achieves stable tracking and maintains trajectory continuity for multiple targets. An annotated dataset containing both detection and tracking labels was constructed using video data from 10 piglet pens for evaluation. Experimental results indicate that SPMF-YOLO achieved a recognition accuracy rate of 95.3% for newborn piglets. When integrated with ByteTrack, it achieves 79.1% HOTA, 92.2% MOTA, and 84.7% IDF1 in multi-object tracking tasks, thereby outperforming existing methods. Building upon this foundation, this study further quantified the cumulative movement distance of each newborn piglet within 30 min after birth and proposed a health-assessment method based on statistical thresholds. The results demonstrated an overall consistency rate of 98.2% across pens and an accuracy rate of 92.9% for identifying abnormal individuals. The results validated the effectiveness of this method for quantifying individual behavior and assessing health status in newborn piglets within complex farming environments, providing a feasible technical pathway and scientific basis for health management and early intervention in precision animal husbandry. Full article

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article

Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article

Micro- and nanoplastic particles (MNPLs) present in the environment have recently become a potential health hazard factor due to the ability to penetrate living organisms, their organs, and cells. MNPLs interact with and absorb chemicals and elements, including metals, such as iron, copper, and zinc, and transport them into the cells. The cells subsequently respond with the altered gene expression profiles. In this study, we applied freely accessible online bioinformatic tools to draw out the sets of genes modulated by the metal ions and MNPLs. We focused on the gene interactome as revealed by The Comparative Toxicogenomics Database (CTD). To achieve a deeper insight into the biological processes that are potentially modulated, the retrieved CTD lists of genes, whose expression was influenced by MNPLs and metals, were subsequently analyzed using online tools: Metascape and String database. The genes from the revealed networks were arranged into functional clusters, annotated mainly as inflammation and immune system activity, regulation of apoptosis, oxidative stress response, Wingless-related Integration Site (WNT) signaling and ferroptosis. The complexity of the interactions between the gene sets altered by MNPLs and metal ions illustrates their pleiotropic effects on living systems. Full article

Identifying concealed explosives in X-ray backscatter (XRBS) imagery remains a critical challenge, primarily due to low image contrasts, cluttered backgrounds, small object sizes, and limited structural details. To address these limitations, we propose YOLOv11-XRBS, an enhanced detection framework tailored to the characteristics of XRBS images. A dedicated dataset (SBCXray) comprising over 10,000 annotated images of simulated explosive scenarios under varied concealment conditions was constructed to support training and evaluation. The proposed framework introduces three targeted improvements: (1) adaptive architectural refinement to enhance multi-scale feature representation and suppress background interference, (2) a Size-Aware Focal Loss (SaFL) strategy to improve the detection of small and weak-feature objects, and (3) a recomposed loss function with scale-adaptive weighting to achieve more accurate bounding box localization. The experiments demonstrated that YOLOv11-XRBS achieves better performance compared to both existing YOLO variants and classical detection models such as Faster R-CNN, SSD512, RetinaNet, DETR, and VGGNet, achieving a mean average precision (mAP) of 94.8%. These results confirm the robustness and practicality of the proposed framework, highlighting its potential deployment in XRBS-based security inspection systems. Full article

Genetic variants in nutrition-related genes exhibit variable functional consequences; however, systematic characterization across different nutritional domains remains limited. This highlights the need for detailed exploration of variant distribution and functional effects across nutritional gene categories. Therefore, the main objective of this computational study is to delve deeper into the distribution and functional impact of missense variants in nutrition-related genes. We analyzed Genetic polymoRphism variants using Personalized Medicine (GRPM) dataset, focusing on ten groups of nutrition-related genes. Missense variants were characterized using ProtVar for functional/structural impact, Pharos for functional classification, network analysis for pathway identification, and Gene Ontology enrichment for biological process annotation. The analysis of 63,581 Single Nucleotide Polymorphisms (SNP) revealed 27,683 missense variants across 1589 genes. Food intolerance (0.23) and food allergy (0.15) groups showed the highest missense/SNP ratio, while obesity-related genes showed the lowest (0.04). Enzymes predominated in xenobiotic and vitamin metabolism groups, while G-protein-coupled receptors were enriched in eating behavior genes. The vitamin metabolism group had the highest proportion of pathogenic variants. Network analysis identified apolipoproteins as central hubs in metabolic groups and inflammatory proteins in allergy-related groups. These findings offer insights into personalized nutrition approaches and underscore the utility of computational variant analysis in elucidating gene-diet interactions. Full article

The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner–Bratzler shear force (WBSF), as well as to perform genome-wide association studies (GWAS) to identify genomic regions and transcription factor (TF) binding sites associated with both traits in Nelore cattle. Genetic parameters were estimated using a bi-trait Bayesian model, and GWAS identified key SNPs explaining over 1% of variance in genomic estimated breeding values. Candidate genes near these SNPs were annotated, TF binding sites predicted, and gene–TF networks constructed. Genetic estimates indicated moderate heritability for ADG, low heritability for WBSF, and a small negative genetic correlation between traits. Genomic regions contained 116 and 151 candidate genes for ADG and WBSF, respectively, with 35 shared between traits. Functional analyses highlighted MYBPC1 and PENK for WBSF, and GHRS and NPY for ADG. TF analysis identified 25 TFs, with 3 key ones highlighted. Gene–TF networks revealed candidates including CAPN1 and LTBP3 for WBSF, and CARM1 and GH1 for ADG. Shared candidate genes identified in the combined network provide valuable insights into the genetic architecture of growth and tenderness in Nelore cattle. Full article