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      The Human Serum Metabolome

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          Abstract

          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 undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.

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          Most cited references 88

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          A simple method for the isolation and purification of total lipides from animal tissues.

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            Reactive oxygen species: metabolism, oxidative stress, and signal transduction.

            Several reactive oxygen species (ROS) are continuously produced in plants as byproducts of aerobic metabolism. Depending on the nature of the ROS species, some are highly toxic and rapidly detoxified by various cellular enzymatic and nonenzymatic mechanisms. Whereas plants are surfeited with mechanisms to combat increased ROS levels during abiotic stress conditions, in other circumstances plants appear to purposefully generate ROS as signaling molecules to control various processes including pathogen defense, programmed cell death, and stomatal behavior. This review describes the mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions. New insights into the complexity and roles that ROS play in plants have come from genetic analyses of ROS detoxifying and signaling mutants. Considering recent ROS-induced genome-wide expression analyses, the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.
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              From genomics to chemical genomics: new developments in KEGG

              The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource () provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                16 February 2011
                : 6
                : 2
                Affiliations
                [1 ]Department of Computing Science, University of Alberta, Edmonton, Canada
                [2 ]Department of Chemistry, University of Alberta, Edmonton, Canada
                [3 ]Department of Clinical Laboratory Medicine, University of Alberta, Edmonton, Canada
                [4 ]Department of Biological Sciences, University of Alberta, Edmonton, Canada
                [5 ]National Institute for Nanotechnology, Edmonton, Canada
                [6 ]James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research and the NCE CECR Centre of Excellence for Prevention of Organ Failure (PROOF Centre), Vancouver, Canada
                [7 ]United States Department of Agriculture, Agricultural Research Service (ARS), Western Human Nutrition Research Center, Davis, California, United States of America
                [8 ]Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
                [9 ]Veterans Administration Hospital and University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
                Aston University, United Kingdom
                Author notes

                Conceived and designed the experiments: NP DDH JP RM SB IS FB RG ZH BM JWN TG DSW. Performed the experiments: NP DDH JP RM SB IS RK ED PH. Analyzed the data: NP DDH JP ACG RM SB IS RK RE BG NY JX CK TLP SS JWN TG. Contributed reagents/materials/analysis tools: ACG RE BG NY JX CK ED PH ZH SS FB TG BM. Wrote the paper: NP DDH JP RM IS ZH TLP RG BM JWN TG DSW.

                PONE-D-10-02036
                10.1371/journal.pone.0016957
                3040193
                21359215
                Psychogios et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Counts
                Pages: 23
                Categories
                Research Article
                Biology
                Biochemistry
                Blood Chemistry
                Metabolism
                Computational Biology
                Chemistry
                Analytical Chemistry
                Applied Chemistry
                Chemical Properties
                Nuclear Magnetic Resonance
                Medicinal Chemistry
                Medicine
                Diagnostic Medicine
                Hematology
                Metabolic Disorders

                Uncategorized

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