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: 1 hour 9 min ago

Antiproliferative and Apoptotic Activity of Chamaecyparis obtusa Leaf Extract against the HCT116 Human Colorectal Cancer Cell Line and Investigation of the Bioactive Compound by Gas Chromatography-Mass Spectrometry-Based Metabolomics.

Thu, 08/10/2015 - 12:58
Related Articles Antiproliferative and Apoptotic Activity of Chamaecyparis obtusa Leaf Extract against the HCT116 Human Colorectal Cancer Cell Line and Investigation of the Bioactive Compound by Gas Chromatography-Mass Spectrometry-Based Metabolomics. Molecules. 2015;20(10):18066-18082 Authors: Kim HY, Lee SG, Oh TJ, Lim SR, Kim SH, Lee HJ, Kim YS, Choi HK Abstract Chamaecyparis obtusa (CO) belongs to the Cupressaceae family, and it is found widely distributed in Japan and Korea. In this study, the anti-proliferative activities of the methanol and water extracts of CO leaves against a human colorectal cancer cell line (HCT116) were investigated. The methanol extract of CO leaves, at a concentration of 1.25 µg/mL, exhibited anti-proliferative activity against HCT116 cells, while displaying no cytotoxicity against Chang liver cells. Comparative global metabolite profiling was performed using gas chromatography-mass spectrometry coupled with multivariate statistical analysis, and it was revealed that anthricin was the major compound contributing to the anti-proliferative activity. The activation of c-Jun N-terminal kinases played a key role in the apoptotic effect of the methanol extract of CO leaves in HCT116 human colon cancer cells. These results suggest that the methanol extract and anthricin derived from CO leaves might be useful in the development of medicines with anti-colorectal cancer activity. PMID: 26445036 [PubMed - as supplied by publisher]

Overview of 'Omics Technologies for Military Occupational Health Surveillance and Medicine.

Thu, 08/10/2015 - 12:58
Related Articles Overview of 'Omics Technologies for Military Occupational Health Surveillance and Medicine. Mil Med. 2015 Oct;180(10S):34-48 Authors: Bradburne C, Graham D, Kingston HM, Brenner R, Pamuku M, Carruth L Abstract Systems biology ('omics) technologies are emerging as tools for the comprehensive analysis and monitoring of human health. In order for these tools to be used in military medicine, clinical sampling and biobanking will need to be optimized to be compatible with downstream processing and analysis for each class of molecule measured. This article provides an overview of 'omics technologies, including instrumentation, tools, and methods, and their potential application for warfighter exposure monitoring. We discuss the current state and the potential utility of personalized data from a variety of 'omics sources including genomics, epigenomics, transcriptomics, metabolomics, proteomics, lipidomics, and efforts to combine their use. Issues in the "sample-to-answer" workflow, including collection and biobanking are discussed, as well as national efforts for standardization and clinical interpretation. Establishment of these emerging capabilities, along with accurate xenobiotic monitoring, for the Department of Defense could provide new and effective tools for environmental health monitoring at all duty stations, including deployed locations. PMID: 26444891 [PubMed - as supplied by publisher]

Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli.

Thu, 08/10/2015 - 12:58
Related Articles Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli. Biotechnol Bioeng. 2015 Oct 7; Authors: Taymaz-Nikerel H, De Mey M, Baart GJ, Maertens J, Foulquié-Moreno MR, Charlier D, Heijnen JJ, van Gulik WM Abstract An aerobic succinate-producing Escherichia coli mutant was compared to its wild type by quantitatively analyzing both the metabolome and fluxome, during glucose-limited steady state and succinate excess dynamic conditions, in order to identify targets for further strain engineering towards a more efficient succinate production. The mutant had four functional mutations under the conditions investigated: increased expression of a succinate exporter (DcuC), deletion of a succinate importer (Dct), deletion of succinate dehydrogenase (SUCDH) and expression of a PEP carboxylase (PPC) with increased capacity due to a point mutation. The steady state and dynamic patterns of the intracellular metabolite levels and fluxes in response to changes were used to locate the quantitative differences in the physiology/metabolism of the mutant strain. Unexpectedly the mutant had higher energy efficiency indicated by a much lower rate of oxygen consumption, under glucose-limited conditions, caused by the deletion of the transcription factors IclR and ArcA. Furthermore the mutant had a much lower uptake capacity for succinate (26 fold) and oxygen (17 fold under succinate excess) compared to the wild type strain. The mutant strain produced 7.9 mmol.CmolX(-1) .h(-1) succinate during chemostat cultivation, showing that the choice of applied genetic modifications was a successful strategy. Furthermore, the applied genetic modifications resulted in multiple large changes in metabolite levels (FBP, pyruvate, 6PG, NAD(+) /NADH ratio, α-ketogluarate) corresponding to large changes in fluxes. Compared to the wild type a considerable flux shift occurred from the tricarboxylic acid (TCA) cycle to the oxidative part of the pentose phosphate pathway, including an inversion of the pyruvate kinase flux. The mutant responded very differently to excess of succinate, with a remarkable possible reversal of the TCA cycle. The mutant and the wild type both showed homeostatic behaviour with respect to the energy charge. In contrast, large changes in redox ratios (NAD(+) /NADH) occurred in the wild type, while the mutant showed even larger changes. This large redox change can be associated to the reversal of flux directions. The observed large flexibility in the central metabolism following genetic (deletions) and environmental (substrate excess) perturbations of the mutant, indicates that introducing a more efficient succinate exporter could result in an even higher succinate production rate. This article is protected by copyright. All rights reserved. PMID: 26444867 [PubMed - as supplied by publisher]

Natural and therapy-induced immunosurveillance in breast cancer.

Thu, 08/10/2015 - 12:58
Related Articles Natural and therapy-induced immunosurveillance in breast cancer. Nat Med. 2015 Oct 7;21(10):1128-1138 Authors: Kroemer G, Senovilla L, Galluzzi L, André F, Zitvogel L Abstract The immunosurveillance theory postulates that tumors evolve and progress in an uncontrolled fashion only when anticancer immune responses fail. Natural immunosurveillance clearly influences human breast cancer (BC) progression because the prognosis of BC patients is dictated by the density, composition and activity of the tumor immune infiltrate at diagnosis. Moreover, chemotherapeutic and radiotherapeutic regimens commonly employed for the treatment of BC affect the tumor immune infiltrate, and accumulating data suggest that the clinical efficacy of these treatments is largely determined by T cell-dependent tumor-specific immune responses. In addition, the mechanism of action of targeted anticancer therapeutics, such as the erb-b2 receptor tyrosine kinase 2 (ERBB2)-targeting agent trastuzumab, involves the innate and adaptive arms of the immune system. In this Review, we discuss these findings as well as preliminary evidence indicating that immunotherapy constitutes a promising option for the treatment of BC. Moreover, we point out that the successful implementation of immunotherapy to BC management requires the optimization of current immunotherapeutic regimens and the identification of immunological biomarkers that enable improved risk stratification and the design of personalized, dynamic treatment plans. PMID: 26444637 [PubMed - as supplied by publisher]

Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni.

Thu, 08/10/2015 - 12:58
Related Articles Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. J Extracell Vesicles. 2015;4:28665 Authors: Nowacki FC, Swain MT, Klychnikov OI, Niazi U, Ivens A, Quintana JF, Hensbergen PJ, Hokke CH, Buck AH, Hoffmann KF Abstract BACKGROUND: Penetration of skin, migration through tissues and establishment of long-lived intravascular partners require Schistosoma parasites to successfully manipulate definitive host defences. While previous studies of larval schistosomula have postulated a function for excreted/secreted (E/S) products in initiating these host-modulatory events, the role of extracellular vesicles (EVs) has yet to be considered. Here, using preparatory ultracentrifugation as well as methodologies to globally analyse both proteins and small non-coding RNAs (sncRNAs), we conducted the first characterization of Schistosoma mansoni schistosomula EVs and their potential host-regulatory cargos. RESULTS: Transmission electron microscopy analysis of EVs isolated from schistosomula in vitro cultures revealed the presence of numerous, 30-100 nm sized exosome-like vesicles. Proteomic analysis of these vesicles revealed a core set of 109 proteins, including homologs to those previously found enriched in other eukaryotic EVs, as well as hypothetical proteins of high abundance and currently unknown function. Characterization of E/S sncRNAs found within and outside of schistosomula EVs additionally identified the presence of potential gene-regulatory miRNAs (35 known and 170 potentially novel miRNAs) and tRNA-derived small RNAs (tsRNAs; nineteen 5' tsRNAs and fourteen 3' tsRNAs). CONCLUSIONS: The identification of S. mansoni EVs and the combinatorial protein/sncRNA characterization of their cargo signifies that an important new participant in the complex biology underpinning schistosome/host interactions has now been discovered. Further work defining the role of these schistosomula EVs and the function/stability of intra- and extra-vesicular sncRNA components presents tremendous opportunities for developing novel schistosomiasis diagnostics or interventions. PMID: 26443722 [PubMed]

Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context.

Thu, 08/10/2015 - 12:58
Related Articles Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context. Annu Rev Genet. 2015 Oct 5; Authors: Shultzaberger RK, Boyd JS, Diamond S, Greenspan RJ, Golden SS Abstract Early research on the cyanobacterial clock focused on characterizing the genes needed to keep, entrain, and convey time within the cell. As the scope of assays used in molecular genetics has expanded to capture systems-level properties (e.g., RNA-seq, ChIP-seq, metabolomics, high-throughput screening of genetic variants), so has our understanding of how the clock fits within and influences a broader cellular context. Here we review the work that has established a global perspective of the clock, with a focus on (a) an emerging network-centric view of clock architecture, (b) mechanistic insights into how temporal and environmental cues are transmitted and integrated within this network, (c) the systematic alteration of gene expression and cellular metabolism by the clock, and (d) insights into the evolution of temporal control in cyanobacteria. Expected final online publication date for the Annual Review of Genetics Volume 49 is November 23, 2015. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates. PMID: 26442846 [PubMed - as supplied by publisher]

Pilot dietary intervention with heat-stabilized rice bran modulates stool microbiota and metabolites in healthy adults.

Thu, 08/10/2015 - 12:58
Related Articles Pilot dietary intervention with heat-stabilized rice bran modulates stool microbiota and metabolites in healthy adults. Nutrients. 2015;7(2):1282-300 Authors: Sheflin AM, Borresen EC, Wdowik MJ, Rao S, Brown RJ, Heuberger AL, Broeckling CD, Weir TL, Ryan EP Abstract Heat-stabilized rice bran (SRB) has been shown to regulate blood lipids and glucose, modulate gut mucosal immunity and inhibit colorectal cancer in animal and human studies. However, SRB's effects on gut microbial composition and metabolism and the resulting implications for health remain largely unknown. A pilot, randomized-controlled trial was developed to investigate the effects of eating 30 g/day SRB on the stool microbiome and metabolome. Seven healthy participants consumed a study meal and snack daily for 28 days. The microbiome and metabolome were characterized using 454 pyrosequencing and gas chromatography-mass spectrometry (GC-MS) at baseline, two and four weeks post-intervention. Increases in eight operational taxonomic units (OTUs), including three from Bifidobacterium and Ruminococcus genera, were observed after two and four weeks of SRB consumption (p<0.01). Branched chain fatty acids, secondary bile acids and eleven other putative microbial metabolites were significantly elevated in the SRB group after four weeks. The largest metabolite change was a rice bran component, indole-2-carboxylic acid, which showed a mean 12% increase with SRB consumption. These data support the feasibility of dietary SRB intervention in adults and support that SRB consumption can affect gut microbial metabolism. These findings warrant future investigations of larger cohorts evaluating SRB's effects on intestinal health. PMID: 25690418 [PubMed - indexed for MEDLINE]

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]

Pages