Search Results (3,189)

Background/Objectives: This study evaluated the effects of a compound probiotic fermented feed (CPFF) containing Lactobacillus plantarum, Bacillus subtilis, yeast, and Aspergillus niger on rumen in vitro fermentation, in situ feed degradation, and growth performance in beef cattle. Methods: We established a control group (CON) and experimental groups with 2%, 4%, and 8% CPFF supplementation for in vitro fermentation. Results: The results indicated that the NH₃-N concentration in the 4% CPFF group was significantly higher than in the other groups (p < 0.001). Similarly, microbial crude protein (MCP) production was significantly greater in the 4% CPFF group compared to the CON group (p = 0.016). The molar proportions of acetate, butyrate, isobutyrate, and valerate were significantly higher in the 2% and 4% CPFF groups than in the control group (p < 0.001), while propionate levels were significantly lower (p < 0.001). After 48 h, gas production was highest in the 4% CPFF group. Based on improvements in gas production, MCP synthesis, and fermentation intensity, the 4% inclusion level was determined to be optimal for further studies. We conducted an in situ degradation trial using 4% CPFF. Results showed that at 12 h, the neutral detergent fiber (NDF) degradation rate in the 4% CPFF group was significantly higher than in the CON group at 4, 8, 12, and 48 h (p < 0.05). At 48 h, the acid detergent fiber (ADF) degradation rate in the 4% CPFF group was also significantly higher than in the CON group (p < 0.001), and this group exhibited a significant increase in crude protein (CP) degradation (p = 0.030). We analyzed rumen fluid samples from both the CON and 4% CPFF groups after in vitro fermentation using 16S rRNA sequencing and untargeted metabolomics. Microbial community analysis revealed significantly increased abundances of functional bacterial groups such as Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group, and UCG-002 in the 4% CPFF group (p < 0.05). Differential metabolites were primarily involved in pathways related to tryptophan metabolism, and tyrosine metabolism signaling. A feeding trial was conducted by adding 4% CPFF to the diet of Angus growing cattle. The results indicated that average daily gain (ADG) (p = 0.004) and average daily feed intake (ADFI) (p = 0.001) were significantly higher in the CPFF group than in the CON group. Conclusions: In conclusion, our results demonstrate that CPFF enhances rumen fermentation activity, optimizes the microbiota and metabolic profiles of rumen fluid, and improves the average daily gain of beef cattle. This research provides a valuable theoretical basis for applying CPFF in beef cattle breeding. Full article

Malania oleifera is an endangered woody oil tree species endemic to China, where light conditions play a key role in seedling establishment. However, responses of seedling-associated bacterial communities to shading remain poorly characterized. This study investigated phyllosphere and rhizosphere bacterial communities under different shading regimes using 16S rRNA amplicon sequencing in two-year-old seedlings. Seedlings were subjected to 75%, 50%, and 25% shading, full-light conditions, and a field-grown reference group. The phyllosphere bacterial community showed lower alpha diversity and stronger compositional variation across shading treatments than the rhizosphere community, indicating higher sensitivity of leaf-associated bacteria to changes in the light environment. The rhizosphere maintained a larger shared bacterial pool and more stable community composition, with treatment-related differences mainly reflected in shifts in relative abundance. Functional prediction using PICRUSt2 indicated that phyllosphere bacterial functions were more responsive to shading than those in the rhizosphere, particularly pathways associated with genetic information processing and metabolism. PICRUSt2-based KEGG predictions suggested that both the phyllosphere and rhizosphere communities in the less-shaded and unshaded treatments were enriched for pathways related to aromatic compound degradation. Co-occurrence network analysis further revealed that phyllosphere association patterns were more sensitive to shading variation, whereas rhizosphere network complexity remained relatively stable. Shading exerted compartment-specific effects on the bacterial communities of M. oleifera seedlings, with the phyllosphere microbiota showing higher sensitivity to light variation than the rhizosphere communities. Full article

The MarR family regulators, widespread in bacteria and archaea, control diverse cellular processes, yet the regulatory mode and molecular signaling mechanism remain unclear in Corynebacterium glutamicum. Here, we functionally characterize AesR (aromatic compounds and environmental stimuli-sensing regulator), a MarR-type transcriptional regulator encoded by ncgl0019 in C. glutamicum. RNA sequencing (RNA-seq) analysis of an aesR-deleted strain (ΔaesR) revealed the down-regulation of genes involved in aromatic compounds degradation, stress response, antibiotic resistance and cell envelope biogenesis, correlating with heightened sensitivity of ΔaesR to adverse conditions. RNA-seq, quantitative reverse transcription-PCR (qRT-PCR) and promoter activity analysis uncovered that AesR represses its own operon (including the Zn-dependent protease with chaperone function gene ncgl0020) and the divergent cytochrome C biosynthesis operon ncgl0018-ncgl0017. AesR binds as a dimer to two side-by-side inverted repeats [5′-ACTATG-N₃-CATAGTCGACTA-N₇-TAGTTG-3′] in the ncgl0018-aesR intergenic region with different affinity, and Cu²⁺/Ni²⁺/Zn²⁺ disrupted binding. These metal ions, along with aromatic compounds, organic peroxides, and bactericidal antibiotics, induce both operons in vivo. Notably, penicillin elevates intracellular Cu²⁺/Ni²⁺/Zn²⁺ levels. Collectively, our findings identify AesR as a novel regulator that senses metal ions as direct signals, relieving autorepression and enabling bacterial defense against aromatic compounds and environmental stressors. Full article

Camel milk is increasingly recognized as a premium functional food, attributed to its rich nutraceutical compounds. Recent research has concentrated on the nanoscale extracellular vesicles derived from camel milk (CM-EVs), which exhibit distinctive properties. This review examines the methodologies for isolating and characterizing CM-EVs, alongside their potential health benefits in functional foods and nutraceuticals. CM-EVs have the capacity to safeguard functional proteins, noncoding RNAs, and bioactive lipids from degradation within the gastrointestinal tract, rendering them particularly suitable for incorporation into infant formulas, adult dietary supplements, and nutraceuticals targeting chronic inflammatory and metabolic disorders. Preclinical models indicate that CM-EVs can mitigate oxidative stress, enhance intestinal barrier integrity, and modulate gut microbiota, thereby contributing to the reduction in colonic injury and inflammation. Nonetheless, the majority of these findings are derived from laboratory and animal studies, highlighting a substantial deficiency in human clinical trials. Critical research gaps remain, necessitating further investigation into the elucidation of molecular mechanisms, assessment of long-term safety, evaluation of bioavailability, and compatibility with dairy processing techniques. This review underscores the significance of CM-EVs as bioactive food components and delineates research priorities, such as standardizing isolation methods, investigating food matrix integration, and providing translational evidence for their application in nutrition and preventive medicine. Full article

Background/Objectives: Autophagy is a key degradative pathway involved in orthodontic tooth movement. DNA damage-regulated autophagy modulator 1 (DRAM1), a protein that plays a central role in the degradation of autophagic cargo, exhibits differential regulation in human periodontal ligament (hPDL) fibroblasts under compressive force. Single-nucleotide polymorphisms (SNPs) may influence force-induced gene expression. Therefore, this study investigated the impact of DRAM1 SNPs on its expression in hPDL fibroblasts under compression force. Methods: The hPDL sample comprised cells of 59 patients. A physiological compressive strain of 2 g/cm³ was used to simulate orthodontic tooth movement. Total RNA from hPDL fibroblasts was isolated to determine DRAM1 relative gene expression under loaded conditions and in a physiological control. Furthermore, a genotyping analysis of six SNPs within the DRAM1 gene (rs756534 (G/T), rs2138257 (C/T), rs2176092 (C/T), rs4622329 (A/G), rs10860812 (A/G), and rs4764657 (A/G)) was performed using real-time polymerase chain reaction. DRAM1 expression was com-pared among genotypes of each SNP using an alpha of 5%. Linear regression analysis was then employed to evaluate SNP-SNP interaction. Results: The relative DRAM1 gene expression was not statistically significantly different (p > 0.05) according to the geno-types. The SNP-SNP interaction did not demonstrate any statistically significant associ-ation either. Conclusions: DRAM1 gene expression in hPDL fibroblasts under orthodontic compression may not be regulated by the studied intronic SNPs in the gene encoding DRAM1. Full article

Background: Eggshell membrane peptides (ESMPs) are natural bioactive compounds with reported chondroprotective properties. However, their regulatory effects on canine chondrocytes remain unclear. This study investigated ESMP in an interleukin-1β (IL-1β)-induced inflammatory model of canine chondrocytes. Methods: Chondrocytes were assigned to control (Cont), IL-1β, and ESMP + IL-1β groups. Cell viability was assessed using the Cell Counting Kit-8 (CCK-8) assay. NF-κB p65 nuclear translocation was evaluated by immunofluorescence staining. Real-time quantitative PCR (RT-qPCR) and Western blotting (WB) were used to measure mRNA and protein expression levels, respectively. Results: ESMP inhibited IL-1β-induced NF-κB p65 nuclear translocation and reduced the IL-1β-induced increases in interleukin-6 (IL-6), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), and matrix metalloproteinase-13 (MMP-13) at both mRNA and protein levels. ESMP also decreased IL-6, nitric oxide (NO), and prostaglandin E₂ (PGE₂) levels in culture supernatants. ESMP reversed the IL-1β-induced reduction in type II collagen α1 chain (COL2A1) and aggrecan (ACAN) expression at both transcriptional and protein levels. Conclusions: ESMP attenuates IL-1β-induced inflammatory responses and extracellular matrix degradation in canine chondrocytes, potentially associated with suppression of NF-κB p65 nuclear translocation. This supports its potential application in promoting joint health in dogs. Full article

Iron overload disrupts cellular homeostasis and drives ferroptosis through dysregulated iron metabolism. Non-coding RNAs (ncRNAs) are considered as key regulators of various biological functions and targets for a new generation of RNA therapeutics and biomarkers. However, few studies have investigated the regulatory roles of ncRNAs, particularly competitive endogenous RNAs (ceRNAs) in iron overload. This study performed whole-transcriptome sequencing to characterize the ceRNA network in ferric ammonium citrate (FAC)-induced iron-overloaded HT-1080 fibrosarcoma cells. A total of 208 differentially expressed mRNAs, 83 lncRNAs, and 170 circRNAs (q < 0.05) were identified, with hierarchical clustering revealing distinct expression patterns between control and iron-treated groups. KEGG enrichment implicated vitamin B6 metabolism (q < 0.001) and lysine degradation (q < 0.001) as key disrupted pathways. ceRNA network was conducted and further demonstrated lncRNA/circRNA-mediated regulation of ferroptosis genes via shared miRNA response elements. Notably, LINC-PINT-232 was implicated in the regulation of both ferritin heavy chain (FTH) and sequestosome 1 (SQSTM1), two ferroptosis-associated mRNAs. FTH upregulation mitigates iron toxicity through ferroxidase activity, while SQSTM1 modulates lipid peroxidation in ferroptosis. These findings provide a preliminary transcriptomic landscape for hypothesis generation regarding ncRNA-mediated regulatory mechanisms in iron overload-induced ferroptosis and offer a computational foundation for future functional and therapeutic investigations. Full article

Antisense oligonucleotides (ASOs) are a class of nucleic acid therapeutics that modulate gene expression through diverse mechanisms. Since their initial demonstration in inhibiting viral genes, advances in medicinal chemistry, pharmacology, and delivery have enabled robust and durable target engagement across multiple tissues. Chemical modifications to the backbone, ribose, and nucleobases have improved nuclease resistance, binding affinity, and pharmacokinetics, while conjugation and delivery technologies have expanded tissue accessibility. Beyond classical RNase H–mediated RNA degradation, ASOs regulate gene expression via splicing modulation, microRNA inhibition, transcriptional activation, and translation modulation, supporting both gene silencing and upregulation strategies. Multiple ASO drugs are now approved, particularly for genetic diseases, with many more in clinical development. This review outlines the evolution of antisense technology, key chemical and delivery innovations, ASO pharmacokinetics and intracellular trafficking, the mechanisms underlying gene regulation, and current clinical applications and future opportunities. Full article

Sustainable agriculture increasingly relies on organic amendments that integrate circular economy principles. Municipal Solid Waste (MSW)-derived compost (MSW-compost) represents a promising candidate as soil amendment in viticulture, yet its impact on soil microbiota remains poorly investigated. This study assessed the effects of MSW-compost application on the bacterial microbiota of a Mediterranean vineyard soil over a twelve-month period, comparing two application methods (surface mulching and tillage incorporation). Soil DNA was analyzed by 16S rRNA gene metabarcoding, complemented by functional prediction (Picrust2) and the Tea Bag Index to assess soil decomposition activity. MSW-compost significantly increased alpha-diversity and affected beta-diversity (p = 0.001) of the microbiota, regardless of the application method, with significant effects persisting throughout the entire observation period despite a clearly diminishing trend. Devosia emerged as the hub taxon of the co-occurrence network and was increased by compost addition. MSW-compost application mode remarkably affected the microbial network, with mulched treatment leading to a more complex, denser, and more interconnected network. While a similar number of taxa were increased or decreased, functional prediction revealed a notable enrichment of metabolic pathways, both synthetic and degradative, in the MSW-compost amended samples; this finding was supported by the enhanced red tea decomposition data (p = 0.007). Our results indicate that MSW-compost acts as a beneficial soil amendment, simultaneously enhancing microbial diversity and soil decomposition activity. This study provides novel evidence supporting the use of MSW-compost as a sustainable tool for improving soil microbiological quality in productive vineyards. Full article

Common bean (Phaseolus vulgaris) is an important crop for human nutrition due to its high protein content and capacity to fix atmospheric nitrogen. However, crop productivity is frequently compromised by biotic and abiotic stresses, among which wounding represents a highly prevalent challenge. Thus, understanding early molecular and biochemical responses to tissue damage is essential for improving plant stress resilience. We have investigated the effects of mechanical wounding on nucleic acid-degrading activities in the common bean. Mechanical wounding of leaves rapidly induced ribonuclease activity, whereas nuclease activities remained unchanged. Gel activity assays revealed a predominant ribonuclease, which was identified by proteomic analysis as PvRNS2, a member of the S-like RNase T2 family. This wound-induced ribonuclease was inhibited more strongly by nucleoside di- and triphosphate than by the corresponding nucleoside monophosphate. The increase in ribonuclease activity correlated with a rapid and transient induction of PvRNS2 expression, which peaked at 2 h after injury (600-fold increase). A similar transcriptional response was observed in radicles subjected to mechanical damage (55-fold increase), indicating that PvRNS2 responds to wounding in both aerial and subterranean tissues. In contrast, the wound-induced increase in PvRNS2 expression was not associated with a coordinated upregulation of genes encoding enzymes involved in downstream nucleotide degradation. Together, these results identify PvRNS2 as a major contributor to wound-induced RNA turnover in the common bean and support the involvement of RNA metabolism in early responses to mechanical damage. The participation of ribonucleases in the wound response of economically vital legumes remains unexplored. This work addresses this knowledge gap, establishing a new framework for understanding nucleic acid degradation during legume defense. Full article

Dental calculus is a highly prevalent oral condition in dogs and is widely recognized as an important risk factor for gingival inflammation and periodontal disease. Effective strategies for its prevention and treatment remain limited, highlighting the significance of exploring novel mechanisms underlying its formation. Neutrophil extracellular traps (NETs), a key component of innate immunity, have been found in various diseases. To investigate the relationship between NETs and canine dental calculus formation, NET-associated markers were assessed in the oral cavities of dogs with dental calculus and healthy controls. Based on previously published full-length 16S rRNA amplicon sequencing data of canine dental calculus, Porphyromonas gulae was selected as a candidate NET-inducing bacterium for subsequent validation experiments. Subsequent neutrophil stimulation experiments were conducted to explore the effects of NETs and related factors on dental calculus formation. Collectively, our findings demonstrate the presence of NETs within canine dental calculus and reveal that P. gulae present in canine dental calculus is capable of inducing NET formation. The level of myeloperoxidase–DNA complex in gingival crevicular fluid was significantly elevated in dogs with dental calculus. NETs promoted aggregation and microcrystal formation from calcium and phosphate ions under both physiological and supersaturated concentrations. By adhering to the surface of dental calculus, NETs facilitated calculus accumulation. This effect showed positive correlation with neutrophil counts and administration frequency, but was independent of the concentration of administered calcium and phosphate solutions. IL-1β promoted the formation of aggregated NETs but did not enhance calculus accumulation. DNase I inhibited this process by degrading NET-DNA. In conclusion, dental calculus and the calculus-inhabiting P. gulae could stimulate oral neutrophils to release NETs, which participate in and facilitate the initial formation, aggregation, and subsequent accumulation of canine dental calculus. Full article

Background/Objectives: West Nile virus (WNV) remains a significant threat to human health, with no approved antiviral treatments or vaccine available. A better understanding of the molecular mechanisms governing flavivirus–host interactions is needed to identify host regulatory pathways involved in infection. This study aimed to investigate how WNV infection remodels the host miRNA–mRNA regulatory landscape. Methods: WNV-induced changes in host miRNA expression in HEK-293 cells were profiled using miRNA-Seq. Transcriptome-wide host gene expression changes in WNV-infected cells were analysed using RNA-Seq. Gene Ontology and pathway enrichment analyses were conducted using DAVID. Integrated miRNA–mRNA network reconstruction was performed using Cytoscape based on the experimentally validated miRNA–mRNA interactions in miRNet database. Results: WNV infection induced global changes in host miRNA expression, with pathogenic NY99 and non-pathogenic Kunjin strains of the virus producing overlapping and strain-specific alterations in the miRNA landscape. Transcriptome analysis showed strong induction of interferon-related responses and activation of NF-κB and MAPK signalling pathways in the infected cells. In contrast, pathways associated with RNA processing, splicing, and proteasomal degradation were downregulated. Integrated miRNA–mRNA network analysis identified miR-197-3p, miR-301b-3p, miR-129-3p, miR-3662, and miR-128-5p as candidate regulatory hubs involved in WNV-induced transcriptome remodelling. These networks suggested that miRNA-mediated regulation may influence antiviral signalling, apoptosis, and RNA metabolism during infection. Conclusions: These findings suggest that WNV infection broadly remodels host miRNA–mRNA regulatory networks and identifies candidate miRNAs that may contribute to the regulation of antiviral and cellular stress responses. These predicted regulatory interactions provide a foundation for future experimental validation. Full article

A chimeric RNase A inhibitor (SUMO-RI) was produced by fusing a SUMO domain to the N-terminus of the murine Rnh1 protein. Functional assays demonstrated that SUMO-RI effectively protects RNA from RNase A-mediated degradation under conditions mimicking real-time RT-PCR, with performance comparable to that of commercial RNase inhibitors. The primary advantage of the chimeric design is its improved technological suitability: SUMO-RI exhibits markedly enhanced storage stability relative to the recombinant Rnh1 inhibitor. However, this benefit comes with a trade-off—SUMO fusion reduces thermostability at temperatures above approximately 47 °C. Together, these findings establish SUMO fusion as a rational engineering strategy for RNase inhibitors, offering improved practical handling at the expense of thermal resilience. Full article

Background: The reversal of liver fibrosis is crucial for improving outcomes in chronic liver disease. The gut–liver axis, mediated by the intestinal microbiota, plays a significant role in this process. However, its dynamic changes and mechanisms during reversal remain unclear. This study aimed to systematically reveal these dynamics and explore the link between gut microbiota and metabolism in a spontaneous reversal model. Methods: Intestinal contents were collected from mouse model groups (fibrosis, 4-week reversal, and 12-week reversal). The use of 16S rRNA gene sequencing was employed to analyze gut microbiota structure, and untargeted metabolomics was used to profile metabolic changes. Differential metabolites and microbial taxa were identified using multivariate statistical analysis, followed by pathway enrichment analysis. Spearman correlation analysis was used to construct metabolite–microbiota association networks across different reversal stages. Results: Metabolomic analysis showed significant alterations in multiple pathways during reversal. Linoleic and α-linolenic acid metabolism had a high impact in later stages. Taurine and biotin metabolism remained active throughout. Branched-chain amino acid degradation was enriched later. Microbiota analysis revealed significant structural shifts via beta-diversity. Bacteroidota decreased while Firmicutes increased in 4 weeks. Butyrate-producing families increased, and Akkermansia was enriched later. Integrated analysis demonstrated significant correlations between specific bacteria and metabolites, indicating a close microbiota–metabolism association during reversal. Conclusions: This integrated multi-omics study delineates the potential dynamic reorganization of the gut microbiota and host metabolism during spontaneous liver fibrosis reversal. These findings provide a theoretical basis for understanding the gut–liver axis mechanism in fibrosis reversal and for developing microbiota-targeted intervention strategies. Full article

C-type lectins (CTLs) are proteins with carbohydrate-recognition domains. These macromolecules interact with pathogen components, thereby playing important roles in the immune system. Current studies indicate that silkworm CTLs are involved in Bombyx mori nucleopolyhedrovirus (BmNPV) infection. Nevertheless, the molecular mechanisms through which these CTLs affect viral infection remain unclear. In this study, B. mori C-type lectin 16 (BmCTL16) was identified in the silkworm. Its expression was significantly downregulated upon BmNPV infection. Functional assays showed that BmCTL16 overexpression suppressed BmNPV proliferation, whereas its knockdown enhanced BmNPV proliferation. Protein–protein interaction assays confirmed that BmCTL16 interacts with BmNPV protein Bm9 in the cytoplasm. Notably, BmCTL16 promoted the degradation of Bm9 via the ubiquitin–proteasome system. Knockdown of Bm9 by siRNA significantly reduced BmNPV proliferation, confirming that Bm9 is the key target for BmCTL16 to exert its antiviral function. Collectively, this study reveals a novel CTL-mediated antiviral mechanism. BmCTL16 interacts with Bm9 and promotes its ubiquitin–proteasome degradation, thereby inhibiting viral proliferation. Furthermore, BmNPV evades this host defense by downregulating BmCTL16 expression. These findings enhance our understanding of silkworm CTL-mediated antiviral defense and offer novel perspectives on host–virus interactions in B. mori. Full article