Search Results (13,110)

Seasonal human coronaviruses (HCoVs) continue to undergo adaptive evolution under structural and immune-mediated constraints. We investigated the molecular epidemiology and spike (S) protein structural variation of circulating coronaviruses in Riyadh, Saudi Arabia, during the 2025–2026 winter season, with particular emphasis on genotype persistence and glycosylation architecture in HCoV-OC43. Among 293 nasopharyngeal aspirates (NPAs) collected from hospitalized patients with acute respiratory illness, HCoV-OC43 was detected in 26 cases (8.87%), whereas other seasonal coronaviruses were not identified. Partial sequencing of the S gene revealed 97.84–98.23% nucleotide identity relative to the prototype strain VR-759, with amino acid substitutions distributed at discrete positions rather than within extended variable domains, indicating structural conservation. Phylogenetic reconstruction demonstrated that all Riyadh isolates clustered within genotype C, together with previously circulating local strains, supporting sustained endemic persistence and in situ evolution. In silico analysis of the S protein glycosylation landscape identified four invariant N-linked glycosylation motifs (N-X-S/T) at residues 46, 121, 134, and 190, reflecting strong structural constraints on glycan-dependent folding and antigenic configuration. A genotype-associated K68N substitution generated an additional N-glycosylation motif (68NGTD) in multiple Riyadh isolates, potentially modifying local glycan shielding without disrupting the overall glycosylation framework. The preservation of core glycosylation sites alongside selective motif acquisition suggests evolutionary fine-tuning of S surface topology rather than large-scale structural remodeling. Collectively, these findings indicate that genotype C persistence in Riyadh is accompanied by conserved S architecture and subtle glycosylation adjustments that may modulate immune recognition while maintaining structural integrity. Continued high-resolution molecular surveillance will be critical for defining the functional consequences of S microevolution in endemic HCoVs. Full article

Multicellular cancer cell aggregates, termed spheroids, are anoikis-resistant, avascular, heterogeneous structures responsible for transcoelomic metastasis of ovarian clear cell carcinoma (OCCC). OCCC is a rare subtype of ovarian cancer with high ARID1A gene mutation rates, resulting in genome-wide changes to H3K27Ac levels and histone deacetylase (HDAC) function. Our study investigated the utility of HDAC inhibitor (HDACi) treatment and H3K27Ac dynamics in OCCC spheroids. By comparing KOC-7c and 105C OCCC cell lines, which have opposing abilities to proliferate as spheroids, we revealed that KOC-7c and 105C spheroids differentially regulated H3K27Ac levels, which correlated with the sensitivity of KOC-7c and the resistance of 105C spheroids to H3K27Ac-altering HDACi treatment. RNA-seq of Entinostat-treated versus vehicle-treated spheroids resulted in a dramatic change in the 105C spheroid transcriptome such that it more closely resembled the proliferative KOC-7c transcriptome over the short term. Comparative pathway analysis identified preferential de-repression of a G2/M checkpoint gene program in 105C spheroids upon Entinostat treatment when compared directly to the KOC-7c spheroids. Our results suggest that the utility of HDACi in OCCC is highly context-dependent. Full article

Virus-like particles (VLPs), nanoscale self-assembled structures lacking viral genetic material, have emerged as a versatile platform for vaccines, targeted delivery systems, and gene-editing applications owing to their strong immunogenicity, favorable biosafety profile, and high engineerability. However, the complex architecture of VLPs, their significant size heterogeneity, and the diversity of process- and product-related impurities generated in different expression systems make downstream purification a major bottleneck limiting product quality, yield, and manufacturability. This review systematically discusses advanced downstream purification strategies for VLPs from the perspective of three major objectives: preservation of structure and biological activity, control of product heterogeneity, and assurance of viral safety. First, strategies for maintaining VLP integrity and function are examined, including optimization of solution conditions, adoption of gentle yet efficient separation operations, and integration of process analytical technology (PAT) to reduce process-induced damage. Second, the review summarizes multi-step purification approaches—spanning clarification, ultrafiltration/diafiltration (UF/DF), chromatography, and disassembly/reassembly—to remove host cell proteins, host cell DNA, and product-related impurities while improving particle homogeneity and stability. Third, viral safety is discussed primarily from the perspective of downstream virus clearance under host-dependent risk, with particular attention to orthogonal clearance steps tailored to VLP properties and expression systems such as CHO cells and insect cell–baculovirus platforms. Overall, this review provides a CQA-oriented framework and practical guidance for the development of robust, scalable, and GMP-compliant downstream purification processes for VLP-based products. Full article

Bisphenol A (BPA) is a widely used endocrine-disrupting chemical that has been linked to oxidative stress and inflammation. This study investigated whether carvacrol (CAR), a natural monoterpene with antioxidant potential, mitigates BPA-induced hepatorenal toxicity in rats. Forty-two male Wistar albino rats were allocated into six groups (n = 7/group): control, vehicle (corn oil), BPA (25 mg/kg/day), and BPA co-administered with CAR (12.5, 25, or 50 mg/kg/day) by oral gavage for 30 days. Oxidative status was assessed in liver and kidney homogenates by measuring malondialdehyde (MDA), reduced glutathione (GSH), and the activities of superoxide dismutase (SOD) and catalase (CAT). In addition, histopathological evaluations were performed, and pro-inflammatory gene expression (NF-κB, TNF-α, and IFN-γ) was quantified by RT-qPCR. BPA induced a consistent pro-oxidant pattern, including increased hepatic MDA with depleted antioxidant defenses, and upregulated inflammatory transcripts. Carvacrol attenuated these alterations in a dose-dependent manner, and the CAR50 group was associated with statistically supported improvements across the oxidative stress panel, pro-inflammatory transcript expression, and histopathology scores. Overall, these findings identify carvacrol as a candidate for further preclinical evaluation against BPA-triggered oxidative and inflammatory disturbances in vivo; however, human-relevant extrapolation will require careful attention to dose scaling, bioavailability, and metabolism. Full article

Endometriosis and endometrial cancer are distinct gynecological conditions that share overlapping biological mechanisms with implications for clinical management. Endometriosis is a chronic, benign disorder characterized by the ectopic implantation of functional tissue lining the uterus, primarily affecting women of reproductive age. It commonly causes chronic pelvic pain, dysmenorrhea, dyspareunia, and infertility. The disease is marked by persistent inflammation, hormonal dysregulation, and alterations in cellular signaling, which mirror some neoplastic processes despite lacking malignant potential. Endometrial cancer is a malignant tumor of the uterine lining, most frequently diagnosed in postmenopausal women. Its incidence is rising due to aging, obesity, and prolonged estrogen exposure. Epidemiological studies suggest a modest increase in endometrial cancer risk among women with endometriosis. However, detection bias and metabolic confounders may influence this association. Both conditions share estrogen dependence, chronic inflammatory microenvironments, and dysregulated pathways such as PI3K/AKT/mTOR. Somatic mutations in genes, including PTEN and ARID1A, further underline molecular intersections. Clinical management is tailored to disease type and severity. Endometriosis therapy emphasizes stepwise hormonal treatment, multidisciplinary pain management, and surgery when indicated. Endometrial cancer management relies on staging, with particular emphasis on molecular classification and histopathology to guide surgery, radiotherapy, chemotherapy, hormone therapy, and immunotherapy in advanced cases. Emerging noninvasive biomarkers and precision medicine strategies may enhance diagnosis, monitoring, and targeted treatment in both conditions. Understanding their shared and divergent mechanisms aids risk stratification, individualized therapy, and improved quality of life. Further prospective studies are needed to optimize patient-specific management and translate mechanistic insights into clinical practice. Full article

This study compared the wound-healing response and osteogenic gene expression profile of osteoblasts exposed to pediatric-equivalent concentrations of dexmedetomidine (DXMT) and propofol (POF). Human osteoblast-like SAOS-2 cells were assigned to control, low- and high-dose DXMT and POF groups based on pharmacokinetically derived free-drug levels. Scratch-wound closure was quantified over 24 h, and expression of osteogenesis- and cytoskeleton-related genes (RANKL, RUNX2, SP7, BMP2, VIM, VCL, OCN, ALP) was measured by SYBR Green quantitative Polymerase Chain Reaction (qPCR). Normality was assessed using the Shapiro–Wilk test, and group differences were analyzed with two-way ANOVA followed by Tukey’s multiple comparisons test (p < 0.05). All groups demonstrated complete scratch closure by 24 h, with no differences at 6 h. At 18 h, POF did not differ from the control, whereas DXMT significantly accelerated closure at both doses in a dose-dependent fashion. High-dose DXMT significantly increased VIM (3.95 ± 3.12, p = 0.0144) and BMP2 (2.28 ± 0.70, p = 0.0002) expression, while RUNX2, SP7, and RANKL remained comparable to controls. ALP (1.68 ± 0.40, p = 0.0005) and OCN (3.31 ± 0.35, p = 0.0108) were significantly elevated only in the high-dose DXMT group, whereas POF showed no significant effects. At clinically relevant concentrations, DXMT was associated with enhanced scratch closure and increased expression of selected osteogenesis- and cytoskeleton-related genes in SAOS-2 cells, whereas POF showed limited effects under the tested conditions. These findings suggest that DXMT may influence early in vitro cellular responses relevant to bone healing and should be further validated in functional differentiation models and in vivo studies. Full article

Background/Objectives: Neuritogenesis and synaptogenesis support learning and cognitive function, and hippocampal neurons play central roles in these processes. Cleistocalyx nervosum var. paniala (CNP), a Southeast Asian berry, has reported neuroprotective activities, but its direct effects on hippocampal neurons remain unclear. We investigated whether CNP extract modulates hippocampal neuronal transcriptomes, neuritogenesis, and synaptogenesis. Methods: Primary hippocampal neurons isolated from male and female Wistar rat pups were treated with CNP extract in vitro. Cytotoxicity was assessed to define non-cytotoxic concentrations. Transcriptomic responses were profiled by RNA sequencing and validated by RT-qPCR. Neuritogenesis was quantified by neurite morphology and Sholl analysis. Synaptogenesis was evaluated by synaptic immunocytochemistry. Molecular docking of cyanidin-3-glucoside (C3G) and resveratrol was used to generate mechanistic hypotheses. Results: At 0.1–10 µg/mL, CNP was non-cytotoxic, whereas a 100 µg/mL dose reduced viability; therefore, 10 µg/mL was used in subsequent experiments. Exploratory RNA-seq profiling identified thousands of differentially expressed genes enriched in synapse- and neurite-related pathways, including synaptogenesis signaling, axon guidance, and neuritogenesis. RT-qPCR showed upregulation of Igf1 in males and Glul in females, with sex-dependent modulation of Bdnf and Cask. CNP increased neurite length, branching, and Sholl complexity in both sexes, with a more pronounced effect in males. A male-biased effect was also observed in synapse-related marker colocalization, with increased Syn1–Psd95 colocalization detected in males. Docking suggested plausible interactions of C3G and resveratrol with regulators such as MYC, TP53, and CREB1. Conclusions: CNP extract alters transcriptional networks and enhances neurite outgrowth in primary hippocampal neurons in a sex-dependent manner, with male-biased effects on Syn1–Psd95 colocalization. These findings support further dose–response, mechanistic, and sex-stratified in vivo studies to evaluate its neurobiological potential. Full article

Leaf-color variation in plants should be associated with chlorophyll metabolism and chloroplast development. Here, we characterized a low-temperature-sensitive pakchoi DH line, 1197, which exhibited green leaves at 25 °C, but showed yellowing at 4 °C. Low temperature significantly reduced chlorophyll accumulation and disrupted chloroplast ultrastructure. After transfer from 4 °C to 25 °C for 7 days, yellow leaves partially regreened, and chlorophyll a content increased by 366.67%. RNA-seq analysis identified 3058 core DEGs associated with the yellowing–regreening transition, which were significantly enriched in photosynthesis–antenna proteins, photosynthesis, and porphyrin metabolism pathways. Leaf yellowing was characterized by repression of chlorophyll biosynthesis genes (e.g., CHLD, CHLM, PORC) and induction of degradation genes (SGR1, SGR2, NYC1, PAO), together with widespread downregulation of chloroplast function-related genes. In addition, GLK2, HBI1, NAC047, and NAC029 were identified as candidate regulators of temperature-dependent leaf-color conversion. This study provides candidate molecular insights into low-temperature-induced yellowing and regreening in pakchoi and offers candidate genes for future functional validation and Brassica breeding. Full article

Low temperature critically influences cellular metabolism by impairing processes such as membrane fluidity, enzyme activity, and protein folding. However, the comprehensive genetic landscape and regulatory mechanisms governing cold acclimation remain poorly understood. Here, we performed high-throughput, pooled genetic screening in the model alga Chlamydomonas reinhardtii (C. reinhardtii) to identify genes essential for cold acclimation. Our screening revealed numerous candidate genes implicated not only in early cold response pathways but also in core cellular processes, including DNA dynamics, protein homeostasis, metabolic regulation, and substrate transport. Notably, we identified a member of the RUS (ROOT UVB SENSITIVE) family, encoding a conserved DUF647 domain protein, designated CrRUS1. CRISPR-generated rus1 mutant alleles in C. reinhardtii display a phenotype consistent with our screening: the mutants did not exhibit any visible growth defects, but show severe growth defects at low temperature. Interestingly, the cold-induced phenotypic changes in rus1 can be reversed by dark conditions, suggesting that CrRUS1 likely promotes cold acclimation in C. reinhardtii through a light-dependent pathway. Our work provides novel genetic resources and mechanistic insights into cold acclimation in C. reinhardtii, with potential translational relevance for enhancing cold tolerance in crop species. Full article

Osteoarthritis (OA) is a complex degenerative joint disease for which early diagnosis and clear molecular characterization remain limited. DNA methylation has been increasingly recognized as an important regulatory factor in OA pathogenesis. In this study, we proposed an integrative computational framework combining statistical analysis, machine learning, deep learning, and functional genomics to identify and validate OA-associated genes and methylation biomarkers for diagnostic and biological interpretation. Candidate CpG sites were obtained using two complementary strategies: differential methylation analysis and selection of loci located near transcription start sites of previously reported OA-related genes. Key features were further refined using support vector machine recursive feature elimination and random forest algorithms. Based on the selected loci, we developed a feature-fusion diagnostic model that combines Transformer and convolutional neural networks with adaptive weighting to capture both global dependency structures and local methylation patterns. A panel of 220 methylation sites demonstrated stable and reproducible diagnostic performance in an independent cohort. Functional annotation and pathway analysis highlighted several established OA-associated genes, including TGFBR2, SMAD3, PPARG, and MAPK3, and suggested INHBB as a potential novel effector gene, with additional support for AMH and INHBE involvement. Overall, this study presents a robust methylation-based framework for identifying key OA-associated genes and provides new insights into the epigenetic mechanisms underlying OA. Full article

In an era marked by rising stress-related disorders and cardiovascular morbidity, understanding how the brain and heart adapt to environmental, physiological, and social stressors has become an urgent biomedical priority. This review advances an integrative framework centered on sociostasis, defined as the dynamic regulation of physiological state through social interaction, and its intersection with hormesis, a biphasic adaptive response to controlled stress that enhances resilience. We focus on four evolutionarily conserved neuropeptides, vasopressin, oxytocin, corticotropin-releasing hormone, and the urocortins, which serve as molecular bridges linking social behavior, neuroendocrine signaling, autonomic regulation, and cardiovascular function. Operating within an organized autonomic architecture, these systems calibrate responses to acute and chronic stress. Their context-dependent synergy enables adaptive flexibility under manageable challenge but may promote maladaptive cardiovascular remodeling when chronically dysregulated. Genetic vulnerability, developmental adversity, and persistent psychosocial stress can shift neuroendocrine–autonomic set points, increasing susceptibility to hypertension, endothelial dysfunction, and stress-induced cardiomyopathy. Conditioning and preconditioning paradigms illustrate how repeated exposure to subthreshold stressors primes cardiovascular tissues for future insults, enhancing ischemic tolerance and adaptive gene expression. We propose that cardiovascular hormesis depends not only on stimulus intensity but also on the integrity of neuroautonomic regulatory mechanisms that support recovery and flexibility. Vagal efficiency, a dynamic index of cardioinhibitory regulation, is discussed as a potential translational metric of adaptive capacity. By integrating molecular, physiological, and psychosocial perspectives, this framework conceptualizes cardiovascular resilience as an emergent property of coordinated hormetic signaling, neuropeptidergic modulation, autonomic regulation, and social buffering. Translational implications include peptide-based therapies, autonomic biofeedback, and behavioral interventions designed to enhance stress adaptability. Full article

Background: Aging is the strongest risk factor for prostate cancer (PCa). It is accompanied by progressive epigenomic divergence, known as epigenetic drift, particularly affecting DNA methylation at regulatory regions. However, the extent to which age-associated promoter methylation contributes to coordinated microRNA (miRNA) expression changes in PCa remains incompletely characterized. Methods: We conducted an integrative in silico analysis of 449 primary tumors from the TCGA-PRAD cohort. Age was modeled as a continuous variable. Age-related miRNA expression changes were estimated from miRNA-seq data using DESeq2. Promoter DNA methylation changes (±2 kb from transcription start sites) were assessed using Illumina 450K arrays and linear regression. MiRNAs showing significant age-associated alterations at both expression and methylation levels were classified as concordant or discordant based on directionality and prioritized using an effect size-based concordance score. We analyzed experimentally validated targets of prioritized miRNAs through functional enrichment and network-based approaches to identify convergent regulatory pathways. Results: Initially, we identified 105 age-associated miRNAs. After filtering, 65 candidates remained. Of these, we found 37 miRNAs with significant age-associated changes at both layers, including 20 concordant and 17 discordant miRNAs. These comprised well-characterized cancer-associated miRNAs and lesser-studied candidates enriched in CpG-rich regulatory regions. Network analyses revealed a limited set of genes under convergent regulation by multiple age-associated miRNAs. These implicated pathways are related to cell cycle control, apoptosis, stress response, and epigenetic regulation. Conclusions: Our findings support a model in which age-dependent promoter methylation drift contributes to coordinated miRNA deregulation in PCa. This convergence highlights biologically plausible miRNA biomarkers and age-sensitive epigenetic circuits relevant to prostate carcinogenesis. Full article

Streptococcus parauberis is a major pathogen responsible for streptococcosis in both marine and freshwater fish species, causing substantial economic losses in aquaculture. The increasing prevalence of multidrug resistance has highlighted the urgent need for alternative disease control strategies. Interference with bacterial quorum sensing (QS) systems represents a promising approach. This study aimed to identify and biochemically characterize an Rgg-family transcriptional regulator and evaluate its potential as a target for quorum sensing-related regulatory interference in vitro. We hypothesized that this Rgg regulator may function as a quorum sensing-associated transcription factor capable of promoter binding and modulation by small molecules. Bioinformatic analyses were used to identify the rgg gene encoding an Rgg-family transcriptional regulator and predict its structural features. The gene was cloned, heterologously expressed, and purified. Promoter binding activity was examined using electrophoretic mobility shift assay (EMSA), and key amino acid residues were identified through site-directed mutagenesis. The inhibitory effect of the cyclic peptide cyclosporin A (CsA) on Rgg-promoter binding was further assessed. The rgg gene (864 bp) encoding a 287-amino-acid protein (34.1 kDa) was successfully identified and expressed. Purified Rgg specifically bound to its own promoter region in a concentration-dependent manner. Mutations at conserved arginine residues R12 and R15 within the helix-turn-helix DNA-binding domain abolished promoter binding activity. Furthermore, CsA disturbed Rgg-promoter binding in a dose-dependent manner. This study provides the first in vitro characterization of an Rgg-family transcriptional regulator in fish-derived S. parauberis. The findings expand current understanding of Rgg-family regulators potentially associated with quorum sensing in aquatic streptococci and provide a preliminary basis for further investigation of quorum sensing-related regulatory interference strategies for controlling streptococcal diseases in aquaculture. Full article

The safe and precise regulation of therapeutic gene expression remains a major challenge for mammalian synthetic biology and cell-based therapies. Many existing inducible systems rely on non-mammalian regulatory components or ligands with limited clinical compatibility. Designer receptors exclusively activated by designer drugs (DREADDs) offer a human G protein-coupled receptor (GPCR)-based framework for pharmacological control of intracellular signaling, yet their application as clinically relevant gene-regulation platforms remains underexplored. Here, we report a clozapine-responsive gene switch that couples a designer GPCR to signaling-dependent transcriptional control. By linking clozapine-activated receptors to cyclic adenosine monophosphate (cAMP)- or calcium-responsive synthetic promoters, receptor activation is converted into robust transgene expression across a broad dynamic range, with sensitivity to sub-nanomolar to low-nanomolar clozapine concentrations. In vivo, alginate-encapsulated reporter cells implanted in C57BL/6J mice responded to systemic or local clozapine administration with efficient secretion of a reporter protein, achieving robust induction at low daily doses (0.3 mg/kg) following either oral administration or local delivery. Together, these results establish a human GPCR-based clozapine-responsive gene switch that integrates regulation by a clinically used small molecule with modular transcriptional outputs, providing an additional approach for pharmacologically controllable gene expression in mammalian cells and in vivo. Full article

Background/Objectives: The impact of antimicrobial susceptibility testing methodology on the categorization and positioning of cefiderocol and aztreonam-avibactam against metallo-β-lactamase (MBL)-producing Gram-negative bacilli remains unclear. This study aimed to evaluate the in vitro activity of cefiderocol and aztreonam-avibactam against clinical MBL-producing isolates and to assess the agreement between different cefiderocol susceptibility testing methods. Methods: A total of 299 non-duplicate clinical MBL-producing Gram-negative isolates were collected from clinical samples between 2022 and 2025. Antimicrobial susceptibility testing was performed using broth microdilution, disc diffusion, and gradient strip diffusion according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Carbapenemase genes were identified by immunochromatography and multiplex PCR. Categorical agreement and error rates between cefiderocol testing methods were analyzed. Results:Klebsiella pneumoniae was the predominant species, mainly producing NDM alone or in combination with OXA-48-like carbapenemases. Aztreonam-avibactam demonstrated complete activity against all Enterobacterales isolates (262/262, 100%) and high activity against Pseudomonas spp. (33/37, 89%). Cefiderocol susceptibility among Enterobacterales varied markedly depending on the testing method. Disc diffusion yielded 14% susceptibility (37/262), which increased to 52% (136/262) after ATU resolution, whereas broth microdilution showed 85% susceptibility (224/262). This resulted in low categorical agreement (42%) and a high rate of major errors (58%), with no very major errors detected. Cefiderocol activity did not differ substantially across carbapenemase types and was highest against VIM-producing Pseudomonas spp. Conclusions: Aztreonam-avibactam showed consistent in vitro activity against MBL-producing Enterobacterales, whereas cefiderocol activity was strongly influenced by the susceptibility testing methodology. Disc diffusion substantially underestimated cefiderocol susceptibility compared with broth microdilution. These findings highlight the critical impact of testing methodology on cefiderocol categorization and support the therapeutic role of last-line agents in the management of MBL-producing Gram-negative infections, with direct implications for clinical microbiology laboratories and antimicrobial stewardship programs. Full article