Search Results (8,696)

Background/Objectives: Short Interspersed Nuclear Elements (SINEs) constitute major components of mammalian genomes, but the structural diversity and evolutionary dynamics of their characteristic 3′ poly(A) tails have not been fully characterized. Methods: Based on the custom-developed SINEtail-scan pipeline, 1,018,332 SINEs with tail in the pig reference genome (Sus scrofa 11.1) were identified and systematically classified, revealing the diversity of tail sequence structures. According to nucleotide composition and microsatellite repeat patterns, the tail sequences were divided into 16 different structural types. Results: A-rich sequences predominated (66.3%), while non-A-rich tails exhibited characteristic architectures including AT-format, AC-format, and AG-format repeats. Temporal analysis spanning 85 million years demonstrated progressive tail modification, with A-rich proportions declining from 84.2% in recent insertions to 31.9% in ancient elements, accompanied by accumulation of complex non-A-rich structures. Comparative genomic analysis across 10 pig genome assemblies identified 308 SINE tail insertions within protein-coding sequences, of which 45 (14.6%) exhibited inter-individual structural polymorphism. Detailed investigation of a polymorphic insertion in the VWA8 gene revealed a 16-bp tail variant causing a frameshift mutation and C-terminal protein structure divergence. Conclusions: These findings establish SINE tail sequences as dynamic evolutionary substrates undergoing continuous modification through slippage-mediated mechanisms, with implications for genome evolution, population genetics, and gene function modulation in mammals. Full article

Background: The subtribe Pleurothallidinae is a diverse group within Orchidaceae with a complex taxonomic history. Comparative plastome analysis can provide insights into genome evolution and facilitate phylogenetic reconstruction. Methods: Here we analyzed 25 complete chloroplast genomes representing 15 genera, including 14 newly assembled genomes, to investigate plastome evolution in this subtribe. Results: All genomes exhibited the typical quadripartite structure (148, 246–158, 138 bp) with conserved gene content (128–134 genes). While most protein-coding genes were under purifying selection, we detected signatures of positive selection in specific lineages. Notably, ndhF in Lepanthes tachirensis showed a markedly elevated Ka/Ks ratio (3.65), which may be associated with adaptation to an extensive distributional range. ENC-plot analysis indicated that natural selection, rather than mutation pressure alone, shapes codon usage bias, with patterns varying among species from different geographic regions. Nucleotide diversity analysis identified eight hypervariable intergenic regions (psbK-psbI, atpI-rps2, petN-psbM, psbB-psbT, petD-rpoA, rpoA-rps11, rps3-rpl22, ccsA-ndhD) suitable as candidate molecular markers. Phylogenetic analysis confirmed that Lepanthes and Pleurothallis are non-monophyletic as traditionally defined. Conclusions: These findings expand plastome resources for Pleurothallidinae, reveal lineage-specific patterns of selection, and provide molecular markers for future taxonomic and evolutionary studies. Full article

Advanced melanoma remains difficult to treat due to its intrinsic resistance to conventional therapies and the frequent development of acquired resistance to targeted agents, such as BRAF inhibitors. Onconase (ONC), an amphibian ribonuclease with established antitumor activity, had been previously shown to have selective cytotoxicity toward melanoma cells. In this study, we investigated the molecular mechanisms underlying ONC-induced cytotoxicity in BRAF-mutated melanoma cell lines that are either sensitive or resistant to the BRAF inhibitor dabrafenib. We focused on oxidative stress regulation, mitochondrial dynamics, and cell death-related signaling pathways. ONC treatment resulted in a marked increase in reactive oxygen species (ROS) levels, concomitant with a pronounced downregulation of NRF2 and multiple NRF2-dependent antioxidant proteins. These effects were particularly evident in dabrafenib-resistant melanoma cells. In parallel, ONC impaired mitochondrial plasticity by inhibiting mitochondrial biogenesis and fission, as evidenced by reduced PGC1α, DRP1, and FIS1 expression. Confocal analysis confirmed the presence of more enlarged mitochondria in ONC-treated cells. Mitophagy and autophagy are hindered by ONC due to the downregulation of PINK1, beclin1, ATG3 expression, as well as the lack of LC3B activation. These mitochondrial defects were associated with mitochondrial-dependent apoptosis, characterized by caspase-9 activation and strong downregulation of the antiapoptotic protein survivin. Lipid peroxidation was also induced by ONC, especially in the A375 cell line. Additionally, ONC inhibited key proliferation-related signaling pathways, including STAT3 and NF-κB, and reduced cyclin-dependent kinase 1, 2, and 4 activities. Collectively, these findings demonstrate that ONC disrupts redox homeostasis, mitochondrial function, and survival signaling in melanoma cells, exerting particularly potent effects in BRAF inhibitor-resistant populations. This study provides mechanistic insight into the anti-melanoma activity of ONC and supports its potential therapeutic application in drug-resistant melanoma. Full article

Background/Objectives: Synovial sarcoma (SS) is a rare and aggressive soft-tissue malignancy characterized by complex molecular alterations and poor prognosis, highlighting the need for targeted immunotherapeutic strategies. This study aimed to design a rational multi-epitope vaccine targeting the FKBP10 oncoprotein to elicit effective immune responses against SS. Methods: Transcriptomic data from the GEO dataset GSE144190, comprising 10 tumor and 9 normal tissue samples, were analyzed to identify differentially expressed genes (DEGs). Results: Our findings revealed significantly upregulated FKBP10 with a log2 fold change of 3.55, baseMean expression of 1521.84, and adjusted p-value of 8.37 × 10⁻²⁶. Mutational analysis across 7782 sarcoma samples indicated a low alteration frequency of ~1.5%, primarily missense variants. Functional mapping showed FKBP10 as a hub interacting with multiple collagen chains and chaperone proteins, implicating its role in extracellular matrix organization and protein folding. Linear B-cell epitope prediction identified 17 epitopes (6–21 amino acids), while T-cell mapping yielded 10 MHC class I and 9 MHC class II high-affinity epitopes, all antigenic (VaxiJen > 0.5) and non-allergenic. A multi-epitope vaccine was constructed incorporating a 50S ribosomal protein L22 adjuvant, linkers, and a 6× histidine tag. Physicochemical analysis showed a molecular weight of 36.43 kDa, pI 6.97, instability index 31.79, aliphatic index 64.88, and GRAVY −0.509, indicating stability and hydrophilicity. Structural modeling validated 82.5% residues in favored regions. Molecular docking revealed strong binding with TLR4 (−9.7 kcal/mol) and TLR9 (−9.4 kcal/mol), and 200 ns molecular dynamics simulations confirmed stable RMSD trajectories, low RMSF at binding residues (<4 Å), persistent hydrogen bonding, compact radius of gyration (38–42 Å for TLR4; ~20 Å for TLR9), favorable total energy (−1400 to −1500 kcal/mol for TLR4; −650 to −720 kcal/mol for TLR9), and stable SASA (~52,000–54,000 Ų). Conclusions: These findings demonstrate that the FKBP10 multi-epitope vaccine is structurally stable, immunogenic, and capable of engaging key innate immune receptors, supporting its potential as a promising immunotherapeutic candidate for synovial sarcoma. Full article

Human prostamide/prostaglandin F synthase (PGFS) catalyzes the NADPH-dependent conversion of prostaglandin H₂ (PGH2) to prostaglandin F₂α that plays a key role in regulating intraocular pressure and labor. Despite its physiological importance, structural and biochemical information of the human PGFS has been limited because of difficulties in obtaining sufficient quality of PGFS wild-type crystal and short half-life of PGH2. Here, we report the crystal structure of human PGFS with two active site mutations, C44S/C47S double mutant (DM), which mimics the reduced active form of the CXXC motif of human PGFS. Structural analysis revealed that PGFS DM adopts a typical thioredoxin (Trx)-like fold. Analysis of B-factors and MD simulations reveals that Tyr108–Asp124 is an intrinsically flexible region, devoid of any stabilizing crystal contacts. Unlike canonical Trx-like proteins, Pro167 in PGFS adopts a trans-conformation, inducing a specific Arg40 side chain localization that creates a positive charge near the CXXC motif. Activation of PGFS by reduction of disulfide bond in the CXXC motif enhanced the thermal stability via core stabilization, yet an unexpected increase in the structural disorder was detected with CD spectroscopy, especially upon ligand binding. These findings collectively establish PGFS as a structurally distinct and redox-regulated enzyme. Our results provide novel molecular insights into PGFS as an underexplored but promising therapeutic target. Full article

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health burden, particularly due to multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Rifampicin, a frontline anti-TB drug that inhibits RNA polymerase, has been central to therapy, but rpoB mutations compromise its efficacy. This highlights the need for Rifampicin analogues that target alternative enzymes to sustain therapeutic effectiveness. In this study, a structure-based computational approach was employed to screen Rifampicin analogues against enoylacyl carrier protein reductase (InhA), a validated enzyme in the biosynthesis of mycolic acids. A library of 399 analogues was retrieved from SwissSimilarity and evaluated using ADMET analysis, with the best candidates showing favourable pharmacokinetic profiles and compliance with Lipinski’s Rule of Five. Molecular docking identified ZINC000013629834 (−10.90 kcal/mol) and ZINC000253411694 (−10.36 kcal/mol) as superior to Rifampicin (−9.05 kcal/mol), with ILE21, SER20, and THR196 consistently stabilizing interactions. Molecular dynamics simulations confirmed the stability of the complexes, with RMSD values of 0.167 nm, 0.175 nm, and 0.297 nm for ZINC000013629834, ZINC000253411694, and Rifampicin, respectively. MM/PBSA analysis showed comparable binding free energies. These findings suggest that optimized Rifampicin analogues targeting InhA may overcome rpoB-associated resistance and serve as promising leads for next-generation anti-TB drug development. Full article

Radar image extrapolation serves as a fundamental methodology in meteorological forecasting, facilitating precise short-term weather prediction through spatiotemporal sequence analysis. Conventional approaches remain constrained by progressive image degradation and artifacts, substantially limiting operational forecasting reliability. This research introduces E-HEOA—an enhanced deep learning architecture with integrated hyperparameter optimization. Our framework incorporates two fundamental innovations: (a) a hybrid metaheuristic optimizer merging a Gaussian-mutated ESOA and Cauchy-mutated HEOA for autonomous learning rate and dropout optimization and (b) embedded ConvLSTM2D modules for enhanced spatiotemporal feature preservation. Experimental validation on 170,000 radar echo samples demonstrates superior performance, demonstrating considerable enhancement in almost all aspects relative to the baseline model while establishing new state-of-the-art benchmarks in prediction fidelity, convergence efficiency, and structural similarity metrics. Full article

Src family tyrosine kinases regulate oocyte maturation and fertilization in many species, yet their physiological roles in Xenopus laevis (X. laevis) remain incompletely defined. Here, we generated three X. laevis Src (xSrc) constructs with defined point mutations allowing for selective immunochemical detection and controlled modulation of kinase activity: wild type (xSrcWT, Arg121His), constitutively active (xSrcKA, Arg121His/Tyr526Phe), and kinase-negative (xSrcKN, Arg121His/Lys294Met). Capped mRNAs were microinjected into immature oocytes, and effects on meiotic maturation and egg activation were analyzed. All constructs produced detectable Src protein within 4–5 h after injection without inducing progesterone-independent maturation. Following progesterone treatment, MAP kinase phosphorylation, CDK1 activation, and germinal vesicle breakdown (GVBD) occurred normally in all groups, although xSrcKA-expressing oocytes showed a modest but reproducible acceleration of MAPK activation and GVBD. Global tyrosine phosphorylation analysis revealed increased phosphorylation of several proteins, including a prominent ~50 kDa substrate, specifically in xSrcKA oocytes. After maturation, oocytes were subjected to artificial activation. xSrcKN-expressing oocytes responded normally to Ca²⁺ ionophore (A23187), indicating that Src activity is not required for direct Ca²⁺-mediated activation. In contrast, xSrcKN oocytes exhibited markedly reduced activation in response to hydrogen peroxide or Cathepsin B, which stimulate membrane-associated signaling pathways. These findings demonstrate that Src kinase activity is required for membrane signal-mediated egg activation but is dispensable for activation driven by direct intracellular Ca²⁺ elevation. Collectively, our results identify Src kinase as a positive regulator of progesterone-induced meiotic maturation and a critical mediator of specific fertilization-like activation pathways in X. laevis. Full article

Objective: We aimed to characterize the somatic mutational landscape of oropharyngeal squamous cell carcinoma (OPSCC) and identify potential genomic drivers of tumor progression and therapeutic resistance using the AACR GENIE database. Study Design: Retrospective genomic analysis was employed. Setting: We used publicly available data from the American Association for Cancer Research (AACR) Project GENIE database accessed via cBioPortal. Methods: We analyzed 412 tumor samples from 401 patients diagnosed with OPSCC. Somatic mutations, clinical variables and tumor characteristics were extracted and analyzed. Statistical comparisons of mutation frequencies across gender and tumor stage (primary vs. metastatic) were conducted. Co-occurrence and mutual exclusivity analyses were performed to identify significant genomic patterns. Results: The most frequently mutated genes included TP53 (30.1%), PIK3CA (26.0%), and KMT2D (21.6%). Gender-specific analyses suggested potential enrichment of TP53 and MET mutations in females and of ZNF750 in males. Distinct mutation patterns were observed between primary and metastatic tumors; primary tumors were enriched for mutations in TP53 and CDKN2A, while metastatic lesions harbored unique alterations in genes like CBLB and BUB1B, suggesting pathways involved in immune evasion and chromosomal instability may drive disease progression. Co-occurrence was noted between PIK3CA and FBXW7, and mutual exclusivity between TP53 and CYLD. Conclusions: This study identifies distinct genomic signatures in OPSCC subgroups, highlighting candidate biomarkers in pathways like PI3K/AKT signaling that warrant further investigation. Validating these markers in prospective trials is a critical next step to translate these findings into personalized therapeutic strategies for OPSCC patients. Full article

Alternative splicing of pre-mRNA is a crucial mechanism in gene expression regulation. As a core component of the spliceosome, the biological function of the Skip protein in Aspergillus flavus remains unknown. Quantitative real-time PCR (qPCR) analysis revealed the presence of two skip gene copies in A. flavus. Single-copy deletion of Skip resulted in slowed growth, reduced conidiation, abolished sclerotial formation, increased aflatoxin biosynthesis, and diminished crop colonization. Meanwhile, Skip was found to regulate the oxidative stress response by modulating the alternative splicing of yapA. Subsequently, immunoprecipitation and Western blot analyses identified lysine 325 (K325) as the benzoylated site on the Skip protein, which catalyzed by the acyltransferase EsaA. Mutation of benzoylated site K325 directly impaired fungal morphogenesis, pathogenicity, and stress adaptation. These findings established the crucial role of Skip and its benzoylation in A. flavus and suggested a potential target for controlling its infection in important crops. Full article

Background: Inherited retinal dystrophies are a heterogeneous group of progressive disorders impacting photoreceptor function, often limiting the usefulness of standard electroretinography in advanced cases. Full-field stimulus test (FST) testing has become a sensitive psychophysical technique for detecting residual visual function when traditional electrophysiology is non-recordable. This study evaluated the ability of chromatic FST to differentiate rod–cone from cone photoreceptor dysfunction in patients with genetically confirmed inherited retinal dystrophies. Methods: Cross-sectional FST data were analyzed from 39 patients (mean age 45.7 ± 20.0 years) with genetically confirmed inherited retinal dystrophies at a tertiary academic center. All participants underwent standardized FST testing using white, red, and blue stimuli. Patients were classified into rod–cone dystrophy (n = 27) or cone dystrophy (n = 12) groups based on genetic and clinical criteria. Group comparisons focused on FST thresholds and especially blue–red threshold differences as markers of photoreceptor-mediated function. Bonferroni correction was applied to adjust for multiple comparisons across four primary FST parameters. Additional analyses by genotype were performed with nonparametric tests. Results: Eight different genetic mutations were represented, including Phosphodiesterase 6A (PDE6A) (n = 10), Rhodopsin (RHO) (n = 7), Phosphodiesterase 6B (PDE6B) (n = 6), Cyclic Nucleotide-Gated Channel Beta 1 (CNGB1) (n = 4), Cyclic Nucleotide-Gated Channel Alpha 3 (CNGA3) (n = 4), Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3) (n = 4), Guanylate Cyclase 2D (GUCY2D) (n = 2), and Cyclic Nucleotide-Gated Channel Beta 3 (CNGB3) (n = 2). Blue–red FST threshold differences exhibited moderate group discrimination in uncorrected analysis, with rod–cone dystrophies averaging −8.35 ± 10.37 dB and cone dystrophies −11.20 ± 14.60 dB. The area under the receiver operating characteristic curve for blue–red difference was 0.74 (95% CI: 0.59–0.90), with 75% sensitivity and 70.4% specificity at a −10 dB cutoff. However, no chromatic FST parameter maintained statistical significance between groups after Bonferroni correction. Inter-eye FST correlation was high (r = 0.758, p < 0.001), supporting test reliability. Conclusions: Chromatic FST testing provides a practical and sensitive means to assess photoreceptor function in advanced inherited retinal dystrophies, particularly when standard electrophysiologic methods are uninformative. Although the blue–red threshold difference offers moderate discrimination between rod–cone and cone dystrophies in uncorrected analysis, no chromatic parameter reached statistical significance after adjustment for multiple testing. Chromatic FST should be considered a supplementary approach for clinical monitoring and therapeutic studies in advanced retinal dystrophies, with further validation needed in larger cohorts. Full article

Background/Objectives: Pheochromocytoma (PHEO) is increasingly detected incidentally or through genetic screening; however, predictors of symptomatic presentation and its perioperative impact remain unclear. We aimed to quantify the prevalence of symptomatic PHEO, identify associated factors, compare perioperative outcomes, and develop a predictive nomogram. Methods: We retrospectively analyzed patients diagnosed and/or operated on for PHEO at a tertiary referral center between 1984 and 2021. Associations with symptomatic presentation were assessed using univariate and multivariable logistic regression analyses. A nomogram was constructed based on independent predictors and evaluated using receiver operating characteristic (ROC) analysis and the area under the curve (AUC). Results: Among 173 patients (mean age 44.4 ± 15.8 years; 53.2% women), 67.1% were symptomatic. In multivariable analysis, male sex (odds ratio [OR] 0.33; p = 0.023) and the presence of a germline mutation (OR 0.15; p = 0.004) were associated with a lower likelihood of symptoms, whereas a noradrenergic secretion profile was associated with a higher likelihood (OR 12.73; p = 0.02). Symptomatic patients had higher rates of intraoperative (OR 2.60; p = 0.032) and postoperative complications (OR 3.09; p = 0.04). The nomogram incorporating sex, genetic status, and noradrenergic profile demonstrated moderate discrimination (AUC 0.799; 95% confidence interval 0.722–0.877; p < 0.001). Conclusions: Symptomatic PHEO is associated with sex, genetic status, and noradrenergic secretion profile and is linked to increased perioperative morbidity. A simple nomogram based on readily available variables may help estimate individual risk and support perioperative management. Full article

Despite the persistent global threat of seasonal influenza viruses such as A(H1N1)pdm09 and A/H3N2, their epidemiological and genetic characteristics in China following the implementation of COVID-19 non-pharmaceutical interventions (NPIs) remain poorly characterized. Between September 2020 and December 2023, we conducted an integrated epidemiological and genomic analysis of influenza A viruses in children in Wuhan. The overall positivity rate for influenza A virus was markedly low at 3.43% (109/3171), reflecting a profound suppression of circulation during the pandemic. Among genotyped positives, H1N1pdm09 was predominant (52.3%), followed by H3N2 (16.5%) and untypeable strains (32.1%). Preschool children showed the highest susceptibility. Phylogenetic analysis revealed that the circulating H1N1 strains (90%) belonged to clade 6B.1A.5a.2, clustering with viruses from Hong Kong and Pakistan. In contrast, H3N2 strains (76.92%) primarily fell into clade 3C.2a1b.2a.2b, closely related to contemporary strains from Europe and North America. Notably, we identified key hemagglutinin mutations associated with antigenic drift (e.g., R240Q in H1N1; E78G, R158G in H3N2) and neuraminidase mutations potentially conferring antiviral resistance (e.g., S247N in H1N1; S245N, a putative novel glycosylation site, in H3N2). Evidence of reassortment events was also detected, underscoring the continued genomic evolution of these viruses despite their low prevalence. Our findings demonstrate that genetically diverse and antigenically drifted influenza A viruses continued to circulate and evolve in Wuhan during the COVID-19 pandemic, albeit at dramatically reduced levels. This highlights the critical need for sustained genomic surveillance and timely updates of vaccine compositions to pre-empt the resurgence of influenza in the post-pandemic era. Full article

Background/Objectives: Thymomas are the most common tumors of the anterior mediastinum. While early-stage disease often has a favorable prognosis, therapeutic options in advanced stages remain limited. Moreover, the molecular profile of thymomas is still poorly characterized. In the present study, we explored the presence of targetable mutations and programmed death-ligand 1 (PD-L1) expression in a cohort of surgically resected thymomas. Furthermore, we investigated the correlation between PD-L1 expression, histological subtype, and risk of recurrence in patients who underwent curative-intent thymectomy. Methods: Mutational profiling was performed using a DNA-based NGS Cancer Panel of 16 genes. PD-L1 expression was evaluated via Tumor Proportion Score (TPS), and thymomas with TPS ≥ 50% were identified as high expressors. The associations with histological subtype and disease-free survival (DFS) were analyzed using logistic regression, Cox proportional hazards models, and Kaplan–Meier survival curves. Results: In our study, 2/37 (5.4%) of tested neoplasms (type AB and B2 thymoma) reported as a PIK3CA mutation; no other targetable mutations were observed. Moreover, high PD-L1 expression (≥50%) was reported in (15/37) 40.5% of patients and was significantly associated with aggressive histological subtypes (B2 and B3) (p < 0.001). Logistic regression analysis showed that high PD-L1 expression was a significant predictor of aggressive histology (McFadden’s R² = 0.268, p < 0.001), with an odds ratio of 15.5 (95% CI: 2.9–83.4; p = 0.001). During follow-up, 5/37 (13.5%) of patients experienced disease recurrence; however, no significant difference in DFS was found between high and low PD-L1 expression groups. Conclusions: Our data confirm the presence of PIK3CA mutations in thymomas and encourage the exploration the potential role of molecular target therapy in this setting. Moreover, we underlined that high PD-L1 expression level is associated with more aggressive thymoma subtypes and may have a role as a prognostic biomarker. These findings support the need for further studies on the potential role of molecular and predictive pathology in thymic epithelial tumors. Full article

Background/Objectives: The prognostic significance of blood tumor mutational burden (bTMB) in metastatic colorectal cancer (mCRC) remains poorly defined. While tissue-based TMB has been associated with favorable outcomes in selected colorectal cancer subgroups, the clinical meaning of bTMB in real-world practice is unclear. This study evaluated the prognostic impact of bTMB measured through liquid biopsy in an unselected cohort of patients with mCRC. Methods: This monocentric, real-world study included 255 adult patients with pMMR/MSS mCRC who underwent routine comprehensive genomic profiling using the FoundationOne^® Liquid CDx assay. bTMB was quantified in mutations per megabase (mut/Mb), and patients were classified into bTMB-low and bTMB-high groups using the cohort median. The primary endpoint was overall survival (OS). Subgroup analyses, including stratification by RAS/BRAF mutation status, were descriptive. Results: The median bTMB was 5 mut/Mb. Patients in the bTMB-high group had an increased risk of death compared with those in the bTMB-low group (hazard ratio (HR) 1.88). The adverse prognostic effect for OS of high bTMB was more pronounced in patients with RAS mutant tumors (HR 2.32) than with RAS/BRAF wild-type tumors (HR 1.81), while no prognostic impact was observed in BRAF^V600E mutant tumors (HR 0.90). bTMB was strongly correlated with ctDNA fraction (p < 0.0001). Conclusions: In routine clinical practice, elevated bTMB is associated with poor prognosis in pMMR/MSS mCRC, particularly in RAS mutant tumors. These results contrast with prior tissue-based studies and indicate that bTMB may reflect tumor burden and aggressive disease biology rather than tumor immunogenicity. Prospective studies integrating bTMB with ctDNA fraction, tumor burden metrics, and longitudinal molecular dynamics are warranted to refine its clinical utility. Full article