Metabolic Profiling Analysis Research Articles

Comparative metabolic profiling and quantitative analysis of metabolites in different tissues of Ajuga turkestanica by ESI-UHPLC-QqTOF-MS and NMR.

Ajuga turkestanica preparations are used as anti-aging cosmeceuticals and for medicinal purposes. Herein we describe the characterization and quantification of its metabolites in different organs using UHPLC-MS and NMR spectroscopy. A total of 51 compounds belonging to various phytochemical classes (11 flavonoids, 10 ecdysteroids, 9 diterpenes, 6 fatty acids, 5 iridoids, 3 phenylpropanoids, 3 sugars, 2 phenolics, 1 coumarin, 1 triterpene) were annotated and tentatively identified by UHPLC-ESI-QqTOF-MS/MS of methanolic extracts obtained separately from the organs. 1D and 2D NMR spectroscopy independently confirmed the identity of six major compounds. The abundances of thesemain constituents in flowers, fruits, leaves, roots, seeds, and stems were compared and quantified using 1H NMR. The results showed that 8-O-acetylharpagide, 20-hydroxyecdysone (ecdysterone) and ajugachin B were the most abundant constituents in the species. The two major compounds, 8-O-acetylharpagide and 20-hydroxyecdysone, were chosen as the markers for the quality assessment of A. turkestanica material. The methanolic extract of the aerial parts of A. turkestanica showed no noteworthy anthelmintic (antihelmintic), antifungal, or cytotoxic effect in in vitro assays.

Lesión bilateral de ligamento cruzado craneal y neuropatía periférica en un canino Golden Retriever con hipotiroidismo: Reporte de caso

The case of a 6 -year -old female Golden Retriever is presented. She was limping in the left posterior limb. A 4/4 grade lameness, pain by palpating the knee, and a negative drawer test, but positive tibial compression was identified. No proprioceptive deficit or signs compatible with lesions joints in X-rays images were found. There was no response to treatment with Meloxicam and Tramadol and because a suspicion of partial rupture of the cranial cruciate ligament, the transposition of tibial tuberosity (TTT) procedure was chosen. The patient returned with lameness in the right hind limb right nine months later and after ruling out other causes of limp, the TTT was successfully performed in the affected limb. However, 18 months later he developed signs of peripheral neuropathy. Metabolic, infectious and hormonal profile analyses revealed increased serum alkaline phosphatase, decreased thyroxine (free T4) and thyroid-stimulating hormone (TSH) values within normal ranges according to the reference laboratory. Based on the patient's history and laboratory findings, the diagnosis was hypothyroidism, and the decision was made to supplement the patient with sodium levothyroxine. Remission of the nervous symptoms was observed 45 days after treatment.

Analysis of volatile compound metabolic profiles during the fermentation of filler tobacco leaves through integrated E-nose, GC–MS, GC-IMS, and sensory evaluation

Tobacco is an agricultural commodity with great economic significance. Producers recognize that the flavor characteristics of filler tobacco clear-out (FTLs) affect the quality of cigar tobacco items. To identify the major volatile organic compounds (VOCs) responsible for differences in FTLs, E-nose, HS-SPME-GC–MS, and HS-GC-IMS were employed for multi-dimensional analysis of nine groups of FTLs at various fermentation stages. The E-nose results indicated a progressive increase in nitrogen-oxygen compounds during fermentation. Coupled with these findings, HS-SPME-GC–MS identified 56 VOCs, and HS-GC-IMS revealed 55 VOCs in the FTLs. Principal component analysis (PCA) suggested that FTLs from various fermentation stages of the Yunxue No 39 tobacco plant exhibit significant differences. Partial least squares discriminant analysis (PLS-DA), along with the variable importance in projection (VIP) method for feature selection, pinpointed 12 VOCs as the essential unmistakable metabolites embroiled within the agrarian fermenting prepare of matured FTLs. During the fermentation process, these crucial metabolites are predominantly enriched in pathways including pyruvate metabolism, phenylalanine metabolism, as well as nicotinate and nicotinamide metabolism. The study provides insights into the differences and diversity of FTLs at agricultural fermentation stages. It offers valuable information for optimizing the quality of agricultural fermentation and guiding the directional fermentation of tobacco leaves.

Metabolic Profiling and Stable Isotope Analysis of Wines: Pilot Study for Cross-Border Authentication.

Globalization and free market dynamics have significantly impacted state economies, particularly in the wine industry. These forces have introduced greater diversity in wine products but have also heightened the risk of food fraud, especially in high-value commodities like wine. Due to its market value and the premium placed on quality, wine is frequently subject to adulteration. This issue is often addressed through regulatory trademarks on wine labels, such as Protected Designation of Origin (PDO) and Protected Geographic Indication (PGI). In this context, the metabolic profiles (organic acids, carbohydrates, and phenols) and stable isotope signatures (δ13C, δ18O, D/HI, and D/HII) of red and white wines from four agroclimatically similar regions were examined. The study explored how factors such as grape variety, harvest year, and geographical origin affect wine composition, with a particular focus on distinguishing samples from cross-border areas. Multivariate statistical analysis was used to assess the variability in wine composition and to identify distinct groups of samples. Preliminary results revealed that organic acids and volatile compounds were found in lower concentrations than carbohydrates but were significantly higher than phenols, with levels ranging between 1617 mg/L and 6258 mg/L. Carbohydrate content in the wines varied from 8285 mg/L to 14662 mg/L. Principal Component Analysis (PCA) indicated certain separation trends based on the variance in carbohydrates (e.g., fructose, glucose, galactose) and isotopic composition. However, Discriminant Analysis (DA) provided clear distinctions based on harvest year, variety, and geographical origin.

Metabolic and Immune Parameters in Pregnant Women with Impaired Glucose Metabolism-A Pilot Study.

Gestational diabetes mellitus (GDM) is a public health problem with increasing prevalence. Analyses of metabolic and immune profiles have great potential for discovering new markers and mechanisms related to the development of GDM. We monitored 61 pregnant women during the first and third trimesters of pregnancy, including 13 pregnant women with GDM, 14 pregnant women with elevated glucose in the first trimester and 34 healthy pregnant women. A number of metabolic and immunological parameters were measured, including glucose, insulin, lipid status, fatty acids, lymphocyte profile, adiponectin, IL-6, IL-10 and TNF-a. A higher number of T-helper lymphocytes and a higher ratio of helper/cytotoxic lymphocytes was found in the control group in the first trimester of pregnancy. Pregnant women whose glucose threshold values were measured in the first trimester, but who did not develop GDM, showed a higher percentage of neutrophils and a lower percentage of lymphocytes in the third trimester. Differences in polyunsaturated fatty acids levels were observed between healthy pregnant women and those with glucose metabolism disorders in the first trimester of pregnancy. The results of this pilot study demonstrate that there are differences in the profiles of T lymphocytes, NK cells and polyunsaturated fatty acids between the examined groups of pregnant women, which can serve as a direction for future research.

Comparative Analysis of Microbial Diversity and Metabolic Profiles during the Spontaneous Fermentation of Jerusalem Artichoke (Helianthus tuberosus L.) Juice.

Jerusalem artichoke juice is valued for its nutritional content and health benefits. Spontaneous fermentation enhances its flavor, quality, and functional components through microbial metabolic activities. This study used high-throughput sequencing to analyze microbial community changes, and LC-MS and GC-MS to detect secondary metabolites and flavor compounds during fermentation. During natural fermentation, beneficial bacteria like Lactobacillus and Pediococcus increased, promoting lactic acid production and inhibiting harmful bacteria, while environmental bacteria decreased. Similarly, fungi shifted from environmental types like Geosmithia and Alternaria to fermentation-associated Pichia and Penicillium. A total of 1666 secondary metabolites were identified, with 595 upregulated and 497 downregulated. Key metabolic pathways included phenylpropanoid biosynthesis, with significant increases in phenylalanine, tryptophan, and related metabolites. Lipid and nucleotide metabolism also showed significant changes. Flavor compounds, including 134 identified alcohols, esters, acids, and ketones, mostly increased in content after fermentation. Notable increases were seen in Phenylethyl Alcohol, Ethyl Benzenepropanoate, 3-Methylbutyl Butanoate, Ethyl 4-Methylpentanoate, 5-Ethyl-3-Hydroxy-4-Methyl-2(5H)-Furanone, Ethyl Decanoate, Hexanoic Acid, and 1-Octanol. γ-aminobutyric acid (GABA) and other functional components enhanced the health value of the juice. This study provides insights into microbial and metabolic changes during fermentation, aiding in optimizing processes and improving the quality of fermented Jerusalem artichoke juice for functional food development.

Unveiling the Molecular Mechanisms of Glioblastoma through an Integrated Network-Based Approach.

Background/Objectives: Despite current treatments extending the lifespan of Glioblastoma (GBM) patients, the average survival time is around 15-18 months, underscoring the fatality of GBM. This study aims to investigate the impact of sample heterogeneity on gene expression in GBM, identify key metabolic pathways and gene modules, and explore potential therapeutic targets. Methods: In this study, we analysed GBM transcriptome data derived from The Cancer Genome Atlas (TCGA) using genome-scale metabolic models (GEMs) and co-expression networks. We examine transcriptome data incorporating tumour purity scores (TPSs), allowing us to assess the impact of sample heterogeneity on gene expression profiles. We analysed the metabolic profile of GBM by generating condition-specific GEMs based on the TPS group. Results: Our findings revealed that over 90% of genes showing brain and glioma specificity in RNA expression demonstrate a high positive correlation, underscoring their expression is dominated by glioma cells. Conversely, negatively correlated genes are strongly associated with immune responses, indicating a complex interaction between glioma and immune pathways and non-tumorigenic cell dominance on gene expression. TPS-based metabolic profile analysis was supported by reporter metabolite analysis, highlighting several metabolic pathways, including arachidonic acid, kynurenine and NAD pathway. Through co-expression network analysis, we identified modules that significantly overlap with TPS-correlated genes. Notably, SOX11 and GSX1 are upregulated in High TPS, show a high correlation with TPS, and emerged as promising therapeutic targets. Additionally, NCAM1 exhibits a high centrality score within the co-expression module, which shows a positive correlation with TPS. Moreover, LILRB4, an immune-related gene expressed in the brain, showed a negative correlation and upregulated in Low TPS, highlighting the importance of modulating immune responses in the GBM mechanism. Conclusions: Our study uncovers sample heterogeneity's impact on gene expression and the molecular mechanisms driving GBM, and it identifies potential therapeutic targets for developing effective treatments for GBM patients.

HIF-1α-HPRT1 axis promotes tumorigenesis and gefitinib resistance by enhancing purine metabolism in EGFR-mutant lung adenocarcinoma

BackgroundThe mutations of oncogenic epidermal growth factor receptor (EGFR) is an important cause of lung adenocarcinoma (LUAD) malignance. It has been knowm that metabolic reprogramming is an important hallmark of malignant tumors, and purine metabolism is a key metabolic pathway for tumor progression and drug resistance, but its relationship with the EGFR-mutant LUAD is unclear.MethodsMetabolic reprogramming was studied through capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS)-based metabolic profiling analysis. Cell proliferation in vitro was evaluated by EdU staining and cell cycle assay. Tumorigenicity in vivo was tested by subcutaneous tumor formation experiment in nude mice. The binding of hypoxia-inducible factor-1 alpha (HIF-1α) and hypoxanthine phosphoribosyltransferase 1 (HPRT1) was detected by DNA pull‑down assay and Chromatin immunoprecipitation (ChIP) assays. HIF-1α, HPRT1, DNA damage and cell apoptosis related genes were examined by western blot. In addition, RNA sequencing, mass spectrometry and bioinformatics analysis were performed.ResultsWe found that mutated EGFR (muEGFR) upregulates HPRT1 to promote purine metabolism and tumorigenesis of EGFR-mutant LUAD. Mechanistically, muEGFR increases HIF-1α expression through protein stability. Meanwhile, up-regulated HIF-1α bound to the promoter of HPRT1 and transcriptionally activates HPRT1 expression, enhancing purine metabolism to maintain rapid tumor cell proliferation in EGFR-mutant LUAD. Further, gefitinib inhibited the synthesis of purine nucleotides, and HPRT1 inhibition increased the sensitivity of gefitinib to EGFR-mutant LUAD.ConclusionsOur study reveals that muEGFR-HIF-1α-HPRT1 axis plays a key role in EGFR-mutant LUAD and provides a new strategy-inhibiting purine metabolism for treating EGFR-mutant LUAD.

Abstract IA-09: Spatiotemporal metabolic networks in pancreatic cancer and associated cachexia

Abstract Cachexia or body wasting is a significant contributing factor to the morbidity and mortality of pancreatic cancer. Despite an unmet need, its metabolic underpinnings remain poorly understood. Here, we characterize an inducible mouse model of pancreatic cancer cachexia that recaptures human disease progression. We present longitudinal systemic metabolic profiling analyses through pre-, early and late cachexia stages in male and female pancreas, its interstitial fluid (IF), plasma, liver, adipose and skeletal muscle. We find that each tissue has a unique metabolome and trajectory across stages, and reveal metabolic signatures with marked lipid enrichment in the pancreatic IF. Using mathematical modeling, we identify metabolites participating in cross-tissue networks and in vivo validate a lactate-hexose connection. We find systemic metabolic changes prior to weight loss, and use feature selection algorithms to identify potential predictive markers of cachexia progression. Our study provides a resource for system-wide metabolic network evolution of pancreatic cancer cachexia, highlighting the potential for prevention and therapy. Citation Format: Blanca Majem, Min-Sik Lee, Kyung Cheul Shin, Insia Naqvi, Courtney Dennis, Lucas Dailey, Sarah Jeanfavre, Mari Mino-Kenudson, Joao B Xavier, Clary B Clish, Deepti Mathur, Nada Y Kalaany. Spatiotemporal metabolic networks in pancreatic cancer and associated cachexia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr IA-09.

Accelerated Exosomal Metabolic Profiling Enabled by Robust On-Target Array Sintering with Metal-Organic Frameworks.

Pancreatic cancer is highly lethal, and survival chances improve only with early detection at a precancerous stage. However, there remains a significant gap in developing tools for large-scale, rapid screening. To this end, a high-throughput On-Target Array Extraction Platform (OTAEP) by direct sintering of a series of metal-organic frameworks (MOFs) for dual in situ extraction, encompassing both exosomes and their metabolic profiles, is developed. Based on the principle of geometry-dependent photothermal conversion efficiency and standard testing, the appropriate MOF functional unit is identified. This unit enables exosome enrichment within 10 min and metabolic fingerprint extraction in under 1 s of laser irradiation, with over five reuse. To further accelerate and enhance the quality of metabolic profile analysis, the application of Surrogate Variable Analysis to eliminate hidden confounding factors within the profiles is proposed, and five biomarkers demonstrated by MS/MS experiments are identified. These biomarkers enable early diagnosis, risk stratification, and staging of pancreatic cancer simultaneously, with sensitivity of 94.1%, specificity of 98.8%, and precision of 94.9%. This work represents a breakthrough for overcoming throughput challenges in large-scale testing and for addressing confounding factors in big data analysis.

Analysis of Metabolic Profiles and Antioxidant Activity of Chinese Cordyceps, Ophiocordyceps sinensis, and Paecilomyces hepiali Based on Untargeted Metabolomics.

Chinese cordyceps (GL) is a traditional medicinal fungus, with Ophiocordyceps sinensis (O. sinensis, BL) and Paecilomyces hepiali (P. hepiali, JSB) being fungi isolated from wild Chinese cordyceps. These three species share similar chemical composition and pharmacological effects. Existing studies have primarily compared the metabolites of Chinese cordyceps and O. sinensis, overlooking the assessment of antioxidant capacity in Chinese cordyceps, P. hepiali, and O. sinensis. In this study, LC-MS/MS was employed to analyze metabolites in GL, JSB, and BL. Utilizing principal component analysis (PCA), supervised orthogonal partial least squares discriminant analysis (OPLS-DA), and hierarchical cluster analysis (HCA), it was observed that the majority of differential metabolites (DMs) primarily accumulated in organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds. Antioxidant activity analysis indicated that GL exhibited the higher 2,2-diphenyl-1-picrylhydrazyl radical scavenging ability (DPPH•, scavenging rate is 81.87 ± 0.97%), hydroxyl free radical scavenging capacity (•OH, scavenging rate is 98.10 ± 0.60%), and superoxide anion radical scavenging capacity (O2•-, scavenging rate is 69.74 ± 4.36%), while JSB demonstrated the higher FRAP total antioxidant capacity of 8.26 μmol Trolox/g (p < 0.05). Correlation analysis revealed a positive correlation between DMs (fatty acyls and amino acids) and DPPH•, FRAP, •OH, and O2•- (p < 0.05). Additionally, glycerophospholipid DMs were found to be positively correlated with FRAP (p < 0.05). Through KEGG pathway analysis, it was determined that the accumulation of DMs in pathways such as cutin, suberine and wax biosynthesis has a higher impact on influencing the antioxidant activity of the samples. These results shed light on the antioxidant capacity and metabolic characteristics of Chinese cordyceps and its substitutes and offer valuable insights into how different DMs impact the strength of antioxidant activity, aiding in the advancement and application of Chinese cordyceps and its substitutes.

Genes to specialized metabolites: accumulation of scopoletin, umbelliferone and their glycosides in natural populations of Arabidopsis thaliana

BackgroundScopoletin and umbelliferone belong to coumarins, which are plant specialized metabolites with potent and wide biological activities, the accumulation of which is induced by various environmental stresses. Coumarins have been detected in various plant species, including medicinal plants and the model organism Arabidopsis thaliana. In recent years, key role of coumarins in maintaining iron (Fe) homeostasis in plants has been demonstrated, as well as their significant impact on the rhizosphere microbiome through exudates secreted into the soil environment. Several mechanisms underlying these processes require clarification. Previously, we demonstrated that Arabidopsis is an excellent model for studying genetic variation and molecular basis of coumarin accumulation in plants.ResultsHere, through targeted metabolic profiling and gene expression analysis, the gene-metabolite network of scopoletin and umbelliferone accumulation was examined in more detail in selected Arabidopsis accessions (Col-0, Est-1, Tsu-1) undergoing different culture conditions and characterized by variation in coumarin content. The highest accumulation of coumarins was detected in roots grown in vitro liquid culture. The expression of 10 phenylpropanoid genes (4CL1, 4CL2, 4CL3, CCoAOMT1, C3’H, HCT, F6’H1, F6’H2,CCR1 and CCR2) was assessed by qPCR in three genetic backgrounds, cultured in vitro and in soil, and in two types of tissues (leaves and roots). We not only detected the expected variability in gene expression and coumarin accumulation among Arabidopsis accessions, but also found interesting polymorphisms in the coding sequences of the selected genes through in silico analysis and resequencing.ConclusionsTo the best of our knowledge, this is the first study comparing accumulation of simple coumarins and expression of phenylpropanoid-related genes in Arabidopsis accessions grown in soil and in liquid cultures. The large variations we detected in the content of coumarins and gene expression are genetically determined, but also tissue and culture dependent. It is particularly important considering that growing plants in liquid media is a widely used technology that provides a large amount of root tissue suitable for metabolomics. Research on differential accumulation of coumarins and related gene expression will be useful in future studies aimed at better understanding the physiological role of coumarins in roots and the surrounding environments.

Aged Brain Metabolomics Study by Metabolic Profiling Analysis of Amino Acids, Organic Acids, and Fatty Acids in Cortex, Cerebellum, Hypothalamus, and Hippocampus of Rats.

Aging is a progressive process characterized by weakness in brain function. Although metabolomics studies on the brain related with aging have been conducted, it is not yet fully understood. A systematic metabolomics study was performed to search for biomarkers and monitor altered metabolism in various brain tissues of the cortex, cerebellum, hypothalamus, and hippocampus of young (8 months old) and old rats (22 months old). Simultaneous profiling analysis of amino acids (AAs), organic acids (OAs), and fatty acids (FAs) in the brain tissues of young and old rats were performed by gas chromatography-tandem mass spectrometry. Under optimal conditions, AA, OA, and FA profiling methods showed good linearity (r ≥0.995) with limit of detection of ≤30 and 73.2 ng and limit of quantification of ≤90.1 and 219.5 ng, respectively. Repeatability varied from 0.4 to 10.4 and 0.8 to 14.8% relative standard deviation and accuracy varied from -11.3 to 10.3 and -12.8 to 14.1% relative error, respectively. In the profiling analysis, total 32, 43, 45, and 30 metabolites were determined in cortex, cerebellum, hypothalamus, and hippocampus, respectively. In statistical analysis, eight AAs (alanine, valine, leucine, isoleucine, threonine, serine, proline, and phenylalanine) in the cortex and four metabolites (alanine, phenylalanine, 3-hydoxypropionic acid, and eicosadienoic acid) in the cerebellum were significantly evaluated (Q-value <0.05, variable importance in projection scores ≥1.0). In all brain tissues, the score plots of orthogonal partial least square discriminant analysis were clearly separated between the young and old groups. Metabolomics results indicate that mechanistic targets of rapamycin complex 1, branched chain-amino acid, and energy metabolism are related to inflammation and mitochondrial dysfunction in the brain during aging. Thus, these results may explain the characteristic metabolism of brain aging.

Metabolic Profiling Analysis of Congenital Adrenal Hyperplasia via an Untargeted Metabolomics Strategy.

Congenital adrenal hyperplasia (CAH) manifests as an autosomal recessive disorder characterized by defects in the enzymes responsible for steroid synthesis. This work aims to perform metabolic profiling of patients with CAH, screen key differential metabolites compared to the control group, and discover the associated metabolic pathways implicated in CAH. Serum samples obtained from 32 pediatric male patients with CAH and 31 healthy control group candidates were subjected to analysis using non-targeted metabolomics strategy using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). A total of 278 differential metabolites were identified and annotated in KEGG. Operating characteristic curves (ROC) measurement exhibited 9 metabolites exhibiting high efficacy in differential diagnosis, as evidenced by an area under ROC curve (AUC) exceeding 0.85. Pathway analysis uncovered notable disruptions in steroid hormone biosynthesis (p <0.0001), purine metabolism and irregularities in lipid metabolism and amino acid metabolism, including tyrosine and alanine, in CAH patients. These findings demonstrate that metabolic pathways of purine, amino acid and lipid metabolism, apart from steroid hormone biosynthesis, may be disrupted and associated with CAH. This study helps provide insight into the metabolic profile of CAH patients and offers a new perspective for monitoring and administering follow-up care to CAH patients.

Identification of the effects of alkalinity exposure on the gills of oriental river prawns, Macrobrachium nipponense

Macrobrachium nipponense is an important commercial freshwater species in China. However, the ability of alkali tolerance of M. nipponense is insufficient to culture in the major saline-alkali water source in China. Thus, it is urgently needed to perform the genetic improvement of alkali tolerance in this species. In the present study, we aimed to analyse the effects of alkali treatment on gills in this species after 96 h alkalinity exposure under the alkali concentrations of 0 mmol/L, 4 mmol/L, 8 mmol/L, and 12 mmol/L through performing the histological observations, measurement of antioxidant enzymes, metabolic profiling analysis, and transcriptome profiling analysis. The results of the present study revealed that alkali treatment stimulated the contents of malondialdehyde, glutathione, glutathione peroxidase in gills, indicating these antioxidant enzymes plays essential roles in the protection of body from the damage, caused by the alkali treatment. In addition, high concentration of alkali treatment (> 8 mmol/L) resulted in the damage of gill membrane and haemolymph vessel, affecting the normal respiratory function of gill. Metabolic profiling analysis revealed that Metabolic pathways, Biosynthesis of secondary metabolites, Biosynthesis of plant secondary metabolites, Microbial metabolism in diverse environments, Biosynthesis of amino acids were identified as the main enriched metabolic pathways of differentially expressed metabolites, which are consistent with the previous publications, treated by the various environmental factors. Transcriptome profiling analyses revealed that the alkali concentration of 12 mmol/L has more regulatory effects on the changes of gene expression than the other alkali concentrations. KEGG analysis revealed that Phagosome, Lysosome, Glycolysis/Gluconeogenesis, Purine Metabolism, Amino sugar and nucleotide sugar metabolism, and Endocytosis were identified as the main enriched metabolic pathways in the present study, predicting these metabolic pathways may be involved in the adaption of alkali treatment in M. nipponense. Phagosome, Lysosome, Purine Metabolism, and Endocytosis are immune-related metabolic pathways, while Glycolysis/Gluconeogenesis, and Amino sugar and nucleotide sugar metabolism are energy metabolism-related metabolic pathways. Quantitative PCR analyses of differentially expressed genes (DEGs) verified the accuracy of the RNA-Seq. Alkali treatment significantly stimulated the expressions of DEGs from the metabolic pathways of Phagosome and Lysosome, suggesting Phagosome and Lysosome play essential roles in the regulation of alkali tolerance in this species, as well as the genes from these metabolic pathways. The present study identified the effects of alkali treatment on gills, providing valuable evidences for the genetic improvement of alkali tolerance in M. nipponense.

Design, Synthesis, Antitumor Activity and NMR-Based Metabolomics of Novel Amino Substituted Tetracyclic Imidazo[4,5-b]Pyridine Derivatives.

Newly prepared tetracyclic imidazo[4,5-b]pyridine derivatives were synthesized to study their antiproliferative activity against human cancer cells. Additionally, the structure-activity was studied to confirm the impact of the N atom position in pyridine nuclei as well as the chosen amino side chains on antiproliferative activity. Targeted amino substituted regioisomers were prepared by using uncatalyzed amination from corresponding chloro substituted precursors. The most active compounds 6 a, 8 and 10 showed improved activity in comparison to standard drug etoposide with IC50 values in a nanomolar range of concentration (0.2-0.9 μM). NMR-based metabolomics is a powerful instrument to elucidate activity mechanism of new chemotherapeutics. Multivariate and univariate statistical analysis of metabolic profiles of non-small cell lung cancer cells before and after exposure to 6 a revealed significant changes in metabolism of essential amino acids, glycerophospholipids and oxidative defense. Insight into the changes of metabolic pathways that are heavily involved in cell proliferation and survival provide valuable guidelines for more detailed analysis of activity metabolism and possible targets of this class of bioactive compounds.

Mass spectrometry-based metabolomics for the investigation of antibiotic-bacterial interactions.

With the development of analytical technologies especially mass spectrometry, metabolomics is becoming increasingly hot in the field of studying antibiotic-bacterial interactions. On the one hand, metabolomics can reveal metabolic perturbations in bacteria in the presence of antibiotics and expose metabolic mechanisms. On the other hand, through in-depth analysis of bacterial metabolic profiles, biomarkers and bioactive secondary metabolites with great potential as drug precursors can be discovered. This review focuses on the experimental workflow of bacterial metabolomics and its application to study the interaction between bacteria and antibiotics. Metabolomics improves the understanding of antibiotic lethality, reveals metabolic perturbations in antibiotic-resistant bacteria, guides the diagnosis and antibiotic treatment of infectious diseases, and aids in the exploration of antibacterial metabolites in nature. Furthermore, current limitations and directions for future developments in this area are discussed.

Association of litter size with the ruminal microbiome structure and metabolomic profile in goats

The Yunshang black goat is a renowned mutton specialist breed mainly originating from China that has excellent breeding ability with varying litter sizes. Litter size is an important factor in the economics of goat farming. However, ruminal microbiome structure might be directly or indirectly regulated by pregnancy-associated factors, including litter sizes. Therefore, the current experiment aimed to evaluate the association of different litter sizes (low versus high) with ruminal microbiome structure by 16S rRNA gene sequencing and metabolomic profiling of Yunshang black does. A total of twenty does of the Yunshang Black breed, approximately aged between 3 and 4 years, were grouped (n = 10 goats/group) into low (D-l) and high (D-h) litter groups according to their litter size (the lower group has ≤ 2 kids/litter and the high group has ≧ 3 kids/litter, respectively). All goats were sacrificed, and collected ruminal fluid samples were subjected to 16S rRNA sequencing and LC–MS/MC Analysis for ruminal microbiome and metabolomic profiling respectively. According to PCoA analysis, the ruminal microbiota was not significantly changed by the litter sizes among the groups. The Firmicutes and Bacteroidetes were the most dominant phyla, with an abundance of 55.34% and 39.62%, respectively. However, Ruminococcaceae_UCG-009, Sediminispirochaeta, and Paraprevotella were significantly increased in the D-h group, whereas Ruminococcaceae_UCG-010 and Howardella were found to be significantly decreased in the D-l group. The metabolic profiling analysis revealed that litter size impacts metabolites as 29 and 50 metabolites in positive and negative ionic modes respectively had significant differences in their regulation. From them, 16 and 24 metabolites of the D-h group were significantly down-regulated in the positive ionic mode, while 26 metabolites were up-regulated in the negative ionic mode for the same group. The most vibrant identified metabolites, including methyl linoleate, acetylursolic acid, O-desmethyl venlafaxine glucuronide, melanostatin, and arginyl-hydroxyproline, are involved in multiple biochemical processes relevant to rumen roles. The identified differential metabolites were significantly enriched in 12 different pathways including protein digestion and absorption, glycerophospholipid metabolism, regulation of lipolysis in adipocytes, and the mTOR signaling pathway. Spearman’s correlation coefficient analysis indicated that metabolites and microbial communities were tightly correlated and had significant differences between the D-l and D-h groups. Based on the results, the present study provides novel insights into the regulation mechanisms of the rumen microbiota and metabolomic profiles leading to different fertility in goats, which can give breeders some enlightenments to further improve the fertility of Yunshang Black goats.

Metabolic Profiling and Transcriptome Analysis Provide Insights into the Anthocyanin Types and Biosynthesis in Zingiber striolatum Diels Flower Buds in Three Planting Modes

The flower buds of Zingiber striolatum Diels are considered a special vegetable in China, and they are rich in anthocyanins. However, the detailed composition types and the molecular mechanism of anthocyanin biosynthesis in Z. striolatum flower buds are still unclear. In this study, targeted metabolites were used to analyze and identify the anthocyanin types of Z. striolatum in three planting modes: monoculture (CK), intercropping with maize (ZP), and intercropping with soybean (SP). A total of 48 anthocyanins were identified with significant differential accumulation in Z. striolatum flower buds. Among them, cyanidin-3-O-glucoside was the main composition type of anthocyanins. Furthermore, the composition types of blue anthocyanin were identified in flower buds. A total of 15 structure genes were obtained from the transcriptome database of Z. striolatum flower buds. The qRT-PCR results revealed that the expression levels of ZsC4H-1, ZsC4H-2, ZsCHS-2, ZsCHI, ZsF3H, ZsF3’H, ZsDFR, ZsF3’5’H-3, and ZsANS genes were the highest in the ZP model. This study showed that the ZP model contributes to anthocyanin synthesis and accumulation of Z. striolatum flower buds among the three planting modes of Z. striolatum. These findings provide valuable information for research on the planting model and anthocyanin biosynthesis in Z. striolatum flower buds.

Integrated network pharmacology and metabolomics reveal vascular protective effects of Ilex pubescens on thromboangiitis obliterans

BackgroundIlex pubescens Hook. et Arn (IP), traditionally known for its properties of promoting blood circulation, swelling and pain relief, heat clearing, and detoxification, has been used in the treatment of thromboangiitis obliterans (TAO). Despite its traditional applications, the specific mechanisms by which IP exerts its therapeutic effects on TAO remain unclear. Aim of the studyThis study aims to uncover the underlying mechanisms in the therapeutic effects of IP on TAO, employing network pharmacology and metabolomic approaches. MethodsIn this study, a rat TAO model was established by injecting sodium laurate through the femoral artery, followed by the oral administration of IP for 7 days. Plasma coagulation parameters were measured to assess the therapeutic effects of IP. The potential influence on the femoral artery and gastrocnemius muscle was histopathologically evaluated. Network pharmacology was employed to predict relevant targets and model pathways for TAO. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) was used for the metabolic profile analysis of rat plasma. Immunohistochemistry (IHC) was used to verify the mechanisms by which IP promotes blood circulation in TAO. ResultsThe study revealed that IP improved blood biochemical function in TAO and played a significant role in vascular protection and maintaining normal blood vessels and gastrocnemius morphologies. Network pharmacology showed that IP compounds play a therapeutic role in modulating lipids and atherosclerosis. Metabolomic analysis revealed that the pathways involved in sphingolipid metabolism and steroid biosynthesis were significantly disrupted. The joint analysis showed a strong correlation between lysophosphatidylcholine and IP components, including triterpenoid and iridoid components, which support the curative action of IP through the modulation of sphingolipid metabolism. Furthermore, decreased expression levels of SPHK1/S1PR1, TNF-α, IL-1β, and IL-6 were observed in the IP-treated group, suggesting that IP exerts a protective effect on the vasculature primarily by regulating of the SPHK1/S1PR1 signaling pathway. ConclusionIn this study, we found that IP protects the vasculature against injury and treats TAO by regulating the steady-state disturbance of the sphingolipid pathway. These findings suggest that IP promotes vasculature by modulating sphingolipid metabolism and SPHK1/S1PR1 signaling pathway and reduce levels of inflammatory factors, offering new insights into its therapeutic potential.