PubMed

Related Articles Host reticulocytes provide metabolic reservoirs that can be exploited by malaria parasites. PLoS Pathog. 2015 Jun;11(6):e1004882 Authors: Srivastava A, Creek DJ, Evans KJ, De Souza D, Schofield L, Müller S, Barrett MP, McConville MJ, Waters AP Abstract Human malaria parasites proliferate in different erythroid cell types during infection. Whilst Plasmodium vivax exhibits a strong preference for immature reticulocytes, the more pathogenic P. falciparum primarily infects mature erythrocytes. In order to assess if these two cell types offer different growth conditions and relate them to parasite preference, we compared the metabolomes of human and rodent reticulocytes with those of their mature erythrocyte counterparts. Reticulocytes were found to have a more complex, enriched metabolic profile than mature erythrocytes and a higher level of metabolic overlap between reticulocyte resident parasite stages and their host cell. This redundancy was assessed by generating a panel of mutants of the rodent malaria parasite P. berghei with defects in intermediary carbon metabolism (ICM) and pyrimidine biosynthesis known to be important for P. falciparum growth and survival in vitro in mature erythrocytes. P. berghei ICM mutants (pbpepc-, phosphoenolpyruvate carboxylase and pbmdh-, malate dehydrogenase) multiplied in reticulocytes and committed to sexual development like wild type parasites. However, P. berghei pyrimidine biosynthesis mutants (pboprt-, orotate phosphoribosyltransferase and pbompdc-, orotidine 5'-monophosphate decarboxylase) were restricted to growth in the youngest forms of reticulocytes and had a severe slow growth phenotype in part resulting from reduced merozoite production. The pbpepc-, pboprt- and pbompdc- mutants retained virulence in mice implying that malaria parasites can partially salvage pyrimidines but failed to complete differentiation to various stages in mosquitoes. These findings suggest that species-specific differences in Plasmodium host cell tropism result in marked differences in the necessity for parasite intrinsic metabolism. These data have implications for drug design when targeting mature erythrocyte or reticulocyte resident parasites. PMID: 26042734 [PubMed - indexed for MEDLINE]

Related Articles Green tea polyphenol (-)-epigallocatechin-3-gallate restores Nrf2 activity and ameliorates crescentic glomerulonephritis. PLoS One. 2015;10(3):e0119543 Authors: Ye T, Zhen J, Du Y, Zhou JK, Peng A, Vaziri ND, Mohan C, Xu Y, Zhou XJ Abstract Crescentic glomerulonephritis (GN) is the most severe form of GN and is associated with significant morbidity and mortality despite aggressive immunotherapy with steroids, cytotoxic drugs, and plasmapheresis. We examined the therapeutic efficacy of the green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG, 50 mg/kg BW/day x3 weeks), a potent anti-inflammatory and anti-oxidant agent, on experimental crescentic GN induced in 129/svJ mice by administration of rabbit anti-mouse glomerular basement membrane sera. Routine histology and key molecules involved in inflammatory and redox signaling were studied. EGCG treatment significantly reduced mortality, decreased proteinuria and serum creatinine, and markedly improved renal histology when compared with vehicle-treated mice. The improvements in renal function and histology were accompanied by the restoration of Nrf2 signaling (which was impaired in vehicle-treated mice) as shown by increased nuclear translocation of Nrf2 and cytoplasmic glutamate cysteine ligase catalytic subunit, glutamate cysteine ligase modifier subunit, and glutathione peroxidase. EGCG-treated mice also showed reduction in p-Akt, p-JNK, p-ERK1/2 and p-P38 as well as restoration of PPARγ and SIRT1 levels. Lower dose of EGCG (25 mg/kg BW/day x2 weeks) treatment also significantly decreased proteinuria and serum creatinine, and markedly improved renal histology when compared with vehicle-treated mice. Thus, our data illustrate the efficacy of EGCG in reversing the progression of crescentic GN in mice by targeting multiple signaling and inflammatory pathways as well as countering oxidative stress. PMID: 25785827 [PubMed - indexed for MEDLINE]

Related Articles Fumarate induces redox-dependent senescence by modifying glutathione metabolism. Nat Commun. 2015;6:6001 Authors: Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, Johnson TI, Gaude E, King A, Leach JD, Edrada-Ebel R, Hedley A, Morrice NA, Kalna G, Blyth K, Ruppin E, Frezza C, Gottlieb E Abstract Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) are associated with a highly malignant form of renal cancer. We combined analytical chemistry and metabolic computational modelling to investigate the metabolic implications of FH loss in immortalized and primary mouse kidney cells. Here, we show that the accumulation of fumarate caused by the inactivation of FH leads to oxidative stress that is mediated by the formation of succinicGSH, a covalent adduct between fumarate and glutathione. Chronic succination of GSH, caused by the loss of FH, or by exogenous fumarate, leads to persistent oxidative stress and cellular senescence in vitro and in vivo. Importantly, the ablation of p21, a key mediator of senescence, in Fh1-deficient mice resulted in the transformation of benign renal cysts into a hyperplastic lesion, suggesting that fumarate-induced senescence needs to be bypassed for the initiation of renal cancers. PMID: 25613188 [PubMed - indexed for MEDLINE]

(1)H NMR Metabolomics Study of Spleen from C57BL/6 Mice Exposed to Gamma Radiation. Metabolomics (Los Angel). 2016;6(1):1-11 Authors: Xiao X, Hu M, Liu M, Hu JZ Abstract Due to the potential risk of accidental exposure to gamma radiation, it's critical to identify the biomarkers of radiation exposed creatures. In the present study, NMR based metabolomics combined with multivariate data analysis to evaluate the metabolites changed in the C57BL/6 mouse spleen after 4 days whole body exposure to 3.0 Gy and 7.8 Gy gamma radiations. Principal component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS) are employed for classification and identification potential biomarkers associated with gamma irradiation. Two different strategies for NMR spectral data reduction (i.e., spectral binning and spectral deconvolution) are combined with normalize to constant sum and unit weight before multivariate data analysis, respectively. The combination of spectral deconvolution and normalization to unit weight is the best way for identifying discriminatory metabolites between the irradiation and control groups. Normalized to the constant sum may achieve some pseudo biomarkers. PCA and OPLS results shown that the exposed groups can be well separated from the control group. Leucine, 2-aminobutyrate, valine, lactate, arginine, glutathione, 2-oxoglutarate, creatine, tyrosine, phenylalanine, π-methylhistidine, taurine, myoinositol, glycerol and uracil are significantly elevated while ADP is decreased significantly. These significantly changed metabolites are associated with multiple metabolic pathways and may be potential biomarkers in the spleen exposed to gamma irradiation. PMID: 27019763 [PubMed - as supplied by publisher]

Novel Metabolite Biomarkers of Huntington's Disease As Detected by High-Resolution Mass Spectrometry. J Proteome Res. 2016 Mar 28; Authors: Graham SF, Kumar P, Bahado-Singh RO, Robinson A, Mann D, Green BD Abstract Huntington's disease (HD) is a fatal autosomal-dominant neurodegenerative disorder that affects approximately 3-10 people per 100 000 in the Western world. The median age of onset is 40 years, with death typically following 15-20 years later. In this study, we biochemically profiled post-mortem frontal lobe and striatum from HD sufferers (n = 14) and compared their profiles with controls (n = 14). LC-LTQ-Orbitrap-MS detected a total of 5579 and 5880 features for frontal lobe and striatum, respectively. An ROC curve combining two spectral features from frontal lobe had an AUC value of 0.916 (0.794 to 1.000) and following statistical cross-validation had an 83% predictive accuracy for HD. Similarly, two striatum biomarkers gave an ROC AUC of 0.935 (0.806 to 1.000) and after statistical cross-validation predicted HD with 91.8% accuracy. A range of metabolite disturbances were evident including but-2-enoic acid and uric acid, which were altered in both frontal lobe and striatum. A total of seven biochemical pathways (three in frontal lobe and four in striatum) were significantly altered as a result of HD. This study highlights the utility of high-resolution metabolomics for the study of HD. Further characterization of the brain metabolome could lead to the identification of new biomarkers and novel treatment strategies for HD. PMID: 27018767 [PubMed - as supplied by publisher]

Effects of chlorpyrifos on the gut microbiome and urine metabolome in mouse (Mus musculus). Chemosphere. 2016 Mar 25;153:287-293 Authors: Zhao Y, Zhang Y, Wang G, Han R, Xie X Abstract In this study, the toxic effects of clorpyrifos (CPF) on the gut microbiome and related urine metabolome in mouse (Mus musculus) were investigated. Mice were exposed to a daily dose of 1 mg kg(-1) bodyweight of CPF for 30 d. As a result, CPF significantly altered the gut microbiota composition in terms of the relative abundance of key microbes. Meanwhile, CPF exposure induced the alterations of urine metabolites related to the metabolism of amino acids, energy, short-chain fatty acids (SCFAs), phenyl derivatives and bile acids. High correlations were observed between perturbed gut microbiome and altered metabolic profiles. These perturbations finally resulted in intestinal inflammation and abnormal intestinal permeability, which were also confirm by the histologic changes in colon and remarkable increase of lipopolysaccharide (LPS) and diamine oxidase (DAO) in the serum of CPF-treated mice. Our findings will provide a new perspective to reveal the mechanism of CPF toxicity. PMID: 27018521 [PubMed - as supplied by publisher]

Chemical Discrimination of Cortex Phellodendri amurensis and Cortex Phellodendri chinensis by Multivariate Analysis Approach. Pharmacogn Mag. 2016 Jan-Mar;12(45):41-9 Authors: Sun H, Wang H, Zhang A, Yan G, Han Y, Li Y, Wu X, Meng X, Wang X Abstract BACKGROUND: As herbal medicines have an important position in health care systems worldwide, their current assessment, and quality control are a major bottleneck. Cortex Phellodendri chinensis (CPC) and Cortex Phellodendri amurensis (CPA) are widely used in China, however, how to identify species of CPA and CPC has become urgent. MATERIALS AND METHODS: In this study, multivariate analysis approach was performed to the investigation of chemical discrimination of CPA and CPC. RESULTS: Principal component analysis showed that two herbs could be separated clearly. The chemical markers such as berberine, palmatine, phellodendrine, magnoflorine, obacunone, and obaculactone were identified through the orthogonal partial least squared discriminant analysis, and were identified tentatively by the accurate mass of quadruple-time-of-flight mass spectrometry. A total of 29 components can be used as the chemical markers for discrimination of CPA and CPC. Of them, phellodenrine is significantly higher in CPC than that of CPA, whereas obacunone and obaculactone are significantly higher in CPA than that of CPC. CONCLUSION: The present study proves that multivariate analysis approach based chemical analysis greatly contributes to the investigation of CPA and CPC, and showed that the identified chemical markers as a whole should be used to discriminate the two herbal medicines, and simultaneously the results also provided chemical information for their quality assessment. SUMMARY: Multivariate analysis approach was performed to the investigate the herbal medicineThe chemical markers were identified through multivariate analysis approachA total of 29 components can be used as the chemical markers. UPLC-Q/TOF-MS-based multivariate analysis method for the herbal medicine samples Abbreviations used: CPC: Cortex Phellodendri chinensis, CPA: Cortex Phellodendri amurensis, PCA: Principal component analysis, OPLS-DA: Orthogonal partial least squares discriminant analysis, BPI: Base peaks ion intensity. PMID: 27018001 [PubMed]

Glycosylation pattern of anti-platelet IgG is stable during pregnancy and predicts clinical outcome in alloimmune thrombocytopenia. Br J Haematol. 2016 Mar 28; Authors: Sonneveld ME, Natunen S, Sainio S, Koeleman CA, Holst S, Dekkers G, Koelewijn J, Partanen J, van der Schoot CE, Wuhrer M, Vidarsson G Abstract Fetal or neonatal alloimmune thrombocytopenia (FNAIT) is a potentially life-threatening disease where fetal platelets are destroyed by maternal anti-platelet IgG alloantibodies. The clinical outcome varies from asymptomatic, to petechiae or intracranial haemorrhage, but no marker has shown reliable correlation with severity, making screening for FNAIT impractical and highly inefficient. We recently found IgG Fc-glycosylation towards platelet and red blood cell antigens to be skewed towards decreased fucosylation, increased galactosylation and sialylation. The lowered core-fucosylation increases the affinity of the pathogenic antibodies to FcγRIIIa and FcγRIIIb, and hence platelet destruction. Here we analysed the N-linked glycans of human platelet antigen (HPA)-1a specific IgG1 with mass spectrometry in large series of FNAIT cases (n = 166) including longitudinal samples (n = 26). Besides a significant decrease in Fc-fucosylation after the first pregnancy (P = 0·0124), Fc-glycosylation levels remained stable during and after pregnancy and in subsequent pregnancies. Multiple logistic regression analysis identified anti-HPA-1a -fucosylation (P = 0·006) combined with galactosylation (P = 0·021) and antibody level (P = 0·038) correlated with bleeding severity, making these parameters a feasible marker in screening for severe cases of FNAIT. PMID: 27017954 [PubMed - as supplied by publisher]

Metabolomic changes in murine serum following inhalation exposure to gasoline and diesel engine emissions. Inhal Toxicol. 2016 Mar 28;:1-10 Authors: Brower JB, Doyle-Eisele M, Moeller B, Stirdivant S, McDonald JD, Campen MJ Abstract The adverse health effects of environmental exposure to gaseous and particulate components of vehicular emissions are a major concern among urban populations. A link has been established between respiratory exposure to vehicular emissions and the development of cardiovascular disease (CVD), but the mechanisms driving this interaction remain unknown. Chronic inhalation exposure to mixed vehicle emissions has been linked to CVD in animal models. This study evaluated the temporal effects of acute exposure to mixed vehicle emissions (MVE; mixed gasoline and diesel emissions) on potentially active metabolites in the serum of exposed mice. C57Bl/6 mice were exposed to a single 6-hour exposure to filtered air (FA) or MVE (100 or 300 μg/m(3)) by whole body inhalation. Immediately after and 18 hours after the end of the exposure period, animals were sacrificed for serum and tissue collection. Serum was analyzed for metabolites that were differentially present between treatment groups and time points. Changes in metabolite levels suggestive of increased oxidative stress (oxidized glutathione, cysteine disulfide, taurine), lipid peroxidation (13-HODE, 9-HODE), energy metabolism (lactate, glycerate, branched chain amino acid catabolites, butrylcarnitine, fatty acids), and inflammation (DiHOME, palmitoyl ethanolamide) were observed immediately after the end of exposure in the serum of animals exposed to MVE relative to those exposed to FA. By 18 hours post exposure, serum metabolite differences between animals exposed to MVE versus those exposed to FA were less pronounced. These findings highlight complex metabolomics alterations in the circulation following inhalation exposure to a common source of combustion emissions. PMID: 27017952 [PubMed - as supplied by publisher]

Anti-phytopathogenic activity of sporothriolide, a metabolite from endophyte Nodulisporium sp. A21 in Ginkgo biloba. Pestic Biochem Physiol. 2016 May;129:7-13 Authors: Cao LL, Zhang YY, Liu YJ, Yang TT, Zhang JL, Zhang ZG, Shen L, Liu JY, Ye YH Abstract Phytopathogenic fungi such as Rhizoctonia solani and Sclerotinia sclerotiorum caused multiple plant diseases resulting in severe loss of crop production. Increasing documents endorsed that endophytes are a striking resource pool for numerous metabolites with various bioactivities such as anti-fungal. Here we reported the characterization and anti-phytopathogenic activity of sporothriolide, a metabolite produced by Nodulisporium sp. A21-an endophytic fungus in the leaves of Ginkgo biloba. Among the total twenty-five endophytic fungi isolated from the healthy leaves of G. biloba, the fermentation broth (FB) of the strain A21 was found potently inhibitory activity against R. solani and S. sclerotiorum using mycelia growth inhibition method. A21 was then identified as Nodulisporium sp., the asexual stage of Hypoxylon sp., by microscopic examination and ITS rDNA sequence data comparison. Under the bioassay-guided fractionation, sporothriolide was isolated from the petroleum ether extract of the FB of A21, whose structure was established by integrated interpretation of HR-ESI-MS and (1)H- and (13)C-NMR. Furthermore, the crystal structure of sporothriolide was first reported. In addition, sporothriolide was validated to be potently antifungal against R. solani, S. sclerotiorum and inhibit conidium germination of Magnaporthe oryzae in vitro and in vivo, indicating that it could be used as a lead compound for new fungicide development. PMID: 27017876 [PubMed - in process]

Related Articles Evolution in miniaturized column liquid chromatography instrumentation and applications: An overview. J Chromatogr A. 2015 Nov 20;1421:18-37 Authors: Nazario CE, Silva MR, Franco MS, Lanças FM Abstract The purpose of this article is to underline the miniaturized LC instrumental system and describe the evolution of commercially available systems by discussing their advantages and drawbacks. Nowadays, there are already many miniaturized LC systems available with a great variety of pump design, interface and detectors as well as efficient columns technologies and reduced connections devices. The solvent delivery systems are able to drive the mobile phase without flow splitters and promote gradient elution using either dual piston reciprocating or syringe-type pumps. The mass spectrometry as detection system is the most widely used detection system; among many alternative ionization sources direct-EI LC-MS is a promising alternative to APCI. In addition, capillary columns are now available showing many possibilities of stationary phases, inner diameters and hardware materials. This review provides a discussion about miniaturized LC demonstrating fundamentals and instrumentals' aspects of the commercially available miniaturized LC instrumental system mainly nano and micro LC formats. This review also covers the recent developments and trends in instrumentation, capillary and nano columns, and several applications of this very important and promising field. PMID: 26381569 [PubMed - indexed for MEDLINE]

Related Articles Moderate alcohol consumption in chronic form enhances the synthesis of cholesterol and C-21 steroid hormones, while treatment with Tinospora cordifolia modulate these events in men. Steroids. 2016 Mar 22; Authors: Kumari S, Mittal A, Dabur R Abstract Chronic and heavy alcohol consumption disrupts lipid metabolism and hormonal balance including testosterone levels. However, studies doubt the relationship between moderate alcohol intake and sex hormone levels. Therefore, the aim of the present investigation was to establish the direct impact of chronic and moderate alcohol intake on cholesterol homeostasis and steroid hormone synthesis. Asymptomatic chronic and moderate alcoholics (n=12) without chronic liver disease and healthy volunteers (n=14) were selected for the study. Furthermore, effects of standardized water extract of Tinospora cordifolia (Willd) Mier. (Menispermaceae) (TCJ), a well reported anti-alcoholic herbal drug, on urinary steroids was studied. This study included four groups, i.e. a) healthy; b) healthy+TCJ; c) alcoholic; d) alcoholic+TCJ. The blood and urine samples from each group were collected on day 0 and 14 of the post-treatment with TCJ and analyzed. Alcoholic blood samples showed the significantly higher values of traditional biomarkers γ-GT and MCV along with cholesterol, LDL, TGL and urinary methylglucuronide compared to healthy. Qualitative analysis of steroids showed that moderate alcohol intake in a chronic manner increased the cholesterol synthesis and directed its flow toward C-21 steroids; shown by increased levels of corticosterone (2.456 fold) and cortisol (3.7 fold). Moreover, alcohol intake also increased the synthesis of estradiol and clearance rate of other steroids through the formation of glucuronides. Therefore, it decreased the synthesis and increased the clearance rate of testosterone (T) and androstenedione (A). Quantitative analysis confirmed decreased T/A ratio from 2.31 to 1.59 in plasma and 2.47 to 1.51 in urine samples of alcoholics. TCJ intervention normalized the levels of steroids and significantly improved the T: A ratio to 2.0 and 2.12 in plasma and urine. The study revealed that TCJ modulated lipid metabolism by inhibiting cholesterol and glucuronides synthesis. PMID: 27016128 [PubMed - as supplied by publisher]

19 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 2016/03/26PubMed 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.

Evaluation of Cancer Metabolomics Using ex vivo High Resolution Magic Angle Spinning (HRMAS) Magnetic Resonance Spectroscopy (MRS). Metabolites. 2016;6(1) Authors: Fuss TL, Cheng LL Abstract According to World Health Organization (WHO) estimates, cancer is responsible for more deaths than all coronary heart disease or stroke worldwide, serving as a major public health threat around the world. High resolution magic angle spinning (HRMAS) magnetic resonance spectroscopy (MRS) has demonstrated its usefulness in the identification of cancer metabolic markers with the potential to improve diagnosis and prognosis for the oncology clinic, due partially to its ability to preserve tissue architecture for subsequent histological and molecular pathology analysis. Capable of the quantification of individual metabolites, ratios of metabolites, and entire metabolomic profiles, HRMAS MRS is one of the major techniques now used in cancer metabolomic research. This article reviews and discusses literature reports of HRMAS MRS studies of cancer metabolomics published between 2010 and 2015 according to anatomical origins, including brain, breast, prostate, lung, gastrointestinal, and neuroendocrine cancers. These studies focused on improving diagnosis and understanding patient prognostication, monitoring treatment effects, as well as correlating with the use of in vivo MRS in cancer clinics. PMID: 27011205 [PubMed - as supplied by publisher]

A Double-Clicking Bis-Azide Fluorogenic Dye for Bioorthogonal Self-Labeling Peptide Tags. Chemistry. 2016 Mar 24; Authors: Demeter O, Fodor EA, Kállay M, Mező G, Németh K, Szabó PT, Kele P Abstract Herein, we give the very first example for the development of a fluorogenic molecular probe that combines the two-point binding specificity of biarsenical-based dyes with the robustness of bioorthogonal click-chemistry. This proof-of-principle study reports on the synthesis and fluorogenic characterization of a new, double-quenched, bis-azide fluorogenic probe suitable for bioorthogonal two-point tagging of small peptide tags by double strain-promoted azide-alkyne cycloaddition. The presented probe exhibits remarkable increase in fluorescence intensity when reacted with bis-cyclooctynylated peptide sequences, which could also serve as possible self-labeling small peptide tag motifs. PMID: 27010966 [PubMed - as supplied by publisher]

Metabolomics reveals positive acceleration(+Gz)-induced metabolic perturbations and the protective effect of Ginkgo biloba extract in a rat model based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. J Pharm Biomed Anal. 2016 Mar 8;125:77-84 Authors: Yang Z, Zhao A, Li Z, Ge H, Li T, Zhang F, Zhan H, Wang J Abstract Positive acceleration (+Gz) in the head-to-foot direction generated by modern high-performance fighter jets during flight maneuvers is characterized by high G values and a rapid rate of acceleration, and is often long in duration and a repeated occurrence. The acceleration overload far exceeds the pilot's physiological tolerance limits and causes considerable strain on several organ systems. Despite the importance of monitoring pathophysiological alterations related to +Gz exposure, we lack a complete explanation of the pathophysiology of +Gz exposure. Ginkgo biloba extract (GBE) is a classic traditional Chinese medicine (TCM) that might exert a protective effect against +Gz exposure. However, its mechanism remains unclear. Here, a metabolomics approach based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOFMS) was used to characterize +Gz-induced metabolic fluctuations in a rat model and to evaluate the protective effect of GBE. Using partial least-squares discriminant analysis for the classification and selection of biomarkers, eighteen serum metabolites related to +Gz exposure were identified, and were found to primarily involve the fatty acid β-oxidation pathway, glycerophospholipid metabolism, phospholipid metabolism, bile acid metabolism, purine metabolism and lysine metabolism. Taking these potential biomarkers as screening indexes, we found that GBE could reverse the pathological process of +Gz exposure by partially regulating the perturbed fatty acid β-oxidation pathway, glycerophospholipid metabolism, purine metabolism and lysine metabolism. This indicates that UHPLC-Q-TOFMS-based metabolomics provides a powerful tool to reveal serum metabolic fluctuations in response to +Gz exposure and to study the mechanism underlying TCM. PMID: 27010354 [PubMed - as supplied by publisher]

MetaboLights: An Open-Access Database Repository for Metabolomics Data. Curr Protoc Bioinformatics. 2016;53:14.13.1-14.13.18 Authors: Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C Abstract MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. © 2016 by John Wiley & Sons, Inc. PMID: 27010336 [PubMed - as supplied by publisher]

Introduction to Cheminformatics. Curr Protoc Bioinformatics. 2016;53:14.1.1-14.1.21 Authors: Wishart DS Abstract Cheminformatics is a field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on small molecule formulas, structures, properties, spectra, and activities (biological or industrial). Cheminformatics originally emerged as a vehicle to help the drug discovery and development process, however cheminformatics now plays an increasingly important role in many areas of biology, chemistry, and biochemistry. The intent of this unit is to give readers some introduction into the field of cheminformatics and to show how cheminformatics not only shares many similarities with the field of bioinformatics, but also enhances much of what is currently done in bioinformatics, molecular biology, and biochemistry. © 2016 by John Wiley & Sons, Inc. PMID: 27010335 [PubMed - as supplied by publisher]

Related Articles Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis. Sci Rep. 2015;5:10604 Authors: He B, Nohara K, Ajami NJ, Michalek RD, Tian X, Wong M, Losee-Olson SH, Petrosino JF, Yoo SH, Shimomura K, Chen Z Abstract Dietary fibers are increasingly appreciated as beneficial nutritional components. However, a requisite role of gut microbiota in fiber function and the overall impact of fibers on metabolomic flux remain unclear. We herein showed enhancing effects of a soluble resistant maltodextrin (RM) on glucose homeostasis in mouse metabolic disease models. Remarkably, fecal microbiota transplantation (FMT) caused pronounced and time-dependent improvement in glucose tolerance in RM recipient mice, indicating a causal relationship between microbial remodeling and metabolic efficacy. Microbial 16S sequencing revealed transmissible taxonomic changes correlated with improved metabolism, notably enrichment of probiotics and reduction of Alistipes and Bacteroides known to associate with high fat/protein diets. Metabolomic profiling further illustrated broad changes, including enrichment of phenylpropionates and decreases in key intermediates of glucose utilization, cholesterol biosynthesis and amino acid fermentation. These studies elucidate beneficial roles of RM-dependent microbial remodeling in metabolic homeostasis, and showcase prevalent health-promoting potentials of dietary fibers. PMID: 26040234 [PubMed - indexed for MEDLINE]

Related Articles Cell-derived extracellular vesicles as a platform to identify low-invasive disease biomarkers. Expert Rev Mol Diagn. 2015;15(7):907-23 Authors: González E, Falcón-Pérez JM Abstract Biomarkers are of great importance for prediction, diagnosis and monitoring the progression and therapeutic success of a disease. Whole body fluids, such as blood or urine, constitute the main desired biological source to identify these markers, mostly due to the minimally invasive procedures used to collect them. An additional benefit of studying these biological fluids that has been demonstrated by many different groups is that they contain cell-released extracellular vesicles, carrying a cargo of lipids, proteins and nucleic acids that reflects cell/tissue origin and, remarkably, cellular status. In this review, the information obtained from the characterization of this body fluid compartment in human samples is discussed in the context of its usefulness as diagnostic resource for several pathologies, including cancer, inflammatory, vascular and metabolic diseases. The review shows the great variety of methods used for this purpose as well as the different types of molecules that could serve as specific or common disease markers. PMID: 25948243 [PubMed - indexed for MEDLINE]