Search Results (4,465)

Bifidobacterium adolescentis is prevalent in the gastrointestinal tract of healthy humans, and significantly influences host health. Recent studies have predominantly investigated the probiotic characteristics of individual strains and their specific metabolic roles, whereas analyses at the population genome level have been limited to date. This study conducted a comparative genomics analysis of 543 B. adolescentis genomes to explore genetic background variations and functional gene differences across geographically diverse populations. The results revealed significant differences in genome size and GC content among populations from Asia, Europe, and North America (p < 0.05). The pan-gene exhibited an open structure, reflecting the substantial genetic diversity within B. adolescentis. Functional annotation demonstrated that B. adolescentis possesses numerous protein-coding genes and abundant carbohydrate-active enzymes (CAZys) implicated in carbohydrate degradation and transformation. Population-specific CAZys were identified, suggesting adaptive evolution driven by distinct regional dietary patterns. Full article

The small-spotted catshark and the smooth-hound are cartilaginous, carnivorous fish with similar depth ranges in their habitats. These two species are among the most abundant elasmobranchs in the Adriatic Sea and are frequently caught by local fishermen using longline fishing. Despite their ecological similarities, little is known about the physiological differences in their digestive processes. The study of enzymatic digestion in these ecologically relevant species helps to fill the knowledge gap in the understanding of nutrient processing in cartilaginous fish. Therefore, the aim of this study was to determine, measure and compare the enzymatic activity of alkaline phosphatase, acid phosphatase, non-specific esterase and aminopeptidase. Fish were caught in the central part of the Adriatic Sea between 2021 and 2023. A total of 60 adult individuals were analyzed, with samples taken from six parts of the digestive tract. Histochemical analysis of 1440 slides revealed clear differences in enzyme activity between the two species. In the small-spotted catshark, cellular protein degradation was most pronounced in esophagus, posterior stomach and rectum, whereas in the smooth-hound, it was concentrated in posterior stomach and spiral intestine. Cellular digestion of lipids in the small-spotted catshark appears to occur primarily in the stomach. The results of this study provide new insights into the distribution of cellular digestive enzymes in cartilaginous fish and emphasize the importance of studying the entire digestive tract as an integrated system rather than focusing on individual parts. This study fills an important knowledge gap and contributes to a deeper understanding of digestive physiology, which in turn has implications for species conservation and biological variability. Full article

In this study, we investigated the effects of air packaging, vacuum packaging and modified atmosphere packaging (CO₂/N₂: 80/20) on the purine metabolism and enzyme activities of refrigerated large yellow croakers. The results showed that modified atmosphere packaging significantly inhibited microbial growth, delayed adenosine triphosphate degradation and maintained higher IMP content (1.93 μmol/g on day 21) compared to the air packaging group (2.82 μmol/g on day 12). The total purine content increased with storage time, with hypoxanthine content increasing significantly and occupying most of the total content, which was the key factor for the elevation of purine, followed by adenine content showing a significant decreasing trend. Hypoxanthine accumulation was significantly suppressed in the modified atmosphere packaging group (2.31 μmol/g on day 18), which was much lower than that in the air packaging group (5.64 μmol/g), whereas xanthine and guanine did not show significant differences among the groups. The key enzymes xanthine oxidase and purine nucleoside phosphorylase were much less active in modified atmosphere packaging, effectively delaying the cascade reaction of inosine monophosphate → hypoxanthine → xanthine. The study confirmed that modified atmosphere packaging intervenes in purine metabolism through enzyme activity regulation, providing a theoretical basis for the preservation of low purine aquatic products. Full article

Contact unmodified antisense DNA biotechnology (CUADb), developed in 2008, employs short antisense DNA oligonucleotides (oligos) as a novel approach to insect pest control. These oligonucleotide-based insecticides target pest mature rRNAs and/or pre-rRNAs and have demonstrated high insecticidal efficacy, particularly against sap-feeding insect pests, which are key vectors of plant DNA viruses and among the most economically damaging herbivorous insects. To further explore the potential of CUADb, this study evaluated the insecticidal efficacy of short 11-mer antisense DNA oligos against Coccus hesperidum, in comparison with long 56-mer single-stranded and double-stranded DNA sequences. The short oligos exhibited higher insecticidal activity. By day 9, the highest mortality rate (97.66 ± 4.04%) was recorded in the Coccus-11 group, while the most effective long sequence was the double-stranded DNA in the dsCoccus-56 group (77.09 ± 6.24%). This study also describes the architecture of the DNA containment (DNAc) mechanism, highlighting the intricate interactions between rRNAs and various types of DNA oligos. During DNAc, the Coccus-11 treatment induced enhanced ribosome biogenesis and ATP production through a metabolic shift from carbohydrates to lipid-based energy synthesis. However, this ultimately led to a ‘kinase disaster’ due to widespread kinase downregulation resulting from insufficient ATP levels. All DNA oligos with high or moderate complementarity to target rRNA initiated hypercompensation, but subsequent substantial rRNA degradation and insect mortality occurred only when the oligo sequence perfectly matched the rRNA. Both short and long oligonucleotide insecticide treatments led to a 3.75–4.25-fold decrease in rRNA levels following hypercompensation, which was likely mediated by a DNA-guided rRNase, such as RNase H1, while crucial enzymes of RNAi (DICER1, Argonaute 2, and DROSHA) were downregulated, indicating fundamental difference in molecular mechanisms of DNAc and RNAi. Consistently, significant upregulation of RNase H1 was detected in the Coccus-11 treatment group. In contrast, treatment with random DNA oligos resulted in only a 2–3-fold rRNA decrease, consistent with the normal rRNA half-life maintained by general ribonucleases. These findings reveal a fundamental new mechanism of rRNA regulation via complementary binding between exogenous unmodified antisense DNA and cellular rRNA. From a practical perspective, this minimalist approach, applying short antisense DNA dissolved in water, offers an effective, eco-friendly and innovative solution for managing sternorrhynchans and other insect pests. The results introduce a promising new concept in crop protection: DNA-programmable insect pest control. Full article

Flammulina filiformis, one of the most delicious and commercially important mushrooms, demonstrates remarkable adaptability to diverse agricultural wastes. However, it is unclear how different substrates affect the degradation of lignocellulosic biomass and the production of lignocellulolytic enzymes in F. filiformis. In this study, label-free comparative proteomic analysis of F. filiformis cultivated on sugarcane bagasse, cotton seed shells, corn cobs, and glucose substrates was conducted to identify degradation mechanism across various substrates. Label-free quantitative proteomics identified 1104 proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of protein expression differences were predominantly enriched in energy metabolism and carbohydrate metabolic pathways. Detailed characterization of carbohydrate-active enzymes among the identified proteins revealed glucanase (GH7, A0A067NSK0) as the key enzyme. F. filiformis secreted higher levels of cellulases and hemicellulases on sugarcane bagasse substrate. In the cotton seed shells substrate, multiple cellulases functioned collaboratively, while in the corn cobs substrate, glucanase predominated among the cellulases. These findings reveal the enzymatic strategies and metabolic flexibility of F. filiformis in lignocellulose utilization, providing novel insights for metabolic engineering applications in biotechnology. The study establishes a theoretical foundation for optimizing biomass conversion and developing innovative substrates using targeted enzyme systems. Full article

Osteoarthritis (OA) is a chronic progressive joint disease characterized by cartilage degradation, subchondral bone remodeling, and synovial inflammation. This complex disorder arises from the interplay between mechanical stress and inflammatory processes, which is mediated by interconnected molecular signaling pathways. This review explores the dual roles of inflammatory and mechanical signaling in OA pathogenesis, focusing on crucial pathways such as NF-kB, JAK/STAT, and MAPK in inflammation, as well as Wnt/β-catenin, Integrin-FAK, and Hippo-YAP/TAZ in mechanotransduction. The interplay between these pathways highlights a vicious cycle wherein mechanical stress exacerbates inflammation, and inflammation weakens cartilage, increasing its vulnerability to mechanical damage. Additionally, we discuss emerging therapeutic strategies targeting these pathways, including inhibitors of cartilage-degrading enzymes, anti-inflammatory biologics, cell-based regenerative approaches, and non-pharmacological mechanical interventions. By dissecting the molecular mechanisms underlying OA, this review aims to provide insights into novel interventions that address both inflammatory and mechanical components of the disease, paving the way for precision medicine in OA management. Full article

Microbial detoxification, as an environmentally friendly strategy, has been widely applied for benzo[a]pyrene (BaP) degradation. Within this approach, food-derived microbial strains offer unique advantages in safety, specificity, and sustainability for detoxifying food-borne BaP. In this study, we aimed to explore the potential of such strains in BaP degradation. Bacillus mojavensis TC-5, a strain that degrades BaP, was isolated from kefir grains. Surprisingly, 12 genes encoding dehydrogenases, synthases, and oxygenases, including betB, fabHB, qdoI, cdoA, and bioI, which are related to BaP degradation, were up-regulated by 2.01-fold to 4.52-fold in TC-5. Two potential degradation pathways were deduced. In pathway I, dioxygenase, betaine aldehyde dehydrogenase, and beta-ketoacyl-ACP synthase III FabHB act sequentially on BaP to form 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl via the phthalic acid pathway. In the presence of the cytochrome P450 enzyme, BaP progressively mediates ring cleavage via the anthracene pathway, eventually forming 3-methyl-5-propylnonane in pathway II. Notably, TC-5 achieved an impressive BaP removal efficiency of up to 63.94%, with a degradation efficiency of 32.89%. These results suggest that TC-5 has significant potential for application in addressing food-borne BaP contamination. Moreover, our findings expand the application possibilities of Xinjiang fermented milk products and add to the available green strategies for BaP degradation in food systems. Full article

Phytate, an antinutritional molecule in poultry feed, can be degraded by applying phytase, but its use in low- and middle-income countries is often limited due to importation instead of local production. Here, inexpensive raw materials were used to optimize the production of a thermostable phytase from an indigenous strain of Bacillus subtilis SP11 that was isolated from a broiler farm in Dhaka. SP11 was identified using 16s rDNA and the fermentation of phytase was optimized using a Plackett–Burman design and response surface methodology, revealing that three substrates, including the raw material mustard meal (2.21% w/v), caused a maximum phytase production of 436 U/L at 37 °C and 120 rpm for 72 h, resulting in a 3.7-fold increase compared to unoptimized media. The crude enzyme showed thermostability up to 80 °C (may withstand the feed pelleting process) with an optimum pH of 6 (near pH of poultry small-intestine), while retaining 96% activity at 41 °C (the body temperature of the chicken). In vitro dephytinization demonstrated its applicability, releasing 978 µg of inorganic phosphate per g of wheat bran per hour. This phytase has the potential to reduce the burden of phytase importation in Bangladesh by making local production and application possible, contributing to sustainable poultry nutrition. Full article

This study aimed to investigate the efficacy of a composite coating composed of 150 mg/L ε-Poly-L-lysine (ε-PL) and 5 g/L chitosan (CTS) in extending the shelf life and maintaining the postharvest quality of fresh Tremella fuciformis. Freshly harvested T. fuciformis were treated by surface spraying, with distilled water serving as the control. The effects of the coating on storage quality, physicochemical properties, reactive oxygen species (ROS) metabolism, and membrane lipid metabolism were evaluated during storage at (25 ± 1) °C. The results showed that the ε-PL/CTS composite coating significantly retarded quality deterioration, as evidenced by reduced weight loss, maintained whiteness and color, and higher retention of soluble sugars, soluble solids, and soluble proteins. The coating also effectively limited water migration and loss. Mechanistically, the coated T. fuciformis exhibited enhanced antioxidant capacity, characterized by increased superoxide anion (O₂⁻) resistance capacity, higher activities of antioxidant enzymes (SOD, CAT, APX), and elevated levels of non-enzymatic antioxidants (AsA, GSH). This led to a significant reduction in malondialdehyde (MDA) accumulation, alongside improved DPPH radical scavenging activity and reducing power. Furthermore, the ε-PL/CTS coating preserved cell membrane integrity by inhibiting the activities of lipid-degrading enzymes (lipase, LOX, PLD), maintaining higher levels of key phospholipids (phosphatidylinositol and phosphatidylcholine), delaying phosphatidic acid accumulation, and consequently reducing cell membrane permeability. In conclusion, the ε-PL/CTS composite coating effectively extends the shelf life and maintains the quality of postharvest T. fuciformis by modulating ROS metabolism and preserving membrane lipid homeostasis. This study provides a theoretical basis and a practical approach for the quality control of fresh T. fuciformis. Full article

Polyvinyl chloride (PVC) is commonly employed as mulch in agriculture to boost crop yields. However, its toxicity is often overlooked. Due to its chemical stability, resistance to degradation, and the inadequacy of the recycling system, PVC tends to persist in farm environments, where it can decompose into microplastics (MPs) or nanoplastics (NPs). The radish (Raphanus sativus L.) was chosen as the model plant for this study to evaluate the underlying toxic mechanisms of PVC NPs on seedling growth through the integration of multi-omics approaches with oxidative stress evaluations. The results indicated that, compared with the control group, the shoot lengths in the 5 mg/L and 150 mg/L treatment groups decreased by 33.7% and 18.0%, respectively, and the root lengths decreased by 28.3% and 11.3%, respectively. However, there was no observable effect on seed germination rates. Except for the peroxidase (POD) activity in the 150 mg/L group, all antioxidant enzyme activities and malondialdehyde (MDA) levels were higher in the treated root tips than in the control group. Both transcriptome and metabolomic analysis profiles showed 2075 and 4635 differentially expressed genes (DEGs) in the high- and low-concentration groups, respectively, and 1961 metabolites under each treatment. PVC NPs predominantly influenced seedling growth by interfering with plant hormone signaling pathways and phenylpropanoid production. Notably, the reported toxicity was more evident at lower concentrations. This can be accounted for by the plant’s “growth-defense trade-off” strategy and the manner in which nanoparticles aggregate. By clarifying how PVC NPs coordinately regulate plant stress responses via hormone signaling and phenylpropanoid biosynthesis pathways, this research offers a scientific basis for assessing environmental concerns related to nanoplastics in agricultural systems. Full article

Ferulic acid (FA) is one of the most abundant hydroxycinnamic acids found in plant cell walls. Its dehydrodimers play an important role in maintaining the structural rigidity of the plant cell wall. Ferulic acid esterases (FAEs) act as debranching enzymes, cleaving the ester bond between FA and the substituted carbohydrate moieties in FA-containing polysaccharides in the plant cell wall. This enzymatic reaction facilitates the degradation of lignocellulosic materials and is crucial for the efficient utilization of biomass resources. This review focuses on the occurrence of ferulic acid in nature and its different forms and outlines the various classification systems of FAEs, their substrate specificity, and the synergistic interactions of these enzymes with other CAZymes. Additionally, it highlights the various methods that have been developed for detecting hydroxycinnamic acids and estimating the enzyme activity, as well as the versatile applications of ferulic acid. Full article

Given the environmental significance of the textile industry, especially the accumulation of nondegradable materials, there is extensive development of greener approaches to fabric waste management. Here, we investigated the biodegradation potential of three Streptomyces strains in model compost on polyamide (PA) and polyamide-elastane (PA-EA) as synthetic, and on cotton (CO) as natural textile materials. Weight change of the materials was followed, while Fourier-Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy (SEM) were used to analyze surface changes of the materials upon biodegradation. The bioluminescence-based toxicity test employing Aliivibrio fischeri confirmed the ecological safety of the tested textiles. After 12 months, the increase of 10 and 16% weight loss, of PA-EA and PA, respectively, was observed in compost augmented with Streptomyces sp. BPS43. Additionally, a 14% increase in cotton degradation was recorded after 2 months in compost augmented with Streptomyces sp. NP10. Genome exploration of the strains was carried out for potential plastic-degrading enzymes. It highlighted BPS43 as the most versatile strain with specific amidases that show sequence identity to UMG-SP-1, UMG-SP-2, and UMG-SP-3 (polyurethane degrading enzymes identified from compost metagenome). Our results showcase the behavior of Streptomyces sp. BPS43 in the degradation of PA and PA-EA textiles in composting conditions, with enzymatic potential that could be further characterized and optimized for increased synthetic textile degradation. Full article

Fungal lytic polysaccharide monooxygenases (LPMOs) have revolutionized the field of biomass degradation by introducing an oxidative mechanism that complements traditional hydrolytic enzymes. These copper-dependent enzymes catalyze the cleavage of glycosidic bonds in recalcitrant polysaccharides such as cellulose, hemicellulose, and chitin, through the activation of molecular oxygen (O₂) or hydrogen peroxide (H₂O₂). Their catalytic versatility is intricately modulated by structural features, including the histidine brace active site, surface-binding loops, and, in some cases, appended carbohydrate-binding modules (CBMs). The oxidation pattern, whether at the C1, C4, or both positions, is dictated by subtle variations in loop architecture, amino acid microenvironments, and substrate interactions. LPMOs are embedded in a highly synergistic fungal enzymatic system, working alongside cellulases, hemicellulases, lignin-modifying enzymes, and oxidoreductases to enable efficient lignocellulose decomposition. Industrial applications of fungal LPMOs are rapidly expanding, with key roles in second-generation biofuels, biorefineries, textile processing, food and feed industries, and the development of sustainable biomaterials. Recent advances in genome mining, protein engineering, and heterologous expression are accelerating the discovery of novel LPMOs with improved functionalities. Understanding the balance between O₂- and H₂O₂-driven mechanisms remains critical for optimizing their catalytic efficiency while mitigating oxidative inactivation. As the demand for sustainable biotechnological solutions grows, this narrative review highlights how fungal LPMOs function as indispensable biocatalysts for the future of the Circular Bioeconomy and green industrial processes. Full article

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole^®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing. Full article

Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant physiology and soil function through diverse molecular mechanisms. PGPB synthesizes indole-3-acetic acid (IAA) to stimulate root development and nutrient uptake and produce ACC deaminase, which lowers ethylene accumulation under stress, mitigating growth inhibition. They also enhance nutrient availability by releasing phosphate-solubilizing enzymes and siderophores that improve iron acquisition. In parallel, PGPB activates jasmonate and salicylate pathways, priming a systemic resistance to biotic and abiotic stress. Through quorum sensing, biofilm formation, and biosynthetic gene clusters encoding antibiotics, lipopeptides, and VOCs, PGPB strengthen rhizosphere colonization and suppress pathogens. These interactions contribute to microbial community recovery, an improved soil structure, and enhanced nutrient cycling. This review synthesizes current evidence on the molecular and physiological mechanisms by which PGPB enhance soil restoration in degraded agroecosystems, highlighting their role beyond biofertilization as key agents in ecological rehabilitation. It examines advances in nutrient mobilization, stress mitigation, and signaling pathways, based on the literature retrieved from major scientific databases, focusing on studies published in the last decade. Full article