Search Results (11,055)

Objective: Emphysema is an important chronic obstructive pulmonary disease (COPD) phenotype characterized by the destruction of air spaces distal to the terminal bronchiole. Aiming to detect potential emphysema biomarkers and to assess the systemic effects of emphysema in blood plasma, we conducted a small cross-sectional shotgun proteomics study. Methods: This study included N = 40 participants divided into four subgroups (N = 10 per group): patients with emphysema and COPD (CE), patients with COPD but without emphysema (CN), healthy smokers (HS) and healthy never-smokers (HN). The participants were sampled non-probabilistically to be similar in terms of age, sex and comorbidities. Participants’ blood plasma was analyzed using liquid chromatography–mass spectrometry. Bioinformatic analysis included detection of differentially expressed proteins (DEPs) and overrepresentation analysis (ORA). Results: Across all groups, a total of 994 proteins were identified, with NADP-dependent malic enzyme (NADP-ME; encoded by ME1) being the only DEP in the CE vs. CN contrast. Proteins such as BMP1, ADAMTSL-2, -4 and IGFBP4, -5, 6 were identified to be upregulated in CE vs. HN. Fibulin-1, -3 and several immunoglobulin components were identified to be downregulated in the CE vs. HN contrast. ORA revealed several enriched processes, including serine-type endopeptidase activity, insulin-like growth factor I and II binding, and signaling receptor binding. Conclusion: We propose NADP-ME, an important enzyme of intermediary metabolism and redox homeostasis, as a potential biomarker candidate of emphysema. Notably, NADP-ME is also implicated in anoikis resistance. Additionally, changes in the expression levels of BMP1, ADAMTSL-2 and -4, and fibulin suggest potential major systemic effects of extracellular matrix perturbation. As all data was derived from LC-MS analysis, these findings need to be further evaluated with complementary methods. Full article

Dietary antioxidants are widely valued for their potential health benefits, but incorporating them into functional foods is not straightforward. Polyphenols are among the most abundant and important antioxidants in foods, and this review focuses on them because the same structural features linked to their health-promoting effects can also cause pronounced bitterness and astringency, ultimately limiting consumer acceptance. This review examines how these challenges are interconnected across three levels: food matrix interactions, bioavailability, and consumer psychobiology. We describe how non-covalent interactions between polyphenols, proteins, and polysaccharides can have both positive and negative effects. While these interactions may alter oral lubrication and flavour release, they also protect highly reactive bioactive compounds from gastric degradation. Furthermore, we broaden the concept of bioavailability by exploring the microbiota-mediated “colonic rescue” of polyphenols that are not released during earlier digestion. We also highlight the role of extraoral bitter taste receptors (TAS2Rs) along the gastrointestinal (GI) tract. Activation of these receptors during digestion can trigger relevant metabolic and endocrine responses, indicating that systemic absorption is not the only pathway to bioactivity. Finally, we connect these mechanisms to individual differences in food acceptance, showing that genetic factors (e.g., TAS2R38 and the salivary proteome) and psychological traits (such as neophobia and reward sensitivity) can shape rejection or flavour-nutrient learning. Overall, the successful development of functional foods will require a “sensory-by-design” approach. This strategy utilises matrix interactions strategically to improve both consumer acceptance and physiological efficacy. Full article

Neuropeptides regulate diverse physiological and behavioural processes in parasites, yet their functional roles in the infective larval stages of Schistosoma mansoni remain poorly defined. In this study, we identified miracidia-derived putative neuropeptides and examined their roles in regulating miracidial behaviour. Peptidomic analysis revealed ten putative neuropeptides, including five whose proteomic identification in this life stage was previously unreported. Neuropeptide precursor proteins were evaluated for stage-specific expression and Schistosoma genus specificity to prioritise candidates with potential functional and biocontrol relevance. Protein–protein interaction analysis identified Smp_176700 as a highly connected neuropeptide precursor associated with proteins implicated in miracidial structure and infection. Eight putative neuropeptides derived from six precursor proteins were synthesised and externally applied to miracidia in acute (1 min) and prolonged (360 min) behavioural assays. During acute exposure, most peptides induced significant concentration-dependent behavioural changes at 3 mg/mL and 0.1 mg/mL, characterised by reduced swimming velocity and increased directional change, with no significant effects at 0.01 mg/mL. Prolonged exposure revealed peptide-specific effects, with ASLSYF-OH and FLLGLPPSLRQH-OH producing the most pronounced behavioural modulation. These findings demonstrate that S. mansoni miracidia express bioactive neuropeptides capable of modulating larval behaviour, providing insight into schistosome neurobiology and identifying potential targets for transmission-blocking interventions. Full article

Nontyphoidal Salmonella (NTS) is a zoonotic pathogen that threatens public health worldwide. This study investigated the prevalence, serotype, virulence, and antimicrobial resistance of NTS isolated from chicken meat in Fukuoka, Japan. Of 50 samples, 64% were positive for Salmonella spp., and 32 NTS strains were isolated from positive samples. Serotyping identified three serotypes: S. enterica ser. Schwarzengrund (78.1%), S. enterica ser. Thompson (15.6%), and S. enterica ser. Oranienburg (6.3%). Multilocus sequence typing revealed three sequence types (STs), and MALDI-TOF MS analysis revealed six distinct clusters, reflecting heterogeneity in protein expression among isolates with the same STs. All isolates harbored the virulence genes hilA, spiC, and ssrB, but not spvC. Microplate assays showed that all S. enterica ser. Schwarzengrund and S. enterica ser. Thompson strains formed biofilms with varying strengths. Antimicrobial susceptibility tests demonstrated that S. enterica ser. Thompson and S. enterica ser. Oranienburg strains were sensitive to all the antimicrobials tested. However, S. enterica ser. Schwarzengrund strains showed resistance to multiple antibiotic classes, and 36% of the isolates were multidrug resistant. These findings suggest a potential public health concern, particularly from S. enterica ser. Schwarzengrund, and underscore the importance of continuous surveillance that integrates both genotypic and phenotypic methods. Full article

Background: Fish skin mucus contains proteins involved in diverse biological pathways, representing a valuable non-invasive diagnostic of fish health. Methods: Skin mucus from three male and three female barramundi was analysed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) following protein extraction and S-Trap digestion. Results and Discussion: A total of 1801 protein groups were matched to the L. calcarifer reference proteome and functionally annotated using Gene Ontology (GO) terms via UniProt ID mapping, with representation across Biological Process, Cellular Component, and Molecular Function categories. Functional classification using eggNOG-mapper further associated leading protein group sequences with Clusters of Orthologous Groups (COGs) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. GO-based screening prioritised 352 putatively immune-relevant protein groups and 24 protein groups associated with sex- and reproduction-related processes, highlighting the functional complexity of the skin mucus proteome. Comparative analysis revealed sex-associated patterns in protein group detection and relative abundance, with differential abundance analysis identifying 244 protein groups exhibiting statistically significant differences between male and female samples. Conclusions: This study provides the first comprehensive discovery-based characterisation of the barramundi skin mucus proteome and establishes a baseline reference dataset for this aquaculture-relevant species. The findings support the utility of skin mucus proteomics for exploring immune and sex-associated molecular patterns and provide a baseline dataset for future validation studies investigating non-invasive health and reproductive monitoring. 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: Cryopreservation induces oxidative stress, membrane disruption, and mitochondrial injury in spermatozoa, leading to impaired motility and fertility. Selenium, as an essential trace element, protects cells from oxidative damage through selenoproteins such as glutathione peroxidase 4 (GPX4), a critical enzyme that detoxifies lipid hydroperoxides and inhibits ferroptosis. This study investigated whether supplementation with L-selenomethionine (L-SeMet), an organic selenium source with superior bioavailability and lower toxicity than inorganic forms, could alleviate cryo-induced sperm injury by suppressing ferroptosis. Methods & Results: Dairy goat sperm were cryopreserved with 0, 2, 4, 6, 8, 10 μM L-SeMet. Supplementation with 6 μM L-SeMet significantly improved motility, membrane and acrosome integrity, and mitochondrial membrane potential. Biochemical assays showed reduced iron, ROS, and MDA levels, alongside increased ATP, SOD, and GSH contents. Proteomic analysis identified 148 differentially expressed proteins, including up-regulation of GPX4, FTH1, VDAC2, and VDAC3—core ferroptosis regulators. Metabolomic profiling further revealed enrichment in unsaturated fatty acid biosynthesis, amino acid metabolism, and the TCA cycle, pathways closely linked to ferroptosis regulation. Transmission electron microscopy confirmed that L-SeMet preserved mitochondrial ultrastructure. Mechanistically, L-SeMet mirrored the ferroptosis inhibitor N-acetyl-L-cysteine and reversed RSL3-induced oxidative damage. Western blotting verified activation of the NRF2–SLC7A11–GPX4 antioxidant axis and inhibition of KEAP1 expression. Conclusions: Collectively, these findings demonstrate that L-SeMet protects spermatozoa from cryo-induced injury by stabilizing redox homeostasis, maintaining mitochondrial function, and inhibiting ferroptosis. The results highlight ferroptosis as a critical mechanism of sperm cryodamage and identify L-SeMet as a promising metabolic intervention to enhance post-thaw sperm quality and fertility. Full article

Background: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and neopeptides, making them a promising additional source of neoantigens. However, SV-derived neoantigen prediction remains challenging due to breakpoint uncertainty, isoform-dependent coding inference, and limited integration of multi-dimensional evidence and reproducibility. Methods: We developed SVNeoPP (Structural Variant Neoantigen Prediction and Prioritization), an end-to-end workflow for SV-derived neoantigen analysis. SVNeoPP takes WGS and RNA-seq as inputs, performs SV calling and annotation, and reconstructs altered transcripts and coding sequences in a traceable, isoform-aware manner to generate candidate peptides. Candidates are prescreened by integrating antigen-processing features with HLA binding prediction, and then hierarchically filtered and prioritized based on transcript expression, LC–MS/MS proteomics evidence, immunogenicity predictions, and sequence similarity to experimentally validated neoantigen databases. SVNeoPP is implemented in Snakemake to enable modular extension, checkpoint-based restarts, and end-to-end reproducibility. Results: Using a hepatocellular carcinoma (HCC) multi-omics dataset as a proof of concept, we demonstrated the performance of SVNeoPP and obtained a high-priority shortlist of candidate peptides. Compared with other methods, SVNeoPP substantially expanded the candidate search space for SV-derived neoantigens and showed more favorable distributions of antigen-processing and HLA binding features. Conclusions: SVNeoPP provides a reusable, traceable, and interpretable multi-dimensional evidence-driven framework for SV-derived neoantigens. As a complementary module to SNV/small-indel pipelines, it broadens the neoantigen candidate repertoire and generates ranked candidates with interpretable evidence to facilitate downstream prioritization and decision-making. Full article

Chlorogenic acid (CGA), which is ubiquitous in diverse botanical sources, demonstrates considerable anticancer potential through modulation of multiple targets or signaling pathways, thereby posing substantial challenges for mechanistic elucidation and target identification. Based on the proteolysis targeting chimera (PROTAC) technology’s ability to induce targeted protein degradation via ubiquitin-proteasome pathway recruitment, we synthesized a panel of CGA-PROTACs. These compounds incorporated the natural product CGA as the target-binding ligand, conjugated to pomalidomide (an E3 ligase-recruiting moiety) via various synthetic linkers. The findings indicated that compound A7, linked with an alkane linker, exhibited a notable anti-proliferative effect on 4T1 and A375 cells in vitro. The IC₅₀ value of A7 on A375 cells reached 69.70 μM, which is 2.2 times better than the effect of the precursor compound CGA (IC₅₀ = 148.80 μM). Mouse double minute 4 (MDM4) was confirmed as a potential target of compound A7 through a combination of proteomics, Western blot analysis and molecular dynamics simulation. CGA-PROTAC A7 treatment led to a dose-dependent reduction in MDM4 protein levels while significantly upregulating p53 and p21 protein expression, and thus inhibited proliferation, induced G2/M phase cell cycle arrest, and markedly enhanced apoptosis in melanoma A375 cells. This study successfully applied an effective strategy for target identification and medication discovery of natural compounds. In addition, CGA-PROTAC A7 was synthesized in one step with an overall yield of 45.96%, providing a feasible route for synthesis and establishing a basis for the combination of natural product polyphenols with PROTAC technology. Full article

Blood platelets are derived from megakaryocytes with functions extending beyond hemostasis to inflammation, immunity, and cancer. Myeloproliferative neoplasms (MPNs) are clonal stem cell disorders driven by somatic mutations affecting JAK-STAT signaling, leading to excessive myeloid proliferation. Thrombosis affects approximately one-fifth of patients at diagnosis and remains elevated throughout the disease course, while the paradoxical coexistence of bleeding further complicates clinical management. In addition, MPNs may progress to advanced disease stages, including bone marrow fibrosis and transformation to acute myeloid leukemia, leading to ineffective hematopoiesis, worsening symptom burden, and poor clinical outcomes. This review outlines how peripherally circulating platelets provide a unique window into MPN pathophysiology, with emphasis on their functional and molecular abnormalities. We summarize current understanding of platelet-mediated hemostatic imbalance across MPN subtypes. We discuss the potential of platelet transcriptomics and proteomics to reveal disease-specific signatures. We further highlight emerging platelet-associated candidates with potential utility as dynamic biomarkers for both the pathological marrow niche and thrombotic and bleeding risk. Together, these insights underscore the potential of platelet-based approaches to complement existing diagnostic and prognostic strategies in MPNs. Full article

Platelets are small circulating blood cells that mediate haemostasis and thrombosis. Platelets respond to vascular damage by adhesion, granule release, and aggregation. Healthy endothelial cells inhibit platelets through prostacyclin-induced cAMP signalling. Intracellular cAMP activates protein kinase A (PKA), a tetrameric kinase composed of two regulatory (R) and two catalytic (C) subunits. cAMP-binding triggers dissociation of C subunits from the PKA complex and phosphorylation of substrate proteins, which mediate platelet inhibition. The R subunits of PKA are known to be attached to A-kinase anchoring proteins (AKAPs), which enable subcellular compartmentalisation of cAMP signalling. Proteomics have identified 22 AKAPs in platelets, but only a few of these have been studied in detail. This review summarises current knowledge about platelet AKAPs, including studies done regarding other cells. Possible integration of AKAPs into platelet signalling is explored with a focus on subcellular localisation, interaction partners, and PKA-mediated substrate phosphorylation. As main platelet compartments, the plasma membrane, endosomes, mitochondria, the Golgi, the dense tubular system, and the cytoskeleton are considered. Potential roles of individual AKAPs in platelet inhibition are discussed, and open questions in the field are defined. Full article

Carnosine (CAR), an endogenous histidine-containing dipeptide, exhibits antioxidant and anti-inflammatory activity in various experimental models; however, its molecular mechanism of action remains poorly understood. Here, we demonstrate that the Michael adduct between CAR and 4-hydroxy-2-nonenal (HNE), which has been detected in previous studies in both in vitro and in vivo settings, mediates its bioactivity, particularly its antioxidant and anti-inflammatory responses, through Nrf2 activation. The CAR–HNE adduct was synthesized and its physicochemical, metabolic, and biological properties were evaluated. CAR–HNE exhibited high stability in biological matrices and retained the ability to transfer HNE to thiol nucleophiles at a slow rate under physiologically relevant conditions, consistent with electrophile-mediated Nrf2 activation. This kinetic behavior limits the cytotoxicity typically associated with free HNE while preserving the redox signaling capacity. CAR–HNE induced dose-dependent Nrf2 activation and NF-κB inhibition in cell-based assays without the hormetic toxicity observed for free HNE. Mechanistically, CAR–HNE may act as a redox-tunable electrophilic reservoir, restoring nucleophilic tone and modulating redox-sensitive transcription factors. In vivo, CAR–HNE attenuated DSS-induced colitis more effectively than equimolar doses of either carnosine or HNE alone. Proteomic analyses revealed modulation of canonical Nrf2-dependent antioxidant pathways. Our findings suggest a conceptual shift in carnosine biology: rather than acting as a classical antioxidant or carbonyl quencher, carnosine functions as a precursor of redox-active electrophilic adducts that transduce anti-inflammatory and antioxidant responses via controlled RCS signaling. Full article

Pyroptosis is a pro-inflammatory form of programmed cell death mediated by inflammasomes and caspases and has been implicated in various inflammatory diseases. However, its function and regulatory role in dairy cows with clinical mastitis (CM) remain poorly understood. This study was conducted to investigate the differentially expressed proteins (DEPs) involved in biological processes (BPs) and the Kyoto Encyclopedia of Genes and Genomes pathways related to inflammasome-mediated pyroptosis based on proteomic data and to further explore their potential involvement in mastitis using in vivo and in vitro models. Histopathological analysis revealed morphological features consistent with pyroptosis in the mammary glands of CM-affected cows, including mammary epithelial cell (MEC) membrane disruption, increased reactive oxygen species production, elevated TUNEL–gasdermin D (GSDMD)-positive staining, and inflammatory cell infiltration. Proteomic profiling identified 276 DEPs and 17 BPs, among which NOD-like receptor family pyrin domain-containing 3 (NLRP3) was identified as a key candidate associated with cytokine production, immune defense, and inflammatory responses. Pathway enrichment analysis indicated that NLRP3, caspase-1 (CASP1), and GSDMD were enriched in the NOD-like receptor signaling pathway and were closely associated with mastitis. Immunohistochemical and molecular analyses demonstrated cytoplasmic localization and significant upregulation of NLRP3, CASP1, and GSDMD at both the mRNA and protein levels in CM-affected tissues. In both in vitro and in vivo models, a dose-dependent increase in the expression of pyroptosis-related targets and pro-inflammatory cytokines was observed with the progression of inflammation. Moreover, the pharmacological inhibition of CASP1 attenuated pyroptosis-associated changes and inflammatory responses in BMECs. Collectively, these findings suggest that the NLRP3–CASP1 axis is associated with inflammation-related pyroptosis in bovine mastitis and may represent a potential therapeutic target for clinical mastitis. Full article

Drought and elevated temperature are major abiotic stresses that limit potato growth and productivity; however, their combined effects on biomass and oxidative damage to proteins remain poorly understood. We investigated individual and interactive effects of drought and elevated temperature on growth traits, yield, protein carbonylation, 20S proteasome activity, and the leaf proteome. Results show that while an elevated temperature alone did not significantly impair vegetative biomass or yield, it markedly intensified the negative impacts of drought during simultaneous exposure. Drought and combined stress substantially reduced stem and leaf mass, as well as assimilation area. Biochemically, drought induced protein carbonylation and stimulated 20S proteasome activity. Interestingly, elevated temperature reduced carbonylation and proteasome activity, yet its presence in combined stress exacerbated oxidative damage compared to drought. Proteomic analysis revealed stress-specific carbonylation of molecular chaperones, antioxidant enzymes, and proteins involved in photosynthesis, glycolysis, and energy metabolism. These results suggest that while potato plants exhibit resilience to moderately elevated temperature, the synergistic effect of heat and drought triggers a more severe oxidative challenge. This requires enhanced proteolytic and antioxidant mechanisms to maintain growth and productivity under complex stress conditions. Full article

Marine byproducts generated from seafood processing represent valuable reservoirs of structurally and functionally distinct biomolecules, whose composition reflects species, habitat, and processing history. This systematic review identified which marine byproducts have been most extensively studied between 2020 and 2025, with emphasis on their composition, valorisation, and suitability for tracing their geographic origin. Following the PRISMA protocol, 6443 publications were initially retrieved, of which 96 peer-reviewed studies were included for data extraction and analysis. The five most frequently investigated byproducts—skin, bones, scales, shells, and roe—were identified as rich sources of proteins (collagen and gelatin), minerals (hydroxyapatite and calcium carbonate), polysaccharides (chitin), lipids (notably polyunsaturated fatty acids (PUFAs), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA)), and vitamin B12. Collagen properties, particularly imino acid content, hydroxylation degree, crosslinking density, and thermal stability, correlate more strongly with environmental temperature than taxonomy, supporting their potential as markers for tracing geographic origin. The mineral fractions, dominated by hydroxyapatite in bones and scales, or calcium carbonate in shells, provided complementary inorganic fingerprints based on calcium-to-phosphorus ratios, carbonate substitution, trace element composition, and thermal analyses. While the lipid profile alone could not completely discriminate fish roe, proteomic techniques, such as MALDI-TOF MS, make it possible to reliably identify species. Collectively, these byproducts offer complementary organic and inorganic markers that support integrated strategies that allow tracing their origin and fostering their sustainable valorisation, overcoming a key technical bottleneck for their use. However, their large-scale conversion into market-ready products remains limited by technical complexity, process variability, and cost-related constraints. Full article