PubMed

Related Articles Nuclear magnetic resonance (NMR) spectroscopy: Metabolic profiling of medicinal plants and their products. Crit Rev Anal Chem. 2015 Nov 17;:0 Authors: Kumar D Abstract NMR spectroscopy has multidisciplinary applications and excellent impact in metabolomics. Analytical capacity of NMR spectroscopy provides information regarding easy qualitative and quantitative assessment of both endogenous and exogenous metabolites present in biological samples. Complexity of a particular metabolite and its contribution in a biological system is critically important for understanding the functional state that governs the organism's phenotypes. This review covers historical aspects of developments in NMR field, its applications in chemical profiling, metabolomics, and quality control of plants and their derived medicine, food etc. The bottlenecks of NMR in metabolic profiling have also been discussed by keeping in view the future scope and more technological interventions. PMID: 26575437 [PubMed - as supplied by publisher]

Related Articles Cyclic di-GMP regulates multiple cellular functions in the symbiotic α-proteobacterium Sinorhizobium meliloti. J Bacteriol. 2015 Nov 16; Authors: Schäper S, Krol E, Skotnicka D, Kaever V, Hilker R, Søgaard-Andersen L, Becker A Abstract Sinorhizobium meliloti undergoes major lifestyle changes between planktonic states, biofilm formation and symbiosis with leguminous plant hosts. In many bacteria, the second messenger 3' ,5' -cyclic diguanylic acid (c-di-GMP, cdG) promotes a sessile lifestyle by regulating a plethora of processes involved in biofilm formation, including motility and biosynthesis of exopolysaccharides (EPS). Here, we systematically investigated the role of cdG in S. meliloti Rm2011 encoding 22 proteins putatively associated with cdG synthesis, degradation or binding. Single mutations in 21 of these genes did not cause evident changes in biofilm formation, motility or EPS biosynthesis. In contrast, manipulation of cdG levels by overproducing endogenous or heterologous diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) affected these processes and accumulation of N-Acyl-homoserine lactones in the culture supernatant. Specifically, individual overexpression of the S. meliloti genes pleD, SMb20523, SMb20447, SMc01464 and SMc03178 encoding putative DGCs, and of SMb21517 encoding a single domain PDE protein had an impact and resulted in increased levels of cdG. Compared to wild type, a S. meliloti cdG(0) strain that did not produce detectable levels of cdG was more sensitive to acid stress. However, it was symbiotically potent, unaffected in motility and only slightly reduced in biofilm formation. The SMc01790-SMc01796 locus, homologous to the Agrobacterium tumefaciens uppABCDEF cluster governing biosynthesis of a unipolarly localized polysaccharide, was found to be required for cdG-stimulated biofilm formation, while the single domain PilZ protein McrA was identified as a cdG receptor protein involved in regulation of motility. IMPORTANCE: We present the first systematic genome-wide investigation of the role of 3' ,5' -cyclic diguanylic acid (c-di-GMP, cdG) in regulation of motility, biosynthesis of exopolysaccharides, biofilm formation, quorum sensing and symbiosis in a symbiotic alpha-rhizobial species. Phenotypes of a S. meliloti cdG(0) strain unable to produce cdG demonstrated that this second messenger is not essential for root nodule symbiosis but may contribute to acid tolerance. Our data further suggest that enhanced levels of cdG promote sessility of S. meliloti and uncovered a single domain PilZ protein as regulator of motility. PMID: 26574513 [PubMed - as supplied by publisher]

Related Articles Mechanotransduction in primary human osteoarthritic chondrocytes is mediated by metabolism of energy, lipids, and amino acids. J Biomech. 2015 Oct 31; Authors: Zignego DL, Hilmer JK, June RK Abstract Chondrocytes are the sole cell type found in articular cartilage and are repeatedly subjected to mechanical loading in vivo. We hypothesized that physiological dynamic compression results in changes in energy metabolism to produce proteins for maintenance of the pericellular and extracellular matrices. The objective of this study was to develop an in-depth understanding for the short term (<30min) chondrocyte response to sub-injurious, physiological compression by analyzing metabolomic profiles for human chondrocytes harvested from femoral heads of osteoarthritic donors. Cell-seeded agarose constructs were randomly assigned to experimental groups, and dynamic compression was applied for 0, 15, or 30min. Following dynamic compression, metabolites were extracted and detected by HPLC-MS. Untargeted analyzes examined changes in global metabolomics profiles and targeted analysis examined the expression of specific metabolites related to central energy metabolism. We identified hundreds of metabolites that were regulated by applied compression, and we report the detection of 16 molecules not found in existing metabolite databases. We observed patient-specific mechanotransduction with aging dependence. Targeted studies found a transient increase in the ratio of NADP+ to NADPH and an initial decrease in the ratio of GDP to GTP, suggesting a flux of energy into the TCA cycle. By characterizing metabolomics profiles of primary chondrocytes in response to applied dynamic compression, this study provides insight into how OA chondrocytes respond to mechanical load. These results are consistent with increases in glycolytic energy utilization by mechanically induced signaling, and add substantial new data to a complex picture of how chondrocytes transduce mechanical loads. PMID: 26573901 [PubMed - as supplied by publisher]

Related Articles The neuroimmune guidance cue netrin-1 controls resolution programs and promotes liver regeneration. Hepatology. 2015 Nov 17; Authors: Schlegel M, Köhler D, Körner A, Granja T, Straub A, Giera M, Mirakaj V Abstract Hepatic ischemia/reperfusion (I/R) is a major adverse reaction to liver transplantation, hemorrhagic shock, or resection. Recently, the anti-inflammatory properties of the axonal guidance cue netrin-1 were reported. Here, we demonstrate that netrin-1 also impacts the resolution of inflammation and promotes hepatic repair and regeneration during liver I/R injury. In initial studies, we investigated the induction of netrin-1 and its receptors in murine liver tissues after I/R injury. Hepatic I/R injury was performed in mice with a partial genetic netrin-1 deficiency (Ntn1(+/-) ) or wild-type C57BL/6 treated with exogenous netrin-1 to examine the endogenous and therapeutically administered impact of netrin-1. These investigations were corroborated by studies determining the characteristics of intravascular leukocyte flow, clearance of apoptotic neutrophils (PMN), production of specialized pro-resolving lipid mediators (SPM), generation of specific growth factors contributing to the resolution of inflammation and liver repair. Hepatic I/R was associated with a significant reduction of netrin-1 transcript and protein in murine liver tissue. Subsequent studies in netrin-1-deficient mice revealed lower efficacies in reducing PMN infiltration, pro-inflammatory cytokine levels and hepatic-specific injury enzymes. Conversely, mice treated with exogenous netrin-1 exhibited increased liver protection and repair, reducing neutrophil influx into the injury site, decreasing pro-inflammatory mediators, increasing efferocytosis of apoptotic PMN, stimulating local endogenous biosynthesis of SPM and the generation of specific growth factors. Lastly, genetic studies implicated the A2B adenosine receptor in netrin-1-mediated protection during hepatic I/R injury. CONCLUSION: The present study indicates a previously unrecognized role for netrin-1 in liver protection and its contribution to tissue homeostasis and regeneration. This article is protected by copyright. All rights reserved. PMID: 26573873 [PubMed - as supplied by publisher]

Related Articles Litomosoides sigmodontis: A jird urine metabolome study. Bioorg Med Chem Lett. 2015 Oct 23; Authors: Globisch D, Specht S, Pfarr KM, Eubanks LM, Hoerauf A, Janda KD Abstract The neglected tropical disease onchocerciasis affects more than 35 million people worldwide with over 95% in Africa. Disease infection initiates from the filarial parasitic nematode Onchocerca volvulus, which is transmitted by the blackfly vector Simulium sp. carrying infectious L3 larvae. New treatments and diagnostics are required to eradicate this parasitic disease. Herein, we describe that a previously discovered biomarker for onchocerciasis, N-acetyltyramine-O-glucuronide (NATOG) is also present in urine samples of jirds infected with the onchocerciasis model nematode Litomosoides sigmodontis. Increased NATOG values paralleled a progressing infection and demonstrated that quantification of NATOG in this rodent model can be utilized to track its infectivity. Moreover, our findings suggest how NATOG monitoring may be used for evaluating potential drug candidates. PMID: 26573416 [PubMed - as supplied by publisher]

Related Articles Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum. BMC Genomics. 2015;16(1):937 Authors: Salo OV, Ries M, Medema MH, Lankhorst PP, Vreeken RJ, Bovenberg RA, Driessen AJ Abstract BACKGROUND: Penicillium chrysogenum is a filamentous fungus that is employed as an industrial producer of β-lactams. The high β-lactam titers of current strains is the result of a classical strain improvement program (CSI) starting with a wild-type like strain more than six decades ago. This involved extensive mutagenesis and strain selection for improved β-lactam titers and growth characteristics. However, the impact of the CSI on the secondary metabolism in general remains unknown. RESULTS: To examine the impact of CSI on secondary metabolism, a comparative genomic analysis of β-lactam producing strains was carried out by genome sequencing of three P. chrysogenum strains that are part of a lineage of the CSI, i.e., strains NRRL1951, Wisconsin 54-1255, DS17690, and the derived penicillin biosynthesis cluster free strain DS68530. CSI has resulted in a wide spread of mutations, that statistically did not result in an over- or underrepresentation of specific gene classes. However, in this set of mutations, 8 out of 31 secondary metabolite genes (20 polyketide synthases and 11 non-ribosomal peptide synthetases) were targeted with a corresponding and progressive loss in the production of a range of secondary metabolites unrelated to β-lactam production. Additionally, key Velvet complex proteins (LeaA and VelA) involved in global regulation of secondary metabolism have been repeatedly targeted for mutagenesis during CSI. Using comparative metabolic profiling, the polyketide synthetase gene cluster was identified that is responsible for sorbicillinoid biosynthesis, a group of yellow-colored metabolites that are abundantly produced by early production strains of P. chrysogenum. CONCLUSIONS: The classical industrial strain improvement of P. chrysogenum has had a broad mutagenic impact on metabolism and has resulted in silencing of specific secondary metabolite genes with the concomitant diversion of metabolism towards the production of β-lactams. PMID: 26572918 [PubMed - as supplied by publisher]

Related Articles From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS. Anal Chim Acta. 2015 Nov 5;900:21-35 Authors: Mastrangelo A, Ferrarini A, Rey-Stolle F, García A, Barbas C Abstract This tutorial provides a comprehensive description of the GC-MS-based untargeted metabolomics workflow including: ethical approval requirement, sample collection and storage, equipment maintenance and setup, sample treatment, monitoring of analytical variability, data pre-processing including deconvolution by free software such as AMDIS, data processing, statistical analysis and validation, detection of outliers and biological interpretation of the results. For each stage tricks will be suggested, pitfalls will be highlighted and advice will be provided on how to get the best from this methodology and technique. In addition, a step-by-step procedure and an example of our in-house library have been included in the supplementary material to lead the user through the concepts described herein. As a case study, an interesting example from one of our experiments at CEMBIO Research Centre is described, presenting an example of the use of this ready-to use protocol for identification of a metabolite that was not previously included in Fiehn commercial target library. PMID: 26572836 [PubMed - in process]

Related Articles Novel Analytical Workflow for Comprehensive Non-targeted Phytochemical Metabolic Profiling. Chimia (Aarau). 2015;69(5):294-5 Authors: Hettich T, Schlotterbeck G Abstract The understanding and interpretation of pharmacological properties on a molecular level is of great importance for many different fields of research. Our study provides a novel model work-flow for comprehensive metabolic profiling by structural identification of relevant metabolites not limited to phytochemistry applications. High resolution liquid chromatography mass spectrometry LC-MS/MS data can be directly correlated with pharmacological test results on a molecular level. Thus the understanding and interpretation of pharmacological properties is supported by structural and chemical information. PMID: 26507349 [PubMed - indexed for MEDLINE]

Related Articles Combination of direct infusion mass spectrometry and gas chromatography mass spectrometry for toxicometabolomic study of red blood cells and serum of mice Mus musculus after mercury exposure. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Mar 15;985:75-84 Authors: García-Sevillano MA, García-Barrera T, Navarro F, Abril N, Pueyo C, López-Barea J, Gómez-Ariza JL Abstract Although mercury (Hg) is an important environmental and occupational pollutant, its toxicological effects, especially in serum and red blood cells (RBCs), have been scarcely studied. A toxicometabolomics workflow based on high resolution mass spectrometry approaches has been applied to investigate the toxicological effects of Hg in Mus musculus mice after subcutaneous injection for 10 days, which produced inflammation and vacuolization, steatosis and karyolysis in the hepatic tissue. To this end, direct infusion mass spectrometry (DIMS) of polar and lipophilic extracts from serum and RBCs, using positive and negative mode of acquisition (ESI+/ESI-), and gas chromatography-mass spectrometry were used. A quantitative analysis of reversible oxidized thiols in serum proteins demonstrated a strong oxidative stress induction in the liver of Hg-exposed mice. Endogenous metabolites alterations were identified by partial least squares-discriminant analysis (PLS-DA). Mercury-exposed mice show perturbations in energy metabolism, amino acid metabolism, membrane phospholipid breakdown and oxidative stress-related metabolites in serum along the exposure. This work reports for the first time the effects of Hg-exposure on RBCs metabolic pathways, and reveals disturbances in glycolysis, membrane turnover, glutathione and ascorbate metabolisms. PMID: 25660718 [PubMed - indexed for MEDLINE]

Related Articles Application of ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to identify curcumin metabolites produced by human intestinal bacteria. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Mar 15;985:38-47 Authors: Lou Y, Zheng J, Hu H, Lee J, Zeng S Abstract Curcumin, a yellow pigment derived from the rhizomes of Curcuma longa Linn, is a natural antioxidant that exhibits a variety of pharmacological activities and therapeutic properties. However, as curcumin is generally conjugated when absorbed through the intestine, free curcumin is present at extremely low levels in the body. Thus, curcumin metabolites are presumed to be responsible for curcumin bioactivity. In this study, we describe a strategy using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF MS) with automated data analysis software (MetaboLynx(XS)) for rapid analysis of the metabolic profile of curcumin in human intestinal flora. The results show that curcumin undergoes extensive phase I and phase II metabolism. A total of 23 curcumin metabolites were detected and identified in vitro. Furthermore, we identified a number of novel metabolic pathways of curcumin in the human intestinal microflora system. PMID: 25658514 [PubMed - indexed for MEDLINE]

Related Articles Study on the pharmacokinetics profiles of polyphyllin I and its bioavailability enhancement through co-administration with P-glycoprotein inhibitors by LC-MS/MS method. J Pharm Biomed Anal. 2015 Mar 25;107:119-24 Authors: Zhu H, Zhu SC, Shakya S, Mao Q, Ding CH, Long MH, Li SL Abstract Polyphyllin I (PPI), one of the steroidal saponins in Paris polyphylla, is a promising natural anticancer candidate. Although the anticancer activity of PPI has been well demonstrated, information regarding the pharmacokinetics and bioavailability is limited. In this study, a series of reliable and rapid liquid chromatography-tandem mass spectrometry methods were developed and successfully applied to determinate PPI in rat plasma, cell incubation media and cell homogenate. Then the pharmacokinetics of PPI in rats was studied and the result revealed that PPI was slowly eliminated with low oral bioavailability (about 0.62%) at a dose of 50 mg/kg, and when co-administrated with verapamil (VPL) and cyclosporine A (CYA), the oral bioavailability of PPI could increase from 0.62% to 3.52% and 3.79% respectively. In addition, in vitro studies showed that with the presence of VPL and CYA in Caco-2 cells, the efflux ratio of PPI decreased from 12.5 to 2.96 and 2.22, and the intracellular concentrations increased 5.8- and 5.0-fold respectively. These results demonstrated that PPI, with poor oral bioavailability, is greatly impeded by P-gp efflux, and inhibition of P-gp can enhance its bioavailability. PMID: 25590941 [PubMed - indexed for MEDLINE]

Related Articles Metabolite profiling for the identification of altered metabolic pathways in Alzheimer's disease. J Pharm Biomed Anal. 2015 Mar 25;107:75-81 Authors: González-Domínguez R, García-Barrera T, Gómez-Ariza JL Abstract Gas chromatography coupled to mass spectrometry is the most frequent tool for metabolomic profiling of low molecular weight metabolites. Its suitability in health survey is beyond doubt, given that primary metabolites involved in central pathways of metabolism are usually altered in diseases. The objective of this work is to investigate metabolic differences in serum between Alzheimer's disease patients and healthy controls in order to elucidate pathological mechanisms underlying to disease. Alterations in levels of 23 metabolites were detected, including increased lactic acid, α-ketoglutarate, isocitric acid, glucose, oleic acid, adenosine and cholesterol, as well as decreased urea, valine, aspartic acid, pyroglutamate, glutamine, phenylalanine, asparagine, ornithine, pipecolic acid, histidine, tyrosine, palmitic and uric acid, tryptophan, stearic acid and cystine. Metabolic pathway analysis revealed the involvement of multiple affected pathways, such as energy deficiencies, oxidative stress, hyperammonemia, and others. Moreover, it is noteworthy that some of these compounds have not been previously described in AD research, such as α-ketoglutarate, isocitrate pipecolic acid, pyroglutamate and adenosine, confirming the potential of this metabolomic approach in the search of novel potential markers for early detection of Alzheimer's disease. PMID: 25575172 [PubMed - indexed for MEDLINE]

Related Articles Biomarkers in nonalcoholic fatty liver disease. Can J Gastroenterol Hepatol. 2014 Dec;28(11):607-18 Authors: Neuman MG, Cohen LB, Nanau RM Abstract BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a chronic liver condition characterized by insulin resistance, type 2 diabetes and fat accumulation in the liver that may cause hepatic inflammation and progressive scarring leading to nonalcoholic steatohepatitis (NASH) and irreversible liver damage (cirrhosis). As a result, there has been increased recognition of the need to assess and closely monitor individuals for risk factors of components of NAFLD and NASH, as well as the severity of these conditions using biomarkers. AIM: To review the biomarkers used to diagnose and define the severity of NAFLD and NASH. METHODS: A comprehensive PubMed and Google Scholar literature search was performed using the terms "non-alcoholic fatty liver disease", "non-alcoholic steatohepatitis", as well as the name of each biomarker known to be used. Articles indexed between 2004 and 2014 were used. Each author read the publications separately and the results were discussed. RESULTS: Biomarkers offer a potential prognostic or diagnostic indicator for disease manifestation, progression or both. Serum biomarkers, including total cholesterol, triglycerides, insulin resistance and C-peptide, have been used for many years. Emerging biomarkers, such as apolipoprotein A1, apolipoprotein B, leptin, adiponectin, free fatty acids, ghrelin and tumour necrosis factor-alpha, have been proposed as tools that could provide valuable complementary information to that obtained from traditional biomarkers. Moreover, markers of cell death and mitochondrial dysfunction (cytokeratins) represent powerful predictors of risk. For biomarkers to be clinically useful in accurately diagnosing and treating disorders, age-specific reference intervals that account for differences in sex and ethnic origin are a necessity. CONCLUSIONS: The present review attempts to provide a comprehensive analysis of the emerging risk biomarkers of NAFLD and NASH, and to use the clinical significance and analytical considerations of each biomarker pointing out sentinel features of disease progression. PMID: 25575111 [PubMed - indexed for MEDLINE]

Related Articles Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing. PLoS Genet. 2014 Sep;10(9):e1004620 Authors: Greaves LC, Nooteboom M, Elson JL, Tuppen HA, Taylor GA, Commane DM, Arasaradnam RP, Khrapko K, Taylor RW, Kirkwood TB, Mathers JC, Turnbull DM Abstract Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. However the dynamics of this process and when these mtDNA mutations occur initially are poorly understood. Using human colorectal epithelium as an exemplar tissue with a well-defined stem cell population, we analysed samples from 207 healthy participants aged 17-78 years using a combination of techniques (Random Mutation Capture, Next Generation Sequencing and mitochondrial enzyme histochemistry), and show that: 1) non-pathogenic mtDNA mutations are present from early embryogenesis or may be transmitted through the germline, whereas pathogenic mtDNA mutations are detected in the somatic cells, providing evidence for purifying selection in humans, 2) pathogenic mtDNA mutations are present from early adulthood (<20 years of age), at both low levels and as clonal expansions, 3) low level mtDNA mutation frequency does not change significantly with age, suggesting that mtDNA mutation rate does not increase significantly with age, and 4) clonally expanded mtDNA mutations increase dramatically with age. These data confirm that clonal expansion of mtDNA mutations, some of which are generated very early in life, is the major driving force behind the mitochondrial dysfunction associated with ageing of the human colorectal epithelium. PMID: 25232829 [PubMed - indexed for MEDLINE]

Related Articles Metabolomic and proteomic analysis of serum from preterm infants with necrotising entercolitis and late onset sepsis. Pediatr Res. 2015 Nov 16; Authors: Stewart CJ, Nelson A, Treumann A, Skeath T, Cummings SP, Embleton ND, Berrington JE Abstract BACKGROUND: Necrotising enterocolitis (NEC) and late onset sepsis (LOS) are the leading causes of death among preterm infants in the developed world. This study aimed to explore the serum proteome and metabolome longitudinally in preterm infants with NEC or LOS, matched to controls. METHODS: Nineteen patients (10 cases, 9 controls) were included. A sample 14 days prior to and following, as well as at disease diagnosis, was included for cases. Controls had serum matched at diagnosis for corresponding case. All samples (n=39) underwent shotgun proteomic analysis and 37 samples also underwent metabolomics analysis using ultra performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS). RESULTS: The proteomic and metabolomic profiles of serum were comparable between all infants. Eight proteins were associated with NEC and four proteins were associated with LOS. C-reactive protein (CRP) was increased in all NEC patients at diagnosisConclusion:No single protein or metabolite was detected in all NEC or LOS cases which was absent from controls, however, several proteins were identified which were associated with disease status. The differing expression of these proteins between diseased infants potentially relates to differing pathophysiology of disease. Thus, it is unlikely a single biomarker exists for NEC and/or LOS.Pediatric Research (2015); doi:10.1038/pr.2015.235. PMID: 26571220 [PubMed - as supplied by publisher]

Related Articles The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol. 2015 Nov 16; Authors: Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H Abstract For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).  Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development. PMID: 26571212 [PubMed - as supplied by publisher]

Related Articles Comparative Lipidomics of Caenorhabditis elegans Metabolic Disease Models by SWATH Non-Targeted Tandem Mass Spectrometry. Metabolites. 2015;5(4):677-696 Authors: Prasain JK, Wilson L, Hoang HD, Moore R, Miller MA Abstract Tandem mass spectrometry (MS/MS) with Sequential Window Acquisition of all Theoretical (SWATH) mass spectra generates a comprehensive archive of lipid species within an extract for retrospective, quantitative MS/MS analysis. Here we apply this new technology in Caenorhabditis elegans (C. elegans) to identify potential lipid mediators and pathways. The DAF-1 type I TGF-β and DAF-2 insulin receptors transmit endocrine signals that couple metabolic status to fertility and lifespan. Mutations in daf-1 and daf-2 reduce prostaglandin-endoperoxide synthase (i.e., Cox)-independent prostaglandin synthesis, increase triacylglyceride storage, and alter transcription of numerous lipid metabolism genes. However, the extent to which DAF-1 and DAF-2 signaling modulate lipid metabolism and the underlying mechanisms are not well understood. MS/MSALL with SWATH analysis across the groups identified significant changes in numerous lipids, including specific triacylglycerols, diacylglycerols, and phosphatidylinositols. Examples are provided, using retrospective neutral loss and precursor ion scans as well as MS/MS spectra, to help identify annotated lipids and search libraries for lipids of interest. As proof of principle, we used comparative lipidomics to investigate the prostaglandin metabolism pathway. SWATH data support an unanticipated model: Cox-independent prostaglandin synthesis may involve lysophosphatidylcholine and other lyso glycerophospholipids. This study showcases the power of comprehensive, retrospectively searchable lipid archives as a systems approach for biological discovery in genetic animal models. PMID: 26569325 [PubMed - as supplied by publisher]

Related Articles Global Profiling of Various Metabolites in Platycodon grandiflorum by UPLC-QTOF/MS. Int J Mol Sci. 2015;16(11):26786-26796 Authors: Lee JW, Ji SH, Kim GS, Song KS, Um Y, Kim OT, Lee Y, Hong CP, Shin DH, Kim CK, Lee SE, Ahn YS, Lee DY Abstract In this study, a method of metabolite profiling based on UPLC-QTOF/MS was developed to analyze Platycodon grandiflorum. In the optimal UPLC, various metabolites, including major platycosides, were separated well in 15 min. The metabolite extraction protocols were also optimized by selecting a solvent for use in the study, the ratio of solvent to sample and sonication time. This method was used to profile two different parts of P. grandiflorum, i.e., the roots of P. grandiflorum (PR) and the stems and leaves of P. grandiflorum (PS), in the positive and negative ion modes. As a result, PR and PS showed qualitatively and quantitatively different metabolite profiles. Furthermore, their metabolite compositions differed according to individual plant samples. These results indicate that the UPLC-QTOF/MS-based profiling method is a good tool to analyze various metabolites in P. grandiflorum. This metabolomics approach can also be applied to evaluate the overall quality of P. grandiflorum, as well as to discriminate the cultivars for the medicinal plant industry. PMID: 26569219 [PubMed - as supplied by publisher]

Related Articles The influence of gut microbiota on drug metabolism and toxicity. Expert Opin Drug Metab Toxicol. 2015 Nov 16; Authors: Li H, He J, Jia W Abstract INTRODUCTION: Gut microbiota plays critical roles in drug metabolism. The variation of gut microbiota contributes to the interindividual differences towards drug therapy including drug-induced toxicity and efficacy. Accordingly, the investigation and elucidation of gut microbial impacts on drug metabolism and toxicity will not only facilitate the way of personalized medicine, but also improve the rational drug design. Areas covered: This review provides an overview on the microbiota-host co-metabolism on drug metabolism and summarizes 30 clinical drugs which are co-metabolized by host and gut microbiota. Moreover, this review is specifically focused on elucidating the gut microbial modulation on some clinical drugs, in which the gut microbial influences on drug metabolism, drug-induced toxicity and efficacy are discussed. Expert opinion: The gut microbial contribution to drug metabolism and toxicity is increasingly recognized, but remains largely unexplored due to the extremely complex relationship between gut microbiota and host. The mechanistic elucidation of gut microbiota in drug metabolism is critical before any practical progress in drug design or personalized medicine could be made by modulating human gut microbiota. Analytical technique innovation is urgently required to strengthen our capability in recognizing microbial functions, including metagenomics, metabolomics, and the integration of multi-disciplinary knowledge. PMID: 26569070 [PubMed - as supplied by publisher]

Related Articles High density lipoprotein efficiently accepts surface but not internal oxidised lipids from oxidised low density lipoprotein. Biochim Biophys Acta. 2015 Nov 10; Authors: Rasmiena AA, Barlow CK, Ng TW, Tull D, Meikle PJ Abstract OBJECTIVE: Oxidised low density lipoprotein (oxLDL) contributes to atherosclerosis, whereas high density lipoprotein (HDL) is known to be atheroprotective due, at least in part, to its ability to remove oxidised lipids from oxLDL. The molecular details of the lipid transfer process are not fully understood. We aimed to identify major oxidised lipid species of oxLDL and investigate their transfer upon co-incubation with HDL with varying levels of oxidation. APPROACH AND RESULTS: A total of 14 major species of oxidised phosphatidylcholine and oxidised cholesteryl ester from oxLDL were identified using an untargeted mass spectrometry approach. HDL obtained from pooled plasma of normolipidemic subjects (N=5) was oxidised under mild and heavy oxidative conditions. Non-oxidised (native) HDL and oxidised HDL were co-incubated with oxLDL, re-isolated and lipidomic analysis was performed. Lipoprotein surface lipids, oxidised phosphatidylcholines and oxidised cholesterols (7-ketocholesterol and 7β-hydroxycholesterol), but not internal oxidised cholesteryl esters, were effectively transferred to native HDL. Saturated and monounsaturated lyso-phosphatidylcholines were also transferred from the oxLDL to native HDL. These processes were attenuated when HDL was oxidised under mild and heavy oxidative conditions. The impaired capacities were accompanied by an increase in a ratio of sphingomyelin to phosphatidylcholine and a reduction in phosphatidylserine content in oxidised HDL, both of which are potentially important regulators of the oxidised lipid transfer capacity of HDL. CONCLUSIONS: Our study has revealed the differential transfer efficiency of surface and internal oxidised lipids from oxLDL and their acceptance onto HDL. These capacities were modulated when HDL was itself oxidised. PMID: 26569052 [PubMed - as supplied by publisher]