Search Results (233)

Background: Lonicerae japonicae flos (LJF), a traditional food and medicine with a history spanning thousands of years, undergoes drying as a critical processing step in modern applications after regular processing. While the by-products of this process are typically discarded as waste, the potential value of LJF condensate water (JYHC) remains largely unexplored. To address this gap and investigate its potential utilization, this study conducted widely targeted metabolome and volatile metabolomics profiling analyses of ‘JYHC’. Methods: This study analyzed the differential metabolites of ‘JYHC’ and dried Lonicerae japonicae flos (JYHG) based on widely targeted metabolomics using UPLC-MS/MS. Additionally, the metabolic differences between fresh Lonicerae japonicae flos (JYHX) and ‘JYHC’ based on GC-MS volatile metabolomics were comprehensively analyzed. Results: A total of 1651 secondary metabolites and 909 volatile metabolites were identified in this study. Among these, flavonoids and terpenoids were the predominant secondary metabolites, while esters and terpenoids dominated the volatile fraction. Further comparison of the ‘JYHC’ and ‘JYHG’ groups revealed that 58 differential metabolites with potential biological activities were significantly up-regulated, with the types being terpenoids, phenolic acids, and alkaloids, which included nootkatone, mandelic acid, sochlorogenic acid B, allantoin, etc. Notably, a total of 186 novel compounds were detected in ‘JYHC’ that had not been previously reported in LJF such as isoborneol, hinokitiol, agarospirol, 5-hydroxymethylfurfural, α-cadinol, etc. Conclusions: This study’s findings highlight the metabolic diversity of ‘JYHC’, offering new theoretical insights into the study of LJF and its by-products. Moreover, this research provides valuable evidence supporting the potential utilization of drying by-products from LJF processing, paving the way for further exploration of their pharmaceutical and industrial applications. Full article

The dynamic metabolic landscape underlying goose meat quality deterioration during refrigerated storage remains incompletely elucidated. Here, ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)-based widely targeted metabolomics was employed to characterize metabolic profiling in refrigerated goose meat. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed 211 differential metabolites, while random forest regression (RFR) identified 30 candidate biomarkers. Seven metabolites, including xanthine, oxidized glutathione, and inosine 5′-monophosphate, exhibited significant correlations with total volatile basic nitrogen (TVB-N). By integrating potential biomarkers, metabolic pathways involving purines, amino acids, and sugars were identified as underlying mechanisms of goose meat spoilage. Notably, through comprehensive analysis of time-dependent correlations between physicochemical properties and metabolic profiles, a temporal threshold for quality deterioration in refrigerated goose meat was identified as day 5. These findings deepen our understanding of metabolite variations in refrigerated goose meat and provide a basis for optimizing storage protocols. The identified biomarkers may enable rapid detection kits and smart packaging systems for poultry industry applications. Full article

Akebia trifoliata is an emerging fruit crop in China, valued for its medicinal and nutritional properties. To elucidate the developmental dynamics of its bioactive compounds, we performed widely targeted metabolomics using Ultra Performance Liquid Chromatography–Tandem Mass Spectrometry (UPLC-MS/MS) across four fruit developmental stages (S1–S4). A total of 1595 metabolites were identified, of which 988 were differentially accumulated and categorized into three distinct accumulation patterns. Flavonoids and phenolic acids exhibited a marked decline during fruit maturation, corresponding with decreasing antioxidant and α-glucosidase inhibitory activities. Conversely, functional oligopeptides and specific terpenoids accumulated significantly at later stages. K-means clustering revealed dynamic shifts in metabolic profiles, and 23 functional oligopeptides with antioxidative, antidiabetic, and ACE-inhibitory activities (angiotensin-converting enzyme, ACE) were predicted. KEGG enrichment highlighted stage-specific pathway transitions from flavonoid biosynthesis during early development to sugar metabolism at ripening. Correlation analysis identified key flavonoids, phenolic acids, and amino acid derivatives associated with antioxidant capacity and α-glucosidase inhibition. This study provides comprehensive metabolomic landscape of A. trifoliata fruit development and offers valuable insights for its functional exploitation in food and medicinal applications. Full article

Off-white or yellowish shoots are common in tea plants (Camellia sinensis L.), and such albino variations are often accompanied by metabolic reprogramming, including increased contents of amino acids and lower levels of polyphenols. Nonetheless, the molecular mechanisms that underlie these albino variations remain to be fully clarified. Here, we examined the ultrastructural characteristics of novel, naturally occurring, yellowish mutated tea leaves and performed metabolomic analyses on green and albino leaves and stems. Then, transcriptomic analyses were also conducted on green and albino leaves to investigate the mechanistic basis of the albino variation. As expected, the cells of albino tea leaves contained fewer and smaller chloroplasts with disorganized thylakoids and smaller starch granules. Widely targeted metabolomics analysis revealed 561 differentially abundant metabolites between green and albino leaves and stems, but there was little difference between green and albino stems. Then, RNA sequencing of green and albino leaves revealed downregulation of genes associated with light harvesting and photosynthesis, and integration of the metabolomic and transcriptomic results indicated that biosynthesis of aromatic amino acids (AAAs) was strongly upregulated in albino leaves. To gain additional insight into the molecular basis of the increased AAA levels, Oxford Nanopore long-read sequencing was performed on green and albino leaves, which enabled us to identify differences in long non-coding RNAs (lncRNAs) and alternatively spliced transcripts between green and albino leaves. Interestingly, the amino acid biosynthesis genes arogenate dehydratase/prephenate dehydratase (ADT) and serine hydroxymethyltransferase (SHMT) were highlighted in the lncRNA and alternative splicing analyses, and the transcription factor genes PLATZ, B3 Os04g0386900, and LRR RLK At1g56140 showed significant changes in both expression and alternative splicing in albino leaves. Together, our data suggest that biosynthesis of AAAs might be crucial for albino mutations in tea plants and could be coordinated with the regulation of lncRNAs and alternative splicing. This is a complex regulatory network, and further exploration of the extensive metabolic reprogramming of albino tea leaves will be beneficial. Full article

This review synthesizes advances in livestock genomics by examining the interplay between candidate genes, molecular markers (MMs), signatures of selection (SSs), and quantitative trait loci (QTLs) in shaping economically vital traits across livestock species. By integrating advances in genomics, bioinformatics, and precision breeding, the study elucidates genetic mechanisms underlying productivity, reproduction, meat quality, milk yield, fibre characteristics, disease resistance, and climate resilience traits pivotal to meeting the projected 70% surge in global animal product demand by 2050. A critical synthesis of 1455 peer-reviewed studies reveals that targeted genetic markers (e.g., SNPs, Indels) and QTL regions (e.g., IGF2 for muscle development, DGAT1 for milk composition) enable precise selection for superior phenotypes. SSs, identified through genome-wide scans and haplotype-based analyses, provide insights into domestication history, adaptive evolution, and breed-specific traits, such as heat tolerance in tropical cattle or parasite resistance in sheep. Functional candidate genes, including leptin (LEP) for feed efficiency and myostatin (MSTN) for double-muscling, are highlighted as drivers of genetic gain in breeding programs. The review underscores the transformative role of high-throughput sequencing, genome-wide association studies (GWASs), and CRISPR-based editing in accelerating trait discovery and validation. However, challenges persist, such as gene interactions, genotype–environment interactions, and ethical concerns over genetic diversity loss. By advocating for a multidisciplinary framework that merges genomic data with phenomics, metabolomics, and advanced biostatistics, this work serves as a guide for researchers, breeders, and policymakers. For example, incorporating DGAT1 markers into dairy cattle programs could elevate milk fat content by 15-20%, directly improving farm profitability. The current analysis underscores the need to harmonize high-yield breeding with ethical practices, such as conserving heat-tolerant cattle breeds, like Sahiwal. Full article

Black tea is widely consumed worldwide, and its characteristic taste and color result from fermentation, where polyphenols are enzymatically oxidized to generate major pigments, including theaflavins (TFs), thearubigins (TRs), and theabrownins (TBs). This study investigated the effects of increased oxygen treatment during fermentation on the flavor attributes and chemical properties of Congou black tea. Fresh tea leaves (variety “Fuyun 6”) were subjected to four oxygen treatments: 0 h (CK), 1 h (TY-1h), 2 h (TY-2h), and 3 h (TY-3h), with oxygen supplied at 8.0 L/min. Sensory evaluation revealed that oxygen-treated samples exhibited tighter and deeper-colored leaves, a redder liquor, fuller taste, and a sweeter fragrance compared with CK. Chromatic analysis showed significant increases in redness (a*) and luminance (L*), alongside reduced yellowness (b*), indicating enhanced liquor color. Chemical analyses demonstrated elevated levels of TFs, TRs, and TBs in oxygen treatments, with TRs showing the most pronounced increase. Non-targeted metabolomics identified 2318 non-volatile and 761 volatile metabolites, highlighting upregulated flavonoids, phenolic acids, and lipids, and downregulated catechins and tannins, which collectively contributed to improved taste and aroma. Optimal results were achieved with 2–3 h of oxygen treatment, balancing pigment formation and sensory quality. These findings can provide a scientific basis for optimizing oxygen conditions in black tea fermentation to improve product quality. Full article

Background: Myeloproliferative neoplasms (MPN), a group of chronic hematologic neoplasms, are driven by inflammatory mechanisms that influence disease initiation and progression. Emerging evidence highlights the gut microbiome and plasma metabolome as pivotal immunomodulators, yet their causal roles in MPN pathogenesis remain uncharacterized. Methods: We conducted a two-sample Mendelian randomization (MR) analysis to systematically evaluate causal relationships between 196 gut microbial taxa, 526 plasma metabolites, and MPN risk. Instrumental variables were derived from genome-wide association studies (GWASs) of microbial/metabolite traits. Validation utilized 16S rRNA sequencing data from NCBI Bioproject PRJNA376506. Mediation and multivariable MR analyses elucidated metabolite-mediated pathways linking microbial taxa to MPN. Results: Our MR analysis revealed that 7 intestinal taxa and 17 plasma metabolites are causally linked to MPN. External validation confirmed the three taxa’s differential abundance in MPN cohorts. Mediation analysis revealed two mediated relationships, of which succinylcarnitine mediated 14.5% of the effect, and lysine 27.9%, linking the Eubacterium xylanophilum group to MPN. Multivariate MR analysis showed that both succinylcarnitine (p = 0.004) and lysine (p = 0.040) had a significant causal effect on MPN. Conclusions: This study identifies novel gut microbiota–metabolite axes driving MPN pathogenesis through immunometabolic mechanisms. The validated biomarkers provide potential therapeutic targets for modulating inflammation in myeloproliferative disorders. Full article

Background: Liquid chromatography-mass spectrometry (LC-MS), widely used in metabolomics, is often limited by low ionization efficiency and ion suppression, which reduce overall metabolite detectability and quantification accuracy. To address these challenges, chemical isotope labeling (CIL) LC-MS has emerged as a powerful approach, offering high sensitivity, accurate quantification, and broad metabolome coverage. This method enables comprehensive profiling by targeting multiple submetabolomes. Specifically, amine-/phenol- and hydroxyl-containing metabolites are labeled using dansyl chloride under distinct reaction conditions. While this strategy provides extensive coverage, the sequential analysis of each submetabolome reduces throughput. To overcome this limitation, we propose a two-channel mixing strategy to improve analytical efficiency. Methods: In this approach, samples labeled separately for the amine/phenol and hydroxyl submetabolomes are combined prior to LC-MS analysis, leveraging the common use of dansyl chloride as the labeling reagent. This integration effectively doubles throughput by reducing LC-MS runtime and associated costs. The method was evaluated using human urine and serum samples, focusing on peak pair detectability and metabolite identification. A proof-of-concept study was also conducted to assess the approach’s applicability in putative biomarker discovery. Results: Results demonstrate that the two-channel mixing strategy enhances throughput while maintaining analytical robustness. Conclusions: This method is particularly suitable for large-scale studies that require rapid sample processing, where high efficiency is essential. Full article

Background: Catalpa bungei ‘Jinsi’ has excellent wood properties and golden texture, which is widely used in producing furniture and crafts. The lignin content and structural composition often determine the use and value of wood. Hence, investigating the characteristics of the annual dynamics of lignin anabolic metabolites in C. bungei ‘Jinsi’ and analyzing their synthesis pathways are particularly important. Methods: We carried out targeted metabolomics analysis of lignin synthesis metabolites using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) on the xylem samples of C. bungei ‘Jinsi’ in February, April, July, October 2022, and January 2023. Results: A total of 10 lignin synthesis–related metabolites were detected: L-phenylalanine, cinnamic acid, p-coumaraldehyde, sinapic acid, p-coumaric acid, coniferaldehyde, ferulic acid, sinapaldehyde, caffeic acid, and sinapyl alcohol (annual total content from high to low). These metabolites were mainly annotated to the synthesis of secondary metabolites and phenylpropane biosynthesis. The annual total content of the 10 metabolites showed the tendency of “decreasing, then increasing, and then decreasing”. Conclusions: C. bungei ‘Jinsi’ is a typical G/S-lignin tree species, and the synthesis of G-lignin occurs earlier than that of S-lignin. The total metabolite content decreased rapidly, and the lignin anabolism process was active from April to July; the metabolites were accumulated, and the lignin anabolism process slowed down from July to October; the total metabolite content remained basically unchanged, and lignin synthesis slowed down or stagnated from October to January of the following year. This reveals the annual dynamic pattern of lignin biosynthesis, which contributes to improving the wood quality and yield of C. bungei ‘Jinsi’ and provides a theoretical basis for its targeted breeding. Full article

Soybean is a dual-purpose crop for food and oil, playing a crucial role in China’s grain production. Seed size and weight are key agronomic traits directly influencing the yield. Cytokinin oxidases/dehydrogenases (CKXs) specifically degrade certain isoforms of endogenous cytokinins (CKs), thereby modulating plant growth and seed development. However, their role in soybeans remains largely uncharacterized. In a previous genome-wide association study of 250 soybean core germplasms, we identified GmCKX3 as a yield-related gene. To elucidate its function, we developed GmCKX3-deficient mutants using CRISPR/Cas9 gene editing in soybean Williams82 and conducted a three-year phenotypic analysis. Loss of GmCKX3 function significantly enhanced the seed size and weight, which was attributed to an increased cell size and fat accumulation in the endosperm. This enhancement was driven by elevated endogenous CK levels resulting from suppressed GmCKX3 expression. Subcellular localization revealed that GmCKX3 resides in the endoplasmic reticulum and predominantly degrades the isopentenyladenine (iP)-type CK. Integrated transcriptomic and metabolomic analyses uncovered key genes and pathways involved in CK regulation, supporting GmCKX3’s central role in seed-trait modulation. These findings advance our understanding of cytokinin-mediated seed development and offer promising targets for molecular breeding aimed at improving the soybean yield. Full article

This study investigated the metabolite dynamic changes and transformation pathways in Diqing Tibetan pig (DTP) hams during fermentation (0, 30, 90, 180, 360, 540 d) by widely targeted metabolomics. A total of 873 metabolites in 17 subclasses were detected, with significant changes in 448 metabolites. Additionally, 65 key metabolites were found to be involved in the top 10 pathways, with the top pathways for metabolite markers in mature hams including protein metabolism (2-oxocarboxylic acid metabolism, tryptophan metabolism and amino acid biosynthesis) and lipid metabolism (unsaturated fatty acid biosynthesis and linoleic acid metabolism). Overall, the unique DTP ham taste, flavor, and nutritional value may be contributed to by the significant accumulation of essential amino acids, MSG-like amino acids, free fatty acids (arachidonic acid, docosahexaenoic acid, and eicosapentaenoic acid), citric acid, oxaloacetic acid, succinic acid, and vitamin B. This study facilitates a comprehensive understanding of metabolic profiling and the transformation pathways of DTP hams during fermentation, providing novel insights into the biochemical mechanisms underlying traditional Tibetan pig hams, bridging traditional knowledge with modern omics technologies. Full article

This study explores the metabolite diversity and potential medicinal value of three Paphiopedilum species—P. dianthum, P. micranthum, and P. barbigerum—using widely targeted metabolomics via HPLC-MS/MS in conjunction with in vitro antioxidant assays. A total of 2201 metabolites were detected across the three species, with flavonoids emerging as the dominant class (480 compounds, accounting for 21.8% of total metabolites). Comparative metabolomic analysis showed that flavonoid levels varied most prominently among the species. Notably, the metabolic profile of P. barbigerum (PB) diverged substantially from those of P. dianthum (PD) and P. micranthum (PM), which shared a higher degree of similarity with each other. Quantitative evaluation of antioxidant-associated metabolites revealed that PB exhibited the greatest enrichment in compounds with antioxidant potential, particularly flavonoids and phenolic acids, followed by PM and PD. These results were corroborated by antioxidant assays, in which PB demonstrated the highest free radical scavenging activity, with PM and PD displaying progressively lower effects. Differences in flavonoid content likely underpin these variations in antioxidant capacity. KEGG pathway enrichment analysis indicated that differentially expressed metabolites were primarily involved in flavonoid-associated biosynthetic routes, notably flavonoid biosynthesis (ko00941) and isoflavonoid biosynthesis (ko00943), with ko00941 being the most enriched. Within this pathway, PB showed eight significantly upregulated flavonoid metabolites, while PM and PD had seven and five, respectively. The observed differences may stem from species-specific expression of key biosynthetic enzymes such as flavonoid 3′-hydroxylase (F3′H) in PM and flavonoid 3′,5′-hydroxylase (F3′5′H) in PB, which influence both flavonoid composition and antioxidant potential. Full article

The plant Synsepalum dulcificum is notable for its considerable edible and medicinal value, with a longstanding history as a folk remedy for diabetes. Its chemical constituents are rich and structurally diverse. However, there is limited information regarding the metabolic basis of these characteristics, and the biological activities and mechanisms underlying its blood glucose-lowering effects remain incompletely understood. In this study, we conducted a widely targeted metabolomics analysis of the stems, leaves, and fruits of S. dulcificum using UPLC-ESI-MS/MS to compare the differences in metabolite profiles among these three tissue types. Our analysis identified a total of 2544 secondary metabolites, primarily consisting of flavonoids and triterpenes, categorized into thirteen distinct compound classes. We selected differential metabolites through multivariate statistical analysis, revealing significant differences among the metabolite profiles of the three tissue types, with flavonoids being the most abundant compounds. Furthermore, we investigated the anti-diabetic mechanisms and potential pharmacological components of S. dulcificum utilizing network pharmacology and molecular docking techniques. Finally, the α-glucosidase inhibitory activity of the potential active components was evaluated using in vitro experiments. These findings establish a foundation for the future application of S. dulcificum in the prevention and treatment of diabetes. Full article

Objectives: To explore the metabolic changes in zebrafish larvae after infection with Mycobacterium marinum, this study adopted a widely targeted metabolomic approach to analyze the changes in the overall metabolic profiles of zebrafish larvae infected for 5 days. Methods: Data were collected by liquid chromatography–tandem mass spectrometry (LC-MS/MS). Mass spectrometry data were processed using Analyst 1.6.3 and MultiQuant 3.0.3 software, and multivariate statistical analysis was carried out. The KEGG database, HMDB database, and CHEBI database were used to screen and identify differential metabolites, and metabolic pathway enrichment analysis was performed through KEGG pathways. Results: A total of 329 metabolites were detected, among which 61 differential metabolites were screened. Specifically, 41 metabolites, such as kynurenine, isoallolithocholic acid, 2′-deoxyguanosine, indole-3-carboxaldehyde, and L-lactic acid, were downregulated, while 20 metabolites, such as L-palmitoylcarnitine, myristoyl-L-carnitine, dodecanoylcarnitine, 2-isopropyl-malic acid, and 2-methylsuccinic acid, were upregulated. KEGG metabolic pathway enrichment analysis indicated that these differential metabolites were mainly involved in metabolic pathways such as pyrimidine metabolism, nucleotide metabolism, the pentose phosphate pathway, and purine metabolism. Conclusions: This study demonstrated that significant changes occurred in multiple metabolites and metabolic pathways in zebrafish larvae after infection with M. marinum. The research results have improved the understanding of zebrafish as a model organism in the field of Mycobacterium research and laid a solid foundation for subsequent metabolomic-related research using zebrafish. Full article

Citral, an organic compound found in lemongrass (Cymbopogon citratus) oil and Litsea cubeba essential oil, has been reported to exhibit notable antifungal activity against Magnaporthe oryzae (M. oryzae), the pathogen of rice blast, which causes significant economic losses in rice production. However, the role of citral in inducing oxidative stress related to antifungal ability and its underlying regulatory networks in M. oryzae remain unclear. In this study, we investigated the oxidative effects of citral on M. oryzae and conducted transcriptomic and widely targeted metabolomic (WTM) analyses on the mycelia. The results showed that citral induced superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) activities but reduced glutathione S-transferase (GST) activity with 25% maximal effective concentration (EC₂₅) and 75% maximal effective concentration (EC₇₅). Importantly, citral at EC₇₅ reduced the activities of mitochondrial respiratory chain complex I, complex III and ATP content, while increasing the activity of mitochondrial respiratory chain complex II. In addition, citral triggered a burst of reactive oxygen species (ROS) and a loss of mitochondrial membrane potential (MMP) through the observation of fluorescence. Furthermore, RNA-seq analysis and metabolomics analysis identified a total of 466 differentially expression genes (DEGs) and 32 differential metabolites (DAMs) after the mycelia were treated with citral. The following multi-omics analysis revealed that the metabolic pathways centered on AsA, GSH and melatonin were obviously suppressed by citral, indicating a disrupted redox equilibrium in the cell. These findings provide further evidences supporting the antifungal activity of citral and offer new insights into the response of M. oryzae under oxidative stress induced by citral. Full article