Search Results (832)

Multi-omics technologies enable parallel quantification of proteomic and metabolomic layers, yet enzyme abundance often shows weak or nonlinear correspondence under diverse biological conditions. This apparent discordance has been attributed to both technical limitations—such as dynamic range compression in LC-MS/MS, metabolite derivatization artifacts, and missing values in proteomic measurements—as well as intrinsic biological properties of metabolic network architecture. While technical factors contribute to cross-omic mismatch, accumulating evidence suggests that constraint-driven network behavior plays a major role in shaping this decoupling. Enzyme abundance constrains catalytic capacity; however, realized flux is selected within this capacity under distributed flux control, as formalized by flux control coefficients in metabolic control analysis, and is further modulated by enzyme kinetics (e.g., km and Vmax), post-translational modifications, substrate availability, and thermodynamic constraints. Metabolite pools, in turn, reflect the physicochemical state of the system, while specific metabolites can also act as regulatory effectors that modulate enzymatic activity and cellular signaling. Because metabolic networks are underdetermined, multiple flux configurations can satisfy identical protein abundance and metabolite concentration data. Static cross-layer correlation is therefore insufficient for mechanistic inference. We synthesize biological mechanisms—including post-translational regulation, allostery, thermodynamic buffering, spatial compartmentalization, feedback amplification, and redox gating—that weaken linear abundance–metabolite expectations. We further outline a constraint-based interpretation framework in which proteomics imposes capacity bounds, metabolomics informs reaction directionality and metabolite pool constraints, and flux-informed approaches reduce solution degeneracy by providing additional information on pathway activity. Moving beyond correlation requires integrating perturbation, temporal resolution, and constraint-aware modeling. Proteome–metabolome discordance should therefore be interpreted not as inconsistency, but as indicative of constraint-driven state selection within high-dimensional biochemical systems. Full article

The present study examined for the first time the effect of native yeasts on the fermentation of artisanal Spondias purpurea L., wine produced in Santa Elena, Ecuador. To achieve this goal, three inoculation strategies were compared: a mixed culture containing Saccharomyces cerevisiae and Candida spp. (CLX), commercial S. cerevisiae (CL), and a spontaneous fermentation without added inoculum (SL). Five yeast isolates were identified from the fermentations, four belonging to Candida spp. and one to Kloeckera spp., using microbiological and biochemical methods. The CLX treatment showed the greatest yeast proliferation on PDA plates (2.7 × 10⁶ CFU/mL) and yielded the highest levels of higher alcohols, while the CL treatment produced the highest ethanol (3.72% ABV) and glycerol content (0.46%). All treatments were free of total and fecal coliforms, and their pH values (2.49–2.56) satisfied the requirements of the current Ecuadorian standard for wine production NTE INEN 374. Residual glucose content was specifically quantified using an enzymatic colorimetric (GOD-POD) assay, confirming the dry character of the wines. Molecular analysis of the final preparation obtained from the variant corresponding to the spontaneous fermentation without inoculum (SL) confirmed the presence of Hanseniaspora spp. (Kloeckera spp.), Diutina rugosa (C. rugosa), C. zeylanoides and Pichia kudriavzevii, after the obtained PCR amplicons using ITS1 and ITS4 were subjected to a blast analysis. Sensory evaluation by panelists (n = 15) favored the CLX wine, particularly for aroma and flavor attributes. The final glucose content reached a low value of 0.28 g/L, indicative of an extremely dry wine, with almost no fermentable sugar. Due to the lack of information related to wines produced from Spondias purpurea L., this study could contribute to a better understanding of the biological behavior and biodiversity of the microorganisms present in this fermentation process. These findings will help to improve wine regionality production, supporting the potential application of native regional yeasts in Spondias purpurea L. wine biotechnology. Full article

Background: Ischemic cholangiopathy (IC) is an under-recognized complication after transarterial chemoembolization (TACE) for hepatocellular carcinoma (HCC). Our goal was to estimate the incidence, timing, clinical presentation, and management of IC after drug-eluting bead TACE. Methods: Single-center retrospective cohort of consecutive drug-eluting bead TACE procedures (1 January 2020–31 December 2023) with imaging follow-up to 31 December 2024 was conducted. IC was defined radiologically as bile duct dilatation without mechanical obstruction, biloma formation, biliary strictures, or ischemic cholecystitis occurring after TACE. The primary outcome was the incidence of IC. Secondary outcomes included clinical presentation, need for hospitalization, and management. Results: Among 106 patients, 14 developed IC (13.2%). Imaging abnormalities were detected a mean of 3.1 months after TACE. Six patients (42.9%) were asymptomatic. Among symptomatic patients, the most common manifestations were abdominal pain (n = 6) and fever (n = 4). Five patients required hospitalization, including 2 with infected bilomas requiring antibiotics and/or drainage. Subsequent HCC therapy was feasible in most cases; no deaths were directly attributed to IC. Conclusions: IC after TACE is not rare and is frequently asymptomatic, often detected incidentally on routine CT follow-up. Systematic biochemical monitoring and selective MRCP could improve detection, particularly when TACE sessions are closely spaced. Full article

As global demand grows for natural health-promoting food ingredients, the agri-food industry’s organic wastes are emerging as promising alternatives thanks to attributes such as biocompatibility, nutritional value and nutraceutical effect. During saffron (Crocus sativus L.) production, approximately 53 kg of petals are obtained as a by-product for every 1 kg of saffron spice. The use of saffron petals and petal extracts in bakery products improves products’ shelf life due to the petals’ high content of nutraceuticals and minerals acting as natural preservatives. Petal-enriched bakery products contain high levels of fiber, minerals and antioxidants. Addition of saffron petals into bread dough reduces gluten network strength, increases crumb hardness, enhances acidity, improves water retention, alters color profiles and increases the duration of the shelf life. The formulation for incorporating saffron petals or petal extracts into food products must address three primary criteria: the maximum concentration of bioactive compounds per 100 g of the finished matrix, the thermal stability of these compounds during the baking process, and their bioavailability (in the food matrix) within the human gastrointestinal tract. Nutraceuticals with pharmacological potential are also influenced by the compositional profile: the proximate composition, minerals, phenolic content, flavonols, and antioxidant capacity of saffron petals and bakery products containing saffron petals. Saffron petals exhibit diverse therapeutic potentials, acting as antidepressants, anxiolytics, anticonvulsants, and neuroprotective agents. They also offer metabolic, cardiovascular, hepatoprotective, and renoprotective benefits, along with anti-inflammatory, antimicrobial, and antitumor activities. This article proposes a roadmap for developing bakery products enriched with saffron petals or petal extracts, targeting both pharmacological applications and consumer goods focused on disease prevention and general wellness. This study investigates the biochemical composition of saffron petals and their integration into bakery products. It evaluates the influence of petal-derived additives on rheological properties, shelf stability, and organoleptic characteristics, alongside an assessment of their bioactivity and toxicological profiles. Furthermore, the analytical methodologies employed for ingredient and biological sample characterization are discussed, emphasizing their role in verifying the authenticity, safety, and nutritional functionality of both raw materials and finished formulations. Full article

Passion fruit (Passiflora edulis) quality is defined by integrated sensory and nutritional traits, including sugar–acid balance, volatile organic compounds (VOCs), pigment-related attributes, and bioactive compounds such as ascorbic acid and phenolics. These traits emerge from coordinated regulation of carbon allocation, mineral nutrition, ripening metabolism, and stress- and defense-related signaling pathways, which are strongly modulated by environmental conditions. Sustainable biological inputs are increasingly explored as tools to influence these regulatory networks; however, evidence linking such interventions to reproducible fruit quality outcomes in Passiflora remains fragmented. This review first synthesizes current knowledge on the physiological, biochemical, and molecular mechanisms underlying passion fruit quality formation and maintenance, and then discusses how biofertilizers; microbial inoculants (including plant growth-promoting rhizobacteria—PGPR and arbuscular mycorrhizal fungi—AMF); fungal-derived elicitors such as chitosan and chitooligosaccharides; and complementary postharvest biological strategies may modulate these processes. Emphasis is placed on traits beyond yield, including sugar–acid balance, aroma and VOC profiles, color, nutritional quality, texture, and shelf life. By integrating genomics, transcriptomics, metabolomics, proteomics, and microbiome-based evidence, we examine how environmental modulation and key signaling pathways intersect with metabolic networks underlying fruit quality. Available studies indicate that responses to biological inputs are context-dependent and often non-linear. Key knowledge gaps and priorities for mechanism-informed sustainable management of passion fruit quality are identified. Full article

Fermented foods hold a significant position in global culinary traditions, particularly within ethnic and traditional diets. They are widely consumed for their distinctive flavors, textures, and health-promoting attributes. Although extensive research exists on fermentation processes, comprehensive insights into the nutraceutical potential and mechanistic health benefits of these foods remain limited. This review highlights key fermented products traditionally consumed in the north-eastern region of India including Hawaijar, Soibum, Ngari, alongside global counterparts such as Natto, Chongkukjang, Miso, Kefir, Tempeh, Kimchi, Kombucha, and Sauerkraut. These foods are rich in bioactive compounds (phenolics, peptides, organic acids, and exopolysaccharides), probiotic microorganisms, and essential nutrients that collectively contribute to their antioxidant, anti-inflammatory, antidiabetic, and cardioprotective effects. Recent in vitro and in vivo studies demonstrate that regular consumption of such foods may support the prevention and management of chronic conditions, including diabetes, cardiovascular diseases, obesity, gastrointestinal disorders, and neurodegenerative diseases. However, mechanistic studies remain insufficient to fully elucidate the synergistic interactions between microbial metabolites, host metabolism, and gut microbiota modulation. The review therefore emphasizes the biochemical and therapeutic mechanisms underlying ethnic fermented foods, advocating for advanced metabolomic and molecular approaches to validate their health-promoting efficacy. This review provides a timely and integrative perspective by critically evaluating preclinical and clinical evidence, highlighting mechanistic insights, translational gaps, and future research priorities. These insights will support the development of functional food formulations and reinforce the integration of traditional fermented foods into modern dietary strategies for disease prevention and overall well-being. Full article

Background/Objective: Apart from the attributes such as cost, yields and consistency that define the feasibility of a manufacturing process, physicochemical and immunological quality traits equally signify the functionality of a biological product. The present study investigates one such promising Meningococcal B vaccine candidate, a chimeric fHbp-PorA protein in Escherichia coli. Methods: The chimeric fHbp–PorA protein, expressed with an N-terminal tag of HIS-MBP-TEV was produced in a 10 L fermenter under two different media and induction strategies: chemically defined (CD) media with lactose induction and complex media (CM) with galactose-mediated autoinduction. Comparative analysis was carried out between the two approaches for cell growth, protein expression, and purification, and the final chimeric proteins were characterized to evaluate for their biochemical, structural, in vitro and in vivo immunochemical properties. Results: Growth in the CD media resulted in several-fold-higher biomass compared to that in CM media in a short cultivation time; however, more than a third of the expressed protein remained in an insoluble state. Meanwhile, almost all of the expressed protein with CM media was recovered in soluble form. Moreover, purification of the unprocessed tagged protein and recovery of chimeric protein (tag removed) resulted in 75% greater yield in CM media when compared to CD media. The final chimeric proteins obtained from each medium varied significantly in their physicochemical characteristics, including their epitope projection and CD spectra. The results of in vivo animal immunogenicity response also showed higher serum bactericidal activity associated with chimeric protein obtained from CM media compared to CD media. Conclusions: The outcomes demonstrate that complex media with galactose-induced expression not only show higher productivity but also exhibit superior quality attributes, qualifying their reliable use in the manufacturing process of this promising vaccine candidate. Full article

Background: Cataract is a progressive lens opacity. According to the World Health Organization, about 45 million people in the world are blind, with about half of these cases attributable to cataracts. Due to the complexity of cataract disease, current research on cataracts is far from sufficient, so it is especially important to understand the development process and the pathogenic factors of cataracts. Myodes rufocanus (M. rufocanus) is an animal of the M. rufocanus of the hamster family Volinae. In developing M. rufocanus, we found an individual of M. rufocanus with a congenital cataract phenotype. We confirmed the symptoms of cataract under natural light and using a slit lamp. Methods: Therefore, we analyzed the mechanism of congenital cataract in M. rufocanus from the aspects of pathological histology, physiology and biochemistry, and gene level, aiming to explore the feasibility of its development into an animal model of cataract. Cataract is a progressive lens opacity and a leading cause of visual impairment. Understanding its pathogenesis requires appropriate animal models. In a laboratory-bred colony of M. rufocanus, we identified individuals with a spontaneous congenital cataract phenotype, confirmed by gross observation and slit lamp examination. To characterize this phenotype and explore its potential as an animal model, we performed pathological, physiological, biochemical, and transcriptomic analyses using three cataract-affected and three normal age-matched male individuals (8 weeks old per group). Results: Blood tests revealed significantly lower white blood cell and lymphocyte counts in the cataract group, while blood glucose and other biochemical parameters showed no significant differences. Histologically, cataractous lenses exhibited eosinophilic aggregation in the nuclear region with disorganized fiber cells. Transcriptome analysis identified 6544 differentially expressed genes, including downregulation of crystallin genes (CRYBB2, CRYBA4, CRYGS) known to be associated with congenital cataract. KEGG pathway enrichment analysis highlighted retinol metabolism, tyrosine metabolism, and cytochrome P450-related pathways. RT-qPCR confirmed reduced CRYBB2 expression in cataractous eyes. Conclusions: This study provides the first transcriptome dataset for M. rufocanus ocular tissues and offers preliminary evidence that this naturally occurring cataract phenotype may serve as a potential model for congenital cataract research. Full article

Fermented foods and probiotics represent complementary yet distinct components of human nutrition. Fermented foods are shaped by biochemical transformations driven by microbial metabolism, whereas probiotics are live microorganisms that may confer health benefits to the host. In both cases, bacteria, yeasts, and filamentous fungi mediate key metabolic activities that generate bioactive compounds and modulate host–microbiota interactions. During fermentation, microbial communities synthesize organic acids, peptides, exopolysaccharides, vitamins, and other metabolites that enhance food safety, sensory attributes, and potential health-promoting properties. Several microbial products, such as bacteriocins, reuterin, hydroxylated fatty acids, and exopolysaccharides, exhibit antimicrobial, immunomodulatory, antioxidant, and cholesterol-lowering activities. Advancing our understanding of microbial metabolism in fermented foods is essential for developing next-generation functional foods and nutraceuticals that leverage microbial biotransformations to support human health. Nonetheless, multiple challenges limit the translation of these advances into commercial products. Inadequately controlled fermentation may introduce microbiological or chemical hazards, regulatory frameworks governing microbial use in foods remain insufficiently defined, and standardized procedures for microbial strain handling and characterization are still lacking. This narrative review integrates current evidence on the nutraceutical properties of fermented foods and probiotics, while also examining the associated safety considerations and the technological factors that influence fermentation processes. Full article

Background/Objectives: Celiac disease (CD) is a chronic, immune-mediated enteropathy induced by dietary gluten exposure in genetically predisposed individuals. Along with non-celiac gluten sensitivity (NCGS), these disorders present with multiple intestinal and extra-intestinal symptoms leading to multisystemic involvement, with complications documented in the oral cavity as well. Persistent immune activation and dysregulation, chronic inflammation, nutrient deficiencies, xerostomia, and microbial dysbiosis found in CD and NCGS constitute shared pathological findings, providing biological plausibility for an association with periodontitis. Methods: A narrative literature review was conducted based on a systematic search of four databases (PubMed, Scopus, Web of Science, Cochrane Library) and the gray literature through January 2026. A comprehensive set of clinical, radiographic, biochemical and immunological parameters was assessed. Two reviewers independently screened and selected studies, with disagreements resolved by consensus. Results: A total of 15 studies met the eligibility criteria and were included in the review. Available evidence, mainly derived from cross-sectional observational studies, remains limited, methodologically heterogeneous, and largely inconclusive. Across adult and pediatric populations, findings do not consistently demonstrate a clinically meaningful association between CD or NCGS and periodontal inflammation, irrespective of gluten-free diet (GFD) adherence. Observed differences, when reported, are modest and inconsistent, and can be mainly attributed to oral hygiene behaviors and dental visit patterns. Conclusions: Despite considerable biological plausibility linking gluten-related disorders with periodontal inflammation, current evidence does not support a definitive conclusion regarding the impact of CD or NCGS on periodontal health. Full article

Functional amyloids are widely distributed in bacteria and play important roles in biofilm formation and microbial physiology. However, most currently known bacterial amyloids have been identified through sequence homology to a limited number of prototype proteins, such as the curli subunit CsgA of Escherichia coli. This approach may overlook amyloidogenic sequences that lack recognizable similarity to these canonical systems. In this study, a cross-species, motif-based computational strategy was used to explore whether conserved sequence features derived from mammalian serum amyloid A (SAA) proteins could provide clues for identifying potential amyloidogenic motifs in bacterial proteomes. Comparative analysis of mammalian SAA isoforms identified a conserved sequence segment with predicted aggregation propensity, within which the hydrophobic motif SIAIILCILIL was observed in murine SAA3. Database searches revealed that similar sequence motifs occur in several proteins encoded by Gram-positive bacteria, including multiple proteins in Clostridioides difficile. To further explore whether C. difficile produces extracellular structures capable of interacting with amyloid-binding dyes, Congo Red-supplemented agar assays were performed. After 48 h of growth, both clinical isolates and a laboratory reference strain exhibited Congo Red-binding colony phenotypes. Because Congo Red binding can arise from several extracellular components and cannot be attributed to a specific protein or sequence motif, these observations should be interpreted cautiously. Taken together, this study presents a motif-based computational framework for identifying candidate amyloidogenic motifs across species and highlights sequence features in bacterial proteomes that may warrant further biochemical and structural investigation. The results should be regarded as hypothesis-generating and provide a basis for future experimental validation of potential amyloid-forming proteins in bacteria. Full article

The initial carbon-to-nitrogen (C/N) ratio is a fundamental parameter for aerobic composting, with a generally recommended optimal range of 25:1 to 30:1. However, in practical applications, the optimal C/N ratio often deviates from the recommended value. We attribute this discrepancy to the limitations of traditional stoichiometric methods in assessing the bioavailability of carbon and nitrogen sources. This study investigated how carbon bioavailability governs composting efficiency and product quality. Laboratory-scale aerobic composting experiments were conducted using six types of raw crop straws and two physically pretreated straws, representing a biodegradability gradient. Results demonstrated that carbon bioavailability significantly modulated the composting performance. Substrates rich in labile carbon pool (LCP), such as wheat straw and extruded cassava plant residue, demonstrated superior thermogenesis, humification, and seed germination indices compared to those dominated by recalcitrant carbon pool (RCP), such as untreated cassava plant residue. Principal component analysis confirmed a strong positive correlation between LCP content and key quality indicators. Microbiological analysis revealed that carbon source variations shaped bacterial succession: Bacteroidota abundance correlated positively with LCP, driving rapid initial degradation, whereas Pseudomonadota were more abundant in RCP-rich treatments, suggesting a role in complex polymer breakdown. This study confirmed that carbon bioavailability, rather than the bulk C/N ratio alone, is a critical limiting factor. This finding logically extends to the role of nitrogen bioavailability, suggesting that a “biochemical C/N ratio”—accounting for the lability of both carbon and nitrogen—could be a more accurate predictor of aerobic composting performance. Full article

Remote sensing advancements have enhanced defoliation monitoring in forests, but distinguishing insect-specific damage from general canopy stress remains challenging due to overlapping spectral signatures. This study addresses this gap by analyzing multispectral reflectance changes in Eucalyptus dunnii caused by Gonipterus sp. n. 2 larval feeding and artificial defoliation (AD). A randomized complete block design with five replicates tested four treatments: No Damage, Medium (100 larvae/tree) and High (200 larvae/tree) larval inoculation, and AD (80% leaf removal). Twenty potted E. dunnii trees were monitored over 16 days using UAV-based multispectral 10-band imagery. Five multispectral flights were conducted during the experiment. The reduction in visible and near-infrared (NIR) reflectance likely reflects structural changes in canopy composition, namely an increased proportion of mature foliage. Both larval feeding and AD treatments decreased reflectance in these spectral regions, probably due to the removal of young leaves and exposure of older, darker leaves. This explanation is inferred from morphological observations; further biochemical measurements would be required to confirm the underlying mechanisms. Larval feeding and AD reduced chlorophyll-related vegetation indices (CVI, NDRE), decreased anthocyanin-related vegetation indices (mARI, ARI), and also caused a drop in relative carotene content (MTVI, CTRI/RE). The effects were strongest in the AD and peaked soon after the treatment, indicating that these pigment effects can mostly and also be attributed to the older leaves becoming more exposed. Statistically significant interactions between date and treatment were found for the pigment-sensitive indices, the Anthocyanin Reflectance Index (ARI) and the Chlorophyll Vegetation Index (CVI). They displayed opposite reflectance trends—CVI increased while ARI decreased—but followed a consistent pattern aligned with insect feeding. EVI values also exhibited a distinguishable pattern that matched this trend. Due to the inherent difficulty of studying insect feeding in natural settings, AD trials may serve as a practical proxy for assessing the impact of pest-induced damage on vegetation reflectance and physiological indices. Full article

As a global environmental problem, biological invasion poses a serious threat to natural ecosystems. To explore the influence mechanism of Alternanthera philoxeroides (Mart.) Griseb on the growth and development of landscape plants, this study systematically analyzed the effects of extracts from different organs (stems, leaves, and roots) of A. philoxeroides on the seed germination and seedling growth of Zinnia elegans Jacq. by combining the Petri dish filter paper method with a pot experiment to reveal the potential mechanism of allelopathy. The results showed that the aqueous extract of A. philoxeroides inhibited the seed germination and seedling growth of Z. elegans. The high concentration (100 mg·mL⁻¹) of stem and leaf extracts significantly reduced the germination rate (by 99.10% and 90.65%) and seedling morphological parameters. The allelopathic inhibition increased with an increase in concentration, and the inhibitory effect of stem and leaf extracts was significantly stronger than that of root extracts. Aqueous extracts from the roots, stems, and leaves of A. philoxeroides at three concentrations (25, 50, and 100 mg·mL⁻¹) induced oxidative stress in seedlings, as evidenced by the elevated malondialdehyde (MDA) content and dysregulated activities of antioxidant enzymes. Specifically, superoxide dismutase (SOD) and catalase (CAT) activities exhibited a concentration-dependent trend of initial induction followed by subsequent inhibition, while root activity was significantly suppressed (p < 0.05), ultimately impairing seedling growth. The aqueous extracts of A. philoxeroides showed a concentration-dependent inhibitory effect on the seed germination and seedling growth of Z. elegans. High concentrations of stem and leaf extracts exerted a significant inhibitory effect on seedling growth, and this growth suppression was attributed to the induction of oxidative stress by the extracts. This study elucidated the phytotoxicity degree and physiological response mechanisms underlying the biochemical allelopathy of A. philoxeroides on Z. elegans. The findings provide a theoretical foundation for the selection of horticultural plant cultivars resistant to allelopathic stress and the development of management strategies for invasive plants. Full article

Edible coatings (ECs) derived from natural biopolymers represent an effective preservation strategy for fruits and vegetables and a promising postharvest approach aligned with the increasing demand for sustainable agricultural practices. These Generally Recognized As Safe (GRAS)-based coatings, which are mainly polysaccharide-, protein-, and lipid-based, can extend shelf-life with minimal impact on texture, flavor, and nutritional value, reducing reliance on synthetic packaging and helping mitigate food loss and waste. Beyond acting as a physical barrier, ECs can significantly influence fruit and vegetable metabolism by modulating biochemical and molecular processes. This review focuses on these effects by summarizing evidence from conventional analytical methods, including targeted metabolite analyses, as well as omics-based approaches, primarily transcriptomics and metabolomics, which remain poorly explored in the current EC research literature. Furthermore, integrated metabolomic and transcriptomic analyses are examined, as they offer a more comprehensive understanding of the molecular mechanisms underlying quality attributes, stress responses, and preservation outcomes. Collectively, this work offers detailed insights into coating-induced changes in metabolite profiles and gene expression in coated fruits and vegetables, including formulations derived from agri-food by-products and coatings enriched with bioactive compounds with antioxidant, antimicrobial, and antifungal properties. Overall, by addressing a current gap in the literature, it provides an integrative and innovative framework for interpreting coating performance at both applied and molecular levels, with potential relevance for the agri-food industry and for future research aimed at developing more sustainable, effective, and commodity-tailored postharvest technologies. Full article