Search Results (9,890)

Gum arabic (GA) is a widely used natural hydrocolloid in food processing because its protein–polysaccharide architecture combines high water solubility, low bulk viscosity, and useful interfacial activity. These attributes make GA valuable as an emulsifier, encapsulating agent, and film-forming material, but native GA is constrained by source-dependent heterogeneity, limited antioxidant functionality, relatively high dosage requirements in some emulsions, and modest barrier and mechanical performance in dried matrices. This review synthesizes recent advances in chemical functionalization, enzymatic and oxidative grafting, physical fractionation and complexation, and Maillard-type bioconjugation as routes to tailor GA for food engineering applications. Emphasis is placed on process-relevant structure–property relationships, including dynamic adsorption, interfacial rheology, emulsifying and encapsulation efficiency, bulk rheology, powder glass transition and hygroscopicity, film barrier behavior, and release kinetics. Across beverage emulsions, spray-dried powders, coacervates, coatings, and delivery systems, the evidence shows that modification must be selected according to the dominant process bottleneck, such as adsorption kinetics, oxidative stability, drying behavior, or humidity-sensitive matrix mobility. This review also identifies priorities for translation, including model-ready measurements, the management of raw-material variability, scale-up-aware processing, and sustainability and regulatory practicality. Overall, modified GA emerges as a versatile platform for designing more robust, application-specific food colloids, encapsulates, and functional coatings. Full article

The membrane fusion process, mediated by the entry fusion complex (EFC) of the monkeypox virus (MPXV), is crucial for host cell invasion. Apolipoprotein B mRNA Editing Catalytic Polypeptide-like 3 (APOBEC3)-driven mutation bias is a key factor in MPXV’s adaptive evolution during its global spread. However, how these mutations affect the structure and function of EFC proteins remains poorly understood. To address this, we performed genomic mutation analysis on globally circulating MPXV clades Ib and IIb, combined with protein monomer, binary, and quaternary complex structure modeling based on AlphaFold 3 and experimental validation by ELISA. We first delineated the mutational spectra of all 11 EFC proteins, revealing that although EFC proteins in clade Ib are highly conserved, lineage IIb B exhibits extensive APOBEC3-driven mutations and the G9 M142I mutation is identified as a lineage-associated APOBEC3-type mutation of lineage IIb B. Structural predictions revealed that while the M142I mutation does not alter G9 monomer folding, it induces a conformational shift in the G9/A16 subcomplex. Furthermore, within the predicted G9/A16/A56/K2 quaternary complex, this mutation enlarges the interfacial gap and reduces docking stability between the G9/A16 subcomplex and A56/K2. Experimental validation demonstrated that the M142I mutation significantly reduces the binding affinity of G9 for A16 and impairs the recruitment of A56/K2 to the quaternary complex, confirming the computationally predicted mechanism of interface destabilization. These findings highlight a dynamic interplay between APOBEC3-driven evolution and EFC protein structure, demonstrating that the M142I mutation alters EFC complex assembly dynamics and may shift the regulatory balance of the membrane fusion system. These structural changes provide molecular insights into MPXV lineage differentiation, though direct functional assays are required to determine the net effect on viral entry efficiency. Full article

Chikungunya virus (CHIKV) is an alphavirus that infects dermal fibroblasts as a primary target cell during natural mosquito-borne transmission. While primary human dermal fibroblasts (hDFs) have been implicated as a key source of type I interferon (IFN-I) during CHIKV infection, the dynamics of this response and its sufficiency for antiviral protection remain incompletely understood. Here, we systematically characterize in vitro CHIKV infection of primary hDFs, evaluating the effects of single-passage viral stock origin (mammalian- vs. mosquito-propagated), donor variability, and multiplicity of infection (MOI) on infection kinetics and innate immune induction. We demonstrate that hDFs support high-titered CHIKV replication at both MOI 1 and 0.01, resulting in universal cell death by 72 hpi despite robust IFNβ transcript induction—reaching up to ~2800-fold over mock—and secretion of pro-inflammatory cytokines, including IFNα2, TNFα, IL-1β, and IL-8. Notably, IFNβ protein levels remained below 10 pg/mL under all infection conditions, revealing a disconnect between transcriptional and translational responses, suggesting CHIKV-mediated translational suppression. Pharmacological inhibition of TBK1/IKKε via amlexanox did not suppress IFNβ transcript induction at any tested concentration, suggesting that canonical PRR signaling through this node—including both RIG-I/MAVS and TLR3/TRIF pathways—is not the major driver of the observed transcriptional response. In contrast, co-inoculation with exogenous IFNβ as low as 20 pg/mL activated IFNAR signaling, robustly upregulated interferon-stimulated genes (ISGs), and fully rescued hDFs from otherwise lethal infection. Together, these findings demonstrate that CHIKV-infected hDFs mount a transcriptionally robust but translationally insufficient innate immune response and that the transcriptional response appears to operate independently of TBK1/IKKε. These results have direct implications for understanding how the skin microenvironment may modulate early CHIKV pathogenesis and suggest that paracrine IFNβ signaling from neighboring cell types may be critical for fibroblast survival during natural infection. Full article

Background: Arginine and related amino acids are widely used to suppress protein aggregation, thereby affecting stability, manufacturability, and therapeutic performance. However, their effectiveness remains limited, necessitating the exploration of alternative strategies. Previous studies have shown that N-acetyl-L-arginine (NA-Arg) can improve protein stability; however, the potential of other N-acetylated amino acids has not been fully explored. Methods: This study aimed to investigate the effects of multiple N-acetylated amino acids as alternative excipients on aggregation, colloidal stability, and viscosity in intravenous immunoglobulin (IVIG) formulations. Dynamic light scattering (DLS) was used to evaluate diffusion behavior and aggregation tendencies, while complementary analyses were performed using size-exclusion chromatography (SEC) and flow-imaging microscopy (FI). Results: Overall, N-acetylation of amino acids improved colloidal stability, shifting the kD values from −5.87 to 6.83 mL/g for arginine and from −8.17 to 16.22 mL/g for histidine, and increased the aggregation onset temperature (Tagg) to above 60 °C. Among the tested compounds, N-acetyl-L-histidine (NA-His) showed the most favorable results, increasing the monomer proportion by approximately 4%, reducing high-molecular-weight species to below 2%, and producing a greater than 10-fold decrease in subvisible particles relative to histidine hydrochloride after 5 days of agitation. At 50 mM, both NA-His and NA-Arg reduced the viscosity of highly concentrated 200 mg/mL IVIG formulations, with NA-His exhibiting the lowest viscosity (7.24 ± 0.12 mPa·s). Protein–protein interaction and surface charge analyses indicated improved colloidal stability relative to parent amino acids, attributable to the presence of the acetyl group. Conclusions: These findings support the potential of N-acetylation as a strategy to modulate interaction-driven instability and suggest NA-His as a promising candidate excipient for stabilizing highly concentrated therapeutic proteins at acidic pH. Full article

Background/Objectives: Bladder cancer treatment is frequently hindered by chemoresistance to agents such as cisplatin, a process in which autophagy is hypothesized to play a cytoprotective role. This study aimed to investigate the time-dependent transcriptional dynamics of autophagy-related genes in response to cisplatin in bladder cancer cell lines to better elucidate the molecular underpinnings of this resistance. Methods: Two human bladder cancer cell lines, T24 and 5637, were exposed to varying concentrations of cisplatin. Cell viability and half-maximal inhibitory concentration (IC₅₀) values were determined at 24 and 48 h using the MTS assay. Subsequently, the relative mRNA expression levels of key autophagy-related genes (ULK1, BECN1, ATG5, ATG7, LC3B, SQSTM1/p62, LAMP1, and TFEB) were quantitatively analyzed via RT-qPCR at 0, 6, 24, and 48 h intervals. Results: Cisplatin exerted a dose- and time-dependent cytotoxic effect, with 5637 cells exhibiting significantly greater sensitivity compared to T24 cells. Transcriptional analysis revealed a dynamic, multiphasic modulation of the autophagic pathway: an early-phase upregulation of initiation genes (ULK1, BECN1), a mid-phase increase in autophagosome formation genes (ATG5, ATG7), and a late-phase alteration in lysosomal regulation genes (LAMP1, TFEB). Notably, the more chemoresistant T24 cells mounted a robust and sustained autophagic transcriptional response, whereas the sensitive 5637 cells demonstrated a more limited and transient reaction. Conclusions: Cisplatin modulates the autophagic pathway at the transcriptional level in a highly dynamic, time-dependent, and cell-line-specific manner. Interpreted alongside established functional evidence in the literature, the sustained autophagic gene expression observed in the resistant cells is consistent with a potential cytoprotective role, warranting further functional validation at the protein level. These findings map the temporal genetic landscape of cisplatin-induced autophagy, providing a theoretical framework for optimizing the timing of autophagy-targeted combination therapies in bladder cancer. Full article

Background: Liquid biopsy-based biomarkers provide valuable insights into tumor biology, dynamics, burden, relapse prediction and therapeutic responsiveness. The stress-inducible heat shock protein 70 (Hsp70), which is frequently overexpressed in highly aggressive solid tumors and is presented on the cell membrane of tumors but not normal cells, is found in the circulation either as a free protein originating from dying cells or in the context of extracellular vesicles (EVs) that are actively released by viable tumor cells. This study demonstrates the potential value of circulating Hsp70 (eHsp70) levels across multiple solid tumor entities as an entity- and stage-dependent diagnostic biomarker reflecting tumor burden and disease stage. Methods: Circulating eHsp70 levels, as determined using the Hsp70-exo ELISA which detects free and EV-associated Hsp70, in plasma samples collected from patients with different tumor entities (n = 389) prior to the initiation of any oncological therapy and healthy controls (n = 108) between 2021 and 2025, were analyzed retrospectively. Tumor stages were categorized as early, locally advanced, or metastatic. The Kruskal–Wallis test was used for group comparisons and the Receiver Operating Characteristic (ROC) curve was used to evaluate the diagnostic performance of eHsp70 levels. DeLong’s test was used to calculate differences between AUC values. Results: In tumor patients (n = 389), circulating eHsp70 levels were significantly higher than those in healthy controls (n = 108) (Kruskal–Wallis, p < 0.001). eHsp70 levels progressively increased from early-stage to locally advanced and metastatic disease in a stage-dependent manner. Although ROC analysis demonstrated the limited discriminatory performance of eHsp70 levels in early-stage disease (AUC 0.569), increased discrimination was apparent in locally advanced disease (AUC 0.751), metastatic tumors (AUC 0.784) and combined advanced tumor diseases (AUC 0.765; significant by DeLong’s Test comparing early-stage to locally advanced and metastatic tumors), irrespective of the tumor entity with the highest AUC values in metastatic breast cancer (AUC 0.872), sarcoma (AUC 0.861) and non-small cell lung cancer (NSCLC) (AUC 0.835). Apart from minor entity-specific differences, the correlation of eHsp70 levels with the tumor stage remained consistent across all measured tumor entities. Conclusions: Circulating eHsp70 levels are markedly elevated in patients with highly malignant solid tumors and show a consistent, stage-dependent increase across multiple tumor types. These findings suggest that circulating eHsp70, as an indicator of tumor-associated cellular stress and overall tumor burden, represents a valuable biomarker for assessing disease stage, monitoring disease progression, and evaluating therapeutic responses. Full article

Potato early blight (EB), caused by Alternaria, is an economically devastating fungal disease affecting global potato production. Using a hybrid population derived from distantly related varieties, we combined resistance evaluation, histological analysis, Bulked Segregant Analysis sequencing, RNA sequencing and molecular dynamics simulation, which successfully identified key candidate resistance genes. Genetic mapping localized three major resistance-associated regions on chromosome 8 spanning positions 25.07–29.20 Mb, 38.05–38.80 Mb, and 39.40–40.78 Mb. Through candidate gene analysis, we identified CND41, encoding an aspartic protease, as the prime candidate. This gene exhibited significantly higher basal expression levels and stronger pathogen-induced upregulation in resistant genotypes. Molecular dynamics simulations further identified six crucial non-synonymous mutations in the TAXI-N domain that likely contribute to enhanced resistance by destabilizing the susceptibility-associated protein conformation. Transient overexpression of CND41 provided functional evidence supporting its likely involvement in early blight resistance (EBR). These findings contribute valuable genetic resources and a strong candidate gene for molecular breeding toward EBR potato varieties. Full article

Senecavirus A (SVA) has rapidly emerged as a globally distributed swine pathogen, with clinical signs mimicking vesicular diseases such as Foot-and-Mouth Disease, posing challenges for timely detection and control. Here, we analyzed 329 complete SVA genomes spanning multiple continents to provide a comprehensive view of its evolutionary dynamics, recombination patterns, haplotype diversity, and global dissemination. Phylogenetic analyses revealed two major lineages: Lineage 1, consisting mainly of early strains from the United States before 2007, and Lineage 2, which emerged post-2007 and subsequently spread across the Americas and East Asia. Recombination was confined to Lineage 2 and concentrated in nonstructural regions, particularly 2C, highlighting intra-lineage genetic exchange as a driver of recent diversification. Haplotype analysis of the 3AB gene identified 170 distinct haplotypes, revealing a star-like network structure consistent with rapid population expansion from a central ancestral variant, while secondary branches reflect ongoing regional diversification. Despite this high genetic variation, genome-wide dN/dS ratios remained below one, and purifying selection was strongest in the N-terminal domains of structural and nonstructural proteins, indicating functional constraints that maintain viral fitness. Time-scaled phylogenetic reconstruction and Bayesian Skyline analysis revealed rapid lineage diversification and a marked increase in effective population size in the early 2010s. Phylogeographic inference further identified repeated introductions from the Americas into East Asia, likely facilitated by swine trade and other anthropogenic factors. Collectively, SVA evolution is driven by frequent mutation and intra-lineage recombination yet constrained by pervasive purifying selection, generating extensive genetic diversity while maintaining functional integrity, with implications for genomic surveillance and targeted control. Full article

This study compared oat yoghurt (OY), almond yoghurt (AY), oat–almond yoghurt (OAY), and an unfermented oat–almond milk (OAM) to clarify how blending and lactic fermentation affect fermented plant-based alternatives to yoghurt. Nutritionally, OAY showed a balanced profile (protein 2.87 g/100 g; fat 5.18 g/100 g), intermediate between AY (3.29 g/100 g, 8.89 g/100 g) and OY (2.39 g/100 g, 3.30 g/100 g). Fermentation enhanced physical stability, as OAY showed higher water-holding capacity (58.08%) and high viscosity (5381.49 mPa·s), together with the highest viable lactic acid bacteria count (7.1 log10 CFU/g). Scanning electron microscopy revealed that co-fermentation formed a denser, more cohesive multiphase gel network with reduced pore size compared with OAM and AY. All samples exhibited shear-thinning behavior; dynamic rheology indicated weak gel features (G′ > G″), and OAY showed the highest G′, implying a reinforced network likely associated with interactions between oat β-glucan and almond proteins during fermentation. Volatile profiling by GC–MS identified 117 compounds, and OAY exhibited the greatest total volatiles (523.02 μg/kg), exceeding OY (397.43 μg/kg) and OAM (195.73 μg/kg), indicating improved aroma complexity and consumer acceptability. In conclusion, our study will provide quantifiable formulations for the development of highly acceptable oat and almond-based plant-based yoghurt. Most importantly, it also offers additional dairy products for individuals with gluten allergies and lactose intolerance. Full article

This article explores the complex interplay between the process of protein translation and DNA methylation, discussing their combined involvement in brain development. We will emphasize on DNA methylation and related proteins such as DNMTs, TETs, and MeCP2, the latter being the prototype of DNA methyl-binding proteins. Collectively, DNA methylation machinery may be involved in controlling the cell fate commitment of brain cells, as well as their neuronal and glial lineage specification. We aim to summarize current knowledge on the dynamics of protein translation, ribosome biogenesis, and relevant cellular pathways, including the mTOR signaling, in the context of brain development. Special attention is given to MeCP2 because of its unique role as an epigenetic factor that influences the chromatin states with a link to protein translation and its relevance to human disease. We also discuss the impact of DNA methylation-mediated chromatin regulation and protein translation in neurodevelopmental disorders. Our discussions include multi-omics techniques and integrative mechanisms that connect DNA methylation with protein translation. Full article

Coastal groundwater in monsoon-dominated regions faces compounding threats from seasonal hydrological extremes and seawater intrusion (SWI), yet the molecular-scale response of dissolved organic matter (DOM) remains poorly understood. We conducted a two-season investigation in Mannar District, Sri Lanka, integrating hydrochemistry, fluorescence spectroscopy, and Fourier-transform ion cyclotron resonance mass spectrometry to characterize DOM dynamics across shallow and deep groundwater. Dry-season chloride averaged 302 mg/L (shallow—5 to 12 m) and 505 mg/L (tube wells—20 to 30 m), then declined by 60–80% during monsoon recharge. Despite this freshening, DOM dynamics were decoupled from salinity: shallow wells showed dry-season DOC peaks (6.64 mg/L) driven by soil concentration, while tube wells exhibited wet-season enrichment (5.02 mg/L). Shallow aquifers maintained consistently high humification indices (around 0.70) and aromatic-rich DOM, indicating sustained buffering by soil-derived inputs. In contrast, wet-season recharge in tube wells appeared to stimulate microbial processing, as indicated by elevated protein-like fluorescence (C2: 26% to 36%) and a higher contribution of nitrogen-bearing formulas (CHONs: 31.4% to 37.1%). Tube wells also accumulated reduced, energy-rich DOM with correspondingly high molecular lability indices. Paradoxically, correlation networks suggested that these saturated aliphatic and halogenated structures persist due to kinetic protection under low oxygen, high-salinity conditions. These findings indicate that aquifer structure and redox conditions control DOM biogeochemistry in coastal groundwater systems. At the molecular level, DOM dynamics are influenced by aquifer depth and seasonal recharge, leading to a decoupling between salinity and organic matter transformation. Full article

Background: Influenza A(H3N2) viruses remain a major public health concern due to their rapid antigenic evolution and association with severe disease, particularly among high-risk populations. During the 2025–2026 influenza season, a marked epidemiological shift was observed in Europe, with the emergence and predominance of the A(H3N2) subclade K (J.2.4.1). Objectives: This narrative review aims to provide an integrated overview of the epidemiology, evolutionary dynamics, and public health implications of subclade K, with a particular focus on its impact on vaccine effectiveness, in comparison with the 2024–2025 influenza season. Methods: A non-systematic literature review was conducted using major scientific databases and official public health sources, including WHO and ECDC reports. Recent surveillance data, genomic analyses, and epidemiological updates were included. Given the rapidly evolving evidence base, selected preprint studies were also considered and interpreted with caution. Results: The 2025–2026 influenza season in Europe was characterized by a relative genetic convergence, with subclade K accounting for the majority of A(H3N2) sequences. This variant demonstrated a clear selective advantage and was associated with an earlier and more intense epidemic peak. Molecular analyses indicate the accumulation of multiple mutations in the hemagglutinin protein, particularly within key antigenic sites, contributing to immune escape. These evolutionary changes have important implications for vaccine effectiveness, with current estimates suggesting moderate protection against infection but preserved effectiveness against severe outcomes. Antigenic mismatch, manufacturing constraints, and host-related factors further contribute to reduced vaccine performance. Conclusions: The emergence and rapid spread of subclade K highlight the dynamic nature of influenza virus evolution and its impact on public health. Continuous genomic surveillance and timely vaccine updates remain essential. Despite suboptimal effectiveness against infection, influenza vaccination continues to provide significant protection against severe disease and should remain a cornerstone of prevention strategies. Full article

Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening “sequence–function gap” exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function. Full article

Neutrophils are the most abundant circulating leukocytes and are characterized by a proteome in which granule-associated proteins synthesized during granulopoiesis constitute a major fraction of total cellular protein, reflecting their preloaded effector nature in innate immune defense. A striking feature of neutrophil biology is the unusual abundance of the calcium-binding proteins S100A8 and S100A9, which together form the heterodimeric complex known as calprotectin. Early biochemical studies estimated that S100A8/A9 constitutes a substantial fraction of the soluble cytosolic proteome in neutrophils, with later studies often describing it as one of the most abundant protein complexes in these cells. Despite extensive studies on the antimicrobial and inflammatory activities of calprotectin, the biological rationale for this unusual abundance remains incompletely understood. In this review, we examine the structural, biochemical, and regulatory features of S100A8/A9 and explore the potential explanations for its high abundance in the neutrophil cytosol. We first discuss the unique organization of the neutrophil proteome and the transcriptional programs governing granulopoiesis that lead to large-scale production of neutrophil effector proteins. We then review the structural and biochemical properties of S100A8/A9, including its calcium-dependent conformational dynamics and high-affinity transition metal binding, which contribute to antimicrobial defense through nutritional immunity. Several functional hypotheses are considered to explain calprotectin abundance, including roles as an antimicrobial reservoir, a metal-sequestering molecule, a regulator of oxidative stress, and a source of damage-associated molecular patterns. Finally, we discuss the evolutionary logic of neutrophil protein preloading and the implications of calprotectin biology in inflammatory diseases and the tumor microenvironment. Resolving the abundance paradox of S100A8/A9 may reveal fundamental principles governing the organization of innate immune cell proteomes and provide new insights into the strategies used by neutrophils to achieve rapid and effective host defense. Full article

Qualitative analysis of biochemical reaction systems reveals fundamental system-level properties that are independent of precise kinetic parameters, often context-dependent, or experimentally inaccessible. By focusing on structural and topological features—such as conservation relations, feedback loops, and pathway interconnections—qualitative analysis identifies invariant behaviors, robustness mechanisms, and potential failure modes inherent to the signaling network. In this study, we use Petri nets as a formal modeling framework to conduct qualitative analysis of the integrated MAPK and PI3K/Akt signaling network. By exploiting structural properties including place invariants, transition invariants, and siphons, the analysis establishes a direct correspondence between the Petri net structure and biologically meaningful conservation laws, signaling modules, and characteristic dynamic behaviors. The results demonstrate that the proposed model is structurally consistent, biologically plausible, and modular. Minimal semi-positive place invariants confirm mass conservation, indicating that proteins and enzymes circulate within closed molecular pools. Minimal semi-positive transition invariants identify canonical kinase–phosphatase cycles underlying sustained and reversible signaling. Hierarchical decomposition reveals a modular organization reducible to reusable enzymatic motifs, reflecting biological reuse across cascades and supporting scalability. Additionally, the identification of sixteen siphons that are also traps highlights persistent subsystems that ensure continuous regulator availability, confirming the robustness and dynamic sustainability of the integrated network. Full article