PubMed

Evidence for the involvement of lipid rafts localized at the ER-mitochondria associated membranes in autophagosome formation. Autophagy. 2016 Apr 28;:1-19 Authors: Garofalo T, Matarrese P, Manganelli V, Marconi M, Tinari A, Gambardella L, Faggioni A, Misasi R, Sorice M, Malorni W Abstract Mitochondria-associated membranes (MAMs) are subdomains of the endoplasmic reticulum (ER) that interact with mitochondria. This membrane scrambling between ER and mitochondria appears to play a critical role in the earliest steps of autophagy. Recently, lipid microdomains, i.e. lipid rafts, have been identified as further actors of the autophagic process. In the present work, a series of biochemical and molecular analyses has been carried out in human fibroblasts with the specific aim of characterizing lipid rafts in MAMs and to decipher their possible implication in the autophagosome formation. In fact, the presence of lipid microdomains in MAMs has been detected and, in these structures, a molecular interaction of the ganglioside GD3, a paradigmatic "brick" of lipid rafts, with core-initiator proteins of autophagy, such as AMBRA1 and WIPI1, was revealed. This association seems thus to take place in the early phases of autophagic process in which MAMs have been hypothesized to play a key role. The functional activity of GD3 was suggested by the experiments carried out by knocking down ST8SIA1 gene expression, i.e., the synthase that leads to the ganglioside formation. This experimental condition results in fact in the impairment of the ER-mitochondria crosstalk and the subsequent hindering of autophagosome nucleation. We thus hypothesize that MAM raft-like microdomains could be pivotal in the initial organelle scrambling activity that finally leads to the formation of autophagosome. PMID: 27123544 [PubMed - as supplied by publisher]

Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling. Metabolomics. 2016;12:93 Authors: Di Guida R, Engel J, Allwood JW, Weber RJ, Jones MR, Sommer U, Viant MR, Dunn WB Abstract INTRODUCTION: The generic metabolomics data processing workflow is constructed with a serial set of processes including peak picking, quality assurance, normalisation, missing value imputation, transformation and scaling. The combination of these processes should present the experimental data in an appropriate structure so to identify the biological changes in a valid and robust manner. OBJECTIVES: Currently, different researchers apply different data processing methods and no assessment of the permutations applied to UHPLC-MS datasets has been published. Here we wish to define the most appropriate data processing workflow. METHODS: We assess the influence of normalisation, missing value imputation, transformation and scaling methods on univariate and multivariate analysis of UHPLC-MS datasets acquired for different mammalian samples. RESULTS: Our studies have shown that once data are filtered, missing values are not correlated with m/z, retention time or response. Following an exhaustive evaluation, we recommend PQN normalisation with no missing value imputation and no transformation or scaling for univariate analysis. For PCA we recommend applying PQN normalisation with Random Forest missing value imputation, glog transformation and no scaling method. For PLS-DA we recommend PQN normalisation, KNN as the missing value imputation method, generalised logarithm transformation and no scaling. These recommendations are based on searching for the biologically important metabolite features independent of their measured abundance. CONCLUSION: The appropriate choice of normalisation, missing value imputation, transformation and scaling methods differs depending on the data analysis method and the choice of method is essential to maximise the biological derivations from UHPLC-MS datasets. PMID: 27123000 [PubMed - as supplied by publisher]

Scientific workflows for bibliometrics. Scientometrics. 2016;107:385-398 Authors: Guler AT, Waaijer CJ, Palmblad M Abstract Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics. PMID: 27122644 [PubMed - as supplied by publisher]

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proc Biol Sci. 2016 Apr 27;283(1829) Authors: Quinn RA, Vermeij MJ, Hartmann AC, Galtier d'Auriac I, Benler S, Haas A, Quistad SD, Lim YW, Little M, Sandin S, Smith JE, Dorrestein PC, Rohwer F Abstract Holobionts are assemblages of microbial symbionts and their macrobial host. As extant representatives of some of the oldest macro-organisms, corals and algae are important for understanding how holobionts develop and interact with one another. Using untargeted metabolomics, we show that non-self interactions altered the coral metabolome more than self-interactions (i.e. different or same genus, respectively). Platelet activating factor (PAF) and Lyso-PAF, central inflammatory modulators in mammals, were major lipid components of the coral holobionts. When corals were damaged during competitive interactions with algae, PAF increased along with expression of the gene encoding Lyso-PAF acetyltransferase; the protein responsible for converting Lyso-PAF to PAF. This shows that self and non-self recognition among some of the oldest extant holobionts involve bioactive lipids identical to those in highly derived taxa like humans. This further strengthens the hypothesis that major players of the immune response evolved during the pre-Cambrian. PMID: 27122568 [PubMed - in process]

Metabolomic patterns associated to QTc interval in shiftworkers: an explorative analysis. Biomarkers. 2016 Apr 28;:1-7 Authors: Campagna M, Locci E, Piras R, Noto A, Lecca LI, Pilia I, Cocco P, d'Aloja E, Scano P Abstract OBJECTIVES: (1)H NMR-metabolomic approach was used to investigate QTc interval correlation with plasma metabolic profiles in shiftworkers. METHODS: Socio-demographic data, electrocardiographic QTc interval and plasma metabolic profiles from 32 male shiftworkers, were correlated by multivariate regression analysis. RESULTS: We found a positive correlation between QTc interval values, body mass index, glycemia and lactate level and a negative correlation between QTc interval and both pyroglutamate and 3-hydroxybutyrate plasma level. CONCLUSIONS: Our analysis provides evidence of the association between clinical, metabolic profiles and QTc interval values. This could be used to identify markers of early effects and/or susceptibility in shiftworkers. PMID: 27121294 [PubMed - as supplied by publisher]

Related Articles Metabolomic Analysis of Blood Plasma after Oral Administration of N-acetyl-d-Glucosamine in Dogs. Mar Drugs. 2015 Aug;13(8):5007-15 Authors: Osaki T, Kurozumi S, Sato K, Terashi T, Azuma K, Murahata Y, Tsuka T, Ito N, Imagawa T, Minami S, Okamoto Y Abstract N-acetyl-d-glucosamine (GlcNAc) is a monosaccharide that polymerizes linearly through (1,4)-β-linkages. GlcNAc is the monomeric unit of the polymer chitin. GlcNAc is a basic component of hyaluronic acid and keratin sulfate found on the cell surface. The aim of this study was to examine amino acid metabolism after oral GlcNAc administration in dogs. Results showed that plasma levels of ectoine were significantly higher after oral administration of GlcNAc than prior to administration (p < 0.001). To our knowledge, there have been no reports of increased ectoine concentrations in the plasma. The mechanism by which GlcNAc administration leads to increased ectoine plasma concentration remains unclear; future studies are required to clarify this mechanism. PMID: 26262626 [PubMed - indexed for MEDLINE]

Related Articles Stable isotope labeling strategy for curcumin metabolite study in human liver microsomes by liquid chromatography-tandem mass spectrometry. J Am Soc Mass Spectrom. 2015 Apr;26(4):686-94 Authors: Gao D, Chen X, Yang X, Wu Q, Jin F, Wen H, Jiang Y, Liu H Abstract The identification of drug metabolites is very important in drug development. Nowadays, the most widely used methods are isotopes and mass spectrometry. However, the commercial isotopic labeled reagents are usually very expensive, and the rapid and convenient identification of metabolites is still difficult. In this paper, an (18)O isotope labeling strategy was developed and the isotopes were used as a tool to identify drug metabolites using mass spectrometry. Curcumin was selected as a model drug to evaluate the established method, and the (18)O labeled curcumin was successfully synthesized. The non-labeled and (18)O labeled curcumin were simultaneously metabolized in human liver microsomes (HLMs) and analyzed by liquid chromatography/mass spectrometry (LC-MS). The two groups of chromatograms obtained from metabolic reaction mixture with and without cofactors were compared and analyzed using Metabolynx software (Waters Corp., Milford, MA, USA). The mass spectra of the newly appearing chromatographic peaks in the experimental sample were further analyzed to find the metabolite candidates. Their chemical structures were confirmed by tandem mass spectrometry. Three metabolites, including two reduction products and a glucuronide conjugate, were successfully detected under their specific HLMs metabolic conditions, which were in accordance with the literature reported results. The results demonstrated that the developed isotope labeling method, together with post-acquisition data processing using Metabolynx software, could be used for fast identification of new drug metabolites. PMID: 25592681 [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 2016/04/28PubMed 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.

20 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 2016/04/27PubMed 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.

Targeted metabolomics of Gammarus pulex following controlled exposures to selected pharmaceuticals in water. Sci Total Environ. 2016 Apr 22;562:777-788 Authors: Gómez-Canela C, Miller TH, Bury NR, Tauler R, Barron LP Abstract The effects of pharmaceuticals and personal care products (PPCPs) on aquatic organisms represent a significant current concern. Herein, a targeted metabolomics approach using liquid chromatography-high resolution mass spectrometry (LC-HRMS) is presented to characterise concentration changes in 29 selected metabolites following exposures of aquatic invertebrates, Gammarus pulex, to pharmaceuticals. Method performance revealed excellent linearity (R(2)>0.99), precision (0.1-19%) and lower instrumental limits of detection (0.002-0.20ng) for all metabolites studied. Three pharmaceuticals were selected representing the low, middle and high range of measured acute measured toxicities (of a total of 26 compounds). Gammarids were exposed to both the no-observed-adverse-effect-level (NOAEL) and the lowest-observed-adverse-effect-level (LOAEL) of triclosan (0.1 and 0.3mgL(-1)), nimesulide (0.5 and 1.4mgL(-1)) and propranolol (100 and 153mgL(-1)) over 24h. Quantitative metabolite profiling was then performed. Significant changes in metabolite concentrations relative to controls are presented and display distinct clustered trends for each pharmaceutical. Approximately 37% (triclosan), 33% (nimesulide) and 46% (propranolol) of metabolites showed statistically significant time-related effects. Observed changes are also discussed with respect to internal concentrations of the three pharmaceuticals measured using a method based on pulverised liquid extraction, solid phase extraction and LC-MS/MS. Potential metabolic pathways that may be affected by such exposures are also discussed. This represents the first study focussing on quantitative, targeted metabolomics of this lower trophic level benthic invertebrate that may elucidate biomarkers for future risk assessment. PMID: 27110989 [PubMed - as supplied by publisher]

Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis. Cancer Metab. 2016;4:10 Authors: Weindl D, Cordes T, Battello N, Sapcariu SC, Dong X, Wegner A, Hiller K Abstract BACKGROUND: Metabolism gained increasing interest for the understanding of diseases and to pinpoint therapeutic intervention points. However, classical metabolomics techniques only provide a very static view on metabolism. Metabolic flux analysis methods, on the other hand, are highly targeted and require detailed knowledge on metabolism beforehand. RESULTS: We present a novel workflow to analyze non-targeted metabolome-wide stable isotope labeling data to detect metabolic flux changes in a non-targeted manner. Furthermore, we show how similarity-analysis of isotopic enrichment patterns can be used for pathway contextualization of unidentified compounds. We illustrate our approach with the analysis of changes in cellular metabolism of human adenocarcinoma cells in response to decreased oxygen availability. Starting without a priori knowledge, we detect metabolic flux changes, leading to an increased glutamine contribution to acetyl-CoA production, reveal biosynthesis of N-acetylaspartate by N-acetyltransferase 8-like (NAT8L) in lung cancer cells and show that NAT8L silencing inhibits proliferation of A549, JHH-4, PH5CH8, and BEAS-2B cells. CONCLUSIONS: Differential stable isotope labeling analysis provides qualitative metabolic flux information in a non-targeted manner. Furthermore, similarity analysis of enrichment patterns provides information on metabolically closely related compounds. N-acetylaspartate and NAT8L are important players in cancer cell metabolism, a context in which they have not received much attention yet. PMID: 27110360 [PubMed]

Modulation of the balance of fatty acid production and secretion is crucial for enhancement of growth and productivity of the engineered mutant of the cyanobacterium Synechococcus elongatus. Biotechnol Biofuels. 2016;9:91 Authors: Kato A, Use K, Takatani N, Ikeda K, Matsuura M, Kojima K, Aichi M, Maeda S, Omata T Abstract BACKGROUND: Among the three model cyanobacterial species that have been used for engineering a system for photosynthetic production of free fatty acids (FFAs), Synechococcus elongatus PCC7942 has been the least successful; the FFA-excreting mutants constructed from this strain could attain lower rates of FFA excretion and lower final FFA concentrations than the mutants constructed from Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002. It has been suggested that S. elongatus PCC7942 cells suffer from toxicity of FFA, but the cause of the low productivity has remained to be determined. RESULTS: By modulating the expression level of the acyl-acyl carrier protein thioesterase and raising the light intensity during cultivation, FFA secretion rates comparable to those obtained with the other cyanobacterial species were attained with an engineered Synechococcus elongatus mutant (dAS1T). The final FFA concentration in the external medium was also higher than previously reported for other S. elongatus mutants. However, about 85 % of the total FFA in the culture was found to remain in the cells, causing severe photoinhibition. Targeted inactivation of the wzt gene in dAS1T, which gene manipulation was previously shown to result in loss of the hydrophilic O-antigen layer on the cell surface, increased FFA secretion, alleviated photoinhibition, and lead to 50 and 45 % increase in the final cell density and the total amount of FFA in the culture (i.e., the sum of the cellular and extracellular FFA), respectively. The average rate of production of total FFA by the culture of the ∆wzt strain was 2.7 mg L(-1) h(-1), being five times higher than those reported for Synechocystis sp. PCC 6803 and comparable to the rates of triacylglycerol production in green algae. CONCLUSION: Synechococcus elongatus PCC7942 has larger capacity of FFA production than Synechocystis sp. PCC6803 but accumulates most of the product in the cell because of the imbalance of the rates of FFA production and secretion. This causes severe photoinhibition and exerts adverse effects on cell growth and FFA productivity. Enhancement of FFA secretion would be required to fully exploiting the capacity of FFA production for the purpose of biofuel production. PMID: 27110287 [PubMed]

Annotation of the human cerebrospinal fluid lipidome using high resolution mass spectrometry and a dedicated data processing workflow. Metabolomics. 2016;12:91 Authors: Seyer A, Boudah S, Broudin S, Junot C, Colsch B Abstract INTRODUCTION: Due to its proximity with the brain, cerebrospinal fluid (CSF) could be a medium of choice for the discovery of biomarkers of neurological and psychiatric diseases using untargeted analytical approaches. OBJECTIVES: This study explored the CSF lipidome in order to generate a robust mass spectral database using an untargeted lipidomic approach. METHODS: Cerebrospinal fluid samples from 45 individuals were analyzed by liquid chromatography coupled to high-resolution mass spectrometry method (LC-HRMS). A dedicated data processing workflow was implemented using XCMS software and adapted filters to select reliable features. In addition, an automatic annotation using an in silico lipid database and several MS/MS experiments were performed to identify CSF lipid species. RESULTS: Using this complete workflow, 771 analytically relevant monoisotopic lipid species corresponding to 550 unique lipids which represent five major lipid families (i.e., free fatty acids, sphingolipids, glycerophospholipids, glycerolipids, and sterol lipids) were detected and annotated. In addition, MS/MS experiments enabled to improve the annotation of 304 lipid species. Thanks to LC-HRMS, it was possible to discriminate between isobaric and also isomeric lipid species; and interestingly, our study showed that isobaric ions represent about 50 % of the total annotated lipid species in the human CSF. CONCLUSION: This work provides an extensive LC/HRMS database of the human CSF lipidome which constitutes a relevant foundation for future studies aimed at finding biomarkers of neurological disorders. PMID: 27110228 [PubMed - as supplied by publisher]

Peptidylation for the determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Analyst. 2016 Apr 25; Authors: Tang F, Cen SY, He H, Liu Y, Yuan BF, Feng YQ Abstract Determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been a great challenge in the analytical research field. Here we developed a universal peptide-based derivatization (peptidylation) strategy for the sensitive analysis of low-molecular-weight compounds by MALDI-TOF-MS. Upon peptidylation, the molecular weights of target analytes increase, thus avoiding serious matrix ion interference in the low-molecular-weight region in MALDI-TOF-MS. Since peptides typically exhibit good signal response during MALDI-TOF-MS analysis, peptidylation endows high detection sensitivities of low-molecular-weight analytes. As a proof-of-concept, we analyzed low-molecular-weight compounds of aldehydes and thiols by the developed peptidylation strategy. Our results showed that aldehydes and thiols can be readily determined upon peptidylation, thus realizing the sensitive and efficient determination of low-molecular-weight compounds by MALDI-TOF-MS. Moreover, target analytes also can be unambiguously detected in biological samples using the peptidylation strategy. The established peptidylation strategy is a universal strategy and can be extended to the sensitive analysis of various low-molecular-weight compounds by MALDI-TOF-MS, which may be potentially used in areas such as metabolomics. PMID: 27109889 [PubMed - as supplied by publisher]

Foodborne pathogens and their toxins. J Proteomics. 2016 Apr 21; Authors: Martinović T, Andjelković U, Gajdošik MŠ, Rešetar D, Josić D Abstract Foodborne pathogens, mostly bacteria and fungi, but also some viruses, prions and protozoa, contaminate food during production and processing, but also during storage and transport before consuming. During their growth these microorganisms can secrete different components, including toxins, into the extracellular environment. Other harmful substances can be also liberated and can contaminate food after disintegration of food pathogens. Some bacterial and fungal toxins can be resistant to inactivation, and can survive harsh treatment during food processing. Many of these molecules are involved in cellular processes and can indicate different mechanisms of pathogenesis of foodborne organisms. More knowledge about food contaminants can also help understand their inactivation. In the present review the use of proteomics, peptidomics and metabolomics, in addition to other foodomic methods for the detection of foodborne pathogenic fungi and bacteria, is overviewed. Furthermore, it is discussed how these techniques can be used for discovering biomarkers for pathogenicity of foodborne pathogens, determining the mechanisms by which they act, and studying their resistance upon inactivation in food of animal and plant origin. BIOLOGICAL SIGNIFICANCE: Comprehensive and comparative view into the genome and proteome of foodborne pathogens of bacterial or fungal origin and foodomic, mostly proteomic, peptidomic and metabolomic investigation of their toxin production and their mechanism of action is necessary in order to get further information about their virulence, pathogenicity and survival under stress conditions. Furthermore, these data pave the way for identification of biomarkers to trace sources of contamination with food-borne microorganisms and their endo- and exotoxins in order to ensure food safety and prevent the outbreak of food-borne diseases. Therefore, detection of pathogens and their toxins during production, transport and before consume of food produce, as well as protection against food spoilage is a task of great social, economic and public health importance. PMID: 27109345 [PubMed - as supplied by publisher]

Anti-stress effects of ginseng total saponins on hindlimb-unloaded rats assessed by a metabolomics study. J Ethnopharmacol. 2016 Apr 21; Authors: Feng L, Liu XM, Cao FR, Wang LS, Chen YX, Pan RL, Liao YH, Wang Q, Chang Q Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Ginseng, the roots and rhizomes of Panax ginseng C.A. Mey. (Araliaceae), is used as a tonic herb for thousands of years in Asian countries. Saponins are recognized as its major active ingredients and reportedly can ease disorders caused by various adverse stimuli. Nevertheless, it is unclear whether ginseng saponins have beneficial effects on stress caused by microgravity. AIM OF THE STUDY: This study aimed to assess the anti-stress effects and corresponding mechanisms of ginseng total saponins (GTSs) on simulated microgravity (SM) hindlimb-unloaded rats using a metabolomics method. MATERIALS AND METHODS: The stressed rats were induced by hindlimb unloading for 7 continuous days. Levels of plasma corticosterone (CORT) and weights of immune organs including the thymuses, spleens, and adrenal glands were determined. Urinary metabolic profiles of the rats under the simulated microgravity condition with and without GTSs intervention were compared using an ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS) based metabolomics method. Multivariate statistical analysis including Principal Component Analysis (PCA) and Partial Least Squares project to latent structures-Discriminant Analysis (PLS-DA) were performed. RESULTS: Compared with control (66.22 ± 10.40 ng/mL), the plasma CORT level of the SM rats (82.67 ± 13.64 ng/mL) were significantly (p < 0.05) elevated, and GTSs could restore this elevation to a lower level (77.75 ± 14.35 ng/mL). GTSs could also significantly alleviate the atrophy of the thymuses and the spleens, as well as the hypertrophy of the adrenal glands of the SM rats. Urinary metabolic profiling showed comprehensive metabolic variation among the three groups. A series of metabolic pathways including taurine and hypotaurine, purine and pyridine, and amino acid were affected. Eleven potential biomarkers such as taurine, adenine, and valine were identified. GTSs could correct the disturbed metabolic pathways and restore the variation of these potential markers. CONCLUSION: GTSs can exert anti-stress effects by reducing the secretion of plasma CORT, enhancing the immune function, and restoring an array of disturbed metabolic pathways and metabolites. The findings of this study provide crucial evidence of a link between metabolic imbalance and microgravity, and reveal a molecular basis for the anti-stress benefits of GTSs in the management of microgravity-related disorders. PMID: 27109340 [PubMed - as supplied by publisher]

Discrimination of Three Panax Species Based on Differences in Volatile Organic Compounds Using a Static Headspace GC-MS-Based Metabolomics Approach. Am J Chin Med. 2016 Apr 24;:1-14 Authors: Chen XJ, Qiu JF, Wang YT, Wan JB Abstract Panax ginseng (Asian ginseng), Panax quinquefolium (American ginseng) and Panax notoginseng (notoginseng) are highly valuable tonic herbs derived from the Panax genus that have similar morphological appearances and odors but different pharmacological activities and clinical indications. Thus, the authentication of these three Panax species is crucial for ensuring the quality, safety and efficacy of medication. In the present study, a static headspace gas chromatography - mass spectrometry (GC-MS) followed by a multivariate statistical analysis was developed to globally characterize the volatile organic compound (VOC) profiles in P. ginseng, P. quinquefolium, and P. notoginseng, and subsequently to discover differentiating chemical markers. Under the optimized conditions, the headspace VOCs of a total of 49 batches of Panax herbs derived from the three Panax species were profiled, and the dataset of sample code, [Formula: see text]-m/z pair and ion intensity was processed by unsupervised principal component analysis (PCA) and by supervised partial least squared discriminant analysis (PLS-DA) to comprehensively compare the chemical differences in Panax across the species. The results demonstrated that Panax herbs derived from three species possess obviously diverse chemical characteristics of VOCs, PCA, and PLS-DA. According to their VOC profiles, 49 tested samples could be clearly differentiated according to species. Chemomarker 1, 2, and 4 might be used as unique chemical markers of P. ginseng, P. notoginseng and P. quinquefolium, respectively. Our findings indicate that static headspace GC-MS-based VOC profiling, combined with multivariate statistical analysis, provide a reliable tool to discriminate between the three Panax species and to identify their differentiation markers, which will be helpful for ensuring their quality, safety and efficacy. PMID: 27109159 [PubMed - as supplied by publisher]

Related Articles MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites. Anal Chem. 2015 Oct 20;87(20):10619-26 Authors: Huan T, Tang C, Li R, Shi Y, Lin G, Li L Abstract We report an analytical tool to facilitate metabolite identification based on an MS/MS spectral match of an unknown to a library of predicted MS/MS spectra of possible human metabolites. To construct the spectral library, the known endogenous human metabolites in the Human Metabolome Database (HMDB) (8,021 metabolites) and their predicted metabolic products via one metabolic reaction in the Evidence-based Metabolome Library (EML) (375,809 predicted metabolites) were subjected to in silico fragmentation to produce the predicted MS/MS spectra. This spectral library is hosted at the public MCID Web site ( www.MyCompoundID.org ), and a spectral search program, MCID MS/MS, has been developed to allow a user to search one or a batch of experimental MS/MS spectra against the library spectra for possible match(s). Using MS/MS spectra generated from standard metabolites and a human urine sample, we demonstrate that this tool is very useful for putative metabolite identification. It allows a user to narrow down many possible structures initially found by using an accurate mass search of an unknown metabolite to only one or a few candidates, thereby saving time and effort in selecting or synthesizing metabolite standard(s) for eventual positive metabolite identification. PMID: 26415007 [PubMed - indexed for MEDLINE]

Related Articles Effects of metformin on metabolite profiles and LDL cholesterol in patients with type 2 diabetes. Diabetes Care. 2015 Oct;38(10):1858-67 Authors: Xu T, Brandmaier S, Messias AC, Herder C, Draisma HH, Demirkan A, Yu Z, Ried JS, Haller T, Heier M, Campillos M, Fobo G, Stark R, Holzapfel C, Adam J, Chi S, Rotter M, Panni T, Quante AS, He Y, Prehn C, Roemisch-Margl W, Kastenmüller G, Willemsen G, Pool R, Kasa K, van Dijk KW, Hankemeier T, Meisinger C, Thorand B, Ruepp A, Hrabé de Angelis M, Li Y, Wichmann HE, Stratmann B, Strauch K, Metspalu A, Gieger C, Suhre K, Adamski J, Illig T, Rathmann W, Roden M, Peters A, van Duijn CM, Boomsma DI, Meitinger T, Wang-Sattler R Abstract OBJECTIVE: Metformin is used as a first-line oral treatment for type 2 diabetes (T2D). However, the underlying mechanism is not fully understood. Here, we aimed to comprehensively investigate the pleiotropic effects of metformin. RESEARCH DESIGN AND METHODS: We analyzed both metabolomic and genomic data of the population-based KORA cohort. To evaluate the effect of metformin treatment on metabolite concentrations, we quantified 131 metabolites in fasting serum samples and used multivariable linear regression models in three independent cross-sectional studies (n = 151 patients with T2D treated with metformin [mt-T2D]). Additionally, we used linear mixed-effect models to study the longitudinal KORA samples (n = 912) and performed mediation analyses to investigate the effects of metformin intake on blood lipid profiles. We combined genotyping data with the identified metformin-associated metabolites in KORA individuals (n = 1,809) and explored the underlying pathways. RESULTS: We found significantly lower (P < 5.0E-06) concentrations of three metabolites (acyl-alkyl phosphatidylcholines [PCs]) when comparing mt-T2D with four control groups who were not using glucose-lowering oral medication. These findings were controlled for conventional risk factors of T2D and replicated in two independent studies. Furthermore, we observed that the levels of these metabolites decreased significantly in patients after they started metformin treatment during 7 years' follow-up. The reduction of these metabolites was also associated with a lowered blood level of LDL cholesterol (LDL-C). Variations of these three metabolites were significantly associated with 17 genes (including FADS1 and FADS2) and controlled by AMPK, a metformin target. CONCLUSIONS: Our results indicate that metformin intake activates AMPK and consequently suppresses FADS, which leads to reduced levels of the three acyl-alkyl PCs and LDL-C. Our findings suggest potential beneficial effects of metformin in the prevention of cardiovascular disease. PMID: 26251408 [PubMed - indexed for MEDLINE]

Related Articles Isolation of Vaginal Lactobacilli and Characterization of Anti-Candida Activity. PLoS One. 2015;10(6):e0131220 Authors: Parolin C, Marangoni A, Laghi L, Foschi C, Ñahui Palomino RA, Calonghi N, Cevenini R, Vitali B Abstract Healthy vaginal microbiota is dominated by Lactobacillus spp., which form a critical line of defence against pathogens, including Candida spp. The present study aims to identify vaginal lactobacilli exerting in vitro activity against Candida spp. and to characterize their antifungal mechanisms of action. Lactobacillus strains were isolated from vaginal swabs of healthy premenopausal women. The isolates were taxonomically identified to species level (L. crispatus B1-BC8, L. gasseri BC9-BC14 and L. vaginalis BC15-BC17) by sequencing the 16S rRNA genes. All strains produced hydrogen peroxide and lactate. Fungistatic and fungicidal activities against C. albicans, C. glabrata, C. krusei, C. tropicalis, C. parapsilosis and C. lusitaniae were evaluated by broth micro-dilution method. The broadest spectrum of activity was observed for L. crispatus BC1, BC4, BC5 and L. vaginalis BC15, demonstrating fungicidal activity against all isolates of C. albicans and C. lusitaniae. Metabolic profiles of lactobacilli supernatants were studied by 1H-NMR analysis. Metabolome was found to be correlated with both taxonomy and activity score. Exclusion, competition and displacement experiments were carried out to investigate the interference exerted by lactobacilli toward the yeast adhesion to HeLa cells. Most Lactobacillus strains significantly reduced C. albicans adhesion through all mechanisms. In particular, L. crispatus BC2, L. gasseri BC10 and L. gasseri BC11 appeared to be the most active strains in reducing pathogen adhesion, as their effects were mediated by both cells and supernatants. Inhibition of histone deacetylases was hypothesised to support the antifungal activity of vaginal lactobacilli. Our results are prerequisites for the development of new therapeutic agents based on probiotics for prophylaxis and adjuvant therapy of Candida infection. PMID: 26098675 [PubMed - indexed for MEDLINE]