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Colorectal cancer (CRC) has a high mortality rate worldwide. Oral and intestinal microbiota members may have an effect on gastrointestinal tumors’ pathogenesis, particularly in CRC. Designed as a pilot study, this study’s aim was to investigate the relationship between CRC and oral microbiota and to identify potential biomarkers for CRC diagnosis. Saliva samples were collected from recently diagnosed CRC patients (n = 14) and healthy controls (n = 14) between March 2023 and December 2023. Microbiota (16S rRNA) analyses were conducted on these saliva samples using a next-generation sequencing method. Phylogenetic analyses, including alpha diversity, principal component analysis (PCA), principal coordinate analysis (PCoA), beta diversity, biomarker, and phenotype analyses, were conducted using the Qiime2 (Quantitative Insights Into Microbial Ecology) platform. Alpha diversity indices (Shannon: p = 0.78, Cho1: p = 0.28, Simpson: p = 0.81) showed no significant difference between CRC and control groups. Beta diversity analysis using Bray–Curtis PCoA indicated significant differences in the microbial community between the two groups (p = 0.003). Examination of OTU distributions revealed that the Mycoplasmatota phylum was undetectable in the oral microbiota of healthy controls but was significantly elevated in CRC patients (CRC: 0.13 ± 0.30, Control: 0.00 ± 0.00, p < 0.05). Additionally, Metamycoplasma salivarium, Bacteroides intestinalis, and Pseudoprevotella muciniphila were undetectable in healthy controls but significantly more prevalent in CRC patients (p < 0.05 for all three species). LEfSe analysis identified eight species with an LDA score > 2, Granulicatella adiacens, Streptococcus thermophilus, Streptococcus gwangjuense, Capnocytophaga sp. FDAARGOS_737, Capnocytophaga gingivalis, Granulicatella elegans, Bacteroides intestinalis, and Pseudoprevotella muciniphila, as potential biomarkers. The results of this study contribute critical evidence of the role of oral microbiota in the pathogenesis of colorectal cancer. Alterations in the microbiota suggest potential biomarkers in understanding the biological mechanisms underlying CRC and developing diagnostic and therapeutic strategies. Full article

The morphology of rice grains represents one of the most vital agronomic characteristics, significantly impacting both grain productivity and the subsequent milling and nutritional quality of the crop. A comprehensive understanding of the genetic basis and molecular drivers of grain shape is vital for the targeted breeding of high-performance rice lines with consistent yield stability. To pinpoint the genomic regions influencing grain dimensions, we conducted a genome-wide association analysis across a panel of 231 distinct rice accessions, focusing on the discovery of loci associated with length and width. Our analysis revealed four consistent quantitative trait loci (QTLs) distributed across chromosomes 3, 4, and 11. Notably, grain length was associated with qGL3.1, qGL3.2, and qGL11. The first two were co-localized with GS3 and SMG3, respectively, whereas qGL11 likely constitutes a novel locus. One QTL, qGW4, which governs grain width, was found to co-localize with the gene OsOFP14. Haplotype analysis further revealed that the characteristic haplotypes of the candidate genes for qGL3.1, qGL3.2, and qGW4 were enriched in eight germplasm accessions (including Newbonnet, Skybonnet, and Lemont), all of which exhibit a slender-grain phenotype. This finding suggests that the specific combination of these characteristic haplotypes is a common genetic signature of slender-grain rice, serving as a potential gene combination for the targeted improvement of rice grain shape. Our results reveal valuable QTLs and candidate genes and highlight specific germplasm resources that can be readily applied in marker-assisted breeding to improve rice grain shape. Full article

DNA methylation, as an important epigenetic modification, plays a key role in shaping hybrid phenotypes. Studies have shown that DNA methylation—specifically, allele-specific methylation (ASM)—can mediate allelic expression imbalance (AEI) and participate in the regulation of plant growth and development. However, since this regulatory mechanism is often sequence-dependent, the prevalence of ASM and the extent to which it influences allelic expression remain poorly characterized. To address this challenge, the present study utilized Camellia azalea, C. amplexicaulis and their F₁ hybrids [C. azalea (♀) × C. amplexicaulis (♂)] as research materials. By performing whole-genome bisulfite sequencing (WGBS), resequencing, and transcriptome sequencing, we assessed the inheritance of DNA methylation patterns and its role in shaping allelic expression in F₁ hybrids. The results showed the following: (1) the overall cytosine methylation level in the F₁ hybrid was intermediate between the two parents; (2) the methylation states of the parental genomes were partly transmitted to the next generation; (3) ASM was not prevalent in the F₁ hybrids, primarily because biparental parent-specific methylation sites (PSMSs) were widespread and randomly distributed, which often act on the same allele pairs; (4) although ASM was not common, it led to biased expression of some alleles related to flower development. The results indicated that ASM was rare in F₁ hybrids, mainly because PSMSs occurred randomly. Instead of causing AEI, the randomly distributed PSMSs played a more important role in balancing allelic expression in F₁ hybrids. Therefore, most of the alleles in F₁ were not biasedly expressed. ASM did not necessarily lead to allele-biased expression; however, its occurrence may hold significant biological implications in modulating AEI and transgressive phenotypes in the F₁ hybrids. These findings elucidate the synergistic effects of genetic and epigenetic controls on transcriptional regulation in hybrid plants, substantially deepening the mechanistic understanding of hybridization at the molecular scale. Full article

Lactiplantibacillus plantarum is widely used in fermented foods and as a probiotic, yet the genomic basis underlying its γ-aminobutyric acid (GABA) production capacity and strain-level functional diversity remains incompletely resolved. We analyzed 1240 publicly available genomes to map species-wide genome architecture, the distribution of GABA-related genes, and accessory drivers of phenotypes. Pangenome analysis identified 45,201 gene families, including 622 strict core genes (1.38%) and 444 soft-core genes (2.36%). The accessory genome dominated (3138 shell and 40,997 cloud genes; 97.64%), indicating a strongly open pangenome. In contrast, the GABA (gad) operon was universally conserved: gadB (glutamate decarboxylase) and gadC (glutamate/GABA antiporter) were present in all genomes regardless of isolates source. Accessory-genome clustering revealed ecological and geographic structure without loss of the operon, suggesting that phenotypes variability relevant to fermentation and probiotic performance is primarily shaped by accessory modules. Accessory features included carbohydrate uptake and processing islands, bacteriocins and immunity systems, stress- and membrane-associated functions, and plasmid-encoded traits. Analysis of complete genomes confirmed substantial variation in plasmid load (median = 2; range = 0–17), highlighting the role of mobile elements in niche-specific adaptation. Carbohydrate-Active Enzymes database (CAZy) and biosynthetic gene cluster (BGC) profiling revealed a conserved enzymatic and metabolic backbone complemented by rare lineage-specific functions. Collectively, these results position L. plantarum as a genetically stable GABA producer with extensive accessory-encoded flexibility and provide a framework for rational strain selection. Full article

Endometritis features an inflammatory milieu in the endometrium, accompanied by the recruitment of immunocompetent cells, including mast cells (MCs). The mechanisms underlying MC involvement in chronic endometritis (CE) and fibrous niche formation remain poorly understood, particularly regarding spatial intercellular interactions in situ. In this study, we used multiplex immunohistochemistry and quantitative immunofluorescence analysis to map the spatial phenotype of MC distribution. Standard histochemical techniques, monoplex and multiplex immunohistochemical staining technologies, light-field microscopy, epifluorescence, and confocal microscopy with multispectral imaging, combined with quantitative immunofluorescence analysis with AI application, were used to identify the spatial phenotyping of quantitative and qualitative features of the endometrial MC population in CE. The increased intensity of endometrial inflammation was accompanied by a rise in the profile of MC content in the endometrium; this accounted for a 0.014% increase in the control and 0.067%, 0.113%, and 0.206% increases in mild, moderate, and severe CE, respectively. We are the first to map the number of MCs that demonstrated loci of accumulations in the endometrium coinciding with foci of fibrous changes. The number of these foci correlated with the severity of chronic endometritis and the development of clinical signs. The frequency of juxtacrine and paracrine MC colocalization with other immunocompetent cells increased with increased CE activity and fibrotic changes: For CD8⁺ lymphocytes, colocalization increased from 4.6% in the control to 11.6%, 18.5%, and 28.0% in mild, moderate, and severe CE, respectively. For monocytes, colocalization increased from 5.6% in the control to 18.7%, 26.8%, and 28.8% in mild, moderate, and severe CE, respectively. For type 1 macrophages, colocalization increased from 5.6% in the control to 13.5%, 17.4%, and 24.6% in mild, moderate, and severe CE, respectively. For type 2 macrophages, colocalization increased from 3.4% in the control to 9.6%, 9.1%, and 21.5% in mild, moderate, and severe CE, respectively. Spatial patterns of juxtacrine and paracrine MC interactions with other immune cells may provide diagnostic algorithms for chronic endometritis, enabling targeted therapy and preventing fibrotic changes. Full article

Methylmercury (MeHg) is a well-known environmental neurotoxicant that preferentially affects sensory neurons in the peripheral nervous system. While sensory-dominant neuropathy has long been described in Minamata disease, the temporal dynamics of dorsal root ganglion (DRG) injury and recovery remain incompletely understood. In this study, Wistar rats were exposed to MeHg for five consecutive days, followed by a two-day treatment-free period; this regimen was repeated once. The DRG and peripheral sensory fibers were analyzed up to 70 days after exposure. Histological and immunohistochemical analyses, DNA microarrays, and mercury quantification and distribution mapping were performed. The A-fiber density was significantly reduced at Day 14 but recovered by Day 70, whereas C-fibers showed no significant change. The total number of DRG neurons remained stable. Immunohistochemical analyses demonstrated that subtype marker-selected neurons (NF, TrkA, FAM19A1, TAC1, SST) decreased at Day 14 and gradually recovered thereafter. DNA microarray analysis at Day 14 revealed a broad downregulation of DRG neuronal subtype marker genes. The mercury concentration in the DRG peaked at Day 14 and declined to the control level by Day 70, with in situ imaging confirming preferential accumulation in DRG neurons. These data suggest that the short-term MeHg exposure caused a transient functional suppression of DRG neurons without widespread neuronal loss. The selective and reversible downregulation of neuronal phenotypes, coupled with preferential Hg accumulation in DRG neurons, underlies the sensory-dominant and potentially reversible features of MeHg neurotoxicity. Full article

Background: This study investigated the phenotypic and genotypic antibiotic resistance profiles of 50 Lactic Acid Bacteria (LAB) strains—25 Lactiplantibacillus plantarum and 25 Lacticaseibacillus paracasei—isolated from traditional Sardinian fermented foods of animal origin. Methods: The sensitivity of the isolates to antibiotics such as β-lactams, tetracyclines, aminoglycosides, macrolides, phenicols, and glycopeptides was initially assessed using disc diffusion and minimum inhibitory concentration (MIC) tests. Subsequently, PCR analyses were performed on both genomic DNA and plasmid DNA to detect blaZ, tet(W), strA, aac(6′)-Ie–aph(2″)-Ia, and vanX genes associated with resistance to ampicillin, tetracycline, streptomycin, gentamicin, and vancomycin. Results: The analysis revealed that L. plantarum strains frequently carried the tet(W) gene on the chromosome and strA on plasmids, while vanX was detected in most strains as a chromosomal determinant. By contrast, L. paracasei strains exhibited a predominantly plasmid-mediated distribution of resistance genes. For example, strA, aac(6′)-Ie–aph(2″)-Ia and blaZ were often found on plasmids, whereas vanX remained chromosomally encoded. Phenotypic assays confirmed high intrinsic resistance to vancomycin in both species, with L. plantarum showing a higher overall frequency and diversity of resistant phenotypes compared to L. paracasei. Conclusions: The co-occurrence of multiple resistance determinants, including plasmid-encoded ones, in most strains suggests that even autochthonous isolates from artisanal products may represent potential reservoirs for transmissible resistance genes. Full article

Nitrogen (N) is essential for maize (Zea mays L.) productivity, yet its acquisition is limited by the low N uptake efficiency of current varieties. Root cortical aerenchyma (RCA) formation provides a carbon-saving strategy that enhances soil exploration and N acquisition by reducing the metabolic cost of root tissue. However, the genetic basis of RCA formation remains poorly characterized. This study employed an association panel of 295 maize inbred lines to dissect the genetic architecture of RCA formation under low nitrogen (LN) stress. Phenotypic analysis demonstrated that LN stress significantly induced RCA area (RCAA) and proportion (RCAP), with responses ranging from −0.31 to 1.16 mm² for RCAA and −11.34% to 40.18% for RCAP. The non-stiff stalk (NSS) subpopulation exhibited 29.19% higher RCAA under LN than the stiff stalk subgroup. Genome-wide association analysis detected a total of 560 significant SNPs and 810 candidate genes associated with RCA-related traits. Transcriptomic profiling further identified 537 differentially expressed genes between inbred lines with contrasting RCA phenotypes. Integrated GWAS and transcriptomic analysis pinpointed 12 co-localized candidates, subsequently refined to four core genes (GRMZM2G033570, GRMZM2G052422, GRMZM2G080603, and GRMZM2G472266), which were implicated in ethylene signaling and stress-responsive root development. Favorable haplotypes of three genes were predominantly distributed in the NSS (25.64–56.00%) and tropical/subtropical (20.51–46.67%) subpopulations. These findings elucidate the genetic basis of LN-responsive RCA formation and provide fundamental resources for marker-assisted breeding of N-efficient maize. Full article

Background: Recent studies have associated the presence of the CYP2C:TG haplotype with increased metabolism of CYP2C19 substrates such as escitalopram and sertraline, suggesting a potential regulatory interaction between CYP2C18 and CYP2C19. However, this association has not been demonstrated for other CYP2C19 substrates. Objective: This study aims to elucidate the role of the CYP2C:TG haplotype in modulating CYP2C19 activity using the omeprazole metabolic ratio (MR) within a cocktail drug approach, to characterize its distribution and prevalence among Native Mexican populations, and to evaluate its potential impact on CYP2C19 metabolic phenotypes. Materials and Methods: A total of 256 volunteers from various ethnic native groups from Mexico were genotyped for CYP2C19 (*2, *3, *4, *5, *17) and the CYP2C haplotype (rs2860840 and rs11188059). The MR of omeprazole to 5-hydroxyomeprazole was analyzed to determine individual CYP2C19 metabolic phenotypes and assess metabolic capacity. Results: The CYP2C:TG haplotype was the most prevalent (42.77%), followed by CYP2C:CG (35.74%) and CYP2C:TA (21.48%). The CYP2C:TG haplotype was consistently associated with the CYP2C19*1 allele. Significant differences in logMR values were observed between individuals with and without the TG haplotype (p = 0.02). A trend toward increased metabolic activity associated with CYP2C:TG was observed across most CYP2C19 metabolizer groups, except for rapid metabolizers. No significant association was found between molecular ancestry and the presence or functionality of the haplotype. Conclusions: The CYP2C:TG haplotype appears to be associated with increased CYP2C19 activity, warranting further functional validation before clinical implementation. Full article

Streptococcus dysgalactiae subsp. equisimilis (SDSE) has historically been recognized as a human pathogen, yet β-hemolytic streptococci consistent with SDSE have been documented in pigs for nearly a century. To investigate the population structure of porcine SDSE and the phylogenetic relationships between swine and human strains, we characterized 41 isolates recovered from diseased pigs in Quebec, Canada (2019–2022). Infected animals spanned all major production stages and frequently presented with invasive disease, including arthritis, endocarditis, and sudden death. Core-genome phylogenetics resolved two heterogeneous porcine clades separated by long internal branches and clearly distinct from dominant human SDSE lineages. Most porcine isolates were emm-negative or contained structurally altered emm regions compared with human strains. Analysis of Lancefield antigen loci identified a predominant group C lineage and a minority group L lineage, recapitulating historical serogroup distributions described since the early-20th century. Phenotypic testing showed susceptibility to β-lactams and florfenicol but high levels of resistance to tetracycline, macrolides and lincosamides. Detected antimicrobial resistance (AMR) genes correlated well with phenotypes, and multidrug resistance was frequent. Hybrid genome assemblies revealed integrative and mobilizable elements carrying AMR determinants. Collectively, our data indicate that porcine SDSE represents a long-standing, genetically structured, host-adapted population with notable AMR potential, underscoring the need for continued swine SDSE genomic surveillance. Full article

This study investigates the reliability and potential genetic utility of data recorded by automatic milking systems by comparing them with official milk recording data. Analyses focused on phenotypic distributions, correlations, systematic differences, and heritability estimates for milk production and quality traits including milk yield, fat and protein percentage, somatic cell count, and electrical conductivity. Automatic milking system data and official milk recording data shared similar distributions. Correlations between the two systems were high for milk yield (r = 0.93), but moderate for fat (r = 0.52) and protein percentage (r = 0.48), and somatic cell count (r = 0.62), suggesting that while the former provides consistent data for quantity traits, quality-related ones may be less reliable. Systematic deviations between automatic milking systems and official milk recordings emerged across different lactation stages. Heritability estimates based on automatic milking system data were generally higher than the official control for production traits, supporting their use in genetic evaluations. Electrical conductivity displayed a similar heritability to somatic cell count, but its measure is insufficiently detailed and its use as an indirect indicator of udder health is not recommended. Automatic milking system data demonstrates potential for integration into genetic selection programs, although further refinement of sensor accuracy is recommended. Full article

Background/Objectives: Knee osteoarthritis (KOA) is a multifactorial and degenerative disease. Growth differentiation factor 5 (GDF5) polymorphism rs143384 G > A is associated with reduced gene expression and musculoskeletal pathologies. This study aimed to evaluate the association between this functional polymorphism and clinical variability and disease severity among patients with KOA in an admixed population. Methods: This cross-sectional observational study enrolled 224 Brazilian patients with KOA, who were evaluated and classified according to disease severity. Results: The median age was 64 (44–84) years; 75.9% of the patients were female, 50.9% were shorter than 1.60 m, and 67.4% were obese or morbidly obese. The disease severity distribution was 64.7% grades I–III and 35.3% IV–V. Patients with KOA who were over 70 years had significantly more advanced grades (OR = 9.3; 95% CI = 3.4–26), in either female group (OR = 8.2; 95% CI = 2.6–26). The minor allele frequency of the GDF5 rs143384 A variant was 41.7% in the overall KOA case group, increasing with disease severity (39.7% in grades I–III versus 45.6% in IV–V). After adjusting for the confounding factors (age and BMI) the GDF5 GA + AA genotype was significantly associated with higher KOA severity IV–V in female patients (OR = 2.5; 95% CI = 1.2–5.3). Additionally, the mean height of female KOA patients with the GDF5 GA + AA genotype (1.56 ± 0.07 m) was significantly shorter than that of patients with the GG genotype (1.59 ± 0.08 m). Conclusions: The GDF5 rs143384 polymorphism was associated with greater KOA severity and shorter stature in female patients. These results suggest that this variant may contribute to phenotypic variability in patients with knee osteoarthritis, helping to refine clinical characterization and stratification in this population, contributing to personalized diagnoses and guiding future changes in treatment guidelines for knee osteoarthritis. Full article

Stem strength is a key factor influencing lodging resistance in soybeans and other crops. To identify quantitative trait loci (QTLs) associated with stem strength in soybean, we assessed the peak forces required to break a 20 cm stem base segment for each individual within a collection of 2138 plants from eight F₂ and F₃ segregating populations in 2023 and 2024. These populations were derived from four crosses between soybean varieties with contrasting stem strength. Most populations exhibited an approximately normal distribution of stem strength. Using BSA-seq, we identified 17 QTLs associated with stem strength from four populations. Among these, one QTL overlapped with a previously reported locus, while the remaining 16 represented novel loci. Notably, nine loci overlapped with known lodging QTLs, suggesting a genetic relationship between stem strength and lodging. Three QTLs were repeatedly detected in multiple populations, indicating their stability. Further linkage mapping with molecular markers confirmed these three stable QTLs. Among them, qSS10 and qSS19-2 were identified as major QTLs, refined to 1.06 Mb and 1.54 Mb intervals, with phenotypic variation explained (PVE) 23.31–25.15% and 14.21–19.93%, respectively. Within these stable QTL regions, we identified 13 candidate genes and analyzed their sequence variation and expression profiles. Collectively, our findings provide a valuable foundation for future research on stem strength in soybeans and reveal novel genetic loci and candidate genes that may be utilized for the genetic improvement of soybean lodging resistance and yield stability. Full article

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a heterogeneous condition shaped by metabolic dysfunction, adipose tissue distribution, inflammatory activation, and body composition. Understanding how these factors interact across distinct clinical phenotypes is essential for improving diagnostic accuracy and risk stratification. This study aimed to compare metabolic, inflammatory, and elastographic profiles between MASLD subgroups defined by adipose tissue dysfunction (ATD) and obesity, and to identify pathways linking metabolic dysregulation to hepatic fibrosis. Methods: We conducted a cross-sectional observational study including 178 adult participants evaluated clinically, biochemically, and by bioimpedance and shear wave elastography. Participants ranged in age from 19 to 82 years. Patients were stratified into a non-MASLD control group and two MASLD subgroups: MASLD with ATD (G1) and MASLD with obesity (G2). Anthropometric data, lipid profile, glycemic markers, cytokines (IL-6, IL-10, TNF-α), liver stiffness, and non-invasive fibrosis indices were compared across groups using standard statistical testing. Results: Patients with MASLD showed higher liver stiffness, triglycerides, and IL-6/IL-10 levels than controls. Between MASLD phenotypes, the ATD group (G1) exhibited a more inflammatory and dysmetabolic profile, with significantly higher triglycerides, IL-6 levels, neutrophil counts, and creatinine, alongside trends suggesting early sarcopenic changes. In contrast, the obese phenotype (G2) demonstrated greater hepatic structural involvement, including higher liver stiffness and BMI, AST/ALT ratio and Diabetes (BARD) scores, despite more favorable inflammatory parameters. Several associations between liver stiffness, IL-6, and glycemic control approached but did not reach statistical significance. Conclusions: MASLD progression appears to follow two complementary but distinct mechanisms: an inflammatory, adipose dysfunction pathway dominated by IL-6 activation and early anabolic decline, and a metabolic-overload pathway driven by obesity. Phenotype-specific evaluation integrating inflammatory markers, metabolic indices, and elastographic parameters may improve risk stratification and inform personalized therapeutic strategies. Full article

This study presents the phenotypic characterization and genomic mining of uric acid catabolism genes in Lactiplantibacillus plantarum YC, a novel food-grade lactic acid bacterium isolated from traditional fermented vegetables with potent uric acid-lowering activity. YC is non-hemolytic, catalase- and gelatinase-negative, exhibits strong adhesion and broad antibacterial activity, and degrades 29.22% of uric acid in vitro, along with complete (100%) degradation of inosine and guanosine. Whole-genome sequencing revealed a 3,214,448 bp chromosome encoding 3026 protein-coding genes. Comparative genomics-based functional annotation highlighted abundant CAZy-related genes and antimicrobial factors, including lysozyme and monooxygenase. Crucially, genomic mining identified a complete uric acid degradation gene cluster, comprising pucK (uric acid permease), hpxO (uric acid hydroxylase), eight copies of hiuH (5-hydroxyisourate hydrolase), allB (allantoinase), and purine nucleoside transport/metabolism genes (rihA, rihB, rihC, pbuG). This work provides the first comparative genomic insight into the genetic architecture and distribution of uric acid metabolism in L. plantarum, elucidating YC’s dual urate-lowering mechanism and delivering key molecular markers for developing enzyme-based functional foods and microbial therapeutics against hyperuricemia. Full article