PubMed

Circ Res. 2025 Jan 31. doi: 10.1161/CIRCRESAHA.124.325639. Online ahead of print.ABSTRACTBACKGROUND: Postmenopausal women (PMW) who complete menopause at a late age (55+ years) have lower cardiovascular disease risk than PMW who complete menopause at a normal age (45-54 years). However, the influence of late-onset menopause on vascular endothelial dysfunction is unknown. Moreover, the mechanisms by which a later age at menopause may modulate endothelial function remain to be determined.METHODS: We measured endothelial function (brachial artery flow-mediated dilation [FMDBA]) in age-matched late- and normal-onset PMW and a young premenopausal reference group. We determined mitochondrial reactive oxygen species (mitoROS)-related suppression of endothelial function (change in FMDBA with an acute dose of the mitochondria-targeted antioxidant MitoQ; ΔFMDBA, MTQ) in PMW. The effects of serum from late- and normal-onset PMW and premenopausal women on mitoROS bioactivity in human aortic endothelial cells in culture were assessed. Metabolomics analyses in combination with serum metabolite level normalization and human aortic endothelial cell serum exposure experiments were performed to identify the circulating factors contributing to the serum effects on endothelial cell mitoROS bioactivity.RESULTS: FMDBA in PMW was lower than in premenopausal women. However, FMDBA was >50% higher in late- versus normal-onset PMW and positively related to age at menopause. ΔFMDBA, MTQ was >50% lower in late- versus normal-onset PMW. Serum from normal-onset PMW but not late-onset PMW induced higher mitoROS bioactivity in human aortic endothelial cells compared with serum from premenopausal women. mitoROS bioactivity was negatively related to FMDBA and age at menopause. Seventeen metabolites significantly differed between late- and normal-onset PMW; 15 were lipid specific; 8 were triglyceride derived. TG(16:0) was most strongly correlated with mitoROS bioactivity. Normalization of TG(16:0) concentrations in serum from premenopausal women and late-onset PMW to match serum levels in normal-onset PMW abrogated differences in mitoROS bioactivity in serum-treated human aortic endothelial cells.CONCLUSIONS: Late-onset menopause is associated with preservation of endothelial function, which is mediated by lower mitoROS-associated oxidative stress. A more favorable profile of circulating lipid metabolites, specifically triglyceride-derived metabolites, contributes to lower endothelial cell mitoROS in late-onset PMW. These findings provide new insight into the possible mechanisms of reduced cardiovascular disease risk in late-onset menopause.PMID:39886766 | DOI:10.1161/CIRCRESAHA.124.325639

Front Plant Sci. 2025 Jan 16;15:1497575. doi: 10.3389/fpls.2024.1497575. eCollection 2024.ABSTRACTThe network of antagonistic, neutral, and synergistic interactions between (micro)organisms has moved into the focus of current research, since in agriculture, this knowledge can help to develop efficient biocontrol strategies. Applying the nematophagous fungus Pochonia chlamydosporia as biocontrol agent to manage the root-knot nematode Meloidogyne hapla is a highly promising strategy. To gain new insight into the systemic response of plants to a plant-parasitic nematode and a nematophagous fungus, Phacelia was inoculated with M. hapla and/or P. chlamydosporia and subjected to transcriptome and metabolome analysis of leaves. While the metabolome proved quite stable except for the early time point of 48 h, comparison of the single P. chlamydosporia with the combined treatment revealed even larger effects after 6 d compared to 48 h, aligning with the later root infestation by P. chlamydosporia compared to M. hapla. Simultaneous exposure to both microorganisms showed a stronger overlap with the single M. hapla treatment than P. chlamydosporia. Changes of transcripts and metabolites were higher in the combined treatment compared to the individual inoculations. The results support the conclusion that P. chlamydosporia induces plant defense in a distinct and beneficial manner if combined with M. hapla although plant defense is partly suppressed by the endophytic growth. The results tentatively suggested that the application of P. chlamydosporia as a biocontrol agent against M. hapla can be more effective by supporting these tritrophic interactions with specific additives, such as phytohormones or amino acids in the formulation.PMID:39886679 | PMC:PMC11779738 | DOI:10.3389/fpls.2024.1497575

Eng Life Sci. 2025 Jan 29;25(1):e70003. doi: 10.1002/elsc.70003. eCollection 2025 Jan.ABSTRACTThe oleaginous yeast Lipomyces starkeyi is recognized for its remarkable lipid accumulation under nitrogen-limited conditions. However, precise control of microbial lipid production in L. starkeyi remains challenging due to the complexity of nutrient media. We developed a two-stage fed-batch fermentation process using a well-defined synthetic medium in a 5-L bioreactor. In the first stage, the specific growth rate was maintained at a designated level by maximizing the cell density through optimizing the feeding rate, molar carbon-to-nitrogen (C/N) ratio, and phosphate concentration in feeding media, achieving a high cell density of 213 ± 10 × 107 cells mL-1. In the second stage, we optimized the molar C/N ratio in the feeding medium for lipid production and achieved high biomass (130 ± 5 g L-1), lipid titer (88 ± 6 g L-1), and lipid content (67% ± 2% of dry cellular weight). Our approach yielded a high lipid titer, comparable to the highest reported value of 68 g L-1 achieved in a nutrient medium, by optimizing cultivation conditions with a synthetic medium in L. starkeyi. This highlights the importance of well-established yet powerful bioprocess approaches for the precise control of microbial cultivation.PMID:39886606 | PMC:PMC11779743 | DOI:10.1002/elsc.70003

Toxicol Rep. 2024 Dec 25;14:101884. doi: 10.1016/j.toxrep.2024.101884. eCollection 2025 Jun.ABSTRACTResistance of cancer cells, especially breast cancer, to therapeutic medicines represents a major clinical obstacle that impedes the stages of treatment. Carcinoma cells that acquire resistance to therapeutic drugs can reprogram their own metabolic processes as a way to overcome the effectiveness of treatment and continue their reproduction processes. Despite the recent developments in medical research in the field of drug resistance, which showed some explanations for this phenomenon, the real explanation, along with the ability to precisely predict the possibility of its occurrence in breast cancer cells, still necessitates a deep consideration of the dynamics of the tumor's response to treatment. For this purpose the current study, combined both in vitro metabolomics and in vivo genomics analysis as the most advanced omics technologies that can provide a potential en route for inventing novel strategies to perform prospective, prognostic and diagnostic biomarkers for drug resistance phenomena in mammary cancer. Doxorubicin is the currently available breast cancer chemotherapeutic medication nevertheless; it was demonstrated to cause drug resistance, which impairs patient survival and prognosis by prompting proliferation, cell cycle progression, and preventing apoptosis, interactions between signaling pathways triggered drug resistance. In this research, in vitro metabolomics analysis based on GC-MS coupled with multivariable analysis was performed on MCF-7 and DOX resistant cell lines; MCF-7/adr cultured cells in addition to, further in vivo confirmation via inducing mammary cancer in rats via two doses of 7,12-dimethylbenz(a) anthracene (DMBA) (50 mg/kg and 25 mg/kg) proceeded by doxorubicin (5 mg/kg) treatment for one month. The metabolomics in vitro results pointed out that mannitol, myoinositol, glycine, α-linolenic acid, oleic acid and stearic acid have AUC values: 0.14, 0.5, 0.7, 0.1, 0.02, -0.02 (1, 1) respectively. Glycine and myoinositol metabolites provided the best discriminative power in the wild and resistance MCF-7 phenotypes. Meanwhile, in vivo results revealed a significant crosstalk between the alternation in oxidative stress biomarkers as well as Arginase II tumor biomarker and the molecular assessment of ABCA1 and P53 gene expression that displayed a marked reduction in addition to, the obvious elevation in resistance and apoptotic biomarkers EGFR/PI3k/AKT/PTEN signaling pathway upon DMBA administration. Data revealed a significant alternation in signaling pathways related to resistance upon doxorubicin administration that affect lipid metabolism in breast cancer. In conclusion, Metabolomics integrated genomics analysis may be promising in understanding multidrug resistance phenotype in MCF-7 breast cancer cells exposed to doxorubicin through modulating ABCA1/EGFR/P53/PI3k/PTEN signaling pathway thus metabolic biomarkers in addition to molecular biomarkers elucidate the challenges fronting profitable therapy of mammary cancer and an pioneering approaches that metabolomics compromises to improve recognizing drug resistance in breast carcinoma.PMID:39886047 | PMC:PMC11780168 | DOI:10.1016/j.toxrep.2024.101884

Front Pharmacol. 2025 Jan 16;15:1431649. doi: 10.3389/fphar.2024.1431649. eCollection 2024.ABSTRACTOBJECTIVE: This study aims to investigate the preventive effect of walnut oil as medicinal food on abnormal lipid metabolism and its influence on liver metabolites and intestinal flora.METHODS: The rat model of abnormal lipid metabolism was established by feeding high-fat diet and administering a high-fat emulsion via gavage. The rats were randomly assigned to one of the five groups: the normal group (ND), the model group (HFD), and three walnut oil intervention groups differing in dosage [low-dose (OL, 2.5 g/kg. BW/day), medium-dose (OM, 5 g/kg. BW/day) and high-dose (OH, 10 g/kg. BW/day)]. Modeling and administration were performed simultaneously for 10 weeks. After the last administration, the serum and organs of the animals were collected under anesthesia, and the organ index was analyzed. Serum total cholesterol (TC), triglyceride (TG), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) were measured. A histopathological examination of the liver was performed, and the intestinal flora was detected by Illumina technology.RESULTS: Compared to the ND group, the HFD group exhibited a significant increase in body weight and Lee's index. Compared to the HFD group, each walnut oil intervention group showed a relatively reduced degree of liver swelling and a significant decrease in fat vacuoles within the cytoplasm. Levels of TC, TG, LDL-C, activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly decreased (p < 0.05), while HDL-C levels were increased (p < 0.05), along with a significant increase in the activity of glutathione peroxidase (GSH-PX) and a decrease in malondialdehyde (MDA) content in serum. These findings indicated that walnut oil could improve the blood lipid profile in hyperlipidemia-model rats. The results of intestinal flora showed that at the genus level, there were significant increases in the relative abundance of Collinsella and Blautia (p < 0.01) while significant decreases of Oscillospira and Allobaculum (p < 0.01) in the HFD group vs. the ND group. However, these flora changes were impeded although only Collinslla (p < 0.05) in the OL group. Metabonomics analysis identified that a total of 19 potential biomarkers were screened out from the differential metabolites with |log2FC| > 1, VIP > 1 and p < 0.05.CONCLUSION: Walnut oil can significantly prevent hyperlipidemia caused by high-fat diet. The mechanism is mainly through significantly reducing the content of MDA and the activities of ALT and AST, significantly increasing the activity of GSH-PX, and improving intestinal flora and liver metabolism.PMID:39885930 | PMC:PMC11780273 | DOI:10.3389/fphar.2024.1431649

Front Pharmacol. 2025 Jan 6;15:1431240. doi: 10.3389/fphar.2024.1431240. eCollection 2024.ABSTRACTBACKGROUND: Gestational diabetes mellitus (GDM), a severe pregnancy disorder, is a temporary form of diabetes that occurs during gestation. Astragaloside IV (AS IV), a natural and effective composition of Astragalus membranaceus, shows pharmacological effects against diabetes. On the contrary, the effects of AS IV on GDM development are still not clear. This study aims to investigate the role of AS IV in alleviating GDM in rats and determine whether AS IV exerts its anti-GDM properties through the regulation of gut microbiota and metabolite modulation.METHODS: There were six pregnant SD rats in each of the four groups. First, the GDM model was induced by the streptozotocin (STZ, 45 mg/kg) injection on gestational days (GDs) 1-4, and AS IV intervention (10 mg/kg/d) was administered from 6 days before pregnancy until delivery. The measurements of relevant indicators pertaining to GDM symptoms and reproductive outcomes, along with the 16S rRNA sequencing data and LC-MS-based metabolomic profiles, were assessed across all groups.RESULTS: After the 25-day intervention, the GDM model + AS IV group showed significantly decreased fasting blood glucose levels (p = 0.0003), mean insulin levels (p = 0.0001), and insulin resistance index (p = 0.0001). AS IV treatment also decreased the malformation rate (p = 0.0373) and increased the average fetal weight (p = 0.0020) of GDM rats. Compared to the control rats, GDM rats showed a significantly higher abundance of Blautia and Anaerobiospirillum. However, the dramatically elevated abundance of these microorganisms was markedly decreased by AS IV treatment. In contrast, compared to GDM rats without treatment, GDM rats treated with AS IV showed a significantly higher abundance of bacteria (p < 0.05), such as Methanobrevibacter, Dubosiella, and Romboutsia, which are beneficial to the rats. Additionally, we observed dramatically elevated production of metabolites, such as N-acetyl-l-leucine and lithocholic acid, after AS IV treatment through metabolomics analysis (p < 0.05). Furthermore, significant associations between most genera of gut bacteria and the altered levels of the metabolites connected to gut microbiota were also discovered.CONCLUSION: Our study demonstrated that AS IV could be an effective nutritional intervention strategy for targeting gut microbiota and metabolome profiles in GDM and provided experimental evidence supporting the use of AS IV to treat GDM.PMID:39885928 | PMC:PMC11780255 | DOI:10.3389/fphar.2024.1431240

BMC Cancer. 2025 Jan 30;25(1):177. doi: 10.1186/s12885-025-13561-x.ABSTRACTOBJECTIVE: This study aims to identify potential lipid biomarkers and metabolic pathways associated with oral cancer (OC). Then to establish and evaluate disease classification models capable of distinguishing OC patients from healthy controls.METHODS: A total of 41 OC patients and 41 controls were recruited from a hospital in Southeast China to examine the serum lipidomics by Ultra-high Performance Liquid Chromatography Q Exactive Mass Spectrometry (UHPLC-QE-MS).RESULTS: The total serum lipid profile showed that triglycerides accounted for the highest proportion of total metabolites, reaching 35.90% of the total. A total of 74 different metabolites were screened (12 up-regulated and 62 down-regulated), mainly enriched in the glycerophospholipid metabolism pathway. The three most significant changes in lipid metabolites were phosphatidylcholine (PC(18:3e/17:2)), acylcarnitine (ACar(14:2)), and glucuronosyldiacylglycerol (GlcADG(14:1/14:1)). The disease classification model, constructed using a KNN algorithm with 13 metabolites selected through LASSO screening, achieved the best performance, with an AUC of 0.978 (0.955-1.000).CONCLUSION: Lipid metabolic biomarkers identified in this study exhibit potential as candidate biomarkers for OC diagnosis. Further validation through prospective studies is required to confirm their clinical utility in early detection.PMID:39885458 | DOI:10.1186/s12885-025-13561-x

J Transl Med. 2025 Jan 30;23(1):138. doi: 10.1186/s12967-024-06040-7.ABSTRACTBACKGROUND: Obesity is associated with varying degrees of metabolic dysfunction. In this study, we aimed to discover markers of the severity of metabolic impairment in men with obesity via a multiomics approach.METHODS: Thirty-two morbidly men with obesity who were candidates for Roux-en-Y gastric bypass (RYGB) surgery were prospectively followed. Nine healthy adults served as controls. Deep phenotyping, including targeted metabolomics, transcriptomics, and brain magnetic resonance imaging (MRI), was performed.RESULTS: Testosterone emerged as a key contributor to phenotypic variability via principal component analysis and was therefore used to further categorize obese patients as having or not having hypogonadotropic hypogonadism (HH). Despite having comparable body mass indices, obese individuals with HH presented with worse metabolic defects than obese individuals without HH, including higher insulin resistance, as well as MRI signs of hypothalamic inflammation and a specific blood transcriptomics signature. The upregulated genes were involved mainly in inflammation, mitochondrial function, and protein translation. Integration of gene expression and clinical data revealed high FGF21 and low cortisol levels as the top markers correlated with the transcriptomic signature of metabolic risk. Following RYGB-induced substantial weight loss, testosterone levels markedly increased in both obese individuals with and without HH, challenging the current definition of hypogonadism. A longitudinal study in a subset of men with obesity following bariatric surgery revealed a unique FGF21 trajectory with a sharp peak at one month post-RYGB that correlated with metabolic and reproductive improvements.CONCLUSIONS: Combining clinical, biochemical, and molecular markers allows adequate stratification of metabolic risk in men with obesity and provides novel tools for personalized care.PMID:39885510 | DOI:10.1186/s12967-024-06040-7

BMC Pregnancy Childbirth. 2025 Jan 30;25(1):96. doi: 10.1186/s12884-025-07224-9.ABSTRACTBACKGROUND: Postpartum hemorrhage (PPH) is the leading cause of maternal mortality worldwide, with uterine atony accounting for approximately 70% of PPH cases. However, there is currently no effective prediction method to promote early management of PPH. In this study, we aimed to screen for potential predictive biomarkers for atonic PPH using combined omics approaches.METHODS: Collection of cervicovaginal fluid (CVF) samples from 27 women with atonic PPH and 32 women with normal delivery was performed for metabolomic (LC-MS/MS) and proteomic (LC-MS/MS) detection and subsequent confirmation experiments in this nested case-control study. Mass spectrum and enzyme-linked immunosorbent assays (ELISA) were used to validate significantly different metabolites and proteins for screening potential biomarkers of atonic PPH. Furthermore, multivariate logistic regressions were performed for the prediction of PPH using the identified biomarkers mentioned above, and the area under the curve (AUC) was computed.RESULTS: We identified 216 and 311 metabolites under positive and negative ion modes, respectively, as well as 1974 proteins. The PPH group had significant differences in metabolites and proteins belonging to the β-alanine metabolic pathway. Specifically, the PPH group had downregulation of critical metabolites, including histidine and protein dihydropyrimidine dehydrogenase (DPYD). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) functional enrichment analysis of significantly differentially expressed proteins revealed that atonic PPH was associated with T cell- and macrophage-related immune inflammatory responses. Furthermore, we verified that concentrations of histidine (350.85 ± 207.87 vs. 648.33 ± 400.87) and DPYD (4.01 ± 2.56 vs. 10.96 ± 10.71), and immune cell-related proteins such as CD163 (0.29 ± 0.19 vs. 1.51 ± 0.83) and FGL2 (5.98 ± 4.23 vs. 11.37 ± 9.42) were significantly lower in the PPH group. Finally, the AUC for independent prediction of PPH using CD163, histidine, DPYD, and FGL2 are 0.969 (0.897-1), 0.722 (0.536-0.874), 0.719 (0.528-0.864), and 0.697 (0.492-0.844), respectively. A relatively high predictive efficiency was obtained when using joint histidine, DPYD, CD163, and FGL2, with AUC = 0. 964 (0.822-1).CONCLUSIONS: This study suggested that immune inflammation may play a role in the occurrence of PPH. The metabolite histidine and proteins of DPYD, CD163, and FGL2 in CVF were associated with uterine atony and could be used as predictive biomarkers for atonic PPH.PMID:39885444 | DOI:10.1186/s12884-025-07224-9

Sci Rep. 2025 Jan 30;15(1):3754. doi: 10.1038/s41598-025-86191-9.ABSTRACTWild tomato species exhibit natural insect resistance, yet the specific secondary metabolites and underlying mechanisms governing the resistance remain unclear. Moreover, defense expression dynamically adapts to insect herbivory, causing significant metabolic changes and species-specific secondary metabolite accumulation. The present study aims to identify the resistance-related metabolites in wild tomato accessions that influence the defense mechanism against whitefly (Bemisia tabaci Asia II 7) and leafminer (Phthorimaea absoluta). In this study, LC-HRMS-based non-targeted metabolomics of resistant wild (Solanum cheesmaniae and Solanum galapagense) and susceptible cultivated (Solanum lycopersicum) accessions following 6- and 12-h post-infestation (hpi) by B. tabaci Asia II 7 and P. absoluta revealed distinct sets of resistance-related constitutive (RRC) and induced (RRI) metabolites. The key resistance-related metabolites were those involved in the fatty acid and associated biosynthesis pathways (e.g., triacontane, di-heptanoic acid, dodecanoic acid, undecanoic acid, N-hexadecanoic acid, pentacosane, monogalactosyldiacylglycerols, sphinganine, and 12-hydroxyjasmonic acid), which are recognized for their direct or indirect role in mediating plant defense against insects. Additionally, the differential accumulation of metabolites was evident through partial least squares-discriminant analysis (PLS-DA), highlighting differences in metabolite profiles between resistant and susceptible accessions at 6 and 12 hpi of B. tabaci and P. absoluta. Volcano plot analysis revealed a higher number of significantly upregulated metabolites in wild accessions following herbivory. Moreover, wild tomato accessions responded uniquely to B. tabaci and P. absoluta, highlighting species-specific metabolic responses of tomato accessions to the two feeding guilds. This study uncovered biochemical mechanisms governing resistance in wild tomato accessions, elucidated the influence of dual herbivory on the plant metabolome, and offered well-characterized parent materials and candidate metabolites for breeding insect-resistant varieties.PMID:39885264 | DOI:10.1038/s41598-025-86191-9

Cell Death Dis. 2025 Jan 30;16(1):55. doi: 10.1038/s41419-025-07365-x.ABSTRACTCell death mediated by executioner caspases is essential during organ development and for organismal homeostasis. The mechanistic role of activated executioner caspases in antibacterial defense during infections with intracellular bacteria, such as Listeria monocytogenes, remains elusive. Cell death upon intracellular bacterial infections is considered altruistic to deprive the pathogens of their protective niche. To establish infections in a human host, Listeria monocytogenes deploy virulence mediators, including membranolytic listeriolysin O (LLO) and the invasion associated protein p60 (Iap), allowing phagosomal escape, intracellular replication and cell-to-cell spread. Here, by means of chemical and genetical modifications, we show that the executioner caspases-3 and -7 efficiently inhibit growth of intracellular Listeria monocytogenes in host cells. Comprehensive proteomics revealed multiple caspase-3 substrates in the Listeria secretome, including LLO, Iap and various other proteins crucially involved in pathogen-host interactions. Listeria secreting caspase-uncleavable LLO or Iap gained significant growth advantage in epithelial cells. With that, we uncovered an underappreciated defense barrier and a non-canonical role of executioner caspases to degrade virulence mediators, thus impairing intracellular Listeria growth.PMID:39885151 | DOI:10.1038/s41419-025-07365-x

Methods Mol Biol. 2025;2895:271-297. doi: 10.1007/978-1-0716-4350-1_18.ABSTRACTThe nematode Caenorhabditis elegans, widely recognized as a model organism due to its ease of breeding and well-characterized genomes, boasts complete digestive, reproductive, and endocrine systems, as well as conserved signaling pathways shared with mammals. It has become an invaluable resource for metabolomics research, particularly in examining responses to chemical or environmental factors and toxicity assessments. In this article, we provide detailed, step-by-step protocols for cultivating C. elegans and conducting metabolomics analyses, specifically focusing on sample preparation for GC-MS analysis in response to toxic compound treatments. We highlight the critical choice of extraction solvent, introducing two representative systems for extracting metabolites from C. elegans.PMID:39885036 | DOI:10.1007/978-1-0716-4350-1_18

Methods Mol Biol. 2025;2895:245-257. doi: 10.1007/978-1-0716-4350-1_16.ABSTRACTIdentifying metabolites in NMR-based plant metabolomics is challenging due to the complexity of plant metabolites. This complexity stems from the abundance and diverse chemical properties of compounds, which vary in concentration across plant specimens. Additionally, the lack of automated identification software complicates the analysis process. Primary metabolites such as amino acids and sugars are widespread in plants, yet their identification is not straightforward due to various stereoisomeric forms and dynamic equilibria. Our protocol offers a manual approach to identify these metabolites, particularly focusing on amino acids and sugars. Through step-by-step guidance, we aim to empower researchers to navigate plant metabolomics complexities effectively.PMID:39885034 | DOI:10.1007/978-1-0716-4350-1_16

Methods Mol Biol. 2025;2895:227-243. doi: 10.1007/978-1-0716-4350-1_15.ABSTRACTProfiling of secondary metabolites within Fragaria sp. (strawberry), Rubus sp. (raspberries and blackberries), and Ribes sp. (blackcurrants and redcurrants) is of key importance with respect to the nutritional (antioxidant) benefits associated with a range of polyphenol classes within such fruits and how they vary between growth environment and season, as well as their deployment as quantitative trait loci (QTL) within breeding populations. This chapter presents an ultra-high-performance liquid chromatography (UHPLC) approach applying aqueous functionalized C18 chromatography combined with mass spectrometry (MS) for the characterization and relative quantification of a wide range of polyphenols such as the pelargonidins, being rich in strawberry; cyanidins, procyanidins, and anthocyanins, being rich in raspberry; and delphinidins and prodelphinidins, being particularly rich in blackcurrant, as well as a range of colorless flavonoids, and amino and organic acids.PMID:39885033 | DOI:10.1007/978-1-0716-4350-1_15

Methods Mol Biol. 2025;2895:177-200. doi: 10.1007/978-1-0716-4350-1_13.ABSTRACTThe metabolic diversity of plants, comprising over a million different metabolites across the plant kingdom, harbors enormous potential for pharmaceutical and biotechnological applications. Resin glycoside (RG) acylsugars from the Convolvulaceae are of interest due to their medicinal and agricultural potential. However, understanding the biological relevance of RGs is challenging as they exhibit a high lineage-specific structural diversity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with computational peak annotation can provide insights into this diversity. Here, we present a comprehensive protocol for the characterization of RG diversity using a sensitive LC-MS/MS instrument, a knowledge-based computational pipeline, and a web tool for peak annotation. The described experimental approach provides a step-by-step guide for RG sampling, extraction, purification for downstream analyses such as bioassays, and structural annotation using LC-MS/MS and computational metabolomics. The protocol focuses on qualitative analysis for putative annotation (Annotation Level 2 as defined by the Metabolomics Standards Initiative) of RGs and can serve as a valuable template for researchers exploring plant metabolic diversity beyond RGs and acylsugars.PMID:39885031 | DOI:10.1007/978-1-0716-4350-1_13

Methods Mol Biol. 2025;2895:99-109. doi: 10.1007/978-1-0716-4350-1_8.ABSTRACTThis chapter presents a comprehensive approach to profiling plant-derived primary metabolites using metabolomics, highlighting its critical role in decoding the biosynthesis of bioactive plant compounds. It details the utilization of gas chromatography-mass spectrometry (GC-MS) for the effective analysis and profiling of these metabolites. The process, encompassing extraction methods, chemical derivatization, and data processing, is thoroughly outlined. This methodology outlines comprehensive procedures for each stage of the workflow, encompassing metabolite extraction, GC-MS analysis, and data alignment, to produce a metabolomics dataset.PMID:39885026 | DOI:10.1007/978-1-0716-4350-1_8

Methods Mol Biol. 2025;2895:15-29. doi: 10.1007/978-1-0716-4350-1_2.ABSTRACTNatural products, particularly plants, remain a vital source of bioactive compounds owing to their unparalleled metabolic diversity across pharmaceuticals, cosmetics, foods, and agriculture. However, this diversity, encompassing not only a multitude of compounds but also their varying chemical and physical properties, presents a challenge in their effective utilization. Targeted analysis of specific metabolites, as well as untargeted approaches covering a wide metabolite range, necessitate optimal extraction solvents tailored to meet diverse requirements. Achieving optimization requires two crucial components: analytical methods capable of capturing a broad spectrum of metabolites and effective data analysis to derive meaningful conclusions. In this regard, 1H nuclear magnetic resonance (NMR) spectroscopy combined with principal component analysis (PCA) emerges as a promising approach for optimization. In this protocol, employing two model plants, leaves of basil (Ocimum basilicum) and lettuce (Lactura sativa), we deduce optimal extraction solvents from mixtures of methanol-water, acetonitrile, and chloroform, leveraging 1H NMR and PCA analyses.PMID:39885020 | DOI:10.1007/978-1-0716-4350-1_2

Methods Mol Biol. 2025;2895:3-13. doi: 10.1007/978-1-0716-4350-1_1.ABSTRACTThis introductory chapter traces the evolution of (bio)chemical assays, emphasizing the critical role of robust protocols in ensuring reproducibility-a fundamental aspect of scientific research. With the advent of systems biology, the need for standardized methods has intensified, particularly for integrating vast datasets in open-access formats. The historical progression from basic plant morphology to advanced chromatographic and spectroscopic techniques in phytochemistry highlights the necessity for precise, reproducible protocols.As metabolomics advances, there is a renewed focus on targeted approaches, shifting from broad, untargeted analyses to more specific, hypothesis-driven studies. This chapter also explores the future of analytical techniques, including cellomics and real-time metabolic flux measurements, which offer new insights into dynamic biochemical processes.Ultimately, this introduction underscores the importance of innovation in developing new methods that address current scientific challenges, particularly in pharmacognosy and analytical phytochemistry. The chapter sets the stage for the broader discussion on the necessity of well-designed protocols that facilitate effective data sharing and collaboration across research disciplines.PMID:39885019 | DOI:10.1007/978-1-0716-4350-1_1

Reprod Sci. 2025 Jan 30. doi: 10.1007/s43032-024-01779-2. Online ahead of print.ABSTRACTThe metabolomic approach has recently been used in the assessment of semen quality and male fertility. Additionally, the crucial roles of branched-chain amino acids (BCAAs) and aromatic amino acids (AAAs) in metabolic syndrome (MetS) were reported. However, little information exists about the association between BCAAs and AAAs with semen parameters, particularly in men with and without MetS. Our objective was to explore the association between BCAAs and AAAs in blood and seminal plasma and sperm parameters in men with MetS (MetS +) and without MetS (MetS-). In a cross-sectional study between January-July 2022, we investigated 98 men (age: 25-42 years; MetS + : n = 28 and MetS-: n = 70) at Royan Institute, Tehran, Iran. All participants underwent anthropometric indices measurements using standard protocols. From each participant, a single fasting blood sample was collected on the same day that the semen sample was collected. The BCAAs and AAAs in blood and seminal plasma were measured using high-performance liquid chromatography (HPLC). The aromatase activity (total testosterone/ estradiol ratio) was significantly lower in MetS + (0.16) than MetS- (0.35) (p = 0.016). Semen parameters were similar between the MetS + and the MetS- groups. All BCAA and AAA family members, except tryptophan, were higher in the blood plasma of men with metabolic syndrome. Meanwhile, the seminal plasma of BCAA and AAAs were similar. Intriguingly, Valine in blood (r = -0.329; p < 0.001) and seminal (r = -0.237; p < 0.05) plasma were correlated with abnormal sperm morphology in patients without metabolic syndrome (MetS-). Further research is necessary to validate these findings and to explore the underlying mechanisms and interactions between the plasma BCAAs and AAAs and sperm parameters.PMID:39885000 | DOI:10.1007/s43032-024-01779-2

Toxicol Appl Pharmacol. 2025 Jan 28:117247. doi: 10.1016/j.taap.2025.117247. Online ahead of print.ABSTRACTOBJECTIVES: Investigating the effect of melatonin (MLT) on the pharmacokinetics and related neurotransmitter and amino acid metabolism of vigabatrin (VGB) in epileptic rats in vivo.METHODS: High performance liquid chromatography was used to examine the pharmacokinetics and tissue distribution of VGB after intragastric administration dosing (50，100，200) mg/kg singly or in combination with melatonin (20 mg/kg) in rats. The single-compartment model of first-order elimination was fitted with the nonlinear mixed-effect model of first-order estimation. Targeting metabolomics were used to measure and analyze the amino acid levels in the hippocampus of kainic acid (KA)-induced epileptic rats treated with VGB alone or coupled melatonin.RESULTS: Melatonin significantly alters the pharmacokinetics of VGB, primarily by lengthening the elimination t1/2, Tmax, MRT and Vz/F, and decreasing the Cmax of both vigabatrin R(-) enantiomer (R-VGB) and vigabatrin S(+) enantiomer (S-VGB). Moreover, the concentrations of R-VGB and S-VGB were increased significantly in the lung and spleen of VGB + MLT group at 15 min compared with that of the VGB group. At 1 h, S-VGB levels increased significantly in spleen. At 4 h, the levels of S-VGB in the hippocampus and R-VGB in the prefrontal cortex increased significantly. Results of targeted metabolomics experiment showed that compared with control group, the level of aminobutyric acid/glutamate (GABA/Glu) in hippocampus of KA-induced epileptic rats was decreased, while glutamate/glutamine (Glu/Gln), tyrosine, dopamine, 3-methoxytyramine, tryptophan, 5-hydroxytryptamine, arginine and phenylalanine were significantly increased. These elevated levels of neurotransmitters and amino acids were decreased in VGB- and VGB + MLT treated group.CONCLUSIONS: MLT affected the pharmacokinetics and tissue distribution of VGB in rats, prolonging its elimination time and improving the tissue distribution. Moreover, it might help VGB improve the imbalance of neurotransmitters and amino acids in the hippocampus of epileptic rats.PMID:39884559 | DOI:10.1016/j.taap.2025.117247