Search Results (22,641)

H9N2 avian influenza viruses inherently carry cross-species transmission potential, making continuous surveillance critical for pandemic prevention. This study focused on monitoring the 2024 H9N2 epidemic in Jiangsu Province’s external environment, analyzing its molecular evolution and receptor binding properties, assessing cross-species transmission and pandemic risks, and investigating serological antibody levels across different human populations. Environmental samples were collected from live poultry markets, farms, slaughterhouses, and bird habitats across Jiangsu, screened via quantitative PCR (qPCR), with positive samples used for virus isolation and whole-genome sequencing. Receptor binding properties were tested by hemagglutination assay, and H9N2 antibody levels were measured in 370 occupationally exposed individuals and 240 non-exposed individuals using hemagglutination inhibition (HI) assays. Among the 5779 collected samples, 6.89% tested H9N2-positive, and 12 strains belonging to the Eurasian lineage Y280-like clade G57 genotype were successfully isolated. All strains carried the HA-Q226L mutation, with 11 showing preferential binding to human α-2,6 receptors and one strain possessing dual receptor binding capability. Internal genes harbored mammalian adaptation mutations, and M2 proteins contained mutations conferring complete resistance to amantadine-class antiviral drugs. Serological tests revealed antibody positive rates of 4.05% in exposed populations and 2.5% in non-exposed populations, with no statistically significant difference between groups. These findings confirm that Jiangsu’s circulating H9N2 viruses have acquired human receptor preference and mammalian adaptation, posing silent infection and pandemic risks. Enhanced surveillance and the development of candidate vaccine stockpiles are strongly recommended. Full article

The aim of this study was to compare carcass composition, meat quality, digestive tract morphometry, and leg bone dimensions of Pekin and Muscovy ducks. The study involved 40 birds, including 10 males and 10 females from each genotype, reared to market age. Carcass traits, physicochemical properties of breast and leg muscles, texture parameters, internal organ development, intestinal measurements, and selected dimensions of the femur and tibia were evaluated. The results demonstrated a significant effect of duck genotype (p < 0.05) on carcass weight, dressing percentage, and the proportion of neck, wings, and skin with subcutaneous fat. Genotype also affected meat color (L*, a*, b*), intramuscular fat and collagen content, cooking loss, pH, electrical conductivity, and selected texture parameters of breast muscles. Differences were also observed in the mass and proportion of internal organs, most intestinal morphometric traits, and selected bone measurements. Sex had a significant effect on body and carcass weight, selected meat quality traits, intestinal measurements, and leg bone dimensions, with males generally showing greater body size and more developed skeletal structures. Significant interactions between genotype and sex were observed for several analyzed traits. The findings indicate that both genotype and sex substantially affect slaughter traits and meat quality characteristics of ducks. Full article

Alpha-1 antitrypsin deficiency (AATD) is a genetically heterogeneous disorder with well-established pulmonary and hepatic manifestations; however, the clinical significance of rare compound heterozygous SERPINA1 variants remains incompletely defined. We report the case of a 61-year-old never-smoking woman with chronically elevated liver transaminase who was found to carry a compound heterozygous SERPINA1 genotype (PI*V/M_procida) previously classified as non-polymerogenic and not previously associated with hepatic inclusions. This case expands the phenotypic spectrum of AATD and highlights the importance of considering SERPINA1 genotyping in adults with unexplained chronic transaminase elevation, while raising clinically relevant questions regarding surveillance and management in atypical AATD phenotypes. Full article

Large language models (LLMs) are increasingly adopted in life-science research for scientific writing, coding, literature synthesis, workflow troubleshooting, and preliminary data interpretation. In microbial genomics and bioinformatics, their appeal is clear because researchers routinely integrate genome annotations, antimicrobial resistance profiles, virulence determinants, taxonomic assignments, microbiome outputs, workflow scripts, and primary literature. Yet this domain also highlights major risks, including hallucinated biological claims, inaccurate citations, irreproducible code, unsupported genotype-to-phenotype inference, and inappropriate clinical or public health framing. This narrative review examines responsible LLM use in microbial genomics as a representative life-science setting where interpretation depends on database provenance, validated workflows, expert assessment, and reproducible evidence chains. It considers applications in genome annotation, antimicrobial resistance interpretation, virulence analysis, microbiome and metagenomics workflows, coding support, and scientific writing. The review further presents MicrobeGuardGPT as a conceptual reliability framework for assessing LLM-assisted microbial genomics outputs before scientific, clinical, or public health use. By connecting task domains, evidence verification, expert validation, and reliability classification, the framework supports risk-aware LLM integration in bioinformatics. Responsible implementation will require domain-specific benchmarks, curated database linkage, transparent reporting, reproducible workflows, human oversight, and governance standards tailored to biological interpretation across research, diagnostic, surveillance, outbreak-response, educational, and translational contexts. Full article

Objective: TNFSF13B, which encodes B-cell-activating factor (BAFF) and peptidylarginine deiminase 4 (PADI4), plays crucial roles in the pathogenesis of ANCA-associated vasculitis (AAV). This study investigated the associations of single-nucleotide polymorphisms (SNPs) in TNFSF13B/BAFF and PADI4 genes with AAV susceptibility, clinical phenotypes, and disease activity in a Guangxi Chinese population. Methods: A case–control study included 324 AAV patients and 324 healthy controls. After propensity score matching (201 pairs), genomic DNA was genotyped for TNFSF13B/BAFF rs3759467 (formerly rs386492354) and rs1041569, and PADI4 rs11203366 and rs874881 using multiplex PCR and high-throughput sequencing. Genetic associations were analyzed via logistic regression, subgroup, haplotype, and clinical correlation analyses. For each of the four SNPs separately, machine learning models (logistic regression, SVM, Random Forest, XGBoost) were built and evaluated via 5-fold cross-validation. No formal adjustment for multiple comparisons was applied due to the exploratory nature of this study. Results: For TNFSF13B/BAFF, the rs3759467 C allele was protective (dominant model OR = 0.60, p = 0.011; log-additive OR = 0.71, p = 0.020; CA haplotype OR = 0.71, p = 0.019), while the rs1041569 T allele was a risk factor (dominant model OR = 1.70, p = 0.016). Subgroup analysis revealed stronger protective effects of rs3759467 in females, Han ethnicity, and MPA patients, and stronger risk effects of rs1041569 in Han ethnicity and MPA patients. Haplotype CA was protective (OR = 0.71, p = 0.019), and TT was risk-associated (OR = 1.55, p = 0.017). Both TNFSF13B/BAFF SNPs were associated with rash and hemoptysis incidence (p < 0.05). rs1041569 was also associated with RBC (red blood cell) count and HB (hemoglobin) levels (p < 0.05). For PADI4, rs11203366 and rs874881 showed no association with AAV susceptibility (all p > 0.05). However, their genotypes were associated with disease activity (BVAS, Birmingham Vasculitis Activity Score), RBC count, and HB levels (p < 0.05). Although machine learning was applied to explore predictive patterns, its performance was suboptimal (AUC < 0.6), indicating limited clinical applicability. Accordingly, the primary findings rely on the genetic model analysis, and the machine learning results should not be overinterpreted as clinically actionable. SHAP analysis indicated that risk-associated genotypes contributed most to model predictions. Conclusions:TNFSF13B/BAFF gene polymorphisms rs3759467 and rs1041569 were associated with AAV susceptibility in this Guangxi cohort, influencing clinical manifestations like rash, hemoptysis, and anemia severity. PADI4 polymorphisms rs11203366 and rs874881 are not associated with susceptibility but may correlate with disease activity and hematological parameters. These findings highlight the ethnic and clinical subtype specificity of genetic influences in AAV. Due to the lack of external validation, these findings are exploratory and require replication. Full article

Cholangiocarcinoma (CCA) is an aggressive and molecularly heterogeneous malignancy characterized by a profoundly immunosuppressive tumor microenvironment (TME) and historically limited therapeutic options. Recent advances have redefined the treatment paradigm, with phase III trials establishing chemoimmunotherapy as a standard of care and multi-omic profiling elucidating the interplay between tumor genomics, stromal architecture, and immune regulation. Despite these gains, durable clinical benefit remains confined to a minority of patients, reflecting convergent mechanisms of primary and acquired resistance—including immune exclusion, myeloid-dominant suppression, and genotype-driven “cold” tumor states. In this review, we synthesize emerging insights into the immune landscape of CCA, integrating data from single-cell, spatial, and translational studies to define the cellular and molecular circuits governing immune evasion. Beyond canonical biomarkers such as mismatch repair and microsatellite status, we highlight how spatial organization of immunity—in particular, tertiary lymphoid structures, dynamic myeloid and stromal interactions, and pathway-level features—shape immunotherapy responsiveness. We also examine how tumor-intrinsic alterations, including IDH1 mutation, FGFR2 fusions, KRAS activation, and MTAP loss, define distinct immunologic phenotypes with direct implications for immunotherapeutic response and biomarker-driven patient selection. We evaluate the expanding clinical trial landscape of immunotherapy in CCA and more broadly in BTC, including adoptive cell therapies and cancer vaccines. Together, these advances position CCA as a paradigm of how tumor genotype and microenvironment co-evolve to define immunotherapy sensitivity and resistance. Full article

The quality of rice grain impacts milling yield, market acceptance, and product value. Physical quality is determined by many traits, such as chalkiness, whiteness, vitreous whiteness, caryopsis length, and width. Breeding for these traits is challenging due to their quantitative nature, environmental effects, and time and labor requirements to evaluate these traits. The digital grain analyzer (S21) equipment determines rice grain physical quality by image-based analysis; however, its use remains restricted. Thus, here we aimed to evaluate S21 efficiency to determine the physical quality of rice grains and estimate the genetic diversity of the trait using a Brazilian panel of 152 irrigated rice genotypes as a working model. We accessed total whiteness, vitreous whiteness, chalkiness degree, chalky grain rate, white belly, grain length, width, and length/width ratio. Our results demonstrated that S21 allowed the characterization of the genotypes according to physical traits, facilitating grouping and separation of accessions and correlation analyses between quality traits. It was also possible to estimate the heritability of quality traits. S21 was efficient in characterizing the physical quality of rice grains and determining their genetic diversity. The equipment is an effective tool exhibiting potential application by breeder programs. Full article

Identifying superior salt-tolerant germplasm and resistance genes is crucial, as wheat (Triticum aestivum L.) seedlings are highly vulnerable to salt stress. Here, using an optimized 150 mM NaCl treatment, we screened 137 Chinese wheat accessions via an organ-specific method. Phenotyping analysis revealed extensive organ-specific divergence, with 48.91% of accessions displaying inconsistent performance between shoot and root length. We then performed comparative transcriptomics on three representative phenotypes at the seedling stage: Gaoyou 2018, representing the salt dual-sensitive group; Huapei 5, representing the salt dual-tolerant group; and Jimai 60, representing the divergent group with higher tolerance in shoots rather than in roots. Analysis of overlapping differentially expressed genes (DEGs) across all three accessions revealed a basal stress response—characterized by induced osmotic defense and suppressed primary growth—exemplifying a classical growth–defense trade-off. Genotype-specific DEG profiling demonstrated that the divergent Jimai 60 maintains its shoot advantage by reinforcing physical barriers and inhibiting apoptosis. Conversely, transcriptomic profiling implies that the systemically tolerant Huapei 5 maintains coordinated shoot and root tolerance at the seedling stage by strongly activating below-ground Na⁺ homeostasis (efflux and compartmentalization) while simultaneously down-regulating non-essential immune responses to optimize defense energy reallocation. Collectively, our findings provide novel insights into the organ-differentiated salt tolerance of wheat, offering well-characterized elite germplasm and compelling genetic targets for future molecular breeding. Full article

Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), poses a serious threat to the global swine industry. Although modified live virus (MLV) vaccines have been widely used in the field for PRRS prevention for decades, the safety and efficacy of these vaccines have long been controversial. Here, we report a rare recombination pattern in China: the emergence of a novel NADC30-like PRRSV strain recombined from two MLV-like strains. Genome comparative analysis reveals that the SCMS2025 isolate has a non-continuous 136-amino acid deletion in the NSP2 protein and shares the highest nucleotide identity of 87.6% with lineage 5 (L5) strains. Phylogenetic analysis showed that SCMS2025 was classified into L1 (NADC30-like) strains based on ORF5 genotyping, whereas it belonged to a single branch between L1 and L5 strains based on the complete genomic sequences. Strikingly, genomic recombination analysis revealed that the newly emerged PRRSV isolate likely resulted from complex recombination events between NADC30-like and two MLV-like strains (RespPRRS MLV and TJbd14-1 MLV-like strains). Furthermore, SCMS2025 infection caused transient overt clinical signs followed by rapid recovery, indicating that the novel PRRSV isolate is a low pathogenic strain. Notably, all SCMS2025-inoculated piglets remained seronegative for PRRSV-specific antibodies throughout the entire 14-day observation period, suggesting a delayed onset of the host humoral immune response. Our study provides evidence for the ongoing evolution of PRRSV through inter lineage recombination and highlights the urgent need for safe and effective vaccines. Full article

Soil salinity is a major constraint on global wheat productivity, yet the genetic and molecular determinants of root system architecture (RSA) adaptation under salt stress remain poorly characterized. We integrated a genome-wide association study (GWAS) of 566 wheat accessions with comparative RNA-seq transcriptomics to identify the genetic and transcriptional determinants of RSA adaptation under 200 mM NaCl. GWAS identified a candidate locus on chromosome 7B harboring TaIAO, which encodes a protein with predicted aldehyde oxidase-like activity consistent with a role in tryptophan-dependent auxin biosynthesis. Accessions carrying the favorable CC allele exhibited significantly greater root volume retention than those carrying the GG genotype (p < 0.001). Comparative RNA-seq revealed that the salt-tolerant Sarajevo 1 exhibited coordinated transcriptional repression of three distinct modules—cell wall expansion (TaExpansin), auxin redistribution (TaPIN-like), and stress-associated ROS defense (TaPOD1)—whereas the sensitive genotype CI 17260 aberrantly induced or incompletely repressed these modules under stress. ELISA-based IAA quantification, ROS imaging, and qRT-PCR analysis provided independent physiological and transcriptional support for these patterns. These findings support a two-tier adaptive model in which constitutive genetic variation at the TaIAO locus may contribute to a developmental baseline, coupled with coordinated stress-responsive transcriptional repression of energy-consuming modules, providing promising targets for marker-assisted breeding of salt-tolerant wheat. Full article

Osteoporosis (OP) is a complex disease in which several immune-related genes have been identified as contributing to susceptibility and disease progression. Despite efforts to achieve functional validation, many of these genes, such as interferon-gamma (IFNG), remain the subject of unresolved mechanisms. The present study aimed to examine whether the IFNG -1616 (G>A, rs2069705) polymorphism was associated with postmenopausal OP. A total of 251 OP patients and 115 healthy controls were genotyped to assess the association between the IFNG -1616 (G>A, rs2069705) polymorphism and osteoporosis. To further investigate the biological role of IFN-γ in bone metabolism, human SaOs-2 osteosarcoma cells were treated with recombinant IFN-γ (2 and 100 U/mL), and calcification and cell viability were evaluated using Alizarin Red staining and the MTT assay, respectively. We found that the IFNG rs2069705 G allele was associated with an increased risk of OP (OR = 1.45, 95% CI = 1.03–2.05, p = 0.03). Furthermore, serum IFN-γ levels did not differ significantly between genotype groups. In SaOs-2 cells, IFN-γ (2 U/mL) significantly increased viability (p = 0.017) and enhanced calcification in a dose-dependent manner. The IFNG rs2069705 G allele may confer susceptibility to postmenopausal OP. IFN-γ promotes osteoblast viability and mineralization at low concentrations, suggesting a potential anabolic role that warrants further investigation in human primary osteoblasts. Full article

Mediterranean organic viticulture requires sustainable pest management strategies that leverage local soil biodiversity. This study isolated endemic entomopathogenic fungi from vineyard soils in Nemea, Greece, using a dual-insect baiting system with Tribolium confusum and Sitophilus spp. The recovered isolates caused complete mortality in bait insects, with mycelial emergence from 93.75% of cadavers. DNA sequencing of the ITS1 region identified the recovered isolates as Purpureocillium lilacinum. Phylogenetic analysis revealed that Nemea isolates (TD and TM series) form a monophyletic clade with 100% bootstrap support, showing distinct genetic divergence from the reference strain P. lilacinum NRRL 895—evidence of a unique “microbial terroir.” Virulence assays demonstrated species-dependent mortality against stored-product pests: Sitophilus granarius was the most susceptible (76.7% mortality; LT₅₀ = 1.9 days), followed by Sitophilus zeamais (61.1%; LT₅₀ = 2.7 days), Tribolium confusum (56.7%; LT₅₀ = 2.8 days), and Sitophilus oryzae (50.0%; LT₅₀ = 3.3 days). Mycosis confirmation (65–83%) and 0% control mortality confirmed pathogenicity. As locally adapted biological control agents, these endemic P. lilacinum strains are highly suitable for protecting crops from major insect pests. Full article

This study evaluated the effects of maternal overfeeding during mid-to-late gestation on maternal productivity, metabolic status, reproductive recovery, and calf performance in Hanwoo cattle using conventional statistics and machine learning (ML) approaches. A total of 243 pregnant cows were assigned to either a control group or an overfeeding group from gestation day 90 to parturition. The overfeeding treatment increased nutrient supply to approximately 140–145% of the control level. Maternal body weight (BW), body condition score (BCS), serum metabolites, and reproductive traits were evaluated throughout gestation and postpartum, while calf growth, morphometrics, and metabolic traits were assessed at birth and weaning. Calves were further classified into growth- or meat-quality-oriented genotypes using SNP-based profiling. Overfeeding increased maternal BW gain and BCS during gestation and reduced circulating non-esterified fatty acid concentrations, indicating improved maternal energy status. However, overfed cows showed a longer interval to postpartum estrus return. Calf birth weight was not significantly affected by maternal overfeeding, whereas calf growth and morphometric traits at weaning were more strongly influenced by parity, sex, and genotype. Machine learning models identified gestational BW, metabolic indicators, calf feed intake, and genotype as major predictors of maternal and calf outcomes, with random forest and XGBoost showing superior predictive performance compared with linear models. These findings suggest that parity- and genotype-informed nutritional management combined with ML-based prediction may support precision feeding strategies in beef cattle production systems. Full article

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu lato (s.l.), is a significant zoonotic disease affecting livestock and public health worldwide, particularly in endemic regions such as La Araucanía, Chile. This study evaluated the role of cattle in the transmission dynamics of E. granulosus sensu stricto (s.s.) by morphologically and molecular characterizing hydatid cysts (HC) collected from cattle, sheep, pigs, and goats. A total of 123 cysts were obtained from a local slaughterhouse, with cattle contributing the majority of samples (n = 94). Fertility was highest in sheep (76.2%) and low in cattle (3.2%), while cysts from pigs and goats were infertile. PCR amplification and sequencing of the cox1 gene confirmed the predominance of genotype G1 (98.1%), with two additional haplotypes (Eg^B and Eg^C) identified in cattle and sheep. Two cattle samples harbored genotype G3. Phylogenetic analyses grouped all sequences within the E. granulosus s.s. complex. The results corroborate the role of cattle as important sentinels for environmental surveillance of CE due to their exposure and traceability but highlight their lower competence in parasite transmission to definitive hosts compared with sheep. The genetic diversity observed aligns with previous findings in Chile, underscoring the epidemiological significance of E. granulosus s.s. and genotype G1 in the region. Full article

Objective: This retrospective cross–sectional study aimed to characterize HIV–1 genotypes, assess drug resistance, and analyze molecular transmission networks in Zhongwei City to inform prevention strategies. Methods: Plasma samples were collected from antiretroviral therapy (ART)–treated patients (2007–2024) with viral load ≥200 copies/mL. HIV–1 pol was amplified by nested PCR; successful sequences were genotyped by maximum likelihood (ML) (IQ–TREE, TVM+F+I+G4, 1000 bootstrap). Drug resistance (DR) was interpreted using Stanford HIV Drug Resistance Database (HIVDB) v9.0; detected mutations represent acquired drug resistance (ADR). Pairwise genetic distances (GD) (TN93 model) were calculated; transmission networks were constructed in Cytoscape 3.10.3. Results: 75 sequences were obtained. Males (84.00%), and heterosexual transmission (64.00%) predominated. CRF07_BC (46.67%) and CRF01_AE (38.67%) were the major subtypes; the overall ADR rate was 40.00%, mainly NNRTIs–associated (30.67% of all participants, including 16.00% single–class NNRTIs and 14.67% dual–class NRTIs–NNRTIs). Network inclusion rate was 40.00% of the 75 sequences; CRF07_BC showed higher betweenness centrality (p = 0.028), while CRF01_AE and CRF85_BC showed higher closeness centrality (p < 0.001). Occupation significantly affected network enrollment (p ≤ 0.05). Conclusion: HIV–1 subtypes are diverse with high ADR. CRF07_BC may act as a transmission bridge, whereas CRF01_AE and CRF85_BC exhibit faster potential spread. Baseline DR testing and network–guided interventions are recommended. Full article