Search Results (3,515)

Protein–DNA and protein–RNA interactions are central to gene regulation and genetic disease, yet experimental identification remains costly and complex. Machine learning (ML) offers an efficient alternative, though challenges persist in representing protein sequences due to residue variability, dimensionality issues, and the risk of losing biological context. Traditional approaches such as k-mer counting or neural network encodings provide standardized sequence representations but often demand high computational resources and may obscure functional information. To address these limitations, a novel encoding method based on interpolation of physicochemical properties (PCPs) is introduced. Discrete PCPs values are transformed into continuous functions using logarithmic enhancement, highlighting residues that contribute most to nucleic acid interactions while preserving biological relevance across variable sequence lengths. Statistical features extracted from the resulting spectra via Tsfresh are then used for binary classification of DNA- and RNA-binding proteins. Six classifiers were evaluated, and the proposed method achieved up to 99% accuracy, precision, recall, and F1 score when amino acid highlighting was applied, compared with 66% without highlighting. Benchmarking against k-mer and neural network approaches confirmed superior efficiency and reliability, underscoring the potential of this method for protein interaction prediction. Our framework may be extended to multiclass problems and applied to the study of protein variants, offering a scalable tool for broader protein interaction prediction. Full article

This study explores the use of a homemade mung bean protein extract solution (MP) as the moisture source in high-moisture extrusion to produce pea–mung bean composite textured protein (PMP). Single-factor experiments assessed the effects of MP addition amount (30–70%), screw speed (140–220 rpm), and extrusion temperature (140–180 °C) on the textural, physicochemical, and structural properties, followed by optimization using response surface methodology (RSM). MP addition amounts between 50% and 60% promoted higher surface hydrophobicity, a higher disulfide bond content, more ordered secondary structures, and a higher intrinsic fluorescence, accompanied by improved water- and oil-holding capacities, bulk density, and texturization degree (p < 0.05). Screw speeds of 160–180 rpm enhanced texturization and texture via increased shear and reduced residence time, whereas higher extrusion temperatures darkened the color (Maillard browning) and reduced texturization and the bulk density. RSM found that the optimal conditions were 53% MP, 160 rpm, and 150 °C, yielding a theoretical maximum texturization degree of 1.55, which was experimentally validated (1.53 ± 0.02). These findings support MP as an effective green moisture source to tailor the structure and functionality of pea-based high-moisture extrudates. Future work will integrate calibrated SME, sensory evaluation, and application testing in meat-analog formats. Full article

Despite promising results, biocomposite research still requires elaboration, particularly with regard to functional properties and applications. In this study, multilayer biocomposites based on gelatin, κ-carrageenan and carboxymethylcellulose were enriched with sage or blackberry extracts. The films were characterized based on their physicochemical traits and bioactivity for application as active packaging and environmental biodegradation. FTIR confirmed extract integration and strong matrix interactions, while UV-VIS analysis showed efficient UV blocking. Water properties remained acceptable (WVTR ≈ 550 g/m² × d); solubility decreased for BB (41.73% vs. 53.45% control). Mechanical testing indicated a plasticizing effect: elongation increased (20.00% control; 35.35% BB; 39.29% SAGE), while tensile strength and Young’s modulus decreased. Antioxidant capacity rose (FRAP: 0.38 control, 1.97 BB, 4.48 SAGE µTrolox/mg; DPPH: 6.38% control, 85.68% BB, 78.25% SAGE; MCA: none). During refrigerated storage, antimicrobial effects were most evident on days 6–9. Lipid oxidation peaked for BB (0.92 mg MDA/kg, day 9), while pH was more stable with SAGE. Biodegradation and phytotoxicity confirmed environmental safety and compostability, with increased humic acid carbon in vermicompost. Overall, the results confirm the relevance of modifying biopolymers using green chemistry and highlight their importance for quality management, food safety and sustainable circular economy strategies. Full article

Ethylene–vinyl acetate (EVA) is a versatile polymer for applications in dental devices; however, its vulnerability to microbial colonization increases with long-term use. This study evaluates EVA composites modified with silver–sodium–hydrogen–zirconium phosphate (SP) particles, aimed at enhancing antimicrobial performance while preserving key functional properties. Composites containing 1–16 wt.% SP were prepared via solvent-based and mechanical compounding routes, with scanning electron microscopy confirming correct filler distribution across processing methods. Antimicrobial assays revealed a pronounced reduction in Streptococcus mutans and Candida albicans levels, reaching 88% and 98% antimicrobial efficacy, respectively, at 16 wt.% SP. Cytotoxicity testing with L-929 fibroblasts demonstrated maintained cell viability above the 70% threshold, confirming non-cytotoxicity. Mechanical characterization indicated marginal increases in hardness, slight tensile strength reduction at higher filler loadings, while other physicochemical and thermal analyses showed minimal impact on polymer performance. These findings indicate balanced antimicrobial activity with other biofunctional properties. Full article

Foods rich in amylose and resistant starch (RS) hold great potential for improving human health. Granule-bound starch synthase (GBSS) is a key enzyme for amylose biosynthesis and its interaction partner, PROTEIN TARGETING TO STARCH1 (PTST1), has been characterized. In this study, we generated overexpression and knockout transgenic plants of StPTST1 to investigate its effect on starch content and physicochemical properties. Aligning with the presence of carbohydrate-binding module in the protein, StPTST1 possesses starch-binding capacity. stptst1 knockout mutants showed a reduction in both total starch and amylose contents in tubers. Analysis of the pasting properties showed that peak viscosity (PV), trough viscosity (TV), breakdown viscosity (BV), final viscosity (FV), and setback viscosity (SV) were all increased in the mutants compared to that in the WT plants. Overexpression of StPTST1 led to an increase in the contents of amylose, RS, and total starch. Moreover, the proportion of short chains (0 < DP < 32) in amylopectin of StPTST1-overexpressing plants was reduced. These data demonstrated that both stptst1 mutants and StPTST1-overexpressing plants were altered in starch content and physicochemical properties. Elucidating the function of StPTST1 deepens our understanding of starch biosynthesis in potato and highlights its potential for enhancing potato nutritional quality. Full article

A good understanding of the effects of different afforestation measures in alpine sandy land on the physicochemical properties, enzymatic activities, and bacterial community structure of such crusts enables elucidation of the succession patterns of biological soil crusts and provides a theoretical basis for precise optimization of desertification control programs in alpine sandy land. In the present study, four afforestation measures—Salix cheilophila+ Populus simonii (WLYY00), S. cheilophila (WL), P. simonii (YY), and Caragana korshinskii (NT00) plantations—were adopted. The physicochemical properties and enzymatic activities of bare sand, algae crust, and moss crust in the four afforested sites were analyzed using Illumina high-throughput sequencing and PICRUSt2 functional prediction to investigate the bacterial community structure and function. Results indicated the following: (1) Water content, nutrient content, enzymatic activities, and bacterial community richness and diversity increased stepwise with succession from the bare sand stage to algae crust and to moss crust. The enhancement effect of YY on the above indicators and fine particle content was most prominent. (2) The primary environmental factors affecting bacterial community structure in algae and moss crusts were adequate phosphorus and organic matter, respectively, and the correlations between the activities of the four enzymes and the bacterial community structure are also quite close. (3) Functional prediction indicated that metabolism was the main primary function of biological soil crusts at the various sample sites. YY maintained the balance of primary functions and provided precise support for the physiological characteristics and ecological needs of different crust types in the secondary functions. In conclusion, among the four types of afforestation measures with a restoration period of 24 years, YY provided a greater advantage in improving the nutrient content, bacterial community structure, and functional potentials of biological soil crusts. The results of this study can serve as a scientific reference for screening of afforestation measures and protecting and utilizing biological soil crusts during the ecological restoration of alpine sandy lands in the present study area and other regions. Full article

Honey is a natural product of high nutritional and therapeutic value, whose biological properties are closely linked to its botanical origin and chemical composition. This study aimed to characterize avocado honey in terms of botanical origin, physicochemical parameters, phenolic content, antioxidant activity, chemical profile by LC-MS/MS, and antibacterial potential. Melissopalynological analysis revealed 86.21% avocado pollen, allowing classification as monofloral honey. The sample presented amber color and a high total phenolic content (269.79 ± 1.10 mg GAE 100 g⁻¹), values higher than those commonly reported for Brazilian and international honeys. Antioxidant activity, assessed by the DPPH method, confirmed the strong radical-scavenging capacity, consistent with the phenolic profile identified (EC₅₀ 10.250 ± 0.003 mg mL⁻¹). LC-MS/MS analysis allowed the annotation of nine compounds, including caffeine, scopoletin, abscisic acid, and vomifoliol, compounds associated with antioxidant, anti-inflammatory, and metabolic regulatory activities. Although no antibacterial effect was detected against the tested oral bacterial strains, the results highlight the chemical diversity and functional potential of avocado honey. Overall, the findings reinforce the bioactive potential of avocado honey, particularly due to its strong antioxidant capacity and diversity of metabolites, supporting its value as a natural resource of nutritional and therapeutic interest. Full article

Lycopene is a carotenoid with strong antioxidant properties, but its therapeutic potential is limited by its poor aqueous solubility. Developing formulations that enhance its solubility and stability may improve its bioavailability and effectiveness. This study aimed to prepare amorphous lycopene–PVP K30 systems via ball milling, a solvent-free and mild technique, and to evaluate their physicochemical properties, solubility, and antioxidant activity. Formulations containing 5%, 10%, and 15% lycopene (w/w) were obtained and characterized using X-ray powder diffraction, differential scanning calorimetry, and Fourier transform infrared spectroscopy. Density Functional Theory calculations were performed to gain molecular-level insights into lycopene–polymer interactions and hydrogen-bond formation. Solubility was determined by high-performance liquid chromatography, and antioxidant activity was evaluated using the DPPH radical scavenging assay. The amorphous dispersions exhibited enhanced solubility compared to crystalline lycopene, with the 10% system showing the highest initial solubility and antioxidant capacity, while the 5% formulation demonstrated superior stability over 24 h. Ball milling proved to be an efficient method for producing amorphous lycopene–PVP K30 dispersions with improved dissolution and bioactive performance. The results indicate that lycopene loadings between 5 and 10% offer the most favorable balance between solubility, stability, and antioxidant activity, supporting their potential use in pharmaceutical formulations. Full article

The TCP gene family plays essential roles in plant growth, development, and stress responses, yet their evolutionary dynamics and functional characteristics remain poorly understood in Juglandaceae species. Here, we aimed to systematically identify, classify, and characterize TCP genes across three nut-producing Juglandaceae species—Carya illinoinensis, Annamocarya sinensis, and Juglans regia—to elucidate their evolutionary relationships and potential functions in fruit development. We identified 44, 35, and 36 TCP genes in C. illinoinensis, A. sinensis, and J. regia, respectively, and classified them into three subfamilies (PCF, CIN, and CYC/TB1). Physicochemical property analysis revealed that most proteins were hydrophilic but relatively unstable. Conserved motif and gene structure analyses showed strong similarity among closely related members, while promoter regions were enriched with cis-acting elements associated with development, hormone signaling, and stress responses. Chromosomal mapping demonstrated an uneven distribution of TCP genes, with frequent clustering, and synteny analysis indicated strong conservation and gene duplication within and across species. Transcriptome profiling revealed that approximately half of the TCP genes were expressed in fruit tissues, with CIN subfamily members showing preferential expression. qRT-PCR validation further highlighted AsTCP23, CiTCP14, and JrTCP09 as highly expressed during fruit development, suggesting potential regulatory roles in fruit maturation. These findings provide new insights into the evolutionary patterns and functional divergence of TCP genes in Juglandaceae and establish a valuable foundation for future studies on fruit development and genetic improvement. Collectively, these findings advance our understanding of TCP gene evolution and provide potential molecular targets for improving fruit development and nut quality in Juglandaceae crops. Full article

Cancer continues to pose a major global health burden, with conventional therapeutic modalities such as surgical resection, chemotherapy, radiotherapy, and immunotherapy often hindered by limited tumor specificity, substantial systemic toxicity, and the emergence of multidrug resistance. The rapid advancement of nanotechnology has introduced functionalized nanomaterials as innovative tools in the realm of precision oncology. These nanoplatforms possess desirable physicochemical properties, including tunable particle size, favorable biocompatibility, and programmable surface chemistry, which collectively enable enhanced tumor targeting and reduced off-target effects. This review systematically examines recent developments in the application of nanomaterials for cancer therapy, with a focus on several representative nanocarrier systems. These include lipid-based formulations, synthetic polymeric nanoparticles, inorganic nanostructures composed of metallic or non-metallic elements, and carbon-based nanomaterials. In addition, the article outlines key strategies for functionalization, such as ligand-mediated targeting, stimulus-responsive drug release mechanisms, and biomimetic surface engineering to improve in vivo stability and immune evasion. These multifunctional nanocarriers have demonstrated significant potential across a range of therapeutic applications, including targeted drug delivery, photothermal therapy, photodynamic therapy, and cancer immunotherapy. When integrated into combinatorial treatment regimens, they have exhibited synergistic therapeutic effects, contributing to improved efficacy by overcoming tumor heterogeneity and resistance mechanisms. A growing body of preclinical evidence supports their ability to suppress tumor progression, minimize systemic toxicity, and enhance antitumor immune responses. This review further explores the design principles of multifunctional nanoplatforms and their comprehensive application in combination therapies, highlighting their preclinical efficacy. In addition, it critically examines major challenges impeding the clinical translation of nanomedicine. By identifying these obstacles, the review provides a valuable roadmap to guide future research and development. Overall, this work serves as an important reference for researchers, clinicians, and regulatory bodies aiming to advance the safe, effective, and personalized application of nanotechnology in cancer treatment. Full article

Aquafaba, a legume cooking water typically discarded as waste, represents a sustainable and plant-based protein source with promising functional applications. In this study, aquafaba hydrolysates were produced by enzymatic treatment with flavourzyme and savinase, yielding two products with distinct degrees of hydrolysis (DH: ~10% and ~29%). Aquafaba hydrolysates obtained using flavourzyme (AFHs) and savinase (ASHs), together with aquafaba isolate (AI), were incorporated into muffin cakes as partial flour substitutes (5%). The addition of hydrolysates significantly influenced cake quality parameters, particularly antioxidant capacity and textural attributes. Enzymatic hydrolysis, particularly with savinase, produced the most pronounced functional improvements. Technologically, ASHs supplementation significantly enhanced cake expansion, with specific volume values (2.23 mL/g) nearly doubling compared to the control (1.04 mL/g). Crust color was markedly altered, with L* decreasing and a* and b* rising, reflecting darker, more browned surfaces due to intensified Maillard reactions. Both ABTS and DPPH assays demonstrated increased radical scavenging activity with higher DH, while SDS-PAGE confirmed the release of smaller peptide fractions. The ABTS radical scavenging activity of the control muffin (CM, 262.53 mg TE/100 g) significantly increased in AIM (muffin cake substituted with aquafaba protein isolate, 481.87 mg TE/100 g) and reached its highest values in muffins containing AFHs (489.74 mg TE/100 g) and ASHs (530.56 mg TE/100 g), respectively. Hardness, a critical quality parameter particularly relevant to storage stability, decreased in hydrolysate-enriched samples compared with both control and isolate formulations. Oxitest results showed that extended induction periods for hydrolysate-containing cakes (18:47 h) were longer relative to control muffins (15:08 h). Thermal analysis also indicated improved thermal stability in the presence of aquafaba. Overall, the findings demonstrate that aquafaba hydrolysates can be effectively utilized in bakery systems to enhance antioxidant activity, oxidative stability, and technological properties, while simultaneously contributing to sustainable food valorization. Full article

Heat stress exacerbated by global warming severely impairs the growth and tea quality of the tea plant (Camellia sinensis). Trehalose is pivotal for regulating plant growth and enhancing stress resistance. However, the molecular characteristics, expression patterns, and regulatory mechanisms of trehalose metabolism genes in tea plants under heat stress remain unclear. Therefore, this study conducted a comprehensive investigation of trehalose metabolism genes in the Tieguanyin tea plant genome. A total of 30 trehalose metabolism genes were identified, including 17 trehalose-6-phosphate synthase (CsTPS), 9 trehalose-6-phosphate phosphatase (CsTPP), and 4 trehalase (CsTRE) genes. These genes were characterized in terms of their chromosomal locations and gene structures; the encoded proteins were characterized in terms of their phylogenetic relationships, conserved motifs, functional domains, physicochemical properties, and subcellular distributions. The results showed that these genes exhibit family-specific structural and functional features, laying a foundation for further functional studies. Collinearity analysis identified 20 homologous gene pairs between tea plants and Arabidopsis thaliana, significantly more than the 3 pairs with Oryza sativa, suggesting a closer evolutionary relationship with A. thaliana. Additionally, five intraspecific duplicated gene pairs were identified, all with Ka/Ks values < 1, indicating they have undergone strong purifying selection during evolution, leading to functional stability. Cis-acting element analysis revealed abundant stress-responsive, light-responsive, and phytohormone-responsive elements in the promoter regions of these trehalose metabolism genes, indicating their potential involvement in tea plant stress resistance regulation. Differential expression analyses under heat stress with exogenous trehalose treatment (CK: control, T: water-sprayed heat stress, TT: 5.0 mM trehalose-sprayed heat stress) identified six differentially expressed genes (DEGs). We further analyzed the expression patterns of these DEGs. Specifically, CsTPS1, CsTPS5, and CsTPS12 were increasingly upregulated in CK, T, and TT, respectively, while CsTPP1 and CsTPP2 were upregulated in TT relative to T. Additionally, CsTRE1, CsTRE2, and CsTRE4 showed downregulation in TT compared to T, though they were not classified as DEGs. These findings indicate that exogenous trehalose application modulates trehalose metabolism by promoting CsTPS and CsTPP expression while inhibiting CsTRE expression, thereby increasing endogenous trehalose content in tea plants under heat stress. Yeast heat stress tolerance assays confirmed that CsTPS1, CsTPS5, CsTPS12, and CsTPP1 enhanced yeast survival at 38 °C, verifying their function in improving organismal heat stress tolerance. In conclusion, these results clarify the roles of trehalose metabolism genes in tea plants’ heat stress response, demonstrating that exogenous trehalose modulates their expression to increase endogenous trehalose levels. This study provides a theoretical foundation for exploring trehalose-mediated heat stress resistance mechanisms and improving tea plant stress tolerance via genetic engineering. Full article

In the production of modern nongxiangxing daqu, mechanical stamping is utilized to compact raw materials into daqu bricks. Nevertheless, variations in stamping frequencies may modify the initial physicochemical properties of daqu, which in turn influence its physicochemical and biochemical parameters, and ultimately affect the quality of baijiu. This study systematically evaluated daqu samples prepared with different stamping frequencies (2 to 5 cycles) in terms of (1) physicochemical and biochemical parameters, (2) volatile compound profiles, (3) microbial community dynamics, and (4) interspecific interactions. The results showed that with the increase in stamping frequency, the moisture content, fermentative power, esterifying power, and liquefying power of daqu were all enhanced, with respective increases of 20.11%, 67.16%, 12.24-fold, and 36.27%. Specifically, the relative abundances of Weissella, Lactobacillus, Aspergillus, and Rasamsonia in daqu exhibited a significant increase with the elevation of pressing cycles. With the reduction in stamping frequency, the primary producers of flavor compounds shifted gradually from bacteria to fungi. These findings verify that stamping frequency exert a substantial regulatory impact on the physicochemical and biochemical parameters, microbial community dynamics, accumulation of flavor substances, and abundance of functional enzymes in daqu. Through a systematic elucidation of the mechanistic links between stamping parameters and daqu functionalities, this research offers actionable insights for optimizing industrial pressing processes and establishes a scientific basis for modern daqu production. Full article

Ectomycorrhizal fungi (ECMF) function as critical mediators connecting plant roots and associated microorganisms. These fungi establish intimate associations with the root systems of diverse higher plants, particularly Pinaceae species, constituting essential components of forest ecosystems. The current understanding of ECMF community structure in Pinus elliottii and its potential associations with soil characteristics remains inadequate. This investigation examined seasonal variations in rhizosphere soil physicochemical properties and fungal community dynamics between susceptible (YB) and healthy (YJ) P. elliottii using amplicon sequencing. The results demonstrated significant seasonal differences in fungal community composition between YB and YJ. Dominant ECMF genera exhibited distinct distribution patterns, with Rhizopogon predominating in YJ and Tricholoma in YB. Correlation analyses revealed strong associations between these ECMF taxa and key soil parameters (available potassium, total phosphorus, and available phosphorus), indicating substantial seasonal influences of phosphorus and potassium cycling on ECMF development. Ericoid mycorrhizal fungi displayed higher abundance in YJ samples during spring, suggesting their dual role in facilitating nutrient acquisition and enhancing host plant resilience against biotic and abiotic stresses. These findings provide novel insights into seasonal dynamics of fungal communities in P. elliottii ecosystems and offer practical implications for sustainable plantation management under global change scenarios. Full article

Oleogels, a semi-solid fat-like material, have emerged as a promising alternative to traditional saturated fats in food products. This study aimed to develop and characterize novel oleogels using starch and extracts from cassava (Manihot esculenta) to be used as a fat replacement in cookies, addressing the growing demand for healthier baked goods. Cassava starch was used as the structuring agent, while extracts provided functional properties to the oleogels. The oleogels were prepared and then incorporated into a cookie formulation, fully replacing the conventional fat. The resulting cookies were analyzed for their physicochemical properties, including texture, moisture content, and color. Rheological and microscopy analyses were also subjected to a sensory evaluation panel. The results demonstrated that the cassava-based oleogels effectively mimicked the functional role of fat, producing cookies with a significantly lower fat content. The cookies made with the oleogels exhibited comparable textural attributes and sensory acceptance to the full-fat control group, with no significant differences in flavor or mouthfeel reported by the panelists. These findings suggest that oleogels derived from cassava are a highly effective and innovative solution for producing healthier cookies without compromising quality, representing a viable strategy for fat reduction in the food industry. Full article