Search Results (265)

Background: Urothelial bladder cancer (UBC) is a molecularly heterogeneous disease, and most sequencing studies have relied on bladder-specific or solid tumor-restricted panels. Whether broader pan-cancer assays provide additional clinically relevant information remains unclear. Methods: We performed targeted next-generation sequencing using an extended gene panel on tumor samples from 100 patients with UBC treated at a tertiary center. Somatic single-nucleotide variants, small insertions/deletions, copy-number alterations, and gene co-occurrence patterns were analyzed and correlated with clinicopathological features, disease-free survival (DFS), and overall survival (OS). Results: Recurrent alterations were identified in FGFR3 (≈50%), TP53 (≈35%), STAG2 (≈25%), and PIK3CA (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in BRCA1 and ALK, were also detected, reflecting the extended coverage of the panel. TP53 mutations were independently associated with worse OS, whereas STAG2 alterations were associated with improved OS, particularly in tumors without concurrent TP53 mutations. FGFR3 mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an FGFR3/PIK3CA-associated pathway and relative mutual exclusivity between FGFR3 and TP53. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of FGFR3 alterations in our cohort, likely reflecting the larger proportion of non–muscle-invasive tumors. Conclusions: Pan-cancer targeted sequencing provided a comprehensive genomic landscape of UBC, capturing canonical drivers and additional alterations that may be overlooked by bladder-restricted assays. The identification of TP53 and STAG2 as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer. Full article

(1) Background: Swine hepatitis E (SHE) is an emerging zoonotic disease caused by the swine hepatitis E virus (SHEV). The open reading frame 3 (ORF3) protein is a recognized virulence factor of SHEV. Jaundice, the typical clinical sign of SHE, primarily results from disruptions in bile production, secretion, and excretion. However, the mechanism by which SHEV ORF3 influences bile metabolism remains unclear. (2) Methods: Building on our previous work involving adenovirus-mediated overexpression of genotype IV SHEV ORF3 in HepG2 cells and subsequent high-throughput lncRNA/transcriptome sequencing, this study performed KEGG enrichment analysis on differentially expressed lncRNAs. Candidate lncRNAs were validated via qRT-PCR. Cis-regulated target genes were predicted by integrating differentially expressed mRNA data. Furthermore, AlphaFold 3.0 was employed to analyze the molecular binding sites between lncRNA UBC (MSTRG.6881.4) and its target, UBC protein. (3) Results: We identified three lncRNAs associated with the bile secretion pathway (ko 04976) in HepG2 cells expressing genotype IV SHEV ORF3, which were further confirmed by qRT-PCR: lncRNA UBC (MSTRG.6881.4), lncRNA UBC (MSTRG.6881.9), and lncRNA UBC (MSTRG.6881.12). Bioinformatics prediction suggested six lncRNA-mRNA regulatory networks involved these lncRNAs and two downregulated UBC mRNA transcripts (ENST00000540700 and ENST00000536769). Molecular docking indicated that nucleotides 395U and 41C of lncRNA UBC (MSTRG.6881.4) could potentially bind to residues 82Lys, 88Thr, and 90Thr of the UBC protein, with predicted binding energies ranging from −4.73 to −0.75 kcal/mol. (4) Conclusions: The successful identification of bile secretion-related lncRNAs, coupled with the prediction of their regulatory networks and molecular interaction sites, has advanced our understanding of SHEV ORF3 function and the pathogenesis of SHEV infection. Full article

Deubiquitinating enzymes (DUBs) play essential roles in diverse plant biological processes, yet the ovarian tumor proteases (OTUs), a major DUB subfamily, have not been systematically characterized in wheat, and their functions in grain development remain unclear. Here, we identified 49 OTU genes (TaOTUs) in the hexaploid wheat genome and classified them into four subfamilies based on phylogenetic relationships, with nomenclature assigned according to homology. TaOTU6-7B was highly expressed during early and mid-grain development and was responsive to gibberellin and jasmonic acid. Its expression differed significantly between large-grain wheat Pindong34 (PD34) and small-grain wheat MY11847 at 7 and 11 days after flowering. To elucidate its function, we used CRISPR/Cas9 to generate loss-of-function mutants by knocking out the three homoeologs (TaOTU6-7A, -7B, and -7D). These mutants exhibited significantly increased grain width and weight relative to wild type. Moreover, TaOTU6-7B directly interacted with TaUBC13, whose expression was markedly elevated in the TaOTU6 knockout background, suggesting that TaUBC13 may positively regulate wheat grain size. Collectively, this study establishes the TaOTU gene family in wheat, reveals TaOTU6 as a negative regulator of grain width and weight, and provides valuable genetic resources and a theoretical foundation for high-yield wheat breeding. Full article

Leukocyte-specific protein 1 (LSP1) is known as an endothelial gatekeeper because it controls endothelial permeability and transendothelial cell migration, including that of leukocytes and potentially metastatic cancer cells. In endothelial cells, LSP1 is predominantly in the nucleus under resting conditions but translocates to extranuclear compartments upon stimulation with TNF-α. The discrepancy between its predicted molecular weight (~37 kDa) and its observed migration on SDS-PAGE (≥52 kDa), along with its dynamic subcellular distribution, suggests a possible post-translational modification by SUMOylation. To investigate this, we examined endogenous LSP1 in murine primary endothelial cells and overexpressed recombinant LSP1 in murine endothelial (SVEC4-10EE2) and HEK293T cells. Our results demonstrate that LSP1 is SUMOylated by SUMO1, with Ubc9 serving as the conjugating enzyme and SENP1 as the deSUMOylating protease. Site-directed mutagenesis of lysines K270 and K318 abolished SUMOylation, resulting in a marked reduction in LSP1 steady-state levels. This reduction was attributed to enhanced ubiquitination and accelerated proteasomal degradation of LSP1 in the SUMOylation-deficient state. Furthermore, deSUMOylation impaired the TNF-α-induced translocation of LSP1 from the nucleus to extranuclear compartments, particularly the cytoskeleton. In summary, our findings establish that LSP1 is a SUMO1-modified protein. SUMOylation stabilizes LSP1 by preventing proteasomal degradation and is essential for its proper subcellular trafficking in endothelial cells in response to inflammatory stimuli. Full article

Fetal growth restriction (FGR) remains a significant problem in obstetrics and is a key risk factor for perinatal brain injury. The fetal neuronal vesicles (FNVs) isolated from maternal blood represent an innovative approach—a “fetal brain liquid biopsy”—enabling early diagnostics of neuronal dysfunction in FGR. Western blotting was used to evaluate the protein pattern expression of FNVs isolated from the blood of pregnant women with FGR and uncomplicated pregnancy. Significant changes in the neurotrophic proteins levels (pro-BDNF, pro-NGF) and presynaptic neurotransmission proteins (SYN1, SYP, SYNPO) were identified. New data were obtained on changes in the expression of proteins of sumoylation (SUMO2/3/4) and neddylation (NAE1, UBC12), which differs in early-onset and late-onset FGR. Moreover, increased SUMO2/3/4 levels can be considered as an endogenous neuroprotective response to cerebral hemodynamic reaction in fetuses with late-onset growth restriction. An association has been established between changes in the expression of the studied proteins and intraventricular hemorrhage (IVH) in newborns with late-onset growth restriction. Full article

The polyphagous pest Oxycetonia jucunda Faldermann can cause substantial damage to a range of economically important crops, with the adult beetles feeding directly on floral tissues and young leaves. RT-qPCR is widely used to analyze gene expression, for which the selection of stable reference genes is essential for enabling an accurate normalization of expression. However, no systematic evaluations of suitable reference genes for RT-qPCR analysis using different tissues of O. jucunda have been conducted. To assess their applicability as reliable normalization controls, we used five computational methods to examine the stability of seven potential reference genes (GAPDH, EF1α, RPS3, RPS18, RPL18, RPS31, and UBC5A) across six adult tissues, with three biological replicates per tissue. The findings revealed RPS3 and RPS31 to be the most stably expressed. This pair of reference genes was further validated by normalizing the expression of the odorant-binding protein 3 (OBP3) target gene. Our findings will provide important foundational data for the accurate analysis of functional gene expression in O. jucunda. Full article

Background: Urothelial bladder carcinoma (UBC) is a disease that lacks robust non-invasive laboratory biomarkers. Recently, urine liquid biopsy has emerged as a promising tool for diagnosis and surveillance of patients with these tumors. The aim of this study was to evaluate the diagnostic potential of a urinary tumor DNA detection panel, which included eight common point mutations in TERT, GPR126, FGFR3, and PIK3CA genes, in UBC. Methods: The study included patients with histologically confirmed UBC (n = 88) and patients with cystitis, bladder leiomyomas, or other non-malignant conditions (control group; n = 72). DNA was extracted from whole urine specimens. ddPCR analysis was performed using the Bio-Rad QX200 AutoDG ddPCR system. Results: Urinary tumor DNA detection panel demonstrated a sensitivity of 78.4% and a specificity of 100% (AUC−ROC = 0.892). Detection rates for the analyzed mutations were the following: 54.5%, 37.5%, 28.4%, and 38.6% for TERT, GPR126, FGFR3, and PIK3CA, respectively. Pairwise comparisons of mutant allele fractions (MAFs) for samples simultaneously positive for ≥2 mutations revealed an absence of significant differences (p > 0.05), except for the pair of FGFR3 vs. PIK3CA (p = 0.03). MAFs were not associated with any clinical and demographic features (p > 0.05), with the only exception being the tumor size: patients with tumors larger than 2.16 cm³ had higher MAFs than the rest (23.4 [1.8; 46.3] vs. 1.6 [0; 24.6] %, respectively, p = 0.02). Conclusions: Upon further validation, the presented tumor DNA detection panel for ddPCR might become a useful tool for diagnostic purposes in UBC. Full article

Fig (Ficus carica L.), a deciduous fruit tree that belongs to the Moraceae family, is cultivated worldwide as an important fruit crop for raw and processed foods. Quantitative real-time PCR (RT-qPCR) is a widely used method in F. carica to elucidate expression of genes related to various physiological responses. However, no studies have identified appropriate reference genes for RT-qPCR normalization in F. carica. In this study, 12 genes were selected from the F. carica genome as candidate reference genes for normalizing target gene expression. All candidate genes exhibited high amplification efficiency and specificity in the absence of primer dimers or extra PCR amplicons. The expression levels of the candidate genes were measured in three different plant tissues (fruit, leaf, and stem) under fungal pathogen infection using RT-qPCR. Their expression stabilities were evaluated using four computational algorithms: geNorm, Normfinder, delta-Ct, and BestKeeper. The RefFinder program was also used to calculate the geometric mean of the stability rankings obtained from these algorithms. The comprehensive ranking revealed that FcYLS8, FcPP2A, and FcAP2M were the most stable reference genes under biotic stress in the fruits, leaves, and stems, respectively. In contrast, traditional reference genes such as FcACT2, FcEF-1α, FcGAPDH, FcUBC21, and FcUBQ5 exhibited relatively low expression stability in all tested tissues. This study identified and validated stable reference genes for RT-qPCR normalization in F. carica, thus providing a valuable resource for accurate gene expression studies under biotic stress and highlighting the importance of validating reference genes to ensure reliable and reproducible RT-qPCR analysis. Full article

Freshwater cladocerans such as Daphnia magna (D. magna) are keystone grazers whose hormone-regulated life history traits make them sensitive sentinels of endocrine-disrupting chemicals (EDCs). The organophosphate flame-retardant tris(2-butoxyethyl) phosphate (TBOEP) and perfluoroethylcyclohexane sulfonate (PFECHS) now co-occur at ng L⁻¹–µg L⁻¹ in surface waters, yet their chronic sub-lethal impacts on invertebrate endocrine networks remain unclear. We analysed two publicly available 21-day microarray datasets (TBOEP: GSE55132; PFECHS: GSE75607) using gene ontology enrichment, STRING protein interaction networks, Drosophila phenotype mapping, and KEGG (Kyoto Encyclopaedia of Genes and Genomes)-anchored frameworks to build putative adverse outcome pathways (AOPs) for D. magna. Differentially expressed genes were clustered into functional modules and hub nodes were ranked by degree and betweenness. TBOEP suppressed moulting and growth, altering 1157 genes enriched for metabolism and membrane processes; hubs VRK1, MIB2, and adenylosuccinate synthetase formed a muscle anatomical development sub-network. PFECHS down-regulated vitellogenin and shifted 879 genes dominated by oxidative-stress and glutathione-metabolism signatures; central nodes UBC9, eIF4A-III, Tra-2α, and HDAC1 linked meiotic-cycle, oogenesis, and cyclic-compound binding. Despite chemical dissimilarity, both compounds converged on Wnt-signalling nodes—TBOEP via presenilin-1, and PFECHS via CK1ε/CK2—thereby reducing TCF/LEF-dependent transcription. Predicted outcomes include impaired oocyte maturation, reduced fecundity, and stunted body size, consistent with observed decreases in length and vitellogenin protein. Our network analysis, based on high-dose, sub-lethal exposures used in the underlying microarray studies, indicates that TBOEP- and PFECHS-induced perturbations can destabilise endocrine, developmental, and metabolic pathways in D. magna without overt lethality, and highlights Wnt-centred key events and hub genes as candidate biomarkers to be evaluated in future low-dose studies that use environmentally realistic exposure scenarios. Hub genes and Wnt-mediated key events emerge as sensitive biomarkers for monitoring mixed EDC exposure. Full article

The Philippines, located along the Pacific Ring of Fire, is highly susceptible to significant seismic activity arising from the active convergence of major tectonic plates. These seismic events often induce ground shaking intense enough to trigger soil liquefaction, particularly in geologically sensitive regions such as Davao del Sur. This study presents a nonlinear static and dynamic analysis of a mat foundation for a proposed midrise building located within the liquefaction-prone zone of Padada, Davao del Sur. Geotechnical data were obtained through rotary drilling and Standard Penetration Tests (SPTs), which provided the basis for developing the numerical model. Liquefaction assessment was conducted using the PLAXIS Liquefaction Model (UBC3D-PLM), confirming that the site adjacent to the Padada–Mainit River exhibits a high liquefaction potential. Subsequently, finite element analyses were performed in PLAXIS 3D using ground motion records from the 2013 Bohol Earthquake, scaled to 1.0 g, and modeled under the Hardening Soil Model with Small-Strain Stiffness (HSsmall). Results showed excess pore pressure ratios approaching 1, and vertical displacements of the mat foundation exceed 100 mm. These results suggest severe degradation in soil strength, as well as reduced friction angles and mobilized pressure. Full article

Bladder cancer (BC), particularly muscle-invasive urothelial bladder carcinoma (UBC), remains a clinical challenge due to frequent recurrence, chemoresistance, and limited treatment options. This study investigates the functional and mechanistic insights of 3-hydroxybutyrate (3-OBA), a ketone body with known metabolic and epigenetic roles, in muscle-invasive UBC models. 3-OBA significantly inhibited cell viability, proliferation, migration, and invasion in T24 and HT1376 cell lines in a dose-dependent manner. In vivo, 3-OBA impaired tumor growth and angiogenesis in the chick chorioallantoic membrane model. Mechanistically, 3-OBA did not alter the expression of the G-protein-coupled lactate receptor GPR81 or associated markers (phospho-ERK1/2, LDHA, MCT1/4, CD147), indicating its antitumor effects are GPR81-independent. Moreover, extracellular lactate modulation upon 3-OBA treatment varied between cell lines, with HT1376 cells showing reduced lactate production under nutrient deprivation, suggesting cell-specific metabolic responses to 3-OBA. These findings highlight 3-OBA’s potential as a metabolic modulator with antitumor efficacy in UBC, particularly in metabolically constrained tumors. However, its dual role—as both a potential energy source and therapeutic agent—demands context-specific investigation. Future studies should focus on patient stratification and preclinical validation to clarify 3-OBA’s therapeutic window and mechanism of action in bladder cancer. Full article

Background: The implementation of shared governance within the nursing practice results in heightened satisfaction among nurses and enhances the quality of care provided. Shared governance fosters collaborative and proactive relationships among nurses and healthcare providers, while also cultivating a sense of confidence among nurses. However, evidence suggests that a lack of awareness, reliance on traditional governance, and inadequate shared governance structures among nurses continue to exist at the unit-based council (UBC) level, including those in the Kingdom of Saudi Arabia (KSA). Purpose: The present study aimed to assess the extent of clinical nurses’ perceptions concerning shared governance at the UBC level, and to examine the variations and relationships in their perceptions based on demographic and work-related characteristics. It further explored the demographic and work-related factors that affect the overall perceptions of shared governance among clinical nurses. Methods: This quantitative study utilized a cross-sectional design and was carried out in three governmental hospitals in the KSA. The sample comprised 669 nurses, who were selected using a convenience sampling method. The Index of Professional Nursing Governance (IPNG) tool was utilized for data collection conducted between February 2025 and April 2025. Descriptive statistics alongside the t-test and analysis of variance (ANOVA), Pearson-r correlation coefficient, and multiple linear regression were utilized for data analysis. Significant findings were drawn when p ≤ 0.05. Results: The average perception of shared governance among clinical nurses at the UBC level was 180.42 out of 430, suggesting that decision-making occurs collaboratively between nurses and management. Significant differences in the average level of clinical nurses’ perceptions of shared governance were noted in relation to their educational qualifications (F = 5.015, p = 0.001) and nursing units (F = 4.157, p = 0.010). The hospital in which clinical nurses were employed (r = 0.098, p = 0.037) and nursing units (r = 0.087, p = 0.020) exhibited significant correlations with their overall shared professional governance. Furthermore, the hospital where clinical nurses were employed (β = 0.406, p = 0.001, 95% confidence interval [CI] = 0.166, 0.646) and nursing units (β = 0.326, p = 0.038, 95% CI = 0.018, 0.314) served as predictors of their overall professional shared governance. Conclusions: Clinical nurses in this study showed an initial or relatively low level of shared governance at the UBC level. The overall finding highlights a critical need for nursing managers and leaders to enhance the level of professional shared governance among clinical nurses, which may result in improved nurse retention and overall quality of nursing care. It is crucial to consider clinical nurses’ educational qualifications and working environment at the UBC level when aiming to enhance their level of professional shared governance. Full article

Mercury adsorption/oxidation plays a crucial role in mercury transformation during coal combustion. To gain an intuitive understanding of the adsorption/oxidation mechanisms between mercury and fly ash, changes in mercury speciation of fly ash before and after Hg adsorption were investigated using temperature-programmed decomposition–atomic fluorescence spectroscopy (TPD-AFS). The results directly reveal that the primary adsorption/oxidation mechanism between mercury and fly ash is the heterogeneous oxidation reaction of Hg⁰ to HgCl₂. The mercury adsorption capacity exhibits a strong positive correlation with both the unburned carbon (UBC) content and the specific surface area (SSA) of the fly ash, whereas the presence of metal oxides has a negligible effect on mercury adsorption. Higher inlet concentrations of Hg⁰ enhance mercury adsorption, while flue gas components such as N₂, O₂, and CO₂ have minimal influence on mercury adsorption. Full article

Accurate normalization of qRT-PCR data in pulmonary tuberculosis (TB) research requires reference genes whose expression is invariant across clinically relevant matrices, yet no studies have addressed this in lesion tissue and blood concurrently. We assessed the expression stability of eight popular housekeeping genes—ACTB, B2M, GAPDH, HPRT1, PPIA, RPL13A, UBC and YWHAZ—in lung tuberculomas and peripheral blood mononuclear cells (PBMCs) from TB patients. Standardized extraction and amplification yielded Cq values that were ranked by geNorm, NormFinder, BestKeeper and comparative Delta CT, with consensus scores generated in RefFinder; and correlation analysis was conducted in order to select the most suitable genes to work collectively for future normalization. The consensus analysis placed PPIA, YWHAZ and HPRT1 at the top, while GAPDH and UBC were the least stable. Our findings endorse a three-gene panel (PPIA, YWHAZ, HPRT1) for robust normalization of host gene-expression studies in both lesion tissue and PBMCs in pulmonary TB and highlight the necessity of context-specific reference-gene validation. Full article

Internal reference genes are a prerequisite for ensuring the accuracy of gene verification experiments, but few relevant studies on Lyophyllum decastes have investigated the growth cycle and different environmental conditions. In this study, the qPCR results of 22 house-keeping genes were analyzed using GeNorm, BestKeeper, NormFinder and RefFinder. The results revealed that the most stable gene differed under different conditions. Across all developmental stages and under hot, cold, acidic, alkaline, and salt conditions, UBCE gene displays the greatest expression stability. However, EF1b, β-ACT, HSD17B3, and Cyb presented the greatest stability under cold, heat, and acidic conditions, and heavy metal exposure, respectively. To screen for genes suitable for all conditions, RefFinder’s ranking results revealed that UBCE and EF1b ranked in the top 2, demonstrating the highest gene expression stability. In contrast, Cyb was positioned at the bottom of the comprehensive ranking table. This study not only revealed potential factors affecting the suitability of reference genes but also identified optimal reference genes from a set of candidate genes across diverse conditions. Full article