Search Results (147)

Background: Epilepsy is a chronic neurological disorder characterized by recurrent seizures, complex neurochemical, and metabolic disturbances. Parishin B, a major bioactive component of Gastrodia elata, has shown neuroprotective potential, but its systemic mechanisms remain unclear. Methods: A pentylenetetrazol (PTZ)-induced seizure model in zebrafish larvae was developed and used to evaluate the anti-seizure effects of Parishin B. Behavioral analysis, ELISA-based biochemical assays, integrated untargeted metabolomics with DIA-based proteomics, and qPCR were performed to decipher underlying molecular mechanisms. Results: Parishin B (0.0625–0.25 mg/mL) significantly alleviated PTZ-induced hyperactivity without developmental toxicity. Parishin B restored neurotransmitter balance by increasing GABA, dopamine, and norepinephrine levels while reducing 5-HT. In addition, it suppressed neuroinflammation and enhanced antioxidant capacity. Integrated multi-omics analysis revealed that Parishin B modulated key metabolic pathways, particularly the TCA cycle and lipid metabolism, and reversed the downregulation of ATP-citrate lyase (ACLY). Parishin B was also associated with the regulation of ferroptosis-related pathways, supported by changes in acsl4a and fth1a expression. qPCR results further confirmed the regulation of aclya, unc13c, and GABAergic signaling genes. Conclusions: Parishin B exerts anti-seizure effects through coordinated regulation of neurotransmitter homeostasis, neuroinflammation, and ACLY-associated energy–lipid metabolism, with potential involvement in ferroptosis-related processes. These findings provide molecular insights supporting Parishin B as a promising candidate for epilepsy therapy. Full article

Conventional extraction of indigo, a vital natural dye, provides low yields and has a negative environmental impact. However, microbial synthesis has emerged as a sustainable alternative. In this study, we describe the optimization of indigo biosynthesis in an engineered Escherichia coli strain called E216. This strain carries, on a replicative plasmid, the styAB genes originating from Pseudomonas putida that constitute the monooxygenase biosynthetic pathway of indigo, as well as mdh, encoding malate dehydrogenase, which plays a role in reducing power generation. In this strain, the overexpression of mtr (a gene encoding a transporter of tryptophan (Trp), the precursor of indigo biosynthesis) and acrA (a gene encoding a protein involved in indigo efflux) was found to substantially enhance indigo yields. Consistently, knocking out these two genes using CRISPR-Cas9 significantly reduced indigo production, whereas it was restored through the complementation of these mutants. This study thus revealed that stimulating tryptophan uptake and indigo efflux, the latter of which limits indigo’s toxic intracellular accumulation, has a positive impact on indigo yields. Furthermore, a comparative mass spectrometry-based proteomic analysis of E216 grown in fermentation medium with or without tryptophan supplementation, integrated with data-independent acquisition (DIA), revealed the global impact of tryptophan supplementation on cellular metabolism. This analysis identified upregulation of key proteins and enriched metabolic pathways under conditions of tryptophan supplementation. Integrating the results of the genetic engineering and proteomic analysis establishes a strong scientific and practical basis for developing a highly efficient method for the green industrial production of indigo using engineered E. coli strains. Full article

Insulin resistance is a multifactorial cellular state involving coordinated alterations in protein homeostasis and organelle function; however, its proteome-wide organization and response to bioactive peptides remain incompletely defined. In this study, we employed DIA-based quantitative proteomics to characterize global protein abundance changes associated with insulin resistance in HepG2 cells and to examine proteomic remodeling following treatment with a camel milk-derived peptide (P2). Comparative proteomic profiling revealed that insulin-resistant cells exhibit extensive reorganization of protein networks linked to redox regulation, endoplasmic reticulum protein processing, mitochondrial metabolism, lysosomal function, and extracellular matrix-associated components. Gene Ontology, KEGG pathway, protein domain, and subcellular localization enrichment analyses consistently indicated disruption of organelle-associated proteomic architecture rather than isolated pathway perturbations. Peptide TYYPPQ treatment was associated with selective, rather than global, proteomic shifts, prominently affecting mitochondrial and peroxisome-associated protein groups as well as extracellular and secretory proteins. Enrichment and localization analyses suggest that peptide exposure reshapes organelle-linked protein representation patterns without implying direct activation of signaling pathways or physiological restoration. Collectively, these results define insulin resistance and peptide responsiveness at a systems-level proteomic resolution and establish an organelle-resolved framework for interpreting peptide-induced proteomic remodeling in insulin-resistant hepatocyte models. This dataset provides a foundation for future targeted functional validation of candidate pathways identified through proteomic association. Full article

Glycosaminoglycans (GAGs) and their degrading enzymes have extensive applications and biotechnology and medicine, and play a crucial role in the recycling of organic matter in oceans. In this study, a potential GAG utilization gene cluster was identified in the genome of a novel marine Bacteroidetes, Roseihalotalea indica gen. nov. sp. nov. TK19036^T, through sole carbon source cultivation and differential proteomic analysis. Multiple GAG-lyases within this locus were purified and characterized. RiPL8 comprises a functionally unknown N-terminal domain and a catalytic C-terminal domain, exhibiting specificity for degrading hyaluronic acid (HA). The activity of RiPL35 is sensitive to Ca²⁺ ion concentration with an optimum at 10 mM. RiPL38 is the first reported member of the PL38 family capable of degrading HA and chondroitin sulfate (CS). In summary, our study reveals Roseihalotalea indica gen. nov. sp. nov. TK19036^T harbors an unpredicted GAG degradation gene cluster, and the encoded GAG-lyases exhibit distinct substrate specificities compared to the host organism. Full article

Background/Objectives: Human milk composition is shaped by gestational age at delivery and stage of lactation; however, proteomic differences between milk from mothers of preterm and term infants and their temporal patterns remain incompletely characterised. Methods: This prospective study enrolled 40 lactating mothers: 20 who delivered preterm infants (<32 weeks’ gestation) and 20 who delivered at term (37–42 weeks). Each provided milk samples during early lactation (first 10 days postpartum) and during later lactation (week five postpartum). Milk serum was analysed using quantitative data-independent acquisition mass spectrometry. Differential protein abundance was assessed separately at each time point; functional annotation was performed using Gene Ontology biological process analysis. Results: Eighty samples were analysed. On average, a total of 662 proteins were identified per sample, of which 169 were consistently quantified across all samples (1% FDR). During early lactation, 10 proteins differed significantly, with bidirectional changes and moderate effect sizes. At week five, 19 proteins were differentially abundant, predominantly higher in preterm samples. Immune-related proteins constituted the largest functional category at both stages. Immunoglobulin heavy constant gamma 4 remained consistently downregulated in preterm milk (1.6-fold lower abundance). Ferritin heavy chain (1.5) and HLA class II histocompatibility antigen gamma chain (1.8) were elevated only early, whereas calprotectin subunits S100A8 (5.6) and S100A9 (5.2) were markedly upregulated later. Conclusions: Proteomic differences vary across lactation stages, highlighting lactation stage as an essential contextual variable in comparative milk proteomics. Full article

Establishing plasma biomarkers in the veterinary field has always been a challenge, due to a lack of significant understanding of pathophysiological attributes of disease. Advances in mass spectrometry-based proteomic techniques have improved plasma biomarker discovery in veterinary medicine. Feline hypertrophic cardiomyopathy is the most common cardiac disease in cats and has a complex and not fully elucidated pathophysiology. This study aimed to use SWATH-MS proteomics to identify novel plasma biomarkers for fHCM and to further elucidate disease pathogenesis. Plasma was collected from 20 cats, consisting of healthy controls (n = 10) and a HCM group (n = 10). Cats with fHCM, were diagnosed by echocardiography and disease statuses were determined by a veterinary cardiologist. Undepleted cat plasma samples were digested using FASP and quantitative analysis was performed using DIA-NN. A total of 40 plasma proteins were found to be dysregulated, primarily associated with innate and humoral responses, including complement C7 and C9 and properdin proteins. Other dysregulated proteins were involved in blood coagulation (fibrinogen, fibulin-1), lipid metabolism (apolipoproteins), and inflammation pathways (transthyretin and plasminogen). These findings provide possible biomarkers for fHCM, with the potential to detect disease before clinical signs become evident, which is a significant outcome for fHCM. These proteomic changes suggest critical pathways for earlier intervention and could potentially lead to more effective treatment outcomes. Furthermore, having significant similarity to human disease strengthens the case for using cats as a potential translational model for hHCM. Full article

Background: Prostate cancer (PCa) shows a marked biological heterogeneity that is closely associated with tumor aggressiveness. A substantial proportion of clinically significant tumors remain undetected by multiparametric magnetic resonance imaging (mpMRI). Elucidating the molecular basis of MRI visibility and identifying non-invasive biomarkers could improve the risk stratification and clinical management of patients. Accordingly, this study aimed to assess tissue and urine proteomic signatures associated with PCa aggressiveness and mpMRI visibility. Methods: In this exploratory study, we performed an integrated proteomic analysis of prostate tissue and preoperative urine samples from 24 patients stratified into four groups: benign prostatic hyperplasia (BPH), indolent PCa (Gleason 6), clinically significant PCa with MRI-visible lesions, and clinically significant PCa with MRI-non-visible lesions. Data-independent acquisition mass spectrometry (DIA workflows) was used to identify differentially expressed proteins associated with malignancy, tumor aggressiveness, and MRI visibility. Results: Pairwise proteomic analyses revealed significant molecular differences between BPH and all PCa groups, identifying 694 non-redundant proteins differentially expressed in tissue and 482 in preoperative urine, showing molecular features associated with both disease presence and progression. Comparative tissue and urine analyses identified 82 proteins, reflecting shared biological pathways in metabolism, cytoskeletal organization, immune processes, and extracellular matrix remodeling. Finally, a direct comparison of MRI-visible and MRI-non-visible clinically significant PCa identified a panel of differentially expressed proteins, including LCN2/NGAL, S100A9, and AOC1/DAO, that showed differential urinary abundance and prognostic relevance in the TCGA-PRAD cohort. Conclusions: Our results suggest that proteomic alterations in PCa are associated with disease progression and aggressiveness and capture biologically relevant differences between tissue and urinary proteomes. These differences are also observed between MRI-visible and MRI-non-visible clinically significant prostate cancers, supporting the potential of urinary proteomics as a non-invasive complement to imaging-based diagnostics. Full article

Type 2 diabetes (T2D) causes systemic metabolic and inflammatory changes that affect the oral cavity, but salivary molecular markers remain poorly characterized. A peptide-centric reanalysis of salivary proteomics data was performed using DIA-NN for peptide-level quantification, without collapsing peptide signals into protein-level summaries. Although the qualitative peptide repertoire was largely conserved between T2D and control samples (>96% overlap), T2D showed coordinated quantitative changes in specific peptide subsets. Differentially abundant peptides primarily originated from complement C3, alpha-2-macroglobulin, serotransferrin, mucins, apolipoproteins, and hemoglobin, with a significant enrichment of oxidized cysteine-containing peptides, indicating redox imbalance and low-grade inflammation. Structural analysis with AlphaFold showed that T2D-associated peptides are located in solvent-exposed and conformationally dynamic regions of proteins. These findings suggest that disease specificity in diabetic saliva occurs mainly at the peptide level, offering mechanistic insight into non-invasive biomarker identification and longitudinal disease monitoring. Full article

Objective: Although Hu sheep are renowned for their high fecundity, the multi-tissue regulatory networks governing spermatogenesis, particularly within the hypothalamic–pituitary–testicular (HPT) axis, remain poorly understood. This study aimed to elucidate these mechanisms by performing a comparative proteomic analysis of the HPT axis in Hu sheep and three other breeds. Methods: We utilized data-independent acquisition (DIA) proteomics to analyze hypothalamic, pituitary, and testis tissues from 36 samples across four breeds. The experimental workflow included protein extraction, enzymatic digestion, LC-MS/MS, and subsequent bioinformatic analyses, complemented by histological examination. Results: Hu sheep exhibited accelerated testicular development and an earlier onset of spermatogenesis. Comprehensive proteomic profiling identified a total of 10,528 proteins, with 771 differentially expressed proteins (DEPs) detected in the testis. These testicular DEPs were significantly enriched in pathways related to spermatogenesis, the blood–testis barrier, and steroid hormone biosynthesis. Notably, the cAMP signaling pathway was consistently enriched across all three tissues, underscoring its pivotal role in regulating spermatogenesis. Protein–protein interaction (PPI) network analysis further highlighted hub proteins, such as MET, suggesting their potential involvement in somatic cell functions and the spermatogenic microenvironment. Key findings were validated by Western blot analysis. Conclusion: This study is the first multi-tissue proteomic investigation proposing a model in which the high reproductive performance of Hu sheep is potentially linked to the efficient, coordinated regulation of spermatogenesis-related proteins and signaling pathways—particularly in the testis. These findings offer novel insights into the molecular mechanisms of male reproduction in sheep and identify potential targets for future research and breeding applications. Full article

Chronic ultraviolet (UV) exposure disrupts dermal collagen homeostasis and accelerates skin aging. This study evaluated the protective effects of black ginseng extract (BGE) against UV-induced photoaging in human dermal fibroblasts. BGE restored collagen-related markers, including COL5A1 and COL7A1, improved fibroblast proliferative capacity, and reduced senescence-associated changes under UV stress. Data-independent acquisition (DIA) proteomics identified broad pathway modulation by BGE, involving extracellular matrix remodeling, chromatin organization, and stress-response processes. To validate genome maintenance-related signals highlighted by proteomics, qPCR showed that BGE increased telomere/replication-associated genes compared with the UV group, including POT1 (2.29-fold) and ORC1 (6.70-fold). In addition, comet assay imaging indicated reduced UV-associated DNA damage features following BGE treatment. Overall, these findings indicate that BGE mitigates UV-induced photoaging phenotypes in fibroblasts, with collagen-related recovery and multi-level protective responses, supporting its potential as a natural bioactive ingredient for anti-photoaging skincare applications. Full article

With intensifying global climate change and human activities, and with regional topography interactions, soil and water salinization has intensified, posing major ecological and environmental challenges worldwide. Here, we integrated histology, transmission electron microscopy, RNA sequencing (RNA-seq) and data-independent acquisition (DIA)-based proteomics to profile hepatopancreas responses of Exopalaemon carinicauda during acute sulfate stress (≤48 h). Sulfate exposure disrupted tubular architecture and organelle integrity, consistent with early cellular injury. Multi-omics analyses revealed metabolic reprogramming marked by suppressed glycolysis (e.g., HK2, ENO) and enhanced oxidative phosphorylation (e.g., ATP5F1B), together with activation of calcium signaling (e.g., SLC8A1, ADCY9) and reinforcement of antioxidant/one-carbon and glucose-branch pathways (e.g., SHMT2, PGAM2). These coordinated transcript–protein changes indicate a shift from rapid cytosolic ATP supply to mitochondrial ATP production while buffering Ca²⁺ overload and reactive oxygen species. Collectively, our results delineate the physiological and molecular adjustments that enable E. carinicauda to cope with sulfate conditions and provide mechanistic targets for selective breeding and water-quality management in saline–alkaline aquaculture. Full article

The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, 3, 3, and 3 EXLAs, alongside 11, 9, 13, and 8 EXLBs, in diploid I. trifida strain Y22, wild tetraploid I. batatas strain Y428B, and hexaploid I. batatas strain Y601, and cultivated sweet potato ‘Nancy Hall’, respectively. A comprehensive bioinformatic analysis of the expansin-like genes and proteins was performed to reveal their potential roles in SR development. Gene expression profiling showed that EXLA members were expressed during SR development, while approximately half of the EXLB members were expressed in Y22, Y428B (pencil root), Y601, and NH, respectively. Proteomic analysis (4D-DIA) detected 2, 1, 1, and 1 EXLAs, and 3, 3, 3, and 3 EXLBs in the mature SRs of the respective species. Integrated transcriptomic and proteomic analyses suggested that downregulating Iba6xEXLB2 and Iba6xEXLB1 may be associated with SR swelling in sweet potato. Furthermore, subcellular localization assays confirmed that Iba6xEXLB2 and Iba6xEXLB8 are localized to the cell wall/membrane. This study enhances the understanding of the expansin-like gene subfamily in sweet potato and its wild relatives and lays the groundwork for future functional studies on the role of expansin-like genes in SR development. Full article

Nocardia seriolae (N. seriolae) is a significant bacterial pathogen in global aquaculture, causing substantial economic losses. Live-attenuated vaccines represent a promising control strategy, but their molecular mechanisms remain poorly understood. This study employed a quantitative proteomic approach to compare the proteomic profiles of a virulent wild-type strain (F1) and an attenuated vaccine strain (F110) of N. seriolae. Using a data-independent acquisition (DIA)-based LC-MS/MS analysis, we identified 4516 proteins, with 540 showing significant differential expression (311 upregulated, 229 downregulated). Bioinformatic analysis revealed that upregulated proteins in F110 were primarily involved in metabolic processes, including phosphatidate cytidylyltransferase and various enzymes related to amino acid and nucleotide metabolism. Conversely, downregulated proteins were enriched in virulence-associated functions, including HtpX and MFS transporter permease. These findings suggest that attenuation involves a complex reprogramming of metabolic pathways coupled with a reduction in key virulence factors, providing insights into the potential molecular basis of vaccine development and potential targets for novel therapeutic strategies. Full article

Wheat is one of the most important crops contributing to global food and nutritional security. However, the gradual increase in soil salt content significantly impairs wheat growth and development, ultimately resulting in reduced yields. Therefore, enhancing the salt tolerance of wheat is of significant importance. Salt stress commonly induces oxidative stress in plants, and nucleoredoxin (NRX) has been shown to effectively maintain redox homeostasis under stress conditions. However, the functional role and molecular mechanism of the NRX gene in regulating salt tolerance in wheat remain to be elucidated. The results of this study demonstrated that TaNRX1-2D homologous overexpression (OE) lines exhibited significantly enhanced tolerance to salt stress. The survival rate and antioxidant enzyme activities (including superoxide dismutase and catalase) in the OE lines were higher than those in the wild type (WT). In contrast, the levels of superoxide anion (O₂⁻), hydrogen peroxide (H₂O₂), and malondialdehyde (MDA) in the OE lines were markedly lower than those in the WT. Conversely, the RNA interference (RNAi) lines displayed opposing trends. The results of yeast one-hybrid (Y1H) and dual luciferase assays (D-LUC) demonstrated that the TaERD15L-3B transcription factor positively regulated the expression of the TaNRX1-2D gene by binding to the ABRERATCAL cis-acting element in the TaNRX1-2D promoter. Through luciferase complementation assay (LCA), bimolecular fluorescence complementation (BiFC) assay, and a “mutation capture strategy”, it was found that TaNRX1-2D (C54, 327S) interacted with TaCAT2-B, indicating that TaCAT2-B was the target protein of TaNRX1-2D. The results of data-independent acquisition (DIA) proteomics analysis indicated that TaNRX1-2D may mediate salt tolerance in wheat through the positive regulation of nsLTP protein abundance and the negative regulation of hexokinase protein abundance. In general, the TaERD15L-3B/TaNRX1-2D regulatory module played a crucial role in conferring salt tolerance in wheat. This study provided an important theoretical basis and identified a potential gene target for developing salt-tolerant wheat varieties through molecular breeding approaches. Full article

The acute gouty arthritis (AGA) to chronic gouty arthritis (CGA) transition is a critical phase leading to irreversible joint damage and systemic complications. However, current molecular mechanism investigations have remained limited to single-omics approaches that lack comprehensive multi-omics explorations. We integrate high-depth data-independent acquisition (DIA) proteomics and untargeted metabolomics to analyze serum samples from healthy controls (n =28), AGA (n = 31), and CGA (n = 14) patients to address this gap. Through differential expression analysis, we identified nine persistently dysregulated pivotal proteins with robust discriminative capacity, including the urate excretion regulator ZBTB20 and inflammation/immune-related proteins (GUCY1A2, CNDP1, LYZ, SERPINA5, GSN). Additionally, 11 consistently altered core metabolites with diagnostic potential were detected, indicating perturbations in sex hormones, thyroid hormones, gut microbiota-derived metabolites, environmental exposures, and nutritional factors. Multi-omics KEGG enrichment analysis highlighted thyroid hormone synthesis, AMPK signaling pathway, and taurine and hypotaurine metabolism as central pathways. Correlation network analysis further revealed significant immune dysregulation, illustrating an evolution from acute immune activation to chronic inflammation during AGA-to-CGA progression. Our study establishes that a coordinated disruption of the thyroid hormone–AMPK–taurine metabolic axis and concomitant immune microenvironment remodeling is associated with chronic gout development. These findings provide critical targets for developing early diagnostic indicators and targeted interventions for CGA. Full article