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      Uncovering mechanisms of global ocean change effects on the Dungeness crab ( Cancer magister) through metabolomics analysis

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          Abstract

          The Dungeness crab is an economically and ecologically important species distributed along the North American Pacific coast. To predict how Dungeness crab may physiologically respond to future global ocean change on a molecular level, we performed untargeted metabolomic approaches on individual Dungeness crab juveniles reared in treatments that mimicked current and projected future pH and dissolved oxygen conditions. We found 94 metabolites and 127 lipids responded in a condition-specific manner, with a greater number of known compounds more strongly responding to low oxygen than low pH exposure. Pathway analysis of these compounds revealed that juveniles may respond to low oxygen through evolutionarily conserved processes including downregulating glutathione biosynthesis and upregulating glycogen storage, and may respond to low pH by increasing ATP production. Most interestingly, we found that the response of juveniles to combined low pH and low oxygen exposure was most similar to the low oxygen exposure response, indicating low oxygen may drive the physiology of juvenile crabs more than pH. Our study elucidates metabolic dynamics that expand our overall understanding of how the species might respond to future ocean conditions and provides a comprehensive dataset that could be used in future ocean acidification response studies.

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          Most cited references 54

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          Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics.

          Accurate profiling of lipidomes relies upon the quantitative and unbiased recovery of lipid species from analyzed cells, fluids, or tissues and is usually achieved by two-phase extraction with chloroform. We demonstrated that methyl-tert-butyl ether (MTBE) extraction allows faster and cleaner lipid recovery and is well suited for automated shotgun profiling. Because of MTBE's low density, lipid-containing organic phase forms the upper layer during phase separation, which simplifies its collection and minimizes dripping losses. Nonextractable matrix forms a dense pellet at the bottom of the extraction tube and is easily removed by centrifugation. Rigorous testing demonstrated that the MTBE protocol delivers similar or better recoveries of species of most all major lipid classes compared with the "gold-standard" Folch or Bligh and Dyer recipes.
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            LIPID MAPS online tools for lipid research

            The LIPID MAPS consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (MS) data. A simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. The structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. Within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. The structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion MS experimental data. The MS prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. The LIPID MAPS online tools are publicly available at www.lipidmaps.org/tools/.
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              Quality control for plant metabolomics: reporting MSI-compliant studies.

              The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study - the metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.
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                Author and article information

                Contributors
                strigg@uw.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                24 July 2019
                24 July 2019
                2019
                : 9
                Affiliations
                [1 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, Division of Biological Sciences, Cell and Developmental Biology Section, , University of California San Diego, ; La Jolla, California USA
                [2 ]ISNI 0000 0001 0662 7144, GRID grid.250671.7, Genomic Analysis Laboratory, , The Salk Institute for Biological Studies, ; La Jolla, California USA
                [3 ]ISNI 0000 0001 1266 2261, GRID grid.3532.7, Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, , National Oceanic and Atmospheric Administration, ; Seattle, Washington USA
                [4 ]ISNI 0000 0001 1266 2261, GRID grid.3532.7, Ocean Acidification Program, , National Oceanic and Atmospheric Administration, ; Seattle, Washington USA
                [5 ]ISNI 0000000122986657, GRID grid.34477.33, Present Address: School of Aquatic and Fishery Sciences, , University of Washington, ; Seattle, Washington USA
                Article
                46947
                10.1038/s41598-019-46947-6
                6656712
                31341175
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Funding
                Funded by: FundRef https://doi.org/10.13039/100000192, United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA);
                Funded by: FundRef https://doi.org/10.13039/100000082, NSF | Directorate for Education & Human Resources | Division of Graduate Education (DGE);
                Award ID: NSF 11-582
                Award Recipient :
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                © The Author(s) 2019

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                metabolomics, biochemical networks, climate-change impacts

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