Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 2 hours 23 min ago

Qualitative characterization of the rat liver mitochondrial lipidome using all ion fragmentation on an Exactive benchtop Orbitrap MS.

Thu, 08/10/2015 - 12:58
Related Articles Qualitative characterization of the rat liver mitochondrial lipidome using all ion fragmentation on an Exactive benchtop Orbitrap MS. Methods Mol Biol. 2015;1264:441-52 Authors: Bird SS, Stavrovskaya IG, Gathungu RM, Tousi F, Kristal BS Abstract Untargeted lipidomics profiling by liquid chromatography-mass spectrometry (LC-MS) allows researchers to observe the occurrences of lipids in a biological sample without showing intentional bias to any specific class of lipids and allows retrospective reanalysis of data collected. Typically, and in the specific method described, a general extraction method followed by LC separation is used to achieve nonspecific class coverage of the lipidome prior to high-resolution accurate mass (HRAM) MS detection. Here we describe a workflow including the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition. We also highlight how, in this method, all-ion fragmentation can be used to identify species of lower abundances, often missed by data-dependent fragmentation techniques. Here we describe the isolation of mitochondria from liver tissue, followed by mitochondrial lipid extraction and the LC-MS conditions used for data acquisition. PMID: 25631033 [PubMed - indexed for MEDLINE]

Integrative methods for studying cardiac energetics.

Thu, 08/10/2015 - 12:58
Related Articles Integrative methods for studying cardiac energetics. Methods Mol Biol. 2015;1264:289-303 Authors: Diolez P, Deschodt-Arsac V, Calmettes G, Gouspillou G, Arsac L, Dos Santos P, Jais P, Haissaguerre M Abstract The more recent studies of human pathologies have essentially revealed the complexity of the interactions involved at the different levels of integration in organ physiology. Integrated organ thus reveals functional properties not predictable by underlying molecular events. It is therefore obvious that current fine molecular analyses of pathologies should be fruitfully combined with integrative approaches of whole organ function. It follows an important issue in the comprehension of the link between molecular events in pathologies, and whole organ function/dysfunction is the development of new experimental strategies aimed at the study of the integrated organ physiology. Cardiovascular diseases are a good example as heart submitted to ischemic conditions has to cope both with a decreased supply of nutrients and oxygen, and the necessary increased activity required to sustain whole body-including the heart itself-oxygenation.By combining the principles of control analysis with noninvasive (31)P NMR measurement of the energetic intermediates and simultaneous measurement of heart contractile activity, we developed MoCA (for Modular Control and Regulation Analysis), an integrative approach designed to study in situ control and regulation of cardiac energetics during contraction in intact beating perfused isolated heart (Diolez et al., Am J Physiol Regul Integr Comp Physiol 293(1):R13-R19, 2007). Because it gives real access to integrated organ function, MoCA brings out a new type of information-the "elasticities," referring to internal responses to metabolic changes-that may be a key to the understanding of the processes involved in pathologies. MoCA can potentially be used not only to detect the origin of the defects associated with the pathology, but also to provide the quantitative description of the routes by which these defects-or also drugs-modulate global heart function, therefore opening therapeutic perspectives. This review presents selected examples of the applications to isolated intact beating heart and a wider application to cardiac energetics under clinical conditions with the direct study of heart pathologies. PMID: 25631023 [PubMed - indexed for MEDLINE]

Detection and differentiation between peroxynitrite and hydroperoxides using mitochondria-targeted arylboronic acid.

Thu, 08/10/2015 - 12:58
Related Articles Detection and differentiation between peroxynitrite and hydroperoxides using mitochondria-targeted arylboronic acid. Methods Mol Biol. 2015;1264:171-81 Authors: Zielonka J, Sikora A, Adamus J, Kalyanaraman B Abstract The development of boronic probes enabled reliable detection and quantitative analysis of hydrogen peroxide and peroxynitrite. The major product, in which boronate moiety of the probe is replaced by the hydroxyl group, is however common for both oxidants. Here, we describe how ortho-isomer of mitochondria-targeted phenylboronic acid can be used to detect and differentiate peroxynitrite-dependent and peroxynitrite-independent probe oxidation. This method highlights the detection and quantification of both the major, phenolic product and the minor, peroxynitrite-specific nitrated product of probe oxidation. PMID: 25631013 [PubMed - indexed for MEDLINE]

Metabolite profiling reveals abiotic stress tolerance in Tn5 mutant of Pseudomonas putida.

Thu, 08/10/2015 - 12:58
Related Articles Metabolite profiling reveals abiotic stress tolerance in Tn5 mutant of Pseudomonas putida. PLoS One. 2015;10(1):e0113487 Authors: Chaudhry V, Bhatia A, Bharti SK, Mishra SK, Chauhan PS, Mishra A, Sidhu OP, Nautiyal CS Abstract Pseudomonas is an efficient plant growth-promoting rhizobacteria (PGPR); however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. Transposon 5 (Tn5) mutagenesis was used to generate a stress tolerant mutant from a PGPR Pseudomonas putida NBRI1108 isolated from chickpea rhizosphere. A mutant NBRI1108T, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. Southern hybridization analysis of EcoRI and XhoI restricted genomic DNA of NBRI1108T confirmed that it had a single Tn5 insertion. The metabolic changes in the polar and non-polar extracts of NBRI1108 and NBRI1108T were examined using 1H, 31P nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS). Thirty six chemically diverse metabolites consisting of amino acids, fatty acids and phospholipids were identified and quantified. Insertion of Tn5 influenced amino acid and phospholipid metabolism and resulted in significantly higher concentration of aspartic acid, glutamic acid, glycinebetaine, glycerophosphatidylcholine (GPC) and putrescine in NBRI1108T as compared to that in NBRI1108. The concentration of glutamic acid, glycinebetaine and GPC increased by 34%, 95% and 100%, respectively in the NBRI1108T as compared to that in NBRI1108. High concentration of glycerophosphatidylethanolamine (GPE) and undetected GPC in NBRI1108 indicates that biosynthesis of GPE may have taken place via the methylation pathway of phospholipid biosynthesis. However, high GPC and low GPE concentration in NBRI1108T suggest that methylation pathway and phosphatidylcholine synthase (PCS) pathway of phospholipid biosynthesis are being followed in the NBRI1108T. Application of multivariate principal component analysis (PCA) on the quantified metabolites revealed clear variations in NBRI1108 and NBRI1108T in polar and non-polar metabolites. Identification of abiotic stress tolerant metabolites from the NBRI1108T suggest that Tn5 mutagenesis enhanced tolerance towards high temperature and drought. Tolerance to drought was further confirmed in greenhouse experiments with maize as host plant, where NBRI1108T showed relatively high biomass under drought conditions. PMID: 25629312 [PubMed - indexed for MEDLINE]

Proteomic adaptations to starvation prepare Escherichia coli for disinfection tolerance.

Thu, 08/10/2015 - 12:58
Related Articles Proteomic adaptations to starvation prepare Escherichia coli for disinfection tolerance. Water Res. 2015 Feb 1;69:110-9 Authors: Du Z, Nandakumar R, Nickerson KW, Li X Abstract Despite the low nutrient level and constant presence of secondary disinfectants, bacterial re-growth still occurs in drinking water distribution systems. The molecular mechanisms that starved bacteria use to survive low-level chlorine-based disinfectants are not well understood. The objective of this study is to investigate these molecular mechanisms at the protein level that prepare starved cells for disinfection tolerance. Two commonly used secondary disinfectants chlorine and monochloramine, both at 1 mg/L, were used in this study. The proteomes of normal and starved Escherichia coli (K12 MG1655) cells were studied using quantitative proteomics. Over 60-min disinfection, starved cells showed significantly higher disinfection tolerance than normal cells based on the inactivation curves for both chlorine and monochloramine. Proteomic analyses suggest that starvation may prepare cells for the oxidative stress that chlorine-based disinfection will cause by affecting glutathione metabolism. In addition, proteins involved in stress regulation and stress responses were among the ones up-regulated under both starvation and chlorine/monochloramine disinfection. By comparing the fold changes under different conditions, it is suggested that starvation prepares E. coli for disinfection tolerance by increasing the expression of enzymes that can help cells survive chlorine/monochloramine disinfection. Protein co-expression analyses show that proteins in glycolysis and pentose phosphate pathway that were up-regulated under starvation are also involved in disinfection tolerance. Finally, the production and detoxification of methylglyoxal may be involved in the chlorine-based disinfection and cell defense mechanisms. PMID: 25463932 [PubMed - indexed for MEDLINE]

Testing tuberculosis drug efficacy in a zebrafish high-throughput translational medicine screen.

Thu, 08/10/2015 - 12:58
Related Articles Testing tuberculosis drug efficacy in a zebrafish high-throughput translational medicine screen. Antimicrob Agents Chemother. 2015 Feb;59(2):753-62 Authors: Ordas A, Raterink RJ, Cunningham F, Jansen HJ, Wiweger MI, Jong-Raadsen S, Bos S, Bates RH, Barros D, Meijer AH, Vreeken RJ, Ballell-Pages L, Dirks RP, Hankemeier T, Spaink HP Abstract The translational value of zebrafish high-throughput screens can be improved when more knowledge is available on uptake characteristics of potential drugs. We investigated reference antibiotics and 15 preclinical compounds in a translational zebrafish-rodent screening system for tuberculosis. As a major advance, we have developed a new tool for testing drug uptake in the zebrafish model. This is important, because despite the many applications of assessing drug efficacy in zebrafish research, the current methods for measuring uptake using mass spectrometry do not take into account the possible adherence of drugs to the larval surface. Our approach combines nanoliter sampling from the yolk using a microneedle, followed by mass spectrometric analysis. To date, no single physicochemical property has been identified to accurately predict compound uptake; our method offers a great possibility to monitor how any novel compound behaves within the system. We have correlated the uptake data with high-throughput drug-screening data from Mycobacterium marinum-infected zebrafish larvae. As a result, we present an improved zebrafish larva drug-screening platform which offers new insights into drug efficacy and identifies potential false negatives and drugs that are effective in zebrafish and rodents. We demonstrate that this improved zebrafish drug-screening platform can complement conventional models of in vivo Mycobacterium tuberculosis-infected rodent assays. The detailed comparison of two vertebrate systems, fish and rodent, may give more predictive value for efficacy of drugs in humans. PMID: 25385118 [PubMed - indexed for MEDLINE]

metabolomics; +17 new citations

Wed, 07/10/2015 - 15:05
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 2015/10/07PubMed 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.

Metabolic Profiling of Alpine and Ecuadorian Lichens.

Tue, 06/10/2015 - 13:42
Metabolic Profiling of Alpine and Ecuadorian Lichens. Molecules. 2015;20(10):18047-18065 Authors: Mittermeier VK, Schmitt N, Volk LP, Suárez JP, Beck A, Eisenreich W Abstract Non-targeted ¹H-NMR methods were used to determine metabolite profiles from crude extracts of Alpine and Ecuadorian lichens collected from their natural habitats. In control experiments, the robustness of metabolite detection and quantification was estimated using replicate measurements of Stereocaulon alpinum extracts. The deviations in the overall metabolite fingerprints were low when analyzing S. alpinum collections from different locations or during different annual and seasonal periods. In contrast, metabolite profiles observed from extracts of different Alpine and Ecuadorian lichens clearly revealed genus- and species-specific profiles. The discriminating functions determining cluster formation in principle component analysis (PCA) were due to differences in the amounts of genus-specific compounds such as sticticin from the Sticta species, but also in the amounts of ubiquitous metabolites, such as sugar alcohols or trehalose. However, varying concentrations of these metabolites from the same lichen species e.g., due to different environmental conditions appeared of minor relevance for the overall cluster formation in PCA. The metabolic clusters matched phylogenetic analyses using nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences of lichen mycobionts, as exemplified for the genus Sticta. It can be concluded that NMR-based non-targeted metabolic profiling is a useful tool in the chemo-taxonomy of lichens. The same approach could also facilitate the discovery of novel lichen metabolites on a rapid and systematical basis. PMID: 26437395 [PubMed - as supplied by publisher]

An efficient and robust fatty acid profiling method for plasma metabolomic studies by gas chromatography-mass spectrometry.

Tue, 06/10/2015 - 13:42
An efficient and robust fatty acid profiling method for plasma metabolomic studies by gas chromatography-mass spectrometry. Clin Chim Acta. 2015 Oct 2; Authors: Chiu HH, Tsai SJ, Tseng YJ, Wu MS, Liao WC, Huang CS, Kuo CH Abstract BACKGROUND: Targeted metabolomic analysis of fatty acids has linked the dysregulation of fatty acids to many diseases. This study selected five frequently used fatty acid derivitization methods for comparison. METHODS: We compared the method precisions and derivatization efficiencies, the most economical and best performing method was subjected to method-validation. Twenty-four fatty acid standards were used to validate the method, which was later applied to the investigation of potential fatty acid markers of breast cancer. RESULTS: The acetyl chloride method was demonstrated to provide the best derivatization efficiency and lowest cost for plasma samples. The ionic liquid column successfully separated positional and geometric fatty acid isomers within 26min under the optimized conditions. Intra-day and inter-day CVsfor most of the fatty acids were <10%. Over 90% of the results showed recoveries within 85%-115%. The validated method was applied to investigate potential fatty acid markers of breast cancer. The fatty acid profiling results revealed 3 fatty acids (C22:0, C24:0, C18:2n6) were significantly lower in both pre- and post-menopausal breast cancer patients (P<0.05). CONCLUSIONS: We demonstrated that the proposed method is an accurate, efficient and economical method for plasma metabolomic studies of fatty acids. PMID: 26436485 [PubMed - as supplied by publisher]

Menopause as a predictor of new-onset asthma: A longitudinal Northern European population study.

Tue, 06/10/2015 - 13:42
Menopause as a predictor of new-onset asthma: A longitudinal Northern European population study. J Allergy Clin Immunol. 2015 Oct 1; Authors: Triebner K, Johannessen A, Puggini L, Benediktsdóttir B, Bertelsen RJ, Bifulco E, Dharmage SC, Dratva J, Franklin KA, Gíslason T, Holm M, Jarvis D, Leynaert B, Lindberg E, Malinovschi A, Macsali F, Norbäck D, Omenaas ER, Rodríguez FJ, Saure E, Schlünssen V, Sigsgaard T, Skorge TD, Wieslander G, Zemp E, Svanes C, Hustad S, Gómez Real F Abstract BACKGROUND: There is limited and conflicting evidence on the effect of menopause on asthma. OBJECTIVES: We sought to study whether the incidence of asthma and respiratory symptoms differ by menopausal status in a longitudinal population-based study with an average follow-up of 12 years. METHODS: The Respiratory Health in Northern Europe study provided questionnaire data pertaining to respiratory and reproductive health at baseline (1999-2001) and follow-up (2010-2012). The study cohort included women aged 45 to 65 years at follow-up, without asthma at baseline, and not using exogenous hormones (n = 2322). Menopausal status was defined as nonmenopausal, transitional, early postmenopausal, and late postmenopausal. Associations with asthma (defined by the use of asthma medication, having asthma attacks, or both) and respiratory symptoms scores were analyzed by using logistic (asthma) and negative binomial (respiratory symptoms) regressions, adjusting for age, body mass index, physical activity, smoking, education, and study center. RESULTS: The odds of new-onset asthma were increased in women who were transitional (odds ratio, 2.40; 95% CI, 1.09-5.30), early postmenopausal (odds ratio, 2.11; 95% CI, 1.06-4.20), and late postmenopausal (odds ratio, 3.44; 95% CI, 1.31-9.05) at follow-up compared with nonmenopausal women. The risk of respiratory symptoms increased in early postmenopausal (coefficient, 0.40; 95% CI, 0.06-0.75) and late postmenopausal (coefficient, 0.69; 95% CI, 0.15-1.23) women. These findings were consistent irrespective of smoking status and across study centers. CONCLUSIONS: New-onset asthma and respiratory symptoms increased in women becoming postmenopausal in a longitudinal population-based study. Clinicians should be aware that respiratory health might deteriorate in women during reproductive aging. PMID: 26435006 [PubMed - as supplied by publisher]

Tri-Omics Analysis of Imatinib Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis.

Tue, 06/10/2015 - 13:42
Tri-Omics Analysis of Imatinib Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis. Anal Chem. 2015 Oct 3; Authors: Breitkopf SB, Yuan M, Helenius KP, Lyssiotis CA, Asara JM Abstract The combination of metabolomics, lipidomics and phosphoproteomics that incorporates triple SILAC protein labeling as well as 13C in vivo metabolite labeling was demonstrated on BCR-ABL positive H929 multiple myeloma cells. From 11,880 phosphorylation sites, we confirm that H929 cells are primarily signaling through the BCR-ABL-ERK pathway and show that imatinib treatment not only down-regulates phosphosites in this pathway, but also up-regulates phosphosites on proteins involved in RNA expression. Metabolomics analyses reveal that BCR-ABL-ERK signaling in H929 cells drives the pentose phosphate pathway (PPP) and RNA biosynthesis, where pathway inhibition via imatinib results in marked PPP impairment and an accumulation of RNA nucleotides and negative regulation of mRNA. Lipidomics data also show an overall reduction in lipid biosynthesis and fatty acid incorporation with a significant decrease in lysophospholipids. RNA immunoprecipitation studies confirm that RNA degradation is inhibited with short imatinib treatment and transcription is inhibited upon long imatinib treatment, validating the "tri-omics" results. These data show the utility of combining mass spectrometry based -omics technologies and reveals that kinase inhibitors may not only down-regulate phosphorylation of their targets but also induce metabolic events via increased phosphorylation of other cellular components. PMID: 26434776 [PubMed - as supplied by publisher]

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

Tue, 06/10/2015 - 13:42
Thermal Degradation of Small Molecules: A Global Metabolomic Investigation. Anal Chem. 2015 Oct 4; Authors: Fang M, Ivanisevic J, Johnson CH, Kurczy ME, Patti GJ, Hoang LT, Uritboonthai W, Benton HP, Siuzdak G Abstract Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolites. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250°C) at different exposure times (30s, 60s, and 300s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online (xcmsonline.scripps.edu). The results showed that heating at an elevated temperature of 100°C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250°C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250°C, 300s) with a significant formation of upregulated, degradation and transformation products. Derivatized samples were similarly affected by thermal degradation. The analysis of the 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30s). For example, tri- and di-organophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was also identified in both the underivatized and derivatized of the plasma metabolites and small molecule standard mixture, and was likely generated from reaction(s) with oleic acid. Overall these analyses show that small molecules and metabolites undergo significant time-sensitive alterations when exposed to elevated temperatures, especially those conditions consistent with GC/MS experiments. PMID: 26434689 [PubMed - as supplied by publisher]

Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections.

Tue, 06/10/2015 - 13:42
Related Articles Using metabolomic and transportomic modeling and machine learning to identify putative novel therapeutic targets for antibiotic resistant Pseudomonad infections. Conf Proc IEEE Eng Med Biol Soc. 2014;2014:314-7 Authors: Larsen PE, Collart FR, Dai Y Abstract Hospital acquired infections sicken or kill tens of thousands of patients every year. These infections are difficult to treat due to a growing prevalence of resistance to many antibiotics. Among these hospital acquired infections, bacteria of the genus Pseudomonas are among the most common opportunistic pathogens. Computational methods for predicting potential novel antimicrobial therapies for hospital acquired Pseudomonad infections, as well as other hospital acquired infectious pathogens, are desperately needed. Using data generated from sequenced Pseudomonad genomes and metabolomic and transportomic computational approaches developed in our laboratory, we present a support vector machine learning method for identifying the most predictive molecular mechanisms that distinguish pathogenic from non-pathogenic Pseudomonads. Predictions were highly accurate, yielding F-scores between 0.84 and 0.98 in leave one out cross validations. These mechanisms are high-value targets for the development of new antimicrobial therapies. PMID: 25569960 [PubMed - indexed for MEDLINE]

Editorial overview: Omics: Methods to monitor and manipulate biological systems: recent advances in 'omics'.

Tue, 06/10/2015 - 13:42
Related Articles Editorial overview: Omics: Methods to monitor and manipulate biological systems: recent advances in 'omics'. Curr Opin Chem Biol. 2015 Feb;24:v-vii Authors: Cravatt BF, Kodadek T PMID: 25549533 [PubMed - indexed for MEDLINE]

Aluminium stress disrupts metabolic performance of Plantago almogravensis plantlets transiently.

Mon, 05/10/2015 - 15:02
Related Articles Aluminium stress disrupts metabolic performance of Plantago almogravensis plantlets transiently. Biometals. 2015 Oct 3; Authors: Grevenstuk T, Moing A, Maucourt M, Deborde C, Romano A Abstract Little is known about how tolerant plants cope with internalized aluminium (Al). Tolerant plants are known to deploy efficient detoxification mechanisms, however it is not known to what extent the primary and secondary metabolism is affected by Al. The aim of this work was to study the metabolic repercussions of Al stress in the tolerant plant Plantago almogravensis. P. almogravensis is well adapted to acid soils where high concentrations of free Al are found and has been classified as a hyperaccumulator. In vitro reared plantlets were used for this purpose in order to control Al exposure rigorously. The metabolome of P. almogravensis plantlets as well as its metabolic response to the supply of sucrose was characterized. The supply of sucrose leads to an accumulation of amino acids and secondary metabolites and consumption of carbohydrates that result from increased metabolic activity. In Al-treated plantlets the synthesis of amino acids and secondary metabolites is transiently impaired, suggesting that P. almogravensis is able to recover from the Al treatment within the duration of the trials. In the presence of Al the consumption of carbohydrate resources is accelerated. The content of some metabolic stress markers also demonstrates that P. almogravensis is highly adapted to Al stress. PMID: 26433896 [PubMed - as supplied by publisher]

Colon-derived uremic biomarkers induced by the acute toxicity of Kansui radix: A metabolomics study of rat plasma and intestinal contents by UPLC-QTOF-MS(E).

Mon, 05/10/2015 - 15:02
Related Articles Colon-derived uremic biomarkers induced by the acute toxicity of Kansui radix: A metabolomics study of rat plasma and intestinal contents by UPLC-QTOF-MS(E). J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Sep 25; Authors: Yang Z, Hou JJ, Qi P, Yang M, Yan BP, Bi QR, Feng RH, Yang WZ, Wu WY, Guo DA Abstract Kansui radix (KR) is a poisonous Chinese herbal medicine recorded in the Chinese Pharmacopoeia, and the acute toxicity obstructs its clinical applications. To explore its acute toxicity mechanism to enhance clinical safety, a metabolomics study based on UPLC-ESI-QTOF-MS(E) was performed. Wistar rats were exposed for 4h to the aqueous and ethyl acetate extracts prepared from KR at a high dose (25g/kg). The contents of six different sections of rat intestine, including the duodenum, jejunum, ileum, cecum, colon, and rectum were collected as samples for the first time, as well as the rat plasma. The interesting results showed that only those rats exposed to the ethyl acetate extract showed a watery diarrhea, similar to the observed acute human toxicity. The identified biomarkers found in the plasma, such as phenol sulfate, indoxyl sulfate, and p-cresol sulfate were significantly perturbed in the rats. These biomarkers are known as colon-derived uremic compounds, which were first reported with respect to KR. The three essential amino acids which produced these biomarkers were only found in the contents of colon and rectum. A hypothesis was proposed that only the colon-derived uremic compounds induced by KR might be responsible for the acute toxicity. Three traditional process methods to reduce the toxicity of KR were compared based on these biomarkers, and different levels of toxicity modulation were observed. These results may be helpful to further understand the mechanism of acute toxicity, and the relevance of the traditional process methods to ameliorate the adverse effects of KR. PMID: 26433353 [PubMed - as supplied by publisher]

UPLC-HRMS based metabolomics reveals the sphingolipids with long fatty chains and olefinic bonds up-regulated in metabolic pathway for hypoxia preconditioning.

Sun, 04/10/2015 - 13:47
UPLC-HRMS based metabolomics reveals the sphingolipids with long fatty chains and olefinic bonds up-regulated in metabolic pathway for hypoxia preconditioning. Chem Biol Interact. 2015 Sep 30; Authors: Zhou T, Wang M, Cheng H, Cui C, Su S, Xu P, Xue M Abstract Hypoxia preconditioning (HPC) could protect cells, tissues, organs and systems from hypoxia injury, but the molecular mechanism still remained unclear. The ultra-high performance liquid chromatography coupled high resolution mass spectrometry (UPLC-HRMS) based metabolomics method was utilized to explore the key endogenous metabolites and metabolic pathways related to HPC. Our results clearly showed that the HPC mice model was established and refined, suggesting that there were significant differences between the control group and 6×HPC group at the molecular levels. A serious of statistical analyses, including univariate analysis and multivariate analysis, were performed by the Progenesis QI software package and MetaboAnalyst web-server. The sphingolipid metabolic pathways were noticed due to the low p-value and high pathway impact calculated by the MetaboAnalyst and the pathways were altered under HPC condition. Especially, the sphingolipid compound sphingomyelin, ceramide, glucosylceramide, galactosylceramide and lactosylceramide were mapping in this metabolic pathway. Interestingly, these sphingolipid metabolites with olefinic bond in the long fatty chain were up-regulated, while those sphingolipids without olefinic bond were down-regulated. The results indicated that C24:1-Cers played a critical role in HPC and had potential in endogenous protective mechanism. Our data provided an insight to further reveal the protection mechanism of HPC. PMID: 26433137 [PubMed - as supplied by publisher]

Biochemical Insights from Population Studies with Genetics and Metabolomics.

Sun, 04/10/2015 - 13:47
Biochemical Insights from Population Studies with Genetics and Metabolomics. Arch Biochem Biophys. 2015 Sep 30; Authors: Suhre K, Raffler J, Kastenmüller G Abstract Genome-wide association studies with concentrations of hundreds of small molecules in samples collected from thousands of individuals (mGWAS) access otherwise inaccessible natural genetic experiments and their influence on the metabolic capacities of the human body. By sampling the natural metabolic and genetic variability that is present in the general population, mGWAS identified over 150 associations between genetic variants and variation in the metabolic composition of human body fluids. Many of these genetic variants were found to be located in enzyme or transporter coding genes, whose functions match the biochemical nature of the associated metabolites. Associations identified by mGWAS can reveal novel biochemical knowledge, such as the function of uncharacterized genes, the biochemical identity of small molecules, and the structure of entire biochemical pathways. Here we review findings of recent mGWAS and discuss concrete examples of how their results can be interpreted in a biochemical context. We describe online resources that are available for mining mGWAS results. In this context, we present two concepts that also find more general applications in the field of metabolomics: strengthening of associations by looking at ratios between metabolite pairs and reconstruction of metabolic pathways by Gaussian graphical modeling. PMID: 26432701 [PubMed - as supplied by publisher]

Exhaled Molecular Fingerprinting in Diagnosis and Monitoring: Validating Volatile Promises.

Sun, 04/10/2015 - 13:47
Exhaled Molecular Fingerprinting in Diagnosis and Monitoring: Validating Volatile Promises. Trends Mol Med. 2015 Oct;21(10):633-44 Authors: Boots AW, Bos LD, van der Schee MP, van Schooten FJ, Sterk PJ Abstract Medical diagnosis and phenotyping increasingly incorporate information from complex biological samples. This has promoted the development and clinical application of non-invasive metabolomics in exhaled air (breathomics). In respiratory medicine, expired volatile organic compounds (VOCs) are associated with inflammatory, oxidative, microbial, and neoplastic processes. After recent proof of concept studies demonstrating moderate to good diagnostic accuracies, the latest efforts in breathomics are focused on optimization of sensor technologies and analytical algorithms, as well as on independent validation of clinical classification and prediction. Current research strategies are revealing the underlying pathophysiological pathways as well as clinically-acceptable levels of diagnostic accuracy. Implementing recent guidelines on validating molecular signatures in medicine will enhance the clinical potential of breathomics and the development of point-of-care technologies. PMID: 26432020 [PubMed - in process]

Global Metabolomic Profiling of Mice Brains following Experimental Infection with the Cyst-Forming Toxoplasma gondii.

Sat, 03/10/2015 - 12:37
Global Metabolomic Profiling of Mice Brains following Experimental Infection with the Cyst-Forming Toxoplasma gondii. PLoS One. 2015;10(10):e0139635 Authors: Zhou CX, Zhou DH, Elsheikha HM, Liu GX, Suo X, Zhu XQ Abstract The interplay between the Apicomplexan parasite Toxoplasma gondii and its host has been largely studied. However, molecular changes at the metabolic level in the host central nervous system and pathogenesis-associated metabolites during brain infection are largely unexplored. We used a global metabolomics strategy to identify differentially regulated metabolites and affected metabolic pathways in BALB/c mice during infection with T. gondii Pru strain at 7, 14 and 21 days post-infection (DPI). The non-targeted Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics analysis detected approximately 2,755 retention time-exact mass pairs, of which more than 60 had significantly differential profiles at different stages of infection. These include amino acids, organic acids, carbohydrates, fatty acids, and vitamins. The biological significance of these metabolites is discussed. Principal Component Analysis and Orthogonal Partial Least Square-Discriminant Analysis showed the metabolites' profile to change over time with the most significant changes occurring at 14 DPI. Correlated metabolic pathway imbalances were observed in carbohydrate metabolism, lipid metabolism, energetic metabolism and fatty acid oxidation. Eight metabolites correlated with the physical recovery from infection-caused illness were identified. These findings indicate that global metabolomics adopted in this study is a sensitive approach for detecting metabolic alterations in T. gondii-infected mice and generated a comparative metabolic profile of brain tissue distinguishing infected from non-infected host. PMID: 26431205 [PubMed - as supplied by publisher]

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