PubMed

Related Articles Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Res. 2019 01;29(1):96-106 Authors: Kooke R, Morgado L, Becker F, van Eekelen H, Hazarika R, Zheng Q, de Vos RCH, Johannes F, Keurentjes JJB Abstract Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map. PMID: 30504416 [PubMed - indexed for MEDLINE]

22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/25PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/25PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

25 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

25 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/23PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/04/23PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Comparative metabolomics of temperature sensitive resistance to wheat streak mosaic virus (WSMV) in resistant and susceptible wheat cultivars. J Plant Physiol. 2019 Apr 12;237:30-42 Authors: Farahbakhsh F, Hamzehzarghani H, Massah A, Tortosa M, Yasayee M, Rodriguez VM Abstract In order to evaluate wheat resistance to wheat streak mosaic virus (WSMV) at low temperature and resistance breakdown at high temperature, metabolic profile of WSMV-resistant (R) and susceptible (S) wheat cultivars were analyzed. Metabolites were detected by UPLC-QTOF/MS in leaves of R and S plants challenged with WSMV at 20 °C and 32 °C, 24, 48 and 72 h post inoculation (hpi). WSMV and mock inoculated plants were used for discriminating the most significant metabolites and metabolic pathways affected at those temperatures. At 24 hpi/20 °C and 48 hpi/20 °C, the most important metabolites in R plants were coumarins, a limited number of lipids, and unknown compounds, while at 72 hpi/20 °C, in addition to coumarins, alkaloids and several amino acids were increased. Compared to 24 and 48 hpi, at 72hpi, in R plants most metabolic pathways were up-regulated at 20 °C. These resistance-related specific pathways included amino acid metabolism, lipid metabolism and alkaloids pathways. Also, several pathways were up-regulated at 32 °C.These combined heat stress and pathogen related pathways, included lipid metabolism and amino acid metabolism. Some carbohydrate metabolism pathways were considered as heat stress related pathways and could be associated with resistance breakdown. On the other hand, the increased expression of lipid compounds, especially 24 hpi at 32 °C in R plant, can be attributed to plant adaptation to combined stressors such as pathogen and high temperature. Increased susceptibility of R plants at 32 °C coincided with a down-regulated expression of components of signal transduction pathways or in a decreased level of metabolites related to this pathway, especially at a later time after infection, leading to decreased metabolite signaling. Decrease of signaling compounds under combined stress is a possible outcome of deactivating WSMV specific signaling networks leading to compatible response in R plants. The significance of these findings considering the recent increase of global temperature and the challenge of breakdown of temperature sensitive resistance to some plant viruses is discussed. PMID: 31005806 [PubMed - as supplied by publisher]

Untargeted gas chromatography-mass spectrometry-based metabolomics analysis of kidney and liver tissue from the Lewis Polycystic Kidney rat. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Apr 12;1118-1119:25-32 Authors: Abbiss H, Maker GL, Gummer JPA, Rawlinson C, Musk GC, Fleming PA, Phillips JK, Boyce MC, Trengove RD Abstract Polycystic kidney disease (PKD) encompasses a spectrum of inherited disorders that lead to end-stage renal disease (ESRD). There is no cure for PKD and current treatment options are limited to renal replacement therapy and transplantation. A better understanding of the pathobiology of PKD is needed for the development of new, less invasive treatments. The Lewis Polycystic Kidney (LPK) rat phenotype has been characterized and classified as a model of nephronophthisis (NPHP9, caused by mutation of the Nek8 gene) for which polycystic kidneys are one of the main pathologic features. The aim of this study was to use a GC-MS-based untargeted metabolomics approach to determine key biochemical changes in kidney and liver tissue of the LPK rat. Tissues from 16-week old LPK (n = 10) and Lewis age- and sex-matched control animals (n = 11) were used. Principal component analysis (PCA) distinguished signal corrected metabolite profiles from Lewis and LPK rats for kidney (PC-1 77%) and liver (PC-1 46%) tissue. There were marked differences in the metabolite profiles of the kidney tissues with 122 deconvoluted features significantly different between the LPK and Lewis strains. The metabolite profiles were less marked between strains for liver samples with 30 features significantly different. Five biochemical pathways showed three or more significantly altered metabolites: transcription/translation, arginine and proline metabolism, alpha-linolenic and linoleic acid metabolism, the citric acid cycle, and the urea cycle. The results of this study validate and complement the current literature and are consistent with the understood pathobiology of PKD. PMID: 31005771 [PubMed - as supplied by publisher]

Protein biomarker discovery is still relevant and has entered a new phase. EBioMedicine. 2019 Apr 18;: Authors: van der Burgt YEM PMID: 31005515 [PubMed - as supplied by publisher]

Stronger anti-obesity effect of white ginseng over red ginseng and the potential mechanisms involving chemically structural/compositional specificity to gut microbiota. Phytomedicine. 2018 Nov 19;:152761 Authors: Zhou SS, Auyeung KK, Yip KM, Ye R, Zhao ZZ, Mao Q, Xu J, Chen HB, Li SL Abstract BACKGROUND: Ginseng has therapeutic potential for treating obesity and the associated gut microbiota dysbiosis. However, whether white ginseng and red ginseng, the two kinds of commonly used processed ginseng, possess different anti-obesity effects remains unknown. PURPOSE: Anti-obesity effects of water extracts of white ginseng and red ginseng (WEWG and WERG) were compared, and the potential mechanisms were discussed. METHODS: Chemical profiles of WEWG and WERG were characterized by ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry (UHPLC-QqQ-MS/MS) and high performance liquid chromatography coupled with evaporative light scattering detector (HPLC-ELSD). Anti-obesity effects of WEWG/WERG were examined by determining fat accumulation, systemic inflammation, enteric metabolic disorders and gut microbiota dysbiosis in high-fat diet (HFD)-fed obese mice. RESULTS: Both WEWG and WERG exerted anti-obesity effects, with WEWG stronger than WERG. Compared to WERG, WEWG contained less contents of carbohydrates (polysaccharides, oligosaccharides, free monosaccharides) and ginsenosides, but chemical structures or compositions of these components in WEWG were characteristic, i.e. narrower molecular weight distribution and higher molar ratios of glucose residues of polysaccharides; higher content ratios of oligosaccharides DP2-3 (di-/tri-saccharides)-to-oligosaccharides DP4-7 (tetra-/penta-/hexa-/hepta-saccharides), sucrose-to-melibiose, maltose-to-trehalose and high-polar-to-low-polar ginsenosides. WEWG better ameliorated fat accumulation, enteric metabolic disorders and gut microbiota dysbiosis in HFD-fed obese mice than WERG. CONCLUSION: The stronger anti-obesity effect of white ginseng appears to correlate with differences in its chemical profile as compared to red ginseng. The carbohydrates and ginsenosides in WEWG potentially present more structural and compositional specificity to the obesity-associated gut bacteria, allowing more beneficial effects of WEWG on the gut microbiota dysbiosis. This consequently better alleviates the enteric metabolic disorders and systemic inflammation, thereby contributing to the stronger anti-obesity effect of WEWG as compared to WERG. PMID: 31005370 [PubMed - as supplied by publisher]

A gas chromatography-mass spectrometry untargeted metabolomics approach to discriminate Fiore Sardo cheese produced from raw or thermized ovine milk. J Dairy Sci. 2019 Apr 17;: Authors: Caboni P, Maxia D, Scano P, Addis M, Dedola A, Pes M, Murgia A, Casula M, Profumo A, Pirisi A Abstract Thermization is a sub-pasteurization heat treatment of cheese milk (at 57-68°C for 15-30 s) aimed to reduce the number of undesirable microbial contaminants with reduced heat damage to the indigenous milk enzymes. In this work, the effects of milk thermization on the compositional parameters, proteolysis indices, free fatty acid levels, and low molecular weight metabolite profiles of ovine cheese were studied. Cheese samples at different ripening stages and produced in 2 different periods of the year were analyzed. While the effects of milk thermization on cheese macro-compositional parameters and free fatty acid levels were not evident due to the predominant effects of milk seasonality and cheese ripening stage, the gas chromatography-mass spectrometry based metabolomics approach of ovine cheese produced from raw and thermized milk highlighted strong differences at the metabolite level. Discriminant analysis applied to gas chromatography-mass spectrometry data provided an excellent classification model where cheese samples were correctly classified as produced from raw or thermized milk. The metabolites that mostly changed due to the thermization process belonged to the classes of free amino acids and saccharides. Gas chromatography-mass spectrometry-based metabolomics has proven to be a valid tool to study the effect of mild heat treatments on the polar metabolite profile in ovine cheese. PMID: 31005329 [PubMed - as supplied by publisher]

An optimized analytical method for cellular targeted quantification of primary metabolites in tricarboxylic acid cycle and glycolysis using gas chromatography-tandem mass spectrometry and its application in three kinds of hepatic cell lines. J Pharm Biomed Anal. 2019 Apr 12;171:171-179 Authors: Xu J, Zhai Y, Feng L, Xie T, Yao W, Shan J, Zhang L Abstract Energy synthesis in aerobic organisms relies on two major metabolic pathways, i.e. tricarboxylic acid (TCA) cycle and glycolysis, the metabolites of which are highly affected by many diseases. Cells are the basic unit of the organism and have independent, ordered and self-controlled metabolic systems. Therefore, it is necessary to quantify intracellular metabolites in TCA cycle and glycolysis. In this study, we established a repeatable gas chromatography-tandem mass spectrometry (GC-MS/MS) method with selected reaction monitoring (SRM) mode for simultaneous quantification of several primary metabolites in these two pathways, including glucose, 3-phosphoglycerate, phosphoenolpyruvate (PEP), pyruvate, lactate, citrate, cis-aconitate, isocitrate, α-ketoglutarate, succinate, fumarate and malate. There are many solvents to extract the metabolites in these two pathways, however, which one is more effective still remains unclear. Sample pretreatment was optimized for solvent types and volumes to advance the extraction efficiency of metabolites. 500 μL of 75% methanol-methyl tert-butyl ether (MTBE) was finally selected for the extraction of targeted metabolites in cells due to its highest extraction efficiency. Activated carbon as an effective adsorbent was successfully applied to the removal of endogenous targeted metabolites in cells for getting the analyte-free surrogate matrices. A series of methodological studies verified the validity of this optimized approach which was applied to quantify and compare the targeted metabolites in three common hepatic cells. The developed GC-MS/MS method provided a better way to determine the metabolites of energy metabolism in cellular metabolomics, facilitating the application of targeted quantification metabolomics to precisely discover the metabolic alterations. PMID: 31005043 [PubMed - as supplied by publisher]

Curcumin attenuates collagen-induced rat arthritis via anti-inflammatory and apoptotic effects. Int Immunopharmacol. 2019 Apr 17;72:292-300 Authors: Wang Q, Ye C, Sun S, Li R, Shi X, Wang S, Zeng X, Kuang N, Liu Y, Shi Q, Liu R Abstract Curcumin is a natural herbal product that has been popularly used to treat autoimmune diseases in China; however, its effects on rheumatoid arthritis and its mechanism are not clear. The main purposes of this study are to explore the therapeutic effects of curcumin on collagen-induced arthritis (CIA) rats and the pharmacological mechanism. In the present study, CIA rats were established by injecting bovine type II collagen. Curcumin and methotrexate were then orally administered daily, and the swelling degree of the hind limb joints was scored every two days. Histopathological changes were observed by hematoxylin-eosin staining. The levels of cytokines (TNF-α, IL-1β, IL-17 and TGF-β) were detected by radioimmunoassay, while the expression of IκBα and COX-2 was detected by Western blot. In addition, cell viability was detected by CCK-8 assay, and the effect of curcumin on macrophage apoptosis was detected by flow cytometry and TUNEL assay. The results indicated that in vivo curcumin attenuated the degree of joint swelling of rats and the further development of joint histopathology. Moreover, it downregulated the levels of cytokines. In vitro curcumin inhibited the degradation of IκBα and reduced the production of COX-2 in LPS-induced inflammatory RAW264.7 cells. Importantly, curcumin significantly induced macrophage apoptosis. In conclusion, in this study, we have demonstrated that curcumin exerts therapeutic effects on arthritis in CIA rats and has a strong pharmacological activity on reducing the inflammatory response in macrophages. Its mechanism may be related to the inhibition of the NF-κB signaling pathway and the promotion of macrophage apoptosis. PMID: 31005039 [PubMed - as supplied by publisher]

What did we learn from multiple omics studies in asthma? Allergy. 2019 Apr 20;: Authors: Ivanova O, Richards LB, Vijverberg SJ, Neerincx AH, Sinha A, Sterk PJ, Maitland van der Zee AH Abstract More than a decade has passed since the finalisation of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired - presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma sub-phenotypes and underlying cellular processes, will likely play a role in asthma management strategies. This article is protected by copyright. All rights reserved. PMID: 31004501 [PubMed - as supplied by publisher]

Related Articles Pro- and anti-inflammatory eicosanoids in psoriatic arthritis. Metabolomics. 2019 Apr 19;15(4):65 Authors: Coras R, Kavanaugh A, Boyd T, Huynh Q, Pedersen B, Armando AM, Dahlberg-Wright S, Marsal S, Jain M, Paravar T, Quehenberger O, Guma M Abstract INTRODUCTION: Eicosanoids are biological lipids that serve as both activators and suppressors of inflammation. Eicosanoid pathways are implicated in synovitis and joint destruction in inflammatory arthritis, yet they might also have a protective function, underscoring the need for a comprehensive understanding of how eicosanoid pathways might be imbalanced. Until recently, sensitive and scalable methods for detecting and quantifying a high number of eicosanoids have not been available. OBJECTIVE: Here, we intend to describe a detailed eicosanoid profiling in patients with psoriatic arthritis (PsA) and evaluate correlations with parameters of disease activity. METHODS: Forty-one patients with PsA, all of whom satisfied the CASPAR classification criteria for PsA, were studied. Outcomes reflecting the activity of peripheral arthritis as well as skin psoriasis, Disease Activity Score (DAS)28, Clinical Disease Index (CDAI) and Body Surface Area (BSA) were assessed. Serum eicosanoids were determined by LC-MS, and the correlation between metabolite levels and disease scores was evaluated. RESULTS: Sixty-six eicosanoids were identified by reverse-phase LC/MS. Certain eicosanoids species including several pro-inflammatory eicosanoids such as PGE2, HXB3 or 6,15-dk,dh,PGF1a correlated with joint disease score. Several eicosapentaenoic acid (EPA)-derived eicosanoids, which associate with anti-inflammatory properties, such as 11-HEPE, 12-HEPE and 15-HEPE, correlated with DAS28 (Disease Activity Score) and CDAI (Clinical Disease Activity Index) as well. Of interest, resolvin D1, a DHA-derived anti-inflammatory eicosanoid, was down-regulated in patients with high disease activity. CONCLUSION: Both pro- and anti-inflammatory eicosanoids were associated with joint disease score, potentially representing pathways of harm as well as benefit. Further studies are needed to determine whether these eicosanoid species might also play a role in the pathogenesis of joint inflammation in PsA. PMID: 31004236 [PubMed - in process]

Related Articles Biomarker Discovery for Cytochrome P450 1A2 Activity Assessment in Rats, Based on Metabolomics. Metabolites. 2019 Apr 18;9(4): Authors: Pu X, Gao Y, Li R, Li W, Tian Y, Zhang Z, Xu F Abstract Cytochrome P450 1A2 (CYP1A2) is one of the major CYP450 enzymes (CYPs) in the liver, and participates in the biotransformation of various xenobiotics and endogenous signaling molecules. The expression and activity of CYP1A2 show large individual differences, due to genetic and environmental factors. In order to discover non-invasive serum biomarkers associated with hepatic CYP1A2, mass spectrometry-based, untargeted metabolomics were first conducted, in order to dissect the metabolic differences in the serum and liver between control rats and β-naphthoflavone (an inducer of CYP1A2)-treated rats. Real-time reverse transcription polymerase chain reaction and pharmacokinetic analysis of phenacetin and paracetamol were performed, in order to determine the changes of mRNA levels and activity of CYP1A2 in these two groups, respectively. Branched-chain amino acids phenylalanine and tyrosine were ultimately focalized, as they were detected in both the serum and liver with the same trends. These findings were further confirmed by absolute quantification via a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted metabolomics approach. Furthermore, the ratio of phenylalanine to tyrosine concentration was also found to be highly correlated with CYP1A2 activity and gene expression. This study demonstrates that metabolomics can be a potentially useful tool for biomarker discovery associated with CYPs. Our findings contribute to explaining interindividual variations in CYP1A2-mediated drug metabolism. PMID: 31003543 [PubMed]

Related Articles Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites. 2019 Apr 18;9(4): Authors: Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, Wishart D Abstract The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized. PMID: 31003499 [PubMed]

Related Articles A metabolomics-based approach for the discrimination of potato varieties (<i>Solanum tuberosum</i>) using UPLC-IMS-QToF. J Agric Food Chem. 2019 Apr 19;: Authors: Claassen C, Kuballa J, Rohn S Abstract One-hundred and eighty-two authentic potato samples (</i>Solanum tuberosum<i>) of known variety were collected from various German regions in 2016 and 2017. Samples were extracted with a liquid-liquid-extraction protocol including isopropanol, methanol, and water in order to focus on lipophilic metabolites. The analysis of nonpolar extracts was performed using an UPLC-IMS-QToF-MS system; data sets obtained were evaluated via multivariate data analysis. A selection of 14 key metabolites with a significant difference in their abundance profiles was identified. This set of markers contained four hydroxylated glucocerebrosides, two phosphoinositols, one phosphocholine, and seven acylated sterol glucosides based on stigmasterol and β-sitosterol, which primarily enable the varietal discrimination. Fragments and neutral losses commonly appearing within one class or subclass of lipids were summarized within a new database including ion mobility data. The performance of the approach was verified with twenty-nine commercial potato samples. PMID: 31002513 [PubMed - as supplied by publisher]

Related Articles Nitrogen utilization and metabolism in maize (Zea mays L.) plants under different rates of biochar addition and nitrogen input conditions. Plant Biol (Stuttg). 2019 Apr 19;: Authors: Sun C, Hao L, Wang D, Li C, Zhang C, Chen X, Fu J, Zhang Y Abstract Biochar (BC) application could improve plant nitrogen (N) utilization and potentially reduce N fertilizer requirements. However, the fate of N in crop-soil systems and the metabolic responses of crops under the condition of BC coapplied with reduced N are not well understood. The urea-15 N isotope and pot experiments with three BC rates (0%, 5% and 15%; w/w) combined with three N fertilizer levels (100%-N, 85%-N and 55%-N) were conducted for maize. The metabolome, 15 N abundance and gene expression in plants were analyzed using nuclear magnetic resonance, gas isotope mass and quantitative real-time reverse transcription-PCR, respectively. The results showed that the recovery of N by maize ranged from 27.4% to 23.6% and decreased as the N application rate decreased (from 100% to 55%) without BC addition, ranged from 24.6% to 29.4% when BC was added at a rate of 5% and increased as the N application rate decreased. BC addition had major effects on global metabolic profiles and metabolic networks at the metabolomics level as well as on the expression of related genes (zmGS1and zmAS1) and the contents of mineral N (NO3 - -N, NO2 - -N and NH4 + -N) in the maize seedlings; however, the interaction effects of the BC application rates and N fertilizer levels were evident (p ≤ 0.001). BC addition induced a decrease in the flux toward sugar hydrolysis and remained a homeostasis in the amino acid pool, which was perturbed by reduced N levels; then, the maize plants adapted to the reduced-N condition, and the N recovery efficiency was ultimately improved with reduced N loss. This article is protected by copyright. All rights reserved. PMID: 31002433 [PubMed - as supplied by publisher]