Search Results (12,226)

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play evolutionarily conserved roles in intracellular vesicle trafficking and membrane fusion across eukaryotes. In pathogenic fungi, various SNARE homologs have been shown to critically regulate host infection processes. Here, we characterize the functional roles of CfSec22 in the sweet potato black rot pathogen Ceratocystis fimbriata. Phylogenetic and domain analyses demonstrate that CfSec22 shares homology with Sec22 proteins from Saccharomyces cerevisiae (ScSec22), Magnaporthe oryzae (MoSec22), and other fungi, containing both the characteristic Longin homology domain and V-SNARE domain. Functional studies reveal that CfSec22 regulates growth, conidiation, and virulence of C. fimbriata. Deletion of CfSEC22 resulted in abnormal vacuole morphology and impaired endocytosis. The ΔCfsec22 mutant displayed heightened sensitivity to diverse stress conditions: oxidative, endoplasmic reticulum, and cell wall stressors. Subcellular localization studies confirmed the endoplasmic reticulum residence of CfSec22. Finally, we established that CfSec22 regulates the secretion of virulence-associated proteins and is required for the induction of ipomeamarone in infected sweet potato tissues. Together, our findings demonstrate that CfSec22-mediated vesicle trafficking serves as a critical regulatory mechanism supporting growth, conidiogenesis, and pathogenicity in C. fimbriata. Full article

Background and Objective: The aim of this study was to evaluate the effects of enamel matrix protein, platelet-rich fibrin (PRF), and bone graft on new bone formation beyond the skeletal system by creating calvarial bone defects in rats. The effects were assessed using histopathological and immunohistochemical analyses. Materials and Methods: In this study, calvarial bone defects were created in male Sprague Dawley rats weighing 500–550 g. The animals were randomly divided into seven groups: Control (n = 13), Emdogain (EMD, n = 13), Emdogain + Bone Graft (EMD + BG, n = 13), Platelet-Rich Fibrin (PRF, n = 13), PRF + Bone Graft (PRF + BG, n = 13), Bone Graft (BG, n = 13), and PRF + Emdogain + Bone Graft (PRF + EMD + BG, n = 13). An additional group of 36 rats was used for PRF preparation. Titanium domes were placed on the calvarial bone defects, and the animals were sacrificed after three months. Bone samples were evaluated histopathologically for new bone formation, numbers of osteoblasts and osteoclasts, angiogenesis, and fibrosis. Immunohistochemical analysis of bone formation was performed using OPG and RANKL staining kits. Data were analyzed statistically. Results: The PRF group showed a significantly higher level of moderate new bone formation compared with the PRF + BG, EMD + BG, and PRF + EMD + BG groups (p ≤ 0.05). No significant differences were observed among the groups in terms of fibrosis or angiogenesis (p > 0.05). Similarly, OPG and RANKL levels, as well as the OPG/RANKL ratio, did not differ significantly between groups (p > 0.05). Conclusions: Based on the findings of this study, the combined use of Emdogain, PRF, and bone graft appears to have beneficial effects on enhancing bone formation in calvarial defects. Full article

Molecularly imprinted polymer (MIP) biosensors offer an attractive strategy for selective biomolecule detection, yet imprinting proteins with structural fidelity remains a major challenge. In this work, we present a rationally designed electrochemical biosensor for matrix metal-loproteinase-8 (MMP-8), a key salivary biomarker of periodontal disease. By integrating graphene oxide (GO) with electropolymerized poly(eriochrome black T, EBT) films on screen-printed carbon electrodes, the partially reduced GO interface enhanced electrical conductivity and facilitated the formation of well-defined poly(EBT) films with re-designed polymerization route, while template extraction generated artificial antibody-like sites capable of specific protein binding. The MIP-based electrodes were comprehensively validated through morphological, spectroscopic, and electrochemical analyses, demonstrating stable and selective recognition of MMP-8 against structurally similar interferents. Complementary density functional theory (DFT) modeling revealed energetically favorable interactions between the EBT monomer and catalytic residues of MMP-8, providing molecular-level insights into imprinting specificity. These experimental and computational findings highlight the importance of rational monomer selection and nanomaterial-assisted polymerization in achieving selective protein imprinting. This work presents a systematic approach that integrates electrochemical engineering, nanomaterial interfaces, and computational validation to address long-standing challenges in protein-based MIP biosensors. By bridging molecular design with practical sensing performance, this study advances the translational potential of MIP-based electrochemical biosensors for point-of-care applications. Full article

Pubertal molting represents a pivotal transition in the life cycle of crustaceans, marking the shift from somatic growth to reproductive development. In mud crabs, mating is known to facilitate this process, yet the molecular mechanisms remain poorly understood. Here, we applied full-length transcriptome sequencing to characterize changes in gene expression and alternative splicing (AS) across post-mating ovarian development. AS analysis revealed extensive transcript diversity, predominantly alternative first exon (AF) and alternative 5′ splice site (A5) events, enriched in genes linked to chromatin remodeling, protein regulation, and metabolism, underscoring AS as a fine-tuning mechanism in ovarian development. Comparative analyses revealed profound molecular reprogramming after mating. In the UM vs. M1 comparison, pathways related to serotonin and catecholamine signaling were enriched, suggesting early neuroendocrine regulation. Serotonin likely promoted, while dopamine inhibited, oocyte maturation, indicating a potential “inhibition–activation” switch. In the UM vs. M3 comparison, pathways associated with oxidative phosphorylation, ATP biosynthesis, and lipid metabolism were upregulated, reflecting heightened energy demands during vitellogenesis. ECM-receptor interaction, HIF-1, and IL-17 signaling pathways further pointed to structural remodeling and tissue regulation. Enhanced antioxidant defenses, including upregulation of SOD2, CAT, GPX4, and GSTO1, highlighted the importance of redox homeostasis. Together, these findings provide the first comprehensive view of transcriptional and splicing dynamics underlying post-mating ovarian maturation in Scylla paramamosain, offering novel insights into the molecular basis of crustacean reproduction. Full article

As native bovine whey (WHEY) poses environmental concerns as a high-water-content by-product, this trial aimed at assessing the effectiveness of a thermal–mechanical microparticulation coupled with a fermentative process to concentrate it into a high-protein soft dairy cream. Compared to native whey, in microparticulated (MPW) and fermented (FMPW) matrices, there was a significant increase in proteins (from 0.7 to 8.8%) and lipids (from 0.3 to 1.3%), and a more brilliant yellowness colour. A factorial discriminant analysis (FDA) showed that FMPW had a higher content of saturated fatty acid (SFA) and some specific polyunsaturated fatty acid (PUFA) n-6, and also identified C14:0, C18:1, C18:1 t-11, C18:2 n-6, and C18:3 n-6 as informative biomarkers of microparticulation and fermentative treatments. The SDS-PAGE indicated no effects on the protein profile but indicated its rearrangement into high molecular weight aggregates. Z-sizer and transmission electron microscopy analyses confirmed a different supramolecular structure corresponding to a higher variability and greater incidence of very large molecular aggregates, suggesting that MPW could be accounted as a colloidal matrix that may have similar ball-bearing lubrication properties. Microparticulation of whey could facilitate its circularity into the dairy supply chain through its re-generation from a waste into a high-value fat replacer for dairy-based food production. Full article

The glyoxalase pathway intermediate S-d-lactoylglutathione was recently implicated in protein post-translational modifications in animal systems. Here, we examined the spontaneous modification of the Arabidopsis thaliana cytosolic glyceraldehyde-3-phosphate dehydrogenase C1 (GAPC1) by this compound. Incubation of GAPC1 with S-d-lactoylglutathione resulted in the inhibition of enzyme activity. The inhibitory effect was concentration dependent and increased at alkaline pHs. Furthermore, the inhibition of GAPC1 by S-d-lactoylglutathione was favored by oxidative conditions and reversed by reduction with dithiothreitol. Analyses of the S-d-lactoylglutathione-treated protein by nanoLC-MS/MS revealed S-glutathionylation of its two Cys residues and N-lactoylation of six Lys residues. Protein structure predictions showed that the double S-glutathionylation is accommodated by the GAPC1 catalytic pocket, which likely explains enzyme inhibition. N-lactoylated sites overlap partially with previously reported N-acetylated sites at the surface of the GAPC1 tetramer. The efficiency of cytosolic glutaredoxin and thioredoxin isoforms was tested for reversing the S-d-lactoylglutathione-induced modification. In these assays, recovery of GAPC1 activity after inhibition by S-d-lactoylglutathione treatment was used as indicator of efficiency. The results show that both types of redoxins were able to reverse inhibition. We propose a model describing the mechanisms involved in the two types of post-translational modifications found on GAPC1 following exposure to S-d-lactoylglutathione. The possible involvement of these findings for the control over glycolytic metabolism is discussed. Full article

Background/Objectives: Galectin-3 (Gal-3), encoded by LGALS3, is a β-galactoside-binding lectin involved in diverse tumor-associated processes, including immune modulation, cell cycle regulation, and stress adaptation. Despite its known roles in cancer biology, the full extent of its molecular functions and prognostic relevance across tumor types remains incompletely understood. This study aimed to systematically investigate the transcriptomic impact of LGALS3 deletion and assess its clinical significance in cancer. Methods: We analyzed CRISPR-Cas9 knockout transcriptomic data from the SigCom LINCS database to characterize the consensus gene signature associated with LGALS3 loss using functional enrichment analyses. Pan-cancer survival analyses were conducted using TIMER2.0. Differential Gal-3 protein levels in ductal adenocarcinoma and normal pancreatic tissues were evaluated using the Human Protein Atlas. Finally, functional analyses were performed in pancreatic ductal adenocarcinoma (PDAC). Results: LGALS3 deletion across multiple cancer cell lines led to transcriptomic changes involving mitotic progression, stress responses, and axonal guidance pathways. High LGALS3 expression was significantly associated with worse overall survival in lower-grade glioma, PDAC, uveal melanoma, and kidney renal papillary cell carcinoma. LGALS3 knockout in YAPC cells recapitulated the pan-cancer findings, linking LGALS3 to cell morphogenesis and proliferation. Conclusions: These findings identify Galectin-3 as a key regulator of oncogenic programs and a potential prognostic biomarker in PDAC and other malignancies, with implications for therapeutic targeting. Full article

This study distinguished male and female individuals by wing morphology (males with long wings, females with short wings) and investigated sexual dimorphism in the chemosensory system of Blaptica dubia through integrated ultrastructural and transcriptomic analyses. Scanning electron microscopy (SEM) was used to characterize the type, number, and distribution of antennal sensilla, while Illumina HiSeq sequencing, Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) annotation, and Quantitative Real-time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) validation were employed to analyze sex-specific gene expression profiles. Both sexes exhibited Böhm’s bristles, chaetic, trichoid, and basiconic sensilla. Males showed significantly more chaetic sensilla on the pedicel and longer type I/II chaetic sensilla on the flagellum, whereas females had longer ST2 sensilla. Basiconic sensilla were predominantly flagellar-distributed and more abundant/longer in males. No sexual differences were observed in Böhm’s bristles. Transcriptomics revealed 5664 differentially expressed genes (DEGs) (2541 upregulated; 3123 downregulated), enriched in oxidation-reduction, extracellular space, lysosome, and glutathione metabolism. KEGG analysis identified five key pathways: lysosome, glutathione metabolism, cytochrome P450-mediated xenobiotic/drug metabolism, and ascorbate/aldarate metabolism. Among 11 chemosensory-related DEGs, chemosensory proteins (CSPs) and odorant binding proteins (OBPs) were downregulated in males, while gustatory receptors (GRs), olfactory receptors (Ors), and ionotropic receptors (IRs) were upregulated. These results demonstrate profound sexual dimorphism in both antennal sensilla morphology and chemosensory gene expression, suggesting divergent sex-specific chemical communication strategies in Blaptica dubia, with implications for understanding adaptive evolution in Blattodea. Full article

High temperature stress is a critical factor affecting the growth and yield of melons (Cucumis melo L.), and improving heat tolerance is therefore crucial for stable production. While the overexpression of the CmDUF239-1 gene is known to improve salt tolerance in melons, its impact on heat tolerance remains unexplored. The role of the CmDUF239-1 gene in enhancing heat tolerance and its underlying mechanisms was investigated in this study. Melon seedlings overexpressing CmDUF239-1 (OEDUF239-1), generated via root transformation, exhibited significantly lower reductions in fresh and dry mass under heat stress compared to controls, indicating enhanced heat tolerance. One day post-stress, antioxidant enzyme activities (SOD, POD, CAT, APX, and GR) increased significantly in OEDUF239-1, while malondialdehyde (MDA) levels decreased. Additionally, proline content and the activity of its synthesizing enzyme (P5CS) rose, whereas the activity of proline dehydrogenase (ProDH) dropped. Transcriptomic and qPCR analyses revealed that CmDUF239-1 overexpression upregulated antioxidant enzyme-related genes (e.g., CmCSD1, CmPOD1) and proline-related genes (e.g., CmP5CS), as well as Heat Shock Protein (HSP) genes (e.g., CmHSP17.6II, CmHSP18.2). In summary, the enhancement of heat tolerance in melon by the CmDUF239-1 gene was mediated through the upregulation of genes involved in antioxidant defense and proline metabolism, together with increased accumulation of HSPs, providing a mechanistic basis for heat-resilient breeding programs. Full article

The recruitment of peripheral membrane proteins is tightly regulated by membrane lipid composition and local electrostatic microenvironments. Our experimental observations revealed that Vp54, a viral matrix protein, exhibited preferential binding to lipid bilayers enriched in anionic lipids such as phosphatidylglycerol (PG) and phosphatidylserine (PS), compared to neutral phosphatidylcholine/phosphatidylethanolamine liposomes, and this occurred in a curvature-dependent manner. To elucidate the molecular basis of this selective interaction, we performed a series of computational analyses including helical wheel projection, electrostatic potential calculations, electric field lines simulations, and electrostatic force analysis. Our results showed that the membrane-proximal region of Vp54 adopted an amphipathic α-helical structure with a positively charged interface. In membranes containing PG or PS, electrostatic potentials at the interface were significantly more negative, enhancing attraction with Vp54. Field line and force analyses further confirmed that both the presence and spatial clustering of anionic lipids intensify membrane–Vp54 electrostatic interactions. These computational findings align with experimental binding data, jointly demonstrating that membrane lipid composition and organization critically modulate Vp54 recruitment. Together, our findings highlight the importance of electrostatic complementarity and membrane heterogeneity in peripheral protein targeting and provide a framework applicable to broader classes of membrane-binding proteins. Full article

Background/Objectives: Neuroblastoma (NB) is an aggressive pediatric malignancy that accounts for nearly 15% of all childhood cancer-related deaths, with high-risk cases showing a poor 20% prognosis and limited response to current therapies. Survivin, encoded by the BIRC5 gene, is an anti-apoptotic protein frequently overexpressed in NB and linked to treatment resistance and unfavorable clinical outcomes. Methods and Results: An analysis of 1235 NB patient datasets revealed a significant association between elevated BIRC5 expression and reduced overall and event-free survival, highlighting survivin as an important therapeutic target in NB. To explore this strategy, we evaluated the efficacy of YM-155, a small-molecule survivin inhibitor, across multiple NB cell lines. YM-155 displayed potent cytotoxic activity in six NB cell lines with IC₅₀ values ranging from 8 to 212 nM and significantly inhibited colony formation and 3D spheroid growth in a dose-dependent manner. Mechanistic analyses revealed that YM-155 downregulated survivin at both mRNA and protein levels, induced apoptosis by about 2–7-fold, and caused G0/G1 phase cell cycle arrest. Moreover, YM-155 treatment enhanced p53 expression, suggesting reactivation of tumor suppressor pathways. Notably, combining YM-155 and the chemotherapeutic agent etoposide resulted in synergistic inhibition of NB growth with ED75 values ranging from 0.17 to 1, compared to either agent alone. In the xenograft mouse model, YM-155 inhibited tumor burden in contrast to controls by about 3-fold, and without any notable toxic effects in vivo. Conclusion: Overall, our findings identify YM-155 as a promising therapeutic agent for high-risk NB by directly targeting survivin and enhancing chemosensitivity. These results support continued preclinical development of survivin inhibitors as part of rational combination strategies in pediatric cancer treatment. Full article

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

Elevated cholesterol levels play important mitogenic roles. Pseurotin A (PsA) is a fermentation product that has recently been reported as a dual inhibitor of proprotein convertase subtilisin/kexin type 9 (PCSK9) secretion and protein-protein interaction (PPI) with the LDLR. PsA showed a high acute safety profile and therapeutic potential against metastatic castration-resistant prostate cancer (mCRPC). The study aims to uncover the chronic safety, distribution, and anti-mCRPC genomic and molecular mechanistic insights of PsA. A 90-day chronic safety assessment of PsA up to 80 mg/kg in Swiss albino mice showed no signs of hematological, biochemical, or major organ toxicity. PsA demonstrated rapid intravenous distribution and elimination in Swiss albino mice. PsA is biodistributed to multiple key organs but was not detected in the brain, indicating its inability to cross the blood-brain barrier. PsA effectively suppressed the recurrence of nude mice xenografted mCRPC, which was subjected to a neoadjuvant docetaxel and enzalutamide regimen, followed by surgical excision. Collected PsA and vehicle control-treated recurrent tumors were subjected to RNA-sequencing and pathway enrichment analysis (PEA) of differentially expressed genes (DEGs). PsA-treated tumors revealed multiple significantly enriched pathways associated with promoting tumor apoptosis and inhibiting both invasion and migration. The PPI network analyses for the downregulated DEGs displayed prominent networks of genes associated with the ubiquitin-proteasome system. Results provide comprehensive mechanistic and preclinical validations for PsA’s potential as a novel PC recurrence suppressive lead entity. Full article

Background/Objectives: Central precocious puberty (CPP) is diagnosed via gonadotropin-releasing hormone (GnRH) stimulation testing, which can be burdensome in pediatric settings. This study evaluated the utility of baseline hormonal markers—particularly insulin-like growth fac-tor 1 (IGF-1) and IGF-binding protein 3 (IGFBP-3)—as auxiliary tools for CPP diagnosis in Korean children. Methods: We retrospectively analyzed patients who underwent GnRH stimulation testing. Baseline LH, FSH, IGF-1, and IGFBP-3 levels were assessed, along with standard deviation scores (SDS) calculated using two different reference intervals. Multivariable logistic regression was performed to improve diagnostic accuracy. Performance was evaluated using area under the curve (AUC) values from receiver operating characteristic (ROC) analyses, stratified by sex. Results: Among 2464 Korean children (2025 girls and 439 boys), CPP diagnosis rates were 54.2% in girls and 65.6% in boys. Among baseline markers, FSH showed the highest AUCs using raw values with sex-specific cutoffs (AUC = 0.767 in girls and 0.895 in boys). Although IGF-1 SDS and IGFBP-3 SDS showed AUCs < 0.7 when used alone, predictive models incorporating these SDS values yielded higher performance (AUC = 0.800 in girls and 0.920 in boys. Conclusions: SDS-based IGF-1 and IGFBP-3 enhance CPP diagnosis when used in predictive models, emphasizing the need for sex-specific interpretation and standardized reference intervals in real-world clinical practice. Full article

Background/Objectives: Sleep is pivotal for recovery, immunity, and energy restoration; however, sleep problems exist in elite athletes. Nutrition and supplementation strategies can play both a positive and negative role in sleep quality and quantity. Elite athletes experience unique psychological and physiological demands above non-elite athletes and may require different nutrition strategies to promote sleep. Nutrient interventions and their effect on sleep in elite athletes is an emerging area, with further research warranted. Methods: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) extension for Scoping Reviews and Joanna Brigg’s Institute Reviewer’s Manual for Scoping Reviews were utilised to assess the available evidence on nutrition strategies used to promote sleep in elite athlete cohorts, and we tried to identify the interventions that could be best researched in the future. NUtrition QUality Evaluation Strengthening Tools (NUQUEST) was used to enhance rigour and assess risk of bias in studies. The Paper to Podium (P2P) Matrix was used to offer practitioners practical recommendations. Results: 12 studies met the inclusion criteria for nutrition interventions or exposures to promote sleep in elite athletes. The median participant group size was 19 and study designs were considered together to ascertain potential sleep promoting strategies. Kiwifruit, Tart Cherry Juice and high dairy intake, limited to females, have demonstrated the highest potential to promote sleep in elite athletes, despite limited sample sizes. A-lactalbumin, carbohydrate pre-bed, casein, tryptophan, probiotic and meeting energy demands showed varying results on sleep quality in elite athletes. Conclusions: Kiwifruit, Tart Cherry Juice and dairy consumption offer potential nutritional interventions to promote sleep in elite athletic populations, while protein-based interventions may have a ceiling effect on sleep quality when elite athletes are already consuming >2.5 g·kg⁻¹ body mass (BM) or are already meeting their sleep duration needs. Full article