Search Results (242)

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches. Full article

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana ‘Miss Manila’. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima’s D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima’s D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of ‘Miss Manila’ are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea. Full article

Background: Influenza A(H3N2) continues to evolve rapidly, frequently eroding population immunity and challenging seasonal vaccine strain selection. During the 2025/26 season, the A(H3N2) subclade K (J.2.4.1) expanded quickly across multiple regions and showed evidence of antigenic divergence in standard assays. Methods: In this study, we combined phylogenetic analyses of hemagglutinin (HA) and neuraminidase (NA) sequences with a systematic synthesis of recent peer-reviewed studies and official surveillance reports to comprehensively define the molecular profile and early epidemiological dynamics of subclade K. Results: Our phylogenetic reconstructions of HA and NA genes confirmed the emergence of a coherent and recently diversified lineage characterized by coordinated evolution of surface glycoproteins and broad geographic representation during 2025. Integration of molecular, temporal, and surveillance evidence further supported rapid expansion with limited early regional structuring. Antigenic analyses reported in peer-reviewed studies described reduced haemagglutination inhibition reactivity to vaccine reference antisera for many subclade K viruses, whereas vaccine effectiveness (VE) estimates from multiple settings remained moderate. Conclusions: Overall, the available genetic, antigenic, and epidemiological evidence indicates that subclade K represents a recently diversified A(H3N2) lineage associated with rapid international spread during the 2025/26 season, highlighting the importance of integrated HA/NA genomic surveillance and timely antigenic characterization to support evidence-based vaccine strain selection. Full article

Background/Objectives: Craniofacial malformations such as orofacial clefts affect ~1 in 700 births; 40–60% lack clear genetic etiology, and many exhibit asymmetry and variable expressivity unexplained by classical Sonic Hedgehog (SHH) morphogen gradient models. We investigated whether integrated molecular modules linking morphogen signaling with metabolic stress responses may better account for craniofacial developmental outcomes. Methods: Sequential UniProt gene set integration identified 186 candidate craniofacial regulators. STRING network analysis revealed modular architecture. Molecular docking profiled 17 compounds against SMO, CK1δ, PINK1, and TIE2 (control). Pathway reconstruction integrated the SHH–CK1δ–HIF1A–HEY1–PINK1 axis with in-silico-predicted CK1δ phosphorylation sites on SMO (S615, T593, S751), HIF1A (Ser247), and GLI1/2/3 transcription factors. A developmental decision tree mapped affinity profiles to node-specific phenotype hypotheses. Results: CK1δ and PINK1 emerged as candidate nodes coupling morphogen signaling with mitochondrial quality control. Cross-docking showed preferential binding to developmental kinases (CK1δ: −8.34 kcal/mol; PINK1: −8.80 kcal/mol) versus TIE2 control (−6.76 kcal/mol; p < 0.001). Pathway reconstruction suggested that CK1δ-mediated Ser247 phosphorylation of HIF1A disrupts ARNT dimerization, redirecting HIF1A toward ARNT-independent HEY1 induction and consequent PINK1 suppression. Based on computed profiles, node-specific associations were proposed as computational hypotheses: SMO perturbation → midline defects; CK1δ → facial asymmetry/clefting; PINK1 → mandibular hypoplasia. Multi-target compounds (e.g., purmorphamine, taladegib) generated composite phenotype predictions consistent with clinical complexity. Conclusions: This strictly in silico study identifies candidate integrated morphogenic modules whose multi-node perturbation may underlie anatomically specific craniofacial malformation patterns. Node–phenotype associations are prioritized computational hypotheses requiring experimental validation; if confirmed, the framework could inform developmental toxicity assessment, therapeutic design, and reclassification of idiopathic craniofacial anomalies. Full article

Objectives: The objective of the study was to investigate the mRNA expression of critical gene patterns, including IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1, and their associations with adverse postoperative outcomes in reconstructive and plastic surgery patients, depending on age. Methods: A total of 95 women participated in this prospective longitudinal cohort study and underwent reconstructive/plastic surgery. The mean age was 35.48 ± 6.61 years (range: 19–57). mRNA expression of IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1 genes was evaluated in peripheral blood leukocytes using a PCR-based method with reverse transcription of cDNA. Results: The risk of postoperative complications significantly increased with elevated expression levels of IL-6 and COL3A1 (7.5-fold, p = 0.007), CCL2 (6.2-fold, p = 0.012), and MAPK1 (25.5-fold, p < 0.001). Increased expression of MAPK8, IL-10, and MMP9 was associated with a 13.2-fold higher risk (p < 0.001). The strongest association was observed for COL1A1 overexpression, which increased complication risk by 58.33-fold (p < 0.001). Risk stratification using the Molecular Complication Risk Index (MCRI), incorporating weighted gene contributions, identified an unfavorable molecular profile predominantly among women aged ≥ 40 years. Receiver operating characteristic analysis confirmed the model’s discriminative ability (AUC = 0.78; 95% CI 0.68–0.87), with an optimal cut-off value of MCRI ≥ 8.5 (sensitivity 76%, specificity 71%, p < 0.05). Conclusions: The transcriptional activity of IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1 is associated with postoperative wound healing risk. Women aged over 40 years are at the highest risk of complications. Implementation of the MCRI model may enable early identification of high-risk patients, support targeted preventive strategies, and improve personalized surgical planning. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

Background/Objectives: Radiotherapy following mastectomy induces persistent structural alterations in the chest wall, including fibrosis, extracellular matrix disorganization, and vascular changes that compromise reconstructive outcomes. Although autologous fat grafting is widely used to improve tissue quality in irradiated breasts, direct human histological evidence remains limited. The aim of this prospective pilot study was to evaluate intra-patient histological remodeling in irradiated postmastectomy breast tissue before and 4 months after autologous fat grafting using paired core needle biopsies. This study should be considered a hypothesis-generating histological pilot study. Methods: Five female patients with prior mastectomy and adjuvant radiotherapy underwent Tru-Cut core needle biopsy of irradiated chest wall tissue before lipofilling and at approximately four months (range between 3 and 12 months) post-procedure. Specimens were processed using formalin fixation, paraffin embedding, and hematoxylin and eosin staining. Histological assessment focused on collagen density, stromal organization, vascular structures, inflammatory infiltrate, and adipocyte integration. Comparative intra-patient analysis was performed descriptively. Results: Baseline biopsies demonstrated consistent post-radiation alterations, including collagen compaction, stromal disorganization, perivascular fibrosis, and variable inflammatory infiltrate. Post-lipofilling specimens showed heterogeneous remodeling characterized by focal collagen fiber insertion between adipocytes, areas of immature connective tissue formation, and variable preservation of adipose architecture. The extent and pattern of remodeling differed among patients. Inflammatory activity decreased or remained mild in most cases. Conclusions: Autologous fat grafting in irradiated postmastectomy tissue is associated with measurable histological remodeling. Structural adaptation appears heterogeneous and patient-specific, suggesting a dynamic multi-stage process rather than uniform regeneration. Further studies incorporating quantitative and molecular analyses are required to clarify the mechanisms underlying these changes. Full article

Background/Objectives: Cardiac embryonic development is a highly coordinated and dynamic process governed by precise spatiotemporal gene regulation. Increasing evidence indicates that cellular heterogeneity and lineage specification during heart development are tightly controlled by complex gene regulatory networks (GRNs) and epigenetic mechanisms. Recent advances in single-cell multi-omics technologies provide unprecedented resolution to dissect these regulatory processes. This review aims to summarise current applications of single-cell multi-omics approaches to elucidate gene regulatory mechanisms underlying cardiac embryogenesis and their implications for congenital heart disease (CHD). Methods: We systematically reviewed recent literature on single-cell RNA sequencing (scRNA-seq), single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), spatial transcriptomics, and integrative multi-omics analyses applied to embryonic heart development. Studies were analysed to evaluate how these technologies contribute to cell-type identification, lineage trajectory reconstruction, GRN inference, and epigenetic landscape characterisation. Results: Single-cell multi-omics approaches have enabled the construction of high-resolution cardiac cell atlases, revealing previously unrecognised cellular heterogeneity and transitional states during heart development. Integrative analyses of transcriptomic and chromatin accessibility data have provided insights into lineage commitment, key transcription factors, enhancer–promoter interactions, and dynamic GRNs. These findings have advanced understanding of developmental genetics in cardiac morphogenesis and offered new perspectives on the molecular mechanisms underlying CHD. Conclusions: Single-cell multi-omics technologies provide a powerful framework for investigating gene regulatory mechanisms during cardiac embryogenesis. Continued methodological refinement and integrative analyses are expected to further clarify developmental processes and facilitate translational insights into CHD. Full article

Background: Velvet worms (Onychophora) occupy a pivotal phylogenetic position for deciphering the evolution of Panarthropoda, yet their exact placement within this clade remains debated. Furthermore, early studies in some onychophoran species revealed extensive gene rearrangements and the truncation or even loss of canonical transfer RNAs (tRNAs), features uncommon in other panarthropods. However, due to sparse representation, the pervasiveness and evolutionary significance of these genomic peculiarities across the phylum remain poorly understood. Methods: We sequenced and assembled three novel mitogenomes representing both extant onychophoran families (Epiperipatus barbadensis [Peripatidae]; Euperipatoides rowelli and Phallocephale tallagandensis [Peripatopsidae]) and conducted comparative analyses with five published species. Results: Onychophoran mitogenomes displayed high A+T content (mean 77.32%) but revealed a family-level divergence in GC skew. All genomes contained the standard 13 protein-coding genes (PCGs) and two ribosomal RNAs, yet tRNA counts varied significantly (ranging from 13 to 22), reflecting lineage-specific tRNA loss. Ancestral state reconstruction uncovered deep architectural divergence: Peripatopsidae retains the ancestral onychophoran gene arrangement, whereas Peripatidae exhibits a stable but derived gene order. Despite this architectural plasticity, synonymous codon usage patterns remained strictly conserved across the phylum, with all but one PCG evolving under strong purifying selection. Maximum likelihood phylogenetic reconstruction based on PCGs strongly supported Onychophora as the sister group to Arthropoda within Panarthropoda. Conclusions: Our findings provide robust molecular evidence supporting the Antennopoda hypothesis over the Tactopoda hypothesis for Panarthropoda phylogeny. Furthermore, we demonstrate extensive mitogenomic remodeling between the two extant onychophoran families, including divergent GC-skew patterns, tRNA contents, and gene arrangements. Full article

Background/Objectives: Mitochondrial DNA (mtDNA) is an important resource for understanding human ancestry, population diversity, and the molecular mechanisms of mitochondrial diseases. However, analyzing mtDNA thoroughly often requires advanced bioinformatics skills and command-line knowledge. To address this challenge, we created Mitochondrial Genome Explorer (MitoGEx), a user-friendly computational pipeline optimized for human mtDNA analysis that combines multiple mtDNA analysis modules within a single graphical user interface. Methods: The platform simplifies key analytical steps, such as quality control, sequence alignment, alignment quality assessment, variant detection, haplogroup classification, and phylogenetic reconstruction. Users can choose between Quick and Advanced modes, which offer default settings or customizable options based on their analysis needs. To demonstrate its effectiveness, we analyzed 15 whole-exome sequencing (WES) samples from Songklanagarind Hospital using MitoGEx. Results: The sequencing data were of high quality, with over 92 percent of bases scoring above a Phred score and consistent GC content across all samples. Variant detection using the GATK mitochondrial pipeline and annotation with ANNOVAR and the MitImpact database revealed multiple high-confidence variants. Haplogroup classification with Haplogrep 3 and phylogenetic analysis with IQ-TREE 2 confirmed diverse maternal lineages within the cohort. Conclusions: Taken together, MitoGEx facilitates mitochondrial genome analysis in a reproducible and accessible manner for both research and clinical bioinformatics applications. The analytical results produced by MitoGEx are concordant with those obtained using standalone bioinformatic tools, demonstrating analytical correctness. By integrating all analysis steps into a single automated workflow, MitoGEx reduces execution time and limits human error inherent to manual, multi-step pipelines. Full article

Background/Objectives: We analyzed the whole-genome sequences of ciprofloxacin-resistant (CIP-R) enteropathogenic Escherichia coli (EPEC) ST752 isolates in South Korea to characterize their molecular epidemiology. This lineage has emerged as the predominant CIP-R EPEC clone in South Korea, accounting for 28.8% of human clinical isolates and circulating within the One Health interface. Methods: We performed whole-genome sequencing (WGS) and reference-based core-genome single-nucleotide polymorphism (SNP) analysis on 26 CIP-R EPEC ST752 isolates (19 human clinical and 7 poultry-derived isolates). To elucidate their evolutionary history and transmission dynamics, Bayesian phylodynamic and phylogeographic reconstructions were implemented by integrating domestic isolates with a global genome dataset (n = 508). Results: Isolates from human and poultry sources clustered together with an identical virulence profile and minimal genetic distance. The Bayesian molecular clock analysis estimated that the time to the most recent common ancestor of the South Korean clade was 2000.65. Moreover, the phylogeographic analysis supported statistical evidence (Bayes factor 32.16) for the introduction of this lineage into South Korea from Denmark and revealed a strongly supported host transition from humans to poultry (Bayes factor > 10,000), although this requires cautious interpretation due to limited temporal sampling of poultry isolates. Conclusions: Continued integrated One Health surveillance across human, animal, and environmental reservoirs is needed to monitor and prevent the spread of high-risk antimicrobial-resistant clones. Full article

Microbial fermentation is attracting attention as a key process in reconstructing the profile of functional components in foods. This review summarizes the main mechanisms by which microbial fermentation generates antioxidants and functional compounds in fermented dairy products. In particular, we focus on (i) the production of bioactive peptides driven by fermentation-induced proteolysis, (ii) modulation of reactive oxygen species (ROS) homeostasis associated with shifts in metabolite composition, and (iii) the remodeling of organic acids, fatty acids, and other low-molecular-weight metabolites. We also discussed an analytical framework for evaluating antioxidant function in various analytical methods such as the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay, 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, and ferric reducing antioxidant power (FRAP) assay, as well as cell-based measurements of reactive oxygen species (ROS)/nitric oxide (NO) and determining oxidative damage in animal models. Overall, the antioxidant functionality of fermented dairy products should be understood not merely as an increase in radical-scavenging capacity but as the outcome of fermentation-driven molecular remodeling and physiological regulatory effects. This review defines fermented dairy products as functional foods, highlighting the need for an omics-based approach in future fermented food studies. Full article

Background and Objectives: The biological state of anterior cruciate ligament (ACL) remnant tissue may influence postoperative healing, yet the molecular changes associated with injury chronicity remain poorly defined. This study evaluated MMP-13 and TGF-β1 expression in human ACL remnants to characterize their regenerative or fibrotic potential. Materials and Methods: ACL remnants from acute (<3 months) and chronic (>6 months) injuries were analyzed using histology, immunohistochemistry, and QuPath-based digital quantification. Clinical outcomes were correlated with marker expression. Protein–protein interaction and KEGG enrichment analyses were performed to identify extracellular matrix (ECM)-related pathways associated with MMP-13 and TGF-β1. Results: Chronic ACL remnants exhibited disorganized ECM structure with significantly higher MMP-13 and TGF-β1 expression across all digital metrics, including DAB-positive area, cell density, optical density, and H-score (p < 0.01). Higher expression of both markers correlated with lower IKDC and Lysholm scores and greater residual pivot-shift positivity. Bioinformatic analysis identified 39 shared proteins enriched in ECM-receptor interaction, TGF-β signaling, and fibrosis-related pathways, aligning with the degenerative phenotype observed in chronic tissue. Conclusions: ACL remnant biology evolves from a reparative profile in acute injuries to a fibrotic, matrix-degradative state in chronic injuries. MMP-13 and TGF-β1 serve as indicators of remnant quality and may help guide timing of surgery and future biologic strategies aimed at improving ACL reconstruction outcomes. Full article

The reconstruction of biological profiles from aged or degraded human skeletal remains represents a major challenge in both forensic and bioarcheological contexts, particularly when conventional identification approaches fail. Recent advances in molecular genetics, biochemical and histological analyses, and biomolecular anthropology have substantially expanded the range of information that can be recovered from compromised remains. This review synthesizes current integrative approaches combining genomic analyses, stable isotope investigations, epigenetic age estimation, proteomic sex determination, and complementary histological techniques to infer sex, ancestry, kinship, age, diet, mobility, and geographic origin. Genetic methods, including next-generation sequencing (NGS), enable increasingly robust inference even from highly degraded samples. Stable isotope analyses provide insights into dietary patterns and mobility, while DNA methylation markers improve age estimation accuracy. Tooth cementum annulation (TCA), although a histological rather than molecular method, contributes an additional chronological indicator within an integrative analytical framework. Rather than treating these approaches independently, this review proposes a multidisciplinary perspective in which complementary datasets collectively support biological profile reconstruction. Integrative interpretation enhances identification potential and provides more nuanced life-history reconstructions, demonstrating the value of combining molecular, biochemical, and histological evidence in forensic and archaeological investigations. Full article

While advanced imaging techniques and ordered porous materials like MOFs have gained prominence, gas sorption remains the indispensable tool for characterizing the multiscale heterogeneity of industrially important disordered solids, such as catalysts and shales. This review examines recent developments in gas sorption methodologies specifically tailored for rigid, disordered porous media. We discuss experimental advances, including the choice of adsorbate and the utility of the overcondensation method for probing macroporosity and ensuring saturation. Furthermore, we critically evaluate theoretical approaches for determining pore size distributions (PSDs), contrasting classical methods with Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) simulations. Special emphasis is placed on the impact of pore-to-pore cooperative effects, such as advanced condensation, cavitation, and pore-blocking, on the interpretation of sorption isotherms. We highlight how complementary techniques, including integrated mercury porosimetry, NMR, and computerized X-ray tomography (CXT), are essential for deconvolving these complex network effects and validating void space descriptors. We conclude that, while “brute force” molecular simulations on image-based reconstructions are progressing, “minimalist” pore network models, which incorporate cooperative mechanisms, currently offer the most empirically adequate approach. Ultimately, gas sorption remains unique in its ability to statistically characterize void spaces from Angstroms to millimeters in a single experiment. Full article