Search Results (11,457)

The exponential growth of genomic and proteomic data has made computational protein–protein interaction (PPI) prediction indispensable, driving the need for a comprehensive and method-aware evaluation of supervised learning approaches. PPIs are fundamental to understanding cellular processes and disease mechanisms, yet experimental identification remains slow, costly, and difficult to scale. This survey systematically investigates ten supervised learning models—Extreme Learning Machine (ELM), Convolutional Neural Networks (CNNs), Graph Neural Networks (GNNs), Deep Neural Networks (DNNs), Naïve Bayes, Probabilistic Decision Tree, Support Vector Machine (SVM), Least Squares SVM (LS-SVM), K-Nearest Neighbor (KNN), and Weighted K-Nearest Neighbor (WKNN)—through a tri-layered framework that integrates Comparative Quantitative Analysis, Comparative Observational Analysis, and Experimental Evaluations. Beyond conventional accuracy summaries, this work provides critical commentary tied to real-world use, analyzing where techniques succeed or fail in practice—for instance, when instance-based methods bottleneck during inference, when kernel choices influence SVM variance, or when deep architectures trade accuracy for computational cost. The survey also offers concrete deployment guidance, such as calibration insights for WKNN versus KNN under varying feature noise or dataset curation quality, delivering operational perspectives that typical surveys omit. Comparative Quantitative Analysis consolidates metrics such as accuracy, F1-score, and computational time from the existing literature, while Comparative Observational Analysis evaluates interpretability, scalability, dataset suitability, and efficiency. Complementing these, Experimental Evaluations conducted by the authors empirically validate model performance on benchmark datasets. Together, these layers provide a unified and evidence-backed perspective on algorithmic strengths, weaknesses, and practical applicability. Findings show that GNNs and DNNs achieve the highest predictive accuracy due to their ability to capture structural and topological relationships, whereas ELM and Naïve Bayes offer superior efficiency. SVM and LS-SVM maintain robust stability under noisy conditions, and CNNs are well-suited for sequence-based prediction tasks. By combining empirical validation, critical insights, and deployment-focused recommendations, this survey delivers decision-grade guidance that bridges theoretical understanding with real-world implementation, thus clarifying the trade-offs among accuracy, efficiency, and scalability in PPI detection research. Full article

Chia seed mucilage (CSM) is a promising plant-derived hydrocolloid characterized by unique physicochemical and functional properties that are strongly influenced by the extraction methodology. In this research, an optimized sonication–freezing-assisted extraction (SFAE) process was developed to obtain mucilage while preserving its structural integrity. Results indicate that the extracted mucilage has a high total dietary fiber content of 75.87% and a moderate protein level of 8.71%. Fourier transform infrared spectroscopy (FTIR) confirmed the presence of hydroxyl and ionized carboxylate (COO⁻) groups associated with uronic acids, highlighting the anionic and polyelectrolyte nature of the system. Rheological characterization of optimized-CSM revealed Newtonian behavior in dilute solutions, indicating minimal intermolecular interactions and permitting accurate measurement of intrinsic viscosity and viscosity-average molecular weight. A critical overlap concentration (c** ≈ 0.2% w/v) was identified, marking the transition to semi-dilute regimes, chain entanglement, and the onset of shear-thinning and viscoplastic behavior. Functionally, the optimized-CSM exhibited high water holding capacity and competitive emulsifying properties (emulsion activity index (EAI): 62.50%; emulsion stability index (ESI): 49.32%), attributed to synergistic interactions between proteins and polysaccharides. Overall, this work provides new insights into how processing conditions influence the chemical composition and molecular structure, which fundamentally govern the rheological and functional performance of CSM. These findings underscore its potential as a versatile hydrocolloid for food and biomedical applications. Full article

Soft spread cheese is highly perishable, and conventional packaging offers limited protection against surface spoilage. Here, we present a sustainable, multifunctional solution: edible films made from whey protein concentrate (WPC), a valuable by-product of the cheese industry, incorporated with the probiotic Lactobacillus acidophilus LA5 (LA5). The objective of this study was to evaluate these films as active coatings for soft cheese, specifically assessing their physicochemical properties, probiotic viability during storage and simulated gastric transit, and their impact on cheese microbial stability and sensory quality over 60 days. Applied as active coatings on soft cheese stored at 4 °C for 60 days, these films were evaluated for their physicochemical properties, probiotic viability, microbial stability, and sensory acceptance. The incorporation of LA5 did not significantly alter film thickness (control: 0.20 ± 0.03 mm; test: 0.18 ± 0.02 mm), moisture content (control: 33.42 ± 0.54%; test: 32.34 ± 1.28%), or water solubility (control: 21.44 ± 1.14%; test: 22.89 ± 0.75%) (p > 0.05). However, mechanical properties were markedly modified: tensile strength decreased from 35.42 ± 5.38 MPa (control) to 6.04 ± 0.55 MPa (test), while elongation at break increased from 4.87 ± 0.93% to 68.23 ± 3.46% (p < 0.05), indicating a transition from rigidity to flexibility upon probiotic incorporation. The probiotic strain exhibited exceptional resilience, retaining 100% viability during simulated gastric exposure at both day 0 and day 30 of storage. During cheese storage, LA5 counts in test film-coated samples remained above the recommended therapeutic threshold (10⁶ cfu/g), starting at 7.44 ± 0.15 log(cfu/g) on day 0 and maintaining 6.56 ± 0.20 log(cfu/g) after 60 days. Critically, yeast and mold spoilage were delayed in probiotic-coated cheese, with detectable growth appearing only at day 60 (1.64 ± 1.34 log(cfu/g)), whereas uncoated cheese showed spoilage as early as day 28 (1.33 ± 1.62 log(cfu/g)). Sensory evaluation revealed no significant differences (p > 0.05) between the coated and uncoated samples for color, appearance, texture, flavor, or overall acceptability. By valorizing a dairy by-product into an active, probiotic-loaded edible film, this approach offers a sustainable, waste-reducing strategy that enhances cheese preservation while delivering added functional value—bridging the gap between food packaging and nutrition. Sensory evaluation (n = 8, preliminary) indicated no significant differences between coated and uncoated samples, but these results require confirmation with a larger, validated panel. Full article

Environmental pollution from plastics is largely driven by inadequate waste management, particularly in food packaging that relies heavily on petroleum-derived materials. This study utilized gelatin capsule waste (GCW) as a sustainable biopolymer and incorporated yellow peacock flower extract (YPE), obtained via ultrasound-assisted extraction (UAE), at various concentrations (0–2%, w/v) to develop biodegradable films with enhanced functional and antioxidant properties. The main phenolic constituents of YPE were flavonoid aglycones and their glycosylated derivatives. YPE showed total phenolic content of 98.44–129.34 mg GAE/g dry extract, with ABTS, DPPH, and FRAP antioxidant activities ranging from 5.51 to 8.11, 3.17–7.63, and 3.86–5.82 mg TE/g dry extract, respectively. Incorporation of YPE into GCW films significantly improved light barrier properties, thermal stability, mechanical strength, and antioxidant activity, along with a reduction in water vapor permeability and an increase in contact angle, indicating enhanced film hydrophobicity. All films exhibited excellent biodegradability, with complete disintegration within 15 days under soil burial conditions. Films containing 2% YPE (GF4) showed significantly higher thickness, tensile strength, and thermal stability, along with increased opacity, compared with the control (GF0), indicating a reinforcing effect. FTIR analysis revealed the interaction between protein and phenolic compounds from YPE. In a food application model, GF4 film pouches (5 × 5 cm²) effectively delayed oxidative deterioration of dried shrimp during storage at 25 ± 2 °C for 15 days. These findings highlight YPE as a promising bioactive ingredient for biodegradable active packaging and demonstrate the feasibility of GCW as a sustainable biopolymer for eco-friendly films. Full article

Sheng Mai San (SMS), a traditional Chinese medicine formula for treating qi and yin deficiency, is widely used in the management of conditions such as cardiovascular diseases and heatstroke. However, its role in mitigating heat stress (HS)-induced liver injury remains underexplored. In this study, a rat model of HS was established under high-temperature and high-humidity conditions, and SMS was administered as an intervention. The pharmacodynamic effects of SMS were comprehensively evaluated through histopathological examination, detection of heat shock protein 70 (HSP70) and heat shock protein 90(HSP90) expression, and analysis of liver function biomarkers (AST, ALT). Meanwhile, oxidative stress indicators were measured using biochemical assay kits (GSH, SOD, CAT, MDA, T-AOC), and transmission electron microscopy was employed to observe mitochondrial ultrastructure, thereby assessing the protective effects of SMS on hepatic oxidative stress and mitochondrial damage induced by HS. In vitro, BRL-3A cells were cultured, subjected to HS, and treated with SMS. Cell viability was assessed using the CCK-8 assay, and changes in mitochondrial reactive oxygen species (ROS) levels, mitochondrial permeability transition pore (MPTP) opening, and mitochondrial membrane potential (MMP) were evaluated using fluorescent probes. The results showed that SMS effectively restored HS-induced histopathological damage in rat liver tissues, reduced serum AST and ALT levels, and downregulated the mRNA expression of HSP70 and HSP90 in liver tissues. Meanwhile, SMS strengthened the hepatic antioxidant system by increasing the levels of GSH, SOD, T-AOC, and CAT, while decreasing MDA content. In vitro experiments confirmed that SMS increased the viability of BRL-3A cells, reduced ROS production, improved MPTP opening/closing regulation, and stabilized MMP. This study provides a clinical reference for its application in treating HS-related conditions in humans and animals. Full article

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by dysbiosis of the gut microbiota. Helminth infections are known to modulate host immunity and intestinal microbial composition; however, the therapeutic use of live parasites poses safety challenges. The recombinant Fasciola hepatica fatty acid-binding protein Fh15 is a helminth-derived molecule with anti-inflammatory effects in models of septic shock and dextran sulfate sodium (DSS)-induced colitis. Whether Fh15 also influences gut microbial composition during colitis remains unknown. Male C57BL/6 mice received 4% DSS in drinking water for 7 days to induce colitis and were treated intraperitoneally with Fh15 (2 mg/kg) on days 1, 3, and 5. Fecal samples were collected on days 2, 4, and 7 for 16S rRNA gene sequencing. Standard microbiota pipelines were used to evaluate community diversity. Acute DSS treatment disrupted gut microbial diversity and community structure compared with non-colitic controls. Fh15 treatment partially restored early microbial balance by shifting microbial composition toward that of healthy mice and reducing microbial dispersion, indicating enhanced community stability despite severe dysbiosis. Although alpha diversity did not return to control levels, Fh15 mitigated the expansion of pro-inflammatory genera (Enterococcus and Turicibacter) and preserved beneficial taxa, including Adlercreutzia. Full article

In the present study, a series of isoxazole derivatives were severally evaluated for their antifungal activity against the yeast Candida albicans and molds such as Aspergillus niger, Aspergillus flavus, and Fusarium oxysporum. The results demonstrate that the isoxazole derivatives exhibit considerable antifungal potential, particularly isoxazole-sulfonate ester 4b (Ar= 4-(Cl)C₆H₄, Ar′= 4-(CH₃)C₆H₄), which was found to be active with significant inhibition zones; the diameters of the C. albicans and F. oxysporum samples were measured at 17.00 ± 0.00 mm and 14.00 ± 0.00 mm, respectively. Furthermore, compounds 4a (Ar= 4-(CH₃)C₆H₄, Ar′= 4-(CH₃)C₆H₄), 4c (Ar: 4-(Cl)C₆H₄, Ar′: 4-(NO₂)C₆H₄) and 4d (Ar: 4-(Cl)C₆H₄, Ar′: 3-(Cl)-2-(OCH₃)C₆H₃) demonstrated MIC and MFC values of 20 µg/mL against C. albicans. In addition, the anti-hemolytic activity of these derivatives was evaluated. Compounds 4a, 4e (Ar: 4-(Cl)C₆H₄, Ar′: 3,4-(OCH₃)₂C₆H₃) and aroylisoxazole 3a (Ar: 4-(CH₃)C₆H₄) demonstrated a high degree of anti-hemolytic activity (>99%) at all concentrations evaluated (10, 15, and 20 mg/mL). Molecular docking and molecular dynamics studies over 200 ns revealed protein–ligand complexes to have high affinity and stability, which agrees with the experimental results. The compounds 4d, 4e, and 3a have shown significant interaction with the target proteins of C. albicans, A. flavus, and F. oxysporum, respectively. The results have revealed that the major interaction sites are hydrogen bonding, hydrophobic interactions, and the presence of a water molecule, especially with key residues like TYR_84, ASP_120, SER_90, and THR_89. The crystal structure of compound 4a was also obtained. Full article

To address the pressing dual challenge of meeting global protein demand while mitigating environmental impacts, the food sector must transition to a circular bioeconomy. In this context, this review comprehensively examines the valorization of plant and animal byproducts, emphasizing how the recovery and application of their inherent bioactive and functional compounds can transform waste into high-value resources. Plant processing residues, such as fruit peels and pomace, and animal residues, such as blood and bones, are increasingly recognized as untapped sources of functional ingredients. These by-products yield bioactive compounds with health benefits. Simultaneously, the same or different compounds serve as structural building blocks, offering valuable technological properties. They improve water-holding capacity, texture, and emulsion stability in both traditional meats and plant-based analogs. While upcycling these materials reduces disposal costs and formulation expenses, challenges remain regarding compositional variability, regulatory barriers, and consumer perception of “waste-derived” ingredients. Ultimately, integrating advanced processing technologies such as enzymatic hydrolysis and fermentation is essential to building a resilient, sustainable, and circular global food system. Full article

Dexamethasone induces systemic toxicity, including oxidative stress, inflammation, hematological disturbances, and organ damage, particularly in the lungs and thyroid. Taurine exhibits antioxidant and anti-inflammatory properties, but poor bioavailability limits its efficacy. Nanoparticle delivery may enhance stability and tissue targeting. This study aimed to evaluate the protective effects of taurine-loaded chitosan nanoparticles (Tau–CS NPs) against dexamethasone-induced tissue injury in rats. Forty-eight male Wistar rats were allocated into control, DEXA, DEXA + silymarin, DEXA + taurine, and DEXA + Tau–CS NPs groups. Tau–CS NPs were characterized by TEM, UV–vis, FTIR, encapsulation efficiency, and drug loading. Hematology, oxidative stress markers (CAT, SOD, GSH, MDA), thyroid hormones (T3, T4, TSH, calcitonin), protein profile, lung and thyroid histopathology, and MPO expression were assessed. Tau–CS NPs showed uniform spherical morphology (11–60 nm), high encapsulation (98.2%), and substantial loading (50.36%). Dexamethasone caused hematological, oxidative, thyroidal, and histological disturbances. Tau–CS NPs markedly restored hematological indices, antioxidant defenses, thyroid function, protein profile, and tissue architecture, outperforming free taurine and silymarin. MPO expression was significantly reduced, indicating decreased inflammation. Taurine nanoparticles effectively mitigate dexamethasone-induced systemic and organ-specific toxicity, offering improved bioavailability and targeted delivery, highlighting their therapeutic potential. Full article

DNA methylation is a fundamental epigenetic modification that regulates gene expression, genome stability, and cell identity across vertebrate development. Disruption of DNA methylation homeostasis contributes to a wide spectrum of human diseases, including developmental disorders, neurological conditions, and cancer. Understanding how DNA methylation patterns are established, maintained, and dynamically remodeled during development is therefore essential for elucidating disease mechanisms and identifying therapeutic opportunities. The zebrafish (Danio rerio) has emerged as a powerful vertebrate model for investigating DNA methylation dynamics in vivo. Its external fertilization, optical transparency, rapid embryogenesis, and high fecundity enable direct observation and experimental manipulation of epigenetic processes at developmental stages that are difficult to access in mammalian systems. In addition, the core enzymatic machinery governing DNA methylation, including DNA methyltransferase (DNMT) and ten-eleven translocation (TET) protein families, is evolutionarily conserved between zebrafish and humans. In this review, we summarize current knowledge of the zebrafish methylome and the enzymatic regulators that control DNA methylation dynamics. We discuss how DNA methylation shapes early embryonic development, organogenesis, and cell fate decisions, and highlight insights gained from zebrafish models of human disease. Finally, we examine emerging technologies that are enabling increasingly precise interrogation of epigenetic regulation in vivo. Together, these advances position zebrafish as an important platform for bridging developmental epigenetics with human disease biology and therapeutic discovery. Full article

Thymol has been granted “Generally Recognized as Safe” status by the US Food and Drug Administration. However, its application as a natural preservative is constrained by limitations such as poor water solubility and high volatility. In this study, a dual-protein complex was prepared using mung bean protein and whey protein isolate to stabilize thymol-loaded oil-in-water (O/W) Pickering emulsions. The results demonstrated that the dual-protein system was driven by hydrogen bonding, electrostatic attraction, and hydrophobic interactions. Compared to single-protein systems, the dual-protein Pickering emulsions possessed smaller droplet sizes, lower polydispersity indices, and higher surface charges and surface hydrophobicity. Additionally, the dual protein enhanced emulsifying activity, thermal stability, and 30-day storage stability. Notably, the complex formed a continuous three-dimensional porous network structure at the mung bean protein (MBP) to whey protein isolate (WPI) ratio of 50%:50%. Benefiting from this structure and high surface hydrophobicity, the 50%:50% formulation achieved the highest thymol encapsulation efficiency. In terms of functional properties, this optimized emulsion demonstrated notable antibacterial activity and antioxidant activity; it demonstrated antibacterial activity against Shewanella putrefaciens and Staphylococcus aureus. Furthermore, the IC₅₀ value for the 50%:50% formulation was 192.25 ± 1.93 μg/mL (DPPH) and 161.74 ± 0.71 μg/mL (ABTS). In summary, the 50%:50% formulation enhanced the emulsifying activity, encapsulation efficiency, and bioactivity of the emulsion. This system provides an effective strategy for the stabilization and encapsulation of hydrophobic active compounds in emulsions. Full article

Colorectal cancer (CRC) is the third most prevalent cancer globally. TASK-1, encoded by the KCNK3 gene, is emerging as a putative target in cancer; it regulates resting membrane potential, cell proliferation, and apoptosis. A series of 27 novel xanthene derivatives, modified at position 9, were synthesized via azide coupling of 2-(9H-xanthen-9-yl)acetohydrazide with selected amines and amino acids, followed by hydrazine-mediated conversion to the corresponding hydrazides. The cytotoxic activity of selected compounds (5a–5g, 6a–6h, 7b, 7f–7h) was evaluated against the HCT-116 cell line in vitro. In addition, molecular docking and molecular dynamics simulations were performed to investigate binding interactions and assess the stability of the protein–ligand complexes. Several compounds (5f, 5g, 6c, 6d, 6f, 6g, 7b, 7f, and 7h) exhibited moderate cytotoxic activity against HCT-116 cells (IC₅₀: 66.97–99.62 µM), compared to cisplatin (IC₅₀: 18.25 µM). Compound 7h demonstrated pronounced antiproliferative effects, evidenced by DAPI staining showing chromatin condensation and apoptotic body formation, along with a marked reduction in cell count and coverage. Molecular docking indicated favorable binding within the TASK-1 potassium channel, and molecular dynamics simulations confirmed the stability of the protein–ligand complex, with consistent interactions, including a key hydrogen bond with Asn240. These findings support 7h as a promising lead candidate. These findings identify xanthene-based derivatives as promising lead compounds for further optimization as TASK-1-targeted therapeutic candidates in colorectal cancer Full article

The continuous increase in atmospheric CO₂ concentration exacerbates global climate change, making carbon reduction an urgent global priority. Carbonic anhydrase (CA), a highly efficient biocatalyst that converts CO₂ into bicarbonate, demonstrates significant potential for carbon capture and resource utilization. However, the stability and catalytic efficiency of native CA in industrial environments are limited, particularly its poor thermal tolerance under flue gas conditions and its sensitivity to impurities, hindering its direct large-scale application. This review systematically summarizes recent advances in modifying microbial CA through protein engineering (e.g., directed evolution, rational design) and immobilization techniques, which have markedly enhanced its thermal stability, adaptability, and reusability. Among these, the integration of machine learning with high-throughput experimentation has emerged as a transformative strategy for CA engineering. Furthermore, we outline CA-driven pathways for CO₂ conversion into high-value chemicals and bioenergy. Finally, future prospects are discussed, including interdisciplinary integration, computational modeling coupled with experimental validation, and comprehensive life-cycle and techno-economic assessments, to facilitate the scaled application of engineered microbial CA in carbon neutrality pathways. Collectively, this review highlights the critical role of engineered CA in bridging biocatalysis with industrial carbon management, offering a viable and sustainable pathway toward carbon neutrality. Full article

Background: Four genotypes of human bocaviruses (HBoVs) have been identified, with only HBoV1 being detected in respiratory specimens, and with HBoV2 being the predominant human bocavirus in fecal specimens, which implies different tissue tropisms for HBoV1 and HBoV2. It is vital to determine the factors that influence the tissue tropisms. Methods: The major capsid proteins VP3 of HBoV1 and HBoV2 were expressed in eukaryotic cells. Then co-immunoprecipitation (Co-IP) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) (IP-MS) was employed, along with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, to screen host proteins interacting with VP3 of different genotypes. Subsequently, in vitro pull-down assays were conducted to verify the direct virus–host interaction proteins with VP3. Furthermore, molecular docking was performed to predict the interaction interfaces between viral and host proteins. Results: Through IP-MS and enrichment analyses, 50 host proteins that displayed ≥10-fold differential binding affinities between HBoV1 VP3 and HBoV2 VP3 were identified. Among these, seven were considered as high-confidence candidate interactors. Notably, SPLUNC1 and VAMP8 showed predominant expression in respiratory and intestinal tissues, respectively. Subsequent in vitro pull-down assays confirmed that SPLUNC1 specifically bound to HBoV1 VP3, whereas VAMP8 specifically interacted with HBoV2 VP3. Molecular docking analysis further revealed that the binding between SPLUNC1 with HBoV1 VP3, as well as VAMP8 with HBoV2 VP3, was stabilized by extensive hydrophobic interfaces along with specific hydrogen bonds. Conclusions: The specific interactions of host proteins SPLUNC1 with HBoV1 VP3 and VAMP8 with HBoV2 VP3, respectively, provided fundamental evidence that the distinct tissue tropisms of HBoVs may be governed by specific host factors. Full article

Artificial intelligence has evolved to generative AI (GenAI), a paradigm shift that has shifted the emphasis away from the evaluation of existing patterns to the generation of novel biological and medical material. This study examines GenAI achievements in biosciences and medical fields the last five years in these fields using databases such as PubMed and Scopus. The paper highlights the recent evolution in biomedical research from virtual screening to de novo design. It illustrates how models like RFdiffusion and ProteinMPNN leverage “inverse folding” to assemble novel of proteins and drugs. Ultimately, these generative methods yield candidate with enhanced binding affinity and structural stability. For example, exploratory studies suggest GenAI has the potential to address inefficiencies via automatic documentation in the therapeutic sector, and it may enhance research capabilities by using Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) to generate synthetic clinical trial data that preserves confidentiality. In addition, the review argues that though GenAI democratizes medical education through scalable simulations, it raises questions about long-term knowledge retention. Finally, GenAI also offers a transformative “write” capability for biology, but its responsible application will require addressing model “hallucinations” and building Explainable AI (XAI) and robust ethical frameworks. Full article