PubMed

Physiol Plant. 2023 Sep-Oct;175(5):e14053. doi: 10.1111/ppl.14053.ABSTRACTMicroRNAs (miRNAs) are small regulatory RNAs that participate in various biological processes by silencing target genes. In Arabidopsis, microRNA163 (miR163) was found to be involved in seed germination, root development, and biotic resistance. However, the regulatory roles of miR163 remain unclear. In the current study, the mir163 mutant was investigated to comprehensively understand and characterize its functions in Arabidopsis. RNA-sequencing and Gene Ontology enrichment analyses revealed that miR163 might be involved in "response to stimulus" and "metabolic process". Interestingly, "response to stress", including heat, cold, and oxidative stress, was enriched under the subcategory of "response to stimulus". We observed that miR163 and PXMT were repressed and induced under heat stress, respectively. Furthermore, the study detected significant differences in seed germination rate, hypocotyl length, and survival rate, indicating a variation in the thermotolerance between WT and mir163 mutant. The results revealed that the mir163 mutant had a lesser degree of germination inhibition by heat treatment than WT. In addition, the mir163 mutant showed a better survival rate and longer hypocotyl length under heat treatment than the WT. The metabolomes of WT and mir163 mutant were further analyzed. The contents of benzene derivatives and flavonoids were affected by miR163, which could enhance plants' defense abilities. In conclusion, miR163/targets regulated the expression of stress-responsive genes and the accumulation of defense-related metabolites to alter stress tolerance.PMID:37882263 | DOI:10.1111/ppl.14053

S Afr Med J. 2023 Aug 3;113(8):8. doi: 10.7196/SAMJ.2023.v113i8.1142.NO ABSTRACTPMID:37882112 | DOI:10.7196/SAMJ.2023.v113i8.1142

Biol Psychiatry Glob Open Sci. 2023 Mar 15;3(4):651-662. doi: 10.1016/j.bpsgos.2023.02.011. eCollection 2023 Oct.ABSTRACTBACKGROUND: Patients with diabetes exhibit an increased prevalence for emotional disorders compared with healthy humans, partially due to a shared pathogenesis including hormone resistance and inflammation, which is also linked to intestinal dysbiosis. The preventive intake of probiotic lactobacilli has been shown to improve dysbiosis along with mood and metabolism. Yet, a potential role of Lactobacillus rhamnosus (Lacticaseibacillus rhamnosus 0030) (LR) in improving emotional behavior in established obesity and the underlying mechanisms are unknown.METHODS: Female and male C57BL/6N mice were fed a low-fat diet (10% kcal from fat) or high-fat diet (HFD) (45% kcal from fat) for 6 weeks, followed by daily oral gavage of vehicle or 1 × 108 colony-forming units of LR, and assessment of anxiety- and depressive-like behavior. Cecal microbiota composition was analyzed using 16S ribosomal RNA sequencing, plasma and cerebrospinal fluid were collected for metabolomic analysis, and gene expression of different brain areas was assessed using reverse transcriptase quantitative polymerase chain reaction.RESULTS: We observed that 12 weeks of HFD feeding induced hyperinsulinemia, which was attenuated by LR application only in female mice. On the contrary, HFD-fed male mice exhibited increased anxiety- and depressive-like behavior, where the latter was specifically attenuated by LR application, which was independent of metabolic changes. Furthermore, LR application restored the HFD-induced decrease of tyrosine hydroxylase, along with normalizing cholecystokinin gene expression in dopaminergic brain regions; both tyrosine hydroxylase and cholecystokinin are involved in signaling pathways impacting emotional disorders.CONCLUSIONS: Our data show that LR attenuates depressive-like behavior after established obesity, with changes in the dopaminergic system in male mice, and mitigates hyperinsulinemia in obese female mice.PMID:37881580 | PMC:PMC10593880 | DOI:10.1016/j.bpsgos.2023.02.011

Curr Res Food Sci. 2023 Oct 11;7:100616. doi: 10.1016/j.crfs.2023.100616. eCollection 2023.ABSTRACTHawthorn, the sliced and dried ripe fruits of Crataegus pinnatifida Bge. Var. Major N. E. Br. (Rosaceae), is an edible and medicinal substance with a variety of health-promoting benefits. Hawthorn needs to be stored in warehouses after harvesting to meet people's perennial demand. However, it is easily infested by insects of Plodia interpunctella and Tribolium castaneum during storage, which inevitably leads to poor quality and causes adverse effects on people's health. So far, there has been no report on insect-infested hawthorn. In this study, we analyzed the changes of metabolites in hawthorn before and after insect infestation and screened out potential biomarkers to effectively and quickly detect the occurrence of insect infestation. A combination analysis of 1H nuclear magnetic resonance (NMR) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was used to identify the primary and secondary metabolites. By the comparison of hawthorn and insect-infested hawthorn samples, it was found that the differences were mainly manifested in the content of metabolites. The metabolites of 32 and 1463 were identified by 1H NMR and UPLC-MS analysis, respectively. According to the parameters of VIP >1 and P < 0.05, 10 differential metabolites were screened from 1H NMR analysis. Based on the parameters of VIP >1.0, P < 0.05, and (FC) > 1 or < 1, 47 differential metabolites were screened from UPLC-MS analysis. Therefore, a total of 57 differential metabolites were considered as differential biomarkers. The heat map analysis showed that the content of some differential biomarkers with significant pharmacological activities decreased after insect infestation. Through receiver operating characteristic (ROC) curve assessment, 52 differential biomarkers (6 of 1H NMR analysis and 46 of UPLC-MS analysis) were screened to distinguish whether insect infestation occurred in hawthorn. This is the first report on the changes of metabolites between hawthorn and insect-infested hawthorn and on the screening of differential biomarkers for monitoring insects. These results contributed to evaluate quality of hawthorn and ensure food safety for consumers. It also laid a foundation for further research on the infestation mechanism and safe storage monitoring in hawthorn.PMID:37881336 | PMC:PMC10594559 | DOI:10.1016/j.crfs.2023.100616

New Phytol. 2023 Oct 25. doi: 10.1111/nph.19353. Online ahead of print.ABSTRACTLegume nodulation requires light perception by plant shoots and precise long-distance communication between shoot and root. Recent studies have revealed that TGACG-motif binding factors (GmSTFs) integrate light signals to promote root nodulation; however, the regulatory mechanisms underlying nodule formation in changing light conditions remain elusive. Here, we applied genetic engineering, metabolite measurement, and transcriptional analysis to study soybean (Glycine max) nodules. We clarify a fine-tuning mechanism in response to ultraviolet B (UV-B) irradiation and rhizobia infection, involving GmUVR8-dependent UV-B perception and GmSTF3/4-GmMYB12-GmCHS-mediated (iso)flavonoid biosynthesis for soybean nodule formation. GmUVR8 receptor-perceived UV-B signal triggered R2R3-MYB transcription factors GmMYB12-dependent flavonoid biosynthesis separately in shoot and root. In shoot, UV-B-triggered flavonoid biosynthesis relied on GmUVR8a, b, c receptor-dependent activation of GmMYB12L-GmCHS8 (chalcone synthase) module. In root, UV-B signaling distinctly promotes the accumulation of the isoflavones, daidzein, and its derivative coumestrol, via GmMYB12B2-GmCHS9 module, resulting in hypernodulation. The mobile transcription factors, GmSTF3/4, bind to cis-regulatory elements in the GmMYB12L, GmMYB12B2, and GmCHS9 promoters, to coordinate UV-B light perception in shoot and (iso)flavonoid biosynthesis in root. Our findings establish a novel shoot-to-root communication module involved in soybean nodulation and reveal an adaptive strategy employed by soybean roots in response to UV-B light.PMID:37881032 | DOI:10.1111/nph.19353

Adv Biol (Weinh). 2023 Oct 25:e2300413. doi: 10.1002/adbi.202300413. Online ahead of print.ABSTRACTAdequate sleep is essential for the biological maintenance of physical energy. Lack of sleep can affect thinking, lead to emotional anxiety, reduce immunity, and interfere with endocrine and metabolic processes, leading to disease. Previous studies have focused on long-term sleep deprivation and the risk of cancer, heart disease, diabetes, and obesity. However, systematic metabolomics analyses of blood, heart, liver, spleen, kidney, brown adipose tissue, and fecal granules have not been performed. This study aims to systematically assess the metabolic changes in the target organs caused by sleep deprivation in vivo, to search for differential metabolites and the involved metabolic pathways, to further understand the impact of sleep deprivation on health, and to provide strong evidence for the need for early intervention.PMID:37880935 | DOI:10.1002/adbi.202300413

Small. 2023 Oct 25:e2306400. doi: 10.1002/smll.202306400. Online ahead of print.ABSTRACTChirality-directed stem-cell-fate determination involves coordinated transcriptional and metabolomics programming that is only partially understood. Here, using high-throughput transcriptional-metabolic profiling and pipeline network analysis, the molecular architecture of chirality-guided mesenchymal stem cell lineage diversification is revealed. A total of 4769 genes and 250 metabolites are identified that are significantly biased by the biomimetic chiral extracellular microenvironment (ECM). Chirality-dependent energetic metabolism analysis has revealed that glycolysis is preferred during left-handed ECM-facilitated osteogenic differentiation, whereas oxidative phosphorylation is favored during right-handed ECM-promoted adipogenic differentiation. Stereo-specificity in the global metabolite landscape is also demonstrated, in which amino acids are enriched in left-handed ECM, while ether lipids and nucleotides are enriched in right-handed ECM. Furthermore, chirality-ordered transcriptomic-metabolic regulatory networks are established, which address the role of positive feedback loops between key genes and central metabolites in driving lineage diversification. The highly integrated genotype-phenotype picture of stereochemical selectivity would provide the fundamental principle of regenerative material design.PMID:37880901 | DOI:10.1002/smll.202306400

Microbiome. 2023 Oct 25;11(1):236. doi: 10.1186/s40168-023-01661-4.ABSTRACTBACKGROUND: Modern dairy diets have shifted from being forage-based to grain and energy dense. However, feeding high-starch diets can lead to a metabolic disturbance that is linked to dysregulation of the gastrointestinal microbiome and systemic inflammatory response. Plant flavonoids have recently attracted extensive interest due to their anti-inflammatory effects in humans and ruminants. Here, multi-omics analysis was conducted to characterize the biological function and mechanisms of citrus flavonoids in modulating the hindgut microbiome of dairy cows fed a high-starch diet.RESULTS: Citrus flavonoid extract (CFE) significantly lowered serum concentrations of lipopolysaccharide (LPS) proinflammatory cytokines (TNF-α and IL-6), acute phase proteins (LPS-binding protein and haptoglobin) in dairy cows fed a high-starch diet. Dietary CFE supplementation increased fecal butyrate production and decreased fecal LPS. In addition, dietary CFE influenced the overall hindgut microbiota's structure and composition. Notably, potentially beneficial bacteria, including Bacteroides, Bifidobacterium, Alistipes, and Akkermansia, were enriched in CFE and were found to be positively correlated with fecal metabolites and host metabolites. Fecal and serum untargeted metabolomics indicated that CFE supplementation mainly emphasized the metabolic feature "sphingolipid metabolism." Metabolites associated with the sphingolipid metabolism pathway were positively associated with increased microorganisms in dairy cows fed CFE, particularly Bacteroides. Serum lipidomics analysis showed that the total contents of ceramide and sphingomyelin were decreased by CFE addition. Some differentially abundant sphingolipid species were markedly associated with serum IL-6, TNF-α, LPS, and fecal Bacteroides. Metaproteomics revealed that dietary supplementation with CFE strongly impacted the overall fecal bacterial protein profile and function. In CFE cows, enzymes involved in carbon metabolism, sphingolipid metabolism, and valine, leucine, and isoleucine biosynthesis were upregulated.CONCLUSIONS: Our research indicates the importance of bacterial sphingolipids in maintaining hindgut symbiosis and homeostasis. Dietary supplementation with CFE can decrease systemic inflammation by maintaining hindgut microbiota homeostasis and regulating sphingolipid metabolism in dairy cows fed a high-starch diet. Video Abstract.PMID:37880759 | DOI:10.1186/s40168-023-01661-4

Chin J Nat Med. 2023 Oct;21(10):759-774. doi: 10.1016/S1875-5364(23)60506-0.ABSTRACTGut microbiota dysbiosis is an avenue for the promotion of atherosclerosis (AS) and this effect is mediated partly via the circulating microbial metabolites. More microbial metabolites related to AS vascular inflammation, and the mechanisms involved need to be clarified urgently. Paeonol (Pae) is an active compound isolated from Paeonia suffruticoas Andr. with anti-AS inflammation effect. However, considering the low oral bioavailability of Pae, it is worth exploring the mechanism by which Pae reduces the harmful metabolites of the gut microbiota to alleviate AS. In this study, ApoE-/- mice were fed a high-fat diet (HFD) to establish an AS model. AS mice were administrated with Pae (200 or 400 mg·kg-1) by oral gavage and fecal microbiota transplantation (FMT) was conducted. 16S rDNA sequencing was performed to investigate the composition of the gut microbiota, while metabolomics analysis was used to identify the metabolites in serum and cecal contents. The results indicated that Pae significantly improved AS by regulating gut microbiota composition and microbiota metabolic profile in AS mice. We also identified α-hydroxyisobutyric acid (HIBA) as a harmful microbial metabolite reduced by Pae. HIBA supplementation in drinking water promoted AS inflammation in AS mice. Furthermore, vascular endothelial cells (VECs) were cultured and stimulated by HIBA. We verified that HIBA stimulation increased intracellular ROS levels, thereby inducing VEC inflammation via the TXNIP/NLRP3 pathway. In sum, Pae reduces the production of the microbial metabolite HIBA, thus alleviating the ROS/TXNIP/NLRP3 pathway-mediated endothelial inflammation in AS. Our study innovatively confirms the mechanism by which Pae reduces the harmful metabolites of gut microbiota to alleviate AS and proposes HIBA as a potential biomarker for AS clinical judgment.PMID:37879794 | DOI:10.1016/S1875-5364(23)60506-0

Chin J Nat Med. 2023 Oct;21(10):745-758. doi: 10.1016/S1875-5364(23)60496-0.ABSTRACTDepression is a mental disorder with high morbidity, disability and relapse rates. Ginkgo biloba extract (GBE), a traditional Chinese medicine, has a long history of clinical application in the treatment of cerebral and mental disorders, but the key mechanism remains incompletely understood. Here we showed that GEB exerted anti-depressant effect in mice through regulating gut microbial metabolism. GBE protected against unpredictable mild stress (UMS)-induced despair, anxiety-like and social avoidance behavior in mice without sufficient brain distribution. Fecal microbiome transplantation transmitted, while antibiotic cocktail abrogated the protective effect of GBE. Spatiotemporal bacterial profiling and metabolomics assay revealed a potential involvement of Parasutterella excrementihominis and the bile acid metabolite ursodeoxycholic acid (UDCA) in the effect of GBE. UDCA administration induced depression-like behavior in mice. Together, these findings suggest that GBE acts on gut microbiome-modulated bile acid metabolism to alleviate stress-induced depression.PMID:37879793 | DOI:10.1016/S1875-5364(23)60496-0

J Ethnopharmacol. 2023 Oct 23:117343. doi: 10.1016/j.jep.2023.117343. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Yiqi Jiedu formula (YQJDF), rooted in the traditional Chinese medicinal principle of "tonifying qi and detoxifying", is remarkably efficacious in the clinical treatment of nasopharyngeal carcinoma (NPC). Previous studies have shed light on some of its anti-NPC effects and mechanisms, but the responsible pharmacological substances and their precise mechanisms of action remain unclear.AIM OF THE STUDY: The purpose of this study was to identify components of YQJDF that entered the bloodstream and to investigate their mechanisms of action against NPC through network pharmacology and serum metabolomics.MATERIAL AND METHODS: Components of YQJDF in serum were identified using liquid chromatography-tandem mass spectrometry. With these serum species as the focus of our research, network pharmacology analysis was used to identify active compounds and target genes that might mediate the efficacy of YQJDF in the treatment of NPC. Following establishment of an NPC xenograft model in nude mice, a non-targeted metabolomics approach was adopted to identify significant serum metabolites and metabolic pathways influenced by YQJDF.RESULTS: Thirty-six components of YQJDF were identified, primarily consisting of alkaloids, phenylpropanoids, and flavonoids. Notably, pathways such as PI3K/AKT, factors associated with Epstein-Barr virus infection, IL-17 signaling, and lipid metabolism, were highlighted as potential therapeutic targets of YQJDF during NPC treatment. Additionally, our findings suggested that YQJDF modified the metabolism of arginine and proline in the serum of mice bearing nasopharyngeal tumor grafts.CONCLUSIONS: This study identified the primary active components of YQJDF, highlighting its holistic role in the treatment of NPC through multiple targets and pathways. Furthermore, our findings provided a roadmap for future research into the mechanism of YQJDF in the therapy of NPC, setting the stage for its clinical application.PMID:37879509 | DOI:10.1016/j.jep.2023.117343

J Ethnopharmacol. 2023 Oct 23:117340. doi: 10.1016/j.jep.2023.117340. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Tetradium ruticarpum (A.Juss.) T.G.Hartley, a traditional Chinese medicine with thousands of years of medicinal history, has been employed to address issues such as indigestion, abdominal pain, and vomiting. Dehydroevodiamine (DHE) is a quinazoline alkaloid extracted from traditional Chinese medicine Tetradium ruticarpum (A.Juss.) T.G.Hartley. Previous studies have shown that DHE has anti-inflammatory, analgesic, and antioxidant activities. However, it is still unclear whether DHE has an effect on ethanol-induced gastric ulcers.AIM OF THE STUDY: The objective of this study is to investigate the therapeutic efficacy and underlying mechanisms of action of DHE on ethanol-induced gastric ulcers using network pharmacology and metabolomics strategies.METHODS: In this study, we used ethanol-induced rats as a model to assess the efficacy of DHE by biochemical indicator assays and pathological tissue detection. The integration of network pharmacology and metabolomics was used to explore possible mechanisms and was validated by western blot experiments. Finally, molecular docking was used to analyze the binding energy between DHE and the targets of PIK3CG and PLA2G2A.RESULTS: DHE was able to reverse ethanol-induced abnormalities in biochemical indicators and improve pathological tissue. Network pharmacology results indicated that DHE may be involved in the regulation of gastric ulcers by modulating 79 targets, and metabolomics results showed that a total of 13 metabolites were changed before and after DHE administration. Integrating network pharmacology and metabolomics, PIK3CG and PLA2G2A were identified as possible targets to exert therapeutic effects. In addition, the MAPKs pathway may also be involved in the regulation of ethanol-induced gastric ulcers. Finally, molecular docking results showed that DHE had low binding energies with both PIK3CG and PLA2G2A.CONCLUSIONS: These findings suggest that DHE was able to exert a protective effect against ethanol-induced gastric ulcers by modulating multiple metabolites with multiple targets. This study provides a valuable reference for the development of antiulcer drugs.PMID:37879508 | DOI:10.1016/j.jep.2023.117340

Sci Total Environ. 2023 Oct 23:168015. doi: 10.1016/j.scitotenv.2023.168015. Online ahead of print.ABSTRACTExposure to single molecules under laboratory conditions has led to a better understanding of the mechanisms of action (MeOAs) and effects of pharmaceutical active compounds (PhACs) on non-target organisms. However, not taking the co-occurrence of contaminants in the environment and their possible interactions into account may lead to underestimation of their impacts. In this study, we combined untargeted metabolomics and proteogenomics approaches to assess the mixture effects of diclofenac, carbamazepine and venlafaxine on marine mussels (Mytilus galloprovincialis). Our multi-omics approach and data fusion strategy highlighted how such xenobiotic cocktails induce important cellular changes that can be harmful to marine bivalves. This response is mainly characterized by energy metabolism disruption, fatty acid degradation, protein synthesis and degradation, and the induction of endoplasmic reticulum stress and oxidative stress. The known MeOAs and molecular signatures of PhACs were taken into consideration to gain insight into the mixture effects, thereby revealing a potential additive effect. Multi-omics approaches on mussels as sentinels offer a comprehensive overview of molecular and cellular responses triggered by exposure to contaminant mixtures, even at environmental concentrations.PMID:37879482 | DOI:10.1016/j.scitotenv.2023.168015

Prostaglandins Other Lipid Mediat. 2023 Oct 23:106789. doi: 10.1016/j.prostaglandins.2023.106789. Online ahead of print.ABSTRACTUrinary eicosanoid concentrations reflect inflammatory processes in multiple diseases and have been used as biomarkers of disease as well as for stratification in precision medicine. However, implementation of urinary eicosanoid profiling in large-scale analyses is restricted due to sample preparation limits. Here we demonstrate a single solid-phase extraction of 300µL urine in 96-well-format for prostaglandins, thromboxanes, isoprostanes, cysteinyl-leukotriene E4 and the linoleic acid-derived dihydroxy-octadecenoic acids (9,10- and 12,13-DiHOME). A simultaneous screening protocol was also developed for cortisol/cortisone and 7 exogenous steroids as well as 3 cyclooxygenase-inhibitors. Satisfactory performance for quantification of eicosanoids with a proper internal standard was demonstrated for intra-plate analyses (CV=8.5-15.1%) as well as for inter-plate (n=35) from multiple studies (CV=22.1-34.9%). Storage stability was evaluated at -20 °C, and polar tetranors evidenced a 50% decrease after 5 months, while the remaining eicosanoids evidenced no significant degradation. All eicosanoids were stable over 3.5-years in urine stored at -80°C. This method will facilitate the implementation of urinary eicosanoid quantification in large scale screening.PMID:37879396 | DOI:10.1016/j.prostaglandins.2023.106789

Biomed Pharmacother. 2023 Oct 23;168:115727. doi: 10.1016/j.biopha.2023.115727. Online ahead of print.ABSTRACTOBJECTIVE: The purpose of this study was to investigate the mechanism through which rosemary essential oil treats atopic dermatitis.METHODS: A dinitrochlorobenzene (DNCB)-induced atopic dermatitis mouse model was established and treated with low (1%), medium (2%), and high (4%) doses of Rosmarinus officinalis essential oil (EORO). Serum levels of interleukin (IL)-6 and tumor necrosis factor-alpha (TNF-α) in each group were determined using enzyme-linked immunosorbent assay (ELISA). Skin tissues were stained with hematoxylin-eosin and toluidine blue. We used network pharmacology and molecular docking techniques to verify the biological activity of essential proteins and their corresponding compounds in the pathway. Gas chromatography-mass spectrometry (GC-MS) was used for metabolomics analysis and multivariate statistical analysis of mouse serum to screen differential metabolites and metabolic pathway analysis. Protein expression of p-JAK1, CD4+ cells, and IL-4 in the skin tissue was detected by immunohistochemistry analysis. Protein levels of STAT3, p-STAT3, P65, and p-P65 in damaged skin tissues were detected using western blotting.RESULT: The skin of mice in the model group showed different degrees of erythema, dryness, scratches, epidermal erosion and shedding, and crusting. After treatment, the serum levels of IL-6 and TNF-α in EORO group were significantly decreased, and the expression of p-JAK1,CD4 + cells, IL-4, p-P65 / P65 and p-STAT3 / STAT3 proteins in skin tissues were decreased.CONCLUSION: EORO can effectively improve DNCB-induced AD-like skin lesions in mice by regulating the JAK/STAT/NF-κB signaling pathway, thereby reducing the production of downstream arachidonic acid metabolites, inhibiting skin inflammation, and restoring epidermal barrier function.PMID:37879216 | DOI:10.1016/j.biopha.2023.115727

Environ Int. 2023 Oct 17;181:108274. doi: 10.1016/j.envint.2023.108274. Online ahead of print.ABSTRACTPerfluorobutane sulfonates (PFBS) have garnered extensive utilization because of their distinctive physicochemical properties. The liver acts as a key target organ for toxicity within the body and is vital for regulating metabolic processes, particularly lipid metabolism. However, there is currently a significant research gap regarding the influences of PFBS on hepatic lipid metabolism, especially in individuals with different dietary statuses. Here, the objective of this research was to examine the effects of PFBS on hepatic function under different dietary conditions. The results suggested that the levels of liver injury biomarkers were significantly upregulated, e.g., transaminase (GPT, GOT), while liver lipid levels were downregulated after exposure to PFBS at concentration of 50 μg/L for 42 days. Moreover, restricted diet further intensified the adverse effects of PFBS on the liver. Metabolomics analysis identified significant alterations in lipid-related metabolites in PFBS-induced hepatotoxicity, PFBS exposure induced a decrease in lysophosphatidylethanolamine and lysophosphatidylcholine. PFBS exposure caused an increase in aldosterone and prostaglandin f2alpha under restricted diet. In PFBS treatment group, histidine metabolism, beta-alanine metabolism, and arginine biosynthesis were the main pathway for PFBS toxicity. Aldosterone-regulated sodium reabsorption as a vital factor in inducing PFBS toxicity in the RD-PFBS treatment group. The analysis of 16S rRNA sequencing revealed that exposure to PFBS resulted in imbalance of gut microbial communities. PFBS exposure induced a decrease in Akkermansia and Lactobacillus, but an increase in Enterococcus. PFBS exposure caused the abundance of Lachnospiraceae_NK4A136_group was significantly elevated under restricted diet. Additionally, disruptions in the expression of genes involved in lipid production and consumption may significantly contribute to lipid imbalance in the liver. This study underscores the importance of recognizing the harmful impact of PFBS on liver function, along with the biotoxicity of contaminant influenced by dietary habits.PMID:37879206 | DOI:10.1016/j.envint.2023.108274

BMC Bioinformatics. 2023 Oct 25;24(1):398. doi: 10.1186/s12859-023-05459-x.ABSTRACTBACKGROUND: In this paper, we are interested in interactions between a high-dimensional -omics dataset and clinical covariates. The goal is to evaluate the relationship between a phenotype of interest and a high-dimensional omics pathway, where the effect of the omics data depends on subjects' clinical covariates (age, sex, smoking status, etc.). For instance, metabolic pathways can vary greatly between sexes which may also change the relationship between certain metabolic pathways and a clinical phenotype of interest. We propose partitioning the clinical covariate space and performing a kernel association test within those partitions. To illustrate this idea, we focus on hierarchical partitions of the clinical covariate space and kernel tests on metabolic pathways.RESULTS: We see that our proposed method outperforms competing methods in most simulation scenarios. It can identify different relationships among clinical groups with higher power in most scenarios while maintaining a proper Type I error rate. The simulation studies also show a robustness to the grouping structure within the clinical space. We also apply the method to the COPDGene study and find several clinically meaningful interactions between metabolic pathways, the clinical space, and lung function.CONCLUSION: TreeKernel provides a simple and interpretable process for testing for relationships between high-dimensional omics data and clinical outcomes in the presence of interactions within clinical cohorts. The method is broadly applicable to many studies.PMID:37880571 | DOI:10.1186/s12859-023-05459-x

Metabolomics. 2023 Oct 25;19(11):90. doi: 10.1007/s11306-023-02051-5.ABSTRACTINTRODUCTION: The cupping test is a widely used method for quality assessment of Arabica coffee. However, the cupping test is limited by the low number of certified panelists and the low throughput. Therefore, an analytical-based quality assessment may be a promising tool to complement the cupping test. A present, there is no report investigating quality marker candidates, focusing only on "specialty" grade Arabica coffee from Indonesia.OBJECTIVE: This study identified the potential quality marker(s) in Arabica Specialty coffee at different stages (green beans, roasted beans, and brewed coffee.METHODS: The metabolite profiles of ten different Arabica specialty-grade coffees were analyzed with different cup scores using gas chromatography-mass spectrometry (GC/MS). From the ten samples, green coffee beans, roasted coffee beans, and brewed coffee were selected. In addition, an orthogonal projection to latent structure (OPLS) regression analysis was conducted to obtain a potential quality marker based on the variable importance in projection (VIP). The potential quality marker(s) were validated by GC/MS metabolome profiling and OPLS analysis of different sets of samples consisting of 35 Arabica specialty-grade coffee samples.RESULTS: In Arabica coffee samples, the OPLS model of the three stages showed galactinol to have a high VIP score. Galactinol showed a consistent positive correlation with cup scores at all stages of coffee production (green beans, roasted beans, and brewed coffee). The correlation suggests galactinol is a potential quality marker after further validation using different samples.CONCLUSION: GC/MS combined with OPLS regression analysis suggested galactinol as a quality marker and provide an early screening method for Arabica coffee quality that complements the cupping test performed by certified panelists.PMID:37880543 | DOI:10.1007/s11306-023-02051-5

Metabolomics. 2023 Oct 25;19(11):91. doi: 10.1007/s11306-023-02055-1.ABSTRACTBACKGROUND: Preterm birth is a leading cause of death in children under the age of five. The risk of preterm birth is increased by maternal HIV infection as well as by certain antiretroviral regimens, leading to a disproportionate burden on low- and medium-income settings where HIV is most prevalent. Despite decades of research, the mechanisms underlying spontaneous preterm birth, particularly in resource limited areas with high HIV infection rates, are still poorly understood and accurate prediction and therapeutic intervention remain elusive.OBJECTIVES: Metabolomics was utilized to identify profiles of preterm birth among pregnant women living with HIV on two different antiretroviral therapy (ART) regimens.METHODS: This pilot study comprised 100 mother-infant dyads prior to antiretroviral initiation, on zidovudine monotherapy or on protease inhibitor-based antiretroviral therapy. Pregnancies that resulted in preterm births were matched 1:1 with controls by gestational age at time of sample collection. Maternal plasma and blood spots at 23-35 weeks gestation and infant dried blood spots at birth, were assayed using an untargeted metabolomics method. Linear regression and random forests classification models were used to identify shared and treatment-specific markers of preterm birth.RESULTS: Classification models for preterm birth achieved accuracies of 95.5%, 95.7%, and 80.7% in the untreated, zidovudine monotherapy, and protease inhibitor-based treatment groups, respectively. Urate, methionine sulfone, cortisone, and 17α-hydroxypregnanolone glucuronide were identified as shared markers of preterm birth. Other compounds including hippurate and N-acetyl-1-methylhistidine were found to be significantly altered in a treatment-specific context.CONCLUSION: This study identified previously known as well as novel metabolomic features of preterm birth in pregnant women living with HIV. Validation of these models in a larger, independent cohort is necessary to ascertain whether they can be utilized to predict preterm birth during a stage of gestation that allows for therapeutic intervention or more effective resource allocation.PMID:37880481 | DOI:10.1007/s11306-023-02055-1

Sci Rep. 2023 Oct 25;13(1):18223. doi: 10.1038/s41598-023-45546-w.ABSTRACTRegular physical effort produces metabolic changes manifested as adaptation to exercise and increasing performance. In humans these changes have been characterized at metabolome level as depending on the discipline. However, all sports involve some level of changes in protein, carbohydrate and lipid metabolism. Recently, also performance horses have been subjected to metabolic analyses, but similar studies were lacking in sports dogs. In this study we performed the metabolomic analysis in plasma of Whippet dogs regularly trained and competing in coursing events, and untrained dogs of the same breed, fed with the same diet. We have also compared the hematological and blood biochemical results in these two groups of dogs. Basic blood tests indicated that enzymes related to lipid metabolism (lipase and gamma-glutamyltransferase) differed considerably between the groups. Metabolomic analysis of plasma confirmed the metabolic shift expressed as the differences in triacylglycerols levels between training and non-training dogs, aimed at improving the use of fatty acids as a source of energy during exertion. Surprisingly, other classes of metabolites were only hardly changed when comparing training and non-training Whippets.PMID:37880383 | DOI:10.1038/s41598-023-45546-w