Search Results (2,327)

Tropical maize often exhibits photoperiod sensitivity, which limits its adaptation to temperate regions. Understanding its proteomic dynamics under long-day conditions is therefore crucial for germplasm improvement. This study employed a Tandem Mass Tag (TMT)-based proteomic approach to investigate stage-specific protein expression patterns in the tropical maize inbred line QR273 under long-day conditions (16 h light/8 h dark). Seeds were cultivated in climate chambers, and leaves were collected at the four-leaf (P4) and nine-leaf (P9) stages. A total of 2881 differentially expressed proteins (DEPs) were quantified between the P4 and P9 stages, among which only 7 were upregulated and 2874 were downregulated at the P9 stage. Gene Ontology (GO) enrichment analysis revealed that these DEPs were significantly enriched in processes related to proteolysis, membrane components, and ATP binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the enrichment of DEPs in amino acid biosynthesis, secondary metabolite biosynthesis, and aminoacyl-tRNA biosynthesis pathways. Protein–protein interaction (PPI) network analysis identified 60S ribosomal protein L12, adenosine 5′-phosphosulfate reductase, and RuvB helicase as core hub proteins. Based on functional annotation of representative DEPs, the DEPs were classified into four categories: 9 proteins related to storage material protection, 14 proteins related to protein modification, 12 proteins related to photosynthesis, and 25 proteins with other biological functions. Comparative analysis demonstrated a decrease in storage material protection, protein modification, and photosynthetic capacity at the P9 stage relative to the P4 stage. These findings provide insights into the proteomic dynamics underlying tropical maize development under long-day conditions and offer a theoretical basis for genetic improvement of tropical maize germplasm. Notably, inferences regarding nutrient reallocation based on DEP downregulation are derived solely from proteomic data and require further experimental validation. Full article

MicroRNAs are important regulators of skeletal muscle development and regeneration; however, the molecular basis by which exercise-induced miRNAs preserve middle-aged muscle function remains to be elucidated. This study aimed to investigate how aerobic exercise delays skeletal muscle attenuation by reversing age-related miRNAs dysregulation in male mice. Twelve-month-old male C57BL/6J mice (MC) (n = 8/group) were randomly assigned to a sedentary control group (OC) or an aerobic exercise group (OE) (12 m/min, 40 min/session, three sessions/week, for 12 weeks). miRNA sequencing identified differentially expressed miRNAs (DEmiRNAs), followed by miRNA–mRNA network construction. The results demonstrated that aerobic exercise improved muscle strength and mass while attenuating early atrophy and fibrosis. Four atrophy-associated DEmiRNAs (miR-150-5p, miR-199a-5p, miR-3535, and miR-329-5p) were reversed after aerobic exercise intervention. GO and KEGG profiling demonstrated that target genes were predominantly involved in protein binding and the Wnt signaling pathway. miR-199a-5p and miR-150-5p, with the most predicted targets, were selected as candidate mechanistic contributors, and FZD4 was confirmed as a common downstream target. Further analysis confirmed that miR-199a-5p and miR-150-5p inhibition attenuated D-galactose-induced C2C12 myotube atrophy, reducing Atrogin-1 and increasing MyoD1, FZD4, and β-catenin expression. These findings suggest that the exercise-induced miR-150-5p/miR-199a-5p axis may alleviate muscle aging in middle age via the restoration of key proteins in Wnt signaling and contribute preliminary observational evidence relevant to the understanding of aerobic exercise intervention in sarcopenia. Full article

Bisphenol A (BPA) is a common industrial chemical primarily used in the manufacture of plastics, and it has been found in more than 90% of people worldwide. As an endocrine disruptor, BPA can impair reproduction, development, immunity, metabolism, and cognition; it also disturbs immune balance and thus fosters chronic inflammation. A number of population-based studies have indicated a link between environmental BPA exposure and atopic dermatitis (AD). Nevertheless, the detailed molecular pathways connecting BPA to AD remain poorly understood. AD is the leading chronic recurrent inflammatory skin disorder, characterized by severe itching and repeated eczema-like lesions. Its prevalence is roughly 13% among children and 5% among adults, and its global incidence continues to rise, imposing heavy health and economic burdens on societies. To clarify whether and how BPA may promote or worsen AD, we carried out a comprehensive computational study that integrated network toxicology, transcriptomic data, machine learning, molecular docking, and molecular dynamics simulations. From the CTD, ChEMBL, and SwissTargetPrediction databases, we collected 5701 potential BPA targets; from GeneCards and OMIM, we obtained 3270 genes linked to AD. The overlap between these two gene sets gave a group of common candidate genes. Enrichment analyses using GO and KEGG showed that these common genes were significantly overrepresented in the PI3K-Akt signaling pathway, Th17 cell differentiation, and the JAK-STAT signaling pathway—all central to immune and inflammatory regulation. We then built a protein–protein interaction (PPI) network by submitting the common genes to the STRING database and employed Cytoscape to extract hub genes from that network. By integrating human AD transcriptomic profiles with the hub genes and applying two machine learning techniques (LASSO and SVM), we identified six core toxic targets of BPA in AD: TIGIT, JAK3, IL22, S100A8, CCL2, and FCER1G. These six targets fall into two main functional categories: immune dysregulation and inflammatory cell infiltration. Subsequent molecular docking and molecular dynamics simulation experiments confirmed that BPA binds well to all six targets and can form stable complexes with them. Collectively, our findings offer a preliminary experimental foundation for future investigations into the pathogenesis of BPA-induced AD and provide important molecular evidence for understanding how environment–gene interactions contribute to complex inflammatory skin diseases such as AD. Full article

To characterize the distinct expression profiles of microRNAs (miRNAs) in serum and tissue and to delineate the heterogeneity of their regulatory mechanisms in early-stage ovarian cancer (EOC), thereby identifying candidate biomarkers for non-invasive early diagnosis. Differentially expressed miRNAs were identified by integrating publicly available datasets of EOC tissues and serum samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Core miRNAs were subsequently screened through integrated differential expression analysis, weighted gene co-expression network analysis (WGCNA), and feature importance ranking derived from optimized machine learning models. Protein–protein interaction (PPI) networks and functional enrichment analyses (GO and KEGG) were performed on predicted target genes to systematically compare the functional discrepancies between serum- and tissue-derived miRNAs. No overlapping core miRNAs were observed between the two compartments. Serum miRNAs exhibited an overall up-regulated trend, whereas tissue miRNAs were predominantly down-regulated. Although the regulatory pathways demonstrated significant heterogeneity, they ultimately converged on the cell cycle and the PI3K-Akt signaling pathway, indicating high functional homology. Furthermore, serum miRNAs are not merely passive leakage products from tissues; current evidence suggests they may be selectively packaged into exosomes to participate in tumor regulation. Despite divergent expression profiles, serum and tissue miRNAs share homologous regulatory functions in EOC. These findings suggest that serum miRNAs accurately reflect the core molecular status of tumor tissues, providing a robust molecular foundation for liquid biopsy-based early detection strategies. Full article

In addition to its role in energy storage, adipose tissue contributes substantially to energy metabolism, endocrine regulation, and inflammatory processes. Sujiang pigs, a hybrid breed approved by the National Livestock and Poultry Genetic Resources Committee of China as a new national breed in 2013, possess a genetic predisposition for substantial fat deposition, making them an ideal model for investigating the mechanisms underlying adipose tissue accumulation. In this study, back fat (BF; subcutaneous adipose tissue), greater omentum (GOM; visceral adipose tissue), and mesenteric adipose tissue (MAD; visceral adipose tissue) were collected from three 6-month-old male Sujiang pigs for RNA-seq analysis. Comparative analyses identified 3005 differentially expressed genes (DEGs) between BF and GOM, 975 DEGs between BF and MAD, and 892 DEGs between GOM and MAD. To validate the reliability of the sequencing data, five DEGs were randomly selected for RT-qPCR verification. The DEGs were further subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. By integrating protein–protein interaction (PPI) networks with bioinformatics analyses, we identified candidate genes potentially associated with lipid metabolism (e.g., WNT9A, WNT5A, and PDGFRA) and inflammatory responses in adipose tissue (e.g., CSF1R, C1QB, and CD4). These findings indicate potential molecular differences between porcine visceral and subcutaneous adipose tissues and may serve as a reference for further studies on the molecular regulation of adipose tissue metabolism. Full article

Granulosa cells (GCs), an element of the ovarian follicle, are crucial for oocyte maturation, folliculogenesis, and steroidogenesis. Granulosa cells play a crucial role in fertilization by providing metabolic and hormonal support to the oocyte, maintaining its quality and regulating its meiotic arrest. Oocyte quality and fertilization efficiency depend on the proper activity of GCs, especially their mutual communication, providing metabolic support and protecting against oxidative stress. When interrupted, they may take part in the pathogenesis of polycystic ovary syndrome, premature ovarian failure, primary ovarian insufficiency, and diminished ovarian reserve. GCs are enclosed in the antrum where they communicate with surrounding cells, create a dynamic microenvironment, and regulate hormone biosynthesis. To analyze molecular mechanisms regulating endogenous signaling, it is important to consider the dynamic transcriptomic response of porcine GCs during in vitro culturing over 48, 96, and 144 h. Transcriptomic analysis revealed a variable and dynamic transcriptional upregulation of genes associated with cellular response to endogenous and external stimuli, chemical compound metabolism, vascular development, and GCs migration. Also, proven by Gene Ontology (GO) enrichment analysis, the following terms were highlighted: “cellular response to chemical stimulus” and “cellular response to organic substance”. Specific genes, such as HSD3B1, POSTN, LOX, SERPINB2, ITGB3, ANKRD1, SLC1A1, and SFRP2, exhibited significant expression changes, suggesting extensive GCs self-regulation and metabolism changes. Further analysis indicates improvements in cellular response to a cytokine stimulus, growth factor response, hormone response, enzyme-linked receptor protein signaling, and positive regulation of cell migration. These findings suggest interweaving of regulatory mechanisms underlying intercellular communication in GCs during in vitro culturing, despite the lack of signals from the native ovarian environment. Further investigating interplays of detecting pathways will provide a more comprehensive understanding and even insights into the potential clinical use of the knowledge about the role of GCs in folliculogenesis, oocyte maturation and ovulation. Full article

The lysosomal enzyme α-galactosidase A (AGAL) degrades globotriaosylceramide (Gb₃). While this enzymatic function in lysosomal metabolism is well characterized, interaction partners and alternative functions are unknown. This study aims to identify new potential AGAL-interacting proteins. AGAL was fused to the mutated biotin ligase BirA from E. coli (TurboID). Expression of the fusion protein was confirmed by Western blot and immunofluorescence, while enzymatic activity was verified by functional assays. In three experimental settings (AGAL wild-type (WT), AGAL missense variant (p.N215S), and the control cell line), TurboID-biotinylated proximal proteins were enriched by streptavidin pull-down and analyzed by mass spectrometry. Gene Ontology (GO) terms were subsequently evaluated to characterize biological functions and localizations of the identified proteins. Selected candidates were co-immunoprecipitated with AGAL to confirm direct interactions. The AGAL-TurboID fusion protein was successfully expressed in AB8/13 podocytes. Immunofluorescence and enzyme activity assays confirmed the presence and functionality of the fusion protein. Subsequent functional analysis (GO term analysis) showed enrichment of driver terms, including extracellular matrix organization (ECM), multicellular organism development, and protein metabolic process, in the biological process category. The identified top-hit proteins were predominantly involved in the organization of ECM, cell proliferation and cytokinesis, unfolded protein response during endoplasmic reticulum stress, and protein ubiquitination. Co-immunoprecipitation confirmed the interaction between AGAL and the candidate Galectin-3-binding protein (Gal-3BP). Our results suggest that AGAL may play a role in other pathways and/or the ECM organization beyond its lysosomal function. The confirmed interaction with Gal-3BP can now be functionally investigated in further studies. Full article

Background/Objectives: IL23R encodes a pivotal component of the IL-23/Th17 signaling axis and represents a validated genetic susceptibility locus for inflammatory bowel disease (IBD), psoriasis, and ankylosing spondylitis. Despite extensive GWAS data, the functional consequences of the full spectrum of IL23R missense single-nucleotide variants (SNVs) have not been systematically characterized. This study aimed to identify high-risk missense SNVs through a multi-tool in silico pipeline. Methods: A total of 723 missense SNVs from NCBI dbSNP were verified against transcript NM_144701.3/Q5VWK5-1 (629 aa) using Ensembl VEP (GRCh38). Sequential filtering was performed using applied SIFT, PolyPhen-2, PROVEAN, E-SNPs&GO, MutPred2, and ConSurf (grade ≥ 7); AlphaMissense and FATHMM-MKL were used as independent annotation layers. Protein stability was assessed with MuPro and DynaMut2 (AlphaFold2 AF-Q5VWK5-F1-v6; pLDDT = 68.19); structural characterization was performed with Project HOPE, and interaction networks were constructed using STRING and GeneMANIA. Results: Sequential filtering identified 37 high-risk missense variants. MuPro predicted destabilizing effects for 36/37 variants, with concordant DynaMut2 results for 35/37. Project HOPE identified disulfide bond disruption in 11 variants, charge-altering substitutions in 8, and glycine/proline backbone conformational changes in 11. STRING analysis identified IL12RB1 (0.999), IL23A (0.999), JAK2 (0.995), IL12B (0.986), and STAT3 (0.980) as the leading IL23R interactors. The protective variant R381Q was appropriately characterized as neutral by PROVEAN (−1.16) and AlphaMissense (likely_benign), supporting the specificity of the pipeline. Conclusions: Comprehensive in silico analysis identified 37 high-risk IL23R missense candidates with convergent computational evidence of predicted deleteriousness, predominantly involving cysteine bridge disruption, charge alteration, and glycine/proline backbone conformational changes. These variants are presented as prioritized candidates for future functional validation and may inform subsequent investigations of IBD susceptibility and IL-23 pathway pharmacogenomics. Full article

The molecular mechanisms of mycelial degeneration during subculturing of Auricularia heimuer strain ‘HWS1908’ were investigated across generations G1 to G20. With successive subculturing, mycelial growth rate and compactness declined, cellulase and laccase activities decreased significantly, whereas antioxidant enzyme activities increased. Comparative transcriptome analysis between G1 and G20 identified 2643 differentially expressed genes (DEGs). Gene Ontology (GO) analysis indicated that the DEGs were significantly enriched in terms associated with protein refolding, response to reactive oxygen species, and ferroxidase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed significant enrichment of DEGs in pathways including phenylpropanoid biosynthesis, peroxisome, fatty acid degradation, and longevity-regulating pathways. Key DEGs, including transcription factors, glycoside hydrolases, lignin-modifying enzymes, chitin synthases, chitinases, ornithine decarboxylase, and Ras/Rho signaling pathway components (Sos, Ras, Rac1), were identified. These genes may be associated with the progressive decline of mycelial vigor, cell wall integrity, and substrate utilization capacity. These findings provide a basis for further exploration of the molecular mechanisms of strain degeneration in A. heimuer, and a practical recommendation to limit subcultures to within 20 generations for maintaining high vitality. Full article

Diabetic neuropathy is typically diagnosed with distal sensory and nerve conduction abnormalities. These symptoms may reflect earlier disturbances of axonal maintenance. This review examines axonal transport and cytoskeletal failure as convergent cellular mechanisms of diabetic axonopathy. Long peripheral axons are particularly vulnerable to damage because their integrity depends on continuous communication between the neuronal soma and distal terminals. This process involves the continuous renewal of cytoskeletal and functional proteins and the involvement of organelles such as mitochondria. Diabetes in experimental models disrupts this system at several levels. It slows cargo transport. The supply of neurofilaments, tubulin and retrograde signaling is reduced, and regenerative growth after injury is weakened. Carbonyl stress and AGEs cause modifications of neural proteins, the extracellular matrix, vascular barriers, and the excitability of sensory neurons. RAGE ligands, including AGEs and the proteins HMGB1 and S100, link the diabetic tissue environment to redox and inflammatory signaling. This occurs in neural and glial compartments, as well as in vascular tissue and the immune system. RAGE interacts with DIAPH1 to activate GTPase signaling and remodel the cytoskeleton. The RAGE–DIAPH1 interaction provides a plausible route from diabetic ligand accumulation to cytoskeletal remodeling. These observations provide a mechanistic context for axonal transport, although not all represent direct measurements of cargo movement. Direct evidence for transport impairment comes mainly from experimental studies showing altered slow cytoskeletal transport, impaired retrograde signaling, and weakened regenerative responses. This work highlights the possibility of developing therapies that go beyond symptomatic relief. Verifying the effectiveness of interventions in protecting axonal transport and nerve fiber integrity in diabetic neuropathy may be therapeutically beneficial. Full article

Shuanghuanglian oral liquid (SHL) is widely used in companion animals and poultry, but its molecular mechanism in pneumonia–myocarditis comorbidity and heart–lung inflammatory crosstalk remains largely unclear. This computational study investigated the conserved AKT1/HIF1A-mediated immunoregulatory mechanism of SHL and its cross-species translational potential in veterinary medicine. Network pharmacology was integrated with GO, KEGG, and Reactome enrichment analyses, protein–protein interaction network construction, ADMET evaluation, cross-species sequence homology analysis (human, dog, cattle, and pig), molecular docking, and molecular dynamics simulation. A total of 61 active compounds, 251 putative targets, and 52 common targets associated with pneumonia and myocarditis were identified. These targets were mainly enriched in inflammation- and immune-related pathways, including TNF, IL-17, AGE–RAGE, and PPAR signaling. AKT1 and HIF1A showed high sequence conservation across species (85–98%). Key compounds exhibited favorable binding affinity to AKT1, and molecular dynamics simulation suggested the stability of the Baicalein–AKT1 complex. ADMET analysis suggested favorable pharmacokinetic properties and low predicted toxicity. These findings suggest that SHL may potentially alleviate pneumonia and myocarditis through modulation of the conserved AKT1/HIF1A axis and support its potential as a complementary therapeutic approach for managing heart–lung inflammatory diseases in multiple livestock species. This entirely computational study highlights promising mechanisms that should be further validated in vivo. Full article

Sports nutrition products are increasingly expected to deliver bioactive compounds that aid in recovery, reduce fatigue, and support physiological regulation, going beyond merely providing energy and nutrients. However, many bioactive compounds face challenges such as poor aqueous dispersibility, limited stability, low bioaccessibility, or inefficient absorption, which hinder their practical use in real food products. This review critically examines food-grade, gel-based delivery systems for bioactive compounds in sports nutrition from a design-driven perspective. It focuses on hydrogels, microgels, emulsion gels, protein gel matrices, and multicomponent gel architectures that prioritize structural stability, digestion-triggered responsiveness, and compatibility with food. Key design principles are discussed, including the need to maintain stability during processing and storage, balance protection with release, and tailor delivery structures to sports-specific constraints such as gastrointestinal tolerance, osmotic load, nutrient timing, and changes in digestion related to exercise. The review also analyzes the effectiveness of gel-based and hybrid systems in liquid, solid, and semi-solid sports nutrition products, emphasizing how the product format and consumption scenario can influence delivery performance. A design decision framework is proposed to align bioactive properties, food format, target release profile, and exercise-stage requirements with appropriate delivery architectures. Current challenges are also addressed, including difficulties in predicting structure–function relationships, limited robustness during scale-up processes, and inadequate functional evaluation. Overall, gel-based food delivery systems provide a promising solution for improving the stability, release behavior, and practical functionality of bioactives in sports nutrition. Full article

Legume–rhizobium symbiosis represents a crucial biological nitrogen fixation system. The AP2/ERF transcription factor ERN1 plays a vital role in nodulation of model legumes; however, its function in peanut (Arachis hypogaea), a typical crack-entry infection legume, remains unclear. To explore this, we performed transcriptome sequencing of peanut roots at 3 days post-inoculation (dpi) with rhizobium. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that differentially expressed genes (DEGs) were mainly enriched in DNA-binding transcription factor activity, plant–pathogen interaction, and plant hormone signal transduction pathways. The most strongly up-regulated gene was AhERN1, which was highly expressed in peanut roots and nodules. Subcellular localization indicated that AhERN1 was a nuclear-localized protein, and yeast transcriptional activation assays confirmed that AhERN1 functions as a transcriptional activator relying on its C-terminal domain. Furthermore, hairy root overexpression of AhERN1 significantly increased the number of peanut nodules. Collectively, these results reveal that AhERN1 acts as a positive regulator to promote rhizobium-induced nodule development in peanut, providing new insights into the regulatory mechanism of nodulation in dalbergoid legumes. Full article

Rapeseed (Brassica napus L.) growth and productivity are severely constrained by drought stress worldwide. Stomata are central regulators of plant transpiration and gas exchange, and therefore, represent key targets for enhancing water-use efficiency and drought tolerance. The transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), a key regulator of the abscisic acid (ABA) signaling pathway, plays crucial roles in plant abiotic stress responses and stomatal regulation. Nevertheless, the biological functions of BnaABI4 in B. napus remain largely unclear. In this study, four BnaABI4 paralogs were identified in the elite rapeseed cultivar ZS11 through genome-wide identification and comprehensive bioinformatic analyses. Each BnaABI4 protein harbors only one conserved AP2 domain, and their promoters contain multiple stress/hormone-responsive cis-regulatory elements (CREs). We subsequently generated BnaABI4-4 overexpression (OE) lines as well as BnaABI4 CRISPR/Cas9-mediated knockout (KO) transgenic lines. Phenotypic assays demonstrated that OE line had reduced transpiration rate (Tr), stomatal conductance (Gs) and stomatal density, along with enhanced drought tolerance, whereas KO lines showed the opposite phenotype. Transcriptome profiling identified numerous differentially expressed genes (DEGs) enriched in biological pathways associated with stomatal regulation, ABA signal transduction, and drought acclimation. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses confirmed significant enrichment of DEGs in processes including stomatal development, stomatal movement, reactive oxygen species (ROS) homeostasis, and drought tolerance. Collectively, our findings demonstrate that BnaABI4 negatively regulates stomatal density while positively contributing to drought tolerance in B. napus. This study lays a mechanistic foundation for genetic improvement and molecular breeding of drought-tolerant rapeseed cultivars. Full article

This study aims to systematically elucidate the influence of various heat treatment methods on the phenolic compounds in highland barley and their potential antihypertensive processes via chemical, in vitro bioactivity, and bioinformatics prediction analyses. This work employed UHPLC-Q Exactive HFX-MS/MS targeted metabolomics technology to ascertain metabolites in barley treated with five different thermal conditions: steaming (ST), boiling at atmospheric pressure (BO), boiling at high pressure (PO), extrusion puffing (EX), and sand-roasting (SR). The data revealed 252 phenolic metabolites, comprising 19 phenolic acids and 233 flavonoids. Moreover, it was observed that, in comparison to the untreated group, various heat treatments yielded substantial differences in the profiles of phenolic compounds. Notably, extrusion puffing (EX) exhibited superior performance: it increased specific flavonoid glycosides such as Clitorin and Quercetin 3-O-rutinoside-(1-2)-O-rhamnoside, while also improving direct antioxidant capabilities such as DPPH and FRAP. In addition, network pharmacology analysis of differentially expressed metabolites in the puffed group identified 44 potential targets, including TNF, IL-6, MMP-9, HIF-1A, and ACE. The KEGG and GO enrichment analyses revealed a substantial enrichment of these targets in classic hypertension-related pathways, including lipid metabolism, atherosclerosis and fluid shear stress. The molecular docking findings indicated that Apigenin 7-O-(2G-rhamnosyl) gentiobioside had significant binding affinities for the target proteins MMP9 and ACE. This study demonstrated that EX is an efficient processing method, with highland barley polyphenols showing potential antihypertensive activity. The findings provide a novel theoretical foundation and research direction for optimizing highland barley processing to maximize functional component utilization and elucidate its food-derived antihypertensive mechanisms. Full article