PubMed

Related Articles Considerations when choosing a genetic model organism for metabolomics studies. Curr Opin Chem Biol. 2016 Dec 22;36:7-14 Authors: Reed LK, Baer CF, Edison AS Abstract Model organisms are important in many areas of chemical biology. In metabolomics, model organisms can provide excellent samples for methods development as well as the foundation of comparative phylometabolomics, which will become possible as metabolomics applications expand. Comparative studies of conserved and unique metabolic pathways will help in the annotation of metabolites as well as provide important new targets of investigation in biology and biomedicine. However, most chemical biologists are not familiar with genetics, which needs to be considered when choosing a model organism. In this review we summarize the strengths and weaknesses of several genetic systems, including natural isolates, recombinant inbred lines, and genetic mutations. We also discuss methods to detect targets of selection on the metabolome. PMID: 28025166 [PubMed - as supplied by publisher]

Related Articles Searching molecular structure databases using tandem MS data: are we there yet? Curr Opin Chem Biol. 2016 Dec 22;36:1-6 Authors: Böcker S Abstract Untargeted metabolomics experiments usually rely on tandem mass spectrometry (MS/MS) to identify the thousands of compounds in a complex sample. Spectral libraries used for identification are incomplete, and many metabolites remain unknown. There has been a recent development to replace spectral libraries by molecular structure databases when searching the MS/MS data of the unknown compound. Several tools have been developed for this task, including CFM-ID, MetFrag, MAGMa(+), FingerID and CSI:FingerID. These methods are already helpful for everyday metabolomics; with further advances, these methods can become indispensable tools for tomorrow's metabolomics. Here, I discuss several questions related to this task, such as: Why not wait for spectral libraries to grow sufficiently? Why evaluate methods outside their 'comfort zone'? Should we use prior information such as citation frequencies? And, ultimately: are we there yet? PMID: 28025165 [PubMed - as supplied by publisher]

Related Articles Comparative systems toxicology analysis of cigarette smoke and aerosol from a candidate modified risk tobacco product in organotypic human gingival epithelial cultures: A 3-day repeated exposure study. Food Chem Toxicol. 2016 Dec 23;: Authors: Zanetti F, Titz B, Sewer A, Lo Sasso G, Scotti E, Schlage WK, Mathis C, Leroy P, Majeed S, Torres LO, Keppler BR, Ashraf E, Trivedi K, Guedj E, Martin F, Frentzel S, Ivanov NV, Peitsch MC, Hoeng J Abstract Smoking is one of the major lifestyle-related risk factors for periodontal diseases. Modified risk tobacco products (MRTP) offer a promising alternative in the harm reduction strategy for adult smokers unable to quit. Using a systems toxicology approach, we investigated and compared the exposure effects of a reference cigarette (3R4F) and a heat-not-burn technology-based candidate MRTP, the Tobacco Heating System (THS) 2.2. Human gingival epithelial organotypic cultures were repeatedly exposed (3 days) for 28 min at two matching concentrations of cigarette smoke (CS) or THS2.2 aerosol. Results showed only minor histopathological alterations and minimal cytotoxicity upon THS2.2 aerosol exposure compared to CS (1% for THS2.2 aerosol vs. 30% for CS, at the high concentration). Among the 14 proinflammatory mediators analyzed, only 5 exhibited significant alterations with THS2.2 exposure compared with 11 upon CS exposure. Transcriptomic and metabolomic analysis indicated a general reduction of the impact in THS2.2 aerosol-exposed samples with respect to CS (∼79% lower biological impact for the high THS2.2 aerosol concentration compared to CS, and 13 metabolites significantly perturbed for THS2.2 vs. 181 for CS). This study indicates that exposure to THS2.2 aerosol had a lower impact on the pathophysiology of human gingival organotypic cultures than CS. PMID: 28025120 [PubMed - as supplied by publisher]

Related Articles Digestomics: an emerging strategy for comprehensive analysis of protein catabolism. Curr Opin Biotechnol. 2016 Dec 22;43:134-140 Authors: Bingeman TS, Perlman DH, Storey DG, Lewis IA Abstract When cells mobilize nutrients from protein, they generate a fingerprint of peptide fragments that reflects the net action of proteases and the identities of the affected proteins. Analyzing these mixtures falls into a grey area between proteomics and metabolomics that is poorly served by existing technology. Herein, we describe an emerging digestomics strategy that bridges this gap and allows mixtures of proteolytic fragments to be quantitatively mapped with an amino acid level of resolution. We describe recent successes using this technique, including a case where digestomics provided the link between hemoglobin digestion by the malaria parasite and the world-wide distribution of chloroquine resistance. We highlight other areas of microbiology and cancer research that are well-suited to this emerging technology. PMID: 28025112 [PubMed - as supplied by publisher]

Related Articles Determination of water-soluble and fat-soluble vitamins in tears and blood serum of infants and parents by liquid chromatography/mass spectrometry. Exp Eye Res. 2016 Dec 23;: Authors: Khaksari M, Mazzoleni LR, Ruan C, Kennedy RT, Minerick AR Abstract Tears serve as a viable diagnostic fluid with advantages including less invasive sample to collect and less complex to prepare for analysis. Several water-soluble and fat-soluble vitamins were detected and quantified in human tears and compared with blood serum levels. Samples from 15 family pairs, each pair consisting of a four-month-old infant and one parent were analyzed; vitamin concentrations were compared between tears and blood serum for individual subjects, between infants and parents, and against self-reported dietary intakes. Water-soluble vitamins B1, B2, B3 (nicotinamide), B5, B9 and fat-soluble vitamin E (α-tocopherol) were routinely detected in tears and blood serum while fat-soluble vitamin A (retinol) was detected only in blood serum. Water-soluble vitamin concentrations measured in tears and blood serum of single subjects were comparable, while higher concentrations were measured in infants compared to their parents. Fat-soluble vitamin E concentrations were lower in tears than blood serum with no significant difference between infants and parents. Serum vitamin A concentrations were higher in parents than infants. Population trends were compiled and quantified using a cross correlation factor. Strong positive correlations were found between tear and blood serum concentrations of vitamin E from infants and parents and vitamin B3 concentrations from parents, while slight positive correlations were detected for infants B3 and parents B1 and B2 concentrations. Correlations between infants and parents were found for the concentrations of B1, B2, B3, and E in tears, and the concentrations of B2, A, and E in blood serum. Stronger vitamin concentration correlations were found between infants and parents for the breast-fed infants, while no significant difference was observed between breast-fed and bottle-fed infants. This work is the first to demonstrate simultaneous vitamin A, B, and E detection and to quantify correlations between vitamin concentrations in tears and blood serum. Our results suggest that tears are a viable biofluid to monitor nutritional health because they sufficiently mirror blood serum data and may enhance the speed of deficiency diagnoses. PMID: 28025000 [PubMed - as supplied by publisher]

Related Articles A Network-based Systems Biology Platform for Predicting Disease-Metabolite Links. Comb Chem High Throughput Screen. 2016 Dec 14; Authors: Wathieu H, Issa NT, Mohandoss M, Byers SW, Dakshanamurthy S Abstract Metabolites constitute phenotypic end products of gene expression, and are key players in biological networks. For this reason, the field of metabolomics has been useful in predicting, explaining, and affecting the mechanisms of disease phenotypes. MSD-MAP (Multi Scale Disease-Metabolite Association Platform) is a powerful computational tool for hypothesizing new links between diseases and metabolites, and characterizing the functional basis of those links in a systems biology context. Upon integrating both predicted and known metabolite-protein associations, MSD-MAP takes a two-pronged approach to associating metabolites to a disease, relying on network-based characterization of disease perturbation at multiple levels of biological activity as well as statistical matching of metabolite- and disease-associated biological profiles. MSD-MAP successfully recapitulated cross-disease links of cancer-associated metabolites, and predicted key metabolites associated with colorectal, esophageal, and prostate cancers after the integration of patient-based gene expression analysis. For example, the catecholamine dopamine was correctly predicted to be strongly associated with colorectal cancer based on statistical coincidence with its disease perturbation network. PMID: 28024464 [PubMed - as supplied by publisher]

Related Articles Exposure of CCRF-CEM cells to acridone derivative 8a triggers tumor death via multiple mechanisms. Proteomics. 2016 Apr;16(7):1177-90 Authors: Wang Y, Gao D, Chu B, Gao C, Cao D, Liu H, Jiang Y Abstract A newly synthesized acridone derivative 8a shows potent antitumor activity against CCRF-CEM leukemia cells. Herein, the first proteomic study of 8a effects in CCRF-CEM cells was performed by 2D nano-LC-ESI-MS/MS to better understand the mechanisms of action of 8a. Data analyses based on PLGS, STRING, Cytoscape, and database for annotation, visualization, and integrated discovery identified 55 proteins that were differentially expressed in response to 8a exposure. Multiple cellular pathways were affected, including chromatin organization, energy metabolism, DNA repair, oxidative-stress, and apoptosis. The changes in protein expression were further verified for PKM2. Moreover, 8a lowered down the expression of HEX and PFK-1. Lactate production was decreased in 8a-treated cells, indicating suppression of glycolysis. The elevated XRCC6 and decreased histone expression levels suggested increased DNA damage in 8a-treated cells, which was confirmed by the increased γ-H2AX foci. Molecular docking of 8a with DNA demonstrated direct interactions of 8a with DNA through three hydrogen bonds and four π-π interactions, potentially explaining the mode of action that 8a damaged to DNA. The differential protein profiling and dysfunction of metabolic pathways induced by 8a provide novel insights into the potential action mechanisms of 8a. PMID: 26867676 [PubMed - indexed for MEDLINE]

Related Articles NMR-based metabonomics for understanding the influence of dormant female genital tuberculosis on metabolism of the human endometrium. Hum Reprod. 2016 Apr;31(4):854-65 Authors: Subramani E, Jothiramajayam M, Dutta M, Chakravorty D, Joshi M, Srivastava S, Mukherjee A, Datta Ray C, Chakravarty BN, Chaudhury K Abstract STUDY QUESTION: Does investigation of metabolic perturbations in endometrial tissue of women with dormant genital tuberculosis (GTB) during the window of implantation (WOI) assist in improving the understanding of endometrial receptivity? SUMMARY ANSWER: In dormant GTB cases significant alterations in endometrial tissue metabolites occur, largely related to energy metabolism and amino acid biosynthesis in dormant GTB cases. WHAT IS KNOWN ALREADY: As an intracellular pathogen, Mycobacterium tuberculosis strongly influences the metabolism of host cells causing metabolic dysregulation. It is also accepted that dormant GTB impairs the receptive status of the endometrium. Global metabolic profiling is useful for an understanding of disease progression and distinguishing between diseased and non-diseased groups. STUDY DESIGN, SIZE, DURATION: Endometrial tissue samples were collected from patients reporting at the tertiary infertility care center during the period September 2011-March 2013. Women having tested positive for GTB were considered as the study group (n = 24). Normal healthy women undergoing sterilization (n = 26) and unexplained infertile women with repeated IVF failure (n = 21) volunteered to participate as controls. PARTICIPANTS/MATERIALS, SETTING, METHODS: Endometrial tissue samples were collected 6-10 days after confirmation of ovulation. PCR and BACTEC-460 culture were used for diagnosing GTB. Proton nuclear magnetic resonance (1H NMR) spectra of tissue were recorded using a 700 MHz Bruker Avance AV III spectrometer. Following phase and baseline correction of all NMR spectra by Bruker Topspin 2.1 software, spectral peak alignment of the data was performed. Multivariate analysis was applied to all spectra and individual metabolites identified and multiple correlation analysis was performed. MAIN RESULTS AND THE ROLE OF CHANCE: Leucine, isoleucine, acetate, lactate, glutamate, glutamine, methionine, lysine, creatine, glycogen, glycine, proline and choline were found to be significantly increased (P < 0.05) in endometrial tissue of women with dormant GTB compared with unexplained infertile women with repeated implantation failure. Valine, citrate, succinate and aspartate were also observed to be significantly up-regulated (P < 0.01). Furthermore, a significant decrease in glucose (P < 0.05), threonine (P < 0.05), tyrosine (P < 0.01) and phenylalanine (P < 0.0001) was observed in women with dormant GTB. Pearson's correlation analysis between the expression of various endometrial receptivity markers and metabolites showed a significant negative correlation (-0.236 to -0.545, P < 0.05). Also, the metabolites were positively correlated with endometrial receptivity markers (0.207 to 0.618, P < 0.05). LIMITATIONS, REASONS FOR CAUTION: It is often difficult to diagnose dormant GTB because it tends to exist without any clinical signs or symptoms. In addition, the diagnosis of GTB by culture remains a challenge due to low detection rates and its paucibacillary nature. Testing for prostate-specific antigen or the Y chromosome in order to account for the possible influences of recent exposure to semen on endometrial metabolism would be important. WIDER IMPLICATIONS OF THE FINDINGS: The metabolic changes associated with the dormant tubercle infection are of potential relevance to clinicians for the treatment of dormant GTB-related infertility. STUDY FUNDING/COMPETING INTERESTS: Government of India, Indian Council of Medical Research. There are no conflicts of interest. PMID: 26851602 [PubMed - indexed for MEDLINE]

17 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 2016/12/27PubMed comprises more than 24 million 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.

Calpain 1 cleaves and inactivates prostacyclin synthase in mesenteric arteries from diabetic mice. Basic Res Cardiol. 2017 Jan;112(1):10 Authors: Randriamboavonjy V, Kyselova A, Elgheznawy A, Zukunft S, Wittig I, Fleming I Abstract Diabetes is associated with a number of co-morbidities including an increased risk of developing cardiovascular diseases. The activation of Ca(2+)-activated proteases of the calpain family has been implicated in platelet activation associated with diabetes and this study aimed to determine the role of calpain activation in the development of endothelial dysfunction. Diabetes induction in mice attenuated acetylcholine-induced relaxation of mesenteric artery rings, an effect prevented in mice receiving a calpain inhibitor. A nitric oxide-independent but diclofenac-sensitive component of the relaxation-response was altered and correlated with a loss of prostacyclin (PGI2) generation and reduced vascular levels of PGI2 synthase. Calpain inhibition was also able to restore PGI2 synthase levels and PGI2 generation in arteries from diabetic animals. The effects of diabetes were reproduced in vitro by a combination of high glucose and palmitate, which elicited calpain activation, PGI2 synthase cleavage and inactivation as well as endothelial dysfunction in mesenteric arteries from wild-type mice. PGI2 cleavage was not observed in arteries from calpain 1(-/-) mice or mice overexpressing the endogenous calpain inhibitor calpastatin. Finally, proteomic analyses revealed that calpain 1 cleaved the C-terminal domain of PGI2 synthase close to the catalytic site of the enzyme. These data demonstrate that diabetes leads to the activation of calpain 1 in mesenteric arteries and can initiate endothelial dysfunction by cleaving and inactivating the PGI2 synthase. Given that calpain inhibition prevented diabetes-induced endothelial dysfunction in mesenteric arteries, calpains represent an interesting therapeutic target for the prevention of cardiovascular complication of diabetes. PMID: 28013348 [PubMed - in process]

Metabolomics study of Populus type propolis. J Pharm Biomed Anal. 2016 Dec 15;: Authors: Anđelković B, Vujisić L, Vučković I, Tešević V, Vajs V, Gođevac D Abstract Herein, we propose rapid and simple spectroscopic methods to determine the chemical composition of propolis derived from various Populus species using a metabolomics approach. In order to correlate variability in Populus type propolis composition with the altitude of its collection, NMR, IR, and UV spectroscopy followed by OPLS was conducted. The botanical origin of propolis was established by comparing propolis spectral data to those of buds of various Populus species. An O2PLS method was utilized to integrate two blocks of data. According to OPLS and O2PLS, the major compounds in propolis samples, collected from temperate continental climate above 500m, were phenolic glycerides originating from P. tremula buds. Flavonoids were predominant in propolis samples collected below 400m, originating from P. nigra and P. x euramericana buds. Samples collected at 400-500m were of mixed origin, with variable amounts of all detected metabolites. PMID: 28012592 [PubMed - as supplied by publisher]

The LC-MS-based metabolomics of hydroxytyrosol administration in rats reveals amelioration of the metabolic syndrome. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Dec 15;1041-1042:45-59 Authors: Lemonakis N, Poudyal H, Halabalaki M, Brown L, Tsarbopoulos A, Skaltsounis AL, Gikas E Abstract Hydroxytyrosol (HT), an important component of olive fruit and olive oil, improves the signs of metabolic syndrome in rats following chronic treatment. At a dose of 20mg/kg/day, HT decreased adiposity and improved cardiovascular and liver structure and function in rats fed with a high-carbohydrate, high-fat diet. An untargeted metabolomics approach has been employed using both UPLC-Orbitrap and -QqTOF methods to identify the changes induced by chronic HT administration on the plasma metabolome. 31 metabolites have been found to be differentially expressed between the examined groups. HT was shown to decrease biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, and the metabolism of linoleic acid, retinol, sphingolipids and arachidonic acid, whereas glycerolipid metabolism is up-regulated. These are plausible mechanisms for the attenuation by HT of cardiovascular, liver and metabolic changes in high-carbohydrate, high-fat diet fed rats. PMID: 28012379 [PubMed - as supplied by publisher]

Related Articles A hepatic metabolomics-based diagnostic approach to assess lethal toxicity of dithiocarbamate fungicide polycarbamate in three marine fish species. Ecotoxicol Environ Saf. 2016 Dec 20;138:64-70 Authors: Hano T, Ohkubo N, Mochida K Abstract The present study was performed to evaluate the toxic effect of the dithiocarbamate fungicide polycarbamate (PC) on the hepatic metabolic profiles of three marine fish species, red sea bream (Pagrus major), spotted halibut (Verasper variegatus), and marbled flounder (Pleuronectes yokohamae). First, juvenile fish were exposed to graded concentrations of PC for 96h; the 96-h LC50 values obtained were 22-29, 239-553, and 301-364µgL(-1) for red sea bream, spotted halibut, and marbled flounder, respectively, indicating that red sea bream possessed higher sensitivity to PC than the two benthic species. Second, the fish were exposed to lethal-equivalent concentration (H group) or sub-lethal (one-tenth of the H group concentrations; L group) for 24 and 96h and gas-chromatography based metabolomics approach was employed to explore the crucial biomarker metabolite associated with lethal toxicity. Of the 53 metabolites identified, only reduced glutathione (GSH) was consistently elevated in the H group for the three fish species at 96h. The calculated cut-off value of GSH (mM) based on receiver operating curve analysis between H group and the other treatment groups (control, solvent control, and L group) was obtained at 0.56mM, which allowed to distinguish between the groups with high confidence for the three fish species. These results are the first to demonstrate the potential of using GSH as a possible biomarker metabolite and its usefulness of threshold cut-off value for diagnosing life-threatening health conditions of fish. PMID: 28011422 [PubMed - as supplied by publisher]

Related Articles Association of atopic dermatitis with cardiovascular risk factors and diseases. J Invest Dermatol. 2016 Dec 20;: Authors: Standl M, Tesch F, Baurecht H, Rodríguez E, Müller-Nurasyid M, Gieger C, Peters A, Wang-Sattler R, Prehn C, Adamski J, Kronenberg F, Schulz H, Koletzko S, Schikowski T, von Berg A, Lehmann I, Berdel D, Heinrich J, Schmitt J, Weidinger S Abstract Epidemiological studies suggested an association between atopic dermatitis (AD) and cardiovascular disease (CVD). Therefore, we investigate associations and potential underlying pathways of AD and CVD in large cohort studies: the AOK PLUS cohort (n=1.2Mio), the GINIplus/LISAplus birth cohorts (n=2286), and the KORA F4 cohort (n=2990). Additionally, metabolomics in KORA F4 and established cardiovascular risk loci in genome-wide data on 10,788 AD cases and 30,047 controls were analyzed. Longitudinal analysis of AD patients in AOK PLUS showed slightly increased risk for incident angina pectoris (AP) (adjusted risk ratio 1.17; 95%-confidence interval 1.12-1.23), hypertension (1.04 (1.02-1.06)) and peripheral arterial disease (PAD) (1.15 (1.11-1.19)) but not for myocardial infarction (MI) (1.05 (0.99-1.12) and stroke (1.02 (0.98-1.07)). In KORA F4 and GINIplus/LISAplus, AD was not associated with cardiovascular risk factors (CVRFs) and no differences in metabolite levels were detected. There was no robust evidence for shared genetic risk variants of AD and CVD. This study indicates only a marginally increased risk for AP, hypertension and PAD and no increased risk for MI or stroke in AD patients. Relevant associations of AD with CVRFs reported in US-populations could not be confirmed. Likewise, AD patients did not have increased genetic risk factors for CVD. PMID: 28011146 [PubMed - as supplied by publisher]

Related Articles An in-source multiple collision-neutral loss filtering based nontargeted metabolomics approach for the comprehensive analysis of malonyl-ginsenosides from Panax ginseng, P. quinquefolius, and P. notoginseng. Anal Chim Acta. 2017 Feb 01;952:59-70 Authors: Shi XJ, Yang WZ, Qiu S, Yao CL, Shen Y, Pan HQ, Bi QR, Yang M, Wu WY, Guo DA Abstract The simultaneous identification and quantification of target metabolites from herbal medicines are difficult to implement by the full-scan MS based nontargeted metabolomics approaches. Here an in-source multiple collision-neutral loss filtering (IMC-NLF) based nontargeted metabolomics approach is developed and applied to identify and quantify the variations of malonyl-ginsenosides, a common group of acyl saponins with potential anti-diabetic activity, among Panax ginseng, P. quinquefolius, and P. notoginseng. The key steps of the IMC-NLF strategy are the acquisition of specific high-resolution neutral loss data and the efficient filtering of target precursor ions from the full-scan spectra. Using a hybrid LTQ-Orbitrap mass spectrometer after UHPLC separation, abundant in-source product ions, [M-H-CO2](-) (due to the vulnerability of the carboxyl group) and [M-H-Mal.](-), were generated at the energies of 70 V and 90 V, respectively. After spectral deconvolution, the generated peak list was screened by dual NLF using a Neutral Loss MS Finder software (NL of 43.9898 Da for CO2 and 86.0004 Da for the malonyl substituent). By combining the precursor ions list-triggered HCD-MS/MS and basic hydrolysis, a total of 101 malonyl-ginsenosides (including 69 from P. ginseng, 52 from P. quinquefolius, and 44 from P. notoginseng) were identified or tentatively characterized. The variations of 81 characterized malonyl-ginsenosides among 45 batches of Ginseng samples were statistically analyzed disclosing ten potential markers. It is the first systematic analysis of malonyl-ginsenosides. The IMC-NLF approach by a single analytical platform is promising in targeted analyses of modification-specific metabolites in metabolomics and drug metabolism. PMID: 28010843 [PubMed - in process]

Related Articles Integrated work-flow for quantitative metabolome profiling of plants, Peucedani Radix as a case. Anal Chim Acta. 2017 Feb 08;953:40-47 Authors: Song Y, Song Q, Liu Y, Li J, Wan JB, Wang Y, Jiang Y, Tu P Abstract Universal acquisition of reliable information regarding the qualitative and quantitative properties of complicated matrices is the premise for the success of metabolomics study. Liquid chromatography-mass spectrometry (LC-MS) is now serving as a workhorse for metabolomics; however, LC-MS-based non-targeted metabolomics is suffering from some shortcomings, even some cutting-edge techniques have been introduced. Aiming to tackle, to some extent, the drawbacks of the conventional approaches, such as redundant information, detector saturation, low sensitivity, and inconstant signal number among different runs, herein, a novel and flexible work-flow consisting of three progressive steps was proposed to profile in depth the quantitative metabolome of plants. The roots of Peucedanum praeruptorum Dunn (Peucedani Radix, PR) that are rich in various coumarin isomers, were employed as a case study to verify the applicability. First, offline two dimensional LC-MS was utilized for in-depth detection of metabolites in a pooled PR extract namely universal metabolome standard (UMS). Second, mass fragmentation rules, notably concerning angular-type pyranocoumarins that are the primary chemical homologues in PR, and available databases were integrated for signal assignment and structural annotation. Third, optimum collision energy (OCE) as well as ion transition for multiple monitoring reaction measurement was online optimized with a reference compound-free strategy for each annotated component and large-scale relative quantification of all annotated components was accomplished by plotting calibration curves via serially diluting UMS. It is worthwhile to highlight that the potential of OCE for isomer discrimination was described and the linearity ranges of those primary ingredients were extended by suppressing their responses. The integrated workflow is expected to be qualified as a promising pipeline to clarify the quantitative metabolome of plants because it could not only holistically provide qualitative information, but also straightforwardly generate accurate quantitative dataset. PMID: 28010741 [PubMed - in process]

Related Articles An efficient data filtering strategy for easy metabolite detection from the direct analysis of a biological fluid using Fourier transform mass spectrometry. Rapid Commun Mass Spectrom. 2016 Dec 23;: Authors: Rathahao-Paris E, Alves S, Debrauwer L, Cravedi JP, Paris A Abstract RATIONALE: High throughput analyses require an overall analytical workflow including robust and high speed technical platform but also dedicated data processing tools able to extract the relevant information. This work aimed at evaluating post-acquisition data mining tools for selective extraction of metabolite species from direct introduction high resolution mass spectrometry data. METHODS: Investigations were performed on spectral data in which seven metabolites of vinclozolin, a dicarboximide fungicide containing two chloride atoms, were previously manually identified. The spectral data obtained from direct introduction (DI) and high resolution mass spectrometry (HRMS) detection were post-processed by plotting the mass defect profiles and applying various data filtering methods based on accurate mass values. RESULTS: Exploration of mass defect profiles highlighted, in a specific plotting region the presence of compounds containing common chemical elements and pairs of conjugated and non-conjugated metabolites resulting from classical metabolic pathways. Additionally, the judicious application of mass defect and/or isotope pattern filters removed many interfering ions from DI-HRMS data, greatly facilitating the detection of vinclozolin metabolites. Compared to previous results obtained by manual data treatment, three additional metabolites of vinclozolin were detected and putatively annotated. CONCLUSIONS: Tracking simultaneously several specific species could be efficiently performed using data mining tools based on accurate mass values. The selectivity of the data extraction was improved when the isotope filter was used for halogenated compounds, facilitating metabolite ion detection even for low abundance species. This article is protected by copyright. All rights reserved. PMID: 28010043 [PubMed - as supplied by publisher]

Related Articles Mass spectrometry-driven drug discovery for development of herbal medicine. Mass Spectrom Rev. 2016 Dec 23;: Authors: Zhang A, Sun H, Wang X Abstract Herbal medicine (HM) has made a major contribution to the drug discovery process with regard to identifying products compounds. Currently, more attention has been focused on drug discovery from natural compounds of HM. Despite the rapid advancement of modern analytical techniques, drug discovery is still a difficult and lengthy process. Fortunately, mass spectrometry (MS) can provide us with useful structural information for drug discovery, has been recognized as a sensitive, rapid, and high-throughput technology for advancing drug discovery from HM in the post-genomic era. It is essential to develop an efficient, high-quality, high-throughput screening method integrated with an MS platform for early screening of candidate drug molecules from natural products. We have developed a new chinmedomics strategy reliant on MS that is capable of capturing the candidate molecules, facilitating their identification of novel chemical structures in the early phase; chinmedomics-guided natural product discovery based on MS may provide an effective tool that addresses challenges in early screening of effective constituents of herbs against disease. This critical review covers the use of MS with related techniques and methodologies for natural product discovery, biomarker identification, and determination of mechanisms of action. It also highlights high-throughput chinmedomics screening methods suitable for lead compound discovery illustrated by recent successes. PMID: 28009933 [PubMed - as supplied by publisher]

Related Articles Metabolomics with Nuclear Magnetic Resonance Spectroscopy in a Drosophila melanogaster Model of Surviving Sepsis. Metabolites. 2016 Dec 21;6(4): Authors: Bakalov V, Amathieu R, Triba MN, Clément MJ, Reyes Uribe L, Le Moyec L, Kaynar AM Abstract Patients surviving sepsis demonstrate sustained inflammation, which has been associated with long-term complications. One of the main mechanisms behind sustained inflammation is a metabolic switch in parenchymal and immune cells, thus understanding metabolic alterations after sepsis may provide important insights to the pathophysiology of sepsis recovery. In this study, we explored metabolomics in a novel Drosophila melanogaster model of surviving sepsis using Nuclear Magnetic Resonance (NMR), to determine metabolite profiles. We used a model of percutaneous infection in Drosophila melanogaster to mimic sepsis. We had three experimental groups: sepsis survivors (infected with Staphylococcus aureus and treated with oral linezolid), sham (pricked with an aseptic needle), and unmanipulated (positive control). We performed metabolic measurements seven days after sepsis. We then implemented metabolites detected in NMR spectra into the MetExplore web server in order to identify the metabolic pathway alterations in sepsis surviving Drosophila. Our NMR metabolomic approach in a Drosophila model of recovery from sepsis clearly distinguished between all three groups and showed two different metabolomic signatures of inflammation. Sham flies had decreased levels of maltose, alanine, and glutamine, while their level of choline was increased. Sepsis survivors had a metabolic signature characterized by decreased glucose, maltose, tyrosine, beta-alanine, acetate, glutamine, and succinate. PMID: 28009836 [PubMed]

Related Articles Metabolic profiles revealed synergistically antidepressant effects of Lilies and Rhizoma Anemarrhenae in a rat model of depression. Biomed Chromatogr. 2016 Dec 23;: Authors: Du H, Zhao H, Lai X, Lin Q, Zhu Z, Chai Y, Lou Z Abstract Depression is the predominant cause of illness and disability. We applied untargeted metabolomics using mass spectrometry to identify metabolic signatures associated with depression in serum and explored the antidepressant effects of Lilies and Rhizoma Anemarrhenae on an experimental model of chronic unpredictable mild stress (CUMS). Meanwhile metabolomics based on UHPLC-Q-TOF-MS, was used to study the change in metabolites in CUMS rat serum and to evaluate the effects of Anemarrhena Rhizoma, Lilies (alone and in combination). Partial least squares-discriminant analysis identified thirty metabolites as decisive marker compounds that discriminated the CUMS rats and the control rats. The majority of these metabolites were involved in amino acid metabolism, the tricarboxylic acid cycle, and phosphoglyceride metabolism. The reliability of the metabolites were evaluated by the administration of Lilies, Rhizoma Anemarrhenas, Fluoxetine, and the combination of Lilies and Rhizoma Anemarrhenas, to the CUMS rats. Behavior studies demonstrated that treatment with the combination of Lilies and Rhizoma Anemarrhenas resulted in optimal antidepressant effects. The combination treatment was almost as effective as Fluoxetine. Our results suggest that Lilies and Rhizoma Anemarrhenae demonstrate synergistically antidepressant effects in CUMS via the regulation of multiple metabolic pathways. These findings provide insight into the pathophysiological mechanisms underlying CUMS and suggest innovative and effective treatments for this disorder. PMID: 28009452 [PubMed - as supplied by publisher]