Search Results (2,270)

Enterohemorrhagic Escherichia coli (EHEC) forms persistent biofilms on meat processing surfaces, posing a significant cross-contamination risk. This study assessed the antagonistic capacity of lactic acid bacteria (LAB) against EHEC under meat-processing-like conditions. Three LAB strains were tested in planktonic co-culture with EHEC at 12 °C, all displaying bactericidal activity. In biofilm assays on stainless steel, LAB reduced EHEC biofilms without affecting their own viability. LAB cell-free supernatants further inhibited EHEC biofilms by 2.6–3.5 log CFU/cm², highlighting the role of secreted antagonistic compounds. Among the tested strains, Pediococcus pentosaceus CRL 2145 showed the strongest effect and was selected for deeper analysis. Fluorescence microscopy confirmed EHEC cell death within mixed biofilms. Proteomic profiling of CRL 2145 under mixed-biofilm conditions revealed 162 differentially expressed proteins, with 156 upregulated. These proteins were mainly associated with metabolism, transcription, translation, and stress response pathways, suggesting a multifactorial inhibitory mechanism involving metabolic dominance, physical competition, and secretion of antagonistic molecules. Overall, this study deepens our understanding of the molecular and physiological aspects of LAB–EHEC interaction. P. pentosaceus CRL 2145 emerges as a promising biocontrol agent that could be applied, alone or with its supernatants, to meat processing surfaces to improve food safety. Proteomic data: ProteomeXchange PXD067300. Full article

miR-71 has been determined to enhance the efficacy of biological control agents against termites. However, it is not clear how miR-71 functions in enhancing the termite control. In this study, we tested the effects of termite miR-71 on the transcriptional and translational profiles of termites via the commercial product miR-71 agomir, and meanwhile developed a cost-effective method using T7 RNA polymerase to synthesize a miR-71 mimic, comparing the effects of the T7-synthesized miR-71 mimic versus the commercial miR-71 agomir on the gene expressions and infection mortality of termites. Comparative bioassays demonstrated that both miR-71 mimic and agomir significantly increased fungus-induced termite mortality with equivalent bioactivity. Mechanistically, transcriptomic and proteomic analyses revealed that commercial miR-71 agomir modulated the expression of defense-related genes, such as hexamerin-1, neuroligin-4, and probable chitinase-10. Meanwhile, RT-qPCR confirmed that T7-synthesized miR-71 mimic induced similar expression changes in the same target genes. Additionally, the dsRNA-mediated silencing of hexamerin-1, neuroligin-4, and probable chitinase-10 made termites more vulnerable to the fungus, respectively. Our study establishes in vitro-transcribed miRNA mimics as potent and cost-effective tools for studying ‘miRNA–mRNA’ interaction, and meanwhile lays the foundation for the microbe-mediated expression of small-RNA mimics in enhancing termite biocontrol. Full article

Ovarian follicular fluid (FF) is a metabolically active and biomarker-rich medium that mirrors the oocyte microenvironment. Its analysis is increasingly recognized in infertility diagnostics and assisted reproductive technologies (ART) for assessing oocyte competence, understanding reproductive disorders, and guiding personalized treatment. However, FF’s high viscosity, complex composition, and biochemical variability challenge reproducibility in sample preparation and molecular profiling. Sonication-based extraction has emerged as an effective approach to address these issues. By exploiting acoustic cavitation, sonication improves protein solubilization, metabolite release, and lipid recovery, while reducing solvent use and processing time. This review synthesizes recent advances in sonication-assisted FF analysis across proteomics, metabolomics, and lipidomics, emphasizing parameter optimization, integration with advanced mass spectrometry workflows, and emerging applications in microfluidics, automation, and point-of-care devices. Clinical implications are discussed in the context of enhanced biomarker discovery pipelines, real-time oocyte selection, and ART outcome prediction. Key challenges, such as preventing biomolecule degradation, standardizing protocols, and achieving inter-laboratory reproducibility, are addressed alongside regulatory considerations. Future directions highlight the potential of combining sonication with multi-omics strategies and AI-driven analytics, paving the way for high-throughput, standardized, and clinically actionable FF analysis to advance precision reproductive medicine. Full article

Gastric diseases represent a significant challenge to global health. A comprehensive understanding of their complex molecular mechanisms, particularly the pathways of molecular progression in precancerous lesions, is essential for enhancing diagnosis and treatment. StomachDB, the first comprehensive multi-omics database dedicated to gastric diseases, has been developed to address these research needs. This database integrates 6 types of biological data: genomics, transcriptomics, emerging single-cell and spatial transcriptomics, proteomics, metabolomics, and therapeutic-related information. It encompasses 44 gastric-related pathologies, including various forms of gastric cancer, gastric ulcers, and gastritis, primarily involving humans and mice as model organisms. The database compiles approximately 2.5 million curated and standardized profiles, along with 268,394 disease-gene associations. The user-friendly analytics platform provides tools for browsing, querying, visualizing, and downloading data, facilitating systematic exploration of multi-omics features. This integrative approach addresses the limitations of single-omics analyses, such as data heterogeneity and insufficient analytical dimensions. Researchers can investigate the clinical significance of target genes (e.g., CDH1) across different omics levels and explore potential regulatory mechanisms. Furthermore, StomachDB emphasizes the discovery of therapeutic targets by cataloging interactions among chemical drugs, traditional herbal medicines, and probiotics. As an open-access resource, it serves as a powerful tool for studying complex biological interactions and regulatory mechanisms. Full article

Background: Fabry disease (FD) is an X-linked lysosomal storage disorder caused by GLA mutations, leading to deficient α-galactosidase A (α-Gal A) activity and progressive glycosphingolipid accumulation. While α-Gal A activity is the diagnostic gold standard, its sensitivity is reduced in late-onset or heterozygous patients. Conventional biomarkers such as lyso-Gb3 provide only limited insight into disease progression and therapeutic response. Exosomes, as stable carriers of disease-specific proteins, may offer complementary biomarkers for early detection and longitudinal monitoring. Methods: Twenty-one pediatric FD patients with confirmed GLA mutations were enrolled. Clinical, enzymatic, renal, and cardiac parameters were assessed. Plasma-derived exosomes were characterized by transmission electron microscopy and proteomic profiling. Differentially expressed proteins were identified using mass spectrometry, analyzed using GO/KEGG enrichment, and validated using RT-PCR, ELISA, and immunofluorescence in patient samples and Gla^−/− mice. Results: Male patients showed markedly reduced α-Gal A activity and elevated lyso-Gb3 compared with females. Although overt renal and cardiac dysfunction was uncommon, several patients exhibited early abnormalities such as proteinuria, an elevated LVMI, or increased cTnI levels. Proteomic analysis identified 2553 proteins, of which 188 were differentially expressed. Fibrosis- and inflammation-related proteins, including THBS1 and CFHR5, were upregulated, while protective factors such as APM1, SERPINA10, and CAB39 were downregulated. IGFBP3 was also elevated and closely linked to tissue remodeling. Enriched pathways were involved in PPAR/AMPK signaling, lipid metabolism, and complement activation. Conclusions: Exosomal proteomic profiling revealed early molecular signatures of cardiorenal involvement in pediatric FD. Key proteins such as THBS1, CFHR5, IGFBP3, APM1, and CAB39 show strong potential as biomarkers for risk stratification, disease monitoring, and therapeutic evaluation. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a multifactorial condition requiring multi-target therapeutic strategies beyond traditional single-marker approaches. In this work, we present a fully in silico nutraceutical screening pipeline that integrates molecular prediction, systemic aggregation, and technological design. A curated panel of ten MASLD-relevant targets, spanning nuclear receptors (FXR, PPAR-α/γ, THR-β), lipogenic and cholesterogenic enzymes (ACC1, FASN, DGAT2, HMGCR), and transport/regulatory proteins (LIPG, FABP4), was assembled from proteomic evidence. Bioactivity records were extracted from ChEMBL, structurally standardized, and converted into RDKit descriptors. Predictive modeling employed a stacked ensemble of Random Forest, XGBoost, and CatBoost with isotonic calibration, yielding robust performance (mean cross-validated ROC-AUC 0.834; independent test ROC-AUC 0.840). Calibrated probabilities were aggregated into total activity (TA) and weighted TA metrics, combined with structural clustering (six structural clusters, twelve MOA clusters) to ensure chemical diversity. We used physiologically based pharmacokinetic (PBPK) modeling to translate probabilistic profiles into minimum simulated doses (MSDs) and chrono-specific exposure (%T>IC50) for three prototype concepts: HepatoBlend (morning powder), LiverGuard Tea (evening aqueous form), and HDL-Chews (postprandial chew). Integration of physicochemical descriptors (MW, logP, TPSA) guided carrier and encapsulation choices, addressing stability and sensory constraints. The results demonstrate that a computationally integrated pipeline can rationally generate multi-target nutraceutical formulations, linking molecular predictions with systemic coverage and practical formulation specifications, and thus provides a transferable framework for MASLD and related metabolic conditions. Full article

Tacrolimus-induced chronic nephrotoxicity (TACN) represents a major barrier to long-term graft survival in kidney transplantation, yet its molecular pathogenesis remains incompletely understood. We have previously reported metabolic abnormalities, including carnitine deficiency, nicotinamide adenine dinucleotide depletion, and elevated asymmetric dimethyl arginine (ADMA), in TACN. To identify upstream regulators associated with these metabolic disturbances, we conducted a comprehensive trans-omic analysis, integrating transcriptomics and proteomics of kidney tissues from male ICR mice with TACN (n = 5/group). Differentially expressed genes and proteins were subjected to functional enrichment and transcription factor binding motif analyses, followed by upstream master regulator identification using the Genome Enhancer platform. A total of 785 genes and 2472 proteins were differentially expressed, with partially discordant regulation between transcriptomic and proteomic profiles, underscoring the limitations of single-omic approaches. Upstream analysis identified protein arginine methyltransferase-1 (PRMT1) and integrins, particularly αVβ6, as potential master regulators and therapeutic targets. PRMT1 is implicated in ADMA-mediated nitric oxide inhibition and fibrosis, whereas integrin αVβ6 is associated with tubular injury and renal fibrogenesis. Notably, PRMT1 may activate STAT3, which in turn regulates integrin β6 expression, suggesting a novel PRMT1–STAT3–integrin αVβ6 axis in TACN pathogenesis. This study represents the first trans-omic approach to TACN, providing a foundation for mechanistic validation and therapeutic exploration of PRMT1 and integrins in both preclinical and clinical settings. Full article

Extracellular particles (EPs), an umbrella term encompassing membrane-enclosed extracellular vesicles (EVs) and non-vesicular extracellular particles ([NVEPs], previously described as extracellular condensates [ECs]) contain a complex cargo of biomolecules, including DNA, RNA, proteins, and lipids, reflecting the physiological state of their cell of origin. Identifying proteins associated with EPs that regulate host responses to physiological and pathophysiological processes is of critical importance. Here, we report the findings of our study to gain insight into the proteins associated with NVEPs. We used samples from human semen, the rat brain, and the rhesus macaque (RM) brain and blood to assess the physical properties and proteome profiles of NVEPs from these specimens. The results show significant differences in the zeta potential, concentration, and size of NVEPs across different species. We identified 938, 51, and 509 total proteins from NVEPs isolated from rat brain tissues, RM blood, and human seminal plasma, respectively. The species-specific protein networks show distinct biological themes, while the species-conserved protein interactome was identified with six proteins (ALB, CST3, FIBA/FGA, GSTP1, PLMN/PLG, PPIA) associated with NVEPs in all samples. The six NVEP-associated proteins are prone to aggregation and formation of wide, insoluble, unbranched filaments with a cross-beta sheet quaternary structure, such as amyloid fibrils. Protein-to-function analysis indicates that the six identified proteins are linked to the release of dopamine, immune-mediated inflammatory disease, replication of RNA viruses, HIV-HCV co-infection, and inflammation. These interesting findings have created an opportunity to evaluate NVEPs for their potential use as biomarkers of health and disease. Additional in-depth studies are needed to clarify when and how these proteins sustain their physiological role or transition to pathogenic roles. Full article

Extracellular vesicles (EVs) express features of parental cells and are fundamental in modulating the crosstalk between cancer cells and their environment. Increasing evidence suggests that EVs have a pivotal role in tumorigenesis, cancer development, and drug resistance. EVs are also involved in controlling the communication between hematopoietic stem cells and the surrounding microenvironment in the bone marrow (BM), during several processes such as self-renewal, mobilization, and lineage differentiation. Proteins expressed in cancer cell-derived EVs can be useful to further understand the regulation of hematopoietic stem cell fate, a fundamental mechanism in acute myeloid leukemia (AML). Furthermore, EVs are implicated in transmitting drug-resistance mechanisms in solid and not-solid cancer types. Here, using a proteomic approach, we analyze and validate the protein profile of EVs from three AML cell lines with different genotypes, namely OCI-AML-2, OCI-AML-3, and HL-60. The majority of the identified proteins were significantly enriched in the Gene Ontology category ‘Extracellular Exosome’. Network model analysis of EV proteins revealed several significantly modulated pathways, including inflammation activation and metastatic processes in AML cell-derived EVs. The EVs proteomic profiling allows us to identify the EVs-associated molecules and pathways that could impact cancer progression and drug resistance. Full article

The mechanistic underlying the favorable meat quality of Tibetan pigs has not been fully elucidated. This study integrated flavor chemistry, histomorphology, and proteomics to explore the structural and molecular features of their meat. Longissimus dorsi samples from Tibetan and Duroc pigs (n = 6 each biological replicates) were quantitatively analyzed for amino acid profiling, histological assessment, and proteomic characteristic. Statistical approaches included weighted correlation network analysis, t-tests, and functional enrichment. Tibetan pork contained 34 mg/100g more total free amino acids, notably sweet-tasting Ala (+49.2%) and Thr (+32.2%). Muscle fiber density was >250% higher and diameter > 30% smaller, indicating finer texture. Proteomics revealed 149 upregulated proteins, including 57 mitochondrial differentially expressed proteins (DEPs)—11 of which belonged to electron transport chain complexes (e.g., NDUFAB1, COX2). The significant enrichment of oxidative phosphorylation pathways may be associated with mitochondrial efficient energy metabolism under hypoxic in Tibetan pigs, potentially linking to the breed’s unique meat characteristics. Ala levels showed strong correlations with metabolic and structural protein modules. The finer fibers and mitochondrial protein profile of Tibetan pigs contribute to higher amino acid content and meat quality. This structural–metabolic–flavor axis supports both hypoxia adaptation and high meat quality. Given the central role of mitochondrial electron transport chain (ETC) proteins in energy metabolism and Ala in flavor presentation, their synergistic action provides a molecular bridge between hypoxia adaptation and meat quality. Therefore, this study suggests that ETC and Ala may serve as key biomarkers for meat quality differences, offering new perspectives for meat quality research. Full article

Postmortem diagnosis of sudden cardiac death (SCD) may escape detection due to the absence of thrombi and slow development of structural and immunohistochemical changes. Therefore, this study explores the possibility of analyzing relevant clinical chemistry biomarkers in myocardial homogenates and serum. Following an initial pilot study, myocardial samples from 113 autopsy cases were homogenized with distilled water, T-PER or 2 M urea. Aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatine kinase (CK-MB), lactate dehydrogenase (LDH), orosomucoid and total protein were analyzed with an IndikoPlus and a subset was also analyzed with a Roche Cobas 8000 c701 analyzer, which also provided results for cardiac Troponin T, myoglobin and NT-proBNP. Although the yields varied with different extraction buffers depending on the analyte, distilled water was often as effective as T-PER and 2 M urea extraction for most analytes. Biomarker levels were consistently higher in the myocardial homogenates than in serum. Proteomic profiling on a subset confirmed higher concentrations of the cardiac markers in the tissue samples than in serum. Finally, we investigated whether selected markers could support the diagnosis of acute cardiac disease by classifying cases as sudden cardiac death (SCD) or controls. There was no significant difference in serum concentrations of the selected biomarkers between SCD cases and controls, whereas a significant loss of several markers was observed in SCD myocardial samples as compared to controls. Hence, our results suggest that analysis of tissue homogenates is likely better for detecting early ischemia, and we show that an in-house benchtop multi-analyzer can provide rapid results to assist the pathologist’s decision-making during autopsy. Full article

Resveratrol may protect against radiation by modulating cellular metabolism and enhancing the cellular response to stress. Here, we explored its effects on human cardiomyocytes exposed to ionizing radiation. Resveratrol (5 µM) was administered for 1, 7, and 30 days before a single 2 Gy dose of irradiation, and then radiation toxicity and changes in the proteome were evaluated. Extended resveratrol treatment (7 or 30 days) induced more profound proteomic changes than one-day treatment and partially counteracted toxic effects of radiation, leading to increased cell survival, reduced cell death, and fewer cells arrested in the G1 phase. Though resveratrol administration itself had a greater impact on the proteome than radiation alone, we identified three subsets of proteins differently affected by radiation depending on the resveratrol context. The first subset (84 differentially expressed proteins; DEPs) represented proteins influenced by radiation in all resveratrol pretreatment regimens. The second subset (228 DEPs), linked to DNA repair, cell cycle checkpoints, and apoptosis, was affected by radiation only in the absence of resveratrol preconditioning, indicating the compound’s protective effect. The third subset (252 DEPs) involved in metabolism regulation appeared only after extended resveratrol preconditioning. In conclusion, the results demonstrate that hypothetical time-dependent cardioprotective effects of resveratrol are linked to significant proteomic reprogramming of cardiomyocytes caused by long-term pretreatment. Full article

The inflammatory and metabolic complexity of colitis necessitates therapies that act on multiple immune pathways. Using serum proteomic profiling, the present study evaluated the systemic immunomodulatory profile of Epilobium angustifolium lyophilized methanol-aqueous extract rich in oenothein B (EAE) in a dextran sulfate sodium (DSS)-induced mouse model of ulcerative colitis in a comparative manner to dexamethasone (DXM). DSS exposure triggered robust inflammatory activation, evidenced by elevated chemokines (CXCL9, CXCL10, CCL11), proinflammatory cytokines (IL-1α, IL-12, PAI-1, RAGE) and metabolic stress mediators (leptin, resistin, FGF-21). Treatment with EAE significantly attenuated this inflammatory profile, notably reducing Th2-skewed chemokines and eosinophil recruitment. In contrast to DXM, EAE uniquely normalized pro-thrombotic and tissue-remodeling markers, including PAI-1 and RAGE, both implicated in intestinal barrier dysfunction and chronic inflammation. Furthermore, EAE demonstrated superior modulation of inflammation-associated growth factors (IGFBP-5, HGF, Flt3L) and adipokines (leptin, resistin), indicating a broader therapeutic scope that includes metabolic dysfunctions. Collectively, our data reveal that EAE exerts a distinct immunoregulatory profile, modulating both innate and adaptive immune pathways while simultaneously addressing metabolic pathologies. These multifaceted actions underscore its promise as a phytotherapeutic candidate for the management of ulcerative colitis and other inflammatory conditions, with potential advantages over conventional steroid treatment. Full article

The human placenta is a complex organ that supports fetal development and is rich in extracellular matrix proteins and growth factors, making it suitable as a biomaterial in wound care. Placenta-derived amnion-only allografts have traditionally been used in the clinic, but they lack the structural and biochemical complexity of the full three-layer placental membrane, which includes the amnion, intermediate, and chorion layers. Advances in tissue engineering have enabled preservation of multiple layers, giving rise to multilayer placental-based Cellular and Acellular Matrix-like Products (CAMPs) such as Full-Thickness (FT; amnion, intermediate, chorion) and ACA (amnion, intermediate, chorion, amnion). Although these advanced CAMPs are increasingly applied clinically, their molecular composition has not been comprehensively defined. This study presents a global proteomic analysis of FT and ACA, complemented by targeted multiplex analysis of soluble proteins and an in vitro angiogenesis assay. Proteomic profiling identified 8908 structural and bioactive components, with 32.5% of proteins associated with tissue repair and remodeling pathways. Multiplex analysis confirmed accessibility of biologically relevant soluble factors. Endothelial tube formation assays further supported biological relevance, demonstrating that soluble proteins in FT and ACA support angiogenesis. These data provide a molecular characterization of multilayer CAMPs and underscore their potential to deliver durable wound coverage while supporting the local microenvironment. Full article

Mitochondrial proteins (mtPs) packaged into extracellular vesicles (EVs), particularly exosomes, have emerged as promising biomarkers and functional mediators in cancer biology. In this study, we investigated whether breast cancer (BC)-derived exosomes selectively incorporate mtPs, thereby providing insights into their diagnostic potential and role in tumor progression. Exosomes were isolated from conditioned media of multiple BC cell lines and non-tumorigenic breast epithelial cells using ultracentrifugation and were characterized by transmission electron microscopy and flow cytometry for canonical markers CD9 and CD81. Proteomic profiling by MALDI-TOF mass spectrometry revealed a distinct enrichment of mtPs in exosomes derived exclusively from tumor cells, while non-tumorigenic cells lacked such cargo. Identified proteins were predominantly associated with the oxidative phosphorylation system, with Complex I subunits most frequently detected, whereas Complex II components were entirely absent. These findings highlight a cancer-specific mechanism of exosomal mtP incorporation, potentially reflecting altered energy metabolism and stress responses in malignant cells. We conclude that mtPs in exosomes represent both functional contributors to tumor progression and promising candidates for liquid biopsy-based BC diagnostics. Full article