Search Results (250)

The impact of seasonality on the aroma quality of tea has been documented in various tea types, but not specifically in oolong tea. This study is the first to explore the complex relationships between seasonality, volatile compounds, and aroma quality in oolong tea. Using Headspace Solid-Phase Microextraction Gas Chromatography–Mass Spectrometry (HS-SPME-GC-MS)-based untargeted metabolomics, we analyzed 266 samples of Tieguanyin oolong tea. The data identified linalool, linalool oxides (trans-linalool oxide (furanoid) and trans-linalool oxide (pyranoid)), and their metabolites (diendiol I; hotrienol) as key seasonal discriminants. Four out of the top ten key differential compounds for distinguishing aroma scores were metabolites from fatty acid degradation, namely trans-3-hexenyl butyrate, trans-2-hexenyl hexanoate, hexyl hexanoate, and hexyl 2-methyl butyrate. Approximately one-fifth of the seasonal discriminant volatile compounds were significant in influencing aroma quality. Overall, the impact of seasonality on the aroma quality of finished Tieguanyin oolong tea is marginal. These findings enhance our understanding of the interplay between seasonal variations, volatile composition, and aroma quality in oolong tea. Full article

Background: Human proteins exist in numerous modifications—proteoforms—which are promising targets for biomarker studies. In this study, we aimed to generate comparative proteomics data, including proteoform patterns, from hepatocellular carcinoma (HCC) and nonmalignant liver tissues. Methods: To investigate protein profiles and proteoform patterns, we employed a panoramic, integrative top-down proteomics approach: two-dimensional gel electrophoresis (2DE) coupled with liquid chromatography–electrospray ionization–tandem mass spectrometry (LC-ESI-MS/MS). Results: We visualized over 2500 proteoform patterns per sample type, enabling the identification of distinct protein signatures and common patterns differentiating nonmalignant and malignant liver cells. Among these, 1270 protein patterns were uniformly observed across all samples. Additionally, 38 proteins—including pyruvate kinase PKM (KPYM), annexin A2 (ANXA2), and others—exhibited pronounced differences in proteoform patterns between nonmalignant and malignant tissues. Conclusions: Most proteoform patterns of the same protein were highly similar, with the dominant peak corresponding to theoretical (unmodified) protein parameters. However, certain proteins displayed altered proteoform patterns and additional proteoforms in cancer compared to controls. These proteins were prioritized for further characterization. Full article

This study aims to investigate the effect of the Pd(II) complex on HeLa cells using computational biology and proteomic analysis. [Pd(dach)Cl₂]-treated HeLa cells were subjected to comparative proteomics analysis using label-free data-independent liquid chromatography-tandem mass spectrometry (LC-MS/MS). In parallel, the informational spectrum method (ISM) was used to predict potential protein interactors of the [Pd(dach)Cl₂] complex in HeLa cells. Proteomics analysis revealed 121 differentially abundant proteins (DAPs). Enrichment analysis of Gene Ontology (GO) annotations revealed ATP hydrolysis and RNA/protein binding as the top molecular functions and RNA splicing and protein–RNA complex organization as the top biological processes. Enrichment analysis of altered canonical pathways pointed out spliceosome and ribosome pathways. The top hub proteins with potential regulatory importance encompassed ribosomal proteins, translational and transcriptional factors, and components of the ribosome assembly machinery. ISM and cross-spectral analysis identified the nucleoplasm and sensor of the single-stranded DNA (SOSS DNA) complex. Proteome analysis showed that [Pd(dach)Cl₂] targets proteins involved in ribosomal biogenesis and RNA splicing, whereas theoretical prediction implies also potential effect on p53 signaling pathway, and thus, alterations of the expression of regulatory proteins involved in cell survival and proliferation. These findings underscore the potential of Pd(II) complexes as anti-cancer agents, warranting further exploration and detailed functional validation. Full article

Among the commercial mollusks from the Black Sea, the ark clam Anadara kagoshimensis, the oyster Crassostrea gigas, the mussel Mytilus galloprovincialis, the scallop Flexopecten glaber ponticus, and the gastropod Rapana venosa hold the top positions in terms of cultivation and harvesting volumes. Mollusk shells are attracting attention due to their potential use in various biotechnological applications, including nutraceutical production. In the present study, using inductively coupled plasma mass spectrometry, concentrations of essential trace elements (Cr, Mn, Fe, Co, Cu, Zn, Se, Mo, and I) were measured in shells of the five mollusks sampled from the same biotope. The essential element concentrations in the mollusk shells differed significantly. The highest concentrations of Cr, Mn, and I were found in Anadara shells; Fe and Co in Crassostrea shells; Zn in Mytilus shells; and Cu and Se in Rapana shells. Principal component analyses demonstrated the overall accumulation of all elements as the main cause of the total data variance and the species-specific accumulation of certain elements as the second most important source of the data dispersion. Matrices of element concentration correlations showed considerable dissimilarity, which suggested species specificity in the concerted or competing element accumulation. Powdered shells of Anadara, Crassostrea, and Rapana are most suitable to fulfill the daily human requirements for many essential elements, and the consumption of these powders in amounts of less than a few tens of grams appears to be sufficient for this purpose. Full article

Background: Rubia schumanniana E. Pritz. (RSP) and Rubia magna P. G. Xiao (RMP) are common adulterants of Rubiae radix et rhizoma (RRR). To realize RRR adulteration analysis, this paper conducted an identification evaluation of RRR based on liquid chromatography–mass spectrometry (LC-MS). Methods: After LC-MS analysis and data conversion, the ion intersections were taken from different batches of RSP, RMP, and RRR. Then, the proprietary ions of three herbs were obtained by taking the de-intersection. Finally, the top-n ions were treated as the “ion identity” of RSP, RMP, and RRR for matching test samples to obtain the recognition index (RI) and combined chemometrics for analysis. Results: The identification evaluation of RRR can be realized based on the “ion identity”, even if 3% RSP (or RMP) in RRR samples can still be recognized. Combined with chemometric analysis, three market samples were identified as adulterants, proving that identification evaluation based on “ion identity” is reasonable. Conclusions: The “ion identity” based on LC-MS, which helps in realizing RRR identification evaluation. It has important reference significance for RRR analysis. Full article

Objective: Secretory factors, termed the secretome, in the conditioned medium (CM) from dental mesenchymal stem cells (MSCs) have shown anti-inflammatory, anti-apoptotic, and tissue regenerative potential. This cell-free product could be further developed by preconditioning cells with various biochemical agents, which lead to a change in secretome and CM profiles. Among the favorable candidates for CM production, metformin as an anti-diabetic medication is currently considered a potential agent for dental hard tissue and periodontal regeneration. Here, we aimed to assess the composition of CM from periodontal ligament stem cells (PDLSCs) grown in metformin-preconditioned media (Met-CM) compared to normal PDLSC-CM and assess the ability of Met-CM to recover the function of inflamed PDLSCs. Methods: Met-CM and normal CM were collected from PDLSCs grown with or without 50 µM metformin, respectively, under healthy culture conditions. Mass spectrometry and liquid chromatography–tandem mass spectrometry (LC–MS/MS) were performed to comparatively evaluate the proteomic profiles in PDLSC-CM versus Met-CM. We then treated the PDLSC cultures with lipopolysaccharide (LPS) from Porphyromonas gingivalis to induce inflammation and evaluated the osteogenic/cementogenic differentiation in the presence of Met-CM or normal PDLSC-CM by assessing alkaline phosphatase activity, intracellular calcium levels, and mRNA expression of osteogenic and cementogenic factors, including RUNX2, OCN, OSX, and CEMP-1. Subsequently, we performed RNA sequencing to identify transcriptomic changes in the treated cells. Results: We identified 202 differentially expressed proteins, 175 of which were significant, in Met-CM versus normal PDLSC-CM. Among the analyzed groups, the top three protein classes were protein-binding activity modulator, cytoskeletal protein, and extracellular matrix (ECM) protein. Treatment of PDLSCs with LPS significantly attenuated ALP activity, [Ca²⁺]_i, and the mRNA expression levels of RUNX2, OCN, OSX, and CEMP-1, whereas treatment with Met-CM alone markedly enhanced PDLSC differentiation activity compared with the control. Moreover, osteogenic/cementogenic differentiation of the LPS-treated PDLSCs was recovered through incubation in Met-CM. Transcriptomic analysis identified 511 and 3591 differentially expressed genes in the control versus Met-CM and LPS versus LPS + Met-CM groups, respectively. The enrichment of biological processes includes positive regulation of DNA-templated transcription and skeletal system morphogenesis in the control versus Met-CM comparison, as well as positive regulation of transcription from the RNA polymerase II promoter and negative regulation of the apoptotic process in the LPS versus LPS + Met-CM comparison. Molecular function analysis demonstrated the enrichment of protein-binding terms among the DEGs from each comparison. Conclusions: Metformin preconditioning enhanced the recovery effect of PDLSC-CM on LPS-induced inflamed PDLSCs. These findings suggest that metformin preconditioning could represent a practical formula for PDLSC-secretome, which may contribute to the development of future cell-free periodontal regenerative strategies. Full article

Background/Objectives: Metabolomics, in combination with genetic data, is a powerful approach to study the biochemical consequences of genetic variation. We assessed the impact of human gene knockouts (KOs) on the metabolite levels of Estonia Biobank (EstBB) participants and integrated the results with electronic health record data. Methods: In 150,000 EstBB genotyped participants, we identified 723 KOs with 152 different predicted loss of function (pLoF) variants in 115 genes. For those KOs and 258 controls, 1387 metabolites were profiled using ultra-high-performance liquid chromatography–tandem mass spectrometry. Results: We identified 48 associations linking rare pLoF variants in 22 genes to 43 metabolites. Out of 48 associations, 27 (56%) were found in genes that cause inborn errors of metabolism. The top associations identified in our analysis included genes and metabolites involved in the degradation pathway of the pyrimidine bases uracil and thymine (DPYD and UPB1). We found DPYD gene KOs to be associated with elevated levels of Uracil, confirming that DPD-deficiency is a leading cause of severe 5-Fluorouracil toxicity. Overall, 54% of reported associations are gene targets of approved drugs or bioactive drug-like compounds. Conclusions: Our findings contribute to assessing the impact of human KOs on metabolite levels and offer insights into gene functions, disease mechanism, and drug target validation. Full article

Turmeric powder has gained widespread popularity due to its culinary and medicinal value and has become a target for economically motivated fraud. The history and exportation of turmeric in Africa were reviewed, and the safety issues of some toxic adulterants were discussed. Priority adulterants were determined from global food safety alerts. A systematic bibliographic search on Scopus, PubMed, Google Scholar, and Web of Science was performed to identify appropriate methods and techniques for authentication and safety. The quality of each study was assessed according to PRISMA guidelines/protocol. African turmeric exportation is on the rise due to recent insights into the suitability of local cultivars, soil and climate for growing high-quality turmeric, with curcumin levels >3%. There are limited data on turmeric adulteration for domestic consumption and export markets. This is important when considering that some turmeric adulterants may serve as risk factors for cancer following exposure. Global alert databases revealed lead chromate as the top hazard identified of all adulterants. Current techniques to detect adulterants are laboratory-based, and while efficient, there is a need for more rapid, field-friendly, non-destructive analytical tools for turmeric fraud/authenticity testing. This enables on-the-spot decision-making to inform rapid alerts. Portable technologies, such as portable X-ray fluorescence, were highlighted as showing potential as a Tier 1 screening tool within a “Food Fortress” systems approach for food safety, combined with validation from mass spectrometry-based Tier 2 testing. Full article

Despite the emerging evidence of the role of transcriptional regulators in schizophrenia as key molecular effectors responsible for the dysregulation of multiple biological processes, limited information is available for brain areas that control higher cognitive functions, such as the cerebellum. To identify transcription factors that could control a wide panel of altered proteins in the cerebellar cortex in schizophrenia, we analyzed a dataset obtained using one-shot liquid chromatography–tandem mass spectrometry on the postmortem human cerebellar cortex in chronic schizophrenia (PXD024937 identifier in the ProteomeXchange repository). Our analysis revealed a panel of 11 enriched transcription factors (SP1, KLF7, SP4, EGR1, HNF4A, CTCF, GABPA, NRF1, NFYA, YY1, and MEF2A) that could be controlling 250 altered proteins. The top three significantly enriched transcription factors were SP1, YY1, and EGR1, and the transcription factors with the largest number of targets were SP1, KLF7, and SP4 which belong to the Krüppel superfamily. An enrichment in vesicle-mediated transport was found for SP1, KLF7, EGR1, HNF4A, CTCF, and MEF2A targets, while pathways related to signaling, inflammation/immune responses, apoptosis, and energy were found for SP1 and KLF7 targets. EGR1 targets were enriched in RNA processing, and GABPA and YY1 targets were mainly involved in organelle organization and assembly. This study provides a reduced panel of transcriptional regulators that could impact multiple pathways through the control of a number of targets in the cerebellum in chronic schizophrenia. These findings suggest that this panel of transcription factors could represent key targets for pharmacological interventions in schizophrenia. Full article

Background/Objectives: Visceral adipose tissue (VAT) may play a direct role in the development of metabolic dysfunction-associated steatotic liver disease (MASLD) and its progression to metabolic dysfunction-associated steatohepatitis (MASH). In this study, we employed untargeted proteomics analyses on paired biopsies from VAT and liver tissues of patients with obesity, MASLD, and MASH. Our objective was to investigate tissue-specific protein expression patterns in search of a potential proteomic signature associated with MASH in both VAT and liver tissue. Methods: VAT and liver tissue were collected from 70 subjects with severe obesity (SWOs) and nine control study subjects without obesity (CON). SWOs were stratified on the basis of liver histology into LS− (no liver steatosis), LS+ (liver steatosis), and MASH. Peptides were extracted from frozen tissue and were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Raw files were analyzed with Spectronaut, proteins were searched against the human FASTA Uniprot database, and the significantly expressed proteins in the two tissues were analyzed. The p-values were false discovery rate (FDR) corrected. Results: A total of 59 VAT and 42 liver proteins were significantly differentially expressed between the four groups: LS−, LS+, MASH, and CON. The majority were upregulated, and many were related to lipid metabolism. In VAT, only one protein, the mitochondrial sulfide:quinone oxidoreductase (SQOR), was significantly downregulated in the MASH group only. In liver tissue from patients with MASH, six proteins were significantly altered compared with the three other groups. Correlation analyses between the top 10 positive VAT and liver proteins were dominated by inflammatory and detoxification proteins. Conclusions: The presence of MASH was not reflected in the VAT proteome, and both the VAT and the liver proteome were generally affected more by the presence of obesity than by MASLD severity. Several immunomodulating proteins correlated significantly between VAT and liver tissue and could reflect common pathophysiological characteristics. Full article

Folate deficiency is a widespread nutritional issue, and biofortifying dairy products through lactic acid bacteria (LAB) is a promising strategy to enhance natural folate levels. This study aimed to develop a reliable method for selecting Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus strains with enhanced folate production for use as functional starter cultures. Initially, a traditional microbiological assay (MA) was used to measure folate production in 36 LAB strains isolated from fermented milks. Due to MA’s limitations, an untargeted and semi-quantitative method combining ultra-high-performance liquid chromatography (UHPLC) with high-resolution mass spectrometry (HRMS) was developed for a more comprehensive folate screening. The MA showed higher folate production in S. thermophilus strains (309–639 µg/L) compared to L. delbrueckii subsp. bulgaricus (up to 48 µg/L). Subsequently, nine selected LAB strains were further analyzed using the UHPLC-HRMS approach, which enabled the identification and semi-quantification of six folate metabolites, namely dihydrofolate, tetrahydrofolate (THF), 10-formyl-THF, 5,10-methenyl-THF, 5,10-methylene-THF, and 5-methyl-THF. Lab-scale yogurt production using the top-performing strains, as identified through the HRMS method, demonstrated an increase in folate content over a 14-day shelf life. These findings revealed the potential of UHPLC-HRMS as a high-throughput alternative method for folates detection, offering a promising tool for screening folate-enhanced LAB strains for biofortification. Full article

Background/Objectives: Metabolomics has recently emerged as a key tool in the biological sciences, offering insights into metabolic pathways and processes. Over the last decade, network-based machine learning approaches have gained significant popularity and application across various fields. While several studies have utilized metabolomics profiles for sample classification, many network-based machine learning approaches remain unexplored for metabolomic-based classification tasks. This study aims to compare the performance of various network-based machine learning approaches, including recently developed methods, in metabolomics-based classification. Methods: A standard data preprocessing procedure was applied to 17 metabolomic datasets, and Bayesian neural network (BNN), convolutional neural network (CNN), feedforward neural network (FNN), Kolmogorov-Arnold network (KAN), and spiking neural network (SNN) were evaluated on each dataset. The datasets varied widely in size, mass spectrometry method, and response variable. Results: With respect to AUC on test data, BNN, CNN, FNN, KAN, and SNN were the top-performing models in 4, 1, 5, 3, and 4 of the 17 datasets, respectively. Regarding F1-score, the top-performing models were BNN (3 datasets), CNN (3 datasets), FNN (4 datasets), KAN (4 datasets), and SNN (3 datasets). For accuracy, BNN, CNN, FNN, KAN, and SNN performed best in 4, 1, 4, 4, and 4 datasets, respectively. Conclusions: No network-based modeling approach consistently outperformed others across the metrics of AUC, F1-score, or accuracy. Our results indicate that while no single network-based modeling approach is superior for metabolomics-based classification tasks, BNN, KAN, and SNN may be underappreciated and underutilized relative to the more commonly used CNN and FNN. Full article

There has been no chemical analysis of the fruit of medicinal plant Jatropha podagrica until now. The current study aimed to qualitatively and quantitatively analyze the J. podagrica fruit using a high-resolution LC-MS strategy, i.e., library-comparison ultra-high-performance liquid chromatography-Quadrupole-Orbitrap-tandem mass spectrometry. The strategy putatively identified 46 compounds from fresh fruit. During the putative identification, 10 isomers (e.g., (vitexin vs. isovitexin) were completely distinguished from each other. Thereafter, all 46 compounds were simultaneously quantified using authentic standard comparison method. Finally, they were also subjected to the 2,2′-azino bis (3-ethylbenzothiazolin-6-sulfonic acid radical (ABTS^+•)-scavenging assay to characterize their relative antioxidant capacities. Their antioxidant capacities were thus multiplied by chemical contents to calculate their antioxidant contribution values, respectively. Corilagin, gallic acid, ellagic acid, and phillygenin exhibited the highest antioxidant contribution percentages and thereby were suggested as the four top antioxidant contributors. The four are recommended to build up a quality-markers (Q-markers) system of J. podagrica fruits. All these findings can help to develop J. podagrica fruits as a potential resource of natural medicine. Full article

The quantification of semi-volatile organic compounds with potential endocrine-disrupting activity contained in fine atmospheric particles (PM_2.5) is essential to understand their temporal behavior, identify their sources, and evaluate the health risks resulting from population exposure to said compounds. Since information and research outcomes regarding their presence in the atmosphere in developing countries are scarce, the main objective of this work was the development of a methodology devoted to extracting, characterizing, and quantifying, for the first time in Mexico, the concentration levels of three important groups of endocrine-disrupting compounds (EDCs) bonded to PM_2.5 and collected during a year, namely: alkylphenols (4-n-nonylphenol (4NP) and 4-tert-octylphenol (4tOP)); bisphenols (bisphenol A (BPA) and bisphenol F (BPF)); natural and synthetic hormones (17β-estradiol (E₂), estriol (E₃) and 17α-ethinyl estradiol (EE₂)). Further, priority polycyclic aromatic hydrocarbons (PAH) that also disrupt endocrine activity were analyzed. All compounds were determined by gas chromatography coupled to tandem mass spectrometry, and the concentration levels were analyzed for different climatic seasons. Cold-dry (CD) season displayed higher levels of 4NP, bisphenols, and hormones (between 0.71 (4NP) and 1860 pg m⁻³ (BPA)), as well as PAH concentrations (9.12 ng m⁻³). Regarding health effects, concentrations of alkylphenols, bisphenols, and hormones quantified had a value of estradiol equivalent concentration (EEQ_E2) between 0.07 and 0.17 ng m⁻³. PAH concentrations did not have carcinogenic and mutagenic risk with BaP_(PEQ) < 1 ng m⁻³. These results can be used by policymakers in the design of strategies for air pollution control. Full article

The European Food Safety Authority (EFSA) monitors the presence and concentration of contaminants in food to mitigate health risks. EU legislation sets maximum levels of heavy metals in foods, including cadmium (Cd), lead (Pb), and total Hg (THg) in seafood, due to their toxicity. In the framework of official control, between 2014 and 2023, 5854 seafood samples were collected and 4300 analyses for THg, 3338 for Cd, and 2171 for Pb were performed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and cold vapor atomic absorption spectrometry (CVAAS). The aim was to assess the proportion of contaminated foods in the dataset, the concentration of contaminants, and the potential health risks associated with their intake. Of the total samples analyzed, 142 (2.43%) were found to be non-compliant (n.c.). Concentrations exceeding the limits for Cd were primarily detected in cephalopods (n = 17), mainly squids. In contrast, Hg levels exceeded the limits in marine fish (n = 118), notably in swordfish (11.30% of n.c. samples among those analyzed for this species), sharks (6.48%), and tuna species (3.11%). Regarding Pb, only a single bivalve sample was found to exceed the maximum limits. A preliminary assessment of weekly exposure to Hg through swordfish consumption raised concerns about the frequent intake of marine top predators, particularly for vulnerable people. Full article