Search Results (26,869)

The AP2/ERF superfamily is a key class of transcription factors involved in plant responses to various stresses. As an ancient species, the olive tree (Olea europaea L.) exhibits considerable stress tolerance and wide adaptability. In this study, we identified 348 AP2/ERF genes in the cultivated olive variety ‘Arbequina’ at the whole-genome level. According to protein sequence alignments and phylogenetic analyses via the Maximum Likelihood method, these genes were classified into four major families: AP2, ERF/DREB, RAV, and Soloist. The ERF/DREB family was further divided into DREB and ERF subfamilies, each encompassing six groups (A1–A6 and B1–B6), with the ERF subfamily being the largest. Members of each group exhibited relatively consistent gene structures and domain/motif compositions of their encoded proteins; however, the distribution of cis-elements and expression patterns varied. Each AP2/ERF gene contained 12 light-responsive, three MeJA-responsive, three ABA-responsive, two anaerobic induction, and one MYB binding site on average. With the threshold of p value < 0.5, control TPM > 0, and |log₂(fold change)| > 0, 50 candidate genes were simultaneously up-regulated (30) or down-regulated (20) under four stress treatments (acid–aluminum, cold, disease, and wound), among which nine showed potential protein–protein interactions. This study provides a comprehensive genomic characterization of the AP2/ERF family in olive and identifies key candidate stress-responsive genes, establishing a foundation for future functional studies on the molecular mechanisms of stress adaptation in the olive tree. Full article

The unfolded protein response (UPR) is a highly conserved adaptive mechanism that restores endoplasmic reticulum (ER) homeostasis under stress. Beyond its canonical roles in proteostasis, the UPR has emerged as a central regulator of immune responses across diverse contexts, including infection, inflammation, cancer, and autoimmunity. IRE1α, PERK, and ATF6 are three principal UPR sensors that coordinate complex signaling networks to regulate antigen presentation, cytokine production, and immune cell differentiation. This review highlights the molecular mechanisms by which small molecules target the UPR to modulate immune responses. In addition, we highlight stress granules (SGs) and the prevalence of protein–protein interactions mediated by intrinsically low-complexity domains (LCDs) in the UPR as potential new avenues for immune modulation. Finally, we discuss future directions for leveraging UPR modulation in immunotherapy, infectious disease, and chronic inflammatory disorders. Full article

The use of food packaging derived from petroleum-based polymers has developed significant environmental problems, as these materials require centuries to degrade and release hazardous pollutants. Consequently, the food industry is shifting toward biodegradable alternatives developed from agro-industrial by-products, such as proteins, polysaccharides, and lipids. Whey protein is a by-product of the cheese industry, which is emerging as a promising material for producing edible and biodegradable films with effective barrier properties. Whey-based films can be incorporated with bioactive compounds, particularly phenolic compounds. These substances, naturally present in fruits, legumes, and vegetable waste, possess potent antimicrobial and antioxidant activities that are essential for extending the shelf life of perishable foods. This review provides a systematic evaluation of how the incorporation of phenolic compounds influences the physicochemical and bioactive properties of whey-based films. Thus, an analysis of film-forming methods, the interaction between protein matrices and phenolic compounds, and a critical discussion of the challenges remaining for their industrial application as active food packaging were evaluated. The discussion focuses on how the incorporation of phenolic extracts influences the physicochemical, mechanical, and barrier properties of the films, as well as their antioxidant and antimicrobial efficiency. The novelty of this review lies in its comprehensive focus on the sustained release of phenolic compounds from a whey protein film and their application in real food systems. By utilizing these natural additives, the industry can provide sustainable alternatives to synthetic preservatives. Active whey protein packaging represents a viable strategy to inhibit food spoilage, prevent lipid oxidation, and maintain sensory quality, while reducing the environmental problems. Full article

The reliance on synthetic repellents such as N,N-diethyl-meta-toluamide (DEET) has raised health and environmental concerns, prompting the search for safer, plant-based alternatives. Catnip (Nepeta cataria L.), a rich source of iridoid monoterpenes, particularly nepetalactones, known for strong insect-repellent activity. However, their efficient extraction and molecular mechanisms in insect inhibition remains challenging. This study examined the chemical composition, protein–ligand interactions, and safety profiles of nepetalactones in comparison with DEET, with particular focus on mosquito odorant-binding proteins (OBPs) from Anopheles gambiae (AgamOBP), Culex quinquefasciatus (CquiOBP), and Aedes aegypti (AaegOBP). GC–MS/MS analysis identified nepetalactone isomers as the predominant constituents in catnip extracts obtained via steam distillation and olive oil extraction from dried leaves. Molecular docking results indicated that cis,cis-, cis,trans-, and nepetalactone isomers exhibited higher binding affinities toward the target OBPs than DEET. Furthermore, molecular dynamics simulations confirmed that all nepetalactone–OBP complexes exhibited stable conformations characterized by low average RMSD values and persistent hydrogen bond formation. Notably, cis,trans-NL–AaegOBP, NL–AaegOBP, and cis,cis-NL–AgamOBP complexes displayed lower binding free energies (ΔG_MM-PBSA) compared to DEET. These findings suggest that nepetalactones stabilize OBP–ligand interactions while inducing subtle conformational flexibility, potentially disrupting mosquito odorant recognition in a manner distinct from DEET. ADMET predictions indicated that nepetalactones exhibit favorable absorption, distribution, and safety profiles with reduced predicted toxicity compared to DEET. Collectively, these results establish nepetalactones as promising candidates for the development of effective, safe, and sustainable plant-based repellents. Full article

Background: Diabetes increases the risk of cataract formation fivefold. Immune-mediated inflammation has been reported to play a role in this process; however, whether alterations in the immune landscape are involved remains unknown. Therefore, we conducted a multi-omics analysis to evaluate the impact of immune inflammation on the lens. Methods: Bulk RNA sequencing was performed on peripheral blood mononuclear cells (PBMCs) from diabetic patients and lens tissues from diabetic rats. Single-cell RNA sequencing was utilized to characterize intercellular interactions. Key gene and protein expressions were validated via laboratory assays. Results: An integrated RNA-seq analysis revealed a disruption of the blood–aqueous barrier integrity in the diabetic group, enhanced monocyte migration and adhesion, increased differentiation from classical to non-classical monocytes, and the upregulation of TNF and IFN-γ signaling pathways. The transcriptomic profiling of rat lenses revealed an increased proportion of monocytes and the activation of apoptotic pathways in lens epithelial cells. Immunohistochemistry and immunofluorescence staining demonstrated elevated caspase-3 and IL-6 levels in lens epithelial cells and increased immune cell infiltration in the diabetic group. The qRT-PCR and ELISA confirmed elevated levels of the pro-inflammatory cytokines IL-6 and IFN-γ, alongside reduced anti-inflammatory cytokine IL-10 in the peripheral blood and aqueous humor of diabetic patients. Conclusions: Diabetes alters the peripheral immune microenvironment and disrupts the blood–aqueous barrier, promoting intraocular inflammation and lens epithelial cell apoptosis, thereby accelerating cataract development. Full article

Lanthanide ions and their complexes have emerged as versatile tools in biology and medicine owing to their unique photophysical, magnetic, and coordination properties. Their applications span bioimaging, sensing, therapy and diagnostics, underpinned by their strong preference for oxygen-donor ligands, kinetic stability, and tunable luminescence. This review integrates current developments in lanthanide coordination chemistry, focusing on the mechanistic basis of their interactions with biomolecules such as nucleic acids, proteins, and peptides. Moreover, this work highlights the design principles governing complex stability and biological compatibility, summarizing key biomedical uses of lanthanides ranging from imaging and drug delivery to anticancer and antioxidant effects, and discusses their toxicity and biodistribution, and their potential for clinical translation. In particular, this review offers a mechanistically oriented synthesis of recent advances, emphasizing the interplay between coordination behavior and biological function, and identifying emerging trends that define the current landscape of lanthanide-based bioinorganic research. By correlating molecular coordination features with biological performance, the review identifies the main trends shaping lanthanide-based bioinorganic research, also including a brief discussion of complexes formed between lanthanides and naturally occurring molecules, such as amino acids. Full article

Aggressive metastatic progression often develops in bladder cancer patients with acquired cisplatin or gemcitabine resistance. The potential of the natural isothiocyanates allyl-isothiocyanate (AITC), butyl-isothiocyanate (BITC), and phenylethyl-isothiocyanate (PEITC) to inhibit adhesion and migration of cisplatin- or gemcitabine-resistant and sensitive RT112, T24, and TCCSUP bladder cancer cell lines was investigated. Parameters determined were: cell interaction with collagen or fibronectin, chemotaxis, and membrane receptors involved in adhesion (total and activated integrins β1, β4, β5, CD44s, and CD44v3-v7). CD44s’ location and adhesion- and migration-related signaling proteins were determined. AITC blocked adhesion of almost all sensitive and resistant cancer cells. PEITC and BITC suppressed fibronectin interaction of sensitive and resistant RT112. All three isothiocyanates diminished chemotaxis in all cell lines. Integrin expression was differentially altered but CD44s and CD44v were not altered. BITC and PEITC translocated CD44s from the cell membrane to cytoplasm. The tumor suppressor E-cadherin increased, whereas focal adhesion kinase (FAK), linked to integrin signaling, was deactivated after isothiocyanate treatment. Blocking FAK, β1, β4, or β5 was associated with reduced chemotaxis. Thus, AITC, BITC, and PEITC blocked adhesion and migration in cisplatin- and gemcitabine-resistant bladder cancer cells. This was associated with altered integrin expression and signaling, CD44s translocation, and enhanced E-cadherin. Full article

Protein phosphorylation modification plays a role in cells’ response to oxidative stress, a key factor leading to postharvest browning of Flammulina filiformis. However, the molecular mechanism by which protein phosphorylation contributes to postharvest browning of F. filiformis remains unclear. This study aimed to characterize the basal phosphoproteomic landscapes associated with variations in different browning phenotypes of F. filiformis. Using data-independent acquisition (DIA) mass spectrometry, we comprehensively profiled the phosphorylation dynamics in susceptible-to-browning (SB) and resistant-to-browning (RB) cultivars at harvest and after 24 h storage. We identified 84,244 phosphorylation sites on 4494 phosphoproteins, with the SB cultivar displaying more altered sites (21,195) than the RB (16,087). Functional enrichment analysis revealed that the differential phosphorylation was significantly implicated in kinases and energy metabolism pathways. Notably, the SB cultivar exhibited a more pronounced phosphorylation profile on key proteins involved in ATP synthesis and glycolysis. Protein–protein interaction (PPI) network analysis further indicated a kinase-mediated regulatory network targeting core energy metabolism components, including ATP synthase and 6-phosphofructokinase. This distinct phosphosignature in the SB cultivar correlated with its more severe browning phenotype and a sharper decline in ATP content during storage. Our findings suggest that divergent phosphorylation-mediated regulation of energy metabolism is strongly associated with the differential postharvest browning susceptibility between these two cultivars, providing a valuable molecular resource for future functional studies. Full article

OGG1 and MUTYH are base excision repair (BER) DNA glycosylases (DGs) from the Helix–hairpin–Helix superfamily responsible for initiating and coordinating the repair of 8-oxo-7,8-dihydroguanine (OG), and its replication-derived mispair with adenine (OG:A), respectively. The DNA repair activities of these DGs are pivotal to safeguarding nuclear and mitochondrial genomes. Indeed, DG functional impairment is associated with numerous pathologies, including neurodegenerative diseases, metabolic syndromes, and cancer. The timely and precise localization and processing of oxidized nucleobases carried out by these DGs are modulated by a complex regulatory network at both transcriptional and posttranslational levels, as well as intricate protein–protein interaction networks. In the absence of regulation, inappropriate and imbalanced DG activity may trigger telomeric instability, changes in transcriptional profiles and cell death. This review focuses on summarizing key features of OGG1 and MUTYH function, with a special emphasis on structure, regulation, and novel emerging roles. Full article

Chronic liver injury is accompanied by coordinated disturbances in lipid trafficking and inflammatory–fibrogenic signaling. Transforming growth factor beta 1 (TGF-β1) signaling has been implicated in hepatic fibrogenesis and tumor-associated remodeling and may co-vary with disturbances in lipid trafficking. Lisosan G (LG), a fermented wheat-derived nutraceutical, has reported antioxidant and anti-inflammatory activity and may influence these interconnected pathways. This study evaluated whether dietary LG alters the lipid composition of plasma lipoprotein fractions and hepatic TGF-β1 levels across distinct liver contexts. Seventy-two female Wistar rats were randomized into nine groups (n = 8/group) defined by liver condition, consisting of healthy control (Control), non-neoplastic liver (PH), and neoplastic liver injury (HCC; PH followed by diethylnitrosamine, DEN), and diet (standard diet, SD + 2.5% LG, or SD + 5% LG). Plasma lipoproteins (VLDL, LDL, HDL₁, HDL₂) were isolated by stepwise KBr density-gradient ultracentrifugation, and cholesterol (TC), phospholipids (PL), and triacylglycerols (TG) were quantified in each fraction. Hepatic TGF-β1 was measured by ELISA and normalized to total protein. LG effects depended strongly on baseline liver status, with significant Condition × Diet interactions for most lipid endpoints and for hepatic TGF-β1. In healthy rats, LG produced fraction-selective remodeling rather than uniform lipid lowering, including increased VLDL-TG at both doses and non-linear changes in cholesterol distribution across LDL and HDL subfractions. After PH, LG broadened lipid remodeling, including reduced VLDL-PL, increased VLDL-TG (both doses), and an increase in LDL-TC at 5% LG, accompanied by marked changes in HDL₁/HDL₂ cholesterol partitioning. In HCC, LG induced pronounced, often dose-dependent increases in LDL-associated lipids (LDL-PL, LDL-TG, LDL-TC) and increased HDL₁-TC while decreasing HDL₂-TC. Hepatic TGF-β1 was elevated in PH and further increased in HCC versus controls; LG reduced hepatic TGF-β1 in a condition-dependent manner, with the strongest reduction at 5% LG in HCC. Dietary Lisosan G remodels circulating lipoprotein lipid composition in a liver-status-dependent manner and is associated with reduced hepatic TGF-β1 abundance in injured liver, most prominently in neoplastic injury. These findings are consistent with the notion that nutraceutical interventions may show stronger phenotypic effects under perturbed metabolic–fibrogenic states than under stable physiology, while highlighting the need for mechanistic work to distinguish altered lipoprotein secretion from changes in peripheral clearance and to assess pathway-level TGF-β signaling. Full article

Osteosarcoma (OS) is the most common primary malignant bone tumor in adolescents, and outcomes for metastatic disease have remained poor, highlighting the need for molecular biomarkers. We integrated three Gene Expression Omnibus (GEO) mRNA expression datasets (GSE12865, GSE14359, and GSE246405) to identify differentially expressed genes (DEGs) between OS and non-malignant bone-related controls. Overlapping DEGs were used to build a protein–protein interaction network, and hub genes were prioritized using multiple network topology algorithms. Prognostic associations were evaluated using the R2 Genomics Platform. Putative upstream miRNAs targeting the top candidate were obtained from prediction databases and intersected with dysregulated circulating miRNAs from GSE65071 (localized OS plasma vs. healthy controls). Functional enrichment analyses (Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and cancer hallmarks) were performed to contextualize the candidate signature. We identified 107 overlapping DEGs and prioritized eight hub genes. CD81 was significantly associated with overall survival (Bonferroni-adjusted p = 0.043) and showed reduced expression in OS tissues and cell line models. hsa-miR-582-5p was nominated as a candidate miRNA predicted to target CD81 and was upregulated in OS plasma. Enrichment results linked the signature to angiogenesis, extracellular matrix remodeling, focal adhesion, and metastasis-associated signatures. These findings support CD81 as a candidate prognostic biomarker and nominate a putative hsa-miR-582-5p–CD81 relationship for future validation. Full article

Functional coatings for food packaging offer innovative approaches to extend shelf life, preserve quality and introduce active properties such as antimicrobial or antioxidant effects. These coatings include natural bio-based films (e.g., polysaccharide or protein-based) and synthetic polymers enhanced with additives or nanomaterials. Despite their advantages (e.g., improved barrier properties, spoilage inhibition, or intelligent sensing) they also pose safety concerns. Migration of chemical constituents and additives into food can lead to toxicological risks, such as cytotoxicity or endocrine disruption. Non-intentionally added substances (NIASs) and nano-sized components further complicate safety assessments. This review outlines the main types of functional coatings, their active mechanisms, and associated safety issues. Particular focus is placed on migration phenomena, chemical interactions and health risks from common migrants including plasticizers, monomers, nanoparticles and essential oils. The EU Packaging and Packaging Waste Regulation (Regulation (EU) 2025/40), adopted in December 2024 and published in the Official Journal in January 2025, introduces comprehensive sustainability and substance-restriction requirements, including strict criteria for food packaging materials that will apply from 12 August 2026. Emerging challenges include the assessment of bio-based and recycled coatings and the toxicology of nanomaterials. Balancing functionality with safety remains crucial for next-generation, sustainable and health-compliant food packaging. Full article

The broadly neutralizing monoclonal antibody 3D1 potently neutralizes SADS-CoV by targeting a conserved epitope within the heptad repeat 1 (HR1) domain of the viral spike protein. Structural and biophysical analyses demonstrate that 3D1 binds with high affinity to a specific linear β-turn motif (residues A804–N809) in HR1. High-resolution crystallography reveals that this motif sits within a deep, electrostatically complementary paratope groove. Critically, 3D1 binding competitively inhibits the essential interaction between HR1 and HR2. Notably, its recognition is not dependent on HR1’s native helical conformation, as it maintains strong binding to conformationally constrained, stapled helical peptides. Collectively, the data indicate that 3D1 neutralizes by capturing a pre-hairpin intermediate state of HR1—a transition state between prefusion and postfusion forms—thereby sterically blocking the formation of the stable postfusion six-helix bundle that is essential for membrane fusion. This work defines a precise, structure-dependent neutralizing epitope and elucidates a mechanism of action that involves trapping a key fusion intermediate, offering a valuable template for the design of broad-spectrum coronavirus therapeutics. Full article

Background/Objectives. Oxidative stress is a key contributor to HIV-associated neurocognitive disorders (HANDs), yet the regional organization and functional engagement of the NRF2 antioxidant pathway in the human brain remain incompletely defined. This study aimed to characterize NRF2 pathway architecture, baseline brain expression, and disease-associated transcriptional and coexpression remodeling across HAND stages. Methods. The NRF2 signaling network was reconstructed using curated pathway data and protein–protein interaction analysis to identify central hub genes. Baseline expression in the normal human cortex was assessed using the Human Protein Atlas. Transcriptomic profiling of postmortem brain samples from individuals with HAND (GSE35864) was performed using differential expression, hierarchical clustering, and region-specific coexpression analyses across white matter, frontal cortex, and basal ganglia. Results. Low-to-medium baseline expression of NRF2-related genes was observed in the normal cortex. Bulk differential expression revealed minimal NRF2 pathway modulation in the frontal cortex and basal ganglia. On the other hand, white matter exhibited robust NRF2 transcriptional activation specifically in HIV encephalitis (HIVE). Coexpression analysis performed specifically within HAND samples revealed a highly coordinated transcriptional organization of the NRF2 signaling network across all analyzed brain regions. Conclusions. NRF2 signaling in HAND is preserved as a coordinated transcriptional network but is selectively activated in white matter during encephalitic disease, highlighting region- and cell-type-targeted therapeutic opportunities. Full article

Background/Objectives: Granulicatella adiacens infective endocarditis is conventionally managed with penicillin, ampicillin, or ceftriaxone in combination with gentamicin, although double beta-lactam regiments have been proposed a safer alternative to reduce aminoglycoside-associated nephrotoxicity. To date, the High-Molecular-Mass Penicillin-Binding Proteins (HMM-PBPs) of G. adiacens and their affinities for beta-lactam antibiotics have not been previously characterized. This study investigated the HMM-PBP profile of G. adiacens, with particular interest on sequence alterations and beta-lactam binding properties, both as single agents and in combination. Methods: Beta-lactam activity, synergistic interactions and PBP binding affinities were evaluated in a clinical isolate (IS 48) and compared with those in the reference strain ATCC 49175. Binding of PBPs to ampicillin, ceftriaxone, and ceftobiprole, alone or in combination, was investigated by Bocillin-FL labeling. PBP homology and conserved active-sites motifs were assessed by sequence alignment, and pbp gene mutations were identified by whole-genome sequencing. Results: The clinical isolate was non-susceptible to ampicillin, resistant to ceftriaxone and exhibited higher minimum inhibitory concentrations (MICs) for ceftobiprole relative to the fully susceptible ATCC reference strain. Five HMM PBPs with high enterococcal homology, were identified. In the IS 48 isolate, the class A PBP showed distinct amino acid substitutions in proximity to the catalytic centers. Despite these alterations, PBP1A and PBP2A were strongly inhibited by the tested beta-lactams, whereas PBP2 and PBP2B demonstrated low acylation rates. Combination of ampicillin with either ceftobiprole or ceftriaxone resulted in enhanced acylation of the three bifunctional HMM PBPs compared with monotreatment. IC₅₀ values were consistently higher for the IS 48 clinical isolate, suggesting decreased target availability and/or reduced beta-lactam affinity under clinical conditions. Conclusions: The resistance phenotype of G. adiacens clinical isolate appears to be primarily associated with altered PBP beta-lactam interactions. Nonetheless, beta-lactam combination regimes remain effective by achieving substantial inhibition of key HMM-PBPs involved in peptidoglycan synthesis, thereby supporting the rationale for dual beta-lactam therapy in this setting. Full article