WorldWideScience

Sample records for based plant metabolomics

  1. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress.

    Science.gov (United States)

    Jorge, Tiago F; Rodrigues, João A; Caldana, Camila; Schmidt, Romy; van Dongen, Joost T; Thomas-Oates, Jane; António, Carla

    2016-09-01

    Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016. PMID:25589422

  2. Chemical Composition and Seasonality of Aromatic Mediterranean Plant Species by NMR-Based Metabolomics

    OpenAIRE

    Monica Scognamiglio; Brigida D’Abrosca; Assunta Esposito; Antonio Fiorentino

    2015-01-01

    An NMR-based metabolomic approach has been applied to analyse seven aromatic Mediterranean plant species used in traditional cuisine. Based on the ethnobotanical use of these plants, the approach has been employed in order to study the metabolic changes during different seasons. Primary and secondary metabolites have been detected and quantified. Flavonoids (apigenin, quercetin, and kaempferol derivatives) and phenylpropanoid derivatives (e.g., chlorogenic and rosmarinic acid) are the main id...

  3. LC-MS-based metabolomics

    OpenAIRE

    Zhou, Bin; Xiao, Jun Feng; Tuli, Leepika; Ressom, Habtom W

    2011-01-01

    Metabolomics aims at identification and quantitation of small molecules involved in metabolic reactions. LC-MS has enjoyed a growing popularity as the platform for metabolomic studies due to its high throughput, soft ionization, and good coverage of metabolites. The success of LC-MS-based metabolomic study often depends on multiple experimental, analytical, and computational steps. This review presents a workflow of a typical LC-MS-based metabolomic analysis for identification and quantitatio...

  4. An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance.

    Science.gov (United States)

    Leiss, Kirsten A; Choi, Young H; Verpoorte, Robert; Klinkhamer, Peter G L

    2011-06-01

    Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for technical reasons, been restricted to the identification of single compounds applying specific chemical analyses adapted to the compound in question. In biological processes however, usually more than one compound is involved. Metabolomics allows the simultaneous detection of a wide range of compounds, providing an immediate image of the metabolome of a plant. One of the most universally used metabolomic approaches comprises nuclear magnetic resonance spectroscopy (NMR). It has been NMR which has been applied as a proof of principle to show that metabolomics can constitute a major advancement in the study of host plant resistance. Here we give an overview on the application of NMR to identify candidate compounds for host plant resistance. We focus on host plant resistance to western flower thrips (Frankliniella occidentalis) which has been used as a model for different plant species. PMID:21765818

  5. Metabolomic profiling of plant tissues.

    Science.gov (United States)

    Rambla, José L; López-Gresa, M P; Bellés, J M; Granell, Antonio

    2015-01-01

    Metabolomics is a powerful discipline aimed at a comprehensive and global analysis of the metabolites present in a cell, tissue, or organism, and to which increasing attention has been paid in the last few years. Given the high diversity in physical and chemical properties of plant metabolites, not a single method is able to analyze them all.Here we describe two techniques for the profiling of two quite different groups of metabolites: polar and semi-polar secondary metabolites, including many of those involved in plant response to biotic and abiotic stress, and volatile compounds, which include those responsible of most of our perception of food flavor. According to these techniques, polar and semi-polar metabolites are extracted in methanol, separated by liquid chromatography (UPLC), and detected by a UV-VIS detector (PDA) and a time-of-flight (ToF) mass spectrometer. Volatile compounds, on the other hand, are extracted by headspace solid phase microextraction (HS-SPME), and separated and detected by gas chromatography coupled to mass spectrometry (GC-MS). PMID:25757775

  6. (1)H NMR and GC-MS Based Metabolomics Reveal Defense and Detoxification Mechanism of Cucumber Plant under Nano-Cu Stress.

    Science.gov (United States)

    Zhao, Lijuan; Huang, Yuxiong; Hu, Jerry; Zhou, Hongjun; Adeleye, Adeyemi S; Keller, Arturo A

    2016-02-16

    Because copper nanoparticles are being increasingly used in agriculture as pesticides, it is important to assess their potential implications for agriculture. Concerns have been raised about the bioaccumulation of nano-Cu and their toxicity to crop plants. Here, the response of cucumber plants in hydroponic culture at early development stages to two concentrations of nano-Cu (10 and 20 mg/L) was evaluated by proton nuclear magnetic resonance spectroscopy ((1)H NMR) and gas chromatography-mass spectrometry (GC-MS) based metabolomics. Changes in mineral nutrient metabolism induced by nano-Cu were determined by inductively coupled plasma-mass spectrometry (ICP-MS). Results showed that nano-Cu at both concentrations interferes with the uptake of a number of micro- and macro-nutrients, such as Na, P, S, Mo, Zn, and Fe. Metabolomics data revealed that nano-Cu at both levels triggered significant metabolic changes in cucumber leaves and root exudates. The root exudate metabolic changes revealed an active defense mechanism against nano-Cu stress: up-regulation of amino acids to sequester/exclude Cu/nano-Cu; down-regulation of citric acid to reduce the mobilization of Cu ions; ascorbic acid up-regulation to combat reactive oxygen species; and up-regulation of phenolic compounds to improve antioxidant system. Thus, we demonstrate that nontargeted (1)H NMR and GC-MS based metabolomics can successfully identify physiological responses induced by nanoparticles. Root exudates metabolomics revealed important detoxification mechanisms. PMID:26751164

  7. NMR-Based Milk Metabolomics

    Directory of Open Access Journals (Sweden)

    Hanne C. Bertram

    2013-04-01

    Full Text Available Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits.

  8. NMR-Based Milk Metabolomics.

    Science.gov (United States)

    Sundekilde, Ulrik K; Larsen, Lotte B; Bertram, Hanne C

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining a better understanding of how milk composition is linked to nutritional or quality traits. PMID:24957988

  9. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    OpenAIRE

    Jun Hong; Litao Yang; Dabing Zhang; Jianxin Shi

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plan...

  10. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality...... and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including...... applications linking the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers...

  11. Chemometric Methods in Plant Metabolomics

    OpenAIRE

    Isomaa, Keijo

    2013-01-01

    This study focuses on chemometric analysis of instrumental data that has been obtained from chemical analysis of plant extracts. Chemometric analysis applies statistical and mathematical tools on chemical data, aiming to find new information or classifying samples in categories defined by the analyst. Chemometric analysis is based on computational pattern recognition and reveals any features that studied samples may have in common. In the literature part of this study, chemometrics and r...

  12. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science.

    Science.gov (United States)

    Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality. PMID:27258266

  13. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

    Science.gov (United States)

    Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

    2016-01-01

    As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality. PMID:27258266

  14. Time-resolved NMR metabolomics of plant cells based on a microfluidic chip.

    Science.gov (United States)

    Maisch, Jan; Kreppenhofer, Kristina; Büchler, Silke; Merle, Christian; Sobich, Shukhrat; Görling, Benjamin; Luy, Burkhard; Ahrens, Ralf; Guber, Andreas E; Nick, Peter

    2016-08-01

    The plant secondary metabolism generates numerous compounds harbouring pharmaceutical activity. In plants, these compounds are typically formed by different and specialised cell types that have to interact constituting a metabolic process chain. This interactivity impedes biotechnological production of secondary compounds, because cell differentiation is suppressed under the conditions of a batch bio-fermenter. We present a novel strategy to address this limitation using a biomimetic approach, where we simulate the situation in a real tissue by a microfluidic chamber system, where plant cells can be integrated into a process flow. We show that walled cells of the plant model tobacco BY-2 can be successfully cultivated in this system and that physiological parameters (such as cell viability, mitotic index and division synchrony) can be preserved over several days. The microfluidic design allows to resolve dynamic changes of specific metabolites over different stages of culture development. These results serve as proof-of-principle that a microfluidic organisation of cultivated plant cells can mimic the metabolic flows in a real plant tissue. PMID:27318870

  15. An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance

    OpenAIRE

    Leiss, Kirsten A.; Choi, Young H.; Verpoorte, Robert; Klinkhamer, Peter G. L.

    2010-01-01

    Secondary metabolites provide a potential source for the generation of host plant resistance and development of biopesticides. This is especially important in view of the rapid and vast spread of agricultural and horticultural pests worldwide. Multiple pests control tactics in the framework of an integrated pest management (IPM) programme are necessary. One important strategy of IPM is the use of chemical host plant resistance. Up to now the study of chemical host plant resistance has, for te...

  16. Plant metabolomics: from holistic data to relevant biomarkers.

    Science.gov (United States)

    Wolfender, Jean-Luc; Rudaz, Serge; Choi, Young Hae; Kim, Hye Kyong

    2013-01-01

    Metabolomics is playing an increasingly important role in plant science. It aims at the comprehensive analysis of the plant metabolome which consists both of primary and secondary metabolites. The goal of metabolomics is ultimately to identify and quantify this wide array of small molecules in biological samples. This new science is included in several systems biology approaches and is based primarily on the unbiased acquisition of mass spectrometric (MS) or nuclear magnetic resonance (NMR) data from carefully selected samples. This approach provides the most ''functional'' information of the 'omics' technologies of a given organism since metabolites are the end products of the cellular regulatory processes. The application of state-of-the-art data mining, that includes various untargeted and targeted multivariate data analysis methods, to the vast amount of data generated by this data-driven approach leads to sample classification and the identification of relevant biomarkers. The biological areas that have been successfully studied by this holistic approach include global metabolite composition assessment, mutant and phenotype characterisation, taxonomy, developmental processes, stress response, interaction with the environment, quality control assessment, lead finding and mode of action of botanicals. This review summarises the main MS- and NMR-based approaches that are used to perform these studies and discusses the potential and current limitations of the various methods. The intent is not to provide an exhaustive overview of the field, which has grown considerably over the past decade, but to summarise the main strategies that are used and to discuss the potential and limitations of the different approaches as well as future trends. PMID:23210790

  17. Metabolomic characteristics of Catharanthus roseus plants in time and space

    OpenAIRE

    Qifang, Pan

    2014-01-01

    The thesis aims at combining metabolomics with other methods to investigate the regulation of the TIA biosynthesis and how this is connected with other pathways and the plant’s physiology and development. It reviews the biosynthesis studies of Catharanthus roseus. An HPLC method is described for both precursors and alkaloids which was validated to analyze alkaloid contents in different organs, its relationship with leaf age and growth of C. roseus plants. A metabolomics investigation of C. ro...

  18. Integrated LC-MS/MS system for plant metabolomics

    Directory of Open Access Journals (Sweden)

    Yuji Sawada

    2013-01-01

    Full Text Available Liquid chromatography-tandem mass spectrometry (LC-MS/MS is highly sensitive, selective, and enables extensive detection of metabolites within a sample. The result allows us to characterize comprehensive metabolite accumulation patterns without dependence on authentic standard compounds and isolation of the individual metabolites. A reference database search is essential for the structural assignment process of un-targeted MS and MS/MS data. Moreover, the characterization of unknown metabolites is challenging, since these cannot be assigned a candidate structure by using a reference database. In this case study, integrated LC-MS/MS based plant metabolomics allows us to detect several hundred metabolites in a sample; and integrated omics analyses, e.g., large-scale reverse genetics, linkage mapping, and association mapping, provides a powerful tool for candidate structure selection or rejection. We also examine emerging technology and applications for LC-MS/MS-based un-targeted plant metabolomics. These activities promote the characterization of massive extended detectable metabolites.

  19. NMR-Based Milk Metabolomics

    OpenAIRE

    Bertram, Hanne C.; Larsen, Lotte B; Sundekilde, Ulrik K

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the ...

  20. Medicinal Plants: A Public Resource for Metabolomics and Hypothesis Development

    Directory of Open Access Journals (Sweden)

    Eve Syrkin Wurtele

    2012-11-01

    Full Text Available Specialized compounds from photosynthetic organisms serve as rich resources for drug development. From aspirin to atropine, plant-derived natural products have had a profound impact on human health. Technological advances provide new opportunities to access these natural products in a metabolic context. Here, we describe a database and platform for storing, visualizing and statistically analyzing metabolomics data from fourteen medicinal plant species. The metabolomes and associated transcriptomes (RNAseq for each plant species, gathered from up to twenty tissue/organ samples that have experienced varied growth conditions and developmental histories, were analyzed in parallel. Three case studies illustrate different ways that the data can be integrally used to generate testable hypotheses concerning the biochemistry, phylogeny and natural product diversity of medicinal plants. Deep metabolomics analysis of Camptotheca acuminata exemplifies how such data can be used to inform metabolic understanding of natural product chemical diversity and begin to formulate hypotheses about their biogenesis. Metabolomics data from Prunella vulgaris, a species that contains a wide range of antioxidant, antiviral, tumoricidal and anti-inflammatory constituents, provide a case study of obtaining biosystematic and developmental fingerprint information from metabolite accumulation data in a little studied species. Digitalis purpurea, well known as a source of cardiac glycosides, is used to illustrate how integrating metabolomics and transcriptomics data can lead to identification of candidate genes encoding biosynthetic enzymes in the cardiac glycoside pathway. Medicinal Plant Metabolomics Resource (MPM [1] provides a framework for generating experimentally testable hypotheses about the metabolic networks that lead to the generation of specialized compounds, identifying genes that control their biosynthesis and establishing a basis for modeling metabolism in less

  1. Plant metabolomics: from holistic hope, to hype, to hot topic

    NARCIS (Netherlands)

    Hall, R.D.

    2006-01-01

    In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with new

  2. Liquid chromatography-quadrupole time of flight tandem mass spectrometry-based targeted metabolomic study for varietal discrimination of grapes according to plant sterols content.

    Science.gov (United States)

    Millán, Laura; Sampedro, M Carmen; Sánchez, Alicia; Delporte, Cédric; Van Antwerpen, Pierre; Goicolea, M Aranzazu; Barrio, Ramón J

    2016-07-01

    Grapevine and derived products are rich in a wide range of compounds and its quality mainly depends on its metabolites, as a result of viticulture practices. Plant sterols, also called phytosterols (PS), are secondary metabolites regarded as bioactive substance present in grape berries and other plant-based food. The present study deals with a metabolomic approach focusing on phytosterols family in six varieties of Rioja grapes (Cabernet Sauvignon, Tempranillo, Graciano, Garnacha, White Garnacha and Viura), in order to find significant differences among them. Liquid chromatography- mass spectrometry with a quadrupole-time of flight mass analyzer (LC-QTOF) was used to find as many metabolites as possible in the different grape berry fractions, and using statistics to help finding significant clustering of the metabolic profile of pulp, peel and seeds in relation to the variety. The best chromatographic and detection conditions were achieved by gas phase ionization via atmospheric pressure chemical ionization (APCI) in positive mode. Furthermore, analysis with electrospray (ESI) is also needed for phytosterol derivatives confirmation. Putative compounds of interest in the analyzed samples were found by an automated compound extraction algorithm (Molecular Feature Extraction, MFE) and an initial differential expression from the data was created with the aid of commercial software. Once the data were collected, the results were filtered, aligned and normalized, and evaluating applying one-way analysis of variance (ANOVA) with a 95% significance level. For sample class prediction, partial least square-discriminant analysis (PLS-DA) is used as a supervised pattern recognition method and excellent separation among the grape varieties is shown. An overall accuracy of 93.3% (pulp samples), 100.0% (peel) or 96.7% (seeds) in discriminating between grape varieties was achieved when comparing the different fractions. In general, 7 PS derivatives were identified with ID scores

  3. Bridging the gap between comprehensive extraction protocols in plant metabolomics studies and method validation.

    Science.gov (United States)

    Bijttebier, Sebastiaan; Van der Auwera, Anastasia; Foubert, Kenn; Voorspoels, Stefan; Pieters, Luc; Apers, Sandra

    2016-09-01

    It is vital to pay much attention to the design of extraction methods developed for plant metabolomics, as any non-extracted or converted metabolites will greatly affect the overall quality of the metabolomics study. Method validation is however often omitted in plant metabolome studies, as the well-established methodologies for classical targeted analyses such as recovery optimization cannot be strictly applied. The aim of the present study is to thoroughly evaluate state-of-the-art comprehensive extraction protocols for plant metabolomics with liquid chromatography-photodiode array-accurate mass mass spectrometry (LC-PDA-amMS) by bridging the gap with method validation. Validation of an extraction protocol in untargeted plant metabolomics should ideally be accomplished by validating the protocol for all possible outcomes, i.e. for all secondary metabolites potentially present in the plant. In an effort to approach this ideal validation scenario, two plant matrices were selected based on their wide versatility of phytochemicals: meadowsweet (Filipendula ulmaria) for its polyphenols content, and spicy paprika powder (from the genus Capsicum) for its apolar phytochemicals content (carotenoids, phytosterols, capsaicinoids). These matrices were extracted with comprehensive extraction protocols adapted from literature and analysed with a generic LC-PDA-amMS characterization platform that was previously validated for broad range phytochemical analysis. The performance of the comprehensive sample preparation protocols was assessed based on extraction efficiency, repeatability and intermediate precision and on ionization suppression/enhancement evaluation. The manuscript elaborates on the finding that none of the extraction methods allowed to exhaustively extract the metabolites. Furthermore, it is shown that depending on the extraction conditions enzymatic degradation mechanisms can occur. Investigation of the fractions obtained with the different extraction methods

  4. Discrimination of conventional and organic white cabbage from a long-term field trial study using untargeted LC-MS-based metabolomics

    DEFF Research Database (Denmark)

    Mie, Axel; Laursen, Kristian Holst; Åberg, K. Magnus;

    2014-01-01

    The influence of organic and conventional farming practices on the content of single nutrients in plants is disputed in the scientific literature. Here, large-scale untargeted LC-MS-based metabolomics was used to compare the composition of white cabbage from organic and conventional agriculture, ...... cases. Thus, it was concluded that the investigated conventional and organic management practices have a systematic impact on the metabolome of white cabbage. This emphasizes the potential of untargeted metabolomics for authenticity testing of organic plant products....

  5. Metabolomics and bioactive substances in plants

    DEFF Research Database (Denmark)

    Khakimov, Bekzod

    and analysis methods. The first study (Journal of Chromatography A, 1266 (2012) 84–94) demonstrated how the application of a multiway decomposition method, PARAFAC2, can help in providing maximum xtraction of metabolite features from the raw LC-MS data obtained from complex plant extracts. The second study...

  6. Metabolomics in Population-Based Research

    Science.gov (United States)

    Metabolomics is the study of small molecules of both endogenous and exogenous origin, such as metabolic substrates and their products, lipids, small peptides, vitamins and other protein cofactors generated by metabolism, which are downstream from genes.

  7. Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

    Science.gov (United States)

    Rivas-Ubach, Albert; Hódar, José A; Sardans, Jordi; Kyle, Jennifer E; Kim, Young-Mo; Oravec, Michal; Urban, Otmar; Guenther, Alex; Peñuelas, Josep

    2016-07-01

    The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but also the entire metabolome. Metabolomes are the final products of genotypes and are constrained by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from three closely related Pinus species with distant coevolutionary histories with the caterpillar of the processionary moth respond similarly to its attack. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of terpenes were in the attacked trees supporting the hypothesis that herbivores avoid plant individuals with higher concentrations. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution. PMID:27386082

  8. MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

    Directory of Open Access Journals (Sweden)

    Bernillon Stéphane

    2011-06-01

    Full Text Available Abstract Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii for queries and visualization of the data, (iii to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

  9. Metabolomics in Plants and Humans: Applications in the Prevention and Diagnosis of Diseases

    Directory of Open Access Journals (Sweden)

    Diego F. Gomez-Casati

    2013-01-01

    Full Text Available In the recent years, there has been an increase in the number of metabolomic approaches used, in parallel with proteomic and functional genomic studies. The wide variety of chemical types of metabolites available has also accelerated the use of different techniques in the investigation of the metabolome. At present, metabolomics is applied to investigate several human diseases, to improve their diagnosis and prevention, and to design better therapeutic strategies. In addition, metabolomic studies are also being carried out in areas such as toxicology and pharmacology, crop breeding, and plant biotechnology. In this review, we emphasize the use and application of metabolomics in human diseases and plant research to improve human health.

  10. Plant metabolomics and its potential application for human nutrition

    NARCIS (Netherlands)

    Hall, R.D.; Brouwer, I.D.; Fitzgerald, M.A.

    2008-01-01

    With the growing interest in the use of metabolomic technologies for a wide range of biological targets, food applications related to nutrition and quality are rapidly emerging. Metabolomics offers us the opportunity to gain deeper insights into, and have better control of, the fundamental biochemic

  11. LC-MS-BASED METABOLOMICS IN DRUG METABOLISM

    OpenAIRE

    Chen, Chi; Frank J. Gonzalez; Idle, Jeffrey R.

    2007-01-01

    Xenobiotic metabolism, a ubiquitous natural response to foreign compounds, elicits initiating signals for many pathophysiological events. Currently, most widely used techniques for identifying xenobiotic metabolites and metabolic pathways are empirical and largely based on in vitro incubation assays and in vivo radiotracing experiments. Recent work in our lab has shown that LC-MS-based metabolomic techniques are useful tools for xenobiotic metabolism research since multivariate data analysis ...

  12. Spatially resolved in vivo plant metabolomics by laser ablation-based mass spectrometry imaging (MSI) techniques: LDI-MSI and LAESI

    OpenAIRE

    Bartels, Benjamin; Svatoš, Aleš

    2015-01-01

    This short review aims to summarize the current developments and applications of mass spectrometry-based methods for in situ profiling and imaging of plants with minimal or no sample pre-treatment or manipulation. Infrared-laser ablation electrospray ionization and UV-laser desorption/ionization methods are reviewed. The underlying mechanisms of the ionization techniques–namely, laser ablation of biological samples and electrospray ionization–as well as variations of the LAESI ion source for ...

  13. Nuclear magnetic resonance (NMR)-based metabolomics.

    Science.gov (United States)

    Keun, Hector C; Athersuch, Toby J

    2011-01-01

    Biofluids are by far the most commonly studied sample type in metabolic profiling studies, encompassing blood, urine, cerebrospinal fluid, cell culture media and many others. A number of these fluids can be obtained at a high sampling frequency with minimal invasion, permitting detailed characterisation of dynamic metabolic events. One of the attractive properties of solution-state metabolomics is the ability to generate profiles from these fluids following simple preparation, allowing the analyst to gain a naturalistic, largely unbiased view of their composition that is highly representative of the in vivo situation. Solution-state samples can also be generated from the extraction of tissue or cellular samples that can be tailored to target metabolites with particular properties. Nuclear magnetic resonance (NMR) provides an excellent technique for profiling these fluids and is especially adept at characterising complex solutions. Profiling biofluid samples by NMR requires appropriate preparation and experimental conditions to overcome the demands of varied sample matrices, including those with high protein, lipid or saline content, as well as the presence of water in aqueous samples. PMID:21207299

  14. Quantification in untargeted mass spectrometry-based metabolomics

    OpenAIRE

    van der Kloet, Frans Meindert

    2014-01-01

    The aim of this thesis was to develop concepts and methods to extract qualitative and quantitative information about metabolites from untargeted mass spectrometric data of biological samples. Several typical challenges in data handling were addressed that prevent a straightforward interpretation (data analysis) of the data acquired with different types of mass spectrometric-based metabolomics methods (GC-MS, LC-MS, CE-MS or DI-MS) methods. The critical parameters causing variation in quantita...

  15. Spatially-resolved in vivo plant metabolomics by laser ablation-based mass spectrometry imaging (MSI techniques: LDI-MSI and LAESI

    Directory of Open Access Journals (Sweden)

    Aleš eSvatoš

    2015-07-01

    Full Text Available This short review aims to summarize the current developments and applications of mass spectrometry-based methods for in situ profiling and imaging of plants with minimal or no sample pre-treatment or manipulation. Infrared-laser ablation electrospray ionization (LAESI and UV-laser desorption/ionization (LDI methods are reviewed. The underlying mechanisms of the ionization techniques - namely, laser ablation of biological samples and electrospray ionization - as well as variations of the LAESI ion source for specific targets of interest are described.

  16. Plastic responses in the metabolome and functional traits of maize plants to temperature variations.

    Science.gov (United States)

    Sun, C X; Gao, X X; Li, M Q; Fu, J Q; Zhang, Y L

    2016-03-01

    Environmentally inducible phenotypic plasticity is a major player in plant responses to climate change. However, metabolic responses and their role in determining the phenotypic plasticity of plants that are subjected to temperature variations remain poorly understood. The metabolomic profiles and metabolite levels in the leaves of three maize inbred lines grown in different temperature conditions were examined with a nuclear magnetic resonance metabolomic technique. The relationship of functional traits to metabolome profiles and the metabolic mechanism underlying temperature variations were then explored. A comparative analysis showed that during heat and cold stress, maize plants shared common plastic responses in biomass accumulation, carbon, nitrogen, sugars, some amino acids and compatible solutes. We also found that the plastic response of maize plants to heat stress was different from that under cold stress, mainly involving biomass allocation, shikimate and its aromatic amino acid derivatives, and other non-polar metabolites. The plastic responsiveness of functional traits of maize lines to temperature variations was low, while the metabolic responsiveness in plasticity was high, indicating that functional and metabolic plasticity may play different roles in maize plant adaptation to temperature variations. A linear regression analysis revealed that the maize lines could adapt to growth temperature variations through the interrelation of plastic responses in the metabolomes and functional traits, such as biomass allocation and the status of carbon and nitrogen. We provide valuable insight into the plastic response strategy of maize plants to temperature variations that will permit the optimisation of crop cultivation in an increasingly variable environment. PMID:26280133

  17. Metabolomic characteristics of Catharanthus roseus plants in time and space

    NARCIS (Netherlands)

    Qifang, Pan; Qifang, Pan

    2014-01-01

    The thesis aims at combining metabolomics with other methods to investigate the regulation of the TIA biosynthesis and how this is connected with other pathways and the plant’s physiology and development. It reviews the biosynthesis studies of Catharanthus roseus. An HPLC method is described for bot

  18. Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology

    NARCIS (Netherlands)

    Allwood, J.W.; Vos, de C.H.; Moing, A.; Deborde, C.; Erban, A.; Kopka, J.; Goodacre, R.; Hall, R.D.

    2011-01-01

    The "metabolome" comprises the entire complement of small molecules in a plant or any other organism. It represents the ultimate phenotype of cells, deduced from the perturbation of gene expression and the modulation of protein function, as well as environmental cues. Extensive advances over the pas

  19. A proposed framework for the description of plant metabolomics experiments and their results

    DEFF Research Database (Denmark)

    Jenkins, H.; Hardy, N.; Beckmann, M-;

    2004-01-01

    The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known...... as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full...... experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http...

  20. LC-MS based Metabolomics Analysis to Identify Potential Allelochemicals in Wedelia trilobata

    Directory of Open Access Journals (Sweden)

    Kamalrul Azlan Azizan

    2016-05-01

    Full Text Available Wedelia trilobata is a noxious invasive weed that has been widely cultivated as a decorative and groundcover plant. The plant has been reported to contain diverse bioactive compounds with a broad spectrum of biological activities including allelochemicals. Allelochemicals contribute to allelopathy interactions that suppress the growth and development of nearby plants. Several studies have reported the allelopathic potential of W. trilobata and its negative effects to crop plants. However, relatively little is known about the allelochemicals’ composition and how allelochemicals contribute to the allelopathic behavior of this plant. In order to prove allelopathy, the identification of the causative allelochemicals is required. The identification of potential allelochemicals that serve as biomarkers could be useful for assessing allelopathy interactions. In this study, a liquid chromatography (LC based metabolomics approach was applied to find biomarkers with allelopathic effects from W. trilobata. Ethanol and water were used to extract metabolites from the leaves of W. trilobata and analyzed using liquid chromatography coupled with quadrupole high-resolution time of flight mass spectrometry (LC-QTOF-MS. Using multivariate statistical analysis (MVA, we identified eight Rt-m/z pairs as candidate marker compounds for assessing allelopathy interactions of W. trilobata. The results highlight the application of metabolomics for understanding of the role of allelochemicals in allelopathy interactions of W. trilobata .

  1. Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants

    Science.gov (United States)

    Doppler, Maria; Kluger, Bernhard; Bueschl, Christoph; Schneider, Christina; Krska, Rudolf; Delcambre, Sylvie; Hiller, Karsten; Lemmens, Marc; Schuhmacher, Rainer

    2016-01-01

    The evaluation of extraction protocols for untargeted metabolomics approaches is still difficult. We have applied a novel stable isotope-assisted workflow for untargeted LC-HRMS-based plant metabolomics , which allows for the first time every detected feature to be considered for method evaluation. The efficiency and complementarity of commonly used extraction solvents, namely 1 + 3 (v/v) mixtures of water and selected organic solvents (methanol, acetonitrile or methanol/acetonitrile 1 + 1 (v/v)), with and without the addition of 0.1% (v/v) formic acid were compared. Four different wheat organs were sampled, extracted and analysed by LC-HRMS. Data evaluation was performed with the in-house-developed MetExtract II software and R. With all tested solvents a total of 871 metabolites were extracted in ear, 785 in stem, 733 in leaf and 517 in root samples, respectively. Between 48% (stem) and 57% (ear) of the metabolites detected in a particular organ were found with all extraction mixtures, and 127 of 996 metabolites were consistently shared between all extraction agent/organ combinations. In aqueous methanol, acidification with formic acid led to pronounced pH dependency regarding the precision of metabolite abundance and the number of detectable metabolites, whereas extracts of acetonitrile-containing mixtures were less affected. Moreover, methanol and acetonitrile have been found to be complementary with respect to extraction efficiency. Interestingly, the beneficial properties of both solvents can be combined by the use of a water-methanol-acetonitrile mixture for global metabolite extraction instead of aqueous methanol or aqueous acetonitrile alone. PMID:27367667

  2. Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants

    Directory of Open Access Journals (Sweden)

    Maria Doppler

    2016-06-01

    Full Text Available The evaluation of extraction protocols for untargeted metabolomics approaches is still difficult. We have applied a novel stable isotope-assisted workflow for untargeted LC-HRMS-based plant metabolomics , which allows for the first time every detected feature to be considered for method evaluation. The efficiency and complementarity of commonly used extraction solvents, namely 1 + 3 (v/v mixtures of water and selected organic solvents (methanol, acetonitrile or methanol/acetonitrile 1 + 1 (v/v, with and without the addition of 0.1% (v/v formic acid were compared. Four different wheat organs were sampled, extracted and analysed by LC-HRMS. Data evaluation was performed with the in-house-developed MetExtract II software and R. With all tested solvents a total of 871 metabolites were extracted in ear, 785 in stem, 733 in leaf and 517 in root samples, respectively. Between 48% (stem and 57% (ear of the metabolites detected in a particular organ were found with all extraction mixtures, and 127 of 996 metabolites were consistently shared between all extraction agent/organ combinations. In aqueous methanol, acidification with formic acid led to pronounced pH dependency regarding the precision of metabolite abundance and the number of detectable metabolites, whereas extracts of acetonitrile-containing mixtures were less affected. Moreover, methanol and acetonitrile have been found to be complementary with respect to extraction efficiency. Interestingly, the beneficial properties of both solvents can be combined by the use of a water-methanol-acetonitrile mixture for global metabolite extraction instead of aqueous methanol or aqueous acetonitrile alone.

  3. MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach

    OpenAIRE

    Nyamundanda, Gift; Gormley, Isobel Claire; Fan, Yue; Gallagher, William M; Brennan, Lorraine

    2013-01-01

    Background: Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot studies are rarely done in metabolomics, currently existing sample size estimation approaches which rely on pilot data can not be applied. Results: In this article, an analysis based approach called MetSizeR is developed to estimate sample size for metabolomic experime...

  4. New frontiers in pharmaceutical analysis: A metabolomic approach to check batch compliance of complex products based on natural substances.

    Science.gov (United States)

    Mattoli, L; Burico, M; Fodaroni, G; Tamimi, S; Bedont, S; Traldi, P; Stocchero, M

    2016-07-15

    Natural substances, particularly medicinal plants and their extracts, are still today intended as source for new Active Pharmaceutical Ingredients (APIs). Alternatively they can be validly employed to prepare medicines, food supplements or medical devices. The most adopted analytical approach used to verify quality of natural substances like medicinal plants is based still today on the traditional quantitative determination of marker compounds and/or active ingredients, besides the acquisition of a fingerprint by TLC, NIR, HPLC, GC. Here a new analytical approach based on untargeted metabolomic fingerprinting by means of Mass Spectrometry (MS) to verify the quality of grinTuss adulti syrup, a complex products based on medicinal plants, is proposed. Recently, untargeted metabolomic has been successfully applied to assess quality of natural substances, plant extracts, as well as corresponding formulated products, being the complexity a resource but not necessarily a limit. The untargeted metabolomic fingerprinting includes the monitoring of the main constituents, giving weighted relevance to the most abundant ones, but also considering minor components, that might be notable in view of an integrated - often synergistic - effect on the biological system. Two different years of production were investigated. The collected samples were analyzed by Flow Injection ElectroSpray Ionization Mass Spectrometry Analysis (FIA-ESI-MS) and a suitable data processing procedure was developed to transform the MS spectra into robust fingerprints. Multivariate Statistical Process Control (MSPC) was applied in order to obtain multivariate control charts that were validated to prove the effectiveness of the proposed method. PMID:27155737

  5. Metabolomics and Epidemiology Working Group

    Science.gov (United States)

    The Metabolomics and Epidemiology (MetEpi) Working Group promotes metabolomics analyses in population-based studies, as well as advancement in the field of metabolomics for broader biomedical and public health research.

  6. Metabolomics-based discovery of diagnostic biomarkers for onchocerciasis.

    Directory of Open Access Journals (Sweden)

    Judith R Denery

    Full Text Available BACKGROUND: Development of robust, sensitive, and reproducible diagnostic tests for understanding the epidemiology of neglected tropical diseases is an integral aspect of the success of worldwide control and elimination programs. In the treatment of onchocerciasis, clinical diagnostics that can function in an elimination scenario are non-existent and desperately needed. Due to its sensitivity and quantitative reproducibility, liquid chromatography-mass spectrometry (LC-MS based metabolomics is a powerful approach to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Analysis of an African sample set comprised of 73 serum and plasma samples revealed a set of 14 biomarkers that showed excellent discrimination between Onchocerca volvulus-positive and negative individuals by multivariate statistical analysis. Application of this biomarker set to an additional sample set from onchocerciasis endemic areas where long-term ivermectin treatment has been successful revealed that the biomarker set may also distinguish individuals with worms of compromised viability from those with active infection. Machine learning extended the utility of the biomarker set from a complex multivariate analysis to a binary format applicable for adaptation to a field-based diagnostic, validating the use of complex data mining tools applied to infectious disease biomarker discovery and diagnostic development. CONCLUSIONS/SIGNIFICANCE: An LC-MS metabolomics-based diagnostic has the potential to monitor the progression of onchocerciasis in both endemic and non-endemic geographic areas, as well as provide an essential tool to multinational programs in the ongoing fight against this neglected tropical disease. Ultimately this technology can be expanded for the diagnosis of other filarial and/or neglected tropical diseases.

  7. LC–MS-based metabolomics in profiling of drug metabolism and bioactivation

    OpenAIRE

    Feng Li; Frank J. Gonzalez; Xiaochao Ma

    2012-01-01

    Since metabolism significantly affects drug safety and efficacy, determining the metabolic profile of a drug is a critical part of drug development. The application of an LC–MS-based metabolomic approach has gained more widespread use in identifying drug metabolites, developing metabolic maps and lending clues to mechanisms of bioactivation. Thus, the LC–MS-based metabolomic approach is a powerful tool for profiling of drug metabolism and bioactivation.

  8. NMR-based metabolomic profiling of overweight adolescents

    DEFF Research Database (Denmark)

    Zheng, Hong; Yde, Christian C; Arnberg, Karina; Mølgaard, Christian; Michaelsen, Kim F.; Larnkjær, Anni; Bertram, Hanne C

    2014-01-01

    The plasma and urine metabolome of 192 overweight 12-15-year-old adolescents (BMI of 25.4 ± 2.3 kg/m(2)) were examined in order to elucidate gender, pubertal development measured as Tanner stage, physical activity measured as number of steps taken daily, and intra-/interindividual differences...... metabolome could be identified. The present study for the first time provides comprehensive information about associations between the metabolome and gender, pubertal development, and physical activity in overweight adolescents, which is an important subject group to approach in the prevention of obesity and...

  9. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-01-01

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

  10. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Directory of Open Access Journals (Sweden)

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  11. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-01-01

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

  12. Heavy Metal Tolerance in Plants: Role of Transcriptomics, Proteomics, Metabolomics, and Ionomics.

    Science.gov (United States)

    Singh, Samiksha; Parihar, Parul; Singh, Rachana; Singh, Vijay P; Prasad, Sheo M

    2015-01-01

    Heavy metal contamination of soil and water causing toxicity/stress has become one important constraint to crop productivity and quality. This situation has further worsened by the increasing population growth and inherent food demand. It has been reported in several studies that counterbalancing toxicity due to heavy metal requires complex mechanisms at molecular, biochemical, physiological, cellular, tissue, and whole plant level, which might manifest in terms of improved crop productivity. Recent advances in various disciplines of biological sciences such as metabolomics, transcriptomics, proteomics, etc., have assisted in the characterization of metabolites, transcription factors, and stress-inducible proteins involved in heavy metal tolerance, which in turn can be utilized for generating heavy metal-tolerant crops. This review summarizes various tolerance strategies of plants under heavy metal toxicity covering the role of metabolites (metabolomics), trace elements (ionomics), transcription factors (transcriptomics), various stress-inducible proteins (proteomics) as well as the role of plant hormones. We also provide a glance of some strategies adopted by metal-accumulating plants, also known as "metallophytes." PMID:26904030

  13. Effect of acute stresses on zebra fish (Danio rerio) metabolome measured by NMR-based metabolomics.

    Science.gov (United States)

    Mushtaq, Mian Yahya; Marçal, Rosilene Moretti; Champagne, Danielle L; van der Kooy, Frank; Verpoorte, Robert; Choi, Young Hae

    2014-09-01

    We applied an acute stress model to zebra fish in order to measure the changes in the metabolome due to biological stress. This was done by submitting the fish to fifteen minutes of acute confinement (netting) stress, and then five minutes for the open field and light/dark field tests. A polar extract of the zebra fish was then subjected to (1)H nuclear magnetic spectroscopy. Multivariate data analysis of the spectra showed a clear separation associated to a wide range of metabolites between zebra fish that were submitted to open field and light/dark field tests. Alanine, taurine, adenosine, creatine, lactate, and histidine were high in zebra fish to which the light/dark field test was applied, regardless of stress, while acetate and isoleucine/lipids appeared to be higher in zebra fish exposed to the open field test. These results show that any change in the environment, even for a small period of time, has a noticeable physiological impact. This research provides an insight of how different mechanisms are activated under different environments to maintain the homeostasis of the body. It should also contribute to establish zebra fish as a model for metabolomics studies. PMID:25098933

  14. Untargeted Metabolomics of Tomato Plants after Root-Knot Nematode Infestation.

    Science.gov (United States)

    Eloh, Kodjo; Sasanelli, Nicola; Maxia, Andrea; Caboni, Pierluigi

    2016-07-27

    After 2 months from the infestation of tomato plants with the root-knot nematode (RKN) Meloidogyne incognita, we performed a gas chromatography-mass spectrometry untargeted fingerprint analysis for the identification of characteristic metabolites and biomarkers. Principal component analysis, and orthogonal projections to latent structures discriminant analysis suggested dramatic local changes of the plant metabolome. In the case of tomato leaves, β-alanine, phenylalanine, and melibiose were induced in response to RKN stimuli, while ribose, glycerol, myristic acid, and palmitic acid were reduced. For tomato stems, upregulated metabolites were ribose, sucrose, fructose, and glucose, while fumaric acid and glycine were downregulated. The variation in molecular strategies to the infestation of RKNs may play an important role in how Solanum lycopersicum and other plants adapt to nematode parasitic stress. PMID:27389052

  15. Metabolomics reveals the origins of antimicrobial plant resins collected by honey bees.

    Science.gov (United States)

    Wilson, Michael B; Spivak, Marla; Hegeman, Adrian D; Rendahl, Aaron; Cohen, Jerry D

    2013-01-01

    The deposition of antimicrobial plant resins in honey bee, Apis mellifera, nests has important physiological benefits. Resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or the benefits of specific resins to bees. We used metabolomic methods as a type of environmental forensics to track individual resin forager behavior through comparisons of global resin metabolite patterns. The resin from the corbiculae of a single bee was sufficient to identify that resin's botanical source without prior knowledge of resin composition. Bees from our apiary discriminately foraged for resin from eastern cottonwood (Populus deltoides), and balsam poplar (P. balsamifera) among many available, even closely related, resinous plants. Cottonwood and balsam poplar resin composition did not show significant seasonal or regional changes in composition. Metabolomic analysis of resin from 6 North American Populus spp. and 5 hybrids revealed peaks characteristic to taxonomic nodes within Populus, while antimicrobial analysis revealed that resin from different species varied in inhibition of the bee bacterial pathogen, Paenibacillus larvae. We conclude that honey bees make discrete choices among many resinous plant species, even among closely related species. Bees also maintained fidelity to a single source during a foraging trip. Furthermore, the differential inhibition of P. larvae by Populus spp., thought to be preferential for resin collection in temperate regions, suggests that resins from closely related plant species many have different benefits to bees. PMID:24204850

  16. Improved batch correction in untargeted MS-based metabolomics

    NARCIS (Netherlands)

    Wehrens, Ron; Hageman, Jos A.; Eeuwijk, van Fred; Kooke, Rik; Flood, Pádraic J.; Wijnker, Erik; Keurentjes, Joost J.B.; Lommen, Arjen; Eekelen, van Henriëtte D.L.M.; Hall, Robert D.; Mumm, Roland; Vos, de Ric C.H.

    2016-01-01

    Introduction: Batch effects in large untargeted metabolomics experiments are almost unavoidable, especially when sensitive detection techniques like mass spectrometry (MS) are employed. In order to obtain peak intensities that are comparable across all batches, corrections need to be performed. S

  17. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

    DEFF Research Database (Denmark)

    Huang, Sijia; Chong, Nicole; Lewis, Nathan;

    2016-01-01

    Background: More accurate diagnostic methods are pressingly needed to diagnose breast cancer, the most common malignant cancer in women worldwide. Blood-based metabolomics is a promising diagnostic method for breast cancer. However, many metabolic biomarkers are difficult to replicate among studies.......993. Moreover, important metabolic pathways, such as taurine and hypotaurine metabolism and the alanine, aspartate, and glutamate pathway, are revealed as critical biological pathways for early diagnosis of breast cancer. Conclusions: We have successfully developed a new type of pathway-based model to study...... metabolomics data for disease diagnosis. Applying this method to blood-based breast cancer metabolomics data, we have discovered crucial metabolic pathway signatures for breast cancer diagnosis, especially early diagnosis. Further, this modeling approach may be generalized to other omics data types for disease...

  18. NMR-based metabolomics of mammalian cell and tissue cultures

    International Nuclear Information System (INIS)

    NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of anti-apoptotic agents to the media on the extracellular and intracellular metabolome indicated changes in metabolic pathways of energy utilization. These results shed light into culture parameters that can be manipulated to optimize growth and protein production. Second, metabolomic analysis was performed on the superfusion media in a common model used for drug metabolism and toxicology studies, in vitro liver slices. In this study, it is demonstrated that two of the 48 standard media components, choline and histidine are depleted at a faster rate than many other nutrients. Augmenting the starting media with extra choline and histidine improves the long-term liver slice viability as measured by higher tissues levels of lactate dehydrogenase (LDH), glutathione and ATP, as well as lower LDH levels in the media at time points out to 94 h after initiation of incubation. In both models, media components and cellular metabolites are measured over time and correlated with currently accepted endpoint measures.

  19. Metabolomics for Biomarker Discovery in Gastroenterological Cancer

    Directory of Open Access Journals (Sweden)

    Shin Nishiumi

    2014-07-01

    Full Text Available The study of the omics cascade, which involves comprehensive investigations based on genomics, transcriptomics, proteomics, metabolomics, etc., has developed rapidly and now plays an important role in life science research. Among such analyses, metabolome analysis, in which the concentrations of low molecular weight metabolites are comprehensively analyzed, has rapidly developed along with improvements in analytical technology, and hence, has been applied to a variety of research fields including the clinical, cell biology, and plant/food science fields. The metabolome represents the endpoint of the omics cascade and is also the closest point in the cascade to the phenotype. Moreover, it is affected by variations in not only the expression but also the enzymatic activity of several proteins. Therefore, metabolome analysis can be a useful approach for finding effective diagnostic markers and examining unknown pathological conditions. The number of studies involving metabolome analysis has recently been increasing year-on-year. Here, we describe the findings of studies that used metabolome analysis to attempt to discover biomarker candidates for gastroenterological cancer and discuss metabolome analysis-based disease diagnosis.

  20. LC-MS-Based Metabolomic Investigation of Chemopreventive Phytochemical-Elicited Metabolic Events.

    Science.gov (United States)

    Wang, Lei; Yao, Dan; Chen, Chi

    2016-01-01

    Phytochemicals are under intensive investigation for their potential use as chemopreventive agents in blocking or suppressing carcinogenesis. Metabolic interactions between phytochemical and biological system play an important role in determining the efficacy and toxicity of chemopreventive phytochemicals. However, complexities of phytochemical biotransformation and intermediary metabolism pose challenges for studying phytochemical-elicited metabolic events. Metabolomics has become a highly effective technical platform to detect subtle changes in a complex metabolic system. Here, using green tea polyphenols as an example, we describe a workflow of LC-MS-based metabolomics study, covering the procedures and techniques in sample collection, preparation, LC-MS analysis, data analysis, and interpretation. PMID:26608291

  1. The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

    Directory of Open Access Journals (Sweden)

    Carroll Adam J

    2010-07-01

    Full Text Available Abstract Background Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Description Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.. Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP their own data to the server for online processing via a novel raw data processing pipeline. Conclusions MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to

  2. Discrimination of conventional and organic white cabbage from a long-term field trial study using untargeted LC-MS-based metabolomics.

    Science.gov (United States)

    Mie, Axel; Laursen, Kristian Holst; Åberg, K Magnus; Forshed, Jenny; Lindahl, Anna; Thorup-Kristensen, Kristian; Olsson, Marie; Knuthsen, Pia; Larsen, Erik Huusfeldt; Husted, Søren

    2014-05-01

    The influence of organic and conventional farming practices on the content of single nutrients in plants is disputed in the scientific literature. Here, large-scale untargeted LC-MS-based metabolomics was used to compare the composition of white cabbage from organic and conventional agriculture, measuring 1,600 compounds. Cabbage was sampled in 2 years from one conventional and two organic farming systems in a rigidly controlled long-term field trial in Denmark. Using Orthogonal Projection to Latent Structures-Discriminant Analysis (OPLS-DA), we found that the production system leaves a significant (p = 0.013) imprint in the white cabbage metabolome that is retained between production years. We externally validated this finding by predicting the production system of samples from one year using a classification model built on samples from the other year, with a correct classification in 83 % of cases. Thus, it was concluded that the investigated conventional and organic management practices have a systematic impact on the metabolome of white cabbage. This emphasizes the potential of untargeted metabolomics for authenticity testing of organic plant products. PMID:24618989

  3. Strategy for nuclear-magnetic-resonance-based metabolomics of human feces

    DEFF Research Database (Denmark)

    Lamichhane, Santosh; Yde, Christian Clement; Schmedes, Mette Søndergaard;

    2015-01-01

    of fresh feces by NMR-based metabolomics. The evaluation of extraction solvents showed that buffer extraction is a suitable approach to extract metabolic information in feces. So, the effects of weight-to-buffer (Wf:Vb) combinations and the effect of sonication and freeze-thaw cycles on the reproducibility...

  4. Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics

    NARCIS (Netherlands)

    Mihaleva, V.V.; Vorst, O.F.J.; Maliepaard, C.A.; Verhoeven, H.A.; Vos, de C.H.; Hall, R.D.; Ham, van R.C.H.J.

    2008-01-01

    Compound identification and annotation in (untargeted) metabolomics experiments based on accurate mass require the highest possible accuracy of the mass determination. Experimental LC/TOF-MS platforms equipped with a time-to-digital converter (TDC) give the best mass estimate for those mass signals

  5. Study of leaf metabolome modifications induced by UV-C radiations in representative Vitis, Cissus and Cannabis species by LC-MS based metabolomics and antioxidant assays.

    Science.gov (United States)

    Marti, Guillaume; Schnee, Sylvain; Andrey, Yannis; Simoes-Pires, Claudia; Carrupt, Pierre-Alain; Wolfender, Jean-Luc; Gindro, Katia

    2014-01-01

    UV-C radiation is known to induce metabolic modifications in plants, particularly to secondary metabolite biosynthesis. To assess these modifications from a global and untargeted perspective, the effects of the UV-C radiation of the leaves of three different model plant species, Cissus antarctica Vent. (Vitaceae), Vitis vinifera L. (Vitaceae) and Cannabis sativa L. (Cannabaceae), were evaluated by an LC-HRMS-based metabolomic approach. The approach enabled the detection of significant metabolite modifications in the three species studied. For all species, clear modifications of phenylpropanoid metabolism were detected that led to an increased level of stilbene derivatives. Interestingly, resveratrol and piceid levels were strongly induced by the UV-C treatment of C. antarctica leaves. In contrast, both flavonoids and stilbene polymers were upregulated in UV-C-treated Vitis leaves. In Cannabis, important changes in cinnamic acid amides and stilbene-related compounds were also detected. Overall, our results highlighted phytoalexin induction upon UV-C radiation. To evaluate whether UV-C stress radiation could enhance the biosynthesis of bioactive compounds, the antioxidant activity of extracts from control and UV-C-treated leaves was measured. The results showed increased antioxidant activity in UV-C-treated V. vinifera extracts. PMID:25197936

  6. Study of Leaf Metabolome Modifications Induced by UV-C Radiations in Representative Vitis, Cissus and Cannabis Species by LC-MS Based Metabolomics and Antioxidant Assays

    Directory of Open Access Journals (Sweden)

    Guillaume Marti

    2014-09-01

    Full Text Available UV-C radiation is known to induce metabolic modifications in plants, particularly to secondary metabolite biosynthesis. To assess these modifications from a global and untargeted perspective, the effects of the UV-C radiation of the leaves of three different model plant species, Cissus antarctica Vent. (Vitaceae, Vitis vinifera L. (Vitaceae and Cannabis sativa L. (Cannabaceae, were evaluated by an LC-HRMS-based metabolomic approach. The approach enabled the detection of significant metabolite modifications in the three species studied. For all species, clear modifications of phenylpropanoid metabolism were detected that led to an increased level of stilbene derivatives. Interestingly, resveratrol and piceid levels were strongly induced by the UV-C treatment of C. antarctica leaves. In contrast, both flavonoids and stilbene polymers were upregulated in UV-C-treated Vitis leaves. In Cannabis, important changes in cinnamic acid amides and stilbene-related compounds were also detected. Overall, our results highlighted phytoalexin induction upon UV-C radiation. To evaluate whether UV-C stress radiation could enhance the biosynthesis of bioactive compounds, the antioxidant activity of extracts from control and UV-C-treated leaves was measured. The results showed increased antioxidant activity in UV-C-treated V. vinifera extracts.

  7. Discovery and validation of urinary exposure markers for different plant foods by untargeted metabolomics

    DEFF Research Database (Denmark)

    Andersen, Maj-Britt Schmidt; Kristensen, Mette; Manach, Claudine;

    2014-01-01

    While metabolomics is increasingly used to investigate the food metabolome and identify new markers of food exposure, limited attention has been given to the validation of such markers. The main objectives of the present study were to (1) discover potential food exposure markers (PEMs) for a range...

  8. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach.

    Science.gov (United States)

    Aw, Wanping; Fukuda, Shinji

    2015-01-01

    Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health. PMID:25338280

  9. A novel approach for LC-MS/MS-based chiral metabolomics fingerprinting and chiral metabolomics extraction using a pair of enantiomers of chiral derivatization reagents.

    Science.gov (United States)

    Takayama, Takahiro; Mochizuki, Toshiki; Todoroki, Kenichiro; Min, Jun Zhe; Mizuno, Hajime; Inoue, Koichi; Akatsu, Hiroyasu; Noge, Ichiro; Toyo'oka, Toshimasa

    2015-10-22

    Chiral metabolites are found in a wide variety of living organisms and some of them are understood to be physiologically active compounds and biomarkers. However, the overall analysis of chiral metabolomics is quite difficult due to the high number of metabolites, the significant diversity in their physicochemical properties, and concentration range from metabolite-to-metabolite. To solve this difficulty, we developed a novel approach for chiral metabolomics fingerprinting and chiral metabolomics extraction, which is based on the labeling of a pair of enantiomers of chiral derivatization reagents (i.e., DMT-(S,R)-Pro-OSu and DMT-3(S,R)-Apy) and precursor ion scan chromatography of the derivatives. The multivariate statistics is also required for this strategy. The proposed procedures were evaluated by the detection of a diagnostic marker (i.e., d-lactic acid) using the saliva of diabetic patients. This method was used for the determination of biomarker candidates of chiral amines and carboxyls in Alzheimer's disease (AD) brain homogenates. As the results, l-phenylalanine (L-Phe) and l-lactic acid (L-LA) were identified as the decreased and increased biomarker candidates in the AD brain, respectively. Therefore, the proposed approach seems to be helpful for the determination of non-target chiral metabolomics possessing amines and carboxyls. PMID:26526912

  10. NMR-based metabolomics in human disease diagnosis: Applications, limitations, and recommendations

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2013-04-03

    Metabolomics is a dynamic and emerging research field, similar to proteomics, transcriptomics and genomics in affording global understanding of biological systems. It is particularly useful in functional genomic studies in which metabolism is thought to be perturbed. Metabolomics provides a snapshot of the metabolic dynamics that reflect the response of living systems to both pathophysiological stimuli and/or genetic modification. Because this approach makes possible the examination of interactions between an organism and its diet or environment, it is particularly useful for identifying biomarkers of disease processes that involve the environment. For example, the interaction of a high fat diet with cardiovascular disease can be studied via such a metabolomics approach by modeling the interaction between genes and diet. The high reproducibility of NMR-based techniques gives this method a number of advantages over other analytical techniques in large-scale and long-term metabolomic studies, such as epidemiological studies. This approach has been used to study a wide range of diseases, through the examination of biofluids, including blood plasma/serum, urine, blister fluid, saliva and semen, as well as tissue extracts and intact tissue biopsies. However, complicating the use of NMR spectroscopy in biomarker discovery is the fact that numerous variables can effect metabolic composition including, fasting, stress, drug administration, diet, gender, age, physical activity, life style and the subject\\'s health condition. To minimize the influence of these variations in the datasets, all experimental conditions including sample collection, storage, preparation as well as NMR spectroscopic parameters and data analysis should be optimized carefully and conducted in an identical manner as described by the local standard operating protocol. This review highlights the potential applications of NMR-based metabolomics studies and gives some recommendations to improve sample

  11. Recent Advances in the Application of Metabolomics to Studies of Biogenic Volatile Organic Compounds (BVOC Produced by Plant

    Directory of Open Access Journals (Sweden)

    Yoko Iijima

    2014-08-01

    Full Text Available In many plants, biogenic volatile organic compounds (BVOCs are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and also influenced by herbivory damage and pathogen infection. Plant-produced BVOCs are receptive to many organisms, from microorganisms to human, as both airborne attractants and repellants. In addition, it is known that some BVOCs act as signals to prime a plant for the defense response in plant-to-plant communications. The compositional profiles of BVOCs can, thus, have profound influences in the physiological and ecological aspects of living organisms. Apart from that, some of them are commercially valuable as aroma/flavor compounds for human. Metabolomic technologies have recently revealed new insights in biological systems through metabolic dynamics. Here, the recent advances in metabolomics technologies focusing on plant-produced BVOC analyses are overviewed. Their application markedly improves our knowledge of the role of BVOCs in chemosystematics, ecological influences, and aroma research, as well as being useful to prove the biosynthetic mechanisms of BVOCs.

  12. Metabolomics-Based Screening of Biofilm-Inhibitory Compounds against Pseudomonas aeruginosa from Burdock Leaf

    Directory of Open Access Journals (Sweden)

    Zaixiang Lou

    2015-09-01

    Full Text Available Screening of anti-biofilm compounds from the burdock leaf based on metabolomics is reported here. The crystal violet assay indicated 34% ethanol elution fraction of burdock leaf could completely inhibit biofilm formation of Pseudomonas aeruginosa at 1 mg·mL−1. Then, the chemical composition of burdock leaf fraction was analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS and 11 active compounds (chlorogenic acid, caffeic acid, p-coumaric acid, quercetin, ursolic acid, rutin, cynarin, luteolin, crocin, benzoic acid, and Tenacissoside I were identified. Lastly, UPLC-MS analysis was employed to obtain the metabolic fingerprints of burdock leaf fractions before and after inhibiting the biofilm of Pseudomonas aeruginosa. The metabolic fingerprints were transformed to data, analyzed with PLS-DA (partial least squares discriminant analysis and the peaks whose area was significantly changed were found out. Thus, 81 compounds were screened as potential anti-biofilm ingredients. Among them, rutin, ursolic acid, caffeic acid, p-coumaric acid and quercetin were identified and confirmed as the main anti-biofilm compounds in burdock leaf. The study provided basic anti-biofilm profile data for the compounds in burdock leaf, as well as provided a convenient method for fast screening of anti-biofilm compounds from natural plants.

  13. Waste materials derived bio-effectors used as growth promoters for strawberry plants. An agronomic and metabolomic study

    Science.gov (United States)

    Vasileva, Brankica; Chami, Ziad Al; De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

    2015-04-01

    Recently, a novel concept of bio-effectors has emerged to describe a group of products that are able to improve plant performance more than fertilizers. In this study, three different agro-industrial residues, i.e. brewers' spent grain (BSG), fennel processing residues (FPR) and lemon processing residues (LPR) were chosen as potential bio-effectors. A greenhouse soilless pot experiment was conducted on strawberry plants (Fragaria x ananassa var. Festival) in order to study the effect of BSG, FPR and LPR water extracts, at different concentrations, on plant growth and fruit quality. Their effect was compared with humic-like substances as a positive/reference control (Ctrl+) and with Hoagland solution as a negative control (Ctrl-). Agronomic parameters and the nutrient uptake were measured on shoots, roots and fruits. Metabolomic profiling tests were carried out on leaves, roots and fruit juices through the NMR technique. Plants treated with the FPR extract showed better vegetative growth, while plants treated with the BSG extract gave higher yield and better fruit size. Metabolomic profiling showed that fruits and roots of plants treated with FPR and LPR extracts had higher concentrations of sucrose, malate and acetate, while BSG treated plants had higher concentrations of citrate and β-glucose. In conclusion, according to the results achieved, the bio-effectors used in this study promote plant growth and fruit quality regardless of their nutritional content. Keywords: bio-effectors, agro-industrial waste, nuclear magnetic resonance (NMR), strawberry, growth promotion, fruit quality.

  14. Metabolomics as a Tool to Investigate Abiotic Stress Tolerance in Plants

    Directory of Open Access Journals (Sweden)

    Aurelio Gómez-Cadenas

    2013-03-01

    Full Text Available Metabolites reflect the integration of gene expression, protein interaction and other different regulatory processes and are therefore closer to the phenotype than mRNA transcripts or proteins alone. Amongst all –omics technologies, metabolomics is the most transversal and can be applied to different organisms with little or no modifications. It has been successfully applied to the study of molecular phenotypes of plants in response to abiotic stress in order to find particular patterns associated to stress tolerance. These studies have highlighted the essential involvement of primary metabolites: sugars, amino acids and Krebs cycle intermediates as direct markers of photosynthetic dysfunction as well as effectors of osmotic readjustment. On the contrary, secondary metabolites are more specific of genera and species and respond to particular stress conditions as antioxidants, Reactive Oxygen Species (ROS scavengers, coenzymes, UV and excess radiation screen and also as regulatory molecules. In addition, the induction of secondary metabolites by several abiotic stress conditions could also be an effective mechanism of cross-protection against biotic threats, providing a link between abiotic and biotic stress responses. Moreover, the presence/absence and relative accumulation of certain metabolites along with gene expression data provides accurate markers (mQTL or MWAS for tolerant crop selection in breeding programs.

  15. NMR-based stable isotope resolved metabolomics in systems biochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Teresa W-M. [University of Louisville, Department of Chemistry (United States); Lane, Andrew N., E-mail: anlane01@louisville.edu [University of Louisville, Center for Regulatory Environmental Analytical Metabolomics (United States)

    2011-04-15

    An important goal of metabolomics is to characterize the changes in metabolic networks in cells or various tissues of an organism in response to external perturbations or pathologies. The profiling of metabolites and their steady state concentrations does not directly provide information regarding the architecture and fluxes through metabolic networks. This requires tracer approaches. NMR is especially powerful as it can be used not only to identify and quantify metabolites in an unfractionated mixture such as biofluids or crude cell/tissue extracts, but also determine the positional isotopomer distributions of metabolites derived from a precursor enriched in stable isotopes such as {sup 13}C and {sup 15}N via metabolic transformations. In this article we demonstrate the application of a variety of 2-D NMR editing experiments to define the positional isotopomers of compounds present in polar and non-polar extracts of human lung cancer cells grown in either [U-{sup 13}C]-glucose or [U-{sup 13}C,{sup 15}N]-glutamine as source tracers. The information provided by such experiments enabled unambiguous reconstruction of metabolic pathways, which is the foundation for further metabolic flux modeling.

  16. Metabolomics-Based Screening of Biofilm-Inhibitory Compounds against Pseudomonas aeruginosa from Burdock Leaf

    OpenAIRE

    Zaixiang Lou; Yuxia Tang; Xinyi Song; Hongxin Wang

    2015-01-01

    Screening of anti-biofilm compounds from the burdock leaf based on metabolomics is reported here. The crystal violet assay indicated 34% ethanol elution fraction of burdock leaf could completely inhibit biofilm formation of Pseudomonas aeruginosa at 1 mg·mL−1. Then, the chemical composition of burdock leaf fraction was analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and 11 active compounds (chlorogenic acid, caffeic acid, p-coumaric acid, quercetin, ursolic aci...

  17. Mass Spectrometry-Based Metabolomics to Elucidate Functions in Marine Organisms and Ecosystems

    OpenAIRE

    Sophie Goulitquer; Philippe Potin; Thierry Tonon

    2012-01-01

    Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices an...

  18. Metabolome based reaction graphs of M. tuberculosis and M. leprae: a comparative network analysis.

    Directory of Open Access Journals (Sweden)

    Ketki D Verkhedkar

    Full Text Available BACKGROUND: Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. METHODOLOGY/PRINCIPAL FINDINGS: Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. CONCLUSIONS: We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a

  19. Mass spectrometry-based metabolomics: applications to biomarker and metabolic pathway research.

    Science.gov (United States)

    Zhang, Aihua; Sun, Hui; Yan, Guangli; Wang, Ping; Wang, Xijun

    2016-01-01

    Mass spectrometry-based metabolomics has become increasingly popular in molecular medicine. High-definition mass spectrometry (MS), coupled with pattern recognition methods, have been carried out to obtain comprehensive metabolite profiling and metabolic pathway of large biological datasets. This sets the scene for a new and powerful diagnostic approach. Analysis of the key metabolites in body fluids has become an important part of improving disease diagnosis. With technological advances in analytical techniques, the ability to measure low-molecular-weight metabolites in bio-samples provides a powerful platform for identifying metabolites that are uniquely correlated with a specific human disease. MS-based metabolomics can lead to enhanced understanding of disease mechanisms and to new diagnostic markers and has a strong potential to contribute to improving early diagnosis of diseases. This review will highlight the importance and benefit with certain characteristic examples of MS-metabolomics for identifying metabolic pathways and metabolites that accurately screen for potential diagnostic biomarkers of diseases. PMID:25739660

  20. PLS-Based and Regularization-Based Methods for the Selection of Relevant Variables in Non-targeted Metabolomics Data.

    Science.gov (United States)

    Bujak, Renata; Daghir-Wojtkowiak, Emilia; Kaliszan, Roman; Markuszewski, Michał J

    2016-01-01

    Non-targeted metabolomics constitutes a part of the systems biology and aims at determining numerous metabolites in complex biological samples. Datasets obtained in the non-targeted metabolomics studies are high-dimensional due to sensitivity of mass spectrometry-based detection methods as well as complexity of biological matrices. Therefore, a proper selection of variables which contribute into group classification is a crucial step, especially in metabolomics studies which are focused on searching for disease biomarker candidates. In the present study, three different statistical approaches were tested using two metabolomics datasets (RH and PH study). The orthogonal projections to latent structures-discriminant analysis (OPLS-DA) without and with multiple testing correction as well as the least absolute shrinkage and selection operator (LASSO) with bootstrapping, were tested and compared. For the RH study, OPLS-DA model built without multiple testing correction selected 46 and 218 variables based on the VIP criteria using Pareto and UV scaling, respectively. For the PH study, 217 and 320 variables were selected based on the VIP criteria using Pareto and UV scaling, respectively. In the RH study, OPLS-DA model built after correcting for multiple testing, selected 4 and 19 variables as in terms of Pareto and UV scaling, respectively. For the PH study, 14 and 18 variables were selected based on the VIP criteria in terms of Pareto and UV scaling, respectively. In the RH and PH study, the LASSO selected 14 and 4 variables with reproducibility between 99.3 and 100%, respectively. In the light of PLS-based models, the larger the search space the higher the probability of developing models that fit the training data well with simultaneous poor predictive performance on the validation set. The LASSO offers potential improvements over standard linear regression due to the presence of the constrain, which promotes sparse solutions. This paper is the first one to date

  1. Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology.

    Science.gov (United States)

    Causon, Tim J; Hann, Stephan

    2016-09-28

    Fermentation and cell culture biotechnology in the form of so-called "cell factories" now play an increasingly significant role in production of both large (e.g. proteins, biopharmaceuticals) and small organic molecules for a wide variety of applications. However, associated metabolic engineering optimisation processes relying on genetic modification of organisms used in cell factories, or alteration of production conditions remain a challenging undertaking for improving the final yield and quality of cell factory products. In addition to genomic, transcriptomic and proteomic workflows, analytical metabolomics continues to play a critical role in studying detailed aspects of critical pathways (e.g. via targeted quantification of metabolites), identification of biosynthetic intermediates, and also for phenotype differentiation and the elucidation of previously unknown pathways (e.g. via non-targeted strategies). However, the diversity of primary and secondary metabolites and the broad concentration ranges encompassed during typical biotechnological processes means that simultaneous extraction and robust analytical determination of all parts of interest of the metabolome is effectively impossible. As the integration of metabolome data with transcriptome and proteome data is an essential goal of both targeted and non-targeted methods addressing production optimisation goals, additional sample preparation steps beyond necessary sampling, quenching and extraction protocols including clean-up, analyte enrichment, and derivatisation are important considerations for some classes of metabolites, especially those present in low concentrations or exhibiting poor stability. This contribution critically assesses the potential of current sample preparation strategies applied in metabolomic studies of industrially-relevant cell factory organisms using mass spectrometry-based platforms primarily coupled to liquid-phase sample introduction (i.e. flow injection, liquid

  2. Electronic Nose and Exhaled Breath NMR-based Metabolomics Applications in Airways Disease.

    Science.gov (United States)

    Santini, Giuseppe; Mores, Nadia; Penas, Andreu; Capuano, Rosamaria; Mondino, Chiara; Trové, Andrea; Macagno, Francesco; Zini, Gina; Cattani, Paola; Martinelli, Eugenio; Motta, Andrea; Macis, Giuseppe; Ciabattoni, Giovanni; Montuschi, Paolo

    2016-01-01

    Breathomics, the multidimensional molecular analysis of exhaled breath, includes analysis of exhaled breath with gas-chromatography/mass spectrometry (GC/MS) and electronic noses (e-noses), and metabolomics of exhaled breath condensate (EBC), a non-invasive technique which provides information on the composition of airway lining fluid, generally by high-resolution nuclear magnetic resonance (NMR) spectroscopy or MS methods. Metabolomics is the identification and quantification of small molecular weight metabolites in a biofluid. Specific profiles of volatile compounds in exhaled breath and metabolites in EBC (breathprints) are potentially useful surrogate markers of inflammatory respiratory diseases. Electronic noses (e-noses) are artificial sensor systems, usually consisting of chemical cross-reactive sensor arrays for characterization of patterns of breath volatile compounds, and algorithms for breathprints classification. E-noses are handheld, portable, and provide real-time data. E-nose breathprints can reflect respiratory inflammation. E-noses and NMR-based metabolomics of EBC can distinguish patients with respiratory diseases such as asthma, COPD, and lung cancer, or diseases with a clinically relevant respiratory component including cystic fibrosis and primary ciliary dyskinesia, and healthy individuals. Breathomics has also been reported to identify patients affected by different types of respiratory diseases. Patterns of breath volatile compounds detected by e-nose and EBC metabolic profiles have been associated with asthma phenotypes. In combination with other -omics platforms, breathomics might provide a molecular approach to respiratory disease phenotyping and a molecular basis to tailored pharmacotherapeutic strategies. Breathomics might also contribute to identify new surrogate markers of respiratory inflammation, thus, facilitating drug discovery. Validation in newly recruited, prospective independent cohorts is essential for development of e

  3. Advances in high-resolution mass spectrometry based on metabolomics studies for food--a review.

    Science.gov (United States)

    Rubert, Josep; Zachariasova, Milena; Hajslova, Jana

    2015-01-01

    Food authenticity becomes a necessity for global food policies, since food placed in the market without fail has to be authentic. It has always been a challenge, since in the past minor components, called also markers, have been mainly monitored by chromatographic methods in order to authenticate the food. Nevertheless, nowadays, advanced analytical methods have allowed food fingerprints to be achieved. At the same time they have been also combined with chemometrics, which uses statistical methods in order to verify food and to provide maximum information by analysing chemical data. These sophisticated methods based on different separation techniques or stand alone have been recently coupled to high-resolution mass spectrometry (HRMS) in order to verify the authenticity of food. The new generation of HRMS detectors have experienced significant advances in resolving power, sensitivity, robustness, extended dynamic range, easier mass calibration and tandem mass capabilities, making HRMS more attractive and useful to the food metabolomics community, therefore becoming a reliable tool for food authenticity. The purpose of this review is to summarise and describe the most recent metabolomics approaches in the area of food metabolomics, and to discuss the strengths and drawbacks of the HRMS analytical platforms combined with chemometrics. PMID:26365870

  4. GC-MS-Based Metabolome and Metabolite Regulation in Serum-Resistant Streptococcus agalactiae.

    Science.gov (United States)

    Wang, Zhe; Li, Min-Yi; Peng, Bo; Cheng, Zhi-Xue; Li, Hui; Peng, Xuan-Xian

    2016-07-01

    Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absence of the plasma, indicating S. agalactiae evolved a way of evading the fish immune system. To determine the events underlying this phenotype, we applied GC-MS-based metabolomics approaches to identify differential metabolomes between S. agalactiae cultured with and without yellow grouper plasma. Through bioinformatics analysis, decreased malic acid and increased adenosine were identified as the most crucial metabolites that distinguish the two groups. Meanwhile, they presented with decreased TCA cycle and elevated purine metabolism, respectively. Finally, exogenous malic acid and adenosine were used to reprogram the plasma-resistant metabolome, leading to elevated and decreased susceptibility to the plasma, respectively. Therefore, our findings reveal for the first time that S. agalactiae utilizes a metabolic trick to respond to plasma killing as a result of serum resistance, which may be reverted or enhanced by exogenous malic acid and adenosine, respectively, suggesting that the metabolic trick can be regulated by metabolites. PMID:27251450

  5. The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit.

    Science.gov (United States)

    Tian, Yuan; Amand, Séverine; Buisson, Didier; Kunz, Caroline; Hachette, François; Dupont, Joëlle; Nay, Bastien; Prado, Soizic

    2014-12-01

    Fungal endophytes live inside plant tissues and some have been found to provide benefits to their host. Nevertheless, their ecological impact is not adequately understood. Considering the fact that endophytes are continuously interacting with their hosts, it is conceivable that both partners have substantial influence on each other's metabolic processes. In this context, we have investigated the action of the endophytic fungus Paraconiothyrium variabile, isolated from the leaves of Cephalotaxus harringtonia, on the secondary metabolome of the host-plant. The alteration of the leaf compounds by the fungus was monitored through metabolomic approaches followed by structural characterization of the altered products. Out of more than a thousand molecules present in the crude extract of the plant leaf, we have observed a specific biotransformation of glycosylated flavonoids by the endophyte. In all cases it led to the production of the corresponding aglycone via deglycosylation. The deglycosylated flavonoids turned out to display significant beneficial effects on the hyphal growth of germinated spores. Our finding, along with the known allelopathic role of flavonoids, illustrates the chemical cooperation underlying the mutualistic relationship between the plant and the endophyte. PMID:25446235

  6. Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias

    Science.gov (United States)

    Imperlini, Esther; Santorelli, Lucia; Orrù, Stefania; Scolamiero, Emanuela; Ruoppolo, Margherita

    2016-01-01

    Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs.

  7. 2-Hydrazinoquinoline as a Derivatization Agent for LC-MS-Based Metabolomic Investigation of Diabetic Ketoacidosis

    Directory of Open Access Journals (Sweden)

    Chi Chen

    2013-10-01

    Full Text Available Short-chain carboxylic acids, aldehydes and ketones are products and regulators of many important metabolic pathways. Their levels in biofluids and tissues reflect the status of specific metabolic reactions, the homeostasis of the whole metabolic system and the wellbeing of a biological entity. In this study, the use of 2-hydrazinoquinoline (HQ as a novel derivatization agent was explored and optimized for simultaneous liquid chromatography-mass spectrometry (LC-MS analysis of carboxylic acids, aldehydes and ketones in biological samples. The formation of carboxylic acid derivative is attributed to the esterification reaction between HQ and a carboxyl group, while the production of aldehyde and ketone derivatives is through the formation of Schiff bases between HQ and a carbonyl group. The compatibility of HQ with biological samples was demonstrated by derivatizing urine, serum and liver extract samples. Using this HQ-based approach, the kinetics of type 1 diabetes-induced metabolic changes was characterized by the LC-MS-based metabolomic analysis of urine samples from streptozotocin (STZ-treated mice. Subsequently, carboxylic acid, aldehyde and ketone metabolites associated with STZ-elicited disruption of nutrient and energy metabolism were conveniently identified and elucidated. Overall, HQ derivatization of carboxylic acids, aldehydes and ketones could serve as a useful tool for the LC-MS-based metabolomic investigation of endogenous metabolism.

  8. NMR-Based Metabolomic Analysis of Huanglongbing-Asymptomatic and -Symptomatic Citrus Trees.

    Science.gov (United States)

    Freitas, Deisy dos Santos; Carlos, Eduardo Fermino; Gil, Márcia Cristina Soares de Souza; Vieira, Luiz Gonzaga Esteves; Alcantara, Glaucia Braz

    2015-09-01

    Huanglongbing (HLB) is one of the most severe diseases that affects citrus trees worldwide and is associated with the yet uncultured bacteria Candidatus Liberibacter spp. To assess the metabolomic differences between HLB-asymptomatic and -symptomatic tissues, extracts from leaf and root samples taken from a uniform 6-year-old commercial orchard of Valencia trees were subjected to nuclear magnetic resonance (NMR) and chemometrics. The results show that the symptomatic trees had higher sucrose content in their leaves and no variation in their roots. In addition, proline betaine and malate were detected in smaller amounts in the HLB-affected symptomatic leaves. The changes in metabolic processes of the plant in response to HLB are corroborated by the relationship between the bacterial levels and the metabolic profiles. PMID:26285838

  9. Bio-effectors from waste materials as growth promoters for tomato plants, an agronomic and metabolomic study

    Science.gov (United States)

    Abou Chehade, Lara; Chami, Ziad Al; De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

    2015-04-01

    In organic farming, where nutrient management is constrained and sustainability is claimed, bio-effectors pave their way. Considering selected bio-effectors, this study integrates metabolomics to agronomy in depicting induced relevant phenomena. Extracts of three agro-industrial wastes (Lemon processing residues, Fennel processing residues and Brewer's spent grain) are being investigated as sources of bio-effectors for the third trial consequently. Corresponding individual and mixture aqueous extracts are assessed for their synergistic and/or single agronomic and qualitative performances on soil-grown tomato, compared to both a control and humic acid treatments. A metabolomic profiling of tomato fruits via the Proton Nuclear Magnetic Resonance (NMR) spectroscopy, as holistic indicator of fruit quality and extract-induced responses, complements crop productivity and organoleptic/nutritional qualitative analyses. Results are expected to show mainly an enhancement of the fruit qualitative traits, and to confirm partly the previous results of better crop productivity and metabolism enhancement. Waste-derived bio-effectors could be, accordingly, demonstrated as potential candidates of plant-enhancing substances. Keywords: bio-effectors, organic farming, agro-industrial wastes, nuclear magnetic resonance (NMR), tomato.

  10. A metabolomics cell-based approach for anticipating and investigating drug-induced liver injury.

    Science.gov (United States)

    García-Cañaveras, Juan Carlos; Castell, José V; Donato, M Teresa; Lahoz, Agustín

    2016-01-01

    In preclinical stages of drug development, anticipating potential adverse drug effects such as toxicity is an important issue for both saving resources and preventing public health risks. Current in vitro cytotoxicity tests are restricted by their predictive potential and their ability to provide mechanistic information. This study aimed to develop a metabolomic mass spectrometry-based approach for the detection and classification of drug-induced hepatotoxicity. To this end, the metabolite profiles of human derived hepatic cells (i.e., HepG2) exposed to different well-known hepatotoxic compounds acting through different mechanisms (i.e., oxidative stress, steatosis, phospholipidosis, and controls) were compared by multivariate data analysis, thus allowing us to decipher both common and mechanism-specific altered biochemical pathways. Briefly, oxidative stress damage markers were found in the three mechanisms, mainly showing altered levels of metabolites associated with glutathione and γ-glutamyl cycle. Phospholipidosis was characterized by a decreased lysophospholipids to phospholipids ratio, suggestive of phospholipid degradation inhibition. Whereas, steatosis led to impaired fatty acids β-oxidation and a subsequent increase in triacylglycerides synthesis. The characteristic metabolomic profiles were used to develop a predictive model aimed not only to discriminate between non-toxic and hepatotoxic drugs, but also to propose potential drug toxicity mechanism(s). PMID:27265840

  11. Assessment of compatibility between extraction methods for NMR- and LC/MS-based metabolomics.

    Science.gov (United States)

    Beltran, Antoni; Suarez, Manuel; Rodríguez, Miguel A; Vinaixa, Maria; Samino, Sara; Arola, Lluís; Correig, Xavier; Yanes, Oscar

    2012-07-17

    Because of the wide range of chemically and structurally diverse metabolites, efforts to survey the complete metabolome rely on the implementation of multiplatform approaches based on nuclear magnetic resonance (NMR) and mass spectrometry (MS). Sample preparation disparities between NMR and MS, however, may limit the analysis of the same samples by both platforms. Specifically, deuterated solvents used in NMR strategies can complicate LC/MS analysis as a result of potential mass shifts, whereas acidic solutions typically used in LC/MS methods to enhance ionization of metabolites can severely affect reproducibility of NMR measurements. These intrinsically different sample preparation requirements result in the application of different procedures for metabolite extraction, which involve additional sample and unwanted variability. To address this issue, we investigated 12 extraction protocols in liver tissue involving different aqueous/organic solvents and temperatures that may satisfy the requirements for both NMR and LC/MS simultaneously. We found that deuterium exchange did not affect LC/MS results, enabling the measurement of metabolites by NMR and, subsequently, the direct analysis of the same samples by using LC/MS with no need for solvent exchange. Moreover, our results show that the choice of solvents rather than the temperature determined the extraction efficiencies of metabolites, a combination of methanol/chloroform/water and methanol/water being the extraction methods that best complement NMR and LC/MS analysis for metabolomic studies. PMID:22697410

  12. Establishing Substantial Equivalence: Metabolomics

    Science.gov (United States)

    Beale, Michael H.; Ward, Jane L.; Baker, John M.

    Modern ‘metabolomic’ methods allow us to compare levels of many structurally diverse compounds in an automated fashion across a large number of samples. This technology is ideally suited to screening of populations of plants, including trials where the aim is the determination of unintended effects introduced by GM. A number of metabolomic methods have been devised for the determination of substantial equivalence. We have developed a methodology, using [1H]-NMR fingerprinting, for metabolomic screening of plants and have applied it to the study of substantial equivalence of field-grown GM wheat. We describe here the principles and detail of that protocol as applied to the analysis of flour generated from field plots of wheat. Particular emphasis is given to the downstream data processing and comparison of spectra by multivariate analysis, from which conclusions regarding metabolome changes due to the GM can be assessed against the background of natural variation due to environment.

  13. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

    Science.gov (United States)

    Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

    2016-01-01

    Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

  14. Overexpression of ORCA3 and G10H in Catharanthus roseus Plants Regulated Alkaloid Biosynthesis and Metabolism Revealed by NMR-Metabolomics

    Science.gov (United States)

    Pan, Qifang; Wang, Quan; Yuan, Fang; Xing, Shihai; Zhao, Jingya; Choi, Young Hae; Verpoorte, Robert; Tian, Yuesheng; Wang, Guofeng; Tang, Kexuan

    2012-01-01

    In order to improve the production of the anticancer dimeric indole alkaloids in Catharanthuse roseus, much research has been dedicated to culturing cell lines, hairy roots, and efforts to elucidate the regulation of the monoterpenoid indole alkaloid (MIA) biosynthesis. In this study, the ORCA3 (Octadecanoid-derivative Responsive Catharanthus AP2-domain) gene alone or integrated with the G10H (geraniol 10-hydroxylase) gene were first introduced into C. roseus plants. Transgenic C. roseus plants overexpressing ORCA3 alone (OR lines), or co-overexpressing G10H and ORCA3 (GO lines) were obtained by genetic modification. ORCA3 overexpression induced an increase of AS, TDC, STR and D4H transcripts but did not affect CRMYC2 and G10H transcription. G10H transcripts showed a significant increase under G10H and ORCA3 co-overexpression. ORCA3 and G10H overexpression significantly increased the accumulation of strictosidine, vindoline, catharanthine and ajmalicine but had limited effects on anhydrovinblastine and vinblastine levels. NMR-based metabolomics confirmed the higher accumulation of monomeric indole alkaloids in OR and GO lines. Multivariate data analysis of 1H NMR spectra showed change of amino acid, organic acid, sugar and phenylpropanoid levels in both OR and GO lines compared to the controls. The result indicated that enhancement of MIA biosynthesis by ORCA3 and G10H overexpression might affect other metabolic pathways in the plant metabolism of C. roseus. PMID:22916202

  15. Overexpression of ORCA3 and G10H in Catharanthus roseus plants regulated alkaloid biosynthesis and metabolism revealed by NMR-metabolomics.

    Directory of Open Access Journals (Sweden)

    Qifang Pan

    Full Text Available In order to improve the production of the anticancer dimeric indole alkaloids in Catharanthuse roseus, much research has been dedicated to culturing cell lines, hairy roots, and efforts to elucidate the regulation of the monoterpenoid indole alkaloid (MIA biosynthesis. In this study, the ORCA3 (Octadecanoid-derivative Responsive Catharanthus AP2-domain gene alone or integrated with the G10H (geraniol 10-hydroxylase gene were first introduced into C. roseus plants. Transgenic C. roseus plants overexpressing ORCA3 alone (OR lines, or co-overexpressing G10H and ORCA3 (GO lines were obtained by genetic modification. ORCA3 overexpression induced an increase of AS, TDC, STR and D4H transcripts but did not affect CRMYC2 and G10H transcription. G10H transcripts showed a significant increase under G10H and ORCA3 co-overexpression. ORCA3 and G10H overexpression significantly increased the accumulation of strictosidine, vindoline, catharanthine and ajmalicine but had limited effects on anhydrovinblastine and vinblastine levels. NMR-based metabolomics confirmed the higher accumulation of monomeric indole alkaloids in OR and GO lines. Multivariate data analysis of (1H NMR spectra showed change of amino acid, organic acid, sugar and phenylpropanoid levels in both OR and GO lines compared to the controls. The result indicated that enhancement of MIA biosynthesis by ORCA3 and G10H overexpression might affect other metabolic pathways in the plant metabolism of C. roseus.

  16. UPLC/Q-TOF MS-based metabolomics and qRT-PCR in enzyme gene screening with key role in triterpenoid saponin biosynthesis of Polygala tenuifolia.

    Directory of Open Access Journals (Sweden)

    Fusheng Zhang

    Full Text Available The dried root of Polygala tenuifolia, named Radix Polygalae, is a well-known traditional Chinese medicine. Triterpenoid saponins are some of the most important components of Radix Polygalae extracts and are widely studied because of their valuable pharmacological properties. However, the relationship between gene expression and triterpenoid saponin biosynthesis in P. tenuifolia is unclear.In this study, ultra-performance liquid chromatography (UPLC coupled with quadrupole time-of-flight mass spectrometry (Q-TOF MS-based metabolomic analysis was performed to identify and quantify the different chemical constituents of the roots, stems, leaves, and seeds of P. tenuifolia. A total of 22 marker compounds (VIP>1 were explored, and significant differences in all 7 triterpenoid saponins among the different tissues were found. We also observed an efficient reference gene GAPDH for different tissues in this plant and determined the expression level of some genes in the triterpenoid saponin biosynthetic pathway. Results showed that MVA pathway has more important functions in the triterpenoid saponin biosynthesis of P. tenuifolia. The expression levels of squalene synthase (SQS, squalene monooxygenase (SQE, and beta-amyrin synthase (β-AS were highly correlated with the peak area intensity of triterpenoid saponins compared with data from UPLC/Q-TOF MS-based metabolomic analysis.This finding suggested that a combination of UPLC/Q-TOF MS-based metabolomics and gene expression analysis can effectively elucidate the mechanism of triterpenoid saponin biosynthesis and can provide useful information on gene discovery. These findings can serve as a reference for using the overexpression of genes encoding for SQS, SQE, and/or β-AS to increase the triterpenoid saponin production of P. tenuifolia.

  17. metaMS: An open-source pipeline for GC–MS-based untargeted metabolomics

    NARCIS (Netherlands)

    Wehrens, H.R.M.J.; Weingart, G.; Mattivi, F.

    2014-01-01

    Untargeted metabolomics are rapidly becoming an important tool for studying complex biological samples. Gas chromatography–mass spectrometry (GC–MS) is the most widely used analytical technology for metabolomic analysis of compounds that are volatile or can be chemically derivatised into volatile co

  18. Impact of metal pollution on shrimp Crangon affinis by NMR-based metabolomics.

    Science.gov (United States)

    Ji, Chenglong; Yu, Deliang; Wang, Qing; Li, Fei; Zhao, Jianmin; Wu, Huifeng

    2016-05-15

    Both cadmium and arsenic are the important metal/metalloid pollutants in the Bohai Sea. In this work, we sampled the dominant species, shrimp Crangon affinis, from three sites, the Middle of the Bohai Sea (MBS), the Yellow River Estuary (YRE) and the Laizhou Bay (LZB) along the Bohai Sea. The concentrations of metals/metalloids in shrimps C. affinis indicated that the YRE site was polluted by Cd and Pb, while the LZB site was contaminated by As. The metabolic differences between shrimps C. affinis from the reference site (MBS) and metal-pollution sites (YRE and LZB) were characterized using NMR-based metabolomics. Results indicated that the metal pollutions in YRE and LZB induced disturbances in osmotic regulation and energy metabolism via different metabolic pathways. In addition, a combination of alanine and arginine might be the biomarker of Cd contamination, while BCAAs and tyrosine could be the biomarkers of arsenic contamination in C. affinis. PMID:26920426

  19. Nuclear magnetic resonance-based metabolomics for prediction of gastric damage induced by indomethacin in rats

    International Nuclear Information System (INIS)

    Highlights: ► NMR based metabolomics – gastric damage by indomethacin. ► Pattern recognition analysis was performed to biomarkers of gastric damage. ► 2-Oxoglutarate, acetate, taurine and hippurate were selected as putative biomarkers. ► The gastric damage induced by NSAIDs can be screened in the preclinical step of drug. - Abstract: Non-steroidal anti-inflammatory drugs (NSAIDs) have side effects including gastric erosions, ulceration and bleeding. In this study, pattern recognition analysis of the 1H-nuclear magnetic resonance (NMR) spectra of urine was performed to develop surrogate biomarkers related to the gastrointestinal (GI) damage induced by indomethacin in rats. Urine was collected for 5 h after oral administration of indomethacin (25 mg kg−1) or co-administration with cimetidine (100 mg kg−1), which protects against GI damage. The 1H-NMR urine spectra were divided into spectral bins (0.04 ppm) for global profiling, and 36 endogenous metabolites were assigned for targeted profiling. The level of gastric damage in each animal was also determined. Indomethacin caused severe gastric damage; however, indomethacin administered with cimetidine did not. Simultaneously, the patterns of changes in their endogenous metabolites were different. Multivariate data analyses were carried out to recognize the spectral pattern of endogenous metabolites related to indomethacin using partial least square-discrimination analysis. In targeted profiling, a few endogenous metabolites, 2-oxoglutarate, acetate, taurine and hippurate, were selected as putative biomarkers for the gastric damage induced by indomethacin. These metabolites changed depending on the degree of GI damage, although the same dose of indomethacin (10 mg kg−1) was administered to rats. The results of global and targeted profiling suggest that the gastric damage induced by NSAIDs can be screened in the preclinical stage of drug development using a NMR based metabolomics approach.

  20. Nuclear magnetic resonance-based metabolomics for prediction of gastric damage induced by indomethacin in rats

    Energy Technology Data Exchange (ETDEWEB)

    Um, So Young [Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk (Korea, Republic of); Division of Life and Pharmaceutical Science and College of Pharmacy, Ewha Womans University, 52 Ewahyeodae-gil, Seodaemun-gu, Seoul (Korea, Republic of); Park, Jung Hyun [Division of Life and Pharmaceutical Science and College of Pharmacy, Ewha Womans University, 52 Ewahyeodae-gil, Seodaemun-gu, Seoul (Korea, Republic of); Chung, Myeon Woo [Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk (Korea, Republic of); Kim, Kyu-Bong [College of Pharmacy, Dankook University, Dandae-ro, Cheonan, Chungnam (Korea, Republic of); Kim, Seon Hwa [Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk (Korea, Republic of); Division of Life and Pharmaceutical Science and College of Pharmacy, Ewha Womans University, 52 Ewahyeodae-gil, Seodaemun-gu, Seoul (Korea, Republic of); College of Pharmacy, Dankook University, Dandae-ro, Cheonan, Chungnam (Korea, Republic of); Choi, Ki Hwan, E-mail: hyokwa11@korea.kr [Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk (Korea, Republic of); Lee, Hwa Jeong, E-mail: hwalee@ewha.ac.kr [Division of Life and Pharmaceutical Science and College of Pharmacy, Ewha Womans University, 52 Ewahyeodae-gil, Seodaemun-gu, Seoul (Korea, Republic of)

    2012-04-13

    Highlights: Black-Right-Pointing-Pointer NMR based metabolomics - gastric damage by indomethacin. Black-Right-Pointing-Pointer Pattern recognition analysis was performed to biomarkers of gastric damage. Black-Right-Pointing-Pointer 2-Oxoglutarate, acetate, taurine and hippurate were selected as putative biomarkers. Black-Right-Pointing-Pointer The gastric damage induced by NSAIDs can be screened in the preclinical step of drug. - Abstract: Non-steroidal anti-inflammatory drugs (NSAIDs) have side effects including gastric erosions, ulceration and bleeding. In this study, pattern recognition analysis of the {sup 1}H-nuclear magnetic resonance (NMR) spectra of urine was performed to develop surrogate biomarkers related to the gastrointestinal (GI) damage induced by indomethacin in rats. Urine was collected for 5 h after oral administration of indomethacin (25 mg kg{sup -1}) or co-administration with cimetidine (100 mg kg{sup -1}), which protects against GI damage. The {sup 1}H-NMR urine spectra were divided into spectral bins (0.04 ppm) for global profiling, and 36 endogenous metabolites were assigned for targeted profiling. The level of gastric damage in each animal was also determined. Indomethacin caused severe gastric damage; however, indomethacin administered with cimetidine did not. Simultaneously, the patterns of changes in their endogenous metabolites were different. Multivariate data analyses were carried out to recognize the spectral pattern of endogenous metabolites related to indomethacin using partial least square-discrimination analysis. In targeted profiling, a few endogenous metabolites, 2-oxoglutarate, acetate, taurine and hippurate, were selected as putative biomarkers for the gastric damage induced by indomethacin. These metabolites changed depending on the degree of GI damage, although the same dose of indomethacin (10 mg kg{sup -1}) was administered to rats. The results of global and targeted profiling suggest that the gastric damage induced by

  1. Effect of the environment on the secondary metabolic profile of Tithonia diversifolia: a model for environmental metabolomics of plants

    Science.gov (United States)

    Sampaio, Bruno Leite; Edrada-Ebel, Ruangelie; da Costa, Fernando Batista

    2016-07-01

    Tithonia diversifolia is an invasive weed commonly found in tropical ecosystems. In this work, we investigate the influence of different abiotic environmental factors on the plant’s metabolite profile by multivariate statistical analyses of spectral data deduced by UHPLC-DAD-ESI-HRMS and NMR methods. Different plant part samples of T. diversifolia which included leaves, stems, roots, and inflorescences were collected from two Brazilian states throughout a 24-month period, along with the corresponding monthly environmental data. A metabolomic approach employing concatenated LC-MS and NMR data was utilised for the first time to study the relationships between environment and plant metabolism. A seasonal pattern was observed for the occurrence of metabolites that included sugars, sesquiterpenes lactones and phenolics in the leaf and stem parts, which can be correlated to the amount of rainfall and changes in temperature. The distribution of the metabolites in the inflorescence and root parts were mainly affected by variation of some soil nutrients such as Ca, Mg, P, K and Cu. We highlight the environment-metabolism relationship for T. diversifolia and the combined analytical approach to obtain reliable data that contributed to a holistic understanding of the influence of abiotic environmental factors on the production of metabolites in various plant parts.

  2. Effect of the environment on the secondary metabolic profile of Tithonia diversifolia: a model for environmental metabolomics of plants

    Science.gov (United States)

    Sampaio, Bruno Leite; Edrada-Ebel, RuAngelie; Da Costa, Fernando Batista

    2016-01-01

    Tithonia diversifolia is an invasive weed commonly found in tropical ecosystems. In this work, we investigate the influence of different abiotic environmental factors on the plant’s metabolite profile by multivariate statistical analyses of spectral data deduced by UHPLC-DAD-ESI-HRMS and NMR methods. Different plant part samples of T. diversifolia which included leaves, stems, roots, and inflorescences were collected from two Brazilian states throughout a 24-month period, along with the corresponding monthly environmental data. A metabolomic approach employing concatenated LC-MS and NMR data was utilised for the first time to study the relationships between environment and plant metabolism. A seasonal pattern was observed for the occurrence of metabolites that included sugars, sesquiterpenes lactones and phenolics in the leaf and stem parts, which can be correlated to the amount of rainfall and changes in temperature. The distribution of the metabolites in the inflorescence and root parts were mainly affected by variation of some soil nutrients such as Ca, Mg, P, K and Cu. We highlight the environment-metabolism relationship for T. diversifolia and the combined analytical approach to obtain reliable data that contributed to a holistic understanding of the influence of abiotic environmental factors on the production of metabolites in various plant parts. PMID:27383265

  3. An inter-laboratory comparison demonstrates that [H-1]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection.

    OpenAIRE

    Ward, J. L.; J.M. Baker; Miller, S J; Deborde, C; Maucourt, M.; Biais, B.; Rolin, D.; Moing, A.; Moco, S.I.A.; Vervoort, J.J.M.; Lommen, A.; Schafer, H; Humpfer, E.; Beale, M.H.

    2010-01-01

    In any metabolomics experiment, robustness and reproducibility of data collection is of vital importance. These become more important in collaborative studies where data is to be collected on multiple instruments. With minimisation of variance in sample preparation and instrument performance it is possible to elucidate even subtle differences in metabolite fingerprints due to genotype or biological treatment. In this paper we report on an inter laboratory comparison of plant derived samples b...

  4. An inter-laboratory comparison demonstrates that [1H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection

    OpenAIRE

    Ward, Jane L.; Baker, John M.; Miller, Sonia J.; Deborde, Catherine; Maucourt, Mickael; Biais, Benoit; Rolin, Dominique; Moing, Annick; Moco, Sofia; Vervoort, Jacques; Lommen, Arjen; Schäfer, Hartmut; Humpfer, Eberhard; Beale, Michael H.

    2010-01-01

    In any metabolomics experiment, robustness and reproducibility of data collection is of vital importance. These become more important in collaborative studies where data is to be collected on multiple instruments. With minimisation of variance in sample preparation and instrument performance it is possible to elucidate even subtle differences in metabolite fingerprints due to genotype or biological treatment. In this paper we report on an inter laboratory comparison of plant derived samples b...

  5. Non-targeted Metabolomics in Diverse Sorghum Breeding Lines Indicates Primary and Secondary Metabolite Profiles Are Associated with Plant Biomass Accumulation and Photosynthesis

    Science.gov (United States)

    Turner, Marie F.; Heuberger, Adam L.; Kirkwood, Jay S.; Collins, Carl C.; Wolfrum, Edward J.; Broeckling, Corey D.; Prenni, Jessica E.; Jahn, Courtney E.

    2016-01-01

    Metabolomics is an emerging method to improve our understanding of how genetic diversity affects phenotypic variation in plants. Recent studies have demonstrated that genotype has a major influence on biochemical variation in several types of plant tissues, however, the association between metabolic variation and variation in morphological and physiological traits is largely unknown. Sorghum bicolor (L.) is an important food and fuel crop with extensive genetic and phenotypic variation. Sorghum lines have been bred for differing phenotypes beneficial for production of grain (food), stem sugar (food, fuel), and cellulosic biomass (forage, fuel), and these varying phenotypes are the end products of innate metabolic programming which determines how carbon is allocated during plant growth and development. Further, sorghum has been adapted among highly diverse environments. Because of this geographic and phenotypic variation, the sorghum metabolome is expected to be highly divergent; however, metabolite variation in sorghum has not been characterized. Here, we utilize a phenotypically diverse panel of sorghum breeding lines to identify associations between leaf metabolites and morpho-physiological traits. The panel (11 lines) exhibited significant variation for 21 morpho-physiological traits, as well as broader trends in variation by sorghum type (grain vs. biomass types). Variation was also observed for cell wall constituents (glucan, xylan, lignin, ash). Non-targeted metabolomics analysis of leaf tissue showed that 956 of 1181 metabolites varied among the lines (81%, ANOVA, FDR adjusted p sorghum. Taken together, this study demonstrates the integration of metabolomics with morpho-physiological datasets to elucidate links between plant metabolism, growth, and architecture. PMID:27462319

  6. RAMAN SPECTROSCOPY-BASED METABOLOMICS FOR DIFFERENTIATING EXPOSURES TO TRIAZOLE FUNGICIDES USING RAT URINE

    Science.gov (United States)

    Normal Raman spectroscopy was evaluated as a metabolomic tool for assessing the impacts of exposure to environmental contaminants, using rat urine collected during the course of a toxicological study. Specifically, one of three triazole fungicides, myclobutanil, propiconazole or ...

  7. IDEOM : an Excel interface for analysis of LC-MS-based metabolomics data

    NARCIS (Netherlands)

    Creek, Darren J.; Jankevics, Andris; Burgess, Karl E. V.; Breitling, Rainer; Barrett, Michael P.; Wren, Jonathan

    2012-01-01

    The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates

  8. Metabolomic profile in pancreatic cancer patients: a consensus-based approach to identify highly discriminating metabolites

    OpenAIRE

    Di Gangi, Iole Maria; Mazza, Tommaso; Fontana, Andrea; Copetti, Massimiliano; Fusilli, Caterina; Ippolito, Antonio; Mattivi, Fulvio; Latiano, Anna; Andriulli, Angelo; Vrhovsek, Urska; Pazienza, Valerio

    2016-01-01

    Purpose pancreatic adenocarcinoma is the fourth leading cause of cancer related deaths due to its aggressive behavior and poor clinical outcome. There is a considerable variability in the frequency of serum tumor markers in cancer' patients. We performed a metabolomics screening in patients diagnosed with pancreatic cancer. Experimental Design Two targeted metabolomic assays were conducted on 40 serum samples of patients diagnosed with pancreatic cancer and 40 healthy controls. Multivariate m...

  9. Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach

    Directory of Open Access Journals (Sweden)

    Redestig Henning

    2011-01-01

    Full Text Available Abstract Background Deciphering the metabolome is essential for a better understanding of the cellular metabolism as a system. Typical metabolomics data show a few but significant correlations among metabolite levels when data sampling is repeated across individuals grown under strictly controlled conditions. Although several studies have assessed topologies in metabolomic correlation networks, it remains unclear whether highly connected metabolites in these networks have specific functions in known tissue- and/or genotype-dependent biochemical pathways. Results In our study of metabolite profiles we subjected root tissues to gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS and used published information on the aerial parts of 3 Arabidopsis genotypes, Col-0 wild-type, methionine over-accumulation 1 (mto1, and transparent testa4 (tt4 to compare systematically the metabolomic correlations in samples of roots and aerial parts. We then applied graph clustering to the constructed correlation networks to extract densely connected metabolites and evaluated the clusters by biochemical-pathway enrichment analysis. We found that the number of significant correlations varied by tissue and genotype and that the obtained clusters were significantly enriched for metabolites included in biochemical pathways. Conclusions We demonstrate that the graph-clustering approach identifies tissue- and/or genotype-dependent metabolomic clusters related to the biochemical pathway. Metabolomic correlations complement information about changes in mean metabolite levels and may help to elucidate the organization of metabolically functional modules.

  10. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health.

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  11. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

    Science.gov (United States)

    Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

    2016-01-01

    The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

  12. Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review.

    OpenAIRE

    Roux, Aurélie; Lison, Dominique; Junot, Christophe; Heillier, Jean-François

    2011-01-01

    International audience The metabolome is the set of small molecular mass organic compounds found in a given biological media. It includes all organic substances naturally occurring from the metabolism of the studied living organism, except biological polymers, but also xenobiotics and their biotransformation products. The metabolic fingerprints of biofluids obtained by mass spectrometry (MS) or nuclear magnetic resonance (NMR)-based methods contain a few hundreds to thousands of signals re...

  13. Non-Targeted Metabolomics in Diverse Sorghum Breeding Lines Indicates Primary and Secondary Metabolite Profiles Are Associated with Plant Biomass Accumulation and Photosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Turner, Marie F.; Heuberger, Adam L.; Kirkwood, Jay S.; Collins, Carl C.; Wolfrum, Edward J.; Broeckling, Corey D.; Prenni, Jessica E.; Jahn, Courtney E.

    2016-07-01

    Metabolomics is an emerging method to improve our understanding of how genetic diversity affects phenotypic variation in plants. Recent studies have demonstrated that genotype has a major influence on biochemical variation in several types of plant tissues, however, the association between metabolic variation and variation in morphological and physiological traits is largely unknown. Sorghum bicolor (L.) is an important food and fuel crop with extensive genetic and phenotypic variation. Sorghum lines have been bred for differing phenotypes beneficial for production of grain (food), stem sugar (food, fuel), and cellulosic biomass (forage, fuel), and these varying phenotypes are the end products of innate metabolic programming which determines how carbon is allocated during plant growth and development. Further, sorghum has been adapted among highly diverse environments. Because of this geographic and phenotypic variation, the sorghum metabolome is expected to be highly divergent; however, metabolite variation in sorghum has not been characterized. Here, we utilize a phenotypically diverse panel of sorghum breeding lines to identify associations between leaf metabolites and morpho-physiological traits. The panel (11 lines) exhibited significant variation for 21 morpho-physiological traits, as well as broader trends in variation by sorghum type (grain vs. biomass types). Variation was also observed for cell wall constituents (glucan, xylan, lignin, ash). Non-targeted metabolomics analysis of leaf tissue showed that 956 of 1181 metabolites varied among the lines (81%, ANOVA, FDR adjusted p < 0.05). Both univariate and multivariate analyses determined relationships between metabolites and morpho-physiological traits, and 384 metabolites correlated with at least one trait (32%, p < 0.05), including many secondary metabolites such as glycosylated flavonoids and chlorogenic acids. The use of metabolomics to explain relationships between two or more morpho

  14. Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

    Directory of Open Access Journals (Sweden)

    Yun Yen

    2013-04-01

    Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

  15. LC-MS-Based Metabolomics Study of Marine Bacterial Secondary Metabolite and Antibiotic Production in Salinispora arenicola

    Directory of Open Access Journals (Sweden)

    Utpal Bose

    2015-01-01

    Full Text Available An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times. We used metabolomics as a tool to investigate the production of rifamycins (antibiotics and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A “chemical profile” link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time.

  16. An UPLC-MS-based metabolomics investigation on the anti-fatigue effect of salidroside in mice.

    Science.gov (United States)

    Ma, Chaoyang; Hu, Liming; Tao, Guanjun; Lv, Wenping; Wang, Hongxin

    2015-02-01

    An ultra-performance liquid chromatography-quadrupole time-of-flight-based metabolomic approach was developed to study influence of salidroside, an anti-fatigue ingredient from Rhoiola rosea, on urinary metabolic profiling of rats to a single dose of 180 mg/kg per day. Unsupervised principal component analysis (PCA) and supervised orthogonal pre-projection to latent structures discriminate analysis (OPLS-DA) on metabolite profiling revealed obvious differentiation between the salidroside treated groups and controls in both positive and negative ion modes. Eleven urinary metabolites contributing to the differentiation were identified as anti-fatigue biomarkers: N-acetylserotonin, 2-Methoxyestrone 3-glucuronide, Taurine, Melatonin, Sorbitol, Geranyl diphosphate, Z-nucleotide, Cortisone, Dihydrocortisol, Sebacic acid, Pregnenolone sulfate. The physiological significance of these biomarkers is discussed. The work showed that metabolomics is a powerful tool in studying the anti-fatigue effects of natural compound salidroside on multiple targets in vivo. PMID:25543286

  17. Evaluation of Pacific white shrimp (Litopenaeus vannamei health during a superintensive aquaculture growout using NMR-based metabolomics.

    Directory of Open Access Journals (Sweden)

    Tracey B Schock

    Full Text Available Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems are being developed that permit year-round production of farmed shrimp at high densities. These systems are intended to overcome problems of disease susceptibility and of water quality issues from waste products, by operating as essentially closed systems that promote beneficial microbial communities (biofloc. The resulting biofloc can assimilate and detoxify wastes, may provide nutrition for the farmed organisms resulting in improved growth, and may aid in reducing disease initiated from external sources. Nuclear magnetic resonance (NMR-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Aberrant shrimp metabolomes were detected from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes in the shrimp that were induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry by providing physiological insight into common environmental stresses that may limit growth or better explain reduced survival and production.

  18. Validation of Metabolic Alterations in Microscale Cell Culture Lysates Using Hydrophilic Interaction Liquid Chromatography (HILIC)-Tandem Mass Spectrometry-Based Metabolomics

    Science.gov (United States)

    Gunda, Venugopal; Yu, Fang; Singh, Pankaj K.

    2016-01-01

    By standard convention, in order to increase the efficacy of metabolite detection from cell culture lysates, metabolite extracts from a large quantity of cells are utilized for multiple reaction monitoring-based metabolomic studies. Metabolomics from a small number of cell extracts offers a potential economical alternative to increased cell numbers, in turn increasing the utility of cell culture-based metabolomics. However, the effect of reduced cell numbers on targeted metabolomic profiling is relatively unstudied. Considering the limited knowledge available of the feasibility and accuracy of microscale cell culture metabolomics, the present study analyzes differences in metabolomic profiles of different cell numbers of three pancreatic cancer cell lines. Specifically, it examines the effects of reduced cell numbers on metabolite profiles by obtaining extracts either directly from microscale culture plates or through serial dilution of increased numbers of cellular metabolite extracts. Our results indicate reduced cell numbers only modestly affect the number of metabolites detected (93% of metabolites detected in cell numbers as low as 104 cells and 97% for 105 cells), independent of the method used to obtain the cells. However, metabolite peak intensities were differentially affected by the reduced cell numbers, with some peak intensities inversely proportional to the cell numbers. To help eliminate such potential inverse relationships, peak intensities for increased cell numbers were excluded from the comparative analysis. Overall, metabolite profiles from microscale culture plates were observed to differ from the serial dilution samples, which may be attributable to the medium-to-cell-number ratios. Finally, findings identify perturbations in metabolomic profiling for cellular extracts from reduced cell numbers, which offer future applications in microscale metabolomic evaluations. PMID:27120458

  19. Application of (1)H NMR-based serum metabolomic studies for monitoring female patients with rheumatoid arthritis.

    Science.gov (United States)

    Zabek, Adam; Swierkot, Jerzy; Malak, Anna; Zawadzka, Iga; Deja, Stanisław; Bogunia-Kubik, Katarzyna; Mlynarz, Piotr

    2016-01-01

    Rheumatoid arthritis is a chronic autoimmune-based inflammatory disease that leads to progressive joint degeneration, disability, and an increased risk of cardiovascular complications, which is the main cause of mortality in this population of patients. Although several biomarkers are routinely used in the management of rheumatoid arthritis, there is a high demand for novel biomarkers to further improve the early diagnosis of rheumatoid arthritis, stratification of patients, and the prediction of a better response to a specific therapy. In this study, the metabolomics approach was used to provide relevant biomarkers to improve diagnostic accuracy, define prognosis and predict and monitor treatment efficacy. The results indicated that twelve metabolites were important for the discrimination of healthy control and rheumatoid arthritis. Notably, valine, isoleucine, lactate, alanine, creatinine, GPC  APC and histidine relative levels were lower in rheumatoid arthritis, whereas 3-hydroxyisobutyrate, acetate, NAC, acetoacetate and acetone relative levels were higher. Simultaneously, the analysis of the concentration of metabolites in rheumatoid arthritis and 3 months after induction treatment revealed that L1, 3-hydroxyisobutyrate, lysine, L5, acetoacetate, creatine, GPC+APC, histidine and phenylalanine were elevated in RA, whereas leucine, acetate, betaine and formate were lower. Additionally, metabolomics tools were employed to discriminate between patients with different IL-17A genotypes. Metabolomics may provide relevant biomarkers to improve diagnostic accuracy, define prognosis and predict and monitor treatment efficacy in rheumatoid arthritis. PMID:26476882

  20. Objective Definition of Monofloral and Polyfloral Honeys Based on NMR Metabolomic Profiling.

    Science.gov (United States)

    Schievano, Elisabetta; Finotello, Claudia; Uddin, Jalal; Mammi, Stefano; Piana, Lucia

    2016-05-11

    In this paper, a remarkably precise, simple, and objective definition of monofloral and polyfloral honey based on NMR metabolomics is proposed. The spectra of organic extracts of 983 samples of 16 botanical origins were used to derive one-versus-all OPLS-DA classification models. The predictive components of the statistical models reveal not only the principal but also the secondary floral origins present in a sample of honey, a novel feature with respect to the methods present in the literature that are able to confirm the authenticity of monofloral honeys but not to characterize a mixture of honey types. This result descends from the peculiar features of the chloroform spectra that show diagnostic resonances for almost each botanical origin, making these NMR spectra suitable fingerprints. The reliability of the method was tested with an additional 120 samples, and the class assignments were compared with those obtained by traditional analysis. The two approaches are in excellent agreement in identifying the floral species present in honeys and in the botanical classification. Therefore, this NMR method may prove to be a valid solution to the huge limitations of traditional classification, which is very demanding and complex. PMID:27086991

  1. Discrimination of the geographical origin of beef by (1)H NMR-based metabolomics.

    Science.gov (United States)

    Jung, Youngae; Lee, Jueun; Kwon, Joseph; Lee, Kwang-Sik; Ryu, Do Hyun; Hwang, Geum-Sook

    2010-10-13

    The geographical origin of beef is of increasing interest to consumers and producers due to "mad cow" disease and the implementation of the Free Trade Agreement (FTA). In this study, (1)H NMR spectroscopy coupled with multivariate statistical analyses was used to differentiate the geographical origin of beef samples. Principal component analysis (PCA) and orthogonal projection to latent structure-discriminant analysis (OPLS-DA) showed significant separation between extracts of beef originating from four countries: Australia, Korea, New Zealand, and the United States. The major metabolites responsible for differentiation in OPLS-DA loading plots were succinate and various amino acids including isoleucine, leucine, methionine, tyrosine, and valine. A one-way ANOVA was performed to statistically certify the difference in metabolite levels. The data suggest that NMR-based metabolomics is an efficient method to distinguish fingerprinting difference between raw beef samples, and several metabolites including various amino acids and succinate can be possible biomarkers for discriminating the geographical origin of beef. PMID:20831251

  2. Metabolomics Reveals the Origins of Antimicrobial Plant Resins Collected by Honey Bees

    OpenAIRE

    Wilson, Michael B.; Spivak, Marla; Hegeman, Adrian D.; Rendahl, Aaron; Cohen, Jerry D.

    2013-01-01

    The deposition of antimicrobial plant resins in honey bee, Apis mellifera, nests has important physiological benefits. Resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or t...

  3. Metabolomics for Quality and food security

    International Nuclear Information System (INIS)

    By the term 'Metabolomics' means the discipline which allows you to determine the set of small molecules (metabolites) produced by an organism in a given time. The metabolomic analysis requires complex technological platforms that allow, in the first place, the separation (chromatography liquid or gaseous) of the different molecules and, subsequently, the identification of the same on the basis of characteristic ratio between their mass and charge (m / z). This study arises by estimates that, between climate change planned for the coming decades, there will also be quick increasing the concentration of Co2 in the atmosphere. In this context, it is essential to predict how these changes weather will impact on product quality plant at the base of our diet.

  4. Metabolomics of genetically modified crops.

    Science.gov (United States)

    Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade. PMID:25334064

  5. Metabolomics of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Carolina Simó

    2014-10-01

    Full Text Available Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.

  6. Comparison of Fruits of Forsythia suspensa at Two Different Maturation Stages by NMR-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Jinping Jia

    2015-05-01

    Full Text Available Forsythiae Fructus (FF, the dried fruit of Forsythia suspensa, has been widely used as a heat-clearing and detoxifying herbal medicine in China. Green FF (GF and ripe FF (RF are fruits of Forsythia suspensa at different maturity stages collected about a month apart. FF undergoes a complex series of physical and biochemical changes during fruit ripening. However, the clinical uses of GF and RF have not been distinguished to date. In order to comprehensively compare the chemical compositions of GF and RF, NMR-based metabolomics coupled with HPLC and UV spectrophotometry methods were adopted in this study. Furthermore, the in vitro antioxidant and antibacterial activities of 50% methanol extracts of GF and RF were also evaluated. A total of 27 metabolites were identified based on NMR data, and eight of them were found to be different between the GF and RF groups. The GF group contained higher levels of forsythoside A, forsythoside C, cornoside, rutin, phillyrin and gallic acid and lower levels of rengyol and β-glucose compared with the RF group. The antioxidant activity of GF was higher than that of RF, but no significant difference was observed between the antibacterial activities of GF and RF. Given our results showing their distinct chemical compositions, we propose that NMR-based metabolic profiling can be used to discriminate between GF and RF. Differences in the chemical and biological activities of GF and RF, as well as their clinical efficacies in traditional Chinese medicine should be systematically investigated in future studies.

  7. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Nagana Gowda, G. A.; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

  8. An untargeted metabolomics approach to contaminant analysis. Pinpointing potential unknown compounds

    NARCIS (Netherlands)

    Lommen, A.; Weg, van der G.; Engelen, M.C.; Bor, G.; Hoogenboom, L.A.P.; Nielen, M.W.F.

    2007-01-01

    This study deals with an automated data analysis strategy to pinpoint potential unknown compounds in full scan mass spectrometry (MS) experiments. Three examples of an untargeted metabolomics approach to contaminant analysis are given. By comparing a plant-oil based hormone cocktail to 90 plant oil

  9. 1H NMR- based metabolomics approaches as non- invasive tools for diagnosis of endometriosis

    Directory of Open Access Journals (Sweden)

    Negar Ghazi

    2016-01-01

    Full Text Available Background: So far, non-invasive diagnostic approaches such as ultrasound, magnetic resonance imaging, or blood tests do not have sufficient diagnostic power for endometriosis disease. Lack of a non-invasive diagnostic test contributes to the long delay between onset of symptoms and diagnosis of endometriosis. Objective: The present study focuses on the identification of predictive biomarkers in serum by pattern recognition techniques and uses partial least square discriminant analysis, multi-layer feed forward artificial neural networks (ANNs and quadratic discriminant analysis (QDA modeling tools for the early diagnosis of endometriosis in a minimally invasive manner by 1H- NMR based metabolomics. Materials and Methods: This prospective cohort study was done in Pasteur Institute, Iran in June 2013. Serum samples of 31 infertile women with endometriosis (stage II and III who confirmed by diagnostic laparoscopy and 15 normal women were collected and analyzed by nuclear magnetic resonance spectroscopy. The model was built by using partial least square discriminant analysis, QDA, and ANNs to determine classifier metabolites for early prediction risk of disease. Results: The levels of 2- methoxyestron, 2-methoxy estradiol, dehydroepiandrostion androstendione, aldosterone, and deoxy corticosterone were enhanced significantly in infertile group. While cholesterol and primary bile acids levels were decreased. QDA model showed significant difference between two study groups. Positive and negative predict value levels obtained about 71% and 78%, respectively. ANNs provided also criteria for detection of endometriosis. Conclusion: The QDA and ANNs modeling can be used as computational tools in noninvasive diagnose of endometriosis. However, the model designed by QDA methods is more efficient compared to ANNs in diagnosis of endometriosis patients.

  10. 1H NMR- based metabolomics approaches as non- invasive tools for diagnosis of endometriosis

    Science.gov (United States)

    Ghazi, Negar; Arjmand, Mohammad; Akbari, Ziba; Mellati, Ali Owsat; Saheb-Kashaf, Hamid; Zamani, Zahra

    2016-01-01

    Background: So far, non-invasive diagnostic approaches such as ultrasound, magnetic resonance imaging, or blood tests do not have sufficient diagnostic power for endometriosis disease. Lack of a non-invasive diagnostic test contributes to the long delay between onset of symptoms and diagnosis of endometriosis. Objective: The present study focuses on the identification of predictive biomarkers in serum by pattern recognition techniques and uses partial least square discriminant analysis, multi-layer feed forward artificial neural networks (ANNs) and quadratic discriminant analysis (QDA) modeling tools for the early diagnosis of endometriosis in a minimally invasive manner by 1H- NMR based metabolomics. Materials and Methods: This prospective cohort study was done in Pasteur Institute, Iran in June 2013. Serum samples of 31 infertile women with endometriosis (stage II and III) who confirmed by diagnostic laparoscopy and 15 normal women were collected and analyzed by nuclear magnetic resonance spectroscopy. The model was built by using partial least square discriminant analysis, QDA, and ANNs to determine classifier metabolites for early prediction risk of disease. Results: The levels of 2- methoxyestron, 2-methoxy estradiol, dehydroepiandrostion androstendione, aldosterone, and deoxy corticosterone were enhanced significantly in infertile group. While cholesterol and primary bile acids levels were decreased. QDA model showed significant difference between two study groups. Positive and negative predict value levels obtained about 71% and 78%, respectively. ANNs provided also criteria for detection of endometriosis. Conclusion: The QDA and ANNs modeling can be used as computational tools in noninvasive diagnose of endometriosis. However, the model designed by QDA methods is more efficient compared to ANNs in diagnosis of endometriosis patients.

  11. Assessment of clam ruditapes philippinarum as Heavy metal bioindicators using NMR-based metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xiaoli; Zhang, Linbao; You, Liping [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); The Graduate School of Chinese Academy of Sciences, Beijing (China); Yu, Junbao; Cong, Ming; Wang, Qing; Li, Fei; Li, Lianzhen; Zhao, Jianmin; Li, Chenghua; Wu, Huifeng [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China)

    2011-08-15

    There are mainly distributed three pedigrees (White, Liangdao Red, and Zebra) of Manila clam Ruditapes philippinarum in Yantai population along the Bohai marine and coast. However, the biological differences to environmental stressors have been ignored in toxicology studies, which could lead to the distortion of biological interpretations of toxicological effects induced by environmental contaminants. In this study, we applied a system biology approach, metabolomics to compare the metabolic profiles in digestive gland from three pedigrees of clam and characterize and compare the metabolic responses induced by mercury in clam digestive gland tissues to determine a sensitive pedigree of clam as a preferable bioindicator for metal pollution monitoring and toxicology research. The most abundant metabolites, respectively, included branched-chain amino acids, alanine, and arginine in White samples, glutamate, dimethylglycine, and glycine in Zebra clams and acetylcholine, betaine, glucose, and glycogen in Liangdao Red clams. After 48 h exposure of 20 {mu}g L{sup -1} Hg{sup 2+}, the metabolic profiles from the three pedigrees of clams showed differentially significant changes in alanine, glutamate, succinate, taurine, hypotaurine, glycine, arginine, glucose, etc. Our findings indicate the toxicological effects of mercury exposure in Manila clams including the neurotoxicity, disturbances in energetic metabolisms and osmoregulation in the digestive glands and suggest that Liangdao Red pedigree of clam could be a preferable bioindicator for the metal pollution monitoring based on the more sensitive classes of metabolic changes from digestive glands compared with other two (White and Zebra) pedigrees of clams. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Metabolomics of Genetically Modified Crops

    OpenAIRE

    Carolina Simó; Clara Ibáez; Alberto Valdés; Alejandro Cifuentes; Virginia García-Cañas

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resul...

  13. Metabolomics by Proton High-Resolution Magic-Angle-Spinning Nuclear Magnetic Resonance of Tomato Plants Treated with Two Secondary Metabolites Isolated from Trichoderma.

    Science.gov (United States)

    Mazzei, Pierluigi; Vinale, Francesco; Woo, Sheridan Lois; Pascale, Alberto; Lorito, Matteo; Piccolo, Alessandro

    2016-05-11

    Trichoderma fungi release 6-pentyl-2H-pyran-2-one (1) and harzianic acid (2) secondary metabolites to improve plant growth and health protection. We isolated metabolites 1 and 2 from Trichoderma strains, whose different concentrations were used to treat seeds of Solanum lycopersicum. The metabolic profile in the resulting 15 day old tomato leaves was studied by high-resolution magic-angle-spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy directly on the whole samples without any preliminary extraction. Principal component analysis (PCA) of HRMAS NMR showed significantly enhanced acetylcholine and γ-aminobutyric acid (GABA) content accompanied by variable amount of amino acids in samples treated with both Trichoderma secondary metabolites. Seed germination rates, seedling fresh weight, and the metabolome of tomato leaves were also dependent upon doses of metabolites 1 and 2 treatments. HRMAS NMR spectroscopy was proven to represent a rapid and reliable technique for evaluating specific changes in the metabolome of plant leaves and calibrating the best concentration of bioactive compounds required to stimulate plant growth. PMID:27088924

  14. NMR-based metabolomics approach to study the toxicity of lambda-cyhalothrin to goldfish (Carassius auratus)

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minghui [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China); Wang, Junsong, E-mail: wang.junsong@gmail.com [Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing 210094 (China); Lu, Zhaoguang; Wei, Dandan; Yang, Minghua [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China); Kong, Lingyi, E-mail: cpu_lykong@126.com [State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009 (China)

    2014-01-15

    Highlights: •A goldfish model was established to investigate the toxicity of lambda-cyhalothrin (LCT) exposure on multiple organs. •NMR based metabolomics approach were firstly used to provide a global view of the toxicity of LCT. •LCT induced neurotransmitters and osmoregulatory imbalances, oxidative stress, energy and amino acid metabolic disorders. •Glutamate–glutamine–GABA axis as a potential target for LCT toxicity was first found. -- Abstract: In this study, a {sup 1}H nuclear magnetic resonance (NMR) based metabolomics approach was applied to investigate the toxicity of lambda-cyhalothrin (LCT) in goldfish (Carassius auratus). LCT showed tissue-specific damage to gill, heart, liver and kidney tissues of goldfish. NMR profiling combined with statistical methods such as orthogonal partial least squares discriminant analysis (OPLS-DA) and two-dimensional statistical total correlation spectroscopy (2D-STOCSY) was developed to discern metabolite changes occurring after one week LCT exposure in brain, heart and kidney tissues of goldfish. LCT exposure influenced levels of many metabolites (e.g., leucine, isoleucine and valine in brain and kidney; lactate in brain, heart and kidney; alanine in brain and kidney; choline in brain, heart and kidney; taurine in brain, heart and kidney; N-acetylaspartate in brain; myo-inositol in brain; phosphocreatine in brain and heart; 2-oxoglutarate in brain; cis-aconitate in brain, and etc.), and broke the balance of neurotransmitters and osmoregulators, evoked oxidative stress, disturbed metabolisms of energy and amino acids. The implication of glutamate–glutamine–gamma-aminobutyric axis in LCT induced toxicity was demonstrated for the first time. Our findings demonstrated the applicability and potential of metabolomics approach for the elucidation of toxicological effects of pesticides and the underlying mechanisms, and the discovery of biomarkers for pesticide pollution in aquatic environment.

  15. NMR-based metabolomics approach to study the toxicity of lambda-cyhalothrin to goldfish (Carassius auratus)

    International Nuclear Information System (INIS)

    Highlights: •A goldfish model was established to investigate the toxicity of lambda-cyhalothrin (LCT) exposure on multiple organs. •NMR based metabolomics approach were firstly used to provide a global view of the toxicity of LCT. •LCT induced neurotransmitters and osmoregulatory imbalances, oxidative stress, energy and amino acid metabolic disorders. •Glutamate–glutamine–GABA axis as a potential target for LCT toxicity was first found. -- Abstract: In this study, a 1H nuclear magnetic resonance (NMR) based metabolomics approach was applied to investigate the toxicity of lambda-cyhalothrin (LCT) in goldfish (Carassius auratus). LCT showed tissue-specific damage to gill, heart, liver and kidney tissues of goldfish. NMR profiling combined with statistical methods such as orthogonal partial least squares discriminant analysis (OPLS-DA) and two-dimensional statistical total correlation spectroscopy (2D-STOCSY) was developed to discern metabolite changes occurring after one week LCT exposure in brain, heart and kidney tissues of goldfish. LCT exposure influenced levels of many metabolites (e.g., leucine, isoleucine and valine in brain and kidney; lactate in brain, heart and kidney; alanine in brain and kidney; choline in brain, heart and kidney; taurine in brain, heart and kidney; N-acetylaspartate in brain; myo-inositol in brain; phosphocreatine in brain and heart; 2-oxoglutarate in brain; cis-aconitate in brain, and etc.), and broke the balance of neurotransmitters and osmoregulators, evoked oxidative stress, disturbed metabolisms of energy and amino acids. The implication of glutamate–glutamine–gamma-aminobutyric axis in LCT induced toxicity was demonstrated for the first time. Our findings demonstrated the applicability and potential of metabolomics approach for the elucidation of toxicological effects of pesticides and the underlying mechanisms, and the discovery of biomarkers for pesticide pollution in aquatic environment

  16. Understanding Metabolomics in Biomedical Research.

    Science.gov (United States)

    Kim, Su Jung; Kim, Su Hee; Kim, Ji Hyun; Hwang, Shin; Yoo, Hyun Ju

    2016-03-01

    The term "omics" refers to any type of specific study that provides collective information on a biological system. Representative omics includes genomics, proteomics, and metabolomics, and new omics is constantly being added, such as lipidomics or glycomics. Each omics technique is crucial to the understanding of various biological systems and complements the information provided by the other approaches. The main strengths of metabolomics are that metabolites are closely related to the phenotypes of living organisms and provide information on biochemical activities by reflecting the substrates and products of cellular metabolism. The transcriptome does not always correlate with the proteome, and the translated proteome might not be functionally active. Therefore, their changes do not always result in phenotypic alterations. Unlike the genome or proteome, the metabolome is often called the molecular phenotype of living organisms and is easily translated into biological conditions and disease states. Here, we review the general strategies of mass spectrometry-based metabolomics. Targeted metabolome or lipidome analysis is discussed, as well as nontargeted approaches, with a brief explanation of the advantages and disadvantages of each platform. Biomedical applications that use mass spectrometry-based metabolomics are briefly introduced. PMID:26676338

  17. Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity

    Directory of Open Access Journals (Sweden)

    Fumio eMatsuda

    2011-08-01

    Full Text Available A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.

  18. Mass spectrometry-based metabolomic fingerprinting for screening cold tolerance in Arabidopsis thaliana accessions

    Czech Academy of Sciences Publication Activity Database

    Václavík, L.; Mishra, Anamika; Mishra, Kumud; Hajslova, J.

    2013-01-01

    Roč. 405, č. 8 (2013), s. 2671-2683. ISSN 1618-2642 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA MŠk OC08055 Institutional support: RVO:67179843 Keywords : cold tolerance * Arabidopsis thaliana * metabolomic fingerprinting * LC-MS * DART-MS * chemometric analysis Subject RIV: EH - Ecology, Behaviour Impact factor: 3.578, year: 2013

  19. A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments

    OpenAIRE

    Everett, Jeremy R.; Dona, Anthony; Kyriakides, Michael; Scott, Flora; Shephard, Elizabeth; Varshavi, Dorsa; Veselkov, Kirill

    2016-01-01

    Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC), in a configuration known as LC–MS. With both NMR and ...

  20. Transcriptome and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Monika eBielecka

    2015-01-01

    Full Text Available Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs using ‘omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

  1. An inter-laboratory comparison demonstrates that [H]-NMR metabolite fingerprinting is a robust technique for collaborative plant metabolomic data collection.

    Science.gov (United States)

    Ward, Jane L; Baker, John M; Miller, Sonia J; Deborde, Catherine; Maucourt, Mickael; Biais, Benoit; Rolin, Dominique; Moing, Annick; Moco, Sofia; Vervoort, Jacques; Lommen, Arjen; Schäfer, Hartmut; Humpfer, Eberhard; Beale, Michael H

    2010-06-01

    In any metabolomics experiment, robustness and reproducibility of data collection is of vital importance. These become more important in collaborative studies where data is to be collected on multiple instruments. With minimisation of variance in sample preparation and instrument performance it is possible to elucidate even subtle differences in metabolite fingerprints due to genotype or biological treatment. In this paper we report on an inter laboratory comparison of plant derived samples by [(1)H]-NMR spectroscopy across five different sites and within those sites utilising instruments with different probes and magnetic field strengths of 9.4 T (400 MHz), 11.7 T (500 MHz) and 14.1 T (600 MHz). Whilst the focus of the study is on consistent data collection across laboratories, aspects of sample stability and the requirement for sample rotation within the NMR magnet are also discussed. Comparability of the datasets from participating laboratories was exceptionally good and the data were amenable to comparative analysis by multivariate statistics. Field strength differences can be adjusted for in the data pre-processing and multivariate analysis demonstrating that [(1)H]-NMR fingerprinting is the ideal technique for large scale plant metabolomics data collection requiring the participation of multiple laboratories. PMID:20526352

  2. NMR-based metabolomic studies on the toxicological effects of cadmium and copper on green mussels Perna viridis

    International Nuclear Information System (INIS)

    Traditional toxicology studies have focused on selected biomarkers to characterize the biological stress induced by metals in marine organisms. In this study, a system biology tool, metabolomics, was applied to the marine mussel Perna viridis to investigate changes in the metabolic profiles of soft tissue as a response to copper (Cu) and cadmium (Cd), both as single metal and as a mixture. The major metabolite changes corresponding to metal exposure are related to amino acids, osmolytes, and energy metabolites. Following metal exposure for 1 week, there was a significant increase in the levels of branched chain amino acids, histidine, glutamate, glutamine, hypotaurine, dimethylglycine, arginine and ATP/ADP. For the Cu + Cd co-exposed mussels, the levels of lactate, branched chain amino acid, succinate, and NAD increased, whereas the levels of glucose, glycogen, and ATP/ADP decreased, indicating a different metabolic profile for the single metal exposure groups. After 2 weeks of exposure, the mussels showed acclimatization to Cd exposure based on the recovery of some metabolites. However, the metabolic profile induced by the metal mixture was very similar to that from Cu exposure, suggesting that Cu dominantly induced the metabolic disturbances. Both Cu and Cd may lead to neurotoxicity, disturbances in energy metabolism, and osmoregulation changes. These results demonstrate the high applicability and reliability of NMR-based metabolomics in interpreting the toxicological mechanisms of metals using global metabolic biomarkers.

  3. (1)H NMR-based metabolomics of Daphnia magna responses after sub-lethal exposure to triclosan, carbamazepine and ibuprofen.

    Science.gov (United States)

    Kovacevic, Vera; Simpson, André J; Simpson, Myrna J

    2016-09-01

    Pharmaceuticals and personal care products are a class of emerging contaminants that are present in wastewater effluents, surface water, and groundwater around the world. There is a need to determine rapid and reliable bioindicators of exposure and the toxic mode of action of these contaminants to aquatic organisms. (1)H nuclear magnetic resonance (NMR)-based metabolomics in combination with multivariate statistical analysis was used to determine the metabolic profile of Daphnia magna after exposure to a range of sub-lethal concentrations of triclosan (6.25-100μg/L), carbamazepine (1.75-14mg/L) and ibuprofen (1.75-14mg/L) for 48h. Sub-lethal triclosan exposure suggested a general oxidative stress condition and the branched-chain amino acids, glutamine, glutamate, and methionine emerged as potential bioindicators. The aromatic amino acids, serine, glycine and alanine are potential bioindicators for sub-lethal carbamazepine exposure that may have altered energy metabolism. The potential bioindicators for sub-lethal ibuprofen exposure are serine, methionine, lysine, arginine and leucine, which showed a concentration-dependent response. The differences in the metabolic changes were related to the dissimilar modes of toxicity of triclosan, carbamazepine and ibuprofen. (1)H NMR-based metabolomics gave an improved understanding of how these emerging contaminants impact the keystone species D. magna. PMID:26809854

  4. Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2016-01-08

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

  5. 1H nuclear magnetic resonance-based metabolomics reveals sex-specific metabolic changes of gastrodin intervention in rats

    Institute of Scientific and Technical Information of China (English)

    Xin Li; Yuan-Wei Jia; Jun-Song Wang; Ming-Hua Yang; Kelvin D G Wang; Ling-Yi Kong

    2014-01-01

    Objective:To explore1H nuclear magnetic resonance-based metabolomics on sex-specific metabolic changes of gastrodin intervention in rats.Methods:In this research,1HNMR-based metabolomics was used for the first time to investigate metabolic changes following chronic intervention with gastrodin in rats.Results:24 endogenous metabolites were identified.Body weight, daily diet and the total volume of urine in in each day of each rat were measured synchronously.Modifications in12 metabolites were observed following gastrodin intervention, indicating gastrodin-induced alterations in carbohydrate and energy metabolism.Interestingly, these metabolic changes were not totally identical in female and male rats.Some metabolic changes arising from gastrodin intervention showed sexual dimorphism includingLDL/VLDL and lactate which were on the decrease in the female but on the increase in the male, together with arginine/ornithine, creatine, and glycerol which were on the increase in the female but on the decrease in the male.While the decrease in pyruvate, succinate and glutamate was only shown in the male and the increase in valine,α-ketoglutarate, glycine and glucose was only in the female. Conclusions:This research shows the sex-specific metabolic response toGAS intervention, weatherGAS is a healthy dietary supplement for the male merits further investigation.

  6. ~1H nuclear magnetic resonance-based metabolomics reveals sex-specific metabolic changes of gastrodin intervention in rats

    Institute of Scientific and Technical Information of China (English)

    Xin; Li; Yuan-Wei; Jia; Jun-Song; Wang; Ming-Hua; Yang; Kelvin; D.G.Wang; Ling-Yi; Kong

    2014-01-01

    Objective:To explore~1H nuclear magnetic resonance-based metabolomics on sex-specific metabolic changes of gastrodin intervention in rats.Methods:In this research,~1H NMR-based metabolomics was used for the first time to investigate metabolic changes following chronic intervention with gastrodin in rats.Results:24 endogenous metabolites were identified.Body weight.daily diet and the total volume of urine in in each day of each rat were measured synchronously.Modifications in 12 metabolites were observsd following gastrodin intervention,indicating gastrodin-induced alterations in carbohydrate and energy metabolism.Interestingly,these metabolic changes were not totally identical in female and male rats.Some metabolic changes arising from gastrodin intervention showed sexual dimorphism including LDL/VLDL and lactate which were on the decrease in the female but on the increase in the male,together with arginine/ornithine,creatine,and glycerol which were on the increase in the female but on the decrease in the male.While the decrease in pyruvate,succinate and glutamate was only shown in the male and the increase in valine,α-ketoglutarate and glucose was only in the female.Conclusions:This resesrch shows the sex-specific metabolic response to GAS intervention,weather GAS is a healthy dietary supplement for the male merits further investigation

  7. Are ant feces nutrients for plants? A metabolomics approach to elucidate the nutritional effects on plants hosting weaver ants

    DEFF Research Database (Denmark)

    Vidkjær, Nanna Hjort; Wollenweber, Bernd; Gislum, René;

    2015-01-01

    Weaver ants (genus Oecophylla) are tropical carnivorous ant species living in high numbers in the canopies of trees. The ants excrete copious amounts of fecal matter on leaf surfaces, and these feces may provide nutrients to host trees. This hypothesis is supported by studies of ant-plant interac...

  8. Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

    Science.gov (United States)

    Treutler, Hendrik; Tsugawa, Hiroshi; Porzel, Andrea; Gorzolka, Karin; Tissier, Alain; Neumann, Steffen; Balcke, Gerd Ulrich

    2016-08-16

    The identification of metabolites by mass spectrometry constitutes a major bottleneck which considerably limits the throughput of metabolomics studies in biomedical or plant research. Here, we present a novel approach to analyze metabolomics data from untargeted, data-independent LC-MS/MS measurements. By integrated analysis of MS(1) abundances and MS/MS spectra, the identification of regulated metabolite families is achieved. This approach offers a global view on metabolic regulation in comparative metabolomics. We implemented our approach in the web application "MetFamily", which is freely available at http://msbi.ipb-halle.de/MetFamily/ . MetFamily provides a dynamic link between the patterns based on MS(1)-signal intensity and the corresponding structural similarity at the MS/MS level. Structurally related metabolites are annotated as metabolite families based on a hierarchical cluster analysis of measured MS/MS spectra. Joint examination with principal component analysis of MS(1) patterns, where this annotation is preserved in the loadings, facilitates the interpretation of comparative metabolomics data at the level of metabolite families. As a proof of concept, we identified two trichome-specific metabolite families from wild-type tomato Solanum habrochaites LA1777 in a fully unsupervised manner and validated our findings based on earlier publications and with NMR. PMID:27452369

  9. NMR-based metabolomics approach to study the toxicity of lambda-cyhalothrin to goldfish (Carassius auratus).

    Science.gov (United States)

    Li, Minghui; Wang, Junsong; Lu, Zhaoguang; Wei, Dandan; Yang, Minghua; Kong, Lingyi

    2014-01-01

    In this study, a (1)H nuclear magnetic resonance (NMR) based metabolomics approach was applied to investigate the toxicity of lambda-cyhalothrin (LCT) in goldfish (Carassius auratus). LCT showed tissue-specific damage to gill, heart, liver and kidney tissues of goldfish. NMR profiling combined with statistical methods such as orthogonal partial least squares discriminant analysis (OPLS-DA) and two-dimensional statistical total correlation spectroscopy (2D-STOCSY) was developed to discern metabolite changes occurring after one week LCT exposure in brain, heart and kidney tissues of goldfish. LCT exposure influenced levels of many metabolites (e.g., leucine, isoleucine and valine in brain and kidney; lactate in brain, heart and kidney; alanine in brain and kidney; choline in brain, heart and kidney; taurine in brain, heart and kidney; N-acetylaspartate in brain; myo-inositol in brain; phosphocreatine in brain and heart; 2-oxoglutarate in brain; cis-aconitate in brain, and etc.), and broke the balance of neurotransmitters and osmoregulators, evoked oxidative stress, disturbed metabolisms of energy and amino acids. The implication of glutamate-glutamine-gamma-aminobutyric axis in LCT induced toxicity was demonstrated for the first time. Our findings demonstrated the applicability and potential of metabolomics approach for the elucidation of toxicological effects of pesticides and the underlying mechanisms, and the discovery of biomarkers for pesticide pollution in aquatic environment. PMID:24291083

  10. Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.

    Science.gov (United States)

    Stenson, Martin; Pedersen, Anders; Hasselblom, Sverker; Nilsson-Ehle, Herman; Karlsson, Bengt Göran; Pinto, Rui; Andersson, Per-Ola

    2016-08-01

    The prognosis for diffuse large B-cell lymphoma (DLBCL) patients with early relapse or refractory disease is dismal. To determine if clinical outcome correlated to diverse serum metabolomic profiles, we used (1)H nuclear magnetic resonance (NMR) spectroscopy and compared two groups of DLBCL patients treated with immunochemotherapy: i) refractory/early relapse (REF/REL; n=27) and ii) long-term progression-free (CURED; n = 60). A supervised multivariate analysis showed a separation between the groups. Among discriminating metabolites higher in the REF/REL group were the amino acids lysine and arginine, the degradation product cadaverine and a compound in oxidative stress (2-hydroxybutyrate). In contrast, the amino acids aspartate, valine and ornithine, and a metabolite in the glutathione cycle, pyroglutamate, were higher in CURED patients. Together, our data indicate that NMR-based serum metabolomics can identify a signature for DLBCL patients with high-risk of failing immunochemotherapy, prompting for larger validating studies which could lead to more individualized treatment of this disease. PMID:26887805

  11. Nutritional Metabolomics

    DEFF Research Database (Denmark)

    Gürdeniz, Gözde

    . Application of multiple analytical strategies may provide comprehensive information to reach a valid answer to these research questions. In this thesis, I investigated several analytical technologies and data handling strategies in order to evaluate their effects on the biological answer. In metabolomics, one...... strategy influences the patterns identified as important for the nutritional question under study. Therefore, in depth understanding of the study design and the specific effects of the analytical technology on the produced data is extremely important to achieve high quality data handling. Besides data...

  12. Metabolomic-Based Study of the Leafy Gall, the Ecological Niche of the Phytopathogen Rhodococcus fascians, as a Potential Source of Bioactive Compounds

    Directory of Open Access Journals (Sweden)

    Pierre Duez

    2013-06-01

    Full Text Available Leafy gall is a plant hyperplasia induced upon Rhodococcus fascians infection. Previously, by genomic and transcriptomic analysis, it has been reported that, at the early stage of symptom development, both primary and secondary metabolisms are modified. The present study is based on the hypothesis that fully developed leafy gall, could represent a potential source of new bioactive compounds. Therefore, non-targeted metabolomic analysis of aqueous and chloroform extracts of leafy gall and non-infected tobacco was carried out by 1H-NMR coupled to principal component analysis (PCA and orthogonal projections to latent structures-discriminant analysis (OPLS-DA. Polar metabolite profiling reflects modifications mainly in the primary metabolites and in some polyphenolics. In contrast, main modifications occurring in non-polar metabolites concern secondary metabolites, and gas chromatography and mass spectrometry (GC-MS evidenced alterations in diterpenoids family. Analysis of crude extracts of leafy galls and non-infected tobacco leaves exhibited a distinct antiproliferative activity against all four tested human cancer cell lines. A bio-guided fractionation of chloroformic crude extract yield to semi-purified fractions, which inhibited proliferation of glioblastoma U373 cells with IC50 between 14.0 and 2.4 µg/mL. Discussion is focused on the consequence of these metabolic changes, with respect to plant defense mechanisms following infection. Considering the promising role of diterpenoid family as bioactive compounds, leafy gall may rather be a propitious source for drug discovery.

  13. Exo-metabolome of some fungal isolates growing on cork-based medium

    DEFF Research Database (Denmark)

    Barreto, M. C.; Frisvad, Jens Christian; Larsen, Thomas Ostenfeld;

    2011-01-01

    are produced by the studied fungal species, both in cork medium or in cork medium added with C. sitophila extracts. However, the addition of C. sitophila extract to the cork medium enhanced the growth of the other studied fungal isolates and altered the respective exo-metabolome profile, leading to......, but also they can be dependent of the remains of former colonizers. In fact, the production of the exo-metabolites by the studied fungal isolates suggests that, under the used experimental conditions, they appear to play an important role in fungal interactions amongst the cork mycoflora....

  14. Metabolomics in transfusion medicine.

    Science.gov (United States)

    Nemkov, Travis; Hansen, Kirk C; Dumont, Larry J; D'Alessandro, Angelo

    2016-04-01

    Biochemical investigations on the regulatory mechanisms of red blood cell (RBC) and platelet (PLT) metabolism have fostered a century of advances in the field of transfusion medicine. Owing to these advances, storage of RBCs and PLT concentrates has become a lifesaving practice in clinical and military settings. There, however, remains room for improvement, especially with regard to the introduction of novel storage and/or rejuvenation solutions, alternative cell processing strategies (e.g., pathogen inactivation technologies), and quality testing (e.g., evaluation of novel containers with alternative plasticizers). Recent advancements in mass spectrometry-based metabolomics and systems biology, the bioinformatics integration of omics data, promise to speed up the design and testing of innovative storage strategies developed to improve the quality, safety, and effectiveness of blood products. Here we review the currently available metabolomics technologies and briefly describe the routine workflow for transfusion medicine-relevant studies. The goal is to provide transfusion medicine experts with adequate tools to navigate through the otherwise overwhelming amount of metabolomics data burgeoning in the field during the past few years. Descriptive metabolomics data have represented the first step omics researchers have taken into the field of transfusion medicine. However, to up the ante, clinical and omics experts will need to merge their expertise to investigate correlative and mechanistic relationships among metabolic variables and transfusion-relevant variables, such as 24-hour in vivo recovery for transfused RBCs. Integration with systems biology models will potentially allow for in silico prediction of metabolic phenotypes, thus streamlining the design and testing of alternative storage strategies and/or solutions. PMID:26662506

  15. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review

    KAUST Repository

    Emwas, Abdul-Hamid M.

    2014-11-21

    The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

  16. {sup 1}H NMR-based metabolomics of time-dependent responses of Eisenia fetida to sub-lethal phenanthrene exposure

    Energy Technology Data Exchange (ETDEWEB)

    Lankadurai, Brian P.; Wolfe, David M.; Simpson, Andre J. [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada); Simpson, Myrna J., E-mail: myrna.simpson@utoronto.ca [Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada (Canada)

    2011-10-15

    {sup 1}H NMR-based metabolomics was used to examine the response of the earthworm Eisenia fetida after exposure to sub-lethal concentrations of phenanthrene over time. Earthworms were exposed to 0.025 mg/cm{sup 2} of phenanthrene (1/64th of the LC{sub 50}) via contact tests over four days. Earthworm tissues were extracted using a mixture of chloroform, methanol and water, resulting in polar and non-polar fractions that were analyzed by {sup 1}H NMR after one, two, three and four days. NMR-based metabolomic analyses revealed heightened E. fetida responses with longer phenanthrene exposure times. Amino acids alanine and glutamate, the sugar maltose, the lipids cholesterol and phosphatidylcholine emerged as potential indicators of phenanthrene exposure. The conversion of succinate to fumarate in the Krebs cycle was also interrupted by phenanthrene. Therefore, this study shows that NMR-based metabolomics is a powerful tool for elucidating time-dependent relationships in addition to the mode of toxicity of phenanthrene in earthworm exposure studies. - Highlights: > NMR-based earthworm metabolomic analysis of the mode of action of phenanthrene is presented. > The earthworm species E. fetida were exposed to sub-lethal phenanthrene concentrations. > Both polar and non-polar metabolites of E. fetida tissue extracts were analyzed by {sup 1}H NMR. > Longer phenanthrene exposure times resulted in heightened earthworm responses. > An interruption of the Krebs cycle was also observed due to phenanthrene exposure. - {sup 1}H NMR metabolomics is used to determine the relationship between phenanthrene exposure and the metabolic response of the earthworm E. fetida over time and also to elucidate the phenanthrene mode of toxicity.

  17. Metabolomics-based prediction models of yeast strains for screening of metabolites contributing to ethanol stress tolerance

    Science.gov (United States)

    Hashim, Z.; Fukusaki, E.

    2016-06-01

    The increased demand for clean, sustainable and renewable energy resources has driven the development of various microbial systems to produce biofuels. One of such systems is the ethanol-producing yeast. Although yeast produces ethanol naturally using its native pathways, production yield is low and requires improvement for commercial biofuel production. Moreover, ethanol is toxic to yeast and thus ethanol tolerance should be improved to further enhance ethanol production. In this study, we employed metabolomics-based strategy using 30 single-gene deleted yeast strains to construct multivariate models for ethanol tolerance and screen metabolites that relate to ethanol sensitivity/tolerance. The information obtained from this study can be used as an input for strain improvement via metabolic engineering.

  18. Discrimination of Citrus reticulata Blanco and Citrus reticulata 'Chachi' by gas chromatograph-mass spectrometry based metabolomics approach.

    Science.gov (United States)

    Duan, Li; Guo, Long; Dou, Li-Li; Zhou, Chang-Lin; Xu, Feng-Guo; Zheng, Guo-Dong; Li, Ping; Liu, E-Hu

    2016-12-01

    Citri Reticulatae Pericarpium, mainly including the pericarp of Citrus reticulata Blanco and the pericarp of Citrus reticulata 'Chachi', has been consumed daily as food and dietary supplement for centuries. In this study, GC-MS based metabolomics was employed to compare comprehensively the volatile constituents in Citrus reticulata Blanco and Citrus reticulata 'Chachi'. Principal component analysis and orthogonal partial least squares discrimination analysis indicated that samples could be distinguished effectively from one another. Fifteen metabolites were finally identified for use as chemical markers in discrimination of Citri Reticulatae Pericarpium samples. The antimicrobial activity against Gram-negative and Gram-positive bacteria of the volatile oil from Citrus reticulata Blanco and Citrus reticulata 'Chachi' was investigated preliminarily. PMID:27374515

  19. NMR-based investigation of the Drosophila melanogaster metabolome under the influence of daily cycles of light and temperature.

    Science.gov (United States)

    Gogna, Navdeep; Singh, Viveka Jagdish; Sheeba, Vasu; Dorai, Kavita

    2015-12-01

    We utilized an NMR-based metabolomic approach to profile the metabolites in Drosophila melanogaster that cycle with a daily rhythm. 1H 1D and 2D NMR experiments were performed on whole-body extracts sampled from flies that experienced strong time cues in the form of both light and temperature cycles. Multivariate and univariate statistical analysis was used to identify those metabolites whose concentrations oscillate diurnally. We compared metabolite levels at two time points twelve hours apart, one close to the end of the day and the other close to the end of the night, and identified metabolites that differed significantly in their relative concentrations. We were able to identify 14 such metabolites whose concentrations differed significantly between the two time points. The concentrations of metabolites such as sterols, fatty acids, amino acids such as leucine, valine, isoleucine, alanine and lysine as well as other metabolites such as creatine, glucose, AMP and NAD were higher close to the end of the night, whereas the levels of lactic acid, and a few amino acids such as histidine and tryptophan were higher close to the end of the day. We compared signal intensities across 12 equally spaced time points for these 14 metabolites, in order to profile the changes in their levels across the day, since the NMR metabolite peak intensity is directly proportional to its molar concentration. Through this report we establish NMR-based metabolomics combined with multivariate statistical analysis as a useful method for future studies on the interactions between circadian clocks and metabolic processes. PMID:26422411

  20. (1)H NMR-based metabolomics investigation of Daphnia magna responses to sub-lethal exposure to arsenic, copper and lithium.

    Science.gov (United States)

    Nagato, Edward G; D'eon, Jessica C; Lankadurai, Brian P; Poirier, David G; Reiner, Eric J; Simpson, Andre J; Simpson, Myrna J

    2013-09-01

    Metal and metalloid contamination constitutes a major concern in aquatic ecosystems. Thus it is important to find rapid and reliable indicators of metal stress to aquatic organisms. In this study, we tested the use of (1)H nuclear magnetic resonance (NMR) - based metabolomics to examine the response of Daphnia magna neonates after a 48h exposure to sub-lethal concentrations of arsenic (49μgL(-1)), copper (12.4μgL(-1)) or lithium (1150μgL(-1)). Metabolomic responses for all conditions were compared to a control using principal component analysis (PCA) and metabolites that contributed to the variation between the exposures and the control condition were identified and quantified. The PCA showed that copper and lithium exposures result in statistically significant metabolite variations from the control. Contributing to this variation was a number of amino acids such as: phenylalanine, leucine, lysine, glutamine, glycine, alanine, methionine and glutamine as well as the nucleobase uracil and osmolyte glycerophosphocholine. The similarities in metabolome changes suggest that lithium has an analogous mode of toxicity to that of copper, and may be impairing energy production and ionoregulation. The PCA also showed that arsenic exposure resulted in a metabolic shift in comparison to the control population but this change was not statistically significant. However, significant changes in specific metabolites such as alanine and lysine were observed, suggesting that energy metabolism is indeed disrupted. This research demonstrates that (1)H NMR-based metabolomics is a viable platform for discerning metabolomic changes and mode of toxicity of D. magna in response to metal stressors in the environment. PMID:23732010

  1. 1H NMR-based metabolomics investigation of copper-laden rat: a model of Wilson's disease.

    Directory of Open Access Journals (Sweden)

    Jingjing Xu

    Full Text Available Wilson's disease (WD, also known as hepatoleticular degeneration (HLD, is a rare autosomal recessive genetic disorder of copper metabolism, which causes copper to accumulate in body tissues. In this study, rats fed with copper-laden diet are used to render the clinical manifestations of WD, and their copper toxicity-induced organ lesions are studied. To investigate metabolic behaviors of 'decoppering' process, penicillamine (PA was used for treating copper-laden rats as this chelating agent could eliminate excess copper through the urine. To date, there has been limited metabolomics study on WD, while metabolic impacts of copper accumulation and PA administration have yet to be established.A combination of 1HNMR spectroscopy and multivariate statistical analysis was applied to examine the metabolic profiles of the urine and blood serum samples collected from the copper-laden rat model of WD with PA treatment.Copper accumulation in the copper-laden rats is associated with increased lactate, creatinine, valine and leucine, as well as decreased levels of glucose and taurine in the blood serum. There were also significant changes in p-hydroxyphenylacetate (p-HPA, creatinine, alpha-ketoglutarate (α-KG, dimethylamine, N-acetylglutamate (NAG, N-acetylglycoprotein (NAC in the urine of these rats. Notably, the changes in p-HPA, glucose, lactate, taurine, valine, leucine, and NAG were found reversed following PA treatment. Nevertheless, there were no changes for dimethylamine, α-KG, and NAC as a result of the treatment. Compared with the controls, the concentrations of hippurate, formate, alanine, and lactate were changed when PA was applied and this is probably due to its side effect. A tool named SMPDB (Small Molecule Pathway Database is introduced to identify the metabolic pathway influenced by the copper-laden diet.The study has shown the potential application of NMR-based metabolomic analysis in providing further insights into the molecular

  2. The Human Serum Metabolome

    OpenAIRE

    Psychogios, Nikolaos; Hau, David. D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul

    2011-01-01

    Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have unde...

  3. Effect of Genotype and Environment on Salvia miltiorrhiza Roots Using LC/MS-Based Metabolomics.

    Science.gov (United States)

    Zhao, Qi; Song, Zhenqiao; Fang, Xinsheng; Pan, Yuling; Guo, Linlin; Liu, Tian; Wang, Jianhua

    2016-01-01

    Salvia miltiorrhiza (S. miltiorrhiza) Bunge is broadly used as herbal medicine for the clinical treatments of cardiovascular and cerebrovascular diseases. Despite its commercial and medicinal values, few systematic studies on the metabolome of S. miltiorrhiza roots have been carried out so far. We systematically described the metabolic profiles of S. miltiorrhiza using high pressure liquid chromatography mass spectrometry (LC/MS) in conjunction with multivariate statistical analyses, aimed at monitoring their biological variations of secondary metabolites related to three locations and four S. miltiorrhiza genotypes. A total of 40 bioactive constituents were putatively annotated in S. miltiorrhiza root samples. This study found that both the same S. miltiorrhiza genotype growing at three different locations and four S. miltiorrhiza genotypes growing at the same location had significant metabonomic differences identified by the principal component analysis (PCA) approach. By using orthogonal projection to latent structure with discriminant analysis (OPLS-DA), 16 and 14 secondary metabolites can be used as potential location-specific and genotype-specific markers in S. miltiorrhiza, respectively. The specificity of LC/MS profiles offered a powerful tool to discriminate S. miltiorrhiza samples according to genotypes or locations. PMID:27023512

  4. [Anti-depressive mechanism of Fufang Chaigui prescription based on neuroendocrine hormone and metabolomic correlation analysis].

    Science.gov (United States)

    Chen, Lei; Liu, Huan; Chen, Jian-li; Gao, Xiao-xia; Zhou, Yu-zhi; Tian, Jun-sheng; Qin, Xue-mei

    2015-10-01

    To elucidate the anti-depressive effect of Fufang Chaigui prescription and its mechanism and investigate its effect on neuroendocrine hormone, rats were included into a chronic unpredictable mild stress (CUMS) model for 28 d, and drugs were administered at the same time. During the period, rats' behaviors were observed and the blood was collected by using ELISA to determine representative hormone concentrations of HPAA, HPTA and HPGA. The changes in endogenous metabolites were analyzed by using H NMR metabolomics to seek the potential biomarkers. Results showed Fufang Chaigui prescription could improve the behaviors of CUMS rats obviously, increase contents of ACTH, CORT, T₃and decrease contents of TSH and TESTO and regulate the levels of lactate, α-glucose, choline, N-acetylglycoprotein, trimethylamine oxide and leucine to get closer to the contents of control group. The results of correlation analysis indicated that HPTA was associated with glycometabolism, amino acid metabolism and choline metabolism. And HPAA was related to glycometabolism and amino acid metabolism. However, HPGA was only correlated with glycometabolism. In conclusion, Fufang Chaigui prescription could show an obvious anti-depressive effect and its underlying mechanism might involve regulations of neuroendocrine function and pathways of glycometabolism, amino acid metabolism and choline metabolism. PMID:27062831

  5. Effect of Genotype and Environment on Salvia miltiorrhiza Roots Using LC/MS-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Qi Zhao

    2016-03-01

    Full Text Available Salvia miltiorrhiza (S. miltiorrhiza Bunge is broadly used as herbal medicine for the clinical treatments of cardiovascular and cerebrovascular diseases. Despite its commercial and medicinal values, few systematic studies on the metabolome of S. miltiorrhiza roots have been carried out so far. We systematically described the metabolic profiles of S. miltiorrhiza using high pressure liquid chromatography mass spectrometry (LC/MS in conjunction with multivariate statistical analyses, aimed at monitoring their biological variations of secondary metabolites related to three locations and four S. miltiorrhiza genotypes. A total of 40 bioactive constituents were putatively annotated in S. miltiorrhiza root samples. This study found that both the same S. miltiorrhiza genotype growing at three different locations and four S. miltiorrhiza genotypes growing at the same location had significant metabonomic differences identified by the principal component analysis (PCA approach. By using orthogonal projection to latent structure with discriminant analysis (OPLS-DA, 16 and 14 secondary metabolites can be used as potential location-specific and genotype-specific markers in S. miltiorrhiza, respectively. The specificity of LC/MS profiles offered a powerful tool to discriminate S. miltiorrhiza samples according to genotypes or locations.

  6. Metabolic Profiling of Human Benign and Malignant Pulmonary Nodules Using Mass Spectrometry-Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Choon Nam Ong

    2013-07-01

    Full Text Available Solitary pulmonary nodule (SPN or coin lesion is a mass in the lung and can be commonly found in chest X-rays or computerized tomography (CT scans. However, despite the advancement of imaging technologies, it is still difficult to distinguish malignant cancer from benign SPNs. Here we investigated the metabolic profiling of patients with benign and malignant pulmonary nodules. A combination of gas chromatography/mass spectrometry (GC/MS and liquid chromatography/mass spectrometry (LC/MS was used to profile the plasma metabolites in 17 patients with malignant SPNs, 15 patients with benign SPNs and 20 healthy controls. The metabolic profiles were assayed using OPLS-DA, and further analyzed to identify marker metabolites related to diseases. Both GC/MS- and LC/MS-derived models showed clear discriminations in metabolic profiles among three groups. It was found that 63 metabolites (12 from GC/MS, 51 from LC/MS contributed to the differences. Of these, 48 metabolites showed same change trend in both malignant and benign SPNs as compared with healthy controls, indicating some common pathways including inflammation and oxidative injury shared by two diseases. In contrast, 14 metabolites constituted distinct profiles that differentiated malignant from benign SPNs, which might be a unique biochemical feature associated with lung cancer. Overall, our data suggested that integration of two highly sensitive and complementary metabolomics platforms could enable a comprehensive metabolic profiling and assist in discrimination malignant from benign SPNs.

  7. Pea Fiber and Wheat Bran Fiber Show Distinct Metabolic Profiles in Rats as Investigated by a 1H NMR-Based Metabolomic Approach

    OpenAIRE

    Guangmang Liu; Liang Xiao; Tingting Fang; Yimin Cai; Gang Jia; Hua Zhao; Jing Wang; Xiaoling Chen; Caimei Wu

    2014-01-01

    This study aimed to examine the effect of pea fiber (PF) and wheat bran fiber (WF) supplementation in rat metabolism. Rats were assigned randomly to one of three dietary groups and were given a basal diet containing 15% PF, 15% WF, or no supplemental fiber. Urine and plasma samples were analyzed by NMR-based metabolomics. PF significantly increased the plasma levels of 3-hydroxybutyrate, and myo-inositol as well as the urine levels of alanine, hydroxyphenylacetate, phenylacetyglycine, and α-k...

  8. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

    OpenAIRE

    Griss, J.; A.R. Jones; Sachsenberg, T.; Walzer, M.; L. Gatto; Hartler, J.; Thallinger, G. G.; Salek, R. M.; Steinbeck, C.; Neuhauser, N.; Cox, J; Neumann, S.; Fan, J; Reisinger, F; Xu, Q.-W.

    2014-01-01

    The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experime...

  9. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

    Directory of Open Access Journals (Sweden)

    Myrna J. Simpson

    2013-08-01

    Full Text Available 1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS, betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA of contaminants is not clearly defined.

  10. 1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil.

    Science.gov (United States)

    Lankadurai, Brian P; Furdui, Vasile I; Reiner, Eric J; Simpson, André J; Simpson, Myrna J

    2013-01-01

    1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

  11. Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran.

    Directory of Open Access Journals (Sweden)

    Mohana Krishna Reddy Mudiam

    Full Text Available Despite recent advances in understanding mechanism of toxicity, the development of biomarkers (biochemicals that vary significantly with exposure to chemicals for pesticides and environmental contaminants exposure is still a challenging task. Carbofuran is one of the most commonly used pesticides in agriculture and said to be most toxic carbamate pesticide. It is necessary to identify the biochemicals that can vary significantly after carbofuran exposure on earthworms which will help to assess the soil ecotoxicity. Initially, we have optimized the extraction conditions which are suitable for high-throughput gas chromatography mass spectrometry (GC-MS based metabolomics for the tissue of earthworm, Metaphire posthuma. Upon evaluation of five different extraction solvent systems, 80% methanol was found to have good extraction efficiency based on the yields of metabolites, multivariate analysis, total number of peaks and reproducibility of metabolites. Later the toxicity evaluation was performed to characterize the tissue specific metabolomic perturbation of earthworm, Metaphire posthuma after exposure to carbofuran at three different concentration levels (0.15, 0.3 and 0.6 mg/kg of soil. Seventeen metabolites, contributing to the best classification performance of highest dose dependent carbofuran exposed earthworms from healthy controls were identified. This study suggests that GC-MS based metabolomic approach was precise and sensitive to measure the earthworm responses to carbofuran exposure in soil, and can be used as a promising tool for environmental eco-toxicological studies.

  12. Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry

    Directory of Open Access Journals (Sweden)

    Jeong Jaesik

    2012-02-01

    Full Text Available Abstract Background Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS has been used for metabolite profiling in metabolomics. However, there is still much experimental variation to be controlled including both within-experiment and between-experiment variation. For efficient analysis, an ideal peak alignment method to deal with such variations is in great need. Results Using experimental data of a mixture of metabolite standards, we demonstrated that our method has better performance than other existing method which is not model-based. We then applied our method to the data generated from the plasma of a rat, which also demonstrates good performance of our model. Conclusions We developed a model-based peak alignment method to process both homogeneous and heterogeneous experimental data. The unique feature of our method is the only model-based peak alignment method coupled with metabolite identification in an unified framework. Through the comparison with other existing method, we demonstrated that our method has better performance. Data are available at http://stage.louisville.edu/faculty/x0zhan17/software/software-development/mspa. The R source codes are available at http://www.biostat.iupui.edu/~ChangyuShen/CodesPeakAlignment.zip. Trial Registration 2136949528613691

  13. Probabilistic Principal Component Analysis for Metabolomic Data.

    LENUS (Irish Health Repository)

    Nyamundanda, Gift

    2010-11-23

    Abstract Background Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model. Results Here, probabilistic principal component analysis (PPCA) which addresses some of the limitations of PCA, is reviewed and extended. A novel extension of PPCA, called probabilistic principal component and covariates analysis (PPCCA), is introduced which provides a flexible approach to jointly model metabolomic data and additional covariate information. The use of a mixture of PPCA models for discovering the number of inherent groups in metabolomic data is demonstrated. The jackknife technique is employed to construct confidence intervals for estimated model parameters throughout. The optimal number of principal components is determined through the use of the Bayesian Information Criterion model selection tool, which is modified to address the high dimensionality of the data. Conclusions The methods presented are illustrated through an application to metabolomic data sets. Jointly modeling metabolomic data and covariates was successfully achieved and has the potential to provide deeper insight to the underlying data structure. Examination of confidence intervals for the model parameters, such as loadings, allows for principled and clear interpretation of the underlying data structure. A software package called MetabolAnalyze, freely available through the R statistical software, has been developed to facilitate implementation of the presented methods in the metabolomics field.

  14. Improving the quality of biomarker candidates in untargeted metabolomics via peak table-based alignment of comprehensive two-dimensional gas chromatography-mass spectrometry data.

    Science.gov (United States)

    Bean, Heather D; Hill, Jane E; Dimandja, Jean-Marie D

    2015-05-15

    The potential of high-resolution analytical technologies like GC×GC/TOF MS in untargeted metabolomics and biomarker discovery has been limited by the development of fully automated software that can efficiently align and extract information from multiple chromatographic data sets. In this work we report the first investigation on a peak-by-peak basis of the chromatographic factors that impact GC×GC data alignment. A representative set of 16 compounds of different chromatographic characteristics were followed through the alignment of 63 GC×GC chromatograms. We found that varying the mass spectral match parameter had a significant influence on the alignment for poorly-resolved peaks, especially those at the extremes of the detector linear range, and no influence on well-chromatographed peaks. Therefore, optimized chromatography is required for proper GC×GC data alignment. Based on these observations, a workflow is presented for the conservative selection of biomarker candidates from untargeted metabolomics analyses. PMID:25857541

  15. LC-MS based Metabolomics Analysis to Identify Potential Allelochemicals in Wedelia trilobata

    OpenAIRE

    Kamalrul Azlan Azizan; Sarah Ibrahim; Nurul Haizun Abdul Ghani; Mohammad Firdaus Nawawi

    2016-01-01

    Wedelia trilobata is a noxious invasive weed that has been widely cultivated as a decorative and groundcover plant. The plant has been reported to contain diverse bioactive compounds with a broad spectrum of biological activities including allelochemicals. Allelochemicals contribute to allelopathy interactions that suppress the growth and development of nearby plants. Several studies have reported the allelopathic potential of W. trilobata and its negative effects to crop plants. However, rel...

  16. Feasibility Study of NMR Based Serum Metabolomic Profiling to Animal Health Monitoring: A Case Study on Iron Storage Disease in Captive Sumatran Rhinoceros (Dicerorhinus sumatrensis).

    Science.gov (United States)

    Watanabe, Miki; Roth, Terri L; Bauer, Stuart J; Lane, Adam; Romick-Rosendale, Lindsey E

    2016-01-01

    A variety of wildlife species maintained in captivity are susceptible to iron storage disease (ISD), or hemochromatosis, a disease resulting from the deposition of excess iron into insoluble iron clusters in soft tissue. Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the rhinoceros species that has evolutionarily adapted to a low-iron diet and is susceptible to iron overload. Hemosiderosis is reported at necropsy in many African black and Sumatran rhinoceroses but only a small number of animals reportedly die from hemochromatosis. The underlying cause and reasons for differences in susceptibility to hemochromatosis within the taxon remains unclear. Although serum ferritin concentrations have been useful in monitoring the progression of ISD in many species, there is some question regarding their value in diagnosing hemochromatosis in the Sumatran rhino. To investigate the metabolic changes during the development of hemochromatosis and possibly increase our understanding of its progression and individual susceptibility differences, the serum metabolome from a Sumatran rhinoceros was investigated by nuclear magnetic resonance (NMR)-based metabolomics. The study involved samples from female rhinoceros at the Cincinnati Zoo (n = 3), including two animals that died from liver failure caused by ISD, and the Sungai Dusun Rhinoceros Conservation Centre in Peninsular Malaysia (n = 4). Principal component analysis was performed to visually and statistically compare the metabolic profiles of the healthy animals. The results indicated that significant differences were present between the animals at the zoo and the animals in the conservation center. A comparison of the 43 serum metabolomes of three zoo rhinoceros showed two distinct groupings, healthy (n = 30) and unhealthy (n = 13). A total of eighteen altered metabolites were identified in healthy versus unhealthy samples. Results strongly suggest that NMR-based metabolomics is a valuable tool for animal health

  17. LC/MS-based metabolomics strategy to assess the amelioration effects of ginseng total saponins on memory deficiency induced by simulated microgravity.

    Science.gov (United States)

    Feng, Li; Yue, Xiao-Fei; Chen, Yi-Xi; Liu, Xin-Min; Wang, Li-Sha; Cao, Fang-Rui; Wang, Qiong; Liao, Yong-Hong; Pan, Rui-le; Chang, Qi

    2016-06-01

    Microgravity-induced memory deficiency seriously affects learning and memory ability of the astronaut during spaceflight, with few effective countermeasures. Panax ginseng C. A. Mey. has been used as a nootropic herb for thousands of years in Asian countries. Saponins are recognized as its major active components. Previous studies have shown that ginseng saponins offer protection against memory deficits caused by various factors. Nevertheless, the underlying mechanisms of their nootropic effects are still largely unknown. In this study, we evaluated the memory-improving effects of ginseng total saponins (GTS) on simulated microgravity hindlimb-unloaded rats using a metabolomics approach. After being exposed to a 7-days hindlimb unloading (HU), variations of plasmatic and hippocampal metabolic profiles of rats with and without GTS intervention were examined by a liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics method. Subsequently, 8 hippocampal neurotransmitters were determined using a LC-MS/MS method. Finally, a LC-MS/MS based targeted metabolomics was performed to validate biomarkers found in the untargeted analysis. Besides, to support the metabolomics results, passive avoidance (PA) test, Nissl staining, and plasmatic corticosterone (CORT) levels determination were performed. The results showed that HU could lead to variations of 7 neurotransmitters and significantly different plasmatic and hippocampal metabolic profiles. GTS could restore most of the imbalanced neurotransmitters, especially glutamic acid and acetylcholine, and correct the levels of various disturbed learning and memory relevant biomarkers such as asparagine, phenylalanine, tyrosine, tryptophan, and choline. In addition, GTS could markedly ameliorate HU-induced memory deficiency, protect hippocampal neurons from damage, and down-regulate elevated CORT levels. In conclusion, GTS exhibits memory-improving effects mainly through regulating the metabolism of amino acids

  18. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum.

    Directory of Open Access Journals (Sweden)

    Theodore R Sana

    data acquisition. Untargeted and targeted data mining workflows, when used together to perform pathway-inferred metabolomics, have the benefit of obviating MS/MS confirmation for every detected compound.

  19. Toxicological effects induced by cadmium in gills of Manila clam ruditapes philippinarum using NMR-based metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Linbao; Liu, Xiaoli; You, Liping; Zhou, Di [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); The Graduate School of Chinese Academy of Sciences, Beijing (China); Yu, Junbao; Zhao, Jianmin; Wu, Huifeng [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); Feng, Jianghua [Department of Electronic Science, Fujian Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen (China)

    2011-11-15

    Cadmium (Cd) has become an important heavy metal contaminant in the sediment and seawater along the Bohai Sea and been of great ecological risk due to its toxic effects to marine organisms. In this work, the toxicological effects caused by environmentally relevant concentrations (10 and 40 {mu}g L{sup -1}) of Cd were studied in the gill tissues of Manila clam Ruditapes philippinarum after exposure for 24, 48, and 96 h. Both low (10 {mu}g L{sup -1}) and high (40 {mu}g L{sup -1}) doses of Cd caused the disturbances in energy metabolism and osmotic regulation and neurotoxicity based on the metabolic biomarkers such as succinate, alanine, branched chain amino acids, betaine, hypotaurine, and glutamate in clam gills after 24 h of exposure. However, the recovery of toxicological effects of Cd after exposure for 96 h was obviously observed in clam to Cd exposures. Overall, these results indicated that NMR-based metabolomics was applicable to elucidate the toxicological effects of heavy metal contaminants in the marine bioindicator. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. Recent Advances in the Application of Metabolomics to Studies of Biogenic Volatile Organic Compounds (BVOC) Produced by Plant

    OpenAIRE

    Yoko Iijima

    2014-01-01

    In many plants, biogenic volatile organic compounds (BVOCs) are produced as specialized metabolites that contribute to the characteristics of each plant. The varieties and composition of BVOCs are chemically diverse by plant species and the circumstances in which the plants grow, and also influenced by herbivory damage and pathogen infection. Plant-produced BVOCs are receptive to many organisms, from microorganisms to human, as both airborne attractants and repellants. In addition, it is know...

  1. Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline.

    Science.gov (United States)

    Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Huber, Christian G

    2015-07-31

    Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the replacement of expensive and laborious animal models. Here we describe a long term repeat dose nephrotoxicity study conducted on the human renal proximal tubular epithelial cell line, RPTEC/TERT1, treated with 10 and 35 μmol·liter(-1) of chloroacetaldehyde, a metabolite of the anti-cancer drug ifosfamide. Our study outlines the establishment of an automated and easy to use untargeted metabolomics workflow for HPLC-high resolution mass spectrometry data. Automated data analysis workflows based on open source software (OpenMS, KNIME) enabled a comprehensive and reproducible analysis of the complex and voluminous metabolomics data produced by the profiling approach. Time- and concentration-dependent responses were clearly evident in the metabolomic profiles. To obtain a more comprehensive picture of the mode of action, transcriptomics and proteomics data were also integrated. For toxicity profiling of chloroacetaldehyde, 428 and 317 metabolite features were detectable in positive and negative modes, respectively, after stringent removal of chemical noise and unstable signals. Changes upon treatment were explored using principal component analysis, and statistically significant differences were identified using linear models for microarray assays. The analysis revealed toxic effects only for the treatment with 35 μmol·liter(-1) for 3 and 14 days. The most regulated metabolites were glutathione and metabolites related to the oxidative stress response of the cells. These findings are corroborated by proteomics and transcriptomics data, which show, among other things, an activation of the Nrf2 and ATF4 pathways. PMID:26055719

  2. From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS.

    Science.gov (United States)

    Mastrangelo, Annalaura; Ferrarini, Alessia; Rey-Stolle, Fernanda; García, Antonia; Barbas, Coral

    2015-11-01

    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

  3. An NMR-based metabolomic approach to investigate the effects of supplementation with glutamic acid in piglets challenged with deoxynivalenol.

    Science.gov (United States)

    Wu, Miaomiao; Xiao, Hao; Ren, Wenkai; Yin, Jie; Hu, Jiayu; Duan, Jielin; Liu, Gang; Tan, Bie; Xiong, Xia; Oso, Abimbola Oladele; Adeola, Olayiwola; Yao, Kang; Yin, Yulong; Li, Tiejun

    2014-01-01

    Deoxynivalenol (DON) has various toxicological effects in humans and pigs that result from the ingestion of contaminated cereal products. This study was conducted to investigate the protective effects of dietary supplementation with glutamic acid on piglets challenged with DON. A total of 20 piglets weaned at 28 d of age were randomly assigned to receive 1 of 4 treatments (5 piglets/treatment): 1) basal diet, negative control (NC); 2) basal diet +4 mg/kg DON (DON); 3) basal diet +2% (g/g) glutamic acid (GLU); 4) basal diet +4 mg/kg DON +2% glutamic acid (DG). A 7-d adaptation period was followed by 30 days of treatment. A metabolite analysis using nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomic technology and the determination of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities for plasma, as well as the activity of Caspase-3 and the proliferation of epithelial cells were conducted. The results showed that contents of low-density lipoprotein, alanine, arginine, acetate, glycoprotein, trimethylamine-N-oxide (TMAO), glycine, lactate, and urea, as well as the glutamate/creatinine ratio were higher but high-density lipoprotein, proline, citrate, choline, unsaturated lipids and fumarate were lower in piglets of DON treatment than that of NC treatment (Pnuclear antigen (PCNA) labeling indexes for the jejunum and ileum (Penergy and amino acid metabolism induced by DON. PMID:25502722

  4. (1)H NMR based metabolomics approach to study the toxic effects of dichlorvos on goldfish (Carassius auratus).

    Science.gov (United States)

    Liu, Yan; Chen, Ting; Li, Ming-Hui; Xu, Hua-Dong; Jia, Ai-Qun; Zhang, Jian-Fa; Wang, Jun-Song

    2015-11-01

    Dichlorvos (DDVP), one of the most widely used organophosphorus pesticides (OPs), has caused serious pollution in environment. In this study, (1)H nuclear magnetic resonance (NMR) based metabolomics approach combined with histopathological and immunohistochemical examination, and biochemical assays were used to investigate toxicities of DDVP on goldfish (Carassius auratus). After 10 days' exposure of DDVP at three dosages of 5.18, 2.59 and 1.73 mg/L, goldfish tissues (gill, brain, liver and kidney) and serum were collected. Histopathology revealed severe impairment of gills, livers and kidneys, and immunohistochemistry disclosed glial fibrillary acidic protein (GFAP) positive reactive astrocytes in brains. Orthogonal signal correction-partial least squares-discriminant analysis (OSC-PLS-DA) of NMR profiles disclosed that DDVP influenced many metabolites (glutamate, aspartate, acetylcholine, 4-aminobutyrate, glutathione, AMP and lactate in brain; glutathione, glucose, histamine in liver; BCAAs, AMP, aspartate, glutamate, riboflavin in kidney) dose-dependently, involved with imbalance of neurotransmitters, oxidative stress, and disorders of energy and amino acid metabolism. Several self-protection mechanisms concerning glutamate degradation and glutathione (GSH) redox system were found in DDVP intoxicated goldfish. PMID:26210017

  5. Nuclear magnetic resonance-based metabolomics reveals that dairy protein fractions affect urinary urea excretion differently in overweight adolescents

    DEFF Research Database (Denmark)

    Zheng, Hong; Yde, Christian Clement; Dalsgaard, Trine Kastrup;

    2015-01-01

    Dairy proteins are an important part of our diet, and recently, there is considerable focus on understanding the effects of the two major dairy proteins fractions constituted by casein and whey. In the present study, the impact of a dietary intervention with casein, whey, and skim milk was invest...... to disclosure exposure effects. In conclusion, the present study demonstrates that casein and whey proteins impact urinary urea excretion differently.......Dairy proteins are an important part of our diet, and recently, there is considerable focus on understanding the effects of the two major dairy proteins fractions constituted by casein and whey. In the present study, the impact of a dietary intervention with casein, whey, and skim milk was...... excretion of urea was found after the 12-week casein and skim milk interventions, while the 12-week whey intervention had no significant effect on the urea excretion. In addition, NMR-based metabolomics revealed a decreased urinary citrate excretion in the whey group and thereby demonstrated its potential...

  6. Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models.

    Science.gov (United States)

    Schultz, Luise; Zurich, Marie-Gabrielle; Culot, Maxime; da Costa, Anaelle; Landry, Christophe; Bellwon, Patricia; Kristl, Theresa; Hörmann, Katrin; Ruzek, Silke; Aiche, Stephan; Reinert, Knut; Bielow, Chris; Gosselet, Fabien; Cecchelli, Romeo; Huber, Christian G; Schroeder, Olaf H-U; Gramowski-Voss, Alexandra; Weiss, Dieter G; Bal-Price, Anna

    2015-12-25

    The present study was performed in an attempt to develop an in vitro integrated testing strategy (ITS) to evaluate drug-induced neurotoxicity. A number of endpoints were analyzed using two complementary brain cell culture models and an in vitro blood-brain barrier (BBB) model after single and repeated exposure treatments with selected drugs that covered the major biological, pharmacological and neuro-toxicological responses. Furthermore, four drugs (diazepam, cyclosporine A, chlorpromazine and amiodarone) were tested more in depth as representatives of different classes of neurotoxicants, inducing toxicity through different pathways of toxicity. The developed in vitro BBB model allowed detection of toxic effects at the level of BBB and evaluation of drug transport through the barrier for predicting free brain concentrations of the studied drugs. The measurement of neuronal electrical activity was found to be a sensitive tool to predict the neuroactivity and neurotoxicity of drugs after acute exposure. The histotypic 3D re-aggregating brain cell cultures, containing all brain cell types, were found to be well suited for OMICs analyses after both acute and long term treatment. The obtained data suggest that an in vitro ITS based on the information obtained from BBB studies and combined with metabolomics, proteomics and neuronal electrical activity measurements performed in stable in vitro neuronal cell culture systems, has high potential to improve current in vitro drug-induced neurotoxicity evaluation. PMID:26026931

  7. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study on colour stability of ovine meat.

    Science.gov (United States)

    Subbaraj, Arvind K; Kim, Yuan H Brad; Fraser, Karl; Farouk, Mustafa M

    2016-07-01

    Meat colour is one of the cues available to the consumer to gauge overall meat quality and wholesomeness. Colour stability of meat is determined by several factors both inherent to the animal and post-slaughter conditions, including ageing, storage/packaging and display times. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study was undertaken to identify and compare polar metabolites between ovine meat samples that were exposed to different durations of ageing, storage conditions, and display times. Primary metabolites comprising amino acids, sugars, nucleotides, nucleosides, organic acids and their breakdown products were mainly identified as discriminating factors. For the first time, boron complexes of sugar and malic acid were also tentatively identified. As expected, most compounds identified were related to myoglobin chemistry, and compounds with antioxidant properties were found in higher levels in colour stable samples. Supplementary studies identifying semi-polar, non-polar and volatile compounds will provide a holistic understanding of the chemical basis of colour stability in ovine meat. PMID:26986230

  8. Untargeted metabolomics: an emerging approach to determine the composition of herbal products

    Directory of Open Access Journals (Sweden)

    Flavia Guzzo

    2013-01-01

    Full Text Available Natural remedies, such as those based on traditional Chinese medicines, have become more popular also in western countries over the last 10 years. The composition of these herbal products is largely unknown and difficult to determine. Moreover, since plants respond to their environment changing the metabolome, the composition of plant material can vary depending on the plant growth conditions.However, there is a growing need of a deeper knowledge on such natural remedies also in view of the growing number of reports of toxicity following the consumption of herbal supplements. Untargeted metabolomics is a useful approach for the simultaneous analysis of many compounds in herbal products. In particular, liquid chromatography/mass spectrometry (LC-MS can determine presence, amount and sometime structures of plant metabolites in complex herbal mixtures, with significant advantages over techniques such as nuclear magnetic resonance (NMR spectroscopy and gas chromatography/mass spectrometry (GC-MS.

  9. Cancer Metabolomics and the Human Metabolome Database

    Directory of Open Access Journals (Sweden)

    David S. Wishart

    2016-03-01

    Full Text Available The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The rapid growth of metabolomics in cancer research is also leading to challenges. In particular, with so many cancer-associate metabolites being identified, it is often difficult to keep track of which compounds are associated with which cancers. It is also challenging to track down information on the specific pathways that particular metabolites, drugs or drug metabolites may be affecting. Even more frustrating are the difficulties associated with identifying metabolites from NMR or MS spectra. Fortunately, a number of metabolomics databases are emerging that are designed to address these challenges. One such database is the Human Metabolome Database (HMDB. The HMDB is currently the world’s largest and most comprehensive, organism-specific metabolomics database. It contains more than 40,000 metabolite entries, thousands of metabolite concentrations, >700 metabolic and disease-associated pathways, as well as information on dozens of cancer biomarkers. This review is intended to provide a brief summary of the HMDB and to offer some guidance on how it can be used in metabolomic studies of cancer.

  10. Metabolomic Heterogeneity of Pulmonary Arterial Hypertension

    OpenAIRE

    Zhao, Yidan; Peng, Jenny; Lu, Catherine; Hsin, Michael; Mura, Marco; Wu, Licun; Chu, Lei; Zamel, Ricardo; Machuca, Tiago; Waddell, Thomas; Liu, Mingyao; Keshavjee, Shaf; Granton, John; de Perrot, Marc

    2014-01-01

    Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of ...

  11. Comparative UPLC-QTOF-MS-based metabolomics and bioactivities analyses of Garcinia oblongifolia.

    Science.gov (United States)

    Li, Ping; AnandhiSenthilkumar, Harini; Wu, Shi-biao; Liu, Bo; Guo, Zhi-yong; Fata, Jimmie E; Kennelly, Edward J; Long, Chun-lin

    2016-02-01

    Garcinia oblongifolia Champ. ex Benth. (Clusiaceae) is a well-known medicinal plant from southern China, with edible fruits. However, the phytochemistry and bioactivity of the different plant parts of G. oblongifolia have not been studied extensively. Comparative metabolic profiling and bioactivities of the leaf, branch, and fruit of G. oblongifolia were investigated. A total of 40 compounds such as biflavonoids, xanthones, and benzophenones were identified using UPLC-QTOF-MS and MS(E), including 15 compounds reported for the first time from this species. Heatmap analyses found that benzophenones, xanthones, and biflavonoids were predominately found in branches, with benzophenones present in relatively high concentrations in all three plant parts. Xanthones were found to have limited distribution in fruit while biflavonoids were present at only low levels in leaves. In addition, the cytotoxic (MCF-7 breast cancer cell line) and antioxidant (ABTS and DPPH chemical tests) activities of the crude extracts of G. oblongifolia indicate that the branch extract exhibits greater bioactivity than either the leaf or the fruit extracts. Orthogonal partial least squares discriminate analysis was used to find 12 marker compounds, mainly xanthones, from the branches, including well-known antioxidants and cytotoxic agents. These G. oblongifolia results revealed that the variation in metabolite profiles can be correlated to the differences in bioactivity of the three plant parts investigated. This UPLC-QTOF-MS strategy can be useful to identify bioactive constituents expressed differentially in the various plant parts of a single species. PMID:26773895

  12. UHPLC/Q-TOFMS-based plasma metabolomics of polycystic ovary syndrome patients with and without insulin resistance.

    Science.gov (United States)

    Chen, Ya-Xiao; Zhang, Xiao-Jing; Huang, Jia; Zhou, Shu-Jun; Liu, Fang; Jiang, Lin-Lin; Chen, Meiwan; Jian-Bo, Wan; Yang, Dong-Zi

    2016-03-20

    Polycystic ovary syndrome (PCOS), characterized with menstrual irregularities, hyperandrogenism and ovulatory abnormalities, is usually companied with insulin resistance (IR) and accounts for one of the most prevalent reproductive dysfunction of premenopausal women. Despite accumulating investigations, diagnostic standards of this pathological condition remain obscure. The aim of present study is to characterize the plasma metabolic characteristics of PCOS patients with and without IR, and subsequently identify the potential biomarkers for the diagnosis of PCOS and its IR complication. A total of 59 plasma samples from eligible healthy controls (CON, n=19), PCOS patients without IR (non-IR PCOS, n=19) and PCOS patients with IR (IR PCOS, n=21) were profiled by an ultra high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOFMS) followed by multivariate statistical analysis. Compared to the healthy controls, significant decrease in the levels of phosphocholines (PCs) and lyso PC (18:2), and increase in trilauric glyceride level were observed in the plasma of IR PCOS. Meanwhile, the significant increase in the levels of saturated fatty acids (palmitic acid and stearic acid) and decanoylcarnitine, and decrease in PC (36:2) and PS (36:0) were found in non-IR PCOS patients. Trilauric glyceride and decanoylcarnitine were identified as the potential biomarkers with the highest sensitivity and specificity for the diagnosis of PCOS patients with and without IR, respectively. Furthermore, based on these alterations of metabolites, MetPA network pathway analysis suggested a profound involvement of the abnormalities of glycerophospholipid, glycerolipid and fatty acid metabolisms in the pathogenesis of PCOS and IR complications. Collectively, LC-MS-based metabolomics provides a promising strategy for complementary diagnosis of PCOS and its IR complication and offers a new insight to understand their pathogenesis mechanisms. PMID:26808063

  13. GC-MS-based metabolomic study on the antidepressant-like effects of diterpene ginkgolides in mouse hippocampus.

    Science.gov (United States)

    Liang, Zihong; Bai, Shunjie; Shen, Peng; Hu, Qingchuan; Wang, Xingfa; Dong, Meixue; Wang, Wei; Li, Juan; Cheng, Ke; Zhang, Shuxiao; Zou, Dezhi; Han, Yu; Wang, Haiyang; Xie, Peng

    2016-11-01

    Ginkgo biloba extract (GBE), including EGb-761, have been suggested to have antidepressant activity based on previous behavioral and biochemical analyses. However, because GBE contain many constituents, the mechanisms underlying this suggested antidepressant activity are unclear. Here, we investigated the antidepressant-like effects of diterpene ginkgolides (DG), an important class of constituents in GBE, and studied their effects in the mouse hippocampus using a GC-MS-based metabolomics approach. Mice were randomly divided into five groups and injected daily until testing with 0.9% NaCl solution, one of three doses of DG (4.06, 12.18, and 36.54mg/kg), or venlafaxine. Sucrose preference (SPT) and tail suspension (TST) tests were then performed to evaluate depressive-like behaviors in mice. DG (12.18 and 36.54mg/kg) and venlafaxine (VLX) administration significantly increased hedonic behavior in mice in the SPT. DG (12.18mg/kg) treatment also shortened immobility time in the TST, suggestive of antidepressant-like effects. Significant differences in the metabolic profile in the DG (12.18mg/kg) compared with the control or VLX group indicative of an antidepressant-like effect were observed using multivariate analysis. Eighteen differential hippocampal metabolites were identified that discriminated the DG (12.18mg/kg) and control groups. These biochemical changes involved neurotransmitter metabolism, oxidative stress, glutathione metabolism, lipid metabolism, energy metabolism, and kynurenic acid, providing clues to the therapeutic mechanisms of DG. Thus, this study showed that DG has antidepressant-like activities in mice and shed light on the biological mechanisms underlying the effects of diterpene ginkgolides on behavior, providing an important drug candidate for the treatment of depression. PMID:27498146

  14. The Time Is Right to Focus on Model Organism Metabolomes

    Directory of Open Access Journals (Sweden)

    Arthur S. Edison

    2016-02-01

    Full Text Available Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.

  15. The food metabolome

    DEFF Research Database (Denmark)

    Scalbert, Augustin; Brennan, Lorraine; Manach, Claudine;

    2014-01-01

    efforts; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health.......The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the...... diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food...

  16. Comparative effects of dexamethasone and bergenin on chronic bronchitis and their anti-inflammatory mechanisms based on NMR metabolomics.

    Science.gov (United States)

    Ren, Xiaolei; Ma, Shuangshuang; Wang, Juan; Tian, Simin; Fu, Xiaorui; Liu, Xinfeng; Li, Zhongfeng; Zhao, Baosheng; Wang, Xueyong

    2016-05-24

    In order to compare the effect of dexamethasone and bergenin on chronic bronchitis and to reveal their anti-inflammatory mechanisms, (1)H NMR-based metabolomics was performed to explore the potential biomarkers of the disease and study the therapeutic mechanisms of the drugs. In this study, 40 Sprague-Dawley male rats were randomly divided into 4 groups, namely control, model, dexamethasone and bergenin groups, with 10 rats in each group. Except for the control group, rats from the other three groups were exposed to tobacco smoke for 1 h d(-1) for 28 days. During the modeling, dexamethasone (0.2 mg kg(-1)) and bergenin (87 mg kg(-1)) were administered orally to dexamethasone or bergenin rats 3 h after exposure every day. On the other hand, control and model rats were intragastrically administered water. According to the results of morphometric analysis of the airway epithelium and the count of white blood cells in the bronchoalveolar lavage fluid (BALF), dexamethasone and bergenin could suppress the infiltration of inflammatory cells, inhibit the secretion of mucus, and reduce white blood cells in BALF. Serum samples from the rats' orbits were collected every week. The metabolic profiles of sera were analyzed by multivariate statistical analyses, including PCA, PLS-DA and OPLS-DA models, and 18 metabolites were identified. The dynamic fluctuations of these biomarkers in sera from different groups were detected. The results suggested that the anti-inflammatory mechanism of dexamethasone may be associated with BCAA metabolism and glycolysis while bergenin could change BCAA metabolism, glycine, serine and threonine metabolism, and glycolysis to treat chronic bronchitis. PMID:27098339

  17. From numbers to a biological sense: How the strategy chosen for metabolomics data treatment may affect final results. A practical example based on urine fingerprints obtained by LC-MS.

    Science.gov (United States)

    Godzien, Joanna; Ciborowski, Michal; Angulo, Santiago; Barbas, Coral

    2013-10-01

    Application of high-throughput technologies in metabolomics studies increases the quantity of data obtained, which in turn imposes several problems during data analysis. Correctly and clearly addressed biological question and comprehensive knowledge about data structure and properties are definitely necessary to select proper chemometric tools. However, there is a broad range of chemometric tools available for use with metabolomics data, which makes this choice challenging. Precisely performed data treatment enables valuable extraction of information and its proper interpretation. The effect of an error made at an early stage will be enhanced throughout the later stages, which in combination with other errors made at each step can accumulate and significantly affect the data interpretation. Moreover, adequate application of these tools may help not only to detect, but sometimes also to correct, biological, analytical, or methodological errors, which may affect truthfulness of obtained results. This report presents steps and tools used for LC-MS based metabolomics data extraction, reduction, and visualization. Following such steps as data reprocessing, data pretreatment, data treatment, and data revision, authors want to show how to extract valuable information and how to avoid misinterpretation of results obtained. The purpose of this work was to emphasize problematic characteristics of metabolomics data and the necessity for their attentive and precise treatment. The dataset used to illustrate metabolomics data properties and to illustrate major data treatment challenges was obtained utilizing an animal model of control and diabetic rats, both with and without rosemary treatment. Urine samples were fingerprinted employing LC-QTOF-MS. PMID:23775708

  18. Potential of human saliva for nuclear magnetic resonance-based metabolomics and for health-related biomarker identification

    DEFF Research Database (Denmark)

    Bertram, Hanne Christine; Eggers, Nina; Eller, Nanna

    2009-01-01

    In the present study, the ability of (1)H nuclear magnetic resonance (NMR) for metabolic profiling of human saliva samples was investigated. High-resolution (1)H NMR spectra were obtained, and signals were assigned to various metabolites mainly representing small organic acids and amino acids. In...... addition, the use of human saliva for metabolomic studies was evaluated, and multivariate data analysis revealed that the 92 morning and night samples from 46 subjects could be discriminated with a predictability of 85%. The diurnal effect on the salivary metabolite profile were ascribed to changes in...... intensities of several metabolites including trimethylamine oxide (TMAO), choline, propionate, alanine, methanol, and N-acetyl groups. No effects of gender and body mass index (BMI) on the salivary metabolite profile were detected. The relationships between the salivary metabolome and glycated hemoglobin...

  19. Metabolomics data normalization with EigenMS.

    Directory of Open Access Journals (Sweden)

    Yuliya V Karpievitch

    Full Text Available Liquid chromatography mass spectrometry has become one of the analytical platforms of choice for metabolomics studies. However, LC-MS metabolomics data can suffer from the effects of various systematic biases. These include batch effects, day-to-day variations in instrument performance, signal intensity loss due to time-dependent effects of the LC column performance, accumulation of contaminants in the MS ion source and MS sensitivity among others. In this study we aimed to test a singular value decomposition-based method, called EigenMS, for normalization of metabolomics data. We analyzed a clinical human dataset where LC-MS serum metabolomics data and physiological measurements were collected from thirty nine healthy subjects and forty with type 2 diabetes and applied EigenMS to detect and correct for any systematic bias. EigenMS works in several stages. First, EigenMS preserves the treatment group differences in the metabolomics data by estimating treatment effects with an ANOVA model (multiple fixed effects can be estimated. Singular value decomposition of the residuals matrix is then used to determine bias trends in the data. The number of bias trends is then estimated via a permutation test and the effects of the bias trends are eliminated. EigenMS removed bias of unknown complexity from the LC-MS metabolomics data, allowing for increased sensitivity in differential analysis. Moreover, normalized samples better correlated with both other normalized samples and corresponding physiological data, such as blood glucose level, glycated haemoglobin, exercise central augmentation pressure normalized to heart rate of 75, and total cholesterol. We were able to report 2578 discriminatory metabolite peaks in the normalized data (p<0.05 as compared to only 1840 metabolite signals in the raw data. Our results support the use of singular value decomposition-based normalization for metabolomics data.

  20. An eco-metabolomic study of host plant resistance to Western flower thrips in cultivated, biofortified and wild carrots.

    Science.gov (United States)

    Leiss, Kirsten A; Cristofori, Gabriele; van Steenis, Rosalinda; Verpoorte, Robert; Klinkhamer, Peter G L

    2013-09-01

    Domestication of plants and selection for agronomic traits may reduce plant secondary defence metabolites relative to their ancestors. Carrot (Daucus carota L.) is an economically important vegetable. Recently, carrot was developed as a functional food with additional health-promoting functions. Biofortified carrots contain increased concentrations of chlorogenic acid as an antioxidant. Chlorogenic acid is involved in host plant resistance to Western Flower Thrips (Frankliniella occidentalis), one of the key agri- and horticultural pests worldwide. The objective of this study was to investigate quantitative host plant resistance to thrips in carrot and to identify candidate compounds for constitutive resistance. As such we explored whether cultivated carrot is more vulnerable to herbivore attack compared to wild carrot. We subjected a set of 14 biofortified, cultivated and wild carrot genotypes to thrips infestation. We compared morphological traits and leaf metabolic profiles of the three most resistant and susceptible carrots using nuclear magnetic resonance spectroscopy (NMR). In contrast to our expectation, wild carrots were not more resistant to thrips than cultivated ones. The most thrips resistant carrot was the cultivar Ingot which is known to be tolerant against carrot root fly (Psila rosae). Biofortified carrots were not resistant to thrips. Plant size, leaf area and number of leaf hairs did not differ between resistant and susceptible carrots. The metabolic profiles of the leaves of resistant carrots were significantly different from those of susceptible carrots. The leaves of resistant carrots contained higher amounts of the flavanoid luteolin, the phenylpropanoid sinapic acid and the amino acid β-alanine. The negative effect of these compounds on thrips was confirmed using in-vitro bioassays. Our results have potential implications for carrot breeders. The natural variation of metabolites present in cultivated carrots can be used for improvement of

  1. Metabolomics in dyslipidemia.

    Science.gov (United States)

    Chen, Hua; Miao, Hua; Feng, Ya-Long; Zhao, Ying-Yong; Lin, Rui-Chao

    2014-01-01

    Hyperlipidemia is an important public health problem with increased incidence and prevalence worldwide. Current clinical biomarkers, triglyceride, total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol lack the necessary specificity and sensitivity and only increase significantly after serious dyslipidemia. Therefore, sensitive biomarkers are needed for hyperlipidemia. Hyperlipidemia-specific biomarkers would improve clinical diagnosis and therapeutic treatment at early disease stages. The aim of metabolomics is to identify untargeted and global small-molecule metabolite profiles from cells, biofluids, and tissues. This method offers the potential for a holistic approach to improve disease diagnoses and our understanding of underlying pathologic mechanisms. This review summarizes analytical techniques, data collection and analysis for metabolomics, and metabolomics in hyperlipidemia animal models and clinical studies. Mechanisms of hypolipemia and antilipemic drug therapy are also discussed. Metabolomics provides a new opportunity to gain insight into metabolic profiling and pathophysiologic mechanisms of hyperlipidemia. PMID:25344987

  2. Metabolomics in multiple sclerosis.

    Science.gov (United States)

    Bhargava, Pavan; Calabresi, Peter A

    2016-04-01

    Multiple sclerosis (MS) is a chronic demyelinating disorder of the central nervous system with inflammatory and degenerative components. The cause of MS remains unknown although genetic and environmental factors appear to play a role in its etiopathogenesis. Metabolomics is a new "omics" technology that aims at measuring small molecules in various biological matrices and can provide information that is not readily obtained from genomics, transcriptomics, or proteomics. Currently, several different analytical platforms exist for metabolomics, and both untargeted and targeted approaches are being employed. Methods of analysis of metabolomics data are also being developed and no consensus currently exists on the optimal approach to analysis and interpretation of these data. Metabolomics has the potential to provide putative biomarkers, insights into the pathophysiology of the disease, and to aid in precision medicine for patients with MS. PMID:26754801

  3. Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics

    Directory of Open Access Journals (Sweden)

    Wei Zou

    2009-04-01

    Full Text Available A robust and complete workflow for metabolic profiling and data mining was described in detail. Three independent and complementary analytical techniques for metabolic profiling were applied: hydrophilic interaction chromatography (HILIC–LC–ESI–MS, reversed-phase liquid chromatography (RP–LC–ESI–MS, and gas chromatography (GC–TOF–MS all coupled to mass spectrometry (MS. Unsupervised methods, such as principle component analysis (PCA and clustering, and supervised methods, such as classification and PCA-DA (discriminatory analysis were used for data mining. Genetic Algorithms (GA, a multivariate approach, was probed for selection of the smallest subsets of potentially discriminative predictors. From thousands of peaks found in total, small subsets selected by GA were considered as highly potential predictors allowing discrimination among groups. It was found that small groups of potential top predictors selected with PCA-DA and GA are different and unique. Annotated GC–TOF–MS data generated identified feature metabolites. Metabolites putatively detected with LC–ESI–MS profiling require further elemental composition assignment with accurate mass measurement by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS and structure elucidation by nuclear magnetic resonance spectroscopy (NMR. GA was also used to generate correlated networks for pathway analysis. Several case studies, comprising groups of plant samples bearing different genotypes and groups of samples of human origin, namely patients and healthy volunteers’ urine samples, demonstrated that such a workflow combining comprehensive metabolic profiling and advanced data mining techniques provides a powerful approach for pattern recognition and biomarker discovery

  4. Metabolomics er fremtiden

    DEFF Research Database (Denmark)

    Pedersern, Birger

    2010-01-01

    Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet......Forskningen i fødevarer har fået et potent redskab i hånden. Metabolomics er vejen frem, mener professor Søren Balling Engelsen fra Københavns Universitet...

  5. Back tracing environmental toxicants in animal-derived food chain based on food metabolomics

    OpenAIRE

    Engel, Erwan; Ratel, Jérémy; Planche, Christelle

    2013-01-01

    Food-producing animals are exposed to toxic micropollutants via their environment and feeds. These micropollutants represent a chemical human health hazard because they are capable of entering the animals and being transferred to edible tissues 1 . Most current approaches to assessing contamination levels in foods are based on high performance analytical methods designed to determine the concentration of targeted micropollutant residues present down to trace levels in the food. Alternative...

  6. Bisphenol A alters n-6 fatty acid composition and decreases antioxidant enzyme levels in rat testes: a LC-QTOF-based metabolomics study.

    Directory of Open Access Journals (Sweden)

    Minjian Chen

    Full Text Available BACKGROUND: Male reproductive toxicity induced by exposure to bisphenol A (BPA has been widely reported. The testes have proven to be a major target organ of BPA toxicity, so studying testicular metabolite variation holds promise for the discovery of mechanisms linked to the toxic effects of BPA on reproduction. METHODOLOGY/PRINCIPAL FINDINGS: Male Sprague-Dawley rats were orally administered doses of BPA at the levels of 0, 50 mg/kg/d for 8 weeks. We used an unbiased liquid chromatography-quadrupole time-of-flight (LC-QTOF-based metabolomics approach to discover, identify, and analyze the variation of testicular metabolites. Two n-6 fatty acids, linoleic acid (LA and arachidonic acid (AA were identified as potential testicular biomarkers. Decreased levels of LA and increased levels of AA as well as AA/LA ratio were observed in the testes of the exposed group. According to these suggestions, testicular antioxidant enzyme levels were detected. Testicular superoxide dismutase (SOD declined significantly in the exposed group compared with that in the non-exposed group, and the glutathione peroxidase (GSH-Px as well as catalase (CAT also showed a decreasing trend in BPA treated group. CONCLUSIONS/SIGNIFICANCE: BPA caused testicular n-6 fatty acid composition variation and decreased antioxidant enzyme levels. This study emphasizes that metabolomics brings the promise of biomarkers identification for the discovery of mechanisms underlying reproductive toxicity.

  7. COnsortium of METabolomics Studies (COMETS)

    Science.gov (United States)

    The COnsortium of METabolomics Studies (COMETS) is an extramural-intramural partnership that promotes collaboration among prospective cohort studies that follow participants for a range of outcomes and perform metabolomic profiling of individuals.

  8. Application of Metabolomics in Thyroid Cancer Research

    Directory of Open Access Journals (Sweden)

    Anna Wojakowska

    2015-01-01

    Full Text Available Thyroid cancer is the most common endocrine malignancy with four major types distinguished on the basis of histopathological features: papillary, follicular, medullary, and anaplastic. Classification of thyroid cancer is the primary step in the assessment of prognosis and selection of the treatment. However, in some cases, cytological and histological patterns are inconclusive; hence, classification based on histopathology could be supported by molecular biomarkers, including markers identified with the use of high-throughput “omics” techniques. Beside genomics, transcriptomics, and proteomics, metabolomic approach emerges as the most downstream attitude reflecting phenotypic changes and alterations in pathophysiological states of biological systems. Metabolomics using mass spectrometry and magnetic resonance spectroscopy techniques allows qualitative and quantitative profiling of small molecules present in biological systems. This approach can be applied to reveal metabolic differences between different types of thyroid cancer and to identify new potential candidates for molecular biomarkers. In this review, we consider current results concerning application of metabolomics in the field of thyroid cancer research. Recent studies show that metabolomics can provide significant information about the discrimination between different types of thyroid lesions. In the near future, one could expect a further progress in thyroid cancer metabolomics leading to development of molecular markers and improvement of the tumor types classification and diagnosis.

  9. Systematic Applications of Metabolomics in Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Robert A. Dromms

    2012-12-01

    Full Text Available The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.

  10. Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation

    Energy Technology Data Exchange (ETDEWEB)

    Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot , Casey M.; Young, VIncent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan A.

    2016-01-19

    Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date analyses of such multi-meta-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites' abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributors. Focusing on two independent vaginal microbiome datasets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that significantly contribute to these predictions. Interestingly, our analysis also detects metabolites for which predicted variation negatively correlates with measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome datasets reveals similar trends,including prediction of bile acid metabolite shifts. This framework is an important first step towards a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease.

  11. Metabolomic heterogeneity of pulmonary arterial hypertension.

    Directory of Open Access Journals (Sweden)

    Yidan Zhao

    Full Text Available Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH, the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH.

  12. GC-MS Based Plasma Metabolomics for Identification of Candidate Biomarkers for Hepatocellular Carcinoma in Egyptian Cohort.

    Directory of Open Access Journals (Sweden)

    Mohammad R Nezami Ranjbar

    Full Text Available This study evaluates changes in metabolite levels in hepatocellular carcinoma (HCC cases vs. patients with liver cirrhosis by analysis of human blood plasma using gas chromatography coupled with mass spectrometry (GC-MS. Untargeted metabolomic analysis of plasma samples from participants recruited in Egypt was performed using two GC-MS platforms: a GC coupled to single quadruple mass spectrometer (GC-qMS and a GC coupled to a time-of-flight mass spectrometer (GC-TOFMS. Analytes that showed statistically significant changes in ion intensities were selected using ANOVA models. These analytes and other candidates selected from related studies were further evaluated by targeted analysis in plasma samples from the same participants as in the untargeted metabolomic analysis. The targeted analysis was performed using the GC-qMS in selected ion monitoring (SIM mode. The method confirmed significant changes in the levels of glutamic acid, citric acid, lactic acid, valine, isoleucine, leucine, alpha tocopherol, cholesterol, and sorbose in HCC cases vs. patients with liver cirrhosis. Specifically, our findings indicate up-regulation of metabolites involved in branched-chain amino acid (BCAA metabolism. Although BCAAs are increasingly used as a treatment for cancer cachexia, others have shown that BCAA supplementation caused significant enhancement of tumor growth via activation of mTOR/AKT pathway, which is consistent with our results that BCAAs are up-regulated in HCC.

  13. Triptolide disrupts fatty acids and peroxisome proliferator-activated receptor (PPAR) levels in male mice testes followed by testicular injury: A GC–MS based metabolomics study

    International Nuclear Information System (INIS)

    Graphical abstract: Heat map of hierarchical clustering of the testicular tissue samples (A) and serum samples (B) at the 2nd week. Red blocks indicate increased intensities whereas blue indicates decreased intensities. The above two columns represent model group and normal group. - Abstract: Triptolide is the major active ingredient of Tripterygium Glycosides (TG), a traditional Chinese medicine with very potent anti-inflammatory effects and has been used in China for the treatment of rheumatoid arthritis and many other inflammatory diseases. However, clinical application of triptolide is restricted due to its multiple side effects, especially male infertility. The mechanism of triptolide on reproduction toxicity remains unclear. In the present study, a GC–MS based metabolomic approach was employed to evaluate the mechanism of triptolide-induced reproductive toxicity as well as identify potential novel biomarkers for the early detection of spermatogenesis dysfunction. In brief, male mice were divided into two groups with or without triptolide intraperitoneal injection at 60 μg/kg/day for 2 weeks and toxic effect of triptolide on testicular tissues were examined by biochemical indicator analysis, testis histopathologic analysis, and sperm quantity analysis. Metabolomics technology was then performed to evaluate systematically the endogenous metabolites profiling. Our results demonstrated that triptolide suppressed the marker-enzymes of spermatogenesis and testosterone levels, decreased sperm counts, reduced the gonad index and destroyed the microstructure of testis. Multivariate data analysis revealed that mice with triptolide induced testicular toxicity could be distinctively differentiated from normal animals and 35 and 39 small molecule metabolites were changed significantly in testis and serum, respectively (Fold-changes >1.5, P < 0.05), in triptolide-treated mice. Abnormal level of fatty acids, an important energy source of sertoli cells with critical role

  14. Comparison of earthworm responses to petroleum hydrocarbon exposure in aged field contaminated soil using traditional ecotoxicity endpoints and 1H NMR-based metabolomics

    International Nuclear Information System (INIS)

    1H NMR metabolomics and conventional ecotoxicity endpoints were used to examine the response of earthworms exposed to petroleum hydrocarbons (PHCs) in soil samples collected from a site that was contaminated with crude oil from a pipeline failure in the mid-1990s. The conventional ecotoxicity tests showed that the soils were not acutely toxic to earthworms (average survival ≥90%), but some soil samples impaired reproduction endpoints by >50% compared to the field control soil. Additionally, metabolomics revealed significant relationships between earthworm metabolic profiles (collected after 2 or 14 days of exposure) and soil properties including soil PHC concentration. Further comparisons by partial least squares regression revealed a significant relationship between the earthworm metabolomic data (collected after only 2 or 14 days) and the reproduction endpoints (measured after 63 days). Therefore, metabolomic responses measured after short exposure periods may be predictive of chronic, ecologically relevant toxicity endpoints for earthworms exposed to soil contaminants. -- Highlights: •Earthworm response to petroleum hydrocarbon exposure in soil is examined. •Metabolomics shows significant changes to metabolic profile after 2 days. •Significant relationships observed between metabolomic and reproduction endpoints. •Metabolomics may have value as a rapid screening tool for chronic toxicity. -- Earthworm metabolomic responses measured after 2 and 14 days are compared to traditional earthworm ecotoxicity endpoints (survival and reproduction) in petroleum hydrocarbon contaminated soil

  15. Linking metabolomics data to underlying metabolic regulation

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2014-11-01

    Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

  16. Bio-effectors from waste materials as growth promoters, an agronomic and metabolomic study

    Science.gov (United States)

    Alwanney, Deaa; Chami, Ziad Al; Angelica De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

    2014-05-01

    Nowadays, improving plant performance by providing growth promoters is a main concern of the organic agriculture. As a consequence of increased food demands, more efficient and alternatives of the current plant nutrition strategies are becoming urgent. Recently, a novel concept "bio-effectors" raised on to describe a group of products that are able to improve plant performance and do not belong to fertilizers or pesticides. Agro-Food processing residues are promising materials as bio-effector. Three plant-derived materials: brewers' spent grain (BSG), fennel processing residues (FPR) and lemon processing residues (LPR) were chosen as bio-effector candidates. Plant-derived materials were characterized in term of total macro and micronutrients content. Green extraction methodology and solvent choice (aqueous; ethanol; and aqueous: ethanol mixture 1:1) was based on the extraction yield as main factor. Optimum extracts, to be used on the tomato test plant, were determined using phytotoxicity test (seed germination test) as main constraint. Thereafter, selected extracts were characterized and secondary metabolites profiling were detected by NMR technique. Selected extracts were applied on tomato in a growth chamber at different doses in comparison to humic-like substances as positive control (Ctrl+) and to a Hoagland solution as negative control (Ctrl-). At the end of the experiment, agronomical parameters were determined and NMR-metabolomic profiling were conducted on tomato seedlings. Results are summarized as follow: (i) raw showed an interesting content, either at nutritional or biological level; (ii) aqueous extraction resulted higher yield than other used solvent; (iii) at high extraction ratio (1:25 for BSG; 1:100 for FPR; and 1:200 for LPR) aqueous extracts were not phytotoxic on the tomato test plant; (iv) all aqueous extract are differently rich in nutrients, aminoacids, sugars and low molecular weight molecules; (v) all extract exhibited a growth promotion at

  17. From models to crop species: caveats and solutions for translational metabolomics

    Directory of Open Access Journals (Sweden)

    Takayuki eTohge

    2011-10-01

    Full Text Available Although plant metabolomics is largely carried out on Arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. However, transfer of between species, or even between different tissues of the same species, is not facile. This is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. In parallel with the diversification of model species it is important to establish good handling and analytic practice, in order to augment computational comparisons between tissues and species. LC-MS-based metabolomics is one of the powerful approaches for metabolite profiling. By using a combination of different extraction methods, separation columns and ion detection, a very wide range of metabolites can be analysed. However, its application requires careful attention to exclude potential pitfalls, including artifactual changes in metabolite levels during sample preparation and analytic errors due to ion-suppression. Here we provide case studies with two different LC-MS-based metabolomics platforms and four species (Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum and Oryza sativa that illustrate how such dangers can be detected and circumvented.

  18. DnsID in MyCompoundID for rapid identification of dansylated amine- and phenol-containing metabolites in LC-MS-based metabolomics.

    Science.gov (United States)

    Huan, Tao; Wu, Yiman; Tang, Chenqu; Lin, Guohui; Li, Liang

    2015-10-01

    High-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is an enabling technology based on rational design of labeling reagents to target a class of metabolites sharing the same functional group (e.g., all the amine-containing metabolites or the amine submetabolome) to provide concomitant improvements in metabolite separation, detection, and quantification. However, identification of labeled metabolites remains to be an analytical challenge. In this work, we describe a library of labeled standards and a search method for metabolite identification in CIL LC-MS. The current library consists of 273 unique metabolites, mainly amines and phenols that are individually labeled by dansylation (Dns). Some of them produced more than one Dns-derivative (isomers or multiple labeled products), resulting in a total of 315 dansyl compounds in the library. These metabolites cover 42 metabolic pathways, allowing the possibility of probing their changes in metabolomics studies. Each labeled metabolite contains three searchable parameters: molecular ion mass, MS/MS spectrum, and retention time (RT). To overcome RT variations caused by experimental conditions used, we have developed a calibration method to normalize RTs of labeled metabolites using a mixture of RT calibrants. A search program, DnsID, has been developed in www.MyCompoundID.org for automated identification of dansyl labeled metabolites in a sample based on matching one or more of the three parameters with those of the library standards. Using human urine as an example, we illustrate the workflow and analytical performance of this method for metabolite identification. This freely accessible resource is expandable by adding more amine and phenol standards in the future. In addition, the same strategy should be applicable for developing other labeled standards libraries to cover different classes of metabolites for comprehensive metabolomics using CIL LC-MS. PMID:26327437

  19. Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system.

    Science.gov (United States)

    Turi, Christina E; Finley, Jamie; Shipley, Paul R; Murch, Susan J; Brown, Paula N

    2015-04-24

    Metabolomics is the qualitative and quantitative analysis of all of the small molecules in a biological sample at a specific time and influence. Technologies for metabolomics analysis have developed rapidly as new analytical tools for chemical separations, mass spectrometry, and NMR spectroscopy have emerged. Plants have one of the largest metabolomes, and it is estimated that the average plant leaf can contain upward of 30 000 phytochemicals. In the past decade, over 1200 papers on plant metabolomics have been published. A standard metabolomics data set contains vast amounts of information and can either investigate or generate hypotheses. The key factors in using plant metabolomics data most effectively are the experimental design, authentic standard availability, extract standardization, and statistical analysis. Using cranberry (Vaccinium macrocarpon) as a model system, this review will discuss and demonstrate strategies and tools for analysis and interpretation of metabolomics data sets including eliminating false discoveries and determining significance, metabolite clustering, and logical algorithms for discovery of new metabolites and pathways. Together these metabolomics tools represent an entirely new pipeline for phytochemical discovery. PMID:25751407

  20. Metabolomic changes of Brassica rapa under biotic stress

    NARCIS (Netherlands)

    Abdel-Farid Ali, Ibrahim Bayoumi

    2009-01-01

    It has been shown by this thesis that plant metabolomics is a promising tool for studying the interaction between B. rapa and pathogenic fungi. It gives a picture of the plant metabolites during the interaction. Brassica rapa has many defense related compounds such as glucosinolates, IAA, phenylprop

  1. The bases of plant introduction

    OpenAIRE

    Karpun Yu N

    2004-01-01

    The main problems of plintroduction are presented as theses. The plants introduction is suggested to regard as process of their cultivation, which has several stages: the mobilization of plant's material, primary test, sec- ond test. The basic terms are offered: introduction point, introduction search, collection number, introduction situation, etc. The peculiarities of plants introduction process are presented. The relationship between native flora and introduction plants are con...

  2. Metabolomics Research Group 2011 Study

    OpenAIRE

    Asara, J. M.; Tolstikov, V.V.; Aronov, P.; Kesler, B.; Shulaev, V.; Turck, C. W.; Wikoff, W R

    2011-01-01

    The ABRF Metabolomics Research Group (MRG) was formed in 2009 and aims to educate research scientists and resource facilities in the analytical approaches and management of data resulting from comprehensive metabolite studies and to promote the science and standardization of metabolomic analyses for a variety of applications. Last year the MRG conducted a ‘Survey Study’ on the current use of metabolomics technologies and procedures in core facilities. This year the MRG is organizing a ‘Resear...

  3. Metabolic regulation of trisporic acid on Blakeslea trispora revealed by a GC-MS-based metabolomic approach.

    Directory of Open Access Journals (Sweden)

    Jie Sun

    Full Text Available The zygomycete Blakeslea trispora is used commercially as natural source of â-carotene. Trisporic acid (TA is secreted from the mycelium of B. trispora during mating between heterothallic strains and is considered as a mediator of the regulation of mating processes and an enhancer of carotene biosynthesis. Gas chromatography-mass spectrometry and multivariate analysis were employed to investigate TA-associated intracellular biochemical changes in B. trispora. By principal component analysis, the differential metabolites discriminating the control groups from the TA-treated groups were found, which were also confirmed by the subsequent hierarchical cluster analysis. The results indicate that TA is a global regulator and its main effects at the metabolic level are reflected on the content changes in several fatty acids, carbohydrates, and amino acids. The carbon metabolism and fatty acids synthesis are sensitive to TA addition. Glycerol, glutamine, and ã-aminobutyrate might play important roles in the regulation of TA. Complemented by two-dimensional electrophoresis, the results indicate that the actions of TA at the metabolic level involve multiple metabolic processes, such as glycolysis and the bypass of the classical tricarboxylic acid cycle. These results reveal that the metabolomics strategy is a powerful tool to gain insight into the mechanism of a microorganism's cellular response to signal inducers at the metabolic level.

  4. Rifaximin Modulates the Vaginal Microbiome and Metabolome in Women Affected by Bacterial Vaginosis

    OpenAIRE

    Laghi, Luca; Picone, Gianfranco; Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Donders, Gilbert; Capozzi, Francesco; Vitali, Beatrice

    2014-01-01

    Bacterial vaginosis (BV) is a common vaginal disorder characterized by the decrease of lactobacilli and overgrowth of Gardnerella vaginalis and resident anaerobic vaginal bacteria. In the present work, the effects of rifaximin vaginal tablets on vaginal microbiota and metabolome of women affected by BV were investigated by combining quantitative PCR and a metabolomic approach based on 1H nuclear magnetic resonance. To highlight the general trends of the bacterial communities and metabolom...

  5. Metabolomics and Atherosclerosis

    OpenAIRE

    Sascha N Goonewardena; Prevette, Lisa E.; Desai, Ankit A

    2010-01-01

    Metabolites reflect the dynamic processes underlying cellular homeostasis. Recent advances in analytical chemistry and molecular biology have set the stage for metabolite profiling to help us understand complex molecular processes and physiology. Metabolomics is the comparative analysis of metabolite flux and how it relates to biological phenotypes. As an intermediate phenotype, metabolite signatures capture a unique aspect of cellular dynamics that is not typically interrogated, providing a ...

  6. FT-ICR/MS and GC-EI/MS Metabolomics Networking Unravels Global Potato Sprout's Responses to Rhizoctonia solani Infection

    OpenAIRE

    Aliferis, Konstantinos A.; Jabaji, Suha

    2012-01-01

    The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The develop...

  7. Metabolomics - the new "omics" of health care

    OpenAIRE

    V.S.Kiranmayi; Srinivasa Rao, P. V. L. N.; Aparna R. Bitla

    2012-01-01

    Metabolic diseases are caused by chronic dysregulations of metabolism that differ among individuals due to interactions of the genetic and environmental influences manifesting as a particular phenotype. These are usually diagnosed with the help of individual metabolites which serve as disease biomarkers. However, single biomarker based diagnostics for metabolism-based diseases fails to identify the cause of the alteration of these surrogate markers. This is where metabolomics come...

  8. Plant-based remediation processes

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Dharmendra Kumar (ed.) [Belgian Nuclear Research Centre (SCK.CEN), Mol (Belgium). Radiological Impact and Performance Assessment Division

    2013-11-01

    A valuable source of information for scientists in the field of environmental pollution and remediation. Describes the latest biotechnological methods for the treatment of contaminated soils. Includes case studies and protocols. Phytoremediation is an emerging technology that employs higher plants for the clean-up of contaminated environments. Basic and applied research have unequivocally demonstrated that selected plant species possess the genetic potential to accumulate, degrade, metabolize and immobilize a wide range of contaminants. The main focus of this volume is on the recent advances of technologies using green plants for remediation of various metals and metalloids. Topics include biomonitoring of heavy metal pollution, amendments of higher uptake of toxic metals, transport of heavy metals in plants, and toxicity mechanisms. Further chapters discuss agro-technological methods for minimizing pollution while improving soil quality, transgenic approaches to heavy metal remediation and present protocols for metal remediation via in vitro root cultures.

  9. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Bhowmik Salil [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Young-Joo; Yi, Hong Jae [College of Pharmacy, Kyung Hee University, Hoegi-dong, Dongdaemun-gu, Seoul 130-791 (Korea, Republic of); Chung, Bong Chul [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); Jung, Byung Hwa, E-mail: jbhluck@kist.re.kr [Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650 (Korea, Republic of); University of Science and Technology, (305-333) 113 Gwahangno, Yuseong-gu, Daejeon (Korea, Republic of)

    2010-02-19

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg{sup -1} day{sup -1} or 250 mg kg{sup -1} day{sup -1} for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

  10. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach

    International Nuclear Information System (INIS)

    In order to develop a safety biomarker for atorvastatin, this drug was orally administrated to hyperlipidemic rats, and a metabolomic study was performed. Atorvastatin was given in doses of either 70 mg kg-1 day-1 or 250 mg kg-1 day-1 for a period of 7 days (n = 4 for each group). To evaluate any abnormal effects of the drug, physiological and plasma biochemical parameters were measured and histopathological tests were carried out. Safety biomarkers were derived by comparing these parameters and using both global and targeted metabolic profiling. Global metabolic profiling was performed using liquid chromatography/time of flight/mass spectrometry (LC/TOF/MS) with multivariate data analysis. Several safety biomarker candidates that included various steroids and amino acids were discovered as a result of global metabolic profiling, and they were also confirmed by targeted metabolic profiling using gas chromatography/mass spectrometry (GC/MS) and capillary electrophoresis/mass spectrometry (CE/MS). Serum biochemical and histopathological tests were used to detect abnormal drug reactions in the liver after repeating oral administration of atorvastatin. The metabolic differences between control and the drug-treated groups were compared using PLS-DA score plots. These results were compared with the physiological and plasma biochemical parameters and the results of a histopathological test. Estrone, cortisone, proline, cystine, 3-ureidopropionic acid and histidine were proposed as potential safety biomarkers related with the liver toxicity of atorvastatin. These results indicate that the combined application of global and targeted metabolic profiling could be a useful tool for the discovery of drug safety biomarkers.

  11. A Generic Multiple Reaction Monitoring Based Approach for Plant Flavonoids Profiling Using a Triple Quadrupole Linear Ion Trap Mass Spectrometry

    Science.gov (United States)

    Yan, Zhixiang; Lin, Ge; Ye, Yang; Wang, Yitao; Yan, Ru

    2014-06-01

    Flavonoids are one of the largest classes of plant secondary metabolites serving a variety of functions in plants and associating with a number of health benefits for humans. Typically, they are co-identified with many other secondary metabolites using untargeted metabolomics. The limited data quality of untargeted workflow calls for a shift from the breadth-first to the depth-first screening strategy when a specific biosynthetic pathway is focused on. Here we introduce a generic multiple reaction monitoring (MRM)-based approach for flavonoids profiling in plants using a hybrid triple quadrupole linear ion trap (QTrap) mass spectrometer. The approach includes four steps: (1) preliminary profiling of major aglycones by multiple ion monitoring triggered enhanced product ion scan (MIM-EPI); (2) glycones profiling by precursor ion triggered EPI scan (PI-EPI) of major aglycones; (3) comprehensive aglycones profiling by combining MIM-EPI and neutral loss triggered EPI scan (NL-EPI) of major glycone; (4) in-depth flavonoids profiling by MRM-EPI with elaborated MRM transitions. Particularly, incorporation of the NH3 loss and sugar elimination proved to be very informative and confirmative for flavonoids screening. This approach was applied for profiling flavonoids in Astragali radix ( Huangqi), a famous herb widely used for medicinal and nutritional purposes in China. In total, 421 flavonoids were tentatively characterized, among which less than 40 have been previously reported in this medicinal plant. This MRM-based approach provides versatility and sensitivity that required for flavonoids profiling in plants and serves as a useful tool for plant metabolomics.

  12. NMR-Based Metabolomic Investigations on the Differential Responses in Adductor Muscles from Two Pedigrees of Manila Clam Ruditapes philippinarum to Cadmium and Zinc

    Directory of Open Access Journals (Sweden)

    Junbao Yu

    2011-09-01

    Full Text Available Manila clam Ruditapes philippinarum is one of the most important economic species in shellfishery in China due to its wide geographic distribution and high tolerance to environmental changes (e.g., salinity, temperature. In addition, Manila clam is a good biomonitor/bioindicator in “Mussel Watch Programs” and marine environmental toxicology. However, there are several pedigrees of R. philippinarum distributed in the marine environment in China. No attention has been paid to the biological differences between various pedigrees of Manila clams, which may introduce undesirable biological variation in toxicology studies. In this study, we applied NMR-based metabolomics to detect the biological differences in two main pedigrees (White and Zebra of R. philippinarum and their differential responses to heavy metal exposures (Cadmium and Zinc using adductor muscle as a target tissue to define one sensitive pedigree of R. philippinarum as biomonitor for heavy metals. Our results indicated that there were significant metabolic differences in adductor muscle tissues between White and Zebra clams, including higher levels of alanine, glutamine, hypotaurine, phosphocholine and homarine in White clam muscles and higher levels of branched chain amino acids (valine, leucine and isoleucine, succinate and 4-aminobutyrate in Zebra clam muscles, respectively. Differential metabolic responses to heavy metals between White and Zebra clams were also found. Overall, we concluded that White pedigree of clam could be a preferable bioindicator/biomonitor in marine toxicology studies and for marine heavy metals based on the relatively high sensitivity to heavy metals.

  13. Robustness of NMR-based metabolomics to generate comparable data sets for olive oil cultivar classification. An inter-laboratory study on Apulian olive oils.

    Science.gov (United States)

    Piccinonna, Sara; Ragone, Rosa; Stocchero, Matteo; Del Coco, Laura; De Pascali, Sandra Angelica; Schena, Francesco Paolo; Fanizzi, Francesco Paolo

    2016-05-15

    Nuclear Magnetic Resonance (NMR) spectroscopy is emerging as a powerful technique in olive oil fingerprinting, but its analytical robustness has to be proved. Here, we report a comparative study between two laboratories on olive oil (1)H NMR fingerprinting, aiming to demonstrate the robustness of NMR-based metabolomics in generating comparable data sets for cultivar classification. Sample preparation and data acquisition were performed independently in two laboratories, equipped with different resolution spectrometers (400 and 500 MHz), using two identical sets of mono-varietal olive oils. Partial Least Squares (PLS)-based techniques were applied to compare the data sets produced by the two laboratories. Despite differences in spectrum baseline, and in intensity and shape of peaks, the amount of shared information was significant (almost 70%) and related to cultivar (same metabolites discriminated between cultivars). In conclusion, regardless of the variability due to operator and machine, the data sets from the two participating units were comparable for the purpose of classification. PMID:26776024

  14. Growing pioneer plants for a lunar base

    Science.gov (United States)

    Kozyrovska, N. O.; Lutvynenko, T. L.; Korniichuk, O. S.; Kovalchuk, M. V.; Voznyuk, T. M.; Kononuchenko, O.; Zaetz, I.; Rogutskyy, I. S.; Mytrokhyn, O. V.; Mashkovska, S. P.; Foing, B. H.; Kordyum, V. A.

    A precursory scenario of cultivating the first plants in a lunar greenhouse was elaborated in frames of a conceptual study to grow plants for a permanently manned lunar base. A prototype plant growth system represents an ornamental plant Tagetes patula L. for growing in a lunar rock anorthosite as a substrate. Microbial community anticipated to be in use to support a growth and development of the plant in a substrate of low bioavailability and provide an acceptable growth and blossoming of T. patula under growth limiting conditions.

  15. Metabolomics for Secondary Metabolite Research

    Directory of Open Access Journals (Sweden)

    Eriko Takano

    2013-11-01

    Full Text Available Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.

  16. Matrix removal in state of the art sample preparation methods for serum by charged aerosol detection and metabolomics-based LC-MS.

    Science.gov (United States)

    Schimek, Denise; Francesconi, Kevin A; Mautner, Anton; Libiseller, Gunnar; Raml, Reingard; Magnes, Christoph

    2016-04-01

    Investigations into sample preparation procedures usually focus on analyte recovery with no information provided about the fate of other components of the sample (matrix). For many analyses, however, and particularly those using liquid chromatography-mass spectrometry (LC-MS), quantitative measurements are greatly influenced by sample matrix. Using the example of the drug amitriptyline and three of its metabolites in serum, we performed a comprehensive investigation of nine commonly used sample clean-up procedures in terms of their suitability for preparing serum samples. We were monitoring the undesired matrix compounds using a combination of charged aerosol detection (CAD), LC-CAD, and a metabolomics-based LC-MS/MS approach. In this way, we compared analyte recovery of protein precipitation-, liquid-liquid-, solid-phase- and hybrid solid-phase extraction methods. Although all methods provided acceptable recoveries, the highest recovery was obtained by protein precipitation with acetonitrile/formic acid (amitriptyline 113%, nortriptyline 92%, 10-hydroxyamitriptyline 89%, and amitriptyline N-oxide 96%). The quantification of matrix removal by LC-CAD showed that the solid phase extraction method (SPE) provided the lowest remaining matrix load (48-123 μg mL(-1)), which is a 10-40 fold better matrix clean-up than the precipitation- or hybrid solid phase extraction methods. The metabolomics profiles of eleven compound classes, comprising 70 matrix compounds showed the trends of compound class removal for each sample preparation strategy. The collective data set of analyte recovery, matrix removal and matrix compound profile was used to assess the effectiveness of each sample preparation method. The best performance in matrix clean-up and practical handling of small sample volumes was showed by the SPE techniques, particularly HLB SPE. CAD proved to be an effective tool for revealing the considerable differences between the sample preparation methods. This detector

  17. Pea fiber and wheat bran fiber show distinct metabolic profiles in rats as investigated by a 1H NMR-based metabolomic approach.

    Directory of Open Access Journals (Sweden)

    Guangmang Liu

    Full Text Available This study aimed to examine the effect of pea fiber (PF and wheat bran fiber (WF supplementation in rat metabolism. Rats were assigned randomly to one of three dietary groups and were given a basal diet containing 15% PF, 15% WF, or no supplemental fiber. Urine and plasma samples were analyzed by NMR-based metabolomics. PF significantly increased the plasma levels of 3-hydroxybutyrate, and myo-inositol as well as the urine levels of alanine, hydroxyphenylacetate, phenylacetyglycine, and α-ketoglutarate. However, PF significantly decreased the plasma levels of isoleucine, leucine, lactate, and pyruvate as well as the urine levels of allantoin, bile acids, and trigonelline. WF significantly increased the plasma levels of acetone, isobutyrate, lactate, myo-inositol, and lipids as well as the urine levels of alanine, lactate, dimethylglycine, N-methylniconamide, and α-ketoglutarate. However, WF significantly decreased the plasma levels of amino acids, and glucose as well as the urine levels of acetate, allantoin, citrate, creatine, hippurate, hydroxyphenylacetate, and trigonelline. Results suggest that PF and WF exposure can promote antioxidant activity and can exhibit common systemic metabolic changes, including lipid metabolism, energy metabolism, glycogenolysis and glycolysis metabolism, protein biosynthesis, and gut microbiota metabolism. PF can also decrease bile acid metabolism. These findings indicate that different fiber diet may cause differences in the biofluid profile in rats.

  18. Integrating candidate metabolites and biochemical factors to elucidate the action mechanism of Xue-sai-tong injection based on (1)H NMR metabolomics.

    Science.gov (United States)

    Jiang, Miaomiao; Zhao, Xiaoping; Wang, Linli; Xu, Lei; Zhang, Yan; Li, Zheng

    2016-07-15

    A strategy of integrating candidate metabolites with crucial biochemical factors was proposed in this study to discover relevant biological functions for interpreting the action mechanism of Traditional Chinese Medicines (TCM). This approach was applied to Xue-Sai-Tong injection (XST) to reveal the action mechanism based on the metabolic response in an ischemia/reperfusion (I/R) rat model by analyzing NMR profile. Partial least squares discriminate analysis (PLS-DA) was used to compare metabolic profiles of serum samples and revealed nine metabolites altered by I/R injury could be restored to normal status (sham-operated group) under the therapy of XST. The pathway enrichment analysis suggested the metabolic changes were mainly involved in pyruvate metabolism, glycolysis, and citrate cycle. The functional roles of the candidate metabolites were further identified by Pearson correlation analysis with the key biochemical factors in serum. The results indicated pyruvate, succinate, acetate and lysine showed significant associations with the oxidative stress factors. Elevated level of pyruvate was found as an essential metabolic response for the major effect of XST against I/R injury by enhancing glycolysis and overcoming the induced reactive oxygen species (ROS). This metabolomics approach provides a better understanding of the mechanisms of TCM and helps to develop a holistic view of TCM efficacy. PMID:26862062

  19. Mealtime, temporal, and daily variability of the human urinary and plasma metabolomes in a tightly controlled environment.

    Directory of Open Access Journals (Sweden)

    Kyoungmi Kim

    Full Text Available While metabolomics has tremendous potential for diagnostic biomarker and therapeutic target discovery, its utility may be diminished by the variability that occurs due to environmental exposures including diet and the influences of the human circadian rhythm. For successful translation of metabolomics findings into the clinical setting, it is necessary to exhaustively define the sources of metabolome variation. To address these issues and to measure the variability of urinary and plasma metabolomes throughout the day, we have undertaken a comprehensive inpatient study in which we have performed non-targeted metabolomics analysis of blood and urine in 26 volunteers (13 healthy subjects with no known disease and 13 healthy subjects with autosomal dominant polycystic kidney disease not taking medication. These individuals were evaluated in a clinical research facility on two separate occasions, over three days, while on a standardized, weight-based diet. Subjects provided pre- and post-prandial blood and urine samples at the same time of day, and all samples were analyzed by "fast lane" LC-MS-based global metabolomics. The largest source of variability in blood and urine metabolomes was attributable to technical issues such as sample preparation and analysis, and less variability was due to biological variables, meals, and time of day. Higher metabolome variability was observed after the morning as compared to the evening meal, yet day-to-day variability was minimal and urine metabolome variability was greater than that of blood. Thus we suggest that blood and urine are suitable biofluids for metabolomics studies, though nontargeted mass spectrometry alone may not offer sufficient precision to reveal subtle changes in the metabolome. Additional targeted analyses may be needed to support the data from nontargeted mass spectrometric analyses. In light of these findings, future metabolomics studies should consider these sources of variability to allow

  20. Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation

    DEFF Research Database (Denmark)

    Zheng, Hong; Lorenzen, J.K.; Astrup, A.; Larsen, Lesli H.; Yde, Christian Clement; Clausen, Morten Rahr; Bertram, Hanne Christine S.

    2016-01-01

    metabolism and gut microbial activity. In addition, a significant time effect on the blood metabolome was attributed to a decrease in blood lipid and lipoprotein levels due to the energy restriction. For the fecal metabolome, a trend for a diet effect was found and a series of metabolites, such as acetate......We investigated the effect of a 24-week energy-restricted intervention with low or high dairy intake (LD or HD) on the metabolic profiles of urine, blood and feces in overweight/obese women by NMR spectroscopy combined with ANOVA-simultaneous component analysis (ASCA). A significant effect of dairy...... intake was found on the urine metabolome. HD intake increased urinary citrate, creatinine and urea excretion, and decreased urinary excretion of trimethylamine-N-oxide (TMAO) and hippurate relative to the LD intake, suggesting that HD intake was associated with alterations in protein catabolism, energy...

  1. Model-based explanation of plant knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Huuskonen, P.J. [VTT Electronics, Oulu (Finland). Embedded Software

    1997-12-31

    This thesis deals with computer explanation of knowledge related to design and operation of industrial plants. The needs for explanation are motivated through case studies and literature reviews. A general framework for analysing plant explanations is presented. Prototypes demonstrate key mechanisms for implementing parts of the framework. Power plants, steel mills, paper factories, and high energy physics control systems are studied to set requirements for explanation. The main problems are seen to be either lack or abundance of information. Design knowledge in particular is found missing at plants. Support systems and automation should be enhanced with ways to explain plant knowledge to the plant staff. A framework is formulated for analysing explanations of plant knowledge. It consists of three parts: 1. a typology of explanation, organised by the class of knowledge (factual, functional, or strategic) and by the target of explanation (processes, automation, or support systems), 2. an identification of explanation tasks generic for the plant domain, and 3. an identification of essential model types for explanation (structural, behavioural, functional, and teleological). The tasks use the models to create the explanations of the given classes. Key mechanisms are discussed to implement the generic explanation tasks. Knowledge representations based on objects and their relations form a vocabulary to model and present plant knowledge. A particular class of models, means-end models, are used to explain plant knowledge. Explanations are generated through searches in the models. Hypertext is adopted to communicate explanations over dialogue based on context. The results are demonstrated in prototypes. The VICE prototype explains the reasoning of an expert system for diagnosis of rotating machines at power plants. The Justifier prototype explains design knowledge obtained from an object-oriented plant design tool. Enhanced access mechanisms into on-line documentation are

  2. A Rough Guide to Metabolite Identification Using High Resolution Liquid Chromatography Mass Spectrometry in Metabolomic Profiling in Metazoans

    Directory of Open Access Journals (Sweden)

    David G Watson

    2013-01-01

    Full Text Available Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.

  3. Taking Metabolomics to the Field: A Pilot Study in a Great Lakes Area of Concern (AOC)

    Science.gov (United States)

    Measurement of changes in endogenous metabolites via 1H-NMR-based metabolomics has shown great potential for assessing organisms exposed to environmental pollutants, and thus could aid the efforts of risk assessors. However, to date, the application of metabolomics to ecologi...

  4. Liquid Chromatography–Mass Spectrometry Based Metabolomics Study of Cloned versus Normal Pigs Fed Either Restricted or Ad Libitum High-Energy Diets

    DEFF Research Database (Denmark)

    Christensen, Kirstine Lykke; Hedemann, Mette Skou; Jørgensen, Henry; Stagsted, Jan; Knudsen, Knud Erik Bach

    2012-01-01

    manner (60% of ad libitum) for 6 months, and plasma was subjected to liquid chromatography–mass spectrometry nontargeted metabolomics and biochemical analyses. Low systemic levels of IGF-1 could indicate altered growth conditions and energy metabolism in cloned pigs. In response to ad libitum feeding...

  5. Controlling design bases inputs to plant modifications

    International Nuclear Information System (INIS)

    The concept of configuration management involves first establishing a baseline where plant design documents are consistent with well-defined design bases and where design documents represent actual plant configuration. From that baseline forward, the design change process assures consistency between design bases, design documents, and as-built configuration. Although the details of the design change procedures vary from utility to utility, that industry consensus is to use some form of design change document or package to effect the change. Although the Final Safety Analysis Reprot(FSAR) and plant technical specification bases are typically changed by the change process, most of the useful design bases information remains only in the archived change package or supporting calculations. This paper discusses several utility programs conceived to document and update their design bases and relates their finished product to improvements in the design modification process

  6. NMR-based metabolomics to determine acute inhalation effects of nano- and fine-sized ZnO particles in the rat lung.

    Science.gov (United States)

    Lee, Sheng-Han; Wang, Ting-Yi; Hong, Jia-Huei; Cheng, Tsun-Jen; Lin, Ching-Yu

    2016-09-01

    Zinc oxide (ZnO) particles induce acute occupational inhalation illness in humans and rats. However, the possible molecular mechanisms of ZnO particles on the respiratory system remain unclear. In this study, metabolic responses of the respiratory system of rats inhaled ZnO particles were investigated by a nuclear magnetic resonance (NMR)-based metabolomic approach. Male Sprague-Dawley rats were treated with a series of doses of nano-sized (35 nm) or fine-sized (250 nm) ZnO particles. The corresponding control groups inhaled filtered air. After 24 h, bronchoalveolar lavage fluid (BALF) and lung tissues were collected, extracted and prepared for (1)H and J-resolved NMR analysis, followed by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). PCA and PLSDA models from analysis of BALF and hydrophilic lung NMR spectra demonstrated that dose response trends were restricted to the 250 nm ZnO particle exposure group and were not observed in the 35 nm ZnO particle exposure group. Increased isoleucine and valine, as well as decreased acetate, trimethylamine n-oxide, taurine, glycine, formate, ascorbate and glycerophosphocholine, were recorded in the BALF of rats treated with moderate and high dose 250 nm ZnO exposures. Decreases in taurine and glucose, as well as an increase of phosphorylcholine-containing lipids and fatty acyl chains, were detected in the lung tissues from 250 nm ZnO-treated rats. These metabolic changes may be associated with cell anti-oxidation, energy metabolism, DNA damage and membrane stability. We also concluded that a metabolic approach provides more complete measurements and suggests potential molecular mechanisms of adverse effects. PMID:27245357

  7. A 1H NMR-based metabolomics approach to evaluate the geographical authenticity of herbal medicine and its application in building a model effectively assessing the mixing proportion of intentional admixtures: A case study of Panax ginseng: Metabolomics for the authenticity of herbal medicine.

    Science.gov (United States)

    Nguyen, Huy Truong; Lee, Dong-Kyu; Choi, Young-Geun; Min, Jung-Eun; Yoon, Sang Jun; Yu, Yun-Hyun; Lim, Johan; Lee, Jeongmi; Kwon, Sung Won; Park, Jeong Hill

    2016-05-30

    Ginseng, the root of Panax ginseng has long been the subject of adulteration, especially regarding its origins. Here, 60 ginseng samples from Korea and China initially displayed similar genetic makeup when investigated by DNA-based technique with 23 chloroplast intergenic space regions. Hence, (1)H NMR-based metabolomics with orthogonal projections on the latent structure-discrimination analysis (OPLS-DA) were applied and successfully distinguished between samples from two countries using seven primary metabolites as discrimination markers. Furthermore, to recreate adulteration in reality, 21 mixed samples of numerous Korea/China ratios were tested with the newly built OPLS-DA model. The results showed satisfactory separation according to the proportion of mixing. Finally, a procedure for assessing mixing proportion of intentionally blended samples that achieved good predictability (adjusted R(2)=0.8343) was constructed, thus verifying its promising application to quality control of herbal foods by pointing out the possible mixing ratio of falsified samples. PMID:26942336

  8. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    Hang Chu; Hui Sun; Guang-Li Yan; Ai-Hua Zhang; Chang Liu; Hui Dong; Xiang-Cai Meng; Xi-Jun Wang

    2015-01-01

    Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL) is an herbal fruit for one year living plant and has been developed into healthy function’s food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its anti-fatigue and antioxidant effects, a novel integrative metabolomics approach was applied. In this study, we present metabolomics analysis applying ultra performance liquid chromatography coupled to quadrupole with time-of-flight mass spectrometry (UPLC-Q/TOF-MS) to determine metabolite alterations after oral administration PPL to rats. Fifteen metabolites in urine were identified as potential biomarkers. Pattern analysis of the UPLC-Q/TOF-MS data disclosed that PPL could relieve fatigue rats by ameliorating the disturbance in amino acids metabolism and energy metabolism, alleviating the oxidative stress from reactive oxygen species and the inflammatory damage, and recovering the destructed regulation. Based on these results, we demonstrated that PPL is a promising source of natural anti-fatigue and antioxidants material for use in functional foods and medicines.

  9. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Hang Chu

    2015-07-01

    Full Text Available Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL is an herbal fruit for one year living plant and has been developed into healthy function's food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its anti-fatigue and antioxidant effects, a novel integrative metabolomics approach was applied. In this study, we present metabolomics analysis applying ultra performance liquid chromatography coupled to quadrupole with time-of-flight mass spectrometry (UPLC-Q/TOF-MS to determine metabolite alterations after oral administration PPL to rats. Fifteen metabolites in urine were identified as potential biomarkers. Pattern analysis of the UPLC-Q/TOF-MS data disclosed that PPL could relieve fatigue rats by ameliorating the disturbance in amino acids metabolism and energy metabolism, alleviating the oxidative stress from reactive oxygen species and the inflammatory damage, and recovering the destructed regulation. Based on these results, we demonstrated that PPL is a promising source of natural anti-fatigue and antioxidants material for use in functional foods and medicines.

  10. Lunar base agriculture: Soils for plant growth

    Science.gov (United States)

    Ming, Douglas W. (Editor); Henninger, Donald L. (Editor)

    1989-01-01

    This work provides information on research and experimentation concerning various aspects of food production in space and particularly on the moon. Options for human settlement of the moon and Mars and strategies for a lunar base are discussed. The lunar environment, including the mineralogical and chemical properties of lunar regolith are investigated and chemical and physical considerations for a lunar-derived soil are considered. It is noted that biological considerations for such a soil include controlled-environment crop production, both hydroponic and lunar regolith-based; microorganisms and the growth of higher plants in lunar-derived soils; and the role of microbes to condition lunar regolith for plant cultivation. Current research in the controlled ecological life support system (CELSS) project is presented in detail and future research areas, such as the growth of higher research plants in CELSS are considered. Optimum plant and microbiological considerations for lunar derived soils are examined.

  11. Model-Based Power Plant Master Control

    Energy Technology Data Exchange (ETDEWEB)

    Boman, Katarina; Thomas, Jean; Funkquist, Jonas

    2010-08-15

    The main goal of the project has been to evaluate the potential of a coordinated master control for a solid fuel power plant in terms of tracking capability, stability and robustness. The control strategy has been model-based predictive control (MPC) and the plant used in the case study has been the Vattenfall power plant Idbaecken in Nykoeping. A dynamic plant model based on nonlinear physical models was used to imitate the true plant in MATLAB/SIMULINK simulations. The basis for this model was already developed in previous Vattenfall internal projects, along with a simulation model of the existing control implementation with traditional PID controllers. The existing PID control is used as a reference performance, and it has been thoroughly studied and tuned in these previous Vattenfall internal projects. A turbine model was developed with characteristics based on the results of steady-state simulations of the plant using the software EBSILON. Using the derived model as a representative for the actual process, an MPC control strategy was developed using linearization and gain-scheduling. The control signal constraints (rate of change) and constraints on outputs were implemented to comply with plant constraints. After tuning the MPC control parameters, a number of simulation scenarios were performed to compare the MPC strategy with the existing PID control structure. The simulation scenarios also included cases highlighting the robustness properties of the MPC strategy. From the study, the main conclusions are: - The proposed Master MPC controller shows excellent set-point tracking performance even though the plant has strong interactions and non-linearity, and the controls and their rate of change are bounded. - The proposed Master MPC controller is robust, stable in the presence of disturbances and parameter variations. Even though the current study only considered a very small number of the possible disturbances and modelling errors, the considered cases are

  12. 基于核磁共振波谱的盐芥盐胁迫代谢组学分析%NMR spectroscopy based metabolomic analysis of Thellungiella salsuginea under salt stress

    Institute of Scientific and Technical Information of China (English)

    王新宇; 王丽华; 于萍; 李楠; 吴惠丰; 阎秀峰

    2012-01-01

    Soil salinity is a critical environmental problem that disrupts plant metabolic homeostasis and requires adjustment of metabolic pathways in plant cells, a process that is usually referred to as acclimation. Metabolomics technologies have made significant contributions to the study of plant stress biology through identification of different compounds, such as signaling molecules and metabolic by-products in response to stress conditions, as well as small molecules involved in the plant acclimation processes. Thellungiella salsuginea is a close relative of Arabidopsis thaliana. It has been proposed as an ideal model for studying molecular mechanisms of salinity tolerance in plants because of its ' extremophile' characteristics manifested by extreme tolerance to high salt conditions. To obtain a better understanding of the molecular mechanisms underlying the response of T. salsuginea to salt stress, an Nuclear Magnetic Resonance ( NMR) -based metabolic profiling approach was used to profile metabolite changes in T. salsuginea after treatment with 150 mmol/L or 300 mmol/L NaCl for 24 h. In general, metabolomic studies should be designed to detect as many metabolites as possible in an organism, and a solvent that can extract a diverse group of metabolites should be employed. In our experiments, metabolites were extracted from the leaf tissues using a solvent system of methanol/water (1/1 ) , known to extract many different metabolites. H-NMR spectroscopy of samples from control, 150 mmol/L and 300 mmol/L NaCl treatment was performed separately. Spectral data were analyzed and interpreted using multivariate statistical analyses. Overall, the original NMR spectra were dominated by one of the organic acids, malate (8 2. 38 and 2. 68) , which is a T. salsuginea metabolite to maintain the osmotic balance in the cells and was approx. 10-100 times higher than other metabolites found in the H-NMR spectra. Principal components analysis ( PCA) was used in this work for the

  13. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells. PMID:27074779

  14. Untargeted Metabolomics Reveals Predominant Alterations in Lipid Metabolism Following Light Exposure in Broccoli Sprouts

    OpenAIRE

    Mariateresa Maldini; Fausta Natella; Simona Baima; Giorgio Morelli; Cristina Scaccini; James Langridge; Giuseppe Astarita

    2015-01-01

    The consumption of vegetables belonging to the family Brassicaceae (e.g., broccoli and cauliflower) is linked to a reduced incidence of cancer and cardiovascular diseases. The molecular composition of such plants is strongly affected by growing conditions. Here we developed an unbiased metabolomics approach to investigate the effect of light and dark exposure on the metabolome of broccoli sprouts and we applied such an approach to provide a bird’s-eye view of the overall metabolic response af...

  15. Optimizing the plant-based diet.

    Science.gov (United States)

    Mann, J I

    2000-09-01

    Any attempt to optimize a plant-based diet necessitates an identification of the features of the diet which confer benefit as well as any which may be associated with detrimental effects. The former task is more difficult than might be assumed as there is no doubt that some of the apparent health benefits observed amongst vegetarians are a consequence of environmental determinants of health which characterize groups of people who choose vegetarian diets, rather than dietary practices. This review will consider the major health benefits of plant-based diets, the specific foods or nutrients which confer the benefits as far as can be ascertained from present knowledge, potential nutrient deficiencies associated with a plant-based diet and nutritional strategies that can be employed to prevent any such deficiencies. PMID:24398280

  16. NMR-Based Metabolomic Study on Isatis tinctoria: Comparison of Different Accessions, Harvesting Dates, and the Effect of Repeated Harvesting.

    Science.gov (United States)

    Guldbrandsen, Niels; Kostidis, Sarantos; Schäfer, Hartmut; De Mieri, Maria; Spraul, Manfred; Skaltsounis, Alexios-Leandros; Mikros, Emmanuel; Hamburger, Matthias

    2015-05-22

    Isatis tinctoria is an ancient dye and medicinal plant with potent anti-inflammatory and antiallergic properties. Metabolic differences were investigated by NMR spectroscopy of accessions from different origins that were grown under identical conditions on experimental plots. For these accessions, metabolite profiles at different harvesting dates were analyzed, and single and repeatedly harvested plants were compared. Leaf samples were shock-frozen in liquid N2 immediately after being harvested, freeze-dried, and cryomilled prior to extraction. Extracts were prepared by pressurized liquid extraction with ethyl acetate and 70% aqueous methanol. NMR spectra were analyzed using a combination of different methods of multivariate data analysis such as principal component analysis (PCA), canonical analysis (CA), and k-nearest neighbor concept (k-NN). Accessions and harvesting dates were well separated in the PCA/CA/k-NN analysis in both extracts. Pairwise statistical total correlation spectroscopy (STOCSY) revealed unsaturated fatty acids, porphyrins, carbohydrates, indole derivatives, isoprenoids, phenylpropanoids, and minor aromatic compounds as the cause of these differences. In addition, the metabolite profile was affected by the repeated harvest regime, causing a decrease of 1,5-anhydroglucitol, sucrose, unsaturated fatty acids, porphyrins, isoprenoids, and a flavonoid. PMID:25946005

  17. Hazard identification based on plant functional modelling

    International Nuclear Information System (INIS)

    A major objective of the present work is to provide means for representing a process plant as a socio-technical system, so as to allow hazard identification at a high level. The method includes technical, human and organisational aspects and is intended to be used for plant level hazard identification so as to identify critical areas and the need for further analysis using existing methods. The first part of the method is the preparation of a plant functional model where a set of plant functions link together hardware, software, operations, work organisation and other safety related aspects of the plant. The basic principle of the functional modelling is that any aspect of the plant can be represented by an object (in the sense that this term is used in computer science) based upon an Intent (or goal); associated with each Intent are Methods, by which the Intent is realized, and Constraints, which limit the Intent. The Methods and Constraints can themselves be treated as objects and decomposed into lower-level Intents (hence the procedure is known as functional decomposition) so giving rise to a hierarchical, object-oriented structure. The plant level hazard identification is carried out on the plant functional model using the Concept Hazard Analysis method. In this, the user will be supported by checklists and keywords and the analysis is structured by pre-defined worksheets. The preparation of the plant functional model and the performance of the hazard identification can be carried out manually or with computer support. (au) (4 tabs., 10 ills., 7 refs.)

  18. Plant-Based Vaccines: Production and Challenges

    Directory of Open Access Journals (Sweden)

    Erna Laere

    2016-01-01

    Full Text Available Plant-based vaccine technologies involve the integration of the desired genes encoding the antigen protein for specific disease into the genome of plant tissues by various methods. Agrobacterium-mediated gene transfer and transformation via genetically modified plant virus are the common methods that have been used to produce effective vaccines. Nevertheless, with the advancement of science and technology, new approaches have been developed to increase the efficiency of former methods such as biolistic, electroporation, agroinfiltration, sonication, and polyethylene glycol treatment. Even though plant-based vaccines provide many benefits to the vaccine industry, there are still challenges that limit the rate of successful production of these third-generation vaccines. Even with all the limitations, continuous efforts are still ongoing in order to produce efficient vaccine for many human and animals related diseases owing to its great potentials. This paper reviews the existing conventional methods as well as the development efforts by researchers in order to improve the production of plant-based vaccines. Several challenges encountered during and after the production process were also discussed.

  19. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review

    OpenAIRE

    Emwas, Abdul-Hamid; Luchinat, Claudio; Turano, Paola; Tenori, Leonardo; Roy, Raja; Salek, Reza M; Ryan, Danielle; Merzaban, Jasmeen S.; Kaddurah-Daouk, Rima; Zeri, Ana Carolina; Nagana Gowda, G. A.; Raftery, Daniel; Wang, Yulan; BRENNAN, Lorraine; Wishart, David S

    2014-01-01

    The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes...

  20. Transcriptome and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis.

    OpenAIRE

    Monika eBielecka; Mutsumi eWatanabe; Wolf Rüdiger Scheible; Rosa eMorcuende; Malcolm John Hawkesford; Holger eHesse; Rainer eHoefgen

    2015-01-01

    Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the...

  1. Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

    OpenAIRE

    Bielecka, Monika; Watanabe, Mutsumi; Morcuende, Rosa; Scheible, Wolf-Rüdiger; Hawkesford, Malcolm J.; Hesse, Holger; Hoefgen, Rainer

    2015-01-01

    Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the dis...

  2. Effect of a traditional Chinese medicine prescription Quzhuotongbi decoction on hyperuricemia model rats studied by using serum metabolomics based on gas chromatography-mass spectrometry.

    Science.gov (United States)

    Chen, Jiao; Zhou, Jia; Wei, Shuangshuang; Xie, Zhijun; Wen, Chengping; Xu, Guowang

    2016-07-15

    Morbidity of hyperuricemia has constantly increased in population in decades, and hyperuricemia has proved to be an important risk factor for gout, cardiovascular diseases and others. Many urate-lowering drugs have unfavorable side effects and drug interactions. Quzhuotongbi decoction (QZTBD) is an empirical traditional Chinese medicine prescription for clinical therapy of hyperuricemia without serious adverse effects. In the study, we investigated the effects of QZTBD on urate and other metabolites in the sera of hyperuricemia model rats. Hyperuricemia model was established by orally administering yeast extract paste, and allopurinol served as a positive control drug. Serum metabolomics was performed by using a gas chromatography-mass spectrometry (GC-MS) method. Student's t-test and the principal component analysis (PCA) were employed to find the metabolic perturbations in hyperuricemia model rats. The levels of urate, lactate, pyruvate and ornithine were significantly increased, and xanthine, glyconic acids (ribonate, galactonate), amino acids (aspartate, proline, glutamine, serine, pyroglutamate, glutamate) and glucose were down-regulated greatly in the model rats. It demonstrated that nucleotide metabolism, amino acid metabolism and glycolytic pathway were disturbed by yeast administration. An orthogonal signal correction-partial least-squares discriminant analysis (OSC-PLS DA) was performed to assess the effects of yeast administering and drug treatment. 11 significantly distinctive metabolites among four groups were defined according to the variable importance for project values (VIP>1) and univariate ANOVA (p value<0.05). As compared to the model rats, the serum uric acid levels were lowered markedly under the treatment of allopurinol or QZTBD. Aspartate and glutamine involved in purine metabolism, were raised to normal level as well. The different influences on xanthine, glutamate pyroglutamate and galactonate suggested there were different mechanisms of

  3. Licensed bases management for advanced nuclear plants

    International Nuclear Information System (INIS)

    Prospective Advanced Nuclear Plant (ANP) owners must have high confidence that the integrity of the licensed bases (LB) of a plant will be effectively maintained over its life cycle. Currently, licensing engineers use text retrieval systems, database managers, and checklists to access, update, and maintain vast and disparate licensing information libraries. This paper describes the demonstration of a ''twin-engine'' approach that integrates a program from the emerging class of concept searching tools with a modern Product Data Management System (PDMS) to enhance the management of LB information for an example ANP design. (author)

  4. Metabolomic elucidation of pork from different crossbreds

    DEFF Research Database (Denmark)

    Bertram, Hanne Christine S.; Straadt, Ida Krestine; Clausen, Morten Rahr;

    )-based metabolomics. Several metabolites including amino acids, organic acids and nucleotides were identified in the obtained proton NMR spectra. Breed-specific differences in the level of several metabolites including inosine, carnosine and lactate were found. Sensory analysis of the cooked pork was performed, and...... correlations between individual metabolites and sensory attributes were elucidated. A high content of carnosine in the meat was associated with a low value of many sensory attributes related to meat flavor/taste. Surprsingly, IMP and inosine were in general not correlated with sensory attributes related to...

  5. YMDB: the Yeast Metabolome Database.

    Science.gov (United States)

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  6. Quality classification of Spanish olive oils by untargeted gas chromatography coupled to hybrid quadrupole-time of flight mass spectrometry with atmospheric pressure chemical ionization and metabolomics-based statistical approach.

    Science.gov (United States)

    Sales, C; Cervera, M I; Gil, R; Portolés, T; Pitarch, E; Beltran, J

    2017-02-01

    The novel atmospheric pressure chemical ionization (APCI) source has been used in combination with gas chromatography (GC) coupled to hybrid quadrupole time-of-flight (QTOF) mass spectrometry (MS) for determination of volatile components of olive oil, enhancing its potential for classification of olive oil samples according to their quality using a metabolomics-based approach. The full-spectrum acquisition has allowed the detection of volatile organic compounds (VOCs) in olive oil samples, including Extra Virgin, Virgin and Lampante qualities. A dynamic headspace extraction with cartridge solvent elution was applied. The metabolomics strategy consisted of three different steps: a full mass spectral alignment of GC-MS data using MzMine 2.0, a multivariate analysis using Ez-Info and the creation of the statistical model with combinations of responses for molecular fragments. The model was finally validated using blind samples, obtaining an accuracy in oil classification of 70%, taking the official established method, "PANEL TEST", as reference. PMID:27596432

  7. Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries.

    Science.gov (United States)

    Hong, Young-Shick; Martinez, Agathe; Liger-Belair, Gérard; Jeandet, Philippe; Nuzillard, Jean-Marc; Cilindre, Clara

    2012-10-01

    Botrytis cinerea is a fungal plant pathogen of grape berries, leading to economic and quality losses in wine production. The global metabolite changes induced by B. cinerea infection in grape have not been established to date, even though B. cinerea infection is known to cause significant changes in chemicals or metabolites. In order to better understand metabolic mechanisms linked to the infection process and to identify the metabolites associated with B. cinerea infection, (1)H NMR spectroscopy was used in global metabolite profiling and multivariate statistical analysis of berries from healthy and botrytized bunches. Pattern recognition methods, such as principal component analysis, revealed clear metabolic discriminations between healthy and botrytized berries of botrytized bunches and healthy berries of healthy bunches. Significantly high levels of proline, glutamate, arginine, and alanine, which are accumulated upon plant stress, were found in healthy and botrytized berries of botrytized bunches. Moreover, largely degraded phenylpropanoids, flavonoid compounds, and sucrose together with markedly produced glycerol, gluconic acid, and succinate, all being directly associated with B. cinerea growth, were only found in botrytized berries of botrytized bunches. This study reports that B. cinerea infection causes significant metabolic changes in grape berry and highlights that both the metabolic perturbations associated with the plant defence system and those directly derived from fungal pathogen growth should be considered to better understand the interaction between metabolic variation and biotic pathogen stress in plants. PMID:22945941

  8. Alterations of the exo- and endometabolite profiles in breast cancer cell lines: A mass spectrometry-based metabolomics approach.

    Science.gov (United States)

    Willmann, Lucas; Schlimpert, Manuel; Hirschfeld, Marc; Erbes, Thalia; Neubauer, Hans; Stickeler, Elmar; Kammerer, Bernd

    2016-06-21

    In recent years, knowledge about metabolite changes which are characteristic for the physiologic state of cancer cells has been acquired by liquid chromatography coupled to mass spectrometry. Distinct molecularly characterized breast cancer cell lines provide an unbiased and standardized in vitro tumor model reflecting the heterogeneity of the disease. Tandem mass spectrometry is a widely applied analytical platform and highly sensitive technique for analysis of complex biological samples. Endo- and exometabolite analysis of the breast cancer cell lines MDA-MB-231, -453 and BT-474 as well as the breast epithelial cell line MCF-10A has been performed using two different analytical platforms: UPLC-ESI-Q-TOF based on a scheduled precursor list has been applied for highlighting of significant differences between cell lines and HPLC-ESI-QqQ using multiple reaction monitoring has been utilized for a targeted approach focusing on RNA metabolism and interconnected pathways, respectively. Statistical analysis enabled a clear discrimination of the breast epithelial from the breast cancer cell lines. As an effect of oxidative stress, a decreased GSH/GSSG ratio has been detected in breast cancer cell lines. The triple negative breast cancer cell line MDA-MB-231 showed an elevation in nicotinamide, 1-ribosyl-nicotinamide and NAD+ reflecting the increased energy demand in triple negative breast cancer, which has a more aggressive clinical course than other forms of breast cancer. Obtained distinct metabolite pattern could be correlated with distinct molecular characteristics of breast cancer cells. Results and methodology of this preliminary in vitro study could be transferred to in vivo studies with breast cancer patients. PMID:27188315

  9. Biomarkers in Transplantation-Proteomics and Metabolomics.

    Science.gov (United States)

    Christians, Uwe; Klawitter, Jelena; Klawitter, Jost

    2016-04-01

    Modern multianalyte "omics" technologies allow for the identification of molecular signatures that confer significantly more information than measurement of a single parameter as typically used in current medical diagnostics. Proteomics and metabolomics bioanalytical assays capture a large set of proteins and metabolites in body fluids, cells, or tissues and, complementing genomics, assess the phenome. Proteomics and metabolomics contribute to the development of novel predictive clinical biomarkers in transplantation in 2 ways: they can be used to generate a diagnostic fingerprint or they can be used to discover individual proteins and metabolites of diagnostic potential. Much fewer metabolomics than proteomics biomarker studies in transplant patients have been reported, and, in contrast to proteomics discovery studies, new lead metabolite markers have yet to emerge. Most clinical proteomics studies have been discovery studies. Several of these studies have assessed diagnostic sensitivity and specificity. Nevertheless, none of these newly discovered protein biomarkers have yet been implemented in clinical decision making in transplantation. The currently most advanced markers discovered in proteomics studies in transplant patients are the chemokines CXCL-9 and CXCL-10, which have successfully been validated in larger multicenter trials in kidney transplant patients. These chemokines can be measured using standard immunoassay platforms, which should facilitate clinical implementation. Based on the published evidence, it is reasonable to expect that these chemokine markers can help guiding and individualizing immunosuppressive regimens, may be able to predict acute and chronic T-cell-mediated and antibody-mediated rejection, and may be useful tools for risk stratification of kidney transplant patients. PMID:26418702

  10. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  11. Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Ishii Jun

    2011-01-01

    Full Text Available Abstract Background The development of novel yeast strains with increased tolerance toward inhibitors in lignocellulosic hydrolysates is highly desirable for the production of bio-ethanol. Weak organic acids such as acetic and formic acids are necessarily released during the pretreatment (i.e. solubilization and hydrolysis of lignocelluloses, which negatively affect microbial growth and ethanol production. However, since the mode of toxicity is complicated, genetic engineering strategies addressing yeast tolerance to weak organic acids have been rare. Thus, enhanced basic research is expected to identify target genes for improved weak acid tolerance. Results In this study, the effect of acetic acid on xylose fermentation was analyzed by examining metabolite profiles in a recombinant xylose-fermenting strain of Saccharomyces cerevisiae. Metabolome analysis revealed that metabolites involved in the non-oxidative pentose phosphate pathway (PPP [e.g. sedoheptulose-7-phosphate, ribulose-5-phosphate, ribose-5-phosphate and erythrose-4-phosphate] were significantly accumulated by the addition of acetate, indicating the possibility that acetic acid slows down the flux of the pathway. Accordingly, a gene encoding a PPP-related enzyme, transaldolase or transketolase, was overexpressed in the xylose-fermenting yeast, which successfully conferred increased ethanol productivity in the presence of acetic and formic acid. Conclusions Our metabolomic approach revealed one of the molecular events underlying the response to acetic acid and focuses attention on the non-oxidative PPP as a target for metabolic engineering. An important challenge for metabolic engineering is identification of gene targets that have material importance. This study has demonstrated that metabolomics is a powerful tool to develop rational strategies to confer tolerance to stress through genetic engineering.

  12. A metabolomics study delineating geographical location-associated primary metabolic changes in the leaves of growing tobacco plants by GC-MS and CE-MS.

    Science.gov (United States)

    Zhao, Yanni; Zhao, Jieyu; Zhao, Chunxia; Zhou, Huina; Li, Yanli; Zhang, Junjie; Li, Lili; Hu, Chunxiu; Li, Wenzheng; Peng, Xiaojun; Lu, Xin; Lin, Fucheng; Xu, Guowang

    2015-01-01

    Ecological conditions and developmental senescence significantly affect the physiological metabolism of plants, yet relatively little is known about the influence of geographical location on dynamic changes in plant leaves during growth. Pseudotargeted gas chromatography-selected ion monitoring-mass spectrometry and capillary electrophoresis-mass spectrometry were used to investigate a time course of the metabolic responses of tobacco leaves to geographical location. Principal component analysis revealed obvious metabolic discrimination between growing districts relative to cultivars. A complex carbon and nitrogen metabolic network was modulated by environmental factors during growth. When the Xuchang and Dali Districts in China were compared, the results indicated that higher rates of photosynthesis, photorespiration and respiration were utilized in Xuchang District to generate the energy and carbon skeletons needed for the biosynthesis of nitrogen-containing metabolites. The increased abundance of defense-associated metabolites generated from the shikimate-phenylpropanoid pathway in Xuchang relative to Dali was implicated in protection against stress. PMID:26549189

  13. Overexpression of ORCA3 and G10H in Catharanthus roseus Plants Regulated Alkaloid Biosynthesis and Metabolism Revealed by NMR-Metabolomics

    OpenAIRE

    Qifang Pan; Quan Wang; Fang Yuan; Shihai Xing; Jingya Zhao; Young Hae Choi; Robert Verpoorte; Yuesheng Tian; Guofeng Wang; Kexuan Tang

    2012-01-01

    In order to improve the production of the anticancer dimeric indole alkaloids in Catharanthuse roseus, much research has been dedicated to culturing cell lines, hairy roots, and efforts to elucidate the regulation of the monoterpenoid indole alkaloid (MIA) biosynthesis. In this study, the ORCA3 (Octadecanoid-derivative Responsive Catharanthus AP2-domain) gene alone or integrated with the G10H (geraniol 10-hydroxylase) gene were first introduced into C. roseus plants. Transgenic C. roseus plan...

  14. Metabolomic Approaches in Cancer Epidemiology

    Directory of Open Access Journals (Sweden)

    Mukesh Verma

    2015-08-01

    Full Text Available Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS and nuclear magnetic resonance spectroscopy (NMR that can measure hundreds of thousands of unique chemical entities (UCEs. The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other “omics” include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs. In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them.

  15. Plant-based Rasayana drugs from Ayurveda.

    Science.gov (United States)

    Balasubramani, Subramani Paranthaman; Venkatasubramanian, Padma; Kukkupuni, Subrahmanya Kumar; Patwardhan, Bhushan

    2011-02-01

    Rasayana tantra is one of the eight specialties of Ayurveda. It is a specialized practice in the form of rejuvenative recipes, dietary regimen, special health promoting behaviour and drugs. Properly administered Rasayana can bestow the human being with several benefits like longevity, memory, intelligence, freedom from diseases, youthful age, excellence of luster, complexion and voice, optimum strength of physique and sense organs, respectability and brilliance. Various types of plant based Rasayana recipes are mentioned in Ayurveda. Review of the current literature available on Rasayanas indicates that anti-oxidant and immunomodulation are the most studied activities of the Rasayana drugs. Querying in Pubmed database on Rasayanas reveals that single plants as well as poly herbal formulations have been researched on. This article reviews the basics of Rasayana therapy and the published research on different Rasayana drugs for specific health conditions. It also provides the possible directions for future research. PMID:21390573

  16. [Transgenics - Plant-Based Drugs (PBD)].

    Science.gov (United States)

    Rocha, Daniele Rachidi da; Marin, Victor Augustus

    2011-07-01

    Plant-Based Drugs - PBD - represent the 4(th) generation of genetically-modified plants and in this case the technology is used to develop and produce pharmaceuticals vaccines and/or products from transgenic seeds. This technology, like all scientific innovations, has inherent risks. However, the current knowledge available about the use of this technology means that no firm conclusions can be drawn about the nature of the risks involved, as well as their significance and the likelihood of causing serious damage or not. Risk analysis should be the starting premise prior to any implementation of techno-scientific innovations. The parameters must be evaluated and precautions taken and research must be conducted in a detailed and broad-ranging manner with respect to the potential risks of any innovation. This article analyzed the applicability of this new technology, as well as risk management and containment in order to guarantee safe use, handling and consumption by human beings. PMID:21808921

  17. Effect of storage time on metabolite profile and alpha-glucosidase inhibitory activity of Cosmos caudatus leaves – GCMS based metabolomics approach

    Directory of Open Access Journals (Sweden)

    Neda Javadi

    2015-09-01

    Full Text Available Cosmos caudatus, which is a commonly consumed vegetable in Malaysia, is locally known as “Ulam Raja”. It is a local Malaysian herb traditionally used as a food and medicinal herb to treat several maladies. Its bioactive or nutritional constituents consist of a wide range of metabolites, including glucosinolates, phenolics, amino acids, organic acids, and sugars. However, many of these metabolites are not stable and easily degraded or modified during storage. In order to investigate the metabolomics changes occurring during post-harvest storage, C. caudatus samples were subjected to seven different storage times (0 hours, 2 hours, 4 hours, 6 hours, 8 hours, 10 hours, and 12 hours at room temperature. As the model experiment, the metabolites identified by gas chromatography-mass spectrometry (GC-MS were correlated with α-glucosidase inhibitory activity analyzed with multivariate data analysis (MVDA to find out the variation among samples and metabolites contributing to the activity. Orthogonal partial least squares (OPLS analysis was applied to investigate the metabolomics changes. A profound chemical alteration, both in primary and secondary metabolites, was observed. The α-tocopherol, catechin, cyclohexen-1-carboxylic acid, benzoic acid, myo-inositol, stigmasterol, and lycopene compounds were found to be the discriminating metabolites at early storage; however, sugars such as sucrose, α-d-galactopyranose, and turanose were detected, which was attributed to the discriminating metabolites for late storage. The result shows that the MVDA method is a promising technique to identify biomarker compounds relative to storage at different times.

  18. Electroacupuncture at Acupoints Reverses Plasma Glutamate, Lipid, and LDL/VLDL in an Acute Migraine Rat Model: A1H NMR-Based Metabolomic Study

    Directory of Open Access Journals (Sweden)

    Zishan Gao

    2014-01-01

    Full Text Available Background. The objective of this study was to identify potential biomarkers of electroacupuncture (EA on relieving acute migraine through metabolomic study. Methods. EA treatments were performed on both acupoints and nonacupoints on the nitroglycerin (NTG-induced migraine rat model. NMR experiments and multivariate analysis were used for metabolomic analysis. Results. The number of head-scratching, the main ethology index of migraine rat model, was significantly increased P<0.01 after NTG injection. The plasma metabolic profile of model group was distinct from that of the control group. Glutamate was significantly increased P<0.01, whereas lipids were significantly decreased P<0.01 in model rats. After EA at acupoints, the metabolic profile of model rats was normalized, with decreased glutamate P<0.05 and increased lipids P<0.01. In contrast, EA at nonacupoints did not restore the metabolic profile, but with six metabolites significantly different from acupoints group. Interestingly, the number of head-scratching and glutamate level were significantly decreased P<0.05 after receiving EA at both acupoints and nonacupoints. Conclusions. EA at acupoints may relieve acute migraine by restoring the plasma metabolic profile and plasma glutamate, while EA at nonacupoints may modestly relieve acute migraine by decreasing plasma glutamate.

  19. Using NMR-Based Metabolomics to Evaluate Postprandial Urinary Responses Following Consumption of Minimally Processed Wheat Bran or Wheat Aleurone by Men and Women

    Directory of Open Access Journals (Sweden)

    Ramandeep Garg

    2016-02-01

    Full Text Available Wheat bran, and especially wheat aleurone fraction, are concentrated sources of a wide range of components which may contribute to the health benefits associated with higher consumption of whole-grain foods. This study used NMR metabolomics to evaluate urine samples from baseline at one and two hours postprandially, following the consumption of minimally processed bran, aleurone or control by 14 participants (7 Females; 7 Males in a randomized crossover trial. The methodology discriminated between the urinary responses of control, and bran and aleurone, but not between the two fractions. Compared to control, consumption of aleurone or bran led to significantly and substantially higher urinary concentrations of lactate, alanine, N-acetylaspartate acid and N-acetylaspartylglutamate and significantly and substantially lower urinary betaine concentrations at one and two hours postprandially. There were sex related differences in urinary metabolite profiles with generally higher hippurate and citrate and lower betaine in females compared to males. Overall, this postprandial study suggests that acute consumption of bran or aleurone is associated with a number of physiological effects that may impact on energy metabolism and which are consistent with longer term human and animal metabolomic studies that used whole-grain wheat diets or wheat fractions.

  20. Variable selection methods in PLS regression - a comparison study on metabolomics data

    DEFF Research Database (Denmark)

    Karaman, İbrahim; Hedemann, Mette Skou; Knudsen, Knud Erik Bach;

    integrated approach. Due to the high number of variables in data sets (both raw data and after peak picking) the selection of important variables in an explorative analysis is difficult, especially when different data sets of metabolomics data need to be related. Variable selection (or removal of irrelevant....... The aim of the metabolomics study was to investigate the metabolic profile in pigs fed various cereal fractions with special attention to the metabolism of lignans using LC-MS based metabolomic approach. References 1. Lê Cao KA, Rossouw D, Robert-Granié C, Besse P: A Sparse PLS for Variable Selection when......Partial least squares regression (PLSR) has been applied to various fields such as psychometrics, consumer science, econometrics and process control. Recently it has been applied to metabolomics based data sets (GC/LC-MS, NMR) and proven to be a very powerful in situations with many variables...

  1. Xenobiotics Produce Distinct Metabolomic Responses in Zebrafish Larvae (Danio rerio).

    Science.gov (United States)

    Huang, Susie S Y; Benskin, Jonathan P; Chandramouli, Bharat; Butler, Heather; Helbing, Caren C; Cosgrove, John R

    2016-06-21

    Sensitive and quantitative protocols for characterizing low-dose effects are needed to meet the demands of 21st century chemical hazard assessment. To test the hypothesis that xenobiotic exposure at environmentally relevant concentrations produces specific biochemical fingerprints in organisms, metabolomic perturbations in zebrafish (Danio rerio) embryo/larvae were measured following 24 h exposures to 13 individual chemicals covering a wide range of contaminant classes. Measured metabolites (208 in total) included amino acids, biogenic amines, fatty acids, bile acids, sugars, and lipids. The 96-120 h post-fertilization developmental stage was the most appropriate model for detecting xenobiotic-induced metabolomic perturbations. Metabolomic fingerprints were largely chemical- and dose-specific and were reproducible in multiple exposures over a 16-month period. Furthermore, chemical-specific responses were detected in the presence of an effluent matrix; importantly, in the absence of morphological response. In addition to improving sensitivity for detecting biological responses to low-level xenobiotic exposures, these data can aid the classification of novel contaminants based on the similarity of metabolomic responses to well-characterized "model" compounds. This approach is clearly of use for rapid, sensitive, and specific analyses of chemical effect on organisms, and can supplement existing methods, such as the Zebrafish Embryo Toxicity assay (OECD TG236), with molecular-level information. PMID:27232715

  2. Metabolomic approach for improving ethanol stress tolerance in Saccharomyces cerevisiae.

    Science.gov (United States)

    Ohta, Erika; Nakayama, Yasumune; Mukai, Yukio; Bamba, Takeshi; Fukusaki, Eiichiro

    2016-04-01

    The budding yeast Saccharomyces cerevisiae is widely used for brewing and ethanol production. The ethanol sensitivity of yeast cells is still a serious problem during ethanol fermentation, and a variety of genetic approaches (e.g., random mutant screening under selective pressure of ethanol) have been developed to improve ethanol tolerance. In this study, we developed a strategy for improving ethanol tolerance of yeast cells based on metabolomics as a high-resolution quantitative phenotypic analysis. We performed gas chromatography-mass spectrometry analysis to identify and quantify 36 compounds on 14 mutant strains including knockout strains for transcription factor and metabolic enzyme genes. A strong relation between metabolome of these mutants and their ethanol tolerance was observed. Data mining of the metabolomic analysis showed that several compounds (such as trehalose, valine, inositol and proline) contributed highly to ethanol tolerance. Our approach successfully detected well-known ethanol stress related metabolites such as trehalose and proline thus, to further prove our strategy, we focused on valine and inositol as the most promising target metabolites in our study. Our results show that simultaneous deletion of LEU4 and LEU9 (leading to accumulation of valine) or INM1 and INM2 (leading to reduction of inositol) significantly enhanced ethanol tolerance. This study shows the potential of the metabolomic approach to identify target genes for strain improvement of S. cerevisiae with higher ethanol tolerance. PMID:26344121

  3. Error Propagation Analysis for Quantitative Intracellular Metabolomics

    Directory of Open Access Journals (Sweden)

    Jana Tillack

    2012-11-01

    Full Text Available Model-based analyses have become an integral part of modern metabolic engineering and systems biology in order to gain knowledge about complex and not directly observable cellular processes. For quantitative analyses, not only experimental data, but also measurement errors, play a crucial role. The total measurement error of any analytical protocol is the result of an accumulation of single errors introduced by several processing steps. Here, we present a framework for the quantification of intracellular metabolites, including error propagation during metabolome sample processing. Focusing on one specific protocol, we comprehensively investigate all currently known and accessible factors that ultimately impact the accuracy of intracellular metabolite concentration data. All intermediate steps are modeled, and their uncertainty with respect to the final concentration data is rigorously quantified. Finally, on the basis of a comprehensive metabolome dataset of Corynebacterium glutamicum, an integrated error propagation analysis for all parts of the model is conducted, and the most critical steps for intracellular metabolite quantification are detected.

  4. Risk-based plant performance indicators

    International Nuclear Information System (INIS)

    Tasked by the 1979 President's Commission on the Accident at Three Mile Island, the U.S. nuclear power industry has put into place a performance indicator program as one means for showing a demonstrable record of achievement. Largely through the efforts of the Institute of Nuclear Power Operations (INPO), plant performance data has, since 1983, been collected and analyzed to aid utility management in measuring their plants' performance progress. The U.S. Nuclear Regulatory Commission (NRC) has also developed a set of performance indicators. This program, conducted by NRC's Office for the Analysis and Evaluation of Operational Data (AEOD), is structured to present information on plant operational performance in a manner that could enhance the staff's ability to recognize changes in the safety performance. Both organizations recognized that performance indicators have limitations and could be subject to misinterpretation and misuse with the potential for an adverse impact on safety. This paper reports on performance indicators presently in use, e.g., unplanned automatic scrams, unplanned safety system actuation, safety system failures, etc., which are logically related to safety. But, a reliability/risk-based method for evaluating either individual indicators or an aggregated set of indicators is not yet available

  5. A Market-Based Virtual Power Plant

    DEFF Research Database (Denmark)

    You, Shi; Træholt, Chresten; Poulsen, Bjarne

    2009-01-01

    The fast growing penetration of Distributed Energy Resources (DER) and the continuing trend towards a more liberalized electricity market requires more efficient energy management strategies to handle both emerging technical and economic issues. In this paper, a market-based Virtual Power Plant...... (MBVPP) model is proposed which provides individual DER units the accesses to current electricity markets. General bidding scenario and price signal scenario as two optional operation scenarios are operated by one MBVPP. In the end, a use case of a MBVPP with micro Combined Heat and Power (μCHP) systems...... demonstrates the potential benefits and operation scenarios of the MBVPP model....

  6. Metabolomic variation of brassica rapa var. rapa (var. raapstelen) and raphanus sativus l. at different developmental stages

    International Nuclear Information System (INIS)

    Brassica rapa (var. raapstelen) and Raphanus sativus (red radish) are being used as food and fodder while also known as model in recent plant research due to the diversity of metabolites as well as genetic resemblance to Arabidopsis. This study explains the change in metabolites (amino acids, organic acids, chlorophyll, carotenoids, tocopherols, ascorbic acid, sucrose, phenylpropanoids and glucosinolates) during plant development. In present study the metabolomic variation in relation to plant growth has been evaluated, for Brassica rapa (var. raapstelen) and red radish (Raphanus sativus) at three different developmental stages. A non-targeted and targeted metabolomic approach by NMR and HPLC in combination with Principal component analysis (PCA) of the data was used to identify phytochemicals being influenced by plant growth. The results lead to the better understanding of metabolic changes during plant development and show the importance of plant age with respect to the metabolomic profile of vegetables. (author)

  7. Biomarker Identification and Pathway Analysis by Serum Metabolomics of Lung Cancer

    OpenAIRE

    2015-01-01

    Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top...

  8. Metabolomics reveals positive acceleration(+Gz)-induced metabolic perturbations and the protective effect of Ginkgo biloba extract in a rat model based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Yang, Zhihui; Zhao, Andong; Li, Zhongdong; Ge, Hua; Li, Tonghua; Zhang, Fucheng; Zhan, Hao; Wang, Jianchang

    2016-06-01

    Positive acceleration (+Gz) in the head-to-foot direction generated by modern high-performance fighter jets during flight maneuvers is characterized by high G values and a rapid rate of acceleration, and is often long in duration and a repeated occurrence. The acceleration overload far exceeds the pilot's physiological tolerance limits and causes considerable strain on several organ systems. Despite the importance of monitoring pathophysiological alterations related to +Gz exposure, we lack a complete explanation of the pathophysiology of +Gz exposure. Ginkgo biloba extract (GBE) is a classic traditional Chinese medicine (TCM) that might exert a protective effect against +Gz exposure. However, its mechanism remains unclear. Here, a metabolomics approach based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOFMS) was used to characterize +Gz-induced metabolic fluctuations in a rat model and to evaluate the protective effect of GBE. Using partial least-squares discriminant analysis for the classification and selection of biomarkers, eighteen serum metabolites related to +Gz exposure were identified, and were found to primarily involve the fatty acid β-oxidation pathway, glycerophospholipid metabolism, phospholipid metabolism, bile acid metabolism, purine metabolism and lysine metabolism. Taking these potential biomarkers as screening indexes, we found that GBE could reverse the pathological process of +Gz exposure by partially regulating the perturbed fatty acid β-oxidation pathway, glycerophospholipid metabolism, purine metabolism and lysine metabolism. This indicates that UHPLC-Q-TOFMS-based metabolomics provides a powerful tool to reveal serum metabolic fluctuations in response to +Gz exposure and to study the mechanism underlying TCM. PMID:27010354

  9. Metabolomic Analysis of Diapausing and Noni-diapausing Larvae of the European Corn Borer Ostrinia nubilalis (Hbn.) (Lepidoptera: Crambidae).

    Science.gov (United States)

    Purać, Jelena; Kojić, Danijela; Popović, Željko D; Vukašinović, Elvira; Tiziani, Stefano; Günther, Ulrich L; Grubor-Lajšić, Gordana

    2015-01-01

    In this study, an (1)H-NMR -based metabolomic approach was used to investigate the biochemical mechanisms of diapause and cold hardiness in diapausing larvae of the European corn borer Ostrinia nubilalis. Metabolomic patterns in polar hemolymph extracts from non-diapausing and diapausing larvae of O. nubilalis were compared. Analysis indicated 13 metabolites: 7 amino acids, glycerol, acetate, citrate, succinate, lactate and putrescine. Results show that diapausing larvae display different metabolomic patterns compared to active non-diapausing larvae, with predominant metabolites identified as glycerol, proline and alanine. In specific diapausing larvae initially kept at 5 °C then gradually chilled to –3 °C and –16 °C, alanine , glycerol and acetate were predominant metabolites. (1)H-NMR spectroscopy provides new insight into the metabolomic patterns associated with cold resistance and diapause in O. nubilalis larvae, suggesting distinct metabolomes function in actively developing and diapausing larvae. PMID:26680702

  10. The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research.

    Science.gov (United States)

    Emwas, Abdul-Hamid M

    2015-01-01

    Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have evolved as the most common techniques in metabolomics studies, and each brings its own advantages and limitations. Unlike MS spectrometry, NMR spectroscopy is quantitative and does not require extra steps for sample preparation, such as separation or derivatization. Although the sensitivity of NMR spectroscopy has increased enormously and improvements continue to emerge steadily, this remains a weak point for NMR compared with MS. MS-based metabolomics provides an excellent approach that can offer a combined sensitivity and selectivity platform for metabolomics research. Moreover, different MS approaches such as different ionization techniques and mass analyzer technology can be used in order to increase the number of metabolites that can be detected. In this chapter, the advantages, limitations, strengths, and weaknesses of NMR and MS as tools applicable to metabolomics research are highlighted. PMID:25677154

  11. GC-TOF/MS-based metabolomic strategy for combined toxicity effects of deoxynivalenol and zearalenone on murine macrophage ANA-1 cells.

    Science.gov (United States)

    Ji, Jian; Zhu, Pei; Pi, Fuwei; Sun, Chao; Jiang, Hui; Sun, Jiadi; Wang, Xiumei; Zhang, Yinzhi; Sun, Xiulan

    2016-09-15

    The actual health risk from exposure to combined mycotoxins is unknown, and few studies have focused on changes to cellular biological systems (e.g., metabolomics) caused by combined mycotoxic effects. To evaluate the combined mycotoxic effects of deoxynivalenol (DON) and zearalenone (ZEN) on the level of cellular biological systems, gas chromatographic, time-of-flight mass spectroscopy (GC-TOF/MS) of the complete murine macrophage ANA-1 cell metabolome was implemented in this study. Using optimized chromatography and mass spectrometry parameters, the metabolites detected by GC-TOF/MS were identified and processed using multivariate statistical analysis, including principal component analysis (PCA) and orthogonal projection on latent-structures discriminant analysis (OPLS-DA). The metabolite sets were screened for further pathway analysis under rules of t-test (P) value  1, and similarity value > 500. The mainly interfered metabolism pathways were categorized into two dominant types: amino acid metabolism and glycometabolism. Four metabolites, palmitic acid, 1-monopalmitin, ribose-5-phosphate and 2-deoxy-D-galactose, occur only under combined "DON + ZEN" treatment, indicating abnormal metabolism in ANA-1 cells. The metabolic state of ANA-1 cells under induction by combined "DON + ZEN" illustrates that DON may inhibit the estrogenic effects of ZEN. Thus, the combined effect of "DON + ZEN" may exacerbate toxicity in the pentose phosphate pathway, while palmitic acid metabolism is likely a new pathway effected by the combination, "DON + ZEN." PMID:27530666

  12. Visualization of Multivariate Metabolomic Data

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jun; CAO Bei; ZHENG Tian; LIU Lin-sheng; GUO Sheng; DUAN Jin-ao; AA Ji-ye; WANG Guang-ji; ZHANG Feng-yi; GU Rong-rong; WANG Xin-wen; ZHAO Chun-yan; LI Meng-jie; SHI Jian

    2011-01-01

    Objective Although principal components analysis profiles greatly facilitate the visualization and interpretation of the multivariate data,the quantitative concepts in both scores plot and loading plot are rather obscure.This article introduced three profiles that assisted the better understanding of metabolomic data.Methods The discriminatory profile,heat map,and statistic profile were developed to visualize the multivariate data obtained from high-throughput GC-TOF-MS analysis.Results The discriminatory profile and heat map obviously showed the discriminatory metabolites between the two groups,while the statistic profile showed the potential markers of statistic significance.Conclusion The three types of profiles greatly facilitate our understanding of the metabolomic data and the identification of the potential markers.

  13. Metabolomics investigation of whey intake

    DEFF Research Database (Denmark)

    Stanstrup, Jan

    interest since it has been shown that it is possible to achieve greater weight loss on a high protein diet as oppose to a high carbohydrate diet. Furthermore, it has been demonstrated that specifically milk-derived whey proteins have certain biological properties that might be beneficial in the treatment...... and prevention of the metabolic syndrome related to obesity and diabetes. In this thesis the effects of whey intake on the human metabolome was investigated using a metabolomics approach. We demonstrated that intake of whey causes a decreased rate of gastric emptying compared to other protein sources....... This is in contrast to previous findings suggesting that whey is cleared faster than other proteins. Paradoxically, we also find disproportionately elevated levels of some amino acids (AAs) following the whey meal. This suggests that whey affects absorption of AAs in a way independent from, or at least...

  14. Evaluation of extracts of Piper sarmentosum for accelerated stability by metabolomic fingerprint profiling

    Directory of Open Access Journals (Sweden)

    K Hussain

    2009-01-01

    Full Text Available Unlike pharmaceuticals, precise stability assessment of herbal products is challenging because of their complex nature. A new trend in natural products is that the extract is considered active as a whole whether active constituents are known or not. Hence, the stability of all the constituents must be taken into account, which is possible by analyzing metabolomic fingerprint profiles. Therefore, present study aimed to evaluate ethanol extracts of fruit of Piper sarmentosum, an important medicinal plant, for accelerated stability using metabolomic fingerprint profiling. The extract was exposed to three storage conditions of different temperature and humidity and analyzed at 0, 1, 2, 4 and 6 months by Fourier transform infrared (FTIR spectroscopy and high performance thin layer chromatography (HPTLC to get metabolomic fingerprints. FTIR fingerprints in combination with chemometrics indicated the changes in metabolomics, stirring with the passage of time at all storage conditions. Visual inspection of HPTLC densitograms revealed metabolomic changes in the extracts stored for 6 months at 60 °C and 85% relative humidity. The results of the study indicate that the products made from this plant ought to be stored at room temperature, below 30 °C and 45% relative humidity, and excessive heating must be avoided during manufacturing process. Moreover, the method may be used by natural product industry as a tool of identification, classification and discrimination (ICD.

  15. Metabolomics in the Rhizosphere

    NARCIS (Netherlands)

    Dam, van Nicole M.; Bouwmeester, Harro J.

    2016-01-01

    The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground ins

  16. The next wave in metabolome analysis

    DEFF Research Database (Denmark)

    Nielsen, Jens; Oliver, S.

    2005-01-01

    The metabolome of a cell represents the amplification and integration of signals from other functional genomic levels, such as the transcriptome and the proteome. Although this makes metabolomics a useful tool for the high-throughput analysis of phenotypes, the lack of a direct connection to the ...

  17. MetaboLights: An Open-Access Database Repository for Metabolomics Data.

    Science.gov (United States)

    Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

    2016-01-01

    MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. © 2016 by John Wiley & Sons, Inc. PMID:27010336

  18. NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review

    International Nuclear Information System (INIS)

    Highlights: ► Procedures for acquisition of different biofluids by NMR. ► Recent developments in metabolic profiling of different biofluids by NMR are presented. ► The crucial steps involved in data preprocessing and multivariate chemometric analysis are reviewed. ► Emphasis is given on recent findings on Multiple Sclerosis via NMR and pattern recognition methods. - Abstract: Metabolomics is the discipline where endogenous and exogenous metabolites are assessed, identified and quantified in different biological samples. Metabolites are crucial components of biological system and highly informative about its functional state, due to their closeness to functional endpoints and to the organism's phenotypes. Nuclear Magnetic Resonance (NMR) spectroscopy, next to Mass Spectrometry (MS), is one of the main metabolomics analytical platforms. The technological developments in the field of NMR spectroscopy have enabled the identification and quantitative measurement of the many metabolites in a single sample of biofluids in a non-targeted and non-destructive manner. Combination of NMR spectra of biofluids and pattern recognition methods has driven forward the application of metabolomics in the field of biomarker discovery. The importance of metabolomics in diagnostics, e.g. in identifying biomarkers or defining pathological status, has been growing exponentially as evidenced by the number of published papers. In this review, we describe the developments in data acquisition and multivariate analysis of NMR-based metabolomics data, with particular emphasis on the metabolomics of Cerebrospinal Fluid (CSF) and biomarker discovery in Multiple Sclerosis (MScl).

  19. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

    Directory of Open Access Journals (Sweden)

    Cseke Leland J

    2011-05-01

    Full Text Available Abstract Background Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. Results We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. Conclusions The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

  20. Metabolomic phenotyping of af cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou;

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and...... possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal...... outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n...

  1. Gas Chromatography/Mass Spectrometry-Based Metabolomic Profiling Reveals Alterations in Mouse Plasma and Liver in Response to Fava Beans

    Science.gov (United States)

    Zhong, Guobing; Yan, Dongjing; Zeng, Huazong; Cai, Wangwei

    2016-01-01

    Favism is a life-threatening hemolytic anemia resulting from the intake of fava beans by susceptible individuals with low erythrocytic glucose 6-phosphate dehydrogenase (G6PD) activity. However, little is known about the metabolomic changes in plasma and liver after the intake of fava beans in G6PD normal and deficient states. In this study, gas chromatography/mass spectrometry was used to analyze the plasma and liver metabolic alterations underlying the effects of fava beans in C3H- and G6PD-deficient (G6PDx) mice, and to find potential biomarkers and metabolic changes associated with favism. Our results showed that fava beans induced oxidative stress in both C3H and G6PDx mice. Significantly, metabolomic differences were observed in plasma and liver between the control and fava bean treated groups of both C3H and G6PDx mice. The levels of 7 and 21 metabolites in plasma showed significant differences between C3H-control (C3H-C)- and C3H fava beans-treated (C3H-FB) mice, and G6PDx-control (G6PDx-C)- and G6PDx fava beans-treated (G6PDx-FB) mice, respectively. Similarly, the levels of 7 and 25 metabolites in the liver showed significant differences between C3H and C3H-FB, and G6PDx and G6PDx-FB, respectively. The levels of oleic acid, linoleic acid, and creatinine were significantly increased in the plasma of both C3H-FB and G6PDx-FB mice. In the liver, more metabolic alterations were observed in G6PDx-FB mice than in C3H-FB mice, and were involved in a sugar, fatty acids, amino acids, cholesterol biosynthesis, the urea cycle, and the nucleotide metabolic pathway. These findings suggest that oleic acid, linoleic acid, and creatinine may be potential biomarkers of the response to fava beans in C3H and G6PDx mice and therefore that oleic acid and linoleic acid may be involved in oxidative stress induced by fava beans. This study demonstrates that G6PD activity in mice can affect their metabolic pathways in response to fava beans. PMID:26981882

  2. Global GPP based on Plant Functional Types

    Science.gov (United States)

    Veroustraete, Frank; Balzarolo, Manuela

    2016-04-01

    Vegetation variables like Gross Primary productivity (GPP) and the Normalized Difference Vegetation Index (NDVI) are key variables in vegetation carbon exchange studies. Field measurements of the NDVI are time consuming due to landscape heterogeneity across time. Typically a sampling protocol adopted during field campaigns is based on the VALERI protocol in that case toe estimate LAI. Field campaign GPP or NDVI measurements can be scaled up to using in-situ FLUXNET radiation raster maps. Regression analysis can then be applied to construct transfer functions for the determination of GPP raster maps raster imagery from Normalized Difference Vegetation Index (NDVI) raster maps derived from in-situ FLUXNET radiation raster maps. Subsequently, in the VALERI approach the scaling up of raster maps is performed by aggregation of high resolution in-situ FLUXNET radiation raster maps data into high resolution raster maps and subsequently aggregating these to 1x1 km MODIS NDVI raster maps by calculating average NDVI values for the low resolution data. The up-scaled 1x1 km pixels are then used to validate the MODIS GPP and NVI products. Hence up scaling based on in-situ FLUXNET radiation measurements are not a luxury for large and heterogeneous sites. Therefore this paper tackles the problem of up scaling using in-situ FLUXNET radiation measurements. Key Words: FLUXNET, GPP, Plant Functional Types, Up-scaling

  3. Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

    OpenAIRE

    Vanessa Aguiar-Pulido; Wenrui Huang; Victoria Suarez-Ulloa; Trevor Cickovski; Kalai Mathee; Giri Narasimhan

    2016-01-01

    Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living organisms. Changes in the microbiome can impact the health of the environmental niche in which they reside. In order to learn more about these communities, different approaches based on data from multiple omics have been pursued. Metagenomics produces a taxonomical profile of the sample, metatranscriptomics helps us to obtain a functional profile, and metabolomics completes the picture by determining which...

  4. Mass spectrometry for high-throughput metabolomics analysis of urine

    OpenAIRE

    Abdelrazig, Salah M.A.

    2015-01-01

    Direct electrospray ionisation-mass spectrometry (direct ESI-MS), by omitting the chromatographic step, has great potential for application as a high-throughput approach for untargeted urine metabolomics analysis compared to liquid chromatography-mass spectrometry (LC-MS). The rapid development and technical innovations revealed in the field of ambient ionisation MS such as nanoelectrospray ionisation (nanoESI) chip-based infusion and liquid extraction surface analysis mass spectrometry (LESA...

  5. Metabolomic analysis of bronchoalveolar lavage fluid from cystic fibrosis patients

    OpenAIRE

    Wolak, Justyna E.; Esther, Charles R.; O’Connell, Thomas M.

    2009-01-01

    Metabolite profiles of bronchoalveolar lavage fluid (BALF) from pediatric patients with cystic fibrosis (CF) were correlated to the degree of airway inflammation using nuclear magnetic resonance spectroscopy-based metabolomics. BALF was collected from 11 children with CF during clinically indicated bronchoscopy. The spectra from BALF with high levels of neutrophilic airway inflammation displayed signals from numerous metabolites, whereas the spectra from subjects with low levels of inflammati...

  6. Biomarkers of Whale Shark Health: A Metabolomic Approach

    OpenAIRE

    Alistair D M Dove; Johannes Leisen; Manshui Zhou; Byrne, Jonathan J; Krista Lim-Hing; Webb, Harry D.; Leslie Gelbaum; Viant, Mark R.; Julia Kubanek; Facundo M Fernández

    2012-01-01

    In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus) from an aquarium collection was explored using (1)H nuclear magnetic resonance (NMR) spectroscopy and direct analysis in real time (DART) mass spectrometry (MS). Principal components analysis (PCA) of spectral data showed that individual animals could be resolved based on the meta...

  7. Diurnal effects of anoxia on the metabolome of the seagrass Zostera marina

    DEFF Research Database (Denmark)

    Hasler-Sheetal, Harald; Holmer, Marianne; Weckwerth, Wolfram;

    2014-01-01

    Environmental metabolomics has become interesting in marine ecological studies. One example is the revealing of new insights in stress response of Zostera marina. This is essential to understand how, at which level and to what extend aquatic plants adapt, tolerate and react to environmental stres...

  8. Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

    DEFF Research Database (Denmark)

    Joseph, Bindu; Corwin, Jason A.; Li, Baohua;

    2013-01-01

    affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a...... central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in...... metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation....

  9. Image-Based Modeling of Plants and Trees

    CERN Document Server

    Kang, Sing Bang

    2009-01-01

    Plants and trees are among the most complex natural objects. Much work has been done attempting to model them, with varying degrees of success. In this book, we review the various approaches in computer graphics, which we categorize as rule-based, image-based, and sketch-based methods. We describe our approaches for modeling plants and trees using images. Image-based approaches have the distinct advantage that the resulting model inherits the realistic shape and complexity of a real plant or tree. We use different techniques for modeling plants (with relatively large leaves) and trees (with re

  10. Proteomics and Metabolomics of Arabidopsis Responses to Perturbation of Glucosinolate Biosynthesis

    Institute of Scientific and Technical Information of China (English)

    Ya-zhou Chen; Qiu-Ying Pang; Yan He; Ning Zhu; Isabel Branstrom; Xiu-Feng Yan; Sixue Chen

    2012-01-01

    To understand plant molecular networks of glucosinolate metabolism,perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis.Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches.Proteins involved in metabolism including photosynthesis and hormone metabolism,protein binding,energy,stress,and defense showed marked responses to glucosinolate perturbation.In parallel,metabolomics revealed major changes in the levels of amino acids,carbohydrates,peptides,and hormones.The metabolomics data were correlated with the proteomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate metabolism.This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.

  11. Ultrahigh-Performance Liquid Chromatography-High-Resolution Quadrupole Time-of-Flight Mass Spectrometry Based Metabolomics Reveals Key Differences between Brachiaria decumbens and B. brizantha, Two Similar Pastures with Different Toxicities.

    Science.gov (United States)

    Pérez, Andy J; Hussain, Syeda M; Pecio, Łukasz; Kowalczyk, Mariusz; Herling, Valdo R; Stochmal, Anna

    2016-06-01

    Several species of Brachiaria (Poaceae) currently cover extensive grazing areas in Brazil, providing valuable source of feed for a large cattle population. However, numerous cases of toxicity outbreaks in livestock have raised concerns on safety of using these plants, especially B. decumbens. In this study, chemometric analysis of ultrahigh-performance liquid chromatography-high-resolution quadrupole time-of-flight mass spectrometry (UHPLC-HR-QTOF-MS) data has for the first time uncovered qualitative and quantitative differences between metabolomes of toxic B. decumbens and nontoxic B. brizantha. The steroidal saponin protoneodioscin was established as the main biomarker for B. decumbens when compared to B. brizantha, and therefore the key explanation for their phytochemical differentiation. Quantification of protodioscin in both plants showed no significant differences; consequently, the idea that this compound is solely responsible for toxicity outbreaks must be discarded. Instead, we propose that the added occurrence of its stereoisomer, protoneodioscin, in B. decumbens, can be considered as the probable cause of these events. Interestingly, the greatest concentrations of saponins for both species were reached during winter (B. decumbens = 53.6 ± 5.1 mg·g(-1) dry weight (D.W.); B. brizantha = 25.0 ± 1.9 mg·g(-1) D.W.) and spring (B. decumbens = 49.4 ± 5.0 mg·g(-1) D.W.; B. brizantha = 27.9 ± 1.4 mg·g(-1) D.W.), although in the case of B. decumbens these values do not vary significantly among seasons. PMID:27192362

  12. Fast Visual Modeling for Plant Based on Real Images

    Institute of Scientific and Technical Information of China (English)

    LI Yun-feng; ZHU Qing-sheng; CAO Yu-kun; LIU Yin-bin; HE Xi-ping

    2004-01-01

    Structures of natural plants are complex and difficult to model. This paper proposes a fast visual modeling for plants based on a small set of images, and establishes a reasonable plant model.Based on knowledge about growth patterns of the plant, image segmentation and 3D reconstruction are first performed to construct the plant skeleton (trunk and major branches), from which the remainder of the plant grows. Then the system produces the realistic plant model images based on image synthesis and validation. It is unnecessary to acquire the complex structure (such as the complex production rules of L-systems). The method provides a high degree of control over the final shape by image validation,resulting in realistic reconstruction.

  13. Fast Construction of Plant Architectural Models Based on Substructure Decomposition

    Institute of Scientific and Technical Information of China (English)

    YAN HongPing (严红平); Philippe de Reffye; PAN ChunHong (潘春洪); HU BaoGang (胡包钢)

    2003-01-01

    Plant structure, representing the physical link among different organs, includes many similar substructures. In this paper, a new method is presented to construct plant architectural models of most plant species. The plant structure is decomposed into a stem, a set of lateral substructures and a terminal substructure, which is called substructure decomposition; then based on substructure decomposition, the plant structures are expressed in an iterative way; and further the derivative formula is employed to compute the number of organs in plant structures to get the geometrical sizes of 3D plant organs by borrowing Hydraulic Model. Using 3D organs, a substructure library is built. Based on the substructures stored in substructure library, one can construct 3D plant structure according to certain topological and geometrical rules. The experiments with different plant species are included in this paper to demonstrate the validity of the new method for constructing plant structures. The experimental results show that the approach follows botanical knowledge with high efficiency in constructing plant structures of most plant species. In addition,this method enables users to check the detail information of plant structure.

  14. Use of Rhizosphere Metabolomics to Investigate Exudation of Phenolics by Arabidopsis Roots

    Science.gov (United States)

    Lee, Yong Jian; Rai, Amit; Reuben, Sheela; Nesati, Victor; Almeida, Reinaldo; Swarup, Sanjay

    2013-04-01

    and anthocyanin metabolites. We describe here the metabolites present in the root exudates using high resolution accurate mass (HRAM) metabolomics approach. Using this approach, biased rhizosphere for another class of PGPR strains can now be created. In this case, lignin- and anthocyanin- utilizing strains will be selectively preferred. We have set up a platform to perform metabolomics of exudates at the root surface. This has allowed us to use the liquid extraction surface analysis (LESA) system using a Thermo Velos Pro Orbitrap-MS to identify differences in exudate profiles along the root system of Arabidopsis. This platform enables direct sampling and measurement from plant roots grown aeroponically. As the metabolites are extracted from root surface and directly injected into the mass spectrometer, there is minimal loss of sample in this process. This method will now allow us to further dissect rhizosphere properties from places such as young root apex, as well as from the more mature base of roots. Taken together, these resources of altered rhizosphere, nutrient utilization pathways in microbes and surface analysis technology will help in extending our understanding of the processes in the plant rhizosphere.

  15. Development of uniformly stable isotope labeling system in higher plants for hetero-nuclear NMR experiments in vitro and in vivo

    International Nuclear Information System (INIS)

    Full text: Novel methods for measurement of living systems are making new breakthroughs in life science. In the era of the metabolome (analysis of all measurable metabolites), a MS-based approach is considered to be the major technology, whereas a NMR-based method is recognized as minor technology due to its low sensitivity. Therefore, my laboratory is currently focusing to develop novel methodologies for an NMR-based metabolomics. This will be achieved by uniform stable isotope labeling of higher plants allowing application of multi-dimensional NMR experiments used in protein structure determination. Using these novel methods, I will analyze the dynamic molecular networks inside tissues. Especially, use of stable isotope labeling methods has enormous advantage for discrimination of incorporated or de novo synthesized compounds. Furthermore, potentiality of in vivo-NMR metabolomics will be discussed in the conference. (author)

  16. Identification of Ornamental Plant Functioned as Medicinal Plant Based on Redundant Discrete Wavelet Transformation

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-03-01

    Full Text Available Human has a duty to preserve the nature. One of the examples is preserving the ornamental plant. Huge economic value of plant trading, escalating esthetical value of one space and medicine efficacy that contained in a plant are some positive values from this plant. However, only few people know about its medicine efficacy. Considering the easiness to obtain and the medicine efficacy, this plant should be an initial treatment of a simple disease or option towards chemical based medicines. In order to let people get acquaint, we need a system that can proper identify this plant. Therefore, we propose to build a system based on Redundant Discrete Wavelet Transformation (RDWT through its leaf. Since its character is translation invariant that able to produce some robust features to identify ornamental plant. This system was successfully resulting 95.83% of correct classification rate.

  17. Amino Acid and Biogenic Amine Profile Deviations in an Oral Glucose Tolerance Test: A Comparison between Healthy and Hyperlipidaemia Individuals Based on Targeted Metabolomics

    Science.gov (United States)

    Li, Qi; Gu, Wenbo; Ma, Xuan; Liu, Yuxin; Jiang, Lidan; Feng, Rennan; Liu, Liyan

    2016-01-01

    Hyperlipidemia (HLP) is characterized by a disturbance in lipid metabolism and is a primary risk factor for the development of insulin resistance (IR) and a well-established risk factor for cardiovascular disease and atherosclerosis. The aim of this work was to investigate the changes in postprandial amino acid and biogenic amine profiles provoked by an oral glucose tolerance test (OGTT) in HLP patients using targeted metabolomics. We used ultra-high-performance liquid chromatography-triple quadrupole mass spectrometry to analyze the serum amino acid and biogenic amine profiles of 35 control and 35 HLP subjects during an OGTT. The amino acid and biogenic amine profiles from 30 HLP subjects were detected as independent samples to validate the changes in the metabolites. There were differences in the amino acid and biogenic amine profiles between the HLP individuals and the healthy controls at baseline and after the OGTT. The per cent changes of 13 metabolites from fasting to the 2 h samples during the OGTT in the HLP patients were significantly different from those of the healthy controls. The lipid parameters were associated with the changes in valine, isoleucine, creatine, creatinine, dimethylglycine, asparagine, serine, and tyrosine (all p < 0.05) during the OGTT in the HLP group. The postprandial changes in isoleucine and γ-aminobutyric acid (GABA) during the OGTT were positively associated with the homeostasis model assessment of insulin resistance (HOMA-IR; all p < 0.05) in the HLP group. Elevated oxidative stress and disordered energy metabolism during OGTTs are important characteristics of metabolic perturbations in HLP. Our findings offer new insights into the complex physiological regulation of metabolism during the OGTT in HLP. PMID:27338465

  18. Amino Acid and Biogenic Amine Profile Deviations in an Oral Glucose Tolerance Test: A Comparison between Healthy and Hyperlipidaemia Individuals Based on Targeted Metabolomics.

    Science.gov (United States)

    Li, Qi; Gu, Wenbo; Ma, Xuan; Liu, Yuxin; Jiang, Lidan; Feng, Rennan; Liu, Liyan

    2016-01-01

    Hyperlipidemia (HLP) is characterized by a disturbance in lipid metabolism and is a primary risk factor for the development of insulin resistance (IR) and a well-established risk factor for cardiovascular disease and atherosclerosis. The aim of this work was to investigate the changes in postprandial amino acid and biogenic amine profiles provoked by an oral glucose tolerance test (OGTT) in HLP patients using targeted metabolomics. We used ultra-high-performance liquid chromatography-triple quadrupole mass spectrometry to analyze the serum amino acid and biogenic amine profiles of 35 control and 35 HLP subjects during an OGTT. The amino acid and biogenic amine profiles from 30 HLP subjects were detected as independent samples to validate the changes in the metabolites. There were differences in the amino acid and biogenic amine profiles between the HLP individuals and the healthy controls at baseline and after the OGTT. The per cent changes of 13 metabolites from fasting to the 2 h samples during the OGTT in the HLP patients were significantly different from those of the healthy controls. The lipid parameters were associated with the changes in valine, isoleucine, creatine, creatinine, dimethylglycine, asparagine, serine, and tyrosine (all p < 0.05) during the OGTT in the HLP group. The postprandial changes in isoleucine and γ-aminobutyric acid (GABA) during the OGTT were positively associated with the homeostasis model assessment of insulin resistance (HOMA-IR; all p < 0.05) in the HLP group. Elevated oxidative stress and disordered energy metabolism during OGTTs are important characteristics of metabolic perturbations in HLP. Our findings offer new insights into the complex physiological regulation of metabolism during the OGTT in HLP. PMID:27338465

  19. The research on Virtual Plants Growth Based on DLA Model

    Science.gov (United States)

    Zou, YunLan; Chai, Bencheng

    This article summarizes the separated Evolutionary Algorithm in fractal algorithm of Diffusion Limited Aggregation model (i.e. DLA model) and put forward the virtual plant growth realization in computer based on DLA model. The method is carried out in the VB6.0 environment to achieve and verify the plant growth based on DLA model.

  20. Biomarker discovery in neurological diseases: a metabolomic approach

    Directory of Open Access Journals (Sweden)

    Afaf El-Ansary

    2009-12-01

    Full Text Available Afaf El-Ansary, Nouf Al-Afaleg, Yousra Al-YafaeeBiochemistry Department, Science College, King Saud University, Riyadh, Saudi ArabiaAbstract: Biomarkers are pharmacological and physiological measurements or specific biochemicals in the body that have a particular molecular feature that makes them useful for measuring the progress of disease or the effects of treatment. Due to the complexity of neurological disorders, it is very difficult to have perfect markers. Brain diseases require plenty of markers to reflect the metabolic impairment of different brain cells. The recent introduction of the metabolomic approach helps the study of neurological diseases based on profiling a multitude of biochemical components related to brain metabolism. This review is a trial to elucidate the possibility to use this approach to identify plasma metabolic markers related to neurological disorders. Previous trials using different metabolomic analyses including nuclear magnetic resonance spectroscopy, gas chromatography combined with mass spectrometry, liquid chromatography combined with mass spectrometry, and capillary electrophoresis will be traced.Keywords: metabolic biomarkers, neurological disorders. metabolome, nuclear magnetic resonance, mass spectrometry, chromatography

  1. A Combined Metabolomic and Proteomic Analysis of Gestational Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Joanna Hajduk

    2015-12-01

    Full Text Available The aim of this pilot study was to apply a novel combined metabolomic and proteomic approach in analysis of gestational diabetes mellitus. The investigation was performed with plasma samples derived from pregnant women with diagnosed gestational diabetes mellitus (n = 18 and a matched control group (n = 13. The mass spectrometry-based analyses allowed to determine 42 free amino acids and low molecular-weight peptide profiles. Different expressions of several peptides and altered amino acid profiles were observed in the analyzed groups. The combination of proteomic and metabolomic data allowed obtaining the model with a high discriminatory power, where amino acids ethanolamine, l-citrulline, l-asparagine, and peptide ions with m/z 1488.59; 4111.89 and 2913.15 had the highest contribution to the model. The sensitivity (94.44% and specificity (84.62%, as well as the total group membership classification value (90.32% calculated from the post hoc classification matrix of a joint model were the highest when compared with a single analysis of either amino acid levels or peptide ion intensities. The obtained results indicated a high potential of integration of proteomic and metabolomics analysis regardless the sample size. This promising approach together with clinical evaluation of the subjects can also be used in the study of other diseases.

  2. 基于NMR代谢组学技术对山药化学成分的研究%Studies on chemical constituents of the yam by 1HNMR-based metabolomics

    Institute of Scientific and Technical Information of China (English)

    张敏; 焦宏; 郭捷

    2014-01-01

    试验采用基于NMR代谢组学的技术,分别对生山药饮片、麸炒山药及食用山药的化学成分进行了研究,检测出30多种化合物,包括腺苷、胆碱、多种氨基酸、有机酸及糖类等物质,其中有14种是3种山药的共有成分。另外,对引起生山药与麸炒山药、食用山药与药用山药差异的化学成分进行了指认,初步了解了炮制对山药化学成分的影响及山药药材与食材的差异。%The studies on chemical constituents of dried yam slices, bran fried yam and edible yam were carried out re-spectively by means of 1HNMR-based metabolomics. Over thirty compounds including adenosine, choline, amino acids, organic acids, sugars and other substances were detected, of which fourteen were common components in three kinds of yams. Their respective characteristic chemical compositions were indicated. Effect of processing on the chemical compo-nents of yam and the differences between edible yam and dried yam slices, bran fried yam were reviewed.

  3. [Plant Spectral Discrimination Based on Phenological Features].

    Science.gov (United States)

    Zhang, Lei; Zhao, Jian-long; Jia, Kun; Li, Xiao-song

    2015-10-01

    Spectral analysis plays a significant role onplant characteristic identification and mechanism recognition, there were many papers published on the aspects of absorption features in the spectra of chlorophyll and moisture, spectral analysis onvegetation red edge effect, spectra profile feature extraction, spectra profile conversion, vegetation leaf structure and chemical composition impacts on the spectra in past years. However, fewer researches issued on spectral changes caused by plant seasonal changes of life form, chlorophyll, leaf area index. This paper studied on spectral observation of 11 plants of various life form, plant leaf structure and its size, phenological characteristics, they include deciduous forest with broad vertical leaf, needle leaf evergreen forest, needle leaf deciduous forest, deciduous forest with broadflat leaf, high shrub with big leaf, high shrub with little leaf, deciduous forest with broad little leaf, short shrub, meadow, steppe and grass. Field spectral data were observed with SVC-HR768 (Spectra Vista company, USA), the band width covers 350-2 500 nm, spectral resolution reaches 1-4 nm. The features of NDVI, spectral maximum absorption depth in green band, and spectral maximum absorption depth in red band were measured after continuum removal processing, the mean, amplitude and gradient of these features on seasonal change profile were analyzed, meanwhile, separability research on plant spectral feature of growth period and maturation period were compared. The paper presents a calculation method of separability of vegetation spectra which consider feature spatial distances. This index is carried on analysis of the vegetation discrimination. The results show that: the spectral features during plant growth period are easier to distinguish than them during maturation period. With the same features comparison, plant separability of growth period is 3 points higher than it during maturation period. The overall separabilityof vegetation

  4. Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome

    OpenAIRE

    Page, Andrew F.; Cseke, Leland J.; Minocha, Rakesh; Turlapati, Swathi A.; Podila, Gopi K.; Ulanov, Alexander; Li, Zhong; Minocha, Subhash C.

    2016-01-01

    Background With the increasing interest in metabolic engineering of plants using genetic manipulation and gene editing technologies to enhance growth, nutritional value and environmental adaptation, a major concern is the potential of undesirable broad and distant effects of manipulating the target gene or metabolic step in the resulting plant. A comprehensive transcriptomic and metabolomic analysis of the product may shed some useful light in this regard. The present study used these two tec...

  5. Two birds with one stone: doing metabolomics with your proteomics kit.

    Science.gov (United States)

    Fischer, Roman; Bowness, Paul; Kessler, Benedikt M

    2013-12-01

    Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple '-OMICS' approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC-MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics-based studies. Limitations and requirements are discussed as well as extensions to the LC-MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC-MS, CE-MS or NMR. PMID:24155035

  6. ECMDB: the E. coli Metabolome Database.

    Science.gov (United States)

    Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S

    2013-01-01

    The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry. PMID:23109553

  7. The prediction of the LWR plant accident based on the measured plant data

    International Nuclear Information System (INIS)

    In case of accident affecting a nuclear reactor, it is essential to anticipate the possible development of the situation to efficiently succeed in emergency response actions, i.e. firstly to be early warned, to get sufficient information on the plant: and as far as possible. The ASTRID (Assessment of Source Term for Emergency Response based on Installation Data) project consists in developing a methodology: of expertise to; structure the work of technical teams and to facilitate cross competence communications among EP players and a qualified computer tool that could be commonly used by the European countries to reliably predict source term in case of an accident in a light water reactor, using the information available on the plant. In many accident conditions the team of analysts may be located far away from the plant experiencing the accident and their decision making is based on the on-line plant data transmitted into the crisis centre in an interval of 30 - 600 seconds. The plant condition has to be diagnosed based on this information, In the ASTRID project the plant status diagnostics has been studied for the European reactor types including BWR, PWR and VVER plants. The directly measured plant data may be used for estimations of the break size from the primary system and its locations. The break size prediction may be based on the pressurizer level, reactor vessel level, primary pressure and steam generator level in the case of the steam generator tube rupture. In the ASTRID project the break predictions concept was developed and its validity for different plant types and is presented in the paper, when the plant data has been created with the plant specific thermohydraulic simulation model. The tracking simulator attempts to follow the plant behavior on-line based on the measured plant data for the main process parameters and most important boundary conditions. When the plant state tracking fails, the plant may be experiencing an accident, and the tracking

  8. Metabolomics continues to flourish: highlights from the 2014 Metabolomics Society Conference

    NARCIS (Netherlands)

    Roessner, U.; Hall, R.D.

    2014-01-01

    The Metabolomics Society has now been organising its annual meetings for 10 years! The 10th annual conference returned, in June, to Tsuruoka, Japan where the very first meeting was also held in 2005—just shortly after our society had been formally established and our journal Metabolomics had brought

  9. OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize

    Directory of Open Access Journals (Sweden)

    Colmsee Christian

    2012-12-01

    Full Text Available Abstract Background Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource for bioenergy. When looking at the problems of limited fossil fuels, the growth of the world’s population or the world’s climate change, it is important to find ways to increase the yield and biomass of maize and to study how it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology project maize plants were grown under a large set of controlled stress conditions, phenotypically characterised and plant material was harvested to analyse the effect of specific environmental conditions or developmental stages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plant material allowing the comparison of results across different omics domains. A data warehouse was developed to store experimental data as well as analysis results of the performed experiments. Description The OPTIMAS Data Warehouse (OPTIMAS-DW is a comprehensive data collection for maize and integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe the functions of the selected unigenes. Several treatment- and plant growth stage experiments were performed and measured data were filled into data templates and imported into the data warehouse by a Java based import tool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is

  10. Systems Analysis Of Advanced Coal-Based Power Plants

    Science.gov (United States)

    Ferrall, Joseph F.; Jennings, Charles N.; Pappano, Alfred W.

    1988-01-01

    Report presents appraisal of integrated coal-gasification/fuel-cell power plants. Based on study comparing fuel-cell technologies with each other and with coal-based alternatives and recommends most promising ones for research and development. Evaluates capital cost, cost of electricity, fuel consumption, and conformance with environmental standards. Analyzes sensitivity of cost of electricity to changes in fuel cost, to economic assumptions, and to level of technology. Recommends further evaluation of integrated coal-gasification/fuel-cell integrated coal-gasification/combined-cycle, and pulverized-coal-fired plants. Concludes with appendixes detailing plant-performance models, subsystem-performance parameters, performance goals, cost bases, plant-cost data sheets, and plant sensitivity to fuel-cell performance.

  11. Metabolomics Analysis of Health Functions of Physalis Pubescens L. using by Ultra-performance Liquid Chromatography/Electrospray Ionization Quadruple Time-of-Flight Mass Spectrometry

    OpenAIRE

    Hang Chu; Hui Sun; Guang-Li Yan; Ai-Hua Zhang; Chang Liu; Hui Dong; Xiang-Cai Meng; Xi-Jun Wang

    2015-01-01

    Herbal medicines may benefit from metabolomics studies, and applying metabolomics may provide answers about which herbal interventions may be effective for individuals, which metabolic processes are triggered, and the subsequent chemical pathways of activity. Physalis pubescens L (PPL) is an herbal fruit for one year living plant and has been developed into healthy function's food. However, the mechanisms of health functions are still unclear. To comprehensively and holistically assess its an...

  12. Dansylation metabolite assay: a simple and rapid method for sample amount normalization in metabolomics.

    Science.gov (United States)

    Wu, Yiman; Li, Liang

    2014-10-01

    Metabolomics involves the comparison of the metabolomes of individual samples from two or more groups to reveal the metabolic differences. In order to measure the metabolite concentration differences accurately, using the same amount of starting materials is essential. In this work, we describe a simple and rapid method for sample amount normalization. It is based on dansylation labeling of the amine and phenol submetabolome of an individual sample, followed by solvent extraction of the labeled metabolites and ultraviolet (UV) absorbance measurement using a microplate reader. A calibration curve of a mixture of 17 dansyl-labeled amino acid standards is used to determine the total concentration of the labeled metabolites in a sample. According to the measured concentrations of individual samples, the volume of an aliquot taken from each sample is adjusted so that the same sample amount is taken for subsequent metabolome comparison. As an example of applications, this dansylation metabolite assay method is shown to be useful in comparative metabolome analysis of two different E. coli strains using a differential chemical isotope labeling LC-MS platform. Because of the low cost of equipment and reagents and the simple procedure used in the assay, this method can be readily implemented. We envisage that, this assay, which is analogous to the bicinchoninic acid (BCA) protein assay widely used in proteomics, will be applicable to many types of samples for quantitative metabolomics. PMID:25215550

  13. The metabolomic study on atherosclerosis mice and its application in a traditional Chinese medicine Sishen granule.

    Science.gov (United States)

    Tian, Feng; Gu, Lei; Si, Aiyong; Yao, Quanbao; Zhang, Xianwei; Zhao, Jihui; Hu, Daode

    2016-06-01

    Although an atherosclerosis (AS) model using low-density lipoprotein receptor deletion mice has been widely applied, its pathological pathway in metabolite level is still not clear. To further reveal the metabolite profile and identify the potential biomarkers in AS development, a serum metabolomic approach was developed based on reversed-phase liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS). The established metabolomic platform was also used for elucidating the therapeutic mechanism of a traditional Chinese medicine named Sishen granule (SSKL). Twenty-one potential biomarkers in AS mouse serum were identified. Through functional analysis of these biomarkers, inflammation, proliferation, dysfunction of energy metabolism and amino acid metabolism were considered the most relevant pathological changes in AS. DNA damage products were found for the first time in the metabolomic study of AS. The network established by 20 biomarkers revealed that pyruvate metabolism, citrate cycle, fatty acid metabolism and urea metabolism were seriously disturbed. This metabolomic study not only supplied a systematic view of the progression of AS but also provided a theoretical basis for the treatment of AS. This metabolomic study also demonstrated that SSKL had therapeutic effectiveness for AS through partly reversing the inflammation reaction and amino acid metabolism dysfunction. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26488619

  14. Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

    Science.gov (United States)

    Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

    2014-01-01

    A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data. PMID:24949426

  15. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

    Science.gov (United States)

    Cottret, Ludovic; Wildridge, David; Vinson, Florence; Barrett, Michael P; Charles, Hubert; Sagot, Marie-France; Jourdan, Fabien

    2010-07-01

    High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr. PMID:20444866

  16. Knowledge based system for fouling assessment of power plant boiler

    International Nuclear Information System (INIS)

    The paper presents the design of an expert system for fouling assessment in power plant boilers. It is an on-line expert system based on selected criteria for the fouling assessment. Using criteria for fouling assessment based on 'clean' and 'not-clean' radiation heat flux measurements, the diagnostic variable are defined for the boiler heat transfer surface. The development of the prototype knowledge-based system for fouling assessment in power plants boiler comprise the integrations of the elements including knowledge base, inference procedure and prototype configuration. Demonstration of the prototype knowledge-based system for fouling assessment was performed on the Sines power plant. It is a 300 MW coal fired power plant. 12 fields are used with 3 on each side of boiler

  17. Metabolomics

    DEFF Research Database (Denmark)

    Kamstrup-Nielsen, Maja Hermann

    ) spectroscopy (Paper II), fluorescence spectroscopy (Paper III) and gas chromatography coupled to mass spectrometry (GC-MS). The principles of the three data acquisition techniques have been briefly described and the methods have been compared. The techniques complement each other, which makes room for data...... analysis (PCA), parallel factor analysis (PARAFAC), PARAFAC2 and partial least squares discriminant analysis (PLS-DA) all being described in depth. It can be a challenge to determine the appropriate number of components in PARAFAC2, since no specific tools have been developed for this purpose. Paper I is a...

  18. Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology.

    Science.gov (United States)

    Weckwerth, Wolfram

    2011-12-10

    biochemical networks up to whole species populations. This process relies on the development of new technologies for the analysis of molecular data, especially genomics, metabolomics and proteomics data. The ambitious aim of these non-targeted 'omic' technologies is to extend our understanding beyond the analysis of separated parts of the system, in contrast to traditional reductionistic hypothesis-driven approaches. The consequent integration of genotyping, pheno/morphotyping and the analysis of the molecular phenotype using metabolomics, proteomics and transcriptomics will reveal a novel understanding of plant metabolism and its interaction with the environment. The analysis of single model systems - plants, fungi, animals and bacteria - will finally emerge in the analysis of populations of plants and other organisms and their adaptation to the ecological niche. In parallel, this novel understanding of ecophysiology will translate into knowledge-based approaches in crop plant biotechnology and marker- or genome-assisted breeding approaches. In this review the foundations of green systems biology are described and applications in ecosystems research are presented. Knowledge exchange of ecosystems research and green biotechnology merging into green systems biology is anticipated based on the principles of natural variation, biodiversity and the genotype-phenotype environment relationship as the fundamental drivers of ecology and evolution. PMID:21802534

  19. Metabolomic phenotyping of a cloned pig model

    Directory of Open Access Journals (Sweden)

    Callesen Henrik

    2011-08-01

    Full Text Available Abstract Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5 was for the first time elucidated by nuclear magnetic resonance (NMR-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6 by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals.

  20. Evaluation of Four Different Analytical Tools to Determine the Regional Origin of Gastrodia elata and Rehmannia glutinosa on the Basis of Metabolomics Study

    Directory of Open Access Journals (Sweden)

    Dong-Kyu Lee

    2014-05-01

    Full Text Available Chemical profiles of medicinal plants could be dissimilar depending on the cultivation environments, which may influence their therapeutic efficacy. Accordingly, the regional origin of the medicinal plants should be authenticated for correct evaluation of their medicinal and market values. Metabolomics has been found very useful for discriminating the origin of many plants. Choosing the adequate analytical tool can be an essential procedure because different chemical profiles with different detection ranges will be produced according to the choice. In this study, four analytical tools, Fourier transform near‑infrared spectroscopy (FT-NIR, 1H-nuclear magnetic resonance spectroscopy (1H‑NMR, liquid chromatography-mass spectrometry (LC-MS, and gas chromatography-mass spectroscopy (GC-MS were applied in parallel to the same samples of two popular medicinal plants (Gastrodia elata and Rehmannia glutinosa cultivated either in Korea or China. The classification abilities of four discriminant models for each plant were evaluated based on the misclassification rate and Q2 obtained from principal component analysis (PCA and orthogonal projection to latent structures-discriminant analysis (OPLS‑DA, respectively. 1H-NMR and LC-MS, which were the best techniques for G. elata and R. glutinosa, respectively, were generally preferable for origin discrimination over the others. Reasoned by integrating all the results, 1H-NMR is the most prominent technique for discriminating the origins of two plants. Nonetheless, this study suggests that preliminary screening is essential to determine the most suitable analytical tool and statistical method, which will ensure the dependability of metabolomics-based discrimination.

  1. Supporting plant operation through computer-based procedures

    International Nuclear Information System (INIS)

    Digital Systems are becoming more important in controlling and monitoring nuclear power plant operations. The capabilities of these systems provide additional functions as well as support operators in making decisions and avoiding errors. Regarding Operation Support Systems, an important way of taking advantage of these features is using computer-based procedures (CBPs) tools that enhance the plant operation. Integrating digital systems in analogue controls at nuclear power plants in operation becomes an extra challenge, in contrast to the integration of Digital Control Systems in new nuclear power plants. Considering the potential advantages of using this technology, Tecnatom has designed and developed a CBP platform taking currently operating nuclear power plants as its design basis. The result is a powerful tool which combines the advantages of CBPs and the conventional analogue control systems minimizing negative effects during plant operation and integrating operation aid-systems to support operators. (authors)

  2. Possible Future SOFC - ST Based Power Plants

    DEFF Research Database (Denmark)

    Rokni, Masoud; Scappin, Fabio

    2009-01-01

    Hybrid systems consisting Solid Oxide Fuel Cell (SOFC) on the top of a Steam Turbine (ST) are investigated. The plants are fired by natural gas. A desulfurization reactor removes the sulfur content in the NG while a pre-reformer break down the heavier hydrocarbons. The pre-treated fuel enters then...... into the anode side of the SOFC. The gases from the SOFC stacks enter into a burner to burn the rest of the fuel. The off-gases now enter into a heat recovery steam generator to produce steam for a Rankine cycle. Different system setups are considered. Cyclic efficiencies up to 67% are achieved which...

  3. Simulation Based Data Reconciliation for Monitoring Power Plant Efficiency

    International Nuclear Information System (INIS)

    Power plant efficiency is analyzed by using measured values, mass/energy balance principles, and several correlations. Since the measured values can have uncertainty depending on the accuracy of instrumentation, the results of plant efficiency should definitely have uncertainty. The certainty may occur due to either the randomness or the malfunctions of a process. In order to improve the accuracy of efficiency analysis, the data reconciliation (DR) is expected as a good candidate because the mathematical algorithm of the DR is based on the first principles such as mass and energy balance considering the uncertainty of instrumentation. It should be noted that the mass and energy balance model for analyzing power plant efficiency is equivalent to a steady-state simulation of a plant system. Therefore the DR for efficiency analysis necessitates the simulation which can deal with the uncertainty of instrumentation. This study will propose the algorithm of the simulation based DR which is applicable to power plant efficiency monitoring

  4. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.

    Directory of Open Access Journals (Sweden)

    Katarzyna Bozek

    2014-05-01

    Full Text Available Metabolite concentrations reflect the physiological states of tissues and cells. However, the role of metabolic changes in species evolution is currently unknown. Here, we present a study of metabolome evolution conducted in three brain regions and two non-neural tissues from humans, chimpanzees, macaque monkeys, and mice based on over 10,000 hydrophilic compounds. While chimpanzee, macaque, and mouse metabolomes diverge following the genetic distances among species, we detect remarkable acceleration of metabolome evolution in human prefrontal cortex and skeletal muscle affecting neural and energy metabolism pathways. These metabolic changes could not be attributed to environmental conditions and were confirmed against the expression of their corresponding enzymes. We further conducted muscle strength tests in humans, chimpanzees, and macaques. The results suggest that, while humans are characterized by superior cognition, their muscular performance might be markedly inferior to that of chimpanzees and macaque monkeys.

  5. Metabolomic analysis of amino acid and energy metabolism in rats supplemented with chlorogenic acid

    Science.gov (United States)

    Ruan, Zheng; Yang, Yuhui; Zhou, Yan; Wen, Yanmei; Ding, Sheng; Liu, Gang; Wu, Xin; Deng, Zeyuan; Assaad, Houssein; Wu, Guoyao

    2016-01-01

    This study was conducted to investigate effects of chlorogenic acid (CGA) supplementation on serum and hepatic metabolomes in rats. Rats received daily intragastric administration of either CGA (60 mg/kg body weight) or distilled water (control) for 4 weeks. Growth performance, serum biochemical profiles, and hepatic morphology were measured. Additionally, serum and liver tissue extracts were analyzed for metabolomes by high-resolution 1H nuclear magnetic resonance-based metabolomics and multivariate statistics. CGA did not affect rat growth performance, serum biochemical profiles, or hepatic morphology. However, supplementation with CGA decreased serum concentrations of lactate, pyruvate, succinate, citrate, β-hydroxybutyrate and acetoacetate, while increasing serum concentrations of glycine and hepatic concentrations of glutathione. These results suggest that CGA supplementation results in perturbation of energy and amino acid metabolism in rats. We suggest that glycine and glutathione in serum may be useful biomarkers for biological properties of CGA on nitrogen metabolism in vivo. PMID:24927697

  6. Performance-based pricing for nuclear power plants

    International Nuclear Information System (INIS)

    State public utility commissions in the United States have implemented incentive regulations to promote the operating efficiency of nuclear power plants. This paper surveys these incentive programs, focusing on the performance-based pricing approach. Our findings suggest that the performance-based price should be set between the electric utility's avoided cost and the marginal cost of generating electricity at the nuclear power plant. 18 refs., 1 fig., 1 tab

  7. The volatile metabolome of grapevine roots: first insights into the metabolic response upon phylloxera attack.

    Science.gov (United States)

    Lawo, Nora C; Weingart, Georg J F; Schuhmacher, Rainer; Forneck, Astrid

    2011-09-01

    Many plant species respond to herbivore attack by an increased formation of volatile organic compounds. In this preliminary study we analysed the volatile metabolome of grapevine roots [Teleki 5C (Vitis berlandieri Planch. × Vitis riparia Michx.)] with the aim to gain insight into the interaction between phylloxera (Daktulosphaira vitifoliae Fitch; Hemiptera: Phylloxeridae) and grapevine roots. In the first part of the study, headspace solid phase microextraction (HS-SPME) coupled to gas chromatography - mass spectrometry (GC-MS) was used to detect and identify volatile metabolites in uninfested and phylloxera-infested root tips of the grapevine rootstock Teleki 5C. Based on the comparison of deconvoluted mass spectra with spectra databases as well as experimentally derived retention indices with literature values, 38 metabolites were identified, which belong to the major classes of plant volatiles including C6-compounds, terpenes (including modified terpenes), aromatic compounds, alcohols and n-alkanes. Based on these identified metabolites, changes in root volatiles were investigated and resulted in metabolite profiles caused by phylloxera infestation. Our preliminary data indicate that defence related pathways such as the mevalonate and/or alternative isopentenyl pyrophosphate-, the lipoxygenase- (LOX) as well as the phenylpropanoid pathway are affected in root galls as a response to phylloxera attack. PMID:21764593

  8. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

    Science.gov (United States)

    Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

    2016-07-01

    The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program's goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. The complete set of training materials including slide sets and videos can be viewed at http://www.uab.edu/proteomics/metabolomics/workshop/workshop_june_2015.php. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27434804

  9. Obesity and Asthma: Microbiome-Metabolome Interactions.

    Science.gov (United States)

    Shore, Stephanie A; Cho, Youngji

    2016-05-01

    Obesity is a risk factor for asthma, but obese subjects with asthma respond poorly to standard asthma drugs. Obesity also alters gut bacterial community structure. Obesity-related changes in gut bacteria contribute to weight gain and other obesity-related conditions, including insulin resistance and systemic inflammation. Here, we review the rationale for the hypothesis that obesity-related changes in gut bacteria may also play a role in obesity-related asthma. The metabolomes of the liver, serum, urine, and adipose tissue are altered in obesity. Gut bacteria produce a large number of metabolites, which can reach the blood and circulate to other organs, and gut bacteria-derived metabolites have been shown to contribute to disease processes outside the gastrointestinal tract, including cardiovascular disease. Here, we describe the potential roles for two such classes of metabolites in obesity-related asthma: short-chain fatty acids and bile acids. Greater understanding of the role of microbiota in obesity-related asthma could lead to novel microbiota-based treatments for these hard-to-treat patients. PMID:26949916

  10. Metal-based nanotoxicity and detoxification pathways in higher plants.

    Science.gov (United States)

    Ma, Chuanxin; White, Jason C; Dhankher, Om Parkash; Xing, Baoshan

    2015-06-16

    The potential risks from metal-based nanoparticles (NPs) in the environment have increased with the rapidly rising demand for and use of nanoenabled consumer products. Plant's central roles in ecosystem function and food chain integrity ensure intimate contact with water and soil systems, both of which are considered sinks for NPs accumulation. In this review, we document phytotoxicity caused by metal-based NPs exposure at physiological, biochemical, and molecular levels. Although the exact mechanisms of plant defense against nanotoxicity are unclear, several relevant studies have been recently published. Possible detoxification pathways that might enable plant resistance to oxidative stress and facilitate NPs detoxification are reviewed herein. Given the importance of understanding the effects and implications of metal-based NPs on plants, future research should focus on the following: (1) addressing key knowledge gaps in understanding molecular and biochemical responses of plants to NPs stress through global transcriptome, proteome, and metablome assays; (2) designing long-term experiments under field conditions at realistic exposure concentrations to investigate the impact of metal-based NPs on edible crops and the resulting implications to the food chain and to human health; and (3) establishing an impact assessment to evaluate the effects of metal-based NPs on plants with regard to ecosystem structure and function. PMID:25974388

  11. Knowledge based diagnostics in nuclear power plants

    International Nuclear Information System (INIS)

    In the paper to be given a special process diagnostic system (PDS) will be presented, taking into account corresponding user experiences. It must be seen the result of a long term work on computerized process surveillance and control on NPP; it includes a model based system for noise analysis of mechanical vibrations, which has been enhanced by using of knowledge based technique (expert systems). The paper will discuss the process diagnostic frame concept and emphasize the vibration analysis expertsystem RADEX, with the parts modelling (building a knowledge base), man-machine communication aspects, implementation. (author). 5 refs, 5 figs

  12. Gas chromatography coupled to mass spectrometry-based metabolomic to screen for anabolic practices in cattle: identification of 5α-androst-2-en-17-one as new biomarker of 4-androstenedione misuse.

    Science.gov (United States)

    Anizan, Sebastien; Bichon, Emmanuelle; Duval, Thibault; Monteau, Fabrice; Cesbron, Nora; Antignac, Jean-Philippe; Le Bizec, Bruno

    2012-01-01

    The use of anabolic steroids as growth promoters for meat-producing animals is banned within the European Union. However, screening for the illegal use of natural steroid hormones still represents a difficult challenge because of the high interindividual and physiological variability of the endogenous concentration levels in animals. In this context, the development of untargeted profiling approaches for identifying new relevant biomarkers of exposure and/or effect has been emerging for a couple of years. The present study deals with an untargeted metabolomics approach on the basis of GC-MS aiming to reveal potential biomarkers signing a fraudulent administration of 4-androstenedione (AED), an anabolic androgenic steroid chosen as template. After a sample preparation based on microextraction by packed sorbent, urinary profiles of the free and deglucurono-conjugates urinary metabolites were acquired by GC-MS in the full-scan acquisition mode. Data processing and chemometric procedures highlighted 125 ions, allowing discrimination between samples collected before and after an administration of 4-AED. After a first evaluation of the signal robustness using additional and independent non-compliant samples, 17 steroid-like metabolites were pointed out as relevant candidate biomarkers. All these metabolites were then monitored using a targeted GC-MS/MS method for an additional assessment of their capacity to be used as biomarkers. Finally, two steroids, namely 5α-androstane-3β,17α-diol and 5α-androst-2-en-17-one, were concluded to be compatible with such a definition and which could be finally usable for screening purpose of AED abuse in cattle. PMID:22282099

  13. Metabolomics for the Authentication of Natural Extracts Used in Flavors and Fragrances: the Case Study of Violet Leaf Absolutes from Viola odorata.

    Science.gov (United States)

    Saint-Lary, Laure; Roy, Céline; Paris, Jean-Philippe; Martin, Jean-François; Thomas, Olivier P; Fernandez, Xavier

    2016-06-01

    Natural extracts used in fine fragrances (alcoholic perfumes) are rare and precious. As such, they represent an interesting target for fraudulent practices called adulterations. Absolutes, important materials used in the creation of perfumes, are obtained by organic solvent extraction of raw plant materials. Because the nonvolatile part of these natural extracts is not normalized and scarcely reported, highlighting potential adulterations present in this fraction appears highly challenging. For the first time, we investigated the use of nontargeted UHPLC-ToFMS metabolomics for this purpose, considering Viola odorata l., a plant largely used in the perfume industry, as a model. Significant differences in the metabolic fingerprints of the violet leaf absolutes were evidenced according to geographical locations, and/or adulterations. Additionally, markers of the geographical origin were detected through their molecular weight/most probable molecular formula and retention time, while adulterations were statistically validated. In this study, we thus clearly demonstrated the efficiency of UHPLC-ToFMS-based metabolomics in accelerating both the identification of the origin of raw materials as well as the search for potential adulterations in absolutes, natural products of high added value. PMID:27135901

  14. Multimedia-based Medicinal Plants Sustainability Management System

    CERN Document Server

    Omogbadegun, Zacchaeus; Ayo, Charles; Mbarika, Victor; Omoregbe, Nicholas; Otofia, Efe; Chieze, Frank

    2011-01-01

    Medicinal plants are increasingly recognized worldwide as an alternative source of efficacious and inexpensive medications to synthetic chemo-therapeutic compound. Rapid declining wild stocks of medicinal plants accompanied by adulteration and species substitutions reduce their efficacy, quality and safety. Consequently, the low accessibility to and non-affordability of orthodox medicine costs by rural dwellers to be healthy and economically productive further threaten their life expectancy. Finding comprehensive information on medicinal plants of conservation concern at a global level has been difficult. This has created a gap between computing technologies' promises and expectations in the healing process under complementary and alternative medicine. This paper presents the design and implementation of a Multimedia-based Medicinal Plants Sustainability Management System addressing these concerns. Medicinal plants' details for designing the system were collected through semi-structured interviews and databas...

  15. Metabolomics to Explore Impact of Dairy Intake

    Directory of Open Access Journals (Sweden)

    Hong Zheng

    2015-06-01

    Full Text Available Dairy products are an important component in the Western diet and represent a valuable source of nutrients for humans. However, a reliable dairy intake assessment in nutrition research is crucial to correctly elucidate the link between dairy intake and human health. Metabolomics is considered a potential tool for assessment of dietary intake instead of traditional methods, such as food frequency questionnaires, food records, and 24-h recalls. Metabolomics has been successfully applied to discriminate between consumption of different dairy products under different experimental conditions. Moreover, potential metabolites related to dairy intake were identified, although these metabolites need to be further validated in other intervention studies before they can be used as valid biomarkers of dairy consumption. Therefore, this review provides an overview of metabolomics for assessment of dairy intake in order to better clarify the role of dairy products in human nutrition and health.

  16. NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review

    Energy Technology Data Exchange (ETDEWEB)

    Smolinska, Agnieszka, E-mail: A.Smolinska@science.ru.nl [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands); Blanchet, Lionel [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands); Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands); Buydens, Lutgarde M.C.; Wijmenga, Sybren S. [Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen (Netherlands)

    2012-10-31

    Highlights: Black-Right-Pointing-Pointer Procedures for acquisition of different biofluids by NMR. Black-Right-Pointing-Pointer Recent developments in metabolic profiling of different biofluids by NMR are presented. Black-Right-Pointing-Pointer The crucial steps involved in data preprocessing and multivariate chemometric analysis are reviewed. Black-Right-Pointing-Pointer Emphasis is given on recent findings on Multiple Sclerosis via NMR and pattern recognition methods. - Abstract: Metabolomics is the discipline where endogenous and exogenous metabolites are assessed, identified and quantified in different biological samples. Metabolites are crucial components of biological system and highly informative about its functional state, due to their closeness to functional endpoints and to the organism's phenotypes. Nuclear Magnetic Resonance (NMR) spectroscopy, next to Mass Spectrometry (MS), is one of the main metabolomics analytical platforms. The technological developments in the field of NMR spectroscopy have enabled the identification and quantitative measurement of the many metabolites in a single sample of biofluids in a non-targeted and non-destructive manner. Combination of NMR spectra of biofluids and pattern recognition methods has driven forward the application of metabolomics in the field of biomarker discovery. The importance of metabolomics in diagnostics, e.g. in identifying biomarkers or defining pathological status, has been growing exponentially as evidenced by the number of published papers. In this review, we describe the developments in data acquisition and multivariate analysis of NMR-based metabolomics data, with particular emphasis on the metabolomics of Cerebrospinal Fluid (CSF) and biomarker discovery in Multiple Sclerosis (MScl).

  17. MetabR: an R script for linear model analysis of quantitative metabolomic data

    Directory of Open Access Journals (Sweden)

    Ernest Ben

    2012-10-01

    Full Text Available Abstract Background Metabolomics is an emerging high-throughput approach to systems biology, but data analysis tools are lacking compared to other systems level disciplines such as transcriptomics and proteomics. Metabolomic data analysis requires a normalization step to remove systematic effects of confounding variables on metabolite measurements. Current tools may not correctly normalize every metabolite when the relationships between each metabolite quantity and fixed-effect confounding variables are different, or for the effects of random-effect confounding variables. Linear mixed models, an established methodology in the microarray literature, offer a standardized and flexible approach for removing the effects of fixed- and random-effect confounding variables from metabolomic data. Findings Here we present a simple menu-driven program, “MetabR”, designed to aid researchers with no programming background in statistical analysis of metabolomic data. Written in the open-source statistical programming language R, MetabR implements linear mixed models to normalize metabolomic data and analysis of variance (ANOVA to test treatment differences. MetabR exports normalized data, checks statistical model assumptions, identifies differentially abundant metabolites, and produces output files to help with data interpretation. Example data are provided to illustrate normalization for common confounding variables and to demonstrate the utility of the MetabR program. Conclusions We developed MetabR as a simple and user-friendly tool for implementing linear mixed model-based normalization and statistical analysis of targeted metabolomic data, which helps to fill a lack of available data analysis tools in this field. The program, user guide, example data, and any future news or updates related to the program may be found at http://metabr.r-forge.r-project.org/.

  18. Maintenance of Ni-based alloy at PWR plant

    International Nuclear Information System (INIS)

    Kansai Electric owns 11 PWR plants. At our PWR plants, we are taking various preventive maintenance measures on Ni-based alloy according to the prediction of possible trouble while past trouble occurred at overseas plants due to Primary Water Stress Corrosion Cracking (PWSCC) being considered. In addition, we are making an effort to put new maintenance techniques into practical use by conducting demonstration tests to confirm their applicability to actual plants. We have replaced reactor vessel heads at 7 plants with new ones. At the other 4 plants, we took, measures to reduce the temperature of reactor vessel head top to delay the timing of PWSCC occurrence. We are carrying out the constant load tests to predict the timing of PWSCC occurrence at these 4 plants. It is planned to conduct non-destructive inspections at an appropriate timing based on the result of the prediction. Based on the prediction of the timing of PWSCC occurrence at bottom-mounted instrumentation (BMI), we have developed water jet peening (WJP) technique to reduce residual stress and applied the technique to our plants successively. Meanwhile, a technique to cut and eliminate cracking has been developed. In addition, capping technique, which covers overall the concerned nozzle on the outer surface of the reactor vessel, has been also established. For alloy 132/82 weld metal for the connection, we are conducting ultrasonic inspection at our plants successively. In order to prepare against PWSCC occurrence, we have also established a technique to replace the entire section of concerned short piping with new one. (author)

  19. Similar local, but different systemic, metabolomic responses of closely related pine subspecies to folivory by caterpillars of the processionary moth

    Czech Academy of Sciences Publication Activity Database

    Rivas-Ubach, A.; Sardans, J.; Hódar, J. A.; Garcia-Porta, J.; Guenther, A.; Oravec, Michal; Urban, Otmar; Penuelas, J.

    2016-01-01

    Roč. 18, č. 3 (2016), s. 484-494. ISSN 1435-8603 R&D Projects: GA MŠk EE2.3.20.0246; GA AV ČR(CZ) M200871201 Institutional support: RVO:67179843 Keywords : folivory * metabolomics * phenolics * plant-insect * stoichiometry * systemic responses Subject RIV: EH - Ecology, Behaviour Impact factor: 2.633, year: 2014

  20. Metabolomics Investigation To Shed Light on Cheese as a Possible Piece in the French Paradox Puzzle

    DEFF Research Database (Denmark)

    Zheng, Hong; Yde, Christian Clement; Clausen, Morten Rahr;

    2015-01-01

    An NMR-based metabolomics approach was used to investigate the differentiation between subjects consuming cheese or milk and to elucidate the potential link to an effect on the blood cholesterol level. Fifteen healthy young men participated in a full cross-over study where they consumed three iso...

  1. Metabolomics Approach to Anabolic Steroid Urine Profiling of Bovines Treated with Prohormones

    NARCIS (Netherlands)

    Rijk, J.C.W.; Lommen, A.; Essers, M.L.; Groot, M.J.; Hende, van J.; Doeswijk, T.G.; Nielen, M.W.F.

    2009-01-01

    In livestock production, illegal use of natural steroids is hard to prove because metabolites are either unknown or not significantly above highly fluctuating endogenous levels. In this work we outlined for the first time a metabolomics based strategy for anabolic steroid urine profiling. Urine prof

  2. Toxicity of a plant based mosquito repellent/killer

    OpenAIRE

    Singh, Bhoopendra; Singh, Prakash Raj; Mohanty, Manoj Kumar

    2012-01-01

    The mission to make humans less attractive to mosquitoes has fuelled decades of scientific research on mosquito behaviour and control. The search for the perfect topical insect repellent/killer continues. This analysis was conducted to review and explore the scientific information on toxicity produced by the ingredients/contents of a herbal product. In this process of systemic review the following methodology was applied. By doing a MEDLINE search with key words of selected plants, plant base...

  3. Time-resolved metabolomics reveals metabolic modulation in rice foliage

    Directory of Open Access Journals (Sweden)

    Arita Masanori

    2008-06-01

    Full Text Available Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS and capillary electrophoresis diode-array detection (CE-DAD, we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the

  4. New Candidates for Plant-Based Repellents Against Aedes aegypti.

    Science.gov (United States)

    Misni, Norashiqin; Nor, Zurainee Mohamed; Ahmad, Rohani

    2016-06-01

    Based on an ethnobotanical study on use for plant species against mosquito bites in the Kota Tinggi District, Johor State, Malaysia, 3 plants selected for study, Citrus aurantifolia (leaves), Citrus grandis (fruit peel), and Alpinia galanga (rhizome), were extracted using hydrodistillation to produce essential oils. These essential oils were then formulated as a lotion using a microencapsulation process and then tested for their repellent effect against Aedes aegypti. N,N-diethyl-m-toluamide (deet) was also prepared in the same formulation and tested for repellency as controls. Four commercial plant-based repellent (KAPS(®), MozAway(®), BioZ Natural(®), and Mosiquard(®)) also were incorporated in the bioassay for comparison purposes. Bioassays revealed that at 20% concentration all repellent formulations demonstrated complete protection for 2 h and >90% for 4 h post-application. The A. galanga-based formulation provided the greatest level of protection (98.91%), which extended for 4 h post-application and was not significantly different from deet at similar concentration. When compared with commercial plant-based repellents (KAPS(®), MozAway(®), and BioZ Natural(®)), the 3 lotion formulations showed significantly better protection against Ae. aegypti bites, providing >90% protection for 4 h. In conclusion, our 3 plant-based lotion formulations provided acceptable levels of protection against host-seeking Ae. aegypti and should be developed. PMID:27280349

  5. Fault Diagnosis Strategies for SOFC-Based Power Generation Plants

    Directory of Open Access Journals (Sweden)

    Paola Costamagna

    2016-08-01

    Full Text Available The success of distributed power generation by plants based on solid oxide fuel cells (SOFCs is hindered by reliability problems that can be mitigated through an effective fault detection and isolation (FDI system. However, the numerous operating conditions under which such plants can operate and the random size of the possible faults make identifying damaged plant components starting from the physical variables measured in the plant very difficult. In this context, we assess two classical FDI strategies (model-based with fault signature matrix and data-driven with statistical classification and the combination of them. For this assessment, a quantitative model of the SOFC-based plant, which is able to simulate regular and faulty conditions, is used. Moreover, a hybrid approach based on the random forest (RF classification method is introduced to address the discrimination of regular and faulty situations due to its practical advantages. Working with a common dataset, the FDI performances obtained using the aforementioned strategies, with different sets of monitored variables, are observed and compared. We conclude that the hybrid FDI strategy, realized by combining a model-based scheme with a statistical classifier, outperforms the other strategies. In addition, the inclusion of two physical variables that should be measured inside the SOFCs can significantly improve the FDI performance, despite the actual difficulty in performing such measurements.

  6. The volatile metabolome of grapevine roots: First insights into the metabolic response upon phylloxera attack

    OpenAIRE

    Nora C Lawo; Weingart, Georg J.F.; Schuhmacher, Rainer; Forneck, Astrid

    2011-01-01

    Many plant species respond to herbivore attack by an increased formation of volatile organic compounds. In this preliminary study we analysed the volatile metabolome of grapevine roots [Teleki 5C (Vitis berlandieri Planch. × Vitis riparia Michx.)] with the aim to gain insight into the interaction between phylloxera (Daktulosphaira vitifoliae Fitch; Hemiptera: Phylloxeridae) and grapevine roots. In the first part of the study, headspace solid phase microextraction (HS-SPME) coupled to gas chro...

  7. Metabolomic profiling and genomic analysis of wheat aneuploid lines to identify genes controlling biochemical pathways in mature grain.

    Science.gov (United States)

    Francki, Michael G; Hayton, Sarah; Gummer, Joel P A; Rawlinson, Catherine; Trengove, Robert D

    2016-02-01

    Metabolomics is becoming an increasingly important tool in plant genomics to decipher the function of genes controlling biochemical pathways responsible for trait variation. Although theoretical models can integrate genes and metabolites for trait variation, biological networks require validation using appropriate experimental genetic systems. In this study, we applied an untargeted metabolite analysis to mature grain of wheat homoeologous group 3 ditelosomic lines, selected compounds that showed significant variation between wheat lines Chinese Spring and at least one ditelosomic line, tracked the genes encoding enzymes of their biochemical pathway using the wheat genome survey sequence and determined the genetic components underlying metabolite variation. A total of 412 analytes were resolved in the wheat grain metabolome, and principal component analysis indicated significant differences in metabolite profiles between Chinese Spring and each ditelosomic lines. The grain metabolome identified 55 compounds positively matched against a mass spectral library where the majority showed significant differences between Chinese Spring and at least one ditelosomic line. Trehalose and branched-chain amino acids were selected for detailed investigation, and it was expected that if genes encoding enzymes directly related to their biochemical pathways were located on homoeologous group 3 chromosomes, then corresponding ditelosomic lines would have a significant reduction in metabolites compared with Chinese Spring. Although a proportion showed a reduction, some lines showed significant increases in metabolites, indicating that genes directly and indirectly involved in biosynthetic pathways likely regulate the metabolome. Therefore, this study demonstrated that wheat aneuploid lines are suitable experimental genetic system to validate metabolomics-genomics networks. PMID:26032167

  8. 76 FR 65165 - Importation of Plants for Planting; Risk-Based Sampling and Inspection Approach and Propagative...

    Science.gov (United States)

    2011-10-20

    ..., to be planted or replanted. The definition of plant in that section includes any plant (including any... October 17, 2011. The risk-based sampling will be implemented following further analysis of the sampling... planting infested with quarantine pests do not enter the United States, while providing a...

  9. [Frost-resistance of subtropical evergreen woody plants: an evaluation based on plant functional traits].

    Science.gov (United States)

    Xu, Yi-Lu; Yang, Xiao-Dong; Xu, Yue; Xie, Yi-Ming; Wang, Liang-Yan; Yan, En-Rong

    2012-12-01

    Evaluating the frost-resistance of evergreen woody plants is of significance in guiding the species selection in forest management in subtropical region. In this paper, an investigation was made on the functional traits (including specific leaf area, stem wood density, leaf area, leaf dry matter content, leaf relative electrical conductance, and twig wood density) of 64 common evergreen broad-leaved and coniferous woody plant species in the Ningbo region of Zhejiang Province, East China, after a severe snowstorm in early 2008, aimed to select the evergreen woody plants with high ability of freeze-tolerance, and to establish a related evaluation system. By using a hierarchy analysis approach, the weight values of the functional traits of each species were determined, and an index system for evaluating the plants tolerance ability against freeze and mechanical damage was established. Based on this system, 23 evergreen plant species with high tolerance ability against freeze and mechanical damage, such as Cyclobalanopsis gilva, Cyclobalanopsis nubium, Neolitsea aurata, and Vacciniuim mandarinorum, were selected. In the meantime, on the basis of the ordering with each of the functional traits, the ordering of the tolerance ability of the 64 plant species against freeze and mechanical damage was made, and a list for the frost-resistance ability of the subtropical evergreen woody plant species in Ningbo region was constituted. PMID:23479868

  10. Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction

    Directory of Open Access Journals (Sweden)

    Taru K Pilvi, Tuulikki Seppänen-Laakso, Helena Simolin, Piet Finckenberg, Anne Huotari, Karl-Heinz Herzig, Riitta Korpela, Matej Orešič, Eero M Mervaala

    2008-07-01

    Full Text Available AIM: To characterise the effect of energy restriction (ER on liver lipid and primary metabolite profile by using metabolomic approach. We also investigated whether the effect of energy restriction can be further enhanced by modification of dietary protein source and calcium.METHODS: Liver metabolomic profile of lean and obese C57Bl/6J mice (n = 10/group were compared with two groups of weight-reduced mice. ER was performed on control diet and whey protein-based high-calcium diet (whey + Ca. The metabolomic analyses were performed using the UPLC/MS based lipidomic platform and the HPLC/MS/MS based primary metabolite platform.RESULTS: ER on both diets significantly reduced hepatic lipid accumulation and lipid droplet size, while only whey + Ca diet significantly decreased blood glucose (P 0.05, vs lean. These changes were accompanied with up-regulated TCA cycle and pentose phosphate pathway metabolites.CONCLUSION: ER-induced changes on hepatic metabolomic profile can be significantly affected by dietary protein source. The therapeutic potential of whey protein and calcium should be further studied.

  11. Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction

    Institute of Scientific and Technical Information of China (English)

    Taru K Pilvi; Tuulikki Sepp(a)nen-Laakso; Helena Simolin; Piet Finckenberg; Anne Huotari; Karl-Heinz Herzig; Riitta Korpela; Matej Ore(s)i(c); Eero M Mervaala

    2008-01-01

    AIM: To characterise the effect of energy restriction (ER) on liver lipid and primary metabolite profile by using metabolomic approach. We also investigated whether the effect of energy restriction can be further enhanced by modification of dietary protein source and calcium.METHODS: Liver metabolomic profile of lean and obese C57BI/6] mice (n = 10/group) were compared with two groups of weight-reduced mice. ER was performed on control diet and whey protein-based high-calcium diet (whey + Ca). The metabolomic an alyses were performed using the UPLC/MS based lipidomic platform and the HPLC/MS/MS based primary metabolite platform.RESULTS: ER on both diets significantly reduced hepatic lipid accumulation and lipid droplet size, while only whey + Ca diet significantly decreased blood glucose (P 0.05, vs lean). These changes were accompanied with up-regulated TCA cycle and pentose phosphate pathway metabolites.CONCLUSION: ER-induced changes on hepatic metabolomic profile can be significantly affected by dietary protein source. The therapeutic potential of whey protein and calcium should be further studied.

  12. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data

    Science.gov (United States)

    Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara J.; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

    2016-01-01

    The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program’s goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. PMID:27434804

  13. Fracture mechanics based life assessment in petrochemical plants

    International Nuclear Information System (INIS)

    The increasing use of thick walled pressure vessels in petrochemical plants operating at high pressure under severe service conditions could lead to catastrophic failure. In the Malaysian Institute for Nuclear Technology Research (MINT), initial efforts are underway to apply fracture mechanics approach for assessment of significance of defects detected during periodic in service inspection (ISI) of industrial plants. This paper outlines the integrity management strategy based on fracture mechanics and proposes a new procedure for life assessment of petrochemical plants based on ASME Boiler and Pressure Vessel Code, Section XI, BSI PD 6493:1991, BSI 6539:1994, BSI Standard 7910:1999 and API 579:2000. Essential relevant data required for the assessment is listed. Several methods available for determination of fracture toughness are reviewed with limitations in their application to petrochemical plants. A new non destructive method for determination of fracture toughness based on hardness testing and normalized key roughness curve is given. Results of fracture mechanics based life assessment conducted for 100 mm thick ammonia converter of Ni r o steel and 70 mm thick plat forming reactor vessel of ASTM A 38 7 grade B steel in operational fertilizer and petroleum refining plants are presented. (Author)

  14. Anti-acetylcholinesterase potential and metabolome classification of 4 Ocimum species as determined via UPLC/qTOF/MS and chemometric tools.

    Science.gov (United States)

    Farag, M A; Ezzat, S M; Salama, M M; Tadros, M G

    2016-06-01

    Ocimum (sweet basil) is a plant of considerable commercial importance in traditional medicine worldwide as well as for the flavor and food industry. The goal of this study was to examine Ocimum extracts anti-acetylcholinesterase activity and to correlate the activity with their secondary metabolites profiles via a metabolome based ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) approach coupled to chemometrics. The metabolomic differences in phenolics from leaves derived from 4 Ocimum species: Ocimum basilicum, Ocimum africanum, Ocimum americanum and Ocimum minimum were assessed. Under optimized conditions, 81 metabolites were identified including 21 hydroxy cinnamic acids, 4 benzoic acid conjugates, 14C/O flavonoid conjugates, 2 alcohols, 5 acyl sugars, 4 triterpenes and 12 fatty acids. Several salviolanic acid derivatives including salviolanic acid A, B, C & I found in Salvia, were found in Ocimum herein for the first time. Unsupervised principal component analysis (PCA) and supervised orthogonal projection to latent structures-discriminant analysis (OPLS-DA) were further used for comparing and classification of samples. A clear separation among the four investigated Ocimum species was revealed, with O. africanum samples found most enriched in hydroxy cinnamates conjugates (HC) and flavonoids. To the best of our knowledge, this is the first report for compositional differences among Ocimum leaves via a metabolomic approach revealing that among examined species O. africanum leaves present a better source of Ocimum bioactive metabolites. The anticholinesrase activity of examined species was further assessed with a potent IC50 values for O. americanum, O. africanum, O. basilicum ranging from 2.5 to 6.6mg/ml, whereas O. minimum was least active with IC50 of 31.4mg/ml. Furthermore, major HC i.e., caftaric, chlorogenic and rosmarinic acids identified in extracts via UPLC-MS analysis exhibited IC50 values of 24, 0.5 and 7.9mg/ml respectively

  15. Physics-based Prognostics for Optimizing Plant Operation

    International Nuclear Information System (INIS)

    Scientists at the Pacific Northwest National Laboratory (PNNL) have examined the necessity for optimization of energy plant operation using ?DSOM? ? Decision Support Operation and Maintenance and this has been deployed at several sites. This approach has been expanded to include a prognostics component and tested on a pilot scale service water system, modeled on the design employed in a nuclear power plant. A key element in plant optimization is understanding and controlling the aging process of both safety-specific nuclear plant components and the infrastructure that supports these processes. This paper reports the development and demonstration of a physics-based approach to prognostic analysis that combines distributed computing, RF data links, the measurement of aging precursor metrics and their correlation with degradation rate and projected machine failure

  16. Photoprotection in Plants Optical Screening-based Mechanisms

    CERN Document Server

    Solovchenko, Alexei

    2010-01-01

    Optical screening of excessive and potentially harmful solar radiation is an important photoprotective mechanism, though it has received much less attention in comparison with other systems preventing photooxidative damage to photoautotrophic organisms. This photoprotection in the form of screening appears to be especially important for juvenile and senescing plants as well as under environmental stresses—i.e. in situations where the efficiency of enzymatic ROS elimination, DNA repair and other ‘classical’ photoprotective systems could be impaired. This book represents an attempt to develop an integral view of optical screening-based photoprotection in microalgae and higher plants. Towards this end, the key groups of pigments involved in the screening of ultraviolet and visible components of solar radiation in microalgae and higher plants, and the patterns of their accumulation and distribution within plant cells and tissues, are described. Special attention is paid to the manifestations of screening pi...

  17. Manufactured soils for plant growth at a lunar base

    Science.gov (United States)

    Ming, Douglas W.

    1989-01-01

    Advantages and disadvantages of synthetic soils are discussed. It is pointed out that synthetic soils may provide the proper physical and chemical properties necessary to maximize plant growth, such as a toxic-free composition and cation exchange capacities. The importance of nutrient retention, aeration, moisture retention, and mechanical support as qualities for synthetic soils are stressed. Zeoponics, or the cultivation of plants in zeolite substrates that both contain essential plant-growth cations on their exchange sites and have minor amounts of mineral phases and/or anion-exchange resins that supply essential plant growth ions, is discussed. It is suggested that synthetic zeolites at lunar bases could provide adsorption media for separation of various gases, act as catalysts and as molecular sieves, and serve as cation exchangers in sewage-effluent treatment, radioactive-waste disposal, and pollution control. A flow chart of a potential zeoponics system illustrates this process.

  18. Physics-Based Prognostics for Optimizing Plant Operation

    Energy Technology Data Exchange (ETDEWEB)

    Leonard J. Bond; Don B. Jarrell

    2005-03-01

    Scientists at the Pacific Northwest National Laboratory (PNNL) have examined the necessity for optimization of energy plant operation using 'DSOM{reg_sign}'--Decision Support Operation and Maintenance and this has been deployed at several sites. This approach has been expanded to include a prognostics components and tested on a pilot scale service water system, modeled on the design employed in a nuclear power plant. A key element in plant optimization is understanding and controlling the aging process of safety-specific nuclear plant components. This paper reports the development and demonstration of a physics-based approach to prognostic analysis that combines distributed computing, RF data links, the measurement of aging precursor metrics and their correlation with degradation rate and projected machine failure.

  19. AI-based alarm processing for a nuclear power plant

    International Nuclear Information System (INIS)

    A real-time expert system is implemented using artificial intelligence and object-oriented technology for alarm processing and presentation in a nuclear power plant. The knowledge base is constructed based on some schemes to process and display alarms to the plant operators. The activated alarms are dynamically prioritized by the reasoning rules, and then, presented on the process mimic overview and by some other means. To demonstrate the proposed system, the alarm processing and presentation is carried out in a simulated environment of the TMI-2 accident

  20. Data analysis strategies in nutritional metabolomics

    NARCIS (Netherlands)

    J. Westerhuis; E. van Velzen; H. Hoefsloot; A. Smilde

    2009-01-01

    In the expanding field of nutritional metabolomics the use of optimized and robust strategies are essential to find meaningful and significant results. Data from nutritional studies can be extremely large, multidimensional and complex. Moreover the data may hide just a subtle biological variation du

  1. Metabolomics in the fight against malaria

    Directory of Open Access Journals (Sweden)

    Jorge L Salinas

    2014-08-01

    Full Text Available Metabolomics uses high-resolution mass spectrometry to provide a chemical fingerprint of thousands of metabolites present in cells, tissues or body fluids. Such metabolic phenotyping has been successfully used to study various biologic processes and disease states. High-resolution metabolomics can shed new light on the intricacies of host-parasite interactions in each stage of the Plasmodium life cycle and the downstream ramifications on the host’s metabolism, pathogenesis and disease. Such data can become integrated with other large datasets generated using top-down systems biology approaches and be utilised by computational biologists to develop and enhance models of malaria pathogenesis relevant for identifying new drug targets or intervention strategies. Here, we focus on the promise of metabolomics to complement systems biology approaches in the quest for novel interventions in the fight against malaria. We introduce the Malaria Host-Pathogen Interaction Center (MaHPIC, a new systems biology research coalition. A primary goal of the MaHPIC is to generate systems biology datasets relating to human and non-human primate (NHP malaria parasites and their hosts making these openly available from an online relational database. Metabolomic data from NHP infections and clinical malaria infections from around the world will comprise a unique global resource.

  2. Microbial metabolomics in open microscale platforms.

    Science.gov (United States)

    Barkal, Layla J; Theberge, Ashleigh B; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A; Wang, Clay C C; Beebe, David J; Keller, Nancy P; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid-liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  3. Data fusion in metabolomic cancer diagnostics

    DEFF Research Database (Denmark)

    Bro, Rasmus; Nielsen, Hans Jørgen; Savorani, Francesco;

    2013-01-01

    We have recently shown that fluorescence spectroscopy of plasma samples has promising abilities regarding early detection of colorectal cancer. In the present paper, these results were further developed by combining fluorescence with the biomarkers, CEA and TIMP-1 and traditional metabolomic meas...

  4. Rifaximin modulates the vaginal microbiome and metabolome in women affected by bacterial vaginosis.

    Science.gov (United States)

    Laghi, Luca; Picone, Gianfranco; Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Donders, Gilbert; Capozzi, Francesco; Vitali, Beatrice

    2014-06-01

    Bacterial vaginosis (BV) is a common vaginal disorder characterized by the decrease of lactobacilli and overgrowth of Gardnerella vaginalis and resident anaerobic vaginal bacteria. In the present work, the effects of rifaximin vaginal tablets on vaginal microbiota and metabolome of women affected by BV were investigated by combining quantitative PCR and a metabolomic approach based on (1)H nuclear magnetic resonance. To highlight the general trends of the bacterial communities and metabolomic profiles in response to the antibiotic/placebo therapy, a multivariate statistical strategy was set up based on the trajectories traced by vaginal samples in a principal component analysis space. Our data demonstrated the efficacy of rifaximin in restoring a health-like condition in terms of both bacterial communities and metabolomic features. In particular, rifaximin treatment was significantly associated with an increase in the lactobacillus/BV-related bacteria ratio, as well as with an increase in lactic acid concentration and a decrease of a pool of metabolites typically produced by BV-related bacteria (acetic acid, succinate, short-chain fatty acids, and biogenic amines). Among the tested dosages of rifaximin (100 and 25 mg for 5 days and 100 mg for 2 days), 25 mg for 5 days was found to be the most effective. PMID:24709255

  5. Biomarkers of whale shark health: a metabolomic approach.

    Science.gov (United States)

    Dove, Alistair D M; Leisen, Johannes; Zhou, Manshui; Byrne, Jonathan J; Lim-Hing, Krista; Webb, Harry D; Gelbaum, Leslie; Viant, Mark R; Kubanek, Julia; Fernández, Facundo M

    2012-01-01

    In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus) from an aquarium collection was explored using (1)H nuclear magnetic resonance (NMR) spectroscopy and direct analysis in real time (DART) mass spectrometry (MS). Principal components analysis (PCA) of spectral data showed that individual animals could be resolved based on the metabolite composition of their serum and that two unhealthy individuals could be discriminated from the remaining healthy animals. The major difference between healthy and unhealthy individuals was the concentration of homarine, here reported for the first time in an elasmobranch, which was present at substantially lower concentrations in unhealthy whale sharks, suggesting that this metabolite may be a useful biomarker of health status in this species. The function(s) of homarine in sharks remain uncertain but it likely plays a significant role as an osmolyte. The presence of trimethylamine oxide (TMAO), another well-known protective osmolyte of elasmobranchs, at 0.1-0.3 mol L(-1) was also confirmed using both NMR and MS. Twenty-three additional potential biomarkers were identified based on significant differences in the frequency of their occurrence between samples from healthy and unhealthy animals, as detected by DART MS. Overall, NMR and MS provided complementary data that showed that metabolomics is a useful approach for biomarker prospecting in poorly studied species like elasmobranchs. PMID:23166652

  6. Biomarkers of whale shark health: a metabolomic approach.

    Directory of Open Access Journals (Sweden)

    Alistair D M Dove

    Full Text Available In a search for biomarkers of health in whale sharks and as exploration of metabolomics as a modern tool for understanding animal physiology, the metabolite composition of serum in six whale sharks (Rhincodon typus from an aquarium collection was explored using (1H nuclear magnetic resonance (NMR spectroscopy and direct analysis in real time (DART mass spectrometry (MS. Principal components analysis (PCA of spectral data showed that individual animals could be resolved based on the metabolite composition of their serum and that two unhealthy individuals could be discriminated from the remaining healthy animals. The major difference between healthy and unhealthy individuals was the concentration of homarine, here reported for the first time in an elasmobranch, which was present at substantially lower concentrations in unhealthy whale sharks, suggesting that this metabolite may be a useful biomarker of health status in this species. The function(s of homarine in sharks remain uncertain but it likely plays a significant role as an osmolyte. The presence of trimethylamine oxide (TMAO, another well-known protective osmolyte of elasmobranchs, at 0.1-0.3 mol L(-1 was also confirmed using both NMR and MS. Twenty-three additional potential biomarkers were identified based on significant differences in the frequency of their occurrence between samples from healthy and unhealthy animals, as detected by DART MS. Overall, NMR and MS provided complementary data that showed that metabolomics is a useful approach for biomarker prospecting in poorly studied species like elasmobranchs.

  7. Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts

    Directory of Open Access Journals (Sweden)

    Lynsey Macintyre

    2014-06-01

    Full Text Available Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS and nuclear magnetic resonance (NMR spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA was employed to differentiate the bacterial strains based on their chemical profiles. NMR 1H and correlation spectroscopy (COSY were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening.

  8. PlantID – DNA-based identification of multiple medicinal plants in complex mixtures

    Directory of Open Access Journals (Sweden)

    Howard Caroline

    2012-07-01

    Full Text Available Abstract Background An efficient method for the identification of medicinal plant products is now a priority as the global demand increases. This study aims to develop a DNA-based method for the identification and authentication of plant species that can be implemented in the industry to aid compliance with regulations, based upon the economically important Hypericum perforatum L. (St John’s Wort or Guan ye Lian Qiao. Methods The ITS regions of several Hypericum species were analysed to identify the most divergent regions and PCR primers were designed to anneal specifically to these regions in the different Hypericum species. Candidate primers were selected such that the amplicon produced by each species-specific reaction differed in size. The use of fluorescently labelled primers enabled these products to be resolved by capillary electrophoresis. Results Four closely related Hypericum species were detected simultaneously and independently in one reaction. Each species could be identified individually and in any combination. The introduction of three more closely related species to the test had no effect on the results. Highly processed commercial plant material was identified, despite the potential complications of DNA degradation in such samples. Conclusion This technique can detect the presence of an expected plant material and adulterant materials in one reaction. The method could be simply applied to other medicinal plants and their problem adulterants.

  9. PlantGL: A Python-based geometric library for 3D plant modelling at different scales

    OpenAIRE

    Pradal, Christophe; Boudon, Frédéric; Nouguier, Christophe; Chopard, Jérôme; Godin, Christophe

    2009-01-01

    International audience In this paper, we present PlantGL, an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants. This C++ geometric library is embedded in the Python language which makes it a powerful user-interactive platform for plant modeling in various biological application domains. PlantGL makes it possible to build and manipulate geometric models of plants or plant parts, ranging from tissues and organs to plant populations. Based on a scene g...

  10. Small Nuclear Co-generation Plants Based on Shipbuilding Technology

    International Nuclear Information System (INIS)

    The development of nuclear cogeneration plants and power desalination complexes of relatively small power, using proven shipbuilding technology, becomes more and more attractive for solving the power supply problems of remote districts of the Extreme North and the Far East with small and medium power grids and for removing the shortage of fresh water in different world regions. The idea of transportation of the power unit with high degree of readiness to the place of its location with minimum construction and mounting activities at the site is very attractive. Compactness typical of RP based on shipbuilding technology allows to develop floating or ground-based plants at minimum use of water area and territory. Small construction scope at the site under conditions of minimum anthropogenic loads and high ecological indices are important arguments in favor of floating nuclear cogeneration plant based on ship power units against the alternative fossil sources. At present, the activities on floating nuclear cogeneration plant design, which is developed on the basis of floating power unit with two KLT-40S reactor plant, which is a modified option of standard KLT-40-type ship plant for icebreaker fleet in Russia are the most advanced. To date, a detailed design of reactor plant has been developed and approved, design activities on floating power unit are in the stage of completion, the site for its location has been selected and licensing by GAN, Russia, is in progress. Besides OKBM has developed some designs of nuclear cogeneration plants of different power on the basis of integral reactor plants, using the experience of transport and stationary power plants designing. Nuclear cogeneration plant investment analysis showed acceptable social and economical efficiency of the design that creates conditions for commercial construction of floating power units with KLT-40S reactor plan. At the same time the reduction of the design recovering terms, increase of budget income and

  11. Shaking table test on base isolated FBR plant model, 1

    International Nuclear Information System (INIS)

    Shaking table test on seismically isolated FBR plant model is carried out. The model is three story steel frame structure supported by nine laminated rubber bearings which are reduced to a scale of 1/15. The effectiveness of base isolation system is verified through this study. (author)

  12. Effects of plant-based diets on plasma lipids.

    Science.gov (United States)

    Ferdowsian, Hope R; Barnard, Neal D

    2009-10-01

    Dyslipidemia is a primary risk factor for cardiovascular disease, peripheral vascular disease, and stroke. Current guidelines recommend diet as first-line therapy for patients with elevated plasma cholesterol concentrations. However, what constitutes an optimal dietary regimen remains a matter of controversy. Large prospective trials have demonstrated that populations following plant-based diets, particularly vegetarian and vegan diets, are at lower risk for ischemic heart disease mortality. The investigators therefore reviewed the published scientific research to determine the effectiveness of plant-based diets in modifying plasma lipid concentrations. Twenty-seven randomized controlled and observational trials were included. Of the 4 types of plant-based diets considered, interventions testing a combination diet (a vegetarian or vegan diet combined with nuts, soy, and/or fiber) demonstrated the greatest effects (up to 35% plasma low-density lipoprotein cholesterol reduction), followed by vegan and ovolactovegetarian diets. Interventions allowing small amounts of lean meat demonstrated less dramatic reductions in total cholesterol and low-density lipoprotein levels. In conclusion, plant-based dietary interventions are effective in lowering plasma cholesterol concentrations. PMID:19766762

  13. Metabolomics of Clostridial Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Rabinowitz, Joshua D [Princeton Univ., NJ (United States); Aristilde, Ludmilla [Cornell Univ., Ithaca, NY (United States); Amador-Noguez, Daniel [Univ. of Wisconsin, Madison, WI (United States)

    2015-09-08

    Members of the genus Clostridium collectively have the ideal set of the metabolic capabilities for fermentative biofuel production: cellulose degradation, hydrogen production, and solvent excretion. No single organism, however, can effectively convert cellulose into biofuels. Here we developed, using metabolomics and isotope tracers, basic science knowledge of Clostridial metabolism of utility for future efforts to engineer such an organism. In glucose fermentation carried out by the biofuel producer Clostridium acetobutylicum, we observed a remarkably ordered series of metabolite concentration changes as the fermentation progressed from acidogenesis to solventogenesis. In general, high-energy compounds decreased while low-energy species increased during solventogenesis. These changes in metabolite concentrations were accompanied by large changes in intracellular metabolic fluxes, with pyruvate directed towards acetyl-CoA and solvents instead of oxaloacetate and amino acids. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources from biomass production into solvent production. In contrast to C. acetobutylicum, which is an avid fermenter, C. cellulolyticum metabolizes glucose only slowly. We find that glycolytic intermediate concentrations are radically different from fast fermenting organisms. Associated thermodynamic and isotope tracer analysis revealed that the full glycolytic pathway in C. cellulolyticum is reversible. This arises from changes in cofactor utilization for phosphofructokinase and an alternative pathway from phosphoenolpyruvate to pyruvate. The net effect is to increase the high-energy phosphate bond yield of glycolysis by 150% (from 2 to 5) at the expense of lower net flux. Thus, C. cellulolyticum prioritizes glycolytic energy efficiency over speed. Degradation of cellulose results in other sugars in addition to glucose. Simultaneous feeding of stable isotope-labeled glucose and unlabeled pentose sugars

  14. Present and foreseeable future of metabolomics in forensic analysis.

    Science.gov (United States)

    Castillo-Peinado, L S; Luque de Castro, M D

    2016-06-21

    The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed. PMID:27188312

  15. Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

    Directory of Open Access Journals (Sweden)

    Nozomu Sakurai

    2014-01-01

    Full Text Available A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal, where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

  16. Biomarkers in bladder cancer: A metabolomic approach using in vitro and ex vivo model systems.

    Science.gov (United States)

    Rodrigues, Daniela; Jerónimo, Carmen; Henrique, Rui; Belo, Luís; de Lourdes Bastos, Maria; de Pinho, Paula Guedes; Carvalho, Márcia

    2016-07-15

    Metabolomics has recently proved to be useful in the area of biomarker discovery for cancers in which early diagnostic and prognostic biomarkers are urgently needed, as is the case of bladder cancer (BC). This article presents a comprehensive review of the literature on the metabolomic studies on BC, highlighting metabolic pathways perturbed in this disease and the altered metabolites as potential biomarkers for BC detection. Current disease model systems used in the study of BC metabolome include in vitro-cultured cancer cells, ex vivo neoplastic bladder tissues and biological fluids, mainly urine but also blood serum/plasma, from BC patients. The major advantages and drawbacks of each model system are discussed. Based on available data, it seems that BC metabolic signature is mainly characterized by alterations in metabolites related to energy metabolic pathways, particularly glycolysis, amino acid and fatty acid metabolism, known to be crucial for cell proliferation, as well as glutathione metabolism, known to be determinant in maintaining cellular redox balance. In addition, purine and pyrimidine metabolism as well as carnitine species were found to be altered in BC. Finally, it is emphasized that, despite the progress made in respect to novel biomarkers for BC diagnosis, there are still some challenges and limitations that should be addressed in future metabolomic studies to ensure their translatability to clinical practice. PMID:26804544

  17. GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Brian; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernard O.; Hyduke, Daniel R.

    2013-11-15

    Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been reported. Results: GIMMME (Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics, and intracellular metabolomics data. GIMMME establishes metabolite utilization requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions, and also provides calculations of the turnover (production / consumption) flux of metabolites. GIMMME was employed to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIMMME has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/

  18. Metabolomic applications to decipher gut microbial metabolic influence in health and disease

    Directory of Open Access Journals (Sweden)

    Francois-Pierre eMartin

    2012-04-01

    Full Text Available Dietary preferences and nutrients composition have been shown to influence human and gut microbial metabolism, which ultimately has specific effects on health and diseases’ risk. Increasingly, results from molecular biology and microbiology demonstrate the key role of the gut microbiota metabolic interface to the overall mammalian host’s health status. There is therefore raising interest in nutrition research to characterize the molecular foundations of the gut microbial mammalian cross-talk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology approaches, such as metabolomics, to underpin the highly complex metabolic exchanges between diverse biological compartments, including organs, systemic biofluids and microbial symbionts. By the development of specific biomarkers for prediction of health and disease, metabolomics is increasingly used in clinical applications as regard to disease aetiology, diagnostic stratification and potentially mechanism of action of therapeutical and nutraceutical solutions. Surprisingly, an increasing number of metabolomics investigations in pre-clinical and clinical studies based on proton nuclear magnetic resonance (1H NMR spectroscopy and mass spectrometry (MS provided compelling evidence that system wide and organ-specific biochemical processes are under the influence of gut microbial metabolism. This review aims at describing recent applications of metabolomics in clinical fields where main objective is to discern the biochemical mechanisms under the influence of the gut microbiota, with insight into gastrointestinal health and diseases diagnostics and improvement of homeostasis metabolic regulation.

  19. Metabolomic variation of brassica rapa var. rapa (var. raapstelen) and raphanus sativus l. at different developmental stages

    OpenAIRE

    Jahangir, M.; Abdel-Farid, I.B.; De Vos; Jonker, H.H.; Choi, Y. H.; Verpoorte, R.

    2014-01-01

    Brassica rapa (var. raapstelen) and Raphanus sativus (red radish) are being used as food and fodder while also known as model in recent plant research due to the diversity of metabolites as well as genetic resemblance to Arabidopsis. This study explains the change in metabolites (amino acids, organic acids, chlorophyll, carotenoids, tocopherols, ascorbic acid, sucrose, phenylpropanoids and glucosinolates) during plant development. In present study the metabolomic variation in relation to plan...

  20. Model-based reasoning and the control of process plants

    International Nuclear Information System (INIS)

    In addition to feedback control, safe and economic operation of industrial process plants requires discrete-event type logic control like for example automatic control sequences, interlocks, etc. A lot of complex routine reasoning is involved in the design and verification and validation (VandV) of such automatics. Similar reasoning tasks are encountered during plant operation in action planning and fault diagnosis. The low-level part of the required problem solving is so straightforward that it could be accomplished by a computer if only there were plant models which allow versatile mechanised reasoning. Such plant models and corresponding inference algorithms are the main subject of this report. Deep knowledge and qualitative modelling play an essential role in this work. Deep knowledge refers to mechanised reasoning based on the first principles of the phenomena in the problem domain. Qualitative modelling refers to knowledge representation formalism and related reasoning methods which allow solving problems on an abstraction level higher than for example traditional simulation and optimisation. Prolog is a commonly used platform for artificial intelligence (Al) applications. Constraint logic languages like CLP(R) and Prolog-III extend the scope of logic programming to numeric problem solving. In addition they allow a programming style which often reduces the computational complexity significantly. An approach to model-based reasoning implemented in constraint logic programming language CLP(R) is presented. The approach is based on some of the principles of QSIM, an algorithm for qualitative simulation. It is discussed how model-based reasoning can be applied in the design and VandV of plant automatics and in action planning during plant operation. A prototype tool called ISIR is discussed and some initial results obtained during the development of the tool are presented. The results presented originate from preliminary test results of the prototype obtained

  1. Plant-based fertilizers for organic vegetable production

    DEFF Research Database (Denmark)

    Sørensen, Jørn Nygaard; Thorup-Kristensen, Kristian

    2011-01-01

    To ensure high yield and quality in organic vegetable production, crops often require additional fertilizer applied during the season. Due to the risk of contamination of edible plant products from slurry, plant-based fertilizers may be used as an alternative. The purpose of our work was to develop...... fertility, the term “mobile green manures” is used for green-manure crops that are harvested in one field and then moved as a whole and used as fertilizer in other fields. To further investigate mobile-green-manure crops for use as efficient fertilizers, pot and field experiments were conducted with...

  2. Healthy pregnancy and prenatal disorders followed by blood plasma metabolomics

    OpenAIRE

    Pinto, Joana Isabel Monteiro

    2015-01-01

    The work presented in this thesis aimed to investigate the impact of healthy pregnancy and selected prenatal disorders on the metabolome and lipidome of maternal blood plasma, in order to define new potential biomarkers for non-invasive prediction and diagnosis. Chapter 1 describes the present status and challenges of the clinically relevant prenatal disorders, along with a presentation of the metabolomics strategy applied and the state of the art of metabolomics in prenatal research. All ...

  3. Metabolome analysis - mass spectrometry and microbial primary metabolites

    OpenAIRE

    Højer-Pedersen, Jesper Juul; Nielsen, Jens; Smedsgaard, Jørn

    2008-01-01

    While metabolite profiling has been carried out for decades, the scope for metabolite analysis have recently been broadened to aim at all metabolites in a living organism – also referred to as the metabolome. This is a great challenge, which requires versatile analytical technologies that are highly sensitive and specific, and to undertake this challenge mass spectrometry (MS) is among the best candidates. Along with analysis of the metabolome the research area of metabolomics has evolved. Me...

  4. METABOLOMICS IN MEDICAL SCIENCES--TRENDS, CHALLENGES AND PERSPECTIVES.

    Science.gov (United States)

    Klupczyńska, Agnieszka; Dereziński, Paweł; Kokot, Zenon J

    2015-01-01

    Metabolomics is the latest of the "omic" technologies that involves comprehensive analysis of small molecule metabolites of an organism or a specific biological sample. Metabolomics provides an insight into the cell status and describes an actual health condition of organisms. Analysis of metabolome offers a unique opportunity to study the influence of genetic variation, disease, applied treatment or diet on endogenous metabolic state of organisms. There are many areas that might benefit from metabolomic research. In the article some applications of this novel "omic" technology in the field of medical sciences are presented. One of the most popular aims of metabolomic studies is biomarker discovery. Despite using the state-of-art analytical techniques along with advanced bioinformatic tools, metabolomic experiments encounter numerous difficulties and pitfalls. Challenges that researchers in the field of analysis of metabolome have to face include i.a., technical limitations, bioinformatic challenges and integration with other "omic" sciences. One of the grand challenges for studies in the field of metabolomics is to tackle the problem of data analysis, which is probably the most time consuming stage of metabolomic workflow and requires close collaboration between analysts, clinicians and experts in chemometric analysis. Implementation of metabolomics into clinical practice will be dependent on establishment of standardized protocols in analytical performance and data analysis and development of fit-for-purpose biomarker method validation. Metabolomics allows to achieve a sophisticated level of information about biological systems and opens up new perspectives in many fields of medicine, especially in oncology. Apart from its extensive cognitive significance, metabolomics manifests also a practical importance as it may lead to design of new non-invasive, sensitive and specific diagnostic techniques and development of new therapies. PMID:26647618

  5. Review: Microfluidic Applications in Metabolomics and Metabolic Profiling

    OpenAIRE

    Kraly, James R.; Holcomb, Ryan E.; Guan, Qian; Charles S. Henry

    2009-01-01

    Metabolomics is an emerging area of research focused on measuring small molecules in biological samples. There are a number of different types of metabolomics, ranging from global profiling of all metabolites in a single sample to measurement of a selected group of analytes. Microfluidics and related technologies have been used in this research area with good success. The aim of this review article is to summarize the use of microfluidics in metabolomics. Direct application of microfluidics t...

  6. Metabolomics of Oxidative Stress in Recent Studies of Endogenous and Exogenously Administered Intermediate Metabolites

    Directory of Open Access Journals (Sweden)

    Jeffrey G. Pelton

    2011-09-01

    Full Text Available Aerobic metabolism occurs in a background of oxygen radicals and reactive oxygen species (ROS that originate from the incomplete reduction of molecular oxygen in electron transfer reactions. The essential role of aerobic metabolism, the generation and consumption of ATP and other high energy phosphates, sustains a balance of approximately 3000 essential human metabolites that serve not only as nutrients, but also as antioxidants, neurotransmitters, osmolytes, and participants in ligand-based and other cellular signaling. In hypoxia, ischemia, and oxidative stress, where pathological circumstances cause oxygen radicals to form at a rate greater than is possible for their consumption, changes in the composition of metabolite ensembles, or metabolomes, can be associated with physiological changes. Metabolomics and metabonomics are a scientific disciplines that focuse on quantifying dynamic metabolome responses, using multivariate analytical approaches derived from methods within genomics, a discipline that consolidated innovative analysis techniques for situations where the number of biomarkers (metabolites in our case greatly exceeds the number of subjects. This review focuses on the behavior of cytosolic, mitochondrial, and redox metabolites in ameliorating or exacerbating oxidative stress. After reviewing work regarding a small number of metabolites—pyruvate, ethyl pyruvate, and fructose-1,6-bisphosphate—whose exogenous administration was found to ameliorate oxidative stress, a subsequent section reviews basic multivariate statistical methods common in metabolomics research, and their application in human and preclinical studies emphasizing oxidative stress. Particular attention is paid to new NMR spectroscopy methods in metabolomics and metabonomics. Because complex relationships connect oxidative stress to so many physiological processes, studies from different disciplines were reviewed. All, however, shared the common goal of ultimately

  7. Preliminary Metabolomic Analysis of Goat Milk from Different Breeds Using Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Mohamad Razlan Abd Rahman

    2015-01-01

    Full Text Available Metabolomics facilitates the identification of numerous metabolites in a sample with mass less than 1 kD. The purpose of this study was to determine the effect of feed on the metabolites in raw goat milk samples obtained from two breeds namely Saanen and Shami that were collected from a farm in Selangor and Negeri Sembilan, Malaysia, respectively. The types of feed given to the goats were recorded. The fat in the samples were removed via centrifugation before analysis using liquid chromatography quadrupole time of flight mass spectrometry (LC-QToF-MS. From the chromatograms obtained the presence of veterinary drug residue, di- and tri-peptides, short and long-chain fatty acids, some components from plants, and insecticide residue were detected using HMP, KEGG, LMP, and METLIN databases identification. It is expected that through metabolomics study it may be possible to formulate the feed and determine the breed that give good quality milk.

  8. An Evaluation of 1-Deoxynojirimycin Oral Administration in Eri Silkworm through Fat Body Metabolomics Based on 1H Nuclear Magnetic Resonance

    Science.gov (United States)

    Wen, Chao-wei; Lin, Xiao-dong; Dong, Min-jian; Deng, Ming-jie

    2016-01-01

    1-Deoxynojirimycin (DNJ), the main hypoglycemic constituent in mulberry (Morus alba) latex, has been extensively researched. Although there is considerable interest in the biological effects of DNJ, the roles of 1-deoxynojirimycin (DNJ) in glycometabolism and energy metabolism in insects have received little attention. In this paper, 1H nuclear magnetic resonance (1H NMR) based metabonomic was performed to study the effects of the oral supplementation of 0.25% DNJ, 0.5% DNJ, latex, and the mixture of 0.5% DNJ and latex (1 : 1) on the fat body glycometabolism and energy metabolism of the fourth-instar larvae of Eri silkworms, Samia cynthia ricini. Metabolic pattern recognition analysis (partial least square-discriminant analysis, PLS-DA) of fat body extracts indicated that the groups of 0.25% DNJ, 0.5% DNJ, latex, and the mixture of 0.5% DNJ and latex (1 : 1) were significantly different from the control group. Further, compared to the control group, the metabolites levels of lactate, trehalose, succinate, malate, and fumarate were remarkably changed in experimental groups, which were involved in glycolysis, hydrolysis of trehalose, and tricarboxylic acid (TCA) cycle. Our results indicate that DNJ has a positive impact on the reverse energy metabolism of Eri silkworms and metabonomic analysis based on NMR can be used as a tool to identify potential biomarkers. PMID:27294120

  9. Laser Vision-Based Plant Geometries Computation in Greenhouses

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2014-04-01

    Full Text Available Plant growth statuses are important parameters in the greenhouse environment control system. It is time-consumed and less accuracy that measuring the plant geometries manually in greenhouses. To find a portable method to measure the growth parameters of plants portably and automatically, a laser vision-based measurement system was developed in this paper, consisting of a camera and a laser sheet that scanned the plant vertically. All equipments were mounted on a metal shelf in size of 30cm*40cm*100cm. The 3D point cloud was obtained with the laser sheet scanning the plant vertically, while the camera videoing the laser lines which projected on the plant. The calibration was conducted by a two solid boards standing together in an angle of 90. The camera’s internal and external parameters were calibrated by Image toolbox in MatLab®. It is useful to take a reference image without laser light and to use difference images to obtain the laser line. Laser line centers were extracted by improved centroid method. Thus, we obtained the 3D point cloud structure of the sample plant. For leaf length measurement, iteration method for point clouds was used to extract the axis of the leaf point cloud set. Start point was selected at the end of the leaf point cloud set as the first point of the leaf axis. The points in a radian of certain distance around the start point were chosen as the subset. The centroid of the subset of points was calculated and taken as the next axis point. Iteration was continued until all points in the leaf point cloud set were selected. Leaf length was calculated by curve fitting on these axis points. In order to increase the accuracy of curve fitting, bi-directional start point selection was useful. For leaf area estimation, exponential regression model was used to describe the grown leaves for sampled plant (water spinach in this paper. To evaluate the method in a sample of 18 water spinaches, planted in the greenhouse (length 16

  10. Effects of Perfluorooctanoic Acid on Metabolic Profiles in Brain and Liver of Mouse Revealed by a High-throughput Targeted Metabolomics Approach

    OpenAIRE

    Nanyang Yu; Si Wei; Meiying Li; Jingping Yang; Kan Li; Ling Jin; Yuwei Xie; Giesy, John P; Xiaowei Zhang; Hongxia Yu

    2016-01-01

    Perfluorooctanoic acid (PFOA), a perfluoroalkyl acid, can result in hepatotoxicity and neurobehavioral effects in animals. The metabolome, which serves as a connection among transcriptome, proteome and toxic effects, provides pathway-based insights into effects of PFOA. Since understanding of changes in the metabolic profile during hepatotoxicity and neurotoxicity were still incomplete, a high-throughput targeted metabolomics approach (278 metabolites) was used to investigate effects of expos...

  11. Introduction of nuclear power plant based on reliability centered maintenance

    International Nuclear Information System (INIS)

    A maintenance program based on RCM (reliability centered maintenance) is used by many countries and increased safety, reliability and economy of plants. RCM and its application conditions to the nuclear power plants in USA and introduction conditions for Japan are explained. The present situation of maintenance and change of maintenance technologies in the world is stated. RCM is the best tool for working out the maintenance program. The basic approach is selection of system and the sphere of activity, identification of accident mode and causes by the FFA (functional failure analysis) and the FMEA (failure modes and effects analysis), and selection of the effective maintenance method for accident mode by the LTA (logic tree analysis) and optimization of maintenance. The maintenance of nuclear power plants and an on-side inspection of RCM in USA are described. The system for maintenance program and construction of the system for keeping the electric power joint technologies in Japan are illustrated. (S.Y.)

  12. Multimedia-based Medicinal Plants Sustainability Management System

    Directory of Open Access Journals (Sweden)

    Zacchaeus Omogbadegun

    2011-09-01

    Full Text Available Medicinal plants are increasingly recognized worldwide as an alternative source of efficacious and inexpensive medications to synthetic chemo-therapeutic compound. Rapid declining wild stocks of medicinal plants accompanied by adulteration and species substitutions reduce their efficacy, quality and safety. Consequently, the low accessibility to and non-affordability of orthodox medicine costs by rural dwellers to be healthy and economically productive further threaten their life expectancy. Finding comprehensive information on medicinal plants of conservation concern at a global level has been difficult. This has created a gap between computing technologies' promises and expectations in the healing process under complementary and alternative medicine. This paper presents the design and implementation of a Multimedia-based Medicinal Plants Sustainability Management System addressing these concerns. Medicinal plants' details for designing the system were collected through semi-structured interviews and databases. Unified Modelling Language, Microsoft-Visual-Studio.Net, C#3.0, Microsoft-Jet-Engine4.0, MySQL, Loquendo Multilingual Text-to-Speech Software, YouTube, and VLC Media Player were used.

  13. Selection of Taste Markers Related to Lactic Acid Bacteria Microflora Metabolism for Chinese Traditional Paocai: A Gas Chromatography-Mass Spectrometry-Based Metabolomics Approach.

    Science.gov (United States)

    Zhao, Nan; Zhang, Chuchu; Yang, Qin; Guo, Zhuang; Yang, Bo; Lu, Wenwei; Li, Dongyao; Tian, Fengwei; Liu, Xiaoming; Zhang, Hao; Chen, Wei

    2016-03-23

    Traditional paocai brine (PB) is continuously propagated by back-slopping and contains numerous lactic acid bacteria (LAB) strains. Although PB is important for the quality of paocai (Chinese sauerkraut), the taste features, taste-related compounds of PB-paocai and the effects of LAB communities from PB on the taste compounds remain unclear. An electronic tongue was used to evaluate the taste features of 13 PB-paocai samples. Umami, saltiness, bitterness, sweetness, and aftertaste astringency were the main taste features of PB-paocai. A total of 14 compounds were identified as discriminant taste markers for PB-paocai via gas chromatography-mass spectrometry (GC-MS)-based multimarker profiling. A LAB co-culture (Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus ethanoliduran) from PB could significantly increase glutamic acid (umami), sucrose (sweetness), glycine (sweetness), lactic acid (sourness), and γ-aminobutyric acid in PB-paocai, which would endow it with important flavor features. Such features could then facilitate starter screening and fermentation optimization to produce paocai-related foods with better nutritional and sensory qualities. PMID:26915389

  14. Strategies to control pollution from coal based thermal power plants

    Energy Technology Data Exchange (ETDEWEB)

    Sengupta, B.; Paliwal, S.K. [Central Pollution Control Board, Delhi (India)

    1997-12-31

    In India, coal based thermal power plants contribute a prime source of energy supply. It has become necessary to adopt an integrated strategy with emphasis on waste minimisation in addition to control at source. Use of clean process technologies such as Fluidised Bed Combustion (FBC, PFBC and AFBC) boilers which not only provide higher combustion efficiency but also emit less amount of pollutants. In order to improve performance of existing power stations and to reduce emission of fly ash, the power plants should use beneficiated coal. Besides the savings in transportation cost and reduction in ash generation, the Plant Load Factor (PLF) of power stations will also be increased considerably after using beneficiated coal. To promote use of flyash for various useful purposes, it is necessary to a adopt dry flyash collection system. Fiscal incentives on equipment and machineries, exemption on excise and custom duties and free availability of land and electricity to the entrepreneur are among the measures required for reducing the problems caused by flyash. The paper provides an overview of the pollution problems in coal based power plants and possible options for waste minimisation and pollution control. 4 tabs.

  15. Plant operator performance evaluation based on cognitive process analysis experiment

    International Nuclear Information System (INIS)

    This paper reports on an experiment to clarify plant operators' cognitive processes that has been performed, to improve the man-machine interface which supports their diagnoses and decisions. The cognitive processes under abnormal conditions were evaluated by protocol analyses interviews, etc. in the experiment using a plant training simulator. A cognitive process model is represented by a stochastic network, based on Rasmussen's decision making model. Each node of the network corresponds to an element of the cognitive process, such as observation, interpretation, execution, etc. Some observations were obtained as follows, by comparison of Monte Carlo simulation results with the experiment results: A process to reconfirm the plant parameters after execution of a task and feedback paths from this process to the observation and the task definition of next task were observed. The feedback probability average and standard deviation should be determined for each incident type to explain correctly the individual differences in the cognitive processes. The tendency for the operator's cognitive level to change from skill-based to knowledge-based via rule-based behavior was observed during the feedback process

  16. Metabolomics to Detect Response of Lettuce (Lactuca sativa) to Cu(OH)2 Nanopesticides: Oxidative Stress Response and Detoxification Mechanisms.

    Science.gov (United States)

    Zhao, Lijuan; Ortiz, Cruz; Adeleye, Adeyemi S; Hu, Qirui; Zhou, Hongjun; Huang, Yuxiong; Keller, Arturo A

    2016-09-01

    There has been an increasing influx of nanopesticides into agriculture in recent years. Understanding the interaction between nanopesticides and edible plants is crucial in evaluating the potential impact of nanotechnology on the environment and agriculture. Here we exposed lettuce plants to Cu(OH)2 nanopesticides (1050-2100 mg/L) through foliar spray for one month. Inductively coupled plasma-mass spectrometry (ICP-MS) results indicate that 97-99% (1353-2501 mg/kg) of copper was sequestered in the leaves and only a small percentage (1-3%) (17.5-56.9 mg/kg) was translocated to root tissues through phloem loading. Gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) based metabolomics combined with partial least squares-discriminant analysis (PLS-DA) multivariate analysis revealed that Cu(OH)2 nanopesticides altered metabolite levels of lettuce leaves. Tricarboxylic (TCA) cycle and a number of amino acid-related biological pathways were disturbed. Some antioxidant levels (cis-caffeic acid, chlorogenic acid, 3,4-dihydroxycinnamic acid, dehydroascorbic acid) were significantly decreased compared to the control, indicating that oxidative stress and a defense response occurred. Nicotianamine, a copper chelator, increased by 12-27 fold compared to the control, which may represent a detoxification mechanism. The up-regulation of polyamines (spermidine and putrescine) and potassium may mitigate oxidative stress and enhance tolerance. The data presented here provide a molecular-scale perspective on the response of plants to copper nanopesticides. PMID:27483188

  17. Application of 1H-NMR metabolomic profiling for reef-building corals.

    Directory of Open Access Journals (Sweden)

    Emilia M Sogin

    Full Text Available In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (1H-NMR-based metabolomics approach in characterizing coral metabolite profiles by 1 investigating technical, intra-, and inter-sample variation, 2 evaluating the ability to recover targeted metabolite spikes, and 3 assessing the potential for this method to differentiate among coral species. Our results indicate 1H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM. Finally, 1H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix. Collectively, these data indicate that 1H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change.

  18. Application of 1H-NMR Metabolomic Profiling for Reef-Building Corals

    Science.gov (United States)

    Sogin, Emilia M.; Anderson, Paul; Williams, Philip; Chen, Chii-Shiarng; Gates, Ruth D.

    2014-01-01

    In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions) across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (1H-NMR)-based metabolomics approach in characterizing coral metabolite profiles by 1) investigating technical, intra-, and inter-sample variation, 2) evaluating the ability to recover targeted metabolite spikes, and 3) assessing the potential for this method to differentiate among coral species. Our results indicate 1H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA) to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM). Finally, 1H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix). Collectively, these data indicate that 1H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change. PMID:25354140

  19. Metabolomic and elemental profiling of melon fruit quality as affected by genotype and environment

    DEFF Research Database (Denmark)

    Bernillon, Stéphane; Biais, Benoit; Deborde, Catherine;

    2013-01-01

    , contrasting agricultural management practices (greenhouse vs. field with or without fruit thinning) and planting date. Two hundred and ninety-one analytes discriminated two contrasting varieties, one from the var. inodorous group and the other from the var. cantaloupensis group. Two hundred and eighty...... tools to characterize the quality of fruits cultivated under commercial conditions. They can also provide knowledge on fruit metabolism and the mechanisms of plant response to environmental modifications, thereby paving the way for metabolomics-guided improvement of cultural practices for better fruit...

  20. Metabolomics analysis of shucked mussels' freshness.

    Science.gov (United States)

    Aru, Violetta; Pisano, Maria Barbara; Savorani, Francesco; Engelsen, Søren Balling; Cosentino, Sofia; Cesare Marincola, Flaminia

    2016-08-15

    In this work a NMR metabolomics approach was applied to analyze changes in the metabolic profile of the bivalve mollusk Mytilus galloprovincialis upon storage at 0°C and 4°C for 10 and 6 days, respectively. The most significant microbial groups involved in spoilage of mussels were also investigated. The time-related metabolic signature of mussels was analysed by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) which revealed a clear discrimination between the fresh samples and those stored at 0°C and 4°C. The results evidenced a noticeable increase in acetate, lactate, succinate, alanine, branched chain amino acids, trimethylamine and a progressive decline of osmolytes like betaine, homarine and taurine during storage. Exploration of the correlations of these metabolites with microbial counts suggested their use as potential biomarkers of spoilage. The results support the use of NMR metabolomics as a valuable tool to provide information on seafood freshness. PMID:27006214

  1. Metabolomic analysis of three Mollicute species.

    Directory of Open Access Journals (Sweden)

    Anna A Vanyushkina

    Full Text Available We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.

  2. An untargeted metabolomics-driven approach based on LC-TOF/MS and LC-MS/MS for the screening of xenobiotics and metabolites of Zhi-Zi-Da-Huang decoction in rat plasma.

    Science.gov (United States)

    Wu, Huan; Li, Xixi; Yan, Xuemei; An, Li; Luo, Kaiwen; Shao, Mingjing; Jiang, Yue; Xie, Rui; Feng, Fang

    2015-11-10

    Zhi-Zi-Da-Huang decoction (ZZDHD), a typical traditional Chinese medicine prescription, is widely used in clinical practice for the treatment of alcoholic liver disease. However, due to lack of holistic metabolic research, the active ingredients of ZZDHD have not been fully elucidated. It entails a huge obstacle for the quality evaluation, pharmacokinetic studies and clinical-safe medication administration of ZZDHD. In this work, an untargeted metabolomics-driven approach was proposed to rapidly screen and characterize xenobiotics and related metabolites in vivo conducted by LC-TOF/MS and LC-QqQ/MS. The tR-m/z pairs which were present in the ZZDHD-dosed group and absent in the control group could be clearly displayed by XCMS Online platform combined with supervised orthogonal partial least squares discriminant analysis. Among them, a total of 61 ZZDHD-related xenobiotics and metabolites including 34 prototype components and 27 metabolites were rapidly identified or tentatively characterized in rat plasma. The results indicated that iridoid glycosides and monoterpenoids from Gardenia jasminoides Ellis, flavonoid glycosides from Citrus aurantium L., as well as anthraquinones from Rheum palmatum L. were the main absorbed chemical components of ZZDHD. Hydrolysis, glucuronidation and sulfation were the main metabolic pathways of ZZDHD in vivo. The present study provided a solid basis for further revealing the relationship between the xenobiotic metabolome and pharmacological activity of ZZDHD. In addition, the application of untargeted metabolomics-driven approach offers a fresh insight for rapid screening and identifying xenobiotics and metabolites of ZZDHD and other multiherb prescription. PMID:26275719

  3. Analysis of axial-induction-based wind plant control using an engineering and a high-order wind plant model

    Energy Technology Data Exchange (ETDEWEB)

    Annoni, Jennifer [Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Aerospace Engineering and Mechanics; Gebraad, Pieter M. O. [National Renewable Energy Laboratory, Golden CO (United States); Scholbrock, Andrew K. [National Renewable Energy Laboratory, Golden CO (United States); Fleming, Paul A. [National Renewable Energy Laboratory, Golden CO (United States); Wingerden, Jan-Willem van [Delft Center for Systems and Control, Delft University of Technology, Delft (Netherlands)

    2015-08-14

    Wind turbines are typically operated to maximize their performance without considering the impact of wake effects on nearby turbines. Wind plant control concepts aim to increase overall wind plant performance by coordinating the operation of the turbines. This paper focuses on axial-induction-based wind plant control techniques, in which the generator torque or blade pitch degrees of freedom of the wind turbines are adjusted. The paper addresses discrepancies between a high-order wind plant model and an engineering wind plant model. Changes in the engineering model are proposed to better capture the effects of axial-induction-based control shown in the high-order model.

  4. Applying computer-based procedures in nuclear power plants

    International Nuclear Information System (INIS)

    Plant operation procedures are used to guide operators in coping with normal, abnormal or emergency situations in a process control system. Historically, the plant procedures have been paper-based (PBP), with the digitalisation trend in these complex systems computer-based procedures (CBPs) are being developed to support procedure use. This work shows briefly the research on CBPs at the Human-System Interface Laboratory (LABIHS). The emergency operation procedure EOP-0 of the LABIHS NPP simulator was implemented in the ImPRO CBP system. The ImPRO system was chosen for test because it is available for download in the Internet. A preliminary operation test using the implemented procedure in the CBP system was realized and the results were compared to the operation through PBP use. (author)

  5. Condition Based and Risk Informed Management for Power Plant Efficiency

    International Nuclear Information System (INIS)

    The efficiency management of power plants is an obvious and tedious topic, but it is still one of the most important pending issues. Efficiency management is not a difficult discipline in terms of academic standard. However, we can realize how we are lack of knowledge from the viewpoint of field practice. Nowadays, utilities are trying to strictly manage plant efficiency because of cost competitiveness with other energy resources. Efficiency management can be widely characterized from the replacement of hardware to the optimization of operation and maintenance using the advanced IT technologies. In this paper, we will overview the advanced efficiency management strategy, which is based on the IT technologies. We named the strategy as condition-based risk-informed efficiency management. This strategy aims at the implementation of predictive as well as proactive maintenance considering the risk in terms of cost

  6. Economic Study of Solar Thermal Plant based on Gas Turbines

    OpenAIRE

    Cabané Fernández, Albert

    2012-01-01

    The goal of this thesis is to carry out an economic analysis of solar thermal plant based on gas turbines. Throughout the project , there is a brief overview of different technologies used today in CSP without going into greater depth in most of them, but emphasizing solar tower technology with solar hybrid gas turbines. Having explained the reason why this technology has been chosen, possible configurations currently found in the solar panorama will be considered. Then, ...

  7. Sustainability of plant-based diets: back to the future.

    Science.gov (United States)

    Sabaté, Joan; Soret, Sam

    2014-07-01

    Plant-based diets in comparison to diets rich in animal products are more sustainable because they use many fewer natural resources and are less taxing on the environment. Given the global population explosion and increase in wealth, there is an increased demand for foods of animal origin. Environmental data are rapidly accumulating on the unsustainability of current worldwide food consumption practices that are high in meat and dairy products. Natural nonrenewable resources are becoming scarce, and environmental degradation is rapidly increasing. At the current trends of food consumption and environmental changes, food security and food sustainability are on a collision course. Changing course (to avoid the collision) will require extreme downward shifts in meat and dairy consumption by large segments of the world's population. Other approaches such as food waste reduction and precision agriculture and/or other technological advances have to be simultaneously pursued; however, they are insufficient to make the global food system sustainable. For millennia, meatless diets have been advocated on the basis of values, and large segments of the world population have thrived on plant-based diets. "Going back" to plant-based diets worldwide seems to be a reasonable alternative for a sustainable future. Policies in favor of the global adoption of plant-based diets will simultaneously optimize the food supply, health, environmental, and social justice outcomes for the world's population. Implementing such nutrition policy is perhaps one of the most rational and moral paths for a sustainable future of the human race and other living creatures of the biosphere that we share. PMID:24898222

  8. Life management of power plant based on structural damage testing

    Energy Technology Data Exchange (ETDEWEB)

    Tallermo, H.; Klevtsov, I. [Thermal Engineering Department of Tallinn Technical University, Tallinn (Estonia); Arras, V. [Eesti Energia, Tallinn (Estonia)

    1998-12-31

    Life management system is based on the valid nowadays in Estonian power plants regulation documentation. The system allows to estimate stress distribution in components, find computational assessment of cumulated creep damage, determine when and where it is necessary to cut off the particular number of microsamples or take replicas. Finally, the real metal condition may be assessed on the basis of metallographic specimen research and reasonable 3-R decision - run, repair, replacement - made on further component use. (orig.) 6 refs.

  9. Siplab, a spatial individual-based plant modelling system

    OpenAIRE

    Oscar Garcia

    2014-01-01

    Spatially-explicit individual-based models are important tools in forestry and plant ecology. They are commonly implemented through custom computer coding that is time-consuming, may cause compatibility and availability problems, and makes difficult the evaluation, comparison and re-use of model components. Siplab is an R package that aims at improving this situation with a flexible computing environment that can handle a variety of model forms, and without requiring advanced programming know...

  10. Adaptive model based control for wastewater treatment plants

    OpenAIRE

    Niet, de, A.; Vrugt, van de, Noëlle Maria; Korving, Hans; Boucherie, Richard J.; Savic, D.A.; Kapelan, Z.; Butler, D.

    2011-01-01

    In biological wastewater treatment, nitrogen and phosphorous are removed by activated sludge. The process requires oxygen input via aeration of the activated sludge tank. Aeration is responsible for about 60% of the energy consumption of a treatment plant. Hence optimization of aeration can contribute considerably to the increase of energy-efficiency in wastewater treatment. To this end, we introduce an adaptive model based control strategy for aeration called adaptive WOMBAT. The strategy is...

  11. Utilization of Low Temperature Heat in Coal based Power Plants

    OpenAIRE

    Sisic, Elmir

    2013-01-01

    Carbon Capture and Storage aims at capturing and storing carbon emissions from large point sources underground. One of three main ways of implementing CCS is in coal based power plants is the pressurized oxy-combustion, an advanced form of oxy-combustion. There are different approaches in designing the heat cycle with CCS. Included in the design is the acid condenser, a heat exchanger which utilizes the low temperature and latent heat of the flue gas for preheating purposes. The objective of ...

  12. Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

    Science.gov (United States)

    Aguiar-Pulido, Vanessa; Huang, Wenrui; Suarez-Ulloa, Victoria; Cickovski, Trevor; Mathee, Kalai; Narasimhan, Giri

    2016-01-01

    Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living organisms. Changes in the microbiome can impact the health of the environmental niche in which they reside. In order to learn more about these communities, different approaches based on data from multiple omics have been pursued. Metagenomics produces a taxonomical profile of the sample, metatranscriptomics helps us to obtain a functional profile, and metabolomics completes the picture by determining which byproducts are being released into the environment. Although each approach provides valuable information separately, we show that, when combined, they paint a more comprehensive picture. We conclude with a review of network-based approaches as applied to integrative studies, which we believe holds the key to in-depth understanding of microbiomes. PMID:27199545

  13. Metabolomics as a diagnostic tool in gastroenterology

    Institute of Scientific and Technical Information of China (English)

    Vicky; De; Preter; Kristin; Verbeke

    2013-01-01

    Metabolomics has increasingly been applied in addition to other "omic" approaches in the study of the pathophysiology of different gastrointestinal diseases.Metabolites represent molecular readouts of the cell status reflecting a physiological phenotype.In addition,changes in metabolite concentrations induced by exogenous factors such as environmental and dietary factors which do not affect the genome,are taken into account.Metabolic reactions initiated by the host or gut microbiota can lead to "marker" metabolites present in different biological fluids that allow differentiation between health and disease.Several lines of evidence implicated the involvement of intestinal microbiota in the pathogenesis of inflammatory bowel disease(IBD).Also in irritable bowel syndrome(IBS),a role of an abnormal microbiota composition,so-called dysbiosis,is supported by experimental data.These compositional alterations could play a role in the aetiology of both diseases by altering the metabolic activities of the gut bacteria.Several studies have applied a metabolomic approach to identify these metabolite signatures.However,before translating a potential metabolite biomarker into clinical use,additional validation studies are required.This review summarizes contributions that metabolomics has made in IBD and IBS and presents potential future directions within the field.

  14. Advanced coal based power plants for the next millennium

    Energy Technology Data Exchange (ETDEWEB)

    Liere, J. van; Burgt, M.J. van der [KEMA, Arnhem (Netherlands)

    1997-12-31

    The global electric power generation demand from the year 2000 to 2015 is estimated to approach 1700 GWe. The global market share of coal is projected to be 38% - a significant market to penetrate for new clean coal technologies. Coal-based power generation has shown continued and steady growth during recent decades, despite drastic changes in political and general economic conditions. This is due to the abundance of global coal resources, their geographical dispersion and a comparatively low price for extraction, transportation and conversion. Demands for reduction of the environmental impact of power generation have so far been met by appropriate technological development, and efforts are made to face the latest challenge - the reduction of CO{sub 2} - emissions. This report presents a utility view on various advanced coal-based technologies for the next millennium: the pulverized coal-fired plant with advanced steam data (PF-USC), the integrated coal gasification/combined cycle plant (IGCC), and the pressurized fluid-bed combustion combined cycle plant (PFBC-CC). Furthermore, the longer-term perspectives of new coal-based technologies are addressed. Key topics are: energy efficiency, economy and ecology. 14 refs., 5 figs., 4 tabs.

  15. Metabolomic analysis of human cirrhosis, hepatocellular carcinoma, non-alcoholic fatty liver disease and non-alcoholic steatohepatitis diseases

    Science.gov (United States)

    Safaei, Akram; Arefi Oskouie, Afsaneh; Mohebbi, Seyed Reza; Rezaei-Tavirani, Mostafa; Mahboubi, Mohammad; Peyvandi, Maryam; Okhovatian, Farshad; Zamanian-Azodi, Mona

    2016-01-01

    Metabolome analysis is used to evaluate the characteristics and interactions of low molecular weight metabolites under a specific set of conditions. In cirrhosis, hepatocellular carcinoma, non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatotic hepatitis (NASH) the liver does not function thoroughly due to long-term damage. Unfortunately the early detection of cirrhosis, HCC, NAFLD and NASH is a clinical problem and determining a sensitive, specific and predictive novel method based on biomarker discovery is an important task. On the other hand, metabolomics has been reported as a new and powerful technology in biomarker discovery and dynamic field that cause global comprehension of system biology. In this review, it has been collected a heterogeneous set of metabolomics published studies to discovery of biomarkers in researches to introduce diagnostic biomarkers for early detection and the choice of patient-specific therapies. PMID:27458508

  16. Application of condition based maintenance to nuclear power plants

    International Nuclear Information System (INIS)

    Device Karte management system which supports application of condition based maintenance to nuclear power plants has been developed. The purpose of this system is to support maintenance personnel in device inspection scheduling based on operating condition monitoring and maintenance histories. There are four functions: field database, degradation estimation, inspection time decision and maintenance planning. The authors have been applying this system to dozens of devices of Onagawa Nuclear Power Station Unit No. 1 for one year. This paper represents the system concept and its application experiences. (author)

  17. Gaharu, from the metabolomic aspect

    International Nuclear Information System (INIS)

    Agarwood, one of the timber woody plant which has the similar response as grand fir toward external invasion and is able to produce oleoresin as the secondary metabolite from plant defense system to inhibit the invader and heal the wound. Species of agarwood found in Malaysia is known as Aquilaria malaccensis, and locally known as karas or depu. A. malaccensis is valuable due to its oleoresin (gaharu). Gaharu is a product produced in the secondary metabolic pathway known as terpenoid synthesis pathway. In order to switch on this pathway, the plant defense system need to be induced and lead to the octadecanoid pathway where the linolenic acid (LA) converts to jasmonic acid (JA). Jasmonic acid is the major key to switch the plant metabolic pathway from primary metabolic pathway to secondary metabolic pathway. To prove this hypothesis, some researches on molecular study such as gene expression and protein expression are conducted to identify key components, which will lead to the manipulation of the metabolic pathway. (Author)

  18. Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures

    Directory of Open Access Journals (Sweden)

    Vogel Hans J

    2008-01-01

    Full Text Available Abstract Background Opium poppy (Papaver somniferum produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a model system to study plant alkaloid metabolism. The plant is cultivated as the only commercial source of the narcotic analgesics morphine and codeine, but also produces many other alkaloids including the antimicrobial agent sanguinarine. Modulations in plant secondary metabolism as a result of environmental perturbations are often associated with the altered regulation of other metabolic pathways. As a key component of our functional genomics platform for opium poppy we have used proton nuclear magnetic resonance (1H NMR metabolomics to investigate the interplay between primary and secondary metabolism in cultured opium poppy cells treated with a fungal elicitor. Results Metabolite fingerprinting and compound-specific profiling showed the extensive reprogramming of primary metabolic pathways in association with the induction of alkaloid biosynthesis in response to elicitor treatment. Using Chenomx NMR Suite v. 4.6, a software package capable of identifying and quantifying individual compounds based on their respective signature spectra, the levels of 42 diverse metabolites were monitored over a 100-hour time course in control and elicitor-treated opium poppy cell cultures. Overall, detectable and dynamic changes in the metabolome of elicitor-treated cells, especially in cellular pools of carbohydrates, organic acids and non-protein amino acids were detected within 5 hours after elicitor treatment. The metabolome of control cultures also showed substantial modulations 80 hours after the start of the time course, particularly in the levels of amino acids and phospholipid pathway intermediates. Specific flux modulations were detected throughout primary metabolism, including glycolysis, the tricarboxylic acid cycle, nitrogen assimilation, phospholipid/fatty acid synthesis and the shikimate pathway, all of which

  19. Functional Metabolomics Uncovers Metabolic Alterations Associated to Severe Oxidative Stress in MCF7 Breast Cancer Cells Exposed to Ascididemin

    OpenAIRE

    Daniel Morvan

    2013-01-01

    Marine natural products are a source of promising agents for cancer treatment. However, there is a need to improve the evaluation of their mechanism of action in tumors. Metabolomics of the response to anti-tumor agents is a tool to reveal candidate biomarkers and metabolic targets. We used two-dimensional high-resolution magic angle spinning proton-NMR spectroscopy-based metabolomics to investigate the response of MCF7 breast cancer cells to ascididemin, a marine alkaloid and lead molecule f...

  20. A metabolomics study on human dietary intervention with apples

    DEFF Research Database (Denmark)

    Dragsted, L. O.; Kristensen, M.; Ravn-Haren, Gitte;

    2009-01-01

    Metabolomics is a promising tool for searching out new biomarkers and the development of hypotheses in nutrition research. This chapter will describe the design of human dietary intervention studies where samples are collected for metabolomics analyses as well as the analytical issues and data...

  1. Metabolomics for Undergraduates: Identification and Pathway Assignment of Mitochondrial Metabolites

    Science.gov (United States)

    Marques, Ana Patrícia; Serralheiro, Maria Luisa; Ferreira, António E. N.; Freire, Ana Ponces; Cordeiro, Carlos; Silva, Marta Sousa

    2016-01-01

    Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening…

  2. HILIC-MS for metabolomics: An attractive and complementary approach to RPLC-MS.

    Science.gov (United States)

    Tang, Dao-Quan; Zou, Ll; Yin, Xiao-Xing; Ong, Choon Nam

    2016-09-01

    Hydrophilic interaction chromatography (HILIC) is an emerging separation mode of liquid chromatography (LC). Using highly hydrophilic stationary phases capable of retaining polar/ionic metabolites, and accompany with high organic content mobile phase that offer readily compatibility with mass spectrometry (MS) has made HILIC an attractive complementary tool to the widely used reverse-phase (RP) chromatographic separations in metabolomic studies. The combination of HILIC and RPLC coupled with an MS detector expands the number of detected analytes and provides more comprehensive metabolite coverage than use of only RP chromatography. This review describes the recent applications of HILIC-MS/MS in metabolomic studies, ranging from amino acids, lipids, nucleotides, organic acids, pharmaceuticals, and metabolites of specific nature. The biological systems investigated include microbials, cultured cell line, plants, herbal medicine, urine, and serum as well as tissues from animals and humans. Owing to its unique capability to measure more-polar biomolecules, the HILIC separation technique would no doubt enhance the comprehensiveness of metabolite detection, and add significant value for metabolomic investigations. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:574-600, 2016. PMID:25284160

  3. Plant-based raw material: Improved food quality for better nutrition via plant genomics

    NARCIS (Netherlands)

    Meer, van der I.M.; Bovy, A.G.; Bosch, H.J.

    2001-01-01

    Plants form the basis of the human food chain. Characteristics of plants are therefore crucial to the quantity and quality of human food. In this review, it is discussed how technological developments in the area of plant genomics and plant genetics help to mobilise the potential of plants to improv

  4. Nuclear Power Plant Operator Reliability Research Based on Fuzzy Math

    International Nuclear Information System (INIS)

    This paper makes use of the concept and theory of fuzzy number in fuzzy mathematics, to research for the response time of operator in accident of Chinese nuclear power plant. Through the quantitative analysis for the performance shape factors (PSFs) which influence the response time of operators, the formula of the operator response time is obtained based on the possibilistic fuzzy linear regression model which is used for the first time in this kind of research. The research result shows that the correct research method can be achieved through the analysis of the information from a small sample. This method breaks through the traditional research method and can be used not only for the reference to the safe operation of nuclear power plant, but also in other areas.

  5. Anthropometric data base for power plant design. Special report

    International Nuclear Information System (INIS)

    The primary study objective is to develop anthropometric data based upon the men and women who operate and maintain nuclear power plants. Age, stature, and weight information were obtained by a questionnaire survey of current operator and maintenance personnel, and the data extracted from the questionnaires were analyzed to derive body-size information for a number of anthropometric variables of interest to designers. Body-size information was developed separately for both men and women. Results achieved for the male population can be utilized by designers with a high level of confidence for the design of general workplaces. While the number of women respondents in the sample proved to be too small to derive results to which a similarly high level of reliability could be attached, the data can nevertheless be used as reasonable indicators of the probable body-size variability to be found among female power plant employees

  6. Concept of laser fusion power plant based on fast ignition

    International Nuclear Information System (INIS)

    Recent progress on fast ignition (FI) and cooled Yb:YAG ceramic laser enable us to design an IFE power plant with a 1MJ-class, compact laser whose output energy is 1/4 of previous central ignition scheme. Basing on the FI scheme, we conceptually designed a laser fusion power plant driven with cooled-Yb:YAG, ceramic lasers. The cooled Yb-YAG ceramic was newly chosen as the laser material. We found that the heating laser for ignition could be constructed with the cooled Yb:YAG ceramics as well as the compression laser with acceptable electricity-laser conversion efficiencies including the electric power for the cooling system. A new reactor scheme for a liquid wall reactor that has no stagnation point of ablated gas was proposed. (author)

  7. Multi-platform metabolomic analyses of ergosterol-induced dynamic changes in Nicotiana tabacum cells.

    Science.gov (United States)

    Tugizimana, Fidele; Steenkamp, Paul A; Piater, Lizelle A; Dubery, Ian A

    2014-01-01

    Metabolomics is providing new dimensions into understanding the intracellular adaptive responses in plants to external stimuli. In this study, a multi-technology-metabolomic approach was used to investigate the effect of the fungal sterol, ergosterol, on the metabolome of cultured tobacco cells. Cell suspensions were treated with different concentrations (0-1000 nM) of ergosterol and incubated for different time periods (0-24 h). Intracellular metabolites were extracted with two methods: a selective dispersive liquid-liquid micro-extraction and a general methanol extraction. Chromatographic techniques (GC-FID, GC-MS, GC × GC-TOF-MS, UHPLC-MS) and (1)H NMR spectroscopy were used for quantitative and qualitative analyses. Multivariate data analyses (PCA and OPLS-DA models) were used to extract interpretable information from the multidimensional data generated from the analytical techniques. The results showed that ergosterol triggered differential changes in the metabolome of the cells, leading to variation in the biosynthesis of secondary metabolites. PCA scores plots revealed dose- and time-dependent metabolic variations, with optimal treatment conditions being found to be 300 nM ergosterol and an 18 h incubation period. The observed ergosterol-induced metabolic changes were correlated with changes in defence-related metabolites. The 'defensome' involved increases in terpenoid metabolites with five antimicrobial compounds (the bicyclic sesquiterpenoid phytoalexins: phytuberin, solavetivone, capsidiol, lubimin and rishitin) and other metabolites (abscisic acid and phytosterols) putatively identified. In addition, various phenylpropanoid precursors, cinnamic acid derivatives and - conjugates, coumarins and lignin monomers were annotated. These annotated metabolites revealed a dynamic reprogramming of metabolic networks that are functionally correlated, with a high complexity in their regulation. PMID:24498209

  8. Plant-based solutions for veterinary immunotherapeutics and prophylactics.

    Science.gov (United States)

    Kolotilin, Igor; Topp, Ed; Cox, Eric; Devriendt, Bert; Conrad, Udo; Joensuu, Jussi; Stöger, Eva; Warzecha, Heribert; McAllister, Tim; Potter, Andrew; McLean, Michael D; Hall, J Christopher; Menassa, Rima

    2014-01-01

    An alarming increase in emergence of antibiotic resistance among pathogens worldwide has become a serious threat to our ability to treat infectious diseases according to the World Health Organization. Extensive use of antibiotics by livestock producers promotes the spread of new resistant strains, some of zoonotic concern, which increases food-borne illness in humans and causes significant economic burden on healthcare systems. Furthermore, consumer preferences for meat/poultry/fish produced without the use of antibiotics shape today's market demand. So, it is viewed as inevitable by the One Health Initiative that humans need to reduce the use of antibiotics and turn to alternative, improved means to control disease: vaccination and prophylactics. Besides the intense research focused on novel therapeutic molecules, both these strategies rely heavily on the availability of cost-effective, efficient and scalable production platforms which will allow large-volume manufacturing for vaccines, antibodies and other biopharmaceuticals. Within this context, plant-based platforms for production of recombinant therapeutic proteins offer significant advantages over conventional expression systems, including lack of animal pathogens, low production costs, fast turnaround and response times and rapid, nearly-unlimited scalability. Also, because dried leaves and seeds can be stored at room temperature for lengthy periods without loss of recombinant proteins, plant expression systems have the potential to offer lucrative benefits from the development of edible vaccines and prophylactics, as these would not require "cold chain" storage and transportation, and could be administered in mass volumes with minimal processing. Several biotechnology companies currently have developed and adopted plant-based platforms for commercial production of recombinant protein therapeutics. In this manuscript, we outline the challenges in the process of livestock immunization as well as the current

  9. FT-ICR/MS and GC-EI/MS metabolomics networking unravels global potato sprout's responses to Rhizoctonia solani infection.

    Science.gov (United States)

    Aliferis, Konstantinos A; Jabaji, Suha

    2012-01-01

    The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents. PMID:22880040

  10. Evaluation of Four Different Analytical Tools to Determine the Regional Origin of Gastrodia elata and Rehmannia glutinosa on the Basis of Metabolomics Study

    OpenAIRE

    Dong-Kyu Lee; Dong Kyu Lim; Jung A. Um; Chang Ju Lim; Ji Yeon Hong; Young A Yoon; Yeonsuk Ryu; Hyo Jin Kim; Hi Jae Cho; Jeong Hill Park; Young Bae Seo; Kyunga Kim; Johan Lim; Sung Won Kwon; Jeongmi Lee

    2014-01-01

    Chemical profiles of medicinal plants could be dissimilar depending on the cultivation environments, which may influence their therapeutic efficacy. Accordingly, the regional origin of the medicinal plants should be authenticated for correct evaluation of their medicinal and market values. Metabolomics has been found very useful for discriminating the origin of many plants. Choosing the adequate analytical tool can be an essential procedure because different chemical profiles with different d...

  11. Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

    Indian Academy of Sciences (India)

    Shivanand M Pudakalakatti; Abhinav Dubey; Hanudatta S Atreya

    2015-06-01

    NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) 13C multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D [1H-1H] TOCSY and (3) 2D [13C-1H] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of 13C. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

  12. A knowledge based method for nuclear plant loading pattern determination

    International Nuclear Information System (INIS)

    This paper deals with the design of a knowledge based system for solving an industrial problem which occurs in nuclear fuel management. The problem lies in determining satisfactory loading patterns for nuclear plants. Its primary feature consists in the huge search space involved. Conventional resolution processes are formally defined and analyzed: there is no general algorithm which guarantees to always provide a reasonable solution in each situation. We propose a new approach to solve this constrained search problem using domain-specific knowledge and general constraint-based heuristics. During a preprocessing step, a problem dependent search algorithm is designed. This procedure is then automatically implemented in FORTRAN. The generated routines have proved to be very efficient finding solutions which could not have been provided using logic programming. A prototype expert system has already been applied to actual reload pattern searches. While combining efficiency and flexibility, this knowledge based system enables human experts to rapidly match new constraints and requirements

  13. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

    OpenAIRE

    Yamanishi, Yoshihiro; Tabei, Yasuo; Kotera, Masaaki

    2015-01-01

    Motivation: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. Results: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-fillin...

  14. Functional Genomics of Novel Secondary Metabolites from Diverse Cyanobacteria Using Untargeted Metabolomics

    OpenAIRE

    Muriel Gugger; Kyrpides, Nikos C.; Ferran Garcia-Pichel; Nick Jose; Ivanova, Natalia N.; Richard Baran; Northen, Trent R.

    2013-01-01

    Mass spectrometry-based metabolomics has become a powerful tool for the detection of metabolites in complex biological systems and for the identification of novel metabolites. We previously identified a number of unexpected metabolites in the cyanobacterium Synechococcus sp. PCC 7002, such as histidine betaine, its derivatives and several unusual oligosaccharides. To test for the presence of these compounds and to assess the diversity of small polar metabolites in other cyanobacteria, we prof...

  15. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part II: New Approaches for Discovery Metabolomics

    OpenAIRE

    Peterson, Amelia C.; Balloon, Allison J.; Westphall, Michael S.; Coon, Joshua J.

    2014-01-01

    Identification of unknown peaks in gas chromatography/mass spectrometry (GC/MS)-based discovery metabolomics is challenging, and remains necessary to permit discovery of novel or unexpected metabolites that may elucidate disease processes and/or further our understanding of how genotypes relate to phenotypes. Here, we introduce two new technologies and an analytical workflow that can facilitate the identification of unknown peaks. First, we report on a GC/Quadrupole-Orbitrap mass spectrometer...

  16. Comparative Metabolomic and Genomic Analyses of TCDD-Elicited Metabolic Disruption in Mouse and Rat Liver

    OpenAIRE

    Forgacs, Agnes L.; Kent, Michael N.; Makley, Meghan K.; Mets, Bryan; DelRaso, Nicholas; Jahns, Gary L.; Burgoon, Lyle D; Zacharewski, Timothy R.; Reo, Nicholas V.

    2011-01-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicits a broad spectrum of species-specific effects that have not yet been fully characterized. This study compares the temporal effects of TCDD on hepatic aqueous and lipid metabolite extracts from immature ovariectomized C57BL/6 mice and Sprague-Dawley rats using gas chromatography-mass spectrometry and nuclear magnetic resonance–based metabolomic approaches and integrates published gene expression data to identify species-specific pathways affect...

  17. The Intervention Effects of Acupuncture on Fatigue Induced by Exhaustive Physical Exercises: A Metabolomics Investigation

    OpenAIRE

    Haifeng Ma; Xia Liu; Ying Wu; Naixia Zhang

    2015-01-01

    In this study, the antifatigue effects of acupuncture had been investigated at the metabolic level on the young male athletes with exhaustive physical exercises. After a series of exhaustive physical exercises and a short-term rest, the athletes either were treated with needling acupuncture on selected acupoints (TA group) or enjoyed an extended rest (TR group). NMR-based metabolomics analysis was then applied to depict the metabolic profiles of urine samples, which were collected from the at...

  18. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton

    OpenAIRE

    Poulson-Ellestad, Kelsey L.; Jones, Christina M.; Roy, Jessie; Viant, Mark R.; Fernández, Facundo M.; Kubanek, Julia; Nunn, Brook L.

    2014-01-01

    Microscopic marine algae (phytoplankton) are responsible for much of Earth's photosynthesis, serving as the base of a massive food web supporting fisheries. Phytoplankton compete for limiting resources, with some species producing noxious compounds that kill competitors or inhibit their growth. The red-tide dinoflagellate Karenia brevis is one such allelopathic species, causing growth suppression of other phytoplankton and negatively impacting coastal ecosystems. Metabolomic and proteomic app...

  19. Metabolomic Analysis of Cerebrospinal Fluid Indicates Iron Deficiency Compromises Cerebral Energy Metabolism in the Infant Monkey

    OpenAIRE

    Rao, Raghavendra; Ennis, Kathleen; Oz, Gulin; Lubach, Gabriele R.; Georgieff, Michael K.; Coe, Christopher L.

    2012-01-01

    Iron deficiency anemia affects many pregnant women and young infants worldwide. The health impact is significant, given iron’s known role in many body functions, including oxidative and lipid metabolism, protein synthesis and brain neurochemistry. The following research determined if 1H NMR spectroscopy-based metabolomic analysis of cerebrospinal fluid (CSF) could detect the adverse influence of early life iron deficiency on the central nervous system. Using a controlled dietary model in 43 i...

  20. NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response

    OpenAIRE

    Cano, Kristin E.; Li, Yi-Jia; Chen, Yuan

    2010-01-01

    Post-translational modifications by the Small Ubiquitin-like Modifier (SUMO) family of proteins have been established as critical events in the cellular response to a wide range of DNA damaging reagents and radiation; however, the detailed mechanism of SUMOylation in DNA damage response is not well understood. In this study, we used nuclear magnetic resonance (NMR) spectroscopy based metabolomics approach to examine the effect of an inhibitor of SUMO-mediated protein-protein interactions on M...

  1. Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

    Directory of Open Access Journals (Sweden)

    Fernandes John F

    2011-06-01

    Full Text Available Abstract Background Under normal solar fluence, UV-B damages macromolecules, but it also elicits physiological acclimation and developmental changes in plants. Excess UV-B decreases crop yield. Using a treatment twice solar fluence, we focus on discovering signals produced in UV-B-irradiated maize leaves that translate to systemic changes in shielded leaves and immature ears. Results Using transcriptome and proteomic profiling, we tracked the kinetics of transcript and protein alterations in exposed and shielded organs over 6 h. In parallel, metabolic profiling identified candidate signaling molecules based on rapid increase in irradiated leaves and increased levels in shielded organs; pathways associated with the synthesis, sequestration, or degradation of some of these potential signal molecules were UV-B-responsive. Exposure of just the top leaf substantially alters the transcriptomes of both irradiated and shielded organs, with greater changes as additional leaves are irradiated. Some phenylpropanoid pathway genes are expressed only in irradiated leaves, reflected in accumulation of pathway sunscreen molecules. Most protein changes detected occur quickly: approximately 92% of the proteins in leaves and 73% in immature ears changed after 4 h UV-B were altered by a 1 h UV-B treatment. Conclusions There were significant transcriptome, proteomic, and metabolomic changes under all conditions studied in both shielded and irradiated organs. A dramatic decrease in transcript diversity in irradiated and shielded leaves occurs between 0 h and 1 h, demonstrating the susceptibility of plants to short term UV-B spikes as during ozone depletion. Immature maize ears are highly responsive to canopy leaf exposure to UV-B.

  2. ECOLOGICAL BASES OF SIMBIOGENIC DEVELOPMENT OF PLANT AT COMPLEX SOWINGS

    Directory of Open Access Journals (Sweden)

    Belyuchenko I. S.

    2015-03-01

    Full Text Available Development of plants in mixed or combined sowings is based on the symbiotic association in the basis of which we have decreased sexual process and its mechanism of genetic exchange among endosymbionts and stimulating of genetic exchange and expansion of the diversity of species among exosymbionts. The exception is the symbiosis of orchids and fungi - activators of orchids mycorrhiza with developed micellar system easily passing on saprophytic option. Coevolution of plant organisms with fungi indicates the specifics symbiogenic conjugate evolution, showing an example of the evolution of a small community with different contact with the external environment. The phenomenon of symbiogenesis has a long history and was manifested in a variety of different types of organisms. Today, some dependence of existence of one species from other organisms is observed at approximately 75% of higher plants and 90% of the animals in varying degrees of symbiogenic dependence from other species and taxa. Originality of symbiogenesis was analyzed by Academician A.A. Takhtadzhyan (1973 during its consideration of origin of eukaryotic cells as process of "assembly" of a complex system. Different approaches to determining the biological essence of symbiosis are known in the history of study of this phenomenon. On the whole phenomenon of symbiosis belongs to the category mutual relations of organisms of different phylogenetic groups

  3. PSA based plant modifications and back-fits

    International Nuclear Information System (INIS)

    The mandate of Principal Working Group No. 5 - Risk Assessment states that 'The group should deal with the technology and methods for identifying contributors to risk and assessing their importance, and appropriate exchanges of information on current research'. Since being formulated in 1982, along with this mandate, the group has also endeavored to develop a common understanding of the different approaches taken in risk assessment. The focus of this report is to provide knowledge to experts on the role Probabilistic Safety Assessment (PSA) has had in safety decision making. PSA is a powerful tool for improving Nuclear Power Plant safety by identifying weaknesses in design or operation and setting priorities for plant modifications and back-fits. While the use is well recognised, it is also true that any safety decision is generally based on several elements, both probabilistic and deterministic. This document provides a general overview of insights gained from the representative set of examples collected from Member countries (Finland, France, Germany, Japan, Korea, Netherlands, Spain, Sweden, Switzerland, United Kingdom, United States). The report starts with basic types of plant modifications which were carried out (e.g. hardware or software, important or minor, etc.) and the characteristics of the PSAs used in the examples (e.g. level and scope, specific or generic, on-going or terminated, etc.). The insights gained from this small collection are then reviewed. The appendix gives a full text version of the Member country contributions

  4. Hypertext-based integration for nuclear plant maintenance and operations

    International Nuclear Information System (INIS)

    A methodology is presented that uses fuzzy graphs in the emerging paradigm of hypertext for the purpose of integrating data, information and multifaceted knowledge resources abounding in power plant operations and maintenance. A hypertext system is viewed as a set of nodes and links where with each link we associate membership functions embodying context-dependent criteria for navigating large information spaces. A general framework for navigation is outlined and graph-theory navigational tools are developed. A numerical example and a HyperCard-based prototype for monitoring special material in the MHTGR-NPR are included. 10 refs., 12 figs

  5. Data warehouse based decision support system in nuclear power plants

    International Nuclear Information System (INIS)

    Safety is an important element in business decision making processes in nuclear power plants. Information about component reliability, structures and systems, data recorded during the nuclear power plant's operation and outage periods, as well as experiences from other power plants are located in different database systems throughout the power plant. It would be possible to create a decision support system which would collect data, transform it into a standardized form and store it in a single location in a format more suitable for analyses and knowledge discovery. This single location where the data would be stored would be a data warehouse. Such data warehouse based decision support system could help make decision making processes more efficient by providing more information about business processes and predicting possible consequences of different decisions. Two main functionalities in this decision support system would be an OLAP (On Line Analytical Processing) and a data mining system. An OLAP system would enable the users to perform fast, simple and efficient multidimensional analysis of existing data and identify trends. Data mining techniques and algorithms would help discover new, previously unknown information from the data as well as hidden dependencies between various parameters. Data mining would also enable analysts to create relevant prediction models that could predict behaviour of different systems during operation and inspection results during outages. The basic characteristics and theoretical foundations of such decision support system are described and the reasons for choosing a data warehouse as the underlying structure are explained. The article analyzes obvious business benefits of such system as well as potential uses of OLAP and data mining technologies. Possible implementation methodologies and problems that may arise, especially in the field of data integration, are discussed and analyzed.(author)

  6. Plasma metabolomics and proteomics profiling after a postprandial challenge reveal subtle diet effects on human metabolic status

    NARCIS (Netherlands)

    Pellis, L.; Erk, M.J. van; Ommen, B. van; Bakker, G.C.M.; Hendriks, H.F.J.; Cnubben, N.H.P.; Kleemann, R.; Someren, E.P. van; Bobeldijk, I.; Rubingh, C.M.; Wopereis, S.

    2012-01-01

    We introduce the metabolomics and proteomics based Postprandial Challenge Test (PCT) to quantify the postprandial response of multiple metabolic processes in humans in a standardized manner. The PCT comprised consumption of a standardized 500 ml dairy shake containing respectively 59, 30 and 12 ener

  7. Understanding Aquatic Rhizosphere Processes Through Metabolomics and Metagenomics Approach

    Science.gov (United States)

    Lee, Yong Jian; Mynampati, Kalyan; Drautz, Daniela; Arumugam, Krithika; Williams, Rohan; Schuster, Stephan; Kjelleberg, Staffan; Swarup, Sanjay

    2013-04-01

    The aquatic rhizosphere is a region around the roots of aquatic plants. Many studies focusing on terrestrial rhizosphere have led to a good understanding of the interactions between the roots, its exudates and its associated rhizobacteria. The rhizosphere of free-floating roots, however, is a different habitat that poses several additional challenges, including rapid diffusion rates of signals and nutrient molecules, which are further influenced by the hydrodynamic forces. These can lead to rapid diffusion and complicates the studying of diffusible factors from both plant and/or rhizobacterial origins. These plant systems are being increasingly used for self purification of water bodies to provide sustainable solution. A better understanding of these processes will help in improving their performance for ecological engineering of freshwater systems. The same principles can also be used to improve the yield of hydroponic cultures. Novel toolsets and approaches are needed to investigate the processes occurring in the aquatic rhizosphere. We are interested in understanding the interaction between root exudates and the complex microbial communities that are associated with the roots, using a systems biology approach involving metabolomics and metagenomics. With this aim, we have developed a RhizoFlowCell (RFC) system that provides a controlled study of aquatic plants, observed the root biofilms, collect root exudates and subject the rhizosphere system to changes in various chemical or physical perturbations. As proof of concept, we have used RFC to test the response of root exudation patterns of Pandanus amaryllifolius after exposure to the pollutant naphthalene. Complexity of root exudates in the aquatic rhizosphere was captured using this device and analysed using LC-qTOF-MS. The highly complex metabolomic profile allowed us to study the dynamics of the response of roots to varying levels of naphthalene. The metabolic profile changed within 5mins after spiking with

  8. First-Trimester Serum Acylcarnitine Levels to Predict Preeclampsia: A Metabolomics Approach

    Directory of Open Access Journals (Sweden)

    Maria P. H. Koster

    2015-01-01

    Full Text Available Objective. To expand the search for preeclampsia (PE metabolomics biomarkers through the analysis of acylcarnitines in first-trimester maternal serum. Methods. This was a nested case-control study using serum from pregnant women, drawn between 8 and 14 weeks of gestational age. Metabolites were measured using an UPLC-MS/MS based method. Concentrations were compared between controls (n=500 and early-onset- (EO- PE (n=68 or late-onset- (LO- PE (n=99 women. Metabolites with a false discovery rate <10% for both EO-PE and LO-PE were selected and added to prediction models based on maternal characteristics (MC, mean arterial pressure (MAP, and previously established biomarkers (PAPPA, PLGF, and taurine. Results. Twelve metabolites were significantly different between EO-PE women and controls, with effect levels between −18% and 29%. For LO-PE, 11 metabolites were significantly different with effect sizes between −8% and 24%. Nine metabolites were significantly different for both comparisons. The best prediction model for EO-PE consisted of MC, MAP, PAPPA, PLGF, taurine, and stearoylcarnitine (AUC = 0.784. The best prediction model for LO-PE consisted of MC, MAP, PAPPA, PLGF, and stearoylcarnitine (AUC = 0.700. Conclusion. This study identified stearoylcarnitine as a novel metabolomics biomarker for EO-PE and LO-PE. Nevertheless, metabolomics-based assays for predicting PE are not yet suitable for clinical implementation.

  9. Metabolomics analysis of metabolic effects of nicotinamide phosphoribosyltransferase (NAMPT inhibition on human cancer cells.

    Directory of Open Access Journals (Sweden)

    Vladimir Tolstikov

    Full Text Available Nicotinamide phosphoribosyltransferase (NAMPT plays an important role in cellular bioenergetics. It is responsible for converting nicotinamide to nicotinamide adenine dinucleotide, an essential molecule in cellular metabolism. NAMPT has been extensively studied over the past decade due to its role as a key regulator of nicotinamide adenine dinucleotide-consuming enzymes. NAMPT is also known as a potential target for therapeutic intervention due to its involvement in disease. In the current study, we used a global mass spectrometry-based metabolomic approach to investigate the effects of FK866, a small molecule inhibitor of NAMPT currently in clinical trials, on metabolic perturbations in human cancer cells. We treated A2780 (ovarian cancer and HCT-116 (colorectal cancer cell lines with FK866 in the presence and absence of nicotinic acid. Significant changes were observed in the amino acids metabolism and the purine and pyrimidine metabolism. We also observed metabolic alterations in glycolysis, the citric acid cycle (TCA, and the pentose phosphate pathway. To expand the range of the detected polar metabolites and improve data confidence, we applied a global metabolomics profiling platform by using both non-targeted and targeted hydrophilic (HILIC-LC-MS and GC-MS analysis. We used Ingenuity Knowledge Base to facilitate the projection of metabolomics data onto metabolic pathways. Several metabolic pathways showed differential responses to FK866 based on several matches to the list of annotated metabolites. This study suggests that global metabolomics can be a useful tool in pharmacological studies of the mechanism of action of drugs at a cellular level.

  10. ITER Fast Plant System Controller prototype based on PXIe platform

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz, M., E-mail: mariano.ruiz@upm.es [Grupo de Investigacion en Instrumentacion y Acustica Aplicada, CAEND CSIC-UPM Universidad Politecnica de Madrid, Crta. Valencia Km-7, Madrid 28031 (Spain); Vega, J.; Castro, R. [Asociacion EURATOM/CIEMAT para Fusion, Madrid (Spain); Sanz, D.; Lopez, J.M.; Arcas, G. de; Barrera, E.; Nieto, J. [Grupo de Investigacion en Instrumentacion y Acustica Aplicada, CAEND CSIC-UPM Universidad Politecnica de Madrid, Crta. Valencia Km-7, Madrid 28031 (Spain); Goncalves, B.; Sousa, J.; Carvalho, B. [Associacao EURATOM/IST, Lisbon (Portugal); Utzel, N.; Makijarvi, P. [ITER Organization, CS 90 046, 13067 St. Paul lez Durance Cedex (France)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer Implementation of Fast Plant System Controller (FPSC) for ITER CODAC. Black-Right-Pointing-Pointer Efficient data acquisition and data movement using EPICS. Black-Right-Pointing-Pointer Performance of PCIe technologies in the implementation of FPSC. - Abstract: The ITER Fast Plant System Controller (FPSC) is based on embedded technologies. The FPSC will be devoted to both data acquisition tasks (sampling rates higher than 1 kHz) and control purposes (feedback loop actuators). Some of the essential requirements of these systems are: (a) data acquisition and data preprocessing; (b) interfacing with different networks and high speed links (Plant Operation Network, timing network based on IEEE1588, synchronous data transference and streaming/archiving networks); and (c) system setup and operation using EPICS (Experimental Physics and Industrial Control System) process variables. CIEMAT and UPM have implemented a prototype of FPSC using a PXIe (PCI eXtension for Instrumentation) form factor in a R and D project developed in two phases. The paper presents the main features of the two prototypes developed that have been named alpha and beta. The former was implemented using LabVIEW development tools as it was focused on modeling the FPSC software modules, using the graphical features of LabVIEW applications, and measuring the basic performance in the system. The alpha version prototype implements data acquisition with time-stamping, EPICS monitoring using waveform process variables (PVs), and archiving. The beta version prototype is a complete IOC implemented using EPICS with different software functional blocks. These functional blocks are integrated and managed using an ASYN driver solution and provide the basic functionalities required by ITER FPSC such as data acquisition, data archiving, data pre-processing (using both CPU and GPU) and streaming.

  11. The exo-metabolome in filamentous fungi

    DEFF Research Database (Denmark)

    Thrane, Ulf; Andersen, Birgitte; Frisvad, Jens Christian;

    2007-01-01

    Filamentous fungi are a diverse group of eukaryotic microorganisms that have a significant impact on human life as spoilers of food and feed by degradation and toxin production. They are also most useful as a source of bulk and fine chemicals and pharmaceuticals. This chapter focuses on the exo......-metabolome in filamentous fungi, which comprises more than 30,000 known secondary metabolites. Profiles of this diverse range of secondary metabolites have, for more than 25 years, been central in development of fungal systematics, taxonomy, and ecology, today integrated in a multidisciplinary and polyphasic approach...

  12. A functional genomics approach using metabolomics and in silico pathway analysis

    DEFF Research Database (Denmark)

    Förster, Jochen; Gombert, Andreas Karoly; Nielsen, Jens

    2002-01-01

    In the field of functional genomics increasing effort is being undertaken to analyze the function of orphan genes using metabolome data. Improved analytical equipment allows screening simultaneously for a high number of metabolites. Such metabolite profiles are analyzed using multivariate data...... analysis techniques and changes in the genotype will in many cases lead to different metabolite profiles. Here, a theoretical framework that may be applied to identify the function of orphan genes is presented. The approach is based on a combination of metabolome analysis combined with in silico pathway...... analysis. Pathway analysis may be carried out using convex analysis and a change in the active pathway structure of deletion mutants expressed in a different metabolite profile may disclose the function or the functional class of an orphan gene. The concept is illustrated using a simplified model for...

  13. Planning for rate base treatment of large power plants

    International Nuclear Information System (INIS)

    This paper addresses two related areas of planning for inclusion in rate base of large generating stations. First, the paper discusses the range of options available as to how the plant is to go into rate base, e.g., phase-in plans. In this connection the process of generating the entire range of options that may be available is described and examined. Second, the paper examines innovative ways of using procedures (e.g., accounting proceedings, settlement procedures, cost caps, and other ideas short of a full-blown rate case) and the resources available in the ratemaking arena, to obtain, in the least painful way possible, the necessary ratemaking orders. The thesis is that there must be better alternatives to the many proceedings that have either begun as, or seem to be leading to, endless retrospective examinations of multiple questions (from load forecasting to construction management to continuation-of-construction decisions) under the label of prudence inquiries

  14. Liposome-Based Delivery Systems in Plant Polysaccharides

    OpenAIRE

    Yitao Wang; Xinsheng Peng; Ping Zhu; Yanfang Zhou; Jingjing Huang; Meiwan Chen

    2012-01-01

    Plant polysaccharides consist of many monosaccharide by α- or β-glycosidic bond which can be extracted by the water, alcohol, lipophile liquid from a variety of plants including Cordyceps sinensis, astragalus, and mushrooms. Recently, many evidences illustrate that natural plant polysaccharides possess various biological activities including strengthening immunity, lowering blood sugar, regulating lipid metabolism, antioxidation, antiaging, and antitumour. Plant polysaccharides have been wide...

  15. Metabolomic and network analysis of astaxanthin-producing Haematococcus pluvialis under various stress conditions.

    Science.gov (United States)

    Su, Yingxue; Wang, Jiangxin; Shi, Mengliang; Niu, Xiangfeng; Yu, Xinheng; Gao, Lianju; Zhang, Xiaoqing; Chen, Lei; Zhang, Weiwen

    2014-10-01

    Various combinations of acetate (Ac), Fe(2+) and high light (HL) stress conditions were evaluated to maximize astaxanthin accumulation and biomass production in Haematococcus pluvialis, and then GC-MS and LC-MS based metabolomics were applied to determine molecular mechanisms responsible for enhancing astaxanthin accumulation under the stress conditions. With the optimized analytical protocols, the GC-MS and LC-MS analyses allowed identification of 93 stable and 24 unstable intracellular metabolites from H. pluvialis, respectively. In addition, a metabolic network was constructed based on GC-MS metabolomic datasets using a weighted correlation network analysis (WGCNA) approach. The network analysis uncovered 2, 1 and 1 distinguished metabolic modules highly associated with HL, Fe(2+) & HL, and Ac & Fe(2+) & HL conditions, respectively. Finally, LC-MS analysis found that AKG, Glu and R5P may be metabolites associated with the Fe(2+) & HL condition. The study provided the first metabolomic view of cell growth and astaxanthin accumulation in H. pluvialis. PMID:25164345

  16. Diagnostic Metabolomic Blood Tests for Endoluminal Gastrointestinal Cancer--A Systematic Review and Assessment of Quality.

    Science.gov (United States)

    Antonowicz, Stefan; Kumar, Sacheen; Wiggins, Tom; Markar, Sheraz R; Hanna, George B

    2016-01-01

    Advances in analytics have resulted in metabolomic blood tests being developed for the detection of cancer. This systematic review aims to assess the diagnostic accuracy of blood-based metabolomic biomarkers for endoluminal gastrointestinal (GI) cancer. Using endoscopic diagnosis as a reference standard, methodologic and reporting quality was assessed using validated tools, in addition to pathway-based informatics to biologically contextualize discriminant features. Twenty-nine studies (15 colorectal, 9 esophageal, 3 gastric, and 2 mixed) with data from 10,835 participants were included. All reported significant differences in hematologic metabolites. In pooled analysis, 246 metabolites were found to be significantly different after multiplicity correction. Incremental metabolic flux with disease progression was frequently reported. Two promising candidates have been validated in independent populations (both colorectal biomarkers), and one has been approved for clinical use. Networks analysis suggested modulation of elements of up to half of Edinburgh Human Metabolic Network subdivisions, and that the poor clinical applicability of commonly modulated metabolites could be due to extensive molecular interconnectivity. Methodologic and reporting quality was assessed as moderate-to-poor. Serum metabolomics holds promise for GI cancer diagnostics; however, future efforts must adhere to consensus standardization initiatives, utilize high-resolution discovery analytics, and compare candidate biomarkers with peer nonendoscopic alternatives. PMID:26598534

  17. Metabolomic Elucidation of the Effects of Curcumin on Fibroblast-Like Synoviocytes in Rheumatoid Arthritis.

    Science.gov (United States)

    Ahn, Joong Kyong; Kim, Sooah; Hwang, Jiwon; Kim, Jungyeon; Lee, You Sun; Koh, Eun-Mi; Kim, Kyoung Heon; Cha, Hoon-Suk

    2015-01-01

    Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease characterized by synovial inflammation and joint disability. Curcumin is known to be effective in ameliorating joint inflammation in RA. To obtain new insights into the effect of curcumin on primary fibroblast-like synoviocytes (FLS, N = 3), which are key effector cells in RA, we employed gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS)-based metabolomics. Metabolomic profiling of tumor necrosis factor (TNF)-α-stimulated and curcumin-treated FLS was performed using GC/TOF-MS in conjunction with univariate and multivariate statistical analyses. A total of 119 metabolites were identified. Metabolomic analysis revealed that metabolite profiles were clearly distinct between TNF-α-stimulated vs. the control group (not stimulated by TNF-α or curcumin). Treatment of FLS with curcumin showed that the metabolic perturbation by TNF-α could be reversed to that of the control group to a considerable extent. Curcumin-treated FLS had higher restoration of amino acid and fatty acid metabolism, as indicated by the prominent metabolic restoration of intermediates of amino acid and fatty acid metabolism, compared with that observed in TNF-α-stimulated FLS. In particular, the abundance of glycine, citrulline, arachidonic acid, and saturated fatty acids in TNF-α-stimulated FLS was restored to the control level after treatment with curcumin, suggesting that the effect of curcumin on preventing joint inflammation may be elucidated with the levels of these metabolites. Our results suggest that GC/TOF-MS-based metabolomic investigation using FLS has the potential for discovering the mechanism of action of curcumin and new targets for therapeutic drugs in RA. PMID:26716989

  18. The design of future central receiver power plants based on lessons learned from the Solar One Pilot Plant

    Science.gov (United States)

    Kolb, G. J.

    The 10-MW(sub e) Solar One Pilot Plant was the world's largest solar central receiver power plant. During its power production years it delivered over 37,000 MWhrs (net) to the utility grid. In this type of electric power generating plant, large sun-tracking mirrors called heliostats reflect and concentrate sunlight onto a receiver mounted on top of a tower. The receiver transforms the solar energy into thermal energy that heats water, turning it into superheated steam that drives a turbine to generate electricity. The Solar One Pilot Plant successfully demonstrated the feasibility of generating electricity with a solar central receiver power plant. During the initial 2 years the plant was tested and 4 years the plant was operated as a power plant, a great deal of data was collected relating to the efficiency and reliability of the plant's various systems. This paper summarizes these statistics and compares them to goals developed by the U.S. Department of Energy. Based on this comparison, improvements in the design and operation of future central receiver plants are recommended. Research at Sandia National Laboratories and the U.S. utility industry suggests that the next generation of central receiver power plants will use a molten salt heat transfer fluid rather than water/steam. Sandia has recently completed the development of the hardware needed in a molten salt power plant. Use of this new technology is expected to solve many of the performance problems encountered at Solar One. Projections for the energy costs from these future central receiver plants are also presented. For reference, these projections are compared to the current energy costs from the SEGS parabolic trough plants now operating in Southern California.

  19. The design of future central receiver power plants based on lessons learned from the Solar One Pilot Plant

    Energy Technology Data Exchange (ETDEWEB)

    Kolb, G.J.

    1991-01-01

    The 10-MW{sub e} Solar One Pilot Plant was the world's largest solar central receiver power plant. During its power production years it delivered over 37,000 MWhrs (net) to the utility grid. In this type of electric power generating plant, large sun-tracking mirrors called heliostats reflect and concentrate sunlight onto a receiver mounted on top a of a tower. The receiver transforms the solar energy into thermal energy that heats water, turning it into superheated steam that drives a turbine to generate electricity. The Solar One Pilot Plant successfully demonstrated the feasibility of generating electricity with a solar central receiver power plant. During the initial 2 years the plant was tested and 4 years the plant was operated as a power plant, a great deal of data was collected relating to the efficiency and reliability of the plant's various systems. This paper summarizes these statistics and compares them to goals developed by the US Department of Energy. Based on this comparison, improvements in the design and operation of future central receiver plants are recommended. Research at Sandia National Laboratories and the US utility industry suggests that the next generation of central receiver power plants will use a molten salt heat transfer fluid rather than water/steam. Sandia has recently completed the development of the hardware needed in a molten salt power plant. Use of this new technology is expected to solve many of the performance problems encountered at Solar One. Projections for the energy costs from these future central receiver plants are also presented. For reference, these projections are compared to the current energy costs from the SEGS parabolic trough plants now operating in Southern California.

  20. Metabolome analysis - mass spectrometry and microbial primary metabolites

    DEFF Research Database (Denmark)

    Højer-Pedersen, Jesper Juul

    2008-01-01

    highly sensitive and specific, and to undertake this challenge mass spectrometry (MS) is among the best candidates. Along with analysis of the metabolome the research area of metabolomics has evolved. Metabolomics combines metabolite profiles, data mining and biochemistry and aims at understanding the...... glucose, galactose or ethanol, and metabolic footprinting by mass spectrometry was used to study the influence of carbon source on the extracellular metabolites. The results showed that footprints clustered according to the carbon source. Advances in technologies for analytical chemistry have mediated...

  1. Metabolomics, a promising approach to translational research in cardiology

    Directory of Open Access Journals (Sweden)

    Martino Deidda

    2015-12-01

    In this article, we will provide a description of metabolomics in comparison with other, better known “omics” disciplines such as genomics and proteomics. In addition, we will review the current rationale for the implementation of metabolomics in cardiology, its basic methodology and the available data from human studies in this discipline. The topics covered will delineate the importance of being able to use the metabolomic information to understand the mechanisms of diseases from the perspective of systems biology, and as a non-invasive approach to the diagnosis, grading and treatment of cardiovascular diseases.

  2. Targeting of the hydrophobic metabolome by pathogens.

    Science.gov (United States)

    Helms, J Bernd; Kaloyanova, Dora V; Strating, Jeroen R P; van Hellemond, Jaap J; van der Schaar, Hilde M; Tielens, Aloysius G M; van Kuppeveld, Frank J M; Brouwers, Jos F

    2015-05-01

    The hydrophobic molecules of the metabolome - also named the lipidome - constitute a major part of the entire metabolome. Novel technologies show the existence of a staggering number of individual lipid species, the biological functions of which are, with the exception of only a few lipid species, unknown. Much can be learned from pathogens that have evolved to take advantage of the complexity of the lipidome to escape the immune system of the host organism and to allow their survival and replication. Different types of pathogens target different lipids as shown in interaction maps, allowing visualization of differences between different types of pathogens. Bacterial and viral pathogens target predominantly structural and signaling lipids to alter the cellular phenotype of the host cell. Fungal and parasitic pathogens have complex lipidomes themselves and target predominantly the release of polyunsaturated fatty acids from the host cell lipidome, resulting in the generation of eicosanoids by either the host cell or the pathogen. Thus, whereas viruses and bacteria induce predominantly alterations in lipid metabolites at the host cell level, eukaryotic pathogens focus on interference with lipid metabolites affecting systemic inflammatory reactions that are part of the immune system. A better understanding of the interplay between host-pathogen interactions will not only help elucidate the fundamental role of lipid species in cellular physiology, but will also aid in the generation of novel therapeutic drugs. PMID:25754025

  3. Comprehensive and Comparative Metabolomic Profiling of Wheat, Barley, Oat and Rye Using Gas Chromatography-Mass Spectrometry and Advanced Chemometrics

    Directory of Open Access Journals (Sweden)

    Bekzod Khakimov

    2014-10-01

    Full Text Available Beyond the main bulk components of cereals such as the polysaccharides and proteins, lower concentration secondary metabolites largely contribute to the nutritional value. This paper outlines a comprehensive protocol for GC-MS metabolomic profiling of phenolics and organic acids in grains, the performance of which is demonstrated through a comparison of the metabolite profiles of the main northern European cereal crops: wheat, barley, oat and rye. Phenolics and organic acids were extracted using acidic hydrolysis, trimethylsilylated using a new method based on trimethylsilyl cyanide and analyzed by GC-MS. In order to extract pure metabolite peaks, the raw chromatographic data were processed by a multi-way decomposition method, Parallel Factor Analysis 2. This approach lead to the semi-quantitative detection of a total of 247 analytes, out of which 89 were identified based on RI and EI-MS library match. The cereal metabolome included 32 phenolics, 30 organic acids, 10 fatty acids, 11 carbohydrates and 6 sterols. The metabolome of the four cereals were compared in detail, including low concentration phenolics and organic acids. Rye and oat displayed higher total concentration of phenolic acids, but ferulic, caffeic and sinapinic acids and their esters were found to be the main phenolics in all four cereals. Compared to the previously reported methods, the outlined protocol provided an efficient and high throughput analysis of the cereal metabolome and the acidic hydrolysis improved the detection of conjugated phenolics.

  4. Diesel power plants based on biomass gasification. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Kurkela, E.; Staahlberg, P.; Solantausta, Y.; Wilen, C.

    1996-12-31

    The aim of the project was to assess the competitiveness and market potential of small-scale power plant concepts based on biomass gasification and on diesel/gas engines, and to study the effect of process parameters on the efficiency of the circulating fluidized-bed gasifier and on the formation of tarry impurities. Alternative diesel/gas engine power plant concepts based on gasification in scale 6-50 MW{sub e} were assessed. In the basic version, where the electricity is generated only by the a diesel/gas engine, the efficiency level of 37 % is achieved in power generation. When steam cycle is added to the process the efficiency of power generation increases to 44-48 %. The efficiencies achieved in the process are very high compared with those of biomass power plant processes on a commercial level or under development. The most significant potential of biomass-based power generation is made up by wastes of sugar industries in south and Central America and in Asia. There are also very extensive growth potentials of bioenergy use in the NAFTA countries (USA, Canada and Mexico) and in Europe. In Europe, the bioenergy use is expected to grow most sharply in Italy, Spain, Germany and Poland. Carbon conversion obtained in the gasifier was in the range of 99.0-99.9 % for sawdust and 96-98 % for forest residue chips. The tar content of the product gas 10-15 g/m- m{sup 3}{sub n}, for sawdust in the gasification temperature of 830-930 deg C and with sand as circulating fluid-bed. When dolomite was used as circulating fluid-bed, the tar contents were 2-3 g/m{sup 3}{sub n} at as low temperatures as 880-890 deg C. The tar content of gas can be reduced sharply by phasing of gasification air and by using catalytic circulating fluid-bed material Bioenergy Research Programme; LIEKKI 2 Research Programme. 26 refs., 40 figs.

  5. Dynamics of Plant Growth; A Theory Based on Riemannian Geometry

    CERN Document Server

    Pulwicki, Julia

    2016-01-01

    In this work, a new model for macroscopic plant tissue growth based on dynamical Riemannian geometry is presented. We treat 1D and 2D tissues as continuous, deformable, growing geometries for sizes larger than 1mm. The dynamics of the growing tissue are described by a set of coupled tensor equations in non-Euclidean (curved) space. These coupled equations represent a novel feedback mechanism between growth and curvature dynamics. For 1D growth, numerical simulations are compared to two measures of root growth. First, modular growth along the simulated root shows an elongation zone common to many species of plant roots. Second, the relative elemental growth rate (REGR) calculated in silico exhibits temporal dynamics recently characterized in high-resolution root growth studies but which thus far lack a biological hypothesis to explain them. Namely, the REGR can evolve from a single peak localized near the root tip to a double-peak structure. In our model, this is a direct consequence of considering growth as b...

  6. Cultivable endophytic bacteria from leaf bases of Agave tequilana and their role as plant growth promoters

    OpenAIRE

    Julia del C. Martínez-Rodríguez; Marcela De la Mora-Amutio; Plascencia-Correa, Luis A.; Esmeralda Audelo-Regalado; Francisco R. Guardado; Elías Hernández-Sánchez; Peña-Ramírez, Yuri J.; Adelfo Escalante; Miguel J. Beltrán-García; Tetsuya Ogura

    2015-01-01

    Agave tequilana Weber var. 'Azul' is grown for the production of tequila, inulin and syrup. Diverse bacteria inhabit plant tissues and play a crucial role for plant health and growth. In this study culturable endophytic bacteria were extracted from leaf bases of 100 healthy Agave tequilana plants. In plant tissue bacteria occurred at mean population densities of 3 million CFU/g of fresh plant tissue. Three hundred endophytic strains were isolated and 16s rDNA sequences grouped the bacteria in...

  7. TVA coal-gasification commercial demonstration plant project. Volume 5. Plant based on Koppers-Totzek gasifier. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1980-11-01

    This volume presents a technical description of a coal gasification plant, based on Koppers-Totzek gasifiers, producing a medium Btu fuel gas product. Foster Wheeler carried out a conceptual design and cost estimate of a nominal 20,000 TPSD plant based on TVA design criteria and information supplied by Krupp-Koppers concerning the Koppers-Totzek coal gasification process. Technical description of the design is given in this volume.

  8. Performance Based Failure Criteria of the Base Isolation System for Nuclear Power Plants

    International Nuclear Information System (INIS)

    The realistic approach to evaluate the failure state of the base isolation system is necessary. From this point of view, several concerns are reviewed and discussed in this study. This is the preliminary study for the performance based risk assessment of a base isolated nuclear power plant. The items to evaluate the capacity and response of an individual base isolator and a base isolation system were briefly outlined. However, the methodology to evaluate the realistic fragility of a base isolation system still needs to be specified. For the quantification of the seismic risk for a nuclear power plant structure, the failure probabilities of the structural component for the various seismic intensity levels need to be calculated. The failure probability is evaluated as the probability when the seismic response of a structure exceeds the failure criteria. Accordingly, the failure mode of the structural system caused by an earthquake vibration should be defined first. The type of a base isolator appropriate for a nuclear power plant structure is regarded as an elastometric rubber bearing with a lead core. The failure limit of the lead-rubber bearing (LRB) is not easy to be predicted because of its high nonlinearity and a complex loading condition by an earthquake excitation. Furthermore, the failure mode of the LRB system installed below the nuclear island cannot be simply determined because the basemat can be sufficiently supported if the number of damaged isolator is not much

  9. Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

    Science.gov (United States)

    Barnes, S; Benton, H P; Casazza, K; Cooper, S J; Cui, X; Du, X; Engler, J A; Kabarowski, J H; Li, S; Pathmasiri, W; Prasain, J K; Renfrow, M B; Tiwari, H K

    2016-07-01

    Metabolomics is perhaps the most challenging of the -omics fields, given the complexity of an organism's metabolome and the rapid rate at which it changes. When one sets out to study metabolism there are numerous dynamic variables that can influence metabolism that must be considered. Recognizing the experimental challenges confronting researchers who undertake metabolism studies, workshops like the one at University of Alabama at Birmingham have been established to offer instructional guidance. A summary of the UAB course training materials is being published as a two-part Special Feature Tutorial. In this month's Part I the authors discuss details of good experimental design and sample collection and handling. In an upcoming Part II, the authors discuss in detail the various aspects of data analysis. PMID:27434812

  10. [Peculicidal activity of plant essential oils and their based preparations].

    Science.gov (United States)

    Lopatina, Iu V; Eremina, O Iu

    2014-01-01

    The peculicidal activity of eight plant essential oils in 75% isopropyl alcohol was in vitro investigated. Of them, the substances that were most active against lice were tea tree (Melaleuca), eucalyptus, neem, citronella (Cymbopogon nardus), and clove (Syzygium aromaticum) oils; KT50 was not more than 3 minutes on average; KT95 was 4 minutes. After evaporating the solvent, only five (tea tree, cassia, clove, anise (Anisum vulgare), and Japanese star anise (Illicium anisatum) oils) of the eight test botanical substances were active against lice. At the same time, KT50 and KT95 showed 1.5-5-fold increases. Citronella and anise oils had incomplete ovicidal activity. Since the lice were permethrin-resistant, the efficacy of preparations based on essential oils was much higher than permethrin. PMID:25296426

  11. Simulation-based biagnostics and control for nuclar power plants

    International Nuclear Information System (INIS)

    Advanced simulation-based diagnostics and control guidance systems for the identification and management of off-normal transient events in nuclear power plants is currently under investigation. To date a great deal of progress has been made in effectively and efficiently combining information obtained through fuzzy pattern recognition and macroscopic mass and energy inventory analysis for use in multiple failure diagnostics. Work has also begun on the unique problem of diagnostics and surveillance methodologies for advanced passively-safe reactors systems utilizing both statistical and fuzzy information. Plans are also being formulated for the development of deterministic optimal control algorithms combined with Monte Carlo incremental learning algorithms to be used for the flexible and efficient control of reactor transients

  12. Plant oil-based shape memory polymer using acrylic monolith

    Directory of Open Access Journals (Sweden)

    T. Tsujimoto

    2015-09-01

    Full Text Available This article deals with the synthesis of a plant oil-based material using acrylic monolith. An acrylic monolith bearing oxirane groups was prepared via simple technique that involved the dissolution of poly(glycidyl methacrylate-comethyl methacrylate (PGMA in ethanolic – aqueous solution by heating and subsequent cooling. The PGMA monolith had topologically porous structure, which was attributed to the phase separation of the polymer solution. The PGMA monolith was impregnated by epoxidized soybean oil (ESO containing thermally-latent catalyst, and the subsequent curing produced a crosslinked material with relatively good transparency. The Young’s modulus and the tensile strength of polyESO/PGMA increased compared with the ESO homopolymer. The strain at break of polyESO/PGMA was larger than that of the ESO homopolymer and crosslinked PGMA. Furthermore, polyESO/PGMA exhibited good shape memory-recovery behavior.

  13. Efficacy of Fluidized Bed Bioartificial Liver in Treating Fulminant Hepatic Failure in Pigs: A Metabolomics Study.

    Science.gov (United States)

    Zhou, Pengcheng; Shao, Li; Zhao, Lifu; Lv, Guoliang; Pan, Xiaoping; Zhang, Anye; Li, Jianzhou; Zhou, Ning; Chen, Deying; Li, Lanjuan

    2016-01-01

    Bioartificial livers may act as a promising therapy for fulminant hepatic failure (FHF) with better accessibility and less injury compared to orthotopic liver transplantation. This study aims to evaluate the efficacy and safety of a fluidized bed bioartificial liver (FBBAL) and to explore its therapeutic mechanisms based on metabolomics. FHF was induced by D-galactosamine. Eighteen hours later, pigs were treated with an FBBAL containing encapsulated primary porcine hepatocytes (B group), with a sham FBBAL (containing cell-free capsules, S group) or with only intensive care (C group) for 6 h. Serum samples were assayed using ultra-performance liquid chromatography-mass spectrometry. The difference in survival time (51.6 ± 7.9 h vs. 49.3 ± 6.6 h) and serum metabolome was negligible between the S and C groups, whereas FBBAL treatment significantly prolonged survival time (70.4 ± 11.5h, P sphingomyelinase, and fatty acids and an increase in conjugated bile acids. The FBBAL exhibits some liver functions and may exert its therapeutic effect by altering the serum metabolome of FHF pigs. Moreover, alginate-chitosan capsules have less influence on serum metabolites. Nevertheless, the alterations were not universally beneficial, revealing that much should be done to improve the FBBAL. PMID:27194381

  14. Metabolomic Effects of Xylitol and Fluoride on Plaque Biofilm in Vivo

    Science.gov (United States)

    Takahashi, N.; Washio, J.

    2011-01-01

    Dental caries is initiated by demineralization of the tooth surface through acid production from sugar by plaque biofilm. Fluoride and xylitol have been used worldwide as caries-preventive reagents, based on in vitro-proven inhibitory mechanisms on bacterial acid production. We attempted to confirm the inhibitory mechanisms of fluoride and xylitol in vivo by performing metabolome analysis on the central carbon metabolism in supragingival plaque using the combination of capillary electrophoresis and a time-of-flight mass spectrometer. Fluoride (225 and 900 ppm F−) inhibited lactate production from 10% glucose by 34% and 46%, respectively, along with the increase in 3-phosphoglycerate and the decrease in phosphoenolpyruvate in the EMP pathway in supragingival plaque. These results confirmed that fluoride inhibited bacterial enolase in the EMP pathway and subsequently repressed acid production in vivo. In contrast, 10% xylitol had no effect on acid production and the metabolome profile in supragingival plaque, although xylitol 5-phosphate was produced. These results suggest that xylitol is not an inhibitor of plaque acid production but rather a non-fermentative sugar alcohol. Metabolome analyses of plaque biofilm can be applied for monitoring the efficacy of dietary components and medicines for plaque biofilm, leading to the development of effective plaque control. PMID:21940519

  15. Integration of datasets from different analytical techniques to assess the impact of nutrition on human metabolome

    Directory of Open Access Journals (Sweden)

    Pamela eVernocchi

    2012-12-01

    Full Text Available Bacteria colonizing the human intestinal tract exhibit a high phylogenetic diversity that reflects their immense metabolic potentials. The catalytic activity of gut microbes has an important impact on gastrointestinal (GI functions and host health. The microbial conversion of carbohydrates and other food components leads to the formation of a large number of compounds that affect the host metabolome and have beneficial or adverse effects on human health. Meabolomics is a metabolic-biology system approach focused on the metabolic responses understanding of living systems to physio-pathological stimuli by using multivariate statistical data on human body fluids obtained by different instrumental techniques. A metabolomic approach based on an analytical platform could be able to separate, detect, characterize and quantify a wide range of metabolites and its metabolic pathways. This approach has been recently applied to study the metabolic changes triggered in the gut microbiota by specific diet components and diet variations, specific diseases, probiotic and synbiotic food intake.This review describes the metabolomic data obtained by analyzing human fluids by using different techniques and particularly Gas Chromatography Mass Spectrometry Solid-phase Micro Extraction (GC-MS/SPME, Proton Nuclear Magnetic Resonance (1H-NMR Spectroscopy and Fourier Transform Infrared (FTIR Spectroscopy. This instrumental approach have a good potential in the identification and detection of specific food intake and diseases biomarkers.

  16. Insights into the impact of silver nanoparticles on human keratinocytes metabolism through NMR metabolomics.

    Science.gov (United States)

    Carrola, Joana; Bastos, Verónica; Ferreira de Oliveira, José Miguel P; Oliveira, Helena; Santos, Conceição; Gil, Ana M; Duarte, Iola F

    2016-01-01

    Due to their antimicrobial properties, silver nanoparticles (AgNPs) are increasingly incorporated into consumer goods and medical products. Their potential toxicity to human cells is however a major concern, and there is a need for improved understanding of their effects on cell metabolism and function. Here, Nuclear Magnetic Resonance (NMR) metabolomics was used to investigate the metabolic profile of human epidermis keratinocytes (HaCaT cell line) exposed for 48 h to 30 nm citrate-stabilized spherical AgNPs (10 and 40 μg/mL). Intracellular aqueous extracts, organic extracts and extracellular culture medium were analysed to provide an integrated view of the cellular metabolic response. The specific metabolite variations, highlighted through multivariate analysis and confirmed by spectral integration, suggested that HaCaT cells exposed to AgNPs displayed upregulated glutathione-based antioxidant protection, increased glutaminolysis, downregulated tricarboxylic acid (TCA) cycle activity, energy depletion and cell membrane modification. Importantly, most metabolic changes were apparent in cells exposed to a concentration of AgNPs which did not affect cell viability at significant levels, thus underlying the sensitivity of NMR metabolomics to detect early biochemical events, even in the absence of a clear cytotoxic response. It can be concluded that NMR metabolomics is an important new tool in the field of in vitro nanotoxicology. PMID:26344855

  17. Revealing disease-associated pathways by network integration of untargeted metabolomics.

    Science.gov (United States)

    Pirhaji, Leila; Milani, Pamela; Leidl, Mathias; Curran, Timothy; Avila-Pacheco, Julian; Clish, Clary B; White, Forest M; Saghatelian, Alan; Fraenkel, Ernest

    2016-09-01

    Uncovering the molecular context of dysregulated metabolites is crucial to understand pathogenic pathways. However, their system-level analysis has been limited owing to challenges in global metabolite identification. Most metabolite features detected by untargeted metabolomics carried out by liquid-chromatography-mass spectrometry cannot be uniquely identified without additional, time-consuming experiments. We report a network-based approach, prize-collecting Steiner forest algorithm for integrative analysis of untargeted metabolomics (PIUMet), that infers molecular pathways and components via integrative analysis of metabolite features, without requiring their identification. We demonstrated PIUMet by analyzing changes in metabolism of sphingolipids, fatty acids and steroids in a Huntington's disease model. Additionally, PIUMet enabled us to elucidate putative identities of altered metabolite features in diseased cells, and infer experimentally undetected, disease-associated metabolites and dysregulated proteins. Finally, we established PIUMet's ability for integrative analysis of untargeted metabolomics data with proteomics data, demonstrating that this approach elicits disease-associated metabolites and proteins that cannot be inferred by individual analysis of these data. PMID:27479327

  18. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.).

    Science.gov (United States)

    Rao, Guodong; Sui, Jinkai; Zhang, Jianguo

    2016-01-01

    The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r(2)≥0.49 and had a false discovery rate (FDR) ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism. PMID:27215321

  19. The Gut Microbiome, Its Metabolome, and Their Relationship to Health and Disease.

    Science.gov (United States)

    Wu, Gary D

    2016-01-01

    Despite its importance in maintaining the health of the host, growing evidence suggests that gut microbiota may also be an important factor in the pathogenesis of various diseases. The composition of the microbiota can be influenced by many factors, including age, genetics, host environment, and diet. There are epidemiologic data associating diet with the development of inflammatory bowel disease as well as evidence that diet can influence both the form and the function of the microbiome. Based on this evidence, studies are now underway to examine the effect of defined formula diets, an effective therapeutic modality in Crohn's disease, on both the gut microbiome and its metabolome as a therapeutic probe. Diet has an impact upon both the composition and the function of the microbiota in part through small-molecule production that may influence the development of both immune-mediated and metabolic diseases. By comparing dietary intake, the gut microbiota, and the plasma metabolome in omnivores versus vegans, we provide evidence that the production of certain bacterial metabolites is constrained by the composition of the gut microbiota. In total, these results demonstrate the potential promise of dietary manipulation of the gut microbiota and its metabolome as a modality to both maintain health and treat disease. PMID:26764479

  20. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.

    Directory of Open Access Journals (Sweden)

    Guodong Rao

    2016-06-01

    Full Text Available The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r2≥0.49 and had a false discovery rate (FDR ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism.