Search Results (6,298)

Porcine group A rotavirus (PoRVA) is a significant cause of viral diarrhea in piglets, necessitating urgent global implementation of effective control strategies. This review assesses advancements in PoRVA in vitro cultivation and amplification, crucial for PoRVA vaccine development. Traditional PoRVA cultivation commonly employs primary porcine kidney cells or finite cell lines like MA-104, posing well-documented challenges in scalability, production cost, and their ability to recapitulate the natural intestinal microenvironment. Consequently, research has increasingly focused on adapting PoRVA to alternative systems, particularly immortalized porcine cell lines or physiologically relevant porcine intestinal organoids. This adaptation process, involving serial passaging, can induce genomic alterations and virulence attenuation in piglets, essential for generating live attenuated vaccine (LAV) candidates. Modern biotechnological tools, such as reverse genetics and synthetic genomics, have expedited the creation of recombinant PoRVA strains with defined antigenic profiles and enhanced in vitro growth characteristics. However, a significant concern regarding LAV candidates derived from cell culture adaptation is the risk of virulence reversion upon pig back-passage, necessitating thorough safety and genetic stability evaluations. Nevertheless, utilizing stable cell lines or organoid platforms presents a feasible and cost-effective approach for large-scale PoRVA vaccine production. Future research should focus on identifying vaccine candidates that provide broad protection and exceptional safety, with an emphasis on cross-protection against divergent epidemic genotypes, while ensuring the economic feasibility of innovative manufacturing approaches. Full article

Familial hypercholesterolemia (FH) and familial hypertriglyceridemia (FHTG) represent a spectrum of inherited conditions with profoundly different etiologies, risk profiles, and therapeutic implications. Despite decades of clinical experience, their formal diagnostic definitions remain rooted in frameworks developed before the genomic era (the Dutch Lipid Clinic Network (DLCN) score), leading to substantial gaps in diagnostic accuracy. This review traces the historical evolution of diagnostic criteria for FH and FHTG from early phenotypic observation to contemporary genomic and biomarker-driven models. It systematically evaluates the major limitations of current criteria, including the (DLCN) score, and integrates evidence from landmark Mendelian randomization (MR) studies to identify persistent gaps. A narrative synthesis of landmark clinical, epidemiological, and genetic studies was performed, encompassing the original discovery of the low-density lipoprotein cholesterol (LDL-C) receptor pathway, the development of international diagnostic criteria, and contemporary mendelian randomization (MR) evidence on the causal roles of LDL-C, lipoprotein (a) [Lp(a)], triglyceride-rich lipoprotein remnants, and apolipoprotein B (ApoB). Current diagnostic frameworks suffer from age-dependent confounding of LDL-C measurements, failure to account for Lp(a)-mediated phenocopies, inadequate discrimination between monogenic and polygenic etiologies, sex differences, ethnicity, and inapplicability to pediatric populations. MR data reveal that the causal architecture of cardiovascular risk in these disorders is particle-centric (ApoB) rather than LDL-C-centric, and that remnant cholesterol, not triglyceride per se, drives atherosclerotic cardiovascular disease risk in FHTG. We evidenced the evolution of treatment options and the morbidity and mortality rates for FH and FHTG from the 1970s until the 2020s. Future diagnostic paradigms should integrate lifetime Lp(a) measurement, polygenic risk scoring, ApoB quantification, and cascade genomic testing to replace phenotype-only approaches. This review concludes by proposing a four-step integrated diagnostic algorithm for FH and FHTG. Full article

Good canine gastrointestinal health depends on the suppression of enteric pathogens and maintenance of epithelial barrier integrity. Limosilactobacillus reuteri ATCC PTA 6127 (Lr6127) is a dog-derived probiotic, but evidence supporting its functional properties remains limited. Here, we evaluated the antimicrobial and epithelial-supportive effects of Lr6127 using a canine epithelial cell model. Cell-free supernatant (CFS) from Lr6127 significantly inhibited the growth of canine-relevant pathogens, including Enterotoxigenic Escherichia coli (52.0 ± 1.3%), Clostridium perfringens (54.0 ± 2.7%), and Salmonella enterica subsp. enterica serovar Typhimurium (48.6 ± 1.2%), compared with the medium control (p < 0.0001). Pathogen inhibition increased in a dose-dependent manner with increasing CFS concentration. Untargeted metabolomic analysis revealed enrichment of multiple antimicrobial-associated metabolites, indicating a multi-component profile consistent with pathogen suppression, with genomic analysis supporting the aromatic amino acid-derived metabolite findings. In addition, viable Lr6127 significantly reduced the epithelial adhesion of all the tested pathogens (p < 0.01). Beyond direct antimicrobial effects, Lr6127 CFS promoted epithelial wound healing at later time points, accompanied by the coordinated modulation of proteins associated with cytoskeletal remodeling and barrier repair. Collectively, these findings support the idea that Lr6127 is associated with antimicrobial and epithelial-related effects, highlighting its potential to contribute to epithelial function under controlled in vitro conditions. Full article

Background: HCC remains one of the leading causes of cancer-related mortality worldwide, and the therapeutic efficacy of sorafenib is limited by the development of acquired resistance. Increasing evidence indicates that the tumor microenvironment, particularly HSCs, plays a pivotal role in modulating drug response; however, the underlying molecular mechanisms remain incompletely elucidated. Methods: Co-culture systems, mouse models, and biochemical assays were employed to evaluate the effects of HSCs on sorafenib sensitivity and ferroptosis in HCC cells. Transcriptomic analyses of data from The Cancer Genome Atlas were performed to identify key long non-coding RNAs (lncRNAs), followed by gain- and loss-of-function experiments to determine their biological roles. The underlying molecular mechanisms were further investigated through expression profiling, correlation analyses, and RNA stability assays. Results: HSCs markedly reduced the sensitivity of HCC cells to sorafenib by inhibiting ferroptosis, as evidenced by decreased levels of ferrous iron, reactive oxygen species, and lipid peroxidation, accompanied by increased glutathione content and activation of the NRF2 signaling pathway. LINC00152 was identified as a critical lncRNA that was upregulated in both HCC tissues and HCC cells co-cultured with HSCs, and its high expression was associated with poor prognosis. Functional studies demonstrated that LINC00152 promoted sorafenib resistance and suppressed ferroptosis both in vitro and in vivo. Mechanistically, LINC00152 enhanced HSPB1 expression by stabilizing its mRNA. Notably, HSPB1 knockdown reversed the effects of LINC00152, restoring ferroptosis and drug sensitivity to sorafenib. Conclusions: These findings reveal a novel HSCs–LINC00152–HSPB1 axis that promotes ferroptosis resistance and sorafenib tolerance in HCC. Targeting this pathway may represent a promising therapeutic strategy for overcoming drug resistance and improving clinical outcomes in patients with HCC. Full article

Single nucleotide polymorphism (SNP) genotyping panels for domesticated ducks are currently lacking, despite their importance for genetic diversity studies and genomic selection. We analyzed whole-genome sequencing data from 74 ducks. To obtain a 40K SNP marker set, we performed SNP calling and applied minor allele frequency (MAF) and linkage disequilibrium (LD) criteria. SNPs from 33 genes associated with Quantitative Trait Loci (QTL) were manually selected and added to the panel. The performance of the resulting SNP panel was validated using genotyping data from 28 additional duck samples. We developed a 40K SNP genotyping panel for ducks. Applying criteria of call rate, MAF, and LD, 37,386 SNP markers were selected. After excluding SNPs near repeats and indels, and incorporating 591 SNPs from 33 duck QTL-associated genes, the final set consisted of 35,613 SNP markers. When evaluating the performance of the SNP panel, genotypes were successfully called for 35,209 out of 35,613 SNPs, achieving a call rate of 98.9%. After applying QC filters, 33,870 SNPs were confirmed to be usable. Our SNP panel design process successfully generated a dataset at a 40K scale without compromising the genetic distances of the whole genome. By minimizing variation at the SNP probe alignment sites, we achieved a high call rate. The panel demonstrated reasonable robustness and suitability for further genomic studies, making it a valuable tool for genetic improvement and trait selection in duck populations. Full article

Grain transparency (GT) is a key determinant of rice appearance quality and consumer preference, yet its genetic basis remains poorly understood. In this study, we evaluated GT in a panel of 450 rice accessions grown in two environments (Guangzhou and Yangjiang). Nineteen quantitative trait loci (QTL) for GT were identified by a genome-wide association study (GWAS), distributed across all rice chromosomes except chromosomes 2 and 12. Among these, four QTL (qGT-1b, qGT-3b, qGT-4b, and qGT-5b) were consistently detected in both environments. Notably, qGT-3b and qGT-5b co-localized with the grain shape genes GRAIN SIZE 3 (GS3) and GRAIN WIDTH 5 (GW5), respectively. For the novel and stable QTL qGT-4b, linkage disequilibrium decay analysis delimited an approximately 300 kb candidate region. Integrative transcriptomic and genomic analyses pointed to two candidate genes: LOC_Os04g40370 (OsFbx142), encoding an F-box domain protein, and LOC_Os04g40720 (OsSUBSrP1), encoding a subtilisin-like serine protease. Haplotype analysis further revealed that specific haplotypes of these genes were significantly associated with GT variation across environments. Our findings provide genetic insights into the regulation of rice grain transparency and offer candidate genes for further functional validation and potential application in improving rice appearance quality. Full article

Background/Objectives: Duodenal epithelial neoplasms are rare; however, the widespread use of surveillance endoscopy and advances in endoscopic imaging technology have increased their incidental detection. Owing to their rarity, the clinicopathological characteristics and natural course of duodenal epithelial neoplasms have not been thoroughly investigated. In this study, we aimed to clarify the genomic profile and clinicopathological characteristics of duodenal epithelial neoplasms. Methods: A total of 158 patients with duodenal epithelial neoplasms were enrolled. Comprehensive genomic profiling and immunohistochemical staining were performed. Immunophenotypes were categorized as gastric type (G-type), gastrointestinal type (GI-type), or intestinal type (I-type). The detection rate of potentially actionable genomic alterations and a high tumor mutational burden (TMB-H ≥ 10 Muts/Mb) were evaluated and compared across tumor types. Results: The median size of adenocarcinomas was larger than that of adenomas (p = 0.002). The age at diagnosis of G-type tumors was higher than that for the other two tumor types (p < 0.001). The median size of I-type tumors was smaller than that of the other two tumor types (p = 0.019). Compared with the other two types, G-type tumors were predominantly located in the superior region (p < 0.001), were macroscopic Type I (p = 0.002), and had significantly higher genomic alteration rates for KRAS (p < 0.001), GNAS (p < 0.001), CDKN2A (p = 0.004), and MDM2 (p < 0.001). Eighteen patients showed TMB-H. Conclusions: TMB-H was observed in >10% duodenal tumors. Additionally, the pathogenesis of G-type duodenal tumors differs from that of other immunophenotypic tumors. These findings could help in understanding the genomic profiles of duodenal tumors and in selecting treatment options. Full article

Pediatric acute myeloid leukemia (AML) is biologically heterogeneous, and genomic profiling increasingly informs risk stratification and treatment. We evaluated the relationship between induction response, genomic risk, transplant allocation, and survival in pediatric AML. We retrospectively analyzed 38 pediatric patients with newly diagnosed AML, treated between 2020 and 2025. Clinical, cytogenetic, molecular, treatment, and outcome data were collected. Genomic alterations were assessed using cytogenetics, fluorescence in situ hybridization (FISH), molecular testing, and next-generation sequencing (NGS). Survival was estimated by Kaplan–Meier analysis, and prognostic factors for event-free survival (EFS) were assessed using univariable Cox regression. This study is exploratory given the limited sample size and should be interpreted accordingly. Complete remission (CR) after the first course of induction was achieved in 25/38 patients (65.8%), partial remission (PR) in 3/38 (7.9%), and refractory disease in 10/38 (26.3%). Twenty-four patients underwent allogeneic hematopoietic stem cell transplantation; 17/24 (70.8%) were alive at last follow-up, with a 2-year overall survival rate of 72.9%. Both induction response and genomic risk stratification showed suggestive associations with outcome; descriptively, induction response showed the strongest prognostic discrimination, with achievement of CR associated with markedly improved survival. High cytogenetic risk and FLT3-ITD were significantly associated with inferior EFS. Post-induction measurable residual disease (MRD) positivity was detected in 16 of 38 patients (42.1%) and was associated with suboptimal induction response; MRD negativity did not uniformly preclude adverse outcomes, particularly in the high-risk genomic subgroup. Genomic profiling refined biological risk and post-remission treatment allocation. Integrated assessment of genomic risk, induction response, and MRD status may improve therapeutic stratification in pediatric AML. Full article

Background: Comprehensive genomic profiling (CGP) via next-generation sequencing (NGS) is pivotal for precision oncology, yet many laboratories face challenges with incomplete genomic coverage, complex bioinformatics workflows, and limited integration of key biomarkers. Methods: We evaluated the analytical performance and clinical utility of a CGP assay using 119 tumor samples representing 18 types of cancer, previously analyzed with an orthogonal NGS panel. Concordance was assessed across 81 genes, covering 176 single-nucleotide variants (SNVs), eight copy number variations (CNVs), four deletions, one duplication, and four gene fusions. Limit of detection (LOD) studies employed AcroMetrix Mutant Hotspot Control and SeraSeq Lung and Brain CNV Mix. Microsatellite instability (MSI) and tumor mutational burden (TMB) were quantified. Inter- and intra-run reproducibility were evaluated to assess precision. Results: The CGP assay demonstrated high analytical performance, with >99% sensitivity, 100% specificity, and complete accuracy for variant detection. LOD studies revealed robust detection of SNVs at ≤5% variant allele frequencies (VAF) and CNVs at three copies. MSI and TMB results were consistent with clinical expectations, showing minimal bias compared to the orthogonal panel. Inter- and intra-run testing confirmed 100% reproducibility, indicating strong assay precision. Post-sequencing variant reporting was streamlined using the iCare platform, enabling direct FASTQ-to-report generation without intermediate bioinformatic steps. Conclusions: These findings support the present assay’s clinical utility in personalized oncology assessment. Full article

Laural (Laurus nobilis) is a Mediterranean plant with reported antibacterial properties, yet the genetic basis of its antibacterial efficacy remains largely unexplored. This study evaluated the antibacterial activity of Laurus nobilis methanolic extracts against Escherichia coli, Staphylococcus aureus, and Bacillus cereus, combined with genome-wide association studies (GWAS) and machine learning (ML) approaches to identify genetic markers and predict antibacterial efficacy in 92 plant samples. Antibacterial tests revealed significant variability in inhibition zones, with E. coli showing the highest inhibition (Canakkale2: 24.5 mm), followed by S. aureus (Aydin2: 26.0 mm). Minimum inhibitory concentration (MIC) analysis demonstrated notable regional differences; extracts from Mersin3 showed the highest efficacy (MIC = 6.25 mg/mL), while Aydin1 exhibited the lowest activity (MIC = 100 mg/mL). Population structure and neighbor joining tree analysis split the germplasm into two groups. GWAS identified significant genetic markers associated with antibacterial traits, including marker 26557159 for EC-MEAN (Escherichia coli-Mean) (p = 1.10 × 10⁻⁴, MarkerR² = 0.1799, genetic variance = 9.41792) and marker 26584774 for BC-MEAN (Bacillus cereus-Mean) (p = 8.89 × 10⁻⁵, MarkerR² = 0.18512, genetic variance = 12.48948). Protein–protein interaction network of loci associated with marker trait association (MTA) marker (26557159) indicated involvement in high-affinity secondary active ammonium transmembrane transporter activity, providing insights into genetic regions influencing antibacterial properties. ML models predicted antibacterial activity with high accuracy. XGBoost achieved the best performance for MIC predictions (R² = 0.999, RMSE = 0.434), while random forest (R² = 0.984) demonstrated robust performance for both MIC and disc diffusion assays. LightGBM performed well for MIC prediction (R² = 0.988) but showed limited accuracy for disc diffusion outcomes (R² = 0.695). This study is the first to combine GWAS and ML for predicting antibacterial efficacy in L. nobilis, identifying specific genetic markers (e.g., 26557159, 26584774) and demonstrating that XGBoost achieves near-perfect MIC prediction (R² = 0.999). These findings provide a genomic and computational foundation for marker-assisted breeding of laurel with enhanced antibacterial properties and support the sustainable use of plant-derived anti-microbials. Full article

Aspartame is a widely used artificial sweetener, but its possible relationship with rheumatoid arthritis (RA) remains insufficiently understood. This study aimed to explore, rather than prove, potential molecular links between aspartame-related targets and RA-associated gene networks. Three public RA transcriptomic datasets (GSE55235, GSE55457, and GSE77298) from the Gene Expression Omnibus (GEO) database were integrated as discovery/training data. Because these datasets included different tissue origins, batch correction was used to reduce dataset-level technical variation, whereas tissue-origin-related biological variation was not assumed to be fully removable. After differential expression analysis, RA-associated differentially expressed genes (DEGs) were identified. The single-cell dataset GSE200815 was used for cell annotation and cellular expression visualization; because its comparator group consists of psoriatic arthritis (PsA) samples rather than healthy controls, single-cell results were interpreted as RA-vs-PsA observations and were not treated as disease-versus-healthy-control evidence. Potential targets of aspartame were retrieved from ChEMBL, SwissTargetPrediction, and the Similarity Ensemble Approach (SEA), and were intersected with RA-related DEGs to construct an aspartame-gene-RA regulatory network. Diagnostic models were developed using 113 machine-learning algorithm combinations to determine an optimal multigene model and its core genes. HLA-DRB1 was selected for exploratory scTenifoldKnk-based virtual knockout mainly because it was included in the optimal model and has a well-established role in RA immunogenetics; the single-cell analysis was used only to describe cellular distribution in the RA/PsA dataset. Molecular docking was then used to evaluate the possible interaction between aspartame and HLA-DRB1. Forty-four intersected genes linked the predicted aspartame targets with RA DEGs. The random forest plus partial least-squares generalized linear model (RF + plsRglm) identified 16 core genes. Network-level interpretation indicated that these genes were distributed across immune/antigen-processing, inflammatory-signaling, protease/extracellular-matrix-remodeling, adhesion, metabolic, and proliferation-related modules; therefore, HLA-DRB1 was treated as a prioritized immune-module candidate rather than as the sole driver of the network. Following virtual knockout of HLA-DRB1, affected genes were enriched in extracellular matrix organization, extracellular structure organization, extracellular matrix, collagen trimer, extracellular matrix structural constituent, and collagen binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included integrin signaling, focal adhesion, proteoglycans in cancer, cytoskeleton in muscle, and phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) signaling. Molecular docking showed a minimum binding energy of −6.7 kcal/mol, which was more negative than the preset stability criterion of −5.0 kcal/mol, and the docking pose suggested contacts around ARG-146. This integrative analysis suggests a hypothesis-generating association between aspartame-related predicted targets and RA-relevant molecular networks involving HLA-DRB1 and other core genes. The findings do not establish causality and require experimental, epidemiological, biophysical, and tissue-stratified validation before any causal or clinical inference can be made. Full article

Background/Objectives: L-2-hydroxyglutaric aciduria (L2HGA) is a rare autosomal recessive neurometabolic disorder marked by developmental delay, intellectual disability, and progressive movement abnormalities. Variants in RYR1 can cause congenital myopathies, but data on the co-occurrence of variants in populations are limited. The aim of this study was to characterize the clinical and genetic basis of the neurometabolic and neuromuscular abnormalities and to investigate the potential interaction between the identified variants. Methods: Patients with complex, previously undiagnosed clinical presentations underwent neurological evaluation, including brain magnetic resonance imaging, electromyography, biochemical testing, and whole-exome sequencing (WES). Identified variants were analyzed in silico and confirmed by Sanger sequencing in the patient and her parents. Three cases were reviewed, and one of these patients exhibited developmental delay, hypotonia, intellectual disability, and progressive motor dysfunction. Biochemical tests revealed markedly elevated urinary 2-hydroxyglutaric acid levels, consistent with L2HGA. Results: WES identified a homozygous likely pathogenic variant in L2HGDH (c.589_590insGGC, p.Q197insG), confirming the molecular diagnosis of L2HGA. In addition, a heterozygous missense variant in RYR1 (c.7268T>A, p.M2423K), classified as a variant of uncertain significance, was detected and was inherited from her mildly affected father. The L2HGDH variant explains the neurometabolic phenotype of the patient, whereas the RYR1 variant remains of uncertain significance, and its clinical contribution cannot be clearly established. Conclusions: To our knowledge, this case illustrates the co-occurrence of a likely pathogenic L2HGDH variant and a heterozygous RYR1 variant of uncertain significance. The findings expand the mutational spectrum of L2HGA and underscore the value of comprehensive genomic testing in complex neurometabolic and neuromuscular disorders. Full article

Pentlandite bioleaching offers a potentially low-energy route for nickel recovery from low-grade sulfide resources, but increasing pulp density may constrain acidophilic microorganisms through metal accumulation, mineral buffering, mass-transfer limitation, and surface-product deposition. This study evaluated pentlandite bioleaching by the nickel-resistant Acidithiobacillus ferriphilus WGS1 at pulp densities of 1%, 5%, and 10% (w/v). Leaching performance and associated interfacial and cellular responses were examined using solution chemistry, mineral and surface characterization, electrochemical measurements under 40 g/L Ni²⁺, and genome-guided transcriptomics. After 30 days at 35 °C, Ni leaching efficiencies reached 99.2%, 97.1%, and 95.7% at 1%, 5%, and 10% pulp densities, respectively, compared with 27.2%, 14.2%, and 0.76% in the corresponding sterile controls. The inoculated systems maintained lower pH and higher ORP than the sterile controls, while the residues showed pentlandite alteration, Ni depletion, secondary Fe-bearing phase formation, and changes in surface sulfur speciation. Under 40 g/L Ni²⁺, the WGS1-containing system showed a lower charge-transfer resistance and a higher corrosion current density than the abiotic system. Transcriptomic comparison between the 10% and 1% pulp-density groups identified 640 differentially expressed genes and highlighted candidate responses associated with Ni homeostasis, Fe/S oxidation, respiratory electron transfer, and energy conservation. Integration of the physicochemical, mineralogical, electrochemical, and transcriptomic results supports a literature-informed working model for WGS1-associated pentlandite bioleaching under high-pulp-density conditions. Full article

Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log₁₀ copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log₁₀ input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds. Full article

Advances in fetal diagnosis and molecular medicine have opened new opportunities for in utero molecular-targeted drug therapy, shifting fetal treatment from purely procedural interventions toward pharmacologic strategies that address disease mechanisms before irreversible organ damage occurs. In this review, we highlight recent advances in in utero drug therapy, focusing on molecular-targeted approaches with emerging clinical or trial-level evidence. Early clinical experience and ongoing trials have demonstrated the feasibility of achieving therapeutically relevant fetal drug exposure, although the strength of evidence varies considerably across therapeutic classes. However, significant challenges remain, including optimization of fetal drug delivery, characterization of fetal pharmacokinetics and pharmacodynamics, long-term safety assessment, and ethical considerations. The current evidence base ranges from single case reports to ongoing Phase 3 clinical trials, underscoring both the promise of prenatal molecular therapeutics and the need for further prospective evaluation. Continued integration of fetal imaging, genomics, ethics and pharmacology will be essential to advance safe and effective prenatal precision therapies. Full article