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Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two major analytical platforms in the field of metabolomics, the other being mass spectrometry (MS). NMR is less sensitive than MS and hence it detects a relatively small number of metabolites. However, NMR exhibits numerous unique characteristics including its high reproducibility and non-destructive nature, its ability to identify unknown metabolites definitively, and its capabilities to obtain absolute concentrations of all detected metabolites, sometimes even without an internal standard. These characteristics outweigh the relatively low sensitivity and resolution of NMR in metabolomics applications. Since biological mixtures are highly complex, increased demand for new methods to improve detection, better identify unknown metabolites, and provide more accurate quantitation continues unabated. Technological and methodological advances to date have helped to improve the resolution and sensitivity and detection of a larger number of metabolite signals. Efforts focused on measuring unknown metabolite signals have resulted in the identification and quantitation of an expanded pool of metabolites including labile metabolites such as cellular redox coenzymes, energy coenzymes, and antioxidants. This chapter describes quantitative NMR methods in metabolomics with an emphasis on recent methodological developments, while highlighting the benefits and challenges of NMR-based metabolomics.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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2
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Miyamoto H, Asano F, Ishizawa K, Suda W, Miyamoto H, Tsuji N, Matsuura M, Tsuboi A, Ishii C, Nakaguma T, Shindo C, Kato T, Kurotani A, Shima H, Moriya S, Hattori M, Kodama H, Ohno H, Kikuchi J. A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155520. [PMID: 35508250 DOI: 10.1016/j.scitotenv.2022.155520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ13C and δ15N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan.
| | - Futo Asano
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Arisa Tsuboi
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeharu Moriya
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
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3
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Kikuchi J, Yamada S. The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science. RSC Adv 2021; 11:30426-30447. [PMID: 35480260 PMCID: PMC9041152 DOI: 10.1039/d1ra03008f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022] Open
Abstract
The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.
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Affiliation(s)
- Jun Kikuchi
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8601 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
| | - Shunji Yamada
- Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
- Prediction Science Laboratory, RIKEN Cluster for Pioneering Research 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
- Data Assimilation Research Team, RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe 650-0047 Japan
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4
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.
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Geier FM, Leroi AM, Bundy JG. 13C Labeling of Nematode Worms to Improve Metabolome Coverage by Heteronuclear Nuclear Magnetic Resonance Experiments. Front Mol Biosci 2019; 6:27. [PMID: 31106208 PMCID: PMC6498324 DOI: 10.3389/fmolb.2019.00027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/04/2019] [Indexed: 11/29/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is widely used as a metabolomics tool, and 1D spectroscopy is overwhelmingly the commonest approach. The use of 2D spectroscopy could offer significant advantages in terms of increased spectral dispersion of peaks, but has a number of disadvantages—in particular, heteronuclear 2D spectroscopy is often much less sensitive than 1D NMR. One factor contributing to this low sensitivity in 13C/1H heteronuclear NMR is the low natural abundance of the 13C stable isotope; as a consequence, where it is possible to label biological material with 13C, there is a potential enhancement of sensitivity of up to around 90fold. However, there are some problems that can reduce the advantages otherwise gained—in particular, the fine structure arising from 13C/13C coupling, which is essentially non-existent at natural abundance, can reduce the possible sensitivity gain and increase the chances of peak overlap. Here, we examined the use of two different heteronuclear single quantum coherence (HSQC) pulse sequences for the analysis of fully 13C-labeled tissue extracts from Caenorhabditis elegans nematodes. The constant time ct-HSQC had improved peak shape, and consequent better peak detection of metabolites from a labeled extract; matching this against reference spectra from the HMDB gave a match to about 300 records (although fewer actual metabolites, as some of these represent false positive matches). This approach gives a rapid and automated initial metabolome assignment, forming an ideal basis for further manual curation.
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Affiliation(s)
- Florian M Geier
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Armand M Leroi
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
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6
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Saborano R, Eraslan Z, Roberts J, Khanim FL, Lalor PF, Reed MAC, Günther UL. A framework for tracer-based metabolism in mammalian cells by NMR. Sci Rep 2019; 9:2520. [PMID: 30792403 PMCID: PMC6385278 DOI: 10.1038/s41598-018-37525-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
Metabolism changes extensively during the normal proliferation and differentiation of mammalian cells, and in cancer and inflammatory diseases. Since changes in the metabolic network reflect interactions between genetic, epigenetic and environmental changes, it is helpful to study the flow of label from isotopically labelled precursors into other metabolites rather than static metabolite levels. For this Nuclear Magnetic Resonance (NMR) spectroscopy is an attractive technique as it can quantify site-specific label incorporation. However, for applications using human cells and cell lines, the challenge is to optimize the process to maximize sensitivity and reproducibility. Here we present a new framework to analyze metabolism in mammalian cell lines and primary cells, covering the workflow from the preparation of cells to the acquisition and analysis of NMR spectra. We have applied this new approach in hematological and liver cancer cell lines and confirm the feasibility of tracer-based metabolism in primary liver cells.
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Affiliation(s)
- Raquel Saborano
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Zuhal Eraslan
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Jennie Roberts
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Farhat L Khanim
- University of Birmingham, School of Biosciences, Birmingham, B15 2TT, England
| | - Patricia F Lalor
- University of Birmingham, Institute of Immunology and Immunotherapy, Birmingham, B15 2TT, England
| | - Michelle A C Reed
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Ulrich L Günther
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England.
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7
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Asakura T, Date Y, Kikuchi J. Application of ensemble deep neural network to metabolomics studies. Anal Chim Acta 2018; 1037:230-236. [DOI: 10.1016/j.aca.2018.02.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 02/05/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022]
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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9
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Osaka T, Moriyama E, Arai S, Date Y, Yagi J, Kikuchi J, Tsuneda S. Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases. Nutrients 2017; 9:nu9121329. [PMID: 29211010 PMCID: PMC5748779 DOI: 10.3390/nu9121329] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 01/10/2023] Open
Abstract
The imbalance of gut microbiota is known to be associated with inflammatory bowel disease, but it remains unknown whether dysbiosis is a cause or consequence of chronic gut inflammation. In order to investigate the effects of gut inflammation on microbiota and metabolome, the sequential changes in gut microbiota and metabolites from the onset of colitis to the recovery in dextran sulfate sodium-induced colitic mice were characterized by using meta 16S rRNA sequencing and proton nuclear magnetic resonance (1H-NMR) analysis. Mice in the colitis progression phase showed the transient expansions of two bacterial families including Bacteroidaceae and Enterobacteriaceae and the depletion of major gut commensal bacteria belonging to the uncultured Bacteroidales family S24-7, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae. After the initiation of the recovery, commensal Lactobacillus members promptly predominated in gut while other normally abundant bacteria excluding the Erysipelotrichaceae remained diminished. Furthermore, 1H-NMR analysis revealed characteristic fluctuations in fecal levels of organic acids (lactate and succinate) associated with the disease states. In conclusion, acute intestinal inflammation is a perturbation factor of gut microbiota but alters the intestinal environments suitable for Lactobacillus members.
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Affiliation(s)
- Toshifumi Osaka
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Eri Moriyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Shunichi Arai
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Junji Yagi
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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Wang J, Zhou L, Lei H, Hao F, Liu X, Wang Y, Tang H. Simultaneous Quantification of Amino Metabolites in Multiple Metabolic Pathways Using Ultra-High Performance Liquid Chromatography with Tandem-mass Spectrometry. Sci Rep 2017; 7:1423. [PMID: 28469184 PMCID: PMC5431165 DOI: 10.1038/s41598-017-01435-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/28/2017] [Indexed: 01/09/2023] Open
Abstract
Metabolites containing amino groups cover multiple pathways and play important roles in redox homeostasis and biosyntheses of proteins, nucleotides and neurotransmitters. Here, we report a new method for simultaneous quantification of 124 such metabolites. This is achieved by derivatization-assisted sensitivity enhancement with 5-aminoisoquinolyl-N-hydroxysuccinimidyl carbamate (5-AIQC) followed with comprehensive analysis using ultra-high performance liquid chromatography and electrospray ionization tandem mass spectrometry (UHPLC-MS/MS). In an one-pot manner, this quantification method enables simultaneous coverage of 20 important metabolic pathways including protein biosynthesis/degradation, biosyntheses of catecholamines, arginine and glutathione, metabolisms of homocysteine, taurine-hypotaurine etc. Compared with the reported ones, this method is capable of simultaneously quantifying thiols, disulfides and other oxidation-prone analytes in a single run and suitable for quantifying aromatic amino metabolites. This method is also much more sensitive for all tested metabolites with LODs well below 50 fmol (at sub-fmol for most tested analytes) and shows good precision for retention time and quantitation with inter-day and intra-day relative standard deviations (RSDs) below 15% and good recovery from renal cancer tissue, rat urine and plasma. The method was further applied to quantify the amino metabolites in silkworm hemolymph from multiple developmental stages showing its applicability in metabolomics and perhaps some clinical chemistry studies.
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Affiliation(s)
- Jin Wang
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.,State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai International Centre for Molecular Phenomics, Collaborative Innovation Center for Genetics and Development, Shanghai, 200438, China.,CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Lihong Zhou
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.,CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hehua Lei
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fuhua Hao
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xin Liu
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310058, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai International Centre for Molecular Phenomics, Collaborative Innovation Center for Genetics and Development, Shanghai, 200438, China.
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11
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Sugiki T, Kobayashi N, Fujiwara T. Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists. Comput Struct Biotechnol J 2017; 15:328-339. [PMID: 28487762 PMCID: PMC5408130 DOI: 10.1016/j.csbj.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data. Owing to the remarkable progress in the past decade, we can easily access suitable and popular analytical resources for NMR structure determination of proteins with high accuracy. Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins. This review should aid NMR specialists aiming to develop new methods that accelerate the structure determination process, and open avenues for non-specialist and life scientists interested in using NMR spectroscopy to solve protein structures.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Kikuchi J, Yamada S. NMR window of molecular complexity showing homeostasis in superorganisms. Analyst 2017; 142:4161-4172. [DOI: 10.1039/c7an01019b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
NMR offers tremendous advantages in the analyses of molecular complexity. The “big-data” are produced during the acquisition of fingerprints that must be stored and shared for posterior analysis and verifications.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science
- Yokohama
- Japan
- Graduate School of Bioagricultural Sciences
- Nagoya University
| | - Shunji Yamada
- RIKEN Center for Sustainable Resource Science
- Yokohama
- Japan
- Graduate School of Bioagricultural Sciences
- Nagoya University
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13
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[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Visualizing Individual and Region-specific Microbial–metabolite Relations by Important Variable Selection Using Machine Learning Approaches. JOURNAL OF COMPUTER AIDED CHEMISTRY 2017. [DOI: 10.2751/jcac.18.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Lee S, Wen H, An YJ, Cha JW, Ko YJ, Hyberts SG, Park S. Carbon Isotopomer Analysis with Non-Unifom Sampling HSQC NMR for Cell Extract and Live Cell Metabolomics Studies. Anal Chem 2016; 89:1078-1085. [DOI: 10.1021/acs.analchem.6b02107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sujin Lee
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - He Wen
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Department
of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yong Jin An
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Jin Wook Cha
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
- Natural
Constituents Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea
| | - Yoon-Joo Ko
- National
Center for Inter-University Research Facilities (NCIRF), Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
| | - Sven G. Hyberts
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sunghyouk Park
- Natural
Product Research Institute, College of Pharmacy, Seoul National University, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea
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15
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Development of chemical isotope labeling liquid chromatography mass spectrometry for silkworm hemolymph metabolomics. Anal Chim Acta 2016; 942:1-11. [DOI: 10.1016/j.aca.2016.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/15/2016] [Accepted: 06/01/2016] [Indexed: 11/24/2022]
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16
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17
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Ogura T, Date Y, Masukujane M, Coetzee T, Akashi K, Kikuchi J. Improvement of physical, chemical, and biological properties of aridisol from Botswana by the incorporation of torrefied biomass. Sci Rep 2016; 6:28011. [PMID: 27313139 PMCID: PMC4911548 DOI: 10.1038/srep28011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/14/2016] [Indexed: 01/14/2023] Open
Abstract
Effective use of agricultural residual biomass may be beneficial for both local and global ecosystems. Recently, biochar has received attention as a soil enhancer, and its effects on plant growth and soil microbiota have been investigated. However, there is little information on how the physical, chemical, and biological properties of soil amended with biochar are affected. In this study, we evaluated the effects of the incorporation of torrefied plant biomass on physical and structural properties, elemental profiles, initial plant growth, and metabolic and microbial dynamics in aridisol from Botswana. Hemicellulose in the biomass was degraded while cellulose and lignin were not, owing to the relatively low-temperature treatment in the torrefaction preparation. Water retentivity and mineral availability for plants were improved in soils with torrefied biomass. Furthermore, fertilization with 3% and 5% of torrefied biomass enhanced initial plant growth and elemental uptake. Although the metabolic and microbial dynamics of the control soil were dominantly associated with a C1 metabolism, those of the 3% and 5% torrefied biomass soils were dominantly associated with an organic acid metabolism. Torrefied biomass was shown to be an effective soil amendment by enhancing water retentivity, structural stability, and plant growth and controlling soil metabolites and microbiota.
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Affiliation(s)
- Tatsuki Ogura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masego Masukujane
- Department of Agricultural Research, Ministry of Agriculture, Private Bag 0033, Gaborone, Botswana
| | - Tidimalo Coetzee
- Department of Agricultural Research, Ministry of Agriculture, Private Bag 0033, Gaborone, Botswana
| | - Kinya Akashi
- Faculty of Agriculture, Tottori University, 4-101 Koyama-cho, Tottori 680-8533, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan
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18
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Yamada H, Kameda T, Kimura Y, Imai H, Matsuda T, Sando S, Toshimitsu A, Aoyama Y, Kondo T. (13)C/(15)N-Enriched l-Dopa as a Triple-Resonance NMR Probe to Monitor Neurotransmitter Dopamine in the Brain and Liver Extracts of Mice. ChemistryOpen 2016; 5:125-8. [PMID: 27308224 PMCID: PMC4906467 DOI: 10.1002/open.201500196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 12/28/2022] Open
Abstract
In an attempt to monitor μm-level trace constituents, we applied here (1)H-{(13)C-(15)N} triple-resonance nuclear magnetic resonance (NMR) to (13)C/(15)N-enriched l-Dopa as the inevitable precursor of the neurotransmitter dopamine in the brain. The perfect selectivity (to render endogenous components silent) and μm-level sensitivity (700 MHz spectrometer equipped with a cryogenic probe) of triple-resonance allowed the unambiguous and quantitative metabolic and pharmacokinetic analyses of administered l-Dopa/dopamine in the brain and liver of mice. The level of dopamine generated in the brain (within the range 7-76 μm, which covers the typical stimulated level of ∼30 μm) could be clearly monitored ex vivo, but was slightly short of the detection limit of a 7 T MR machine for small animals. This work suggests that μm-level trace constituents are potential targets of ex vivo monitoring as long as they contain N atom(s) and their appropriate (13)C/(15)N-enrichment is synthetically accessible.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering Research UnitCenter for the Promotion of Interdisciplinary Education and ResearchKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
- Department of Life SystemsInstitute of Technology and Science Graduate SchoolTokushima UniversityTokushima770-8506Japan
| | - Tetsuro Kameda
- Department of Energy and Hydrocarbon ChemistryGraduate School of EngineeringKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
| | - Yu Kimura
- Department of Energy and Hydrocarbon ChemistryGraduate School of EngineeringKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
- Research and Educational Unit of Leaders for Integrated Medical SystemCenter for the Promotion of Interdisciplinary Education and ResearchKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
| | - Hirohiko Imai
- Department of Systems ScienceGraduate School of InformaticsKyoto University, Yoshida-honmachi, Sakyo-kuKyoto606-8501Japan
| | - Tetsuya Matsuda
- Department of Systems ScienceGraduate School of InformaticsKyoto University, Yoshida-honmachi, Sakyo-kuKyoto606-8501Japan
| | - Shinsuke Sando
- Department of Chemistry and BiotechnologyThe University of Tokyo, 7-3-1 Hongo, Bunkyo-kuTokyo113-8656Japan
| | - Akio Toshimitsu
- Department of Energy and Hydrocarbon ChemistryGraduate School of EngineeringKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
- Division of Multidisciplinary ChemistryInstitute for Chemical ResearchKyoto University, Gokanosho, UjiKyoto611-0011Japan
| | | | - Teruyuki Kondo
- Advanced Biomedical Engineering Research UnitCenter for the Promotion of Interdisciplinary Education and ResearchKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
- Department of Energy and Hydrocarbon ChemistryGraduate School of EngineeringKyoto University, Katsura, Nishikyo-kuKyoto615-8510Japan
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19
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Visualization of Microfloral Metabolism for Marine Waste Recycling. Metabolites 2016; 6:metabo6010007. [PMID: 26828528 PMCID: PMC4812336 DOI: 10.3390/metabo6010007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/16/2015] [Accepted: 01/21/2016] [Indexed: 12/26/2022] Open
Abstract
Marine biomass including fishery products are precious protein resources for human foods and are an alternative to livestock animals in order to reduce the virtual water problem. However, a large amount of marine waste can be generated from fishery products and it is not currently recycled. We evaluated the metabolism of digested marine waste using integrated analytical methods, under anaerobic conditions and the fertilization of abandoned agricultural soils. Dynamics of fish waste digestion revealed that samples of meat and bony parts had similar dynamics under anaerobic conditions in spite of large chemical variations in input marine wastes. Abandoned agricultural soils fertilized with fish waste accumulated some amino acids derived from fish waste, and accumulation of l-arginine and l-glutamine were higher in plant seedlings. Therefore, we have proposed an analytical method to visualize metabolic dynamics for recycling of fishery waste processes.
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20
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Kikuchi J, Tsuboi Y, Komatsu K, Gomi M, Chikayama E, Date Y. SpinCouple: Development of a Web Tool for Analyzing Metabolite Mixtures via Two-Dimensional J-Resolved NMR Database. Anal Chem 2015; 88:659-65. [PMID: 26624790 DOI: 10.1021/acs.analchem.5b02311] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A new Web-based tool, SpinCouple, which is based on the accumulation of a two-dimensional (2D) (1)H-(1)H J-resolved NMR database from 598 metabolite standards, has been developed. The spectra include both J-coupling and (1)H chemical shift information; those are applicable to a wide array of spectral annotation, especially for metabolic mixture samples that are difficult to label through the attachment of (13)C isotopes. In addition, the user-friendly application includes an absolute-quantitative analysis tool. Good agreement was obtained between known concentrations of 20-metabolite mixtures versus the calibration curve-based quantification results obtained from 2D-Jres spectra. We have examined the web tool availability using nine series of biological extracts, obtained from animal gut and waste treatment microbiota, fish, and plant tissues. This web-based tool is publicly available via http://emar.riken.jp/spincpl.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University , 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Komatsu
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Masahiro Gomi
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Eisuke Chikayama
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Information Systems, Niigata University of International and Information Studies , 3-1-1 Mizukino, Nishi-ku, Niigata-shi, Niigata 950-2292, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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21
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Identification of Reliable Components in Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS): a Data-Driven Approach across Metabolic Processes. Sci Rep 2015; 5:15710. [PMID: 26531245 PMCID: PMC4632111 DOI: 10.1038/srep15710] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/27/2015] [Indexed: 02/08/2023] Open
Abstract
There is an increasing need to use multivariate statistical methods for understanding biological functions, identifying the mechanisms of diseases, and exploring biomarkers. In addition to classical analyses such as hierarchical cluster analysis, principal component analysis, and partial least squares discriminant analysis, various multivariate strategies, including independent component analysis, non-negative matrix factorization, and multivariate curve resolution, have recently been proposed. However, determining the number of components is problematic. Despite the proposal of several different methods, no satisfactory approach has yet been reported. To resolve this problem, we implemented a new idea: classifying a component as “reliable” or “unreliable” based on the reproducibility of its appearance, regardless of the number of components in the calculation. Using the clustering method for classification, we applied this idea to multivariate curve resolution-alternating least squares (MCR-ALS). Comparisons between conventional and modified methods applied to proton nuclear magnetic resonance (1H-NMR) spectral datasets derived from known standard mixtures and biological mixtures (urine and feces of mice) revealed that more plausible results are obtained by the modified method. In particular, clusters containing little information were detected with reliability. This strategy, named “cluster-aided MCR-ALS,” will facilitate the attainment of more reliable results in the metabolomics datasets.
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22
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Nagana Gowda GA, Raftery D. Can NMR solve some significant challenges in metabolomics? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:144-60. [PMID: 26476597 PMCID: PMC4646661 DOI: 10.1016/j.jmr.2015.07.014] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 05/04/2023]
Abstract
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.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States; Department of Chemistry, University of Washington, Seattle, WA 98195, United States; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States.
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23
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Ogura T, Date Y, Tsuboi Y, Kikuchi J. Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan. ACS Chem Biol 2015; 10:1908-15. [PMID: 25997449 DOI: 10.1021/cb500609p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new metabolic dynamics analysis approach has been developed in which massive data sets from time-series of (1)H and (13)C NMR spectra are integrated in combination with microbial variability to characterize the biomass degradation process using field soil microbial communities. On the basis of correlation analyses that revealed relationships between various metabolites and bacteria, we efficiently monitored the metabolic dynamics of saccharides, amino acids, and organic acids, by assessing time-course changes in the microbial and metabolic profiles during biomass degradation. Specific bacteria were found to support specific steps of metabolic pathways in the degradation process of biomass to short chain fatty acids. We evaluated samples from agricultural and abandoned fields contaminated by the tsunami that followed the Great East earthquake in Japan. Metabolic dynamics and activities in the biomass degradation process differed considerably between soil from agricultural and abandoned fields. In particular, production levels of short chain fatty acids, such as acetate and propionate, which were considered to be produced by soil bacteria such as Sedimentibacter sp. and Coprococcus sp., were higher in the soil from agricultural fields than from abandoned fields. Our approach could characterize soil activity based on the metabolic dynamics of microbial communities in the biomass degradation process and should therefore be useful in future investigations of the environmental effects of natural disasters on soils.
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Affiliation(s)
- Tatsuki Ogura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan
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24
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Dubey A, Rangarajan A, Pal D, Atreya HS. Pattern Recognition-Based Approach for Identifying Metabolites in Nuclear Magnetic Resonance-Based Metabolomics. Anal Chem 2015; 87:7148-55. [DOI: 10.1021/acs.analchem.5b00990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Abhinav Dubey
- IISc Mathematics Initiative, ‡NMR Research Centre, §Department of Molecular Reproduction,
Development and Genetics, ∥Supercomputer Education
and Research Centre, and ⊥Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Annapoorni Rangarajan
- IISc Mathematics Initiative, ‡NMR Research Centre, §Department of Molecular Reproduction,
Development and Genetics, ∥Supercomputer Education
and Research Centre, and ⊥Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Debnath Pal
- IISc Mathematics Initiative, ‡NMR Research Centre, §Department of Molecular Reproduction,
Development and Genetics, ∥Supercomputer Education
and Research Centre, and ⊥Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hanudatta S. Atreya
- IISc Mathematics Initiative, ‡NMR Research Centre, §Department of Molecular Reproduction,
Development and Genetics, ∥Supercomputer Education
and Research Centre, and ⊥Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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25
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Mori T, Tsuboi Y, Ishida N, Nishikubo N, Demura T, Kikuchi J. Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of (13)C-labeled Plant Metabolites and Lignocellulose. Sci Rep 2015; 5:11848. [PMID: 26143886 PMCID: PMC4491710 DOI: 10.1038/srep11848] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 06/08/2015] [Indexed: 01/18/2023] Open
Abstract
Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components.
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Affiliation(s)
- Tetsuya Mori
- 1] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan [2] Biotechnology Laboratory, Toyota Central R&D Labs, Inc., 41-1, Nagakute 480-1192, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Nobuhiro Ishida
- Biotechnology Laboratory, Toyota Central R&D Labs, Inc., 41-1, Nagakute 480-1192, Japan
| | - Nobuyuki Nishikubo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Taku Demura
- 1] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [2] Biomass Engineering Program, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Jun Kikuchi
- 1] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan [3] Biomass Engineering Program, RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako 351-0198, Japan [4] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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26
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Tokuda G, Tsuboi Y, Kihara K, Saitou S, Moriya S, Lo N, Kikuchi J. Metabolomic profiling of 13C-labelled cellulose digestion in a lower termite: insights into gut symbiont function. Proc Biol Sci 2015; 281:20140990. [PMID: 25009054 PMCID: PMC4100516 DOI: 10.1098/rspb.2014.0990] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Termites consume an estimated 3–7 billion tonnes of lignocellulose annually, a role in nature which is unique for a single order of invertebrates. Their food is digested with the help of microbial symbionts, a relationship that has been recognized for 200 years and actively researched for at least a century. Although DNA- and RNA-based approaches have greatly refined the details of the process and the identities of the participants, the allocation of roles in space and time remains unclear. To resolve this issue, a pioneer study is reported using metabolomics to chart the in situ catabolism of 13C-cellulose fed to the dampwood species Hodotermopsis sjostedti. The results confirm that the secretion of endogenous cellulases by the host may be significant to the digestive process and indicate that a major contribution by hindgut bacteria is phosphorolysis of cellodextrins or cellobiose. This study provides evidence that essential amino acid acquisition by termites occurs following the lysis of microbial tissue obtained via proctodaeal trophallaxis.
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Affiliation(s)
- Gaku Tokuda
- Tropical Biosphere Research Center, COMB, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kumiko Kihara
- RIKEN Antibiotics Laboratory, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Seikou Saitou
- Tropical Biosphere Research Center, COMB, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Sigeharu Moriya
- RIKEN Antibiotics Laboratory, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Nathan Lo
- School of Biological Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya 464-8601, Japan
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27
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Zhou L, Li H, Hao F, Li N, Liu X, Wang G, Wang Y, Tang H. Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.). J Proteome Res 2015; 14:2331-47. [PMID: 25825269 DOI: 10.1021/acs.jproteome.5b00159] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Silkworm (Bombyx mori) is a lepidopteran-holometabolic model organism. To understand its developmental biochemistry, we characterized the larval hemolymph metabonome from the third instar to prepupa stage using (1)H NMR spectroscopy whilst hemolymph fatty acid composition using GC-FID/MS. We unambiguously assigned more than 60 metabolites, among which tyrosine-o-β-glucuronide, mesaconate, homocarnosine, and picolinate were reported for the first time from the silkworm hemolymph. Phosphorylcholine was the most abundant metabolite in all developmental stages with exception for the periods before the third and fourth molting. We also found obvious developmental dependence for the hemolymph metabonome involving multiple pathways including protein biosyntheses, glycolysis, TCA cycle, the metabolisms of choline amino acids, fatty acids, purines, and pyrimidines. Most hemolymph amino acids had two elevations during the feeding period of the fourth instar and prepupa stage. Trehalose was the major blood sugar before day 8 of the fifth instar, whereas glucose became the major blood sugar after spinning. C16:0, C18:0 and its unsaturated forms were dominant fatty acids in hemolymph. The developmental changes of hemolymph metabonome were associated with dietary nutrient intakes, biosyntheses of cell membrane, pigments, proteins, and energy metabolism. These findings offered essential biochemistry information in terms of the dynamic metabolic changes during silkworm development.
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Affiliation(s)
- Lihong Zhou
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Huihui Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fuhua Hao
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ning Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xin Liu
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoliang Wang
- ¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Yulan Wang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,⊥Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Huiru Tang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,§State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200433, China
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Misawa T, Date Y, Kikuchi J. Human Metabolic, Mineral, and Microbiota Fluctuations Across Daily Nutritional Intake Visualized by a Data-Driven Approach. J Proteome Res 2015; 14:1526-34. [DOI: 10.1021/pr501194k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Takuma Misawa
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
- Biomass
Engineering Program, RIKEN Research Cluster for Innovation, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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29
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Watanabe M, Ohta Y, Licang S, Motoyama N, Kikuchi J. Profiling contents of water-soluble metabolites and mineral nutrients to evaluate the effects of pesticides and organic and chemical fertilizers on tomato fruit quality. Food Chem 2015; 169:387-95. [DOI: 10.1016/j.foodchem.2014.07.155] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 10/24/2022]
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Multi-Spectroscopic Analysis of Seed Quality and 13C-Stable-Iotopologue Monitoring in Initial Growth Metabolism of Jatropha curcas L. Metabolites 2014; 4:1018-33. [PMID: 25401292 PMCID: PMC4279157 DOI: 10.3390/metabo4041018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/10/2014] [Accepted: 11/05/2014] [Indexed: 12/20/2022] Open
Abstract
In the present study, we applied nuclear magnetic resonance (NMR), as well as near-infrared (NIR) spectroscopy, to Jatropha curcas to fulfill two objectives: (1) to qualitatively examine the seeds stored at different conditions, and (2) to monitor the metabolism of J. curcas during its initial growth stage under stable-isotope-labeling condition (until 15 days after seeding). NIR spectra could non-invasively distinguish differences in storage conditions. NMR metabolic analysis of water-soluble metabolites identified sucrose and raffinose family oligosaccharides as positive markers and gluconic acid as a negative marker of seed germination. Isotopic labeling patteren of metabolites in germinated seedlings cultured in agar-plate containg 13C-glucose and 15N-nitrate was analyzed by zero-quantum-filtered-total correlation spectroscopy (ZQF-TOCSY) and 13C-detected 1H-13C heteronuclear correlation spectroscopy (HETCOR). 13C-detected HETOCR with 13C-optimized cryogenic probe provided high-resolution 13C-NMR spectra of each metabolite in molecular crowd. The 13C-13C/12C bondmer estimated from 1H-13C HETCOR spectra indicated that glutamine and arginine were the major organic compounds for nitrogen and carbon transfer from roots to leaves.
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31
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Yoshida S, Date Y, Akama M, Kikuchi J. Comparative metabolomic and ionomic approach for abundant fishes in estuarine environments of Japan. Sci Rep 2014; 4:7005. [PMID: 25387575 PMCID: PMC4228347 DOI: 10.1038/srep07005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 09/17/2014] [Indexed: 12/23/2022] Open
Abstract
Environmental metabolomics or ionomics is widely used to characterize the effects of environmental stressors on the health of aquatic organisms. However, most studies have focused on liver and muscle tissues of fish, and little is known about how the other organs are affected by environmental perturbations and effects such as metal pollutants or eutrophication. We examined the metabolic and mineral profiles of three kinds of abundant fishes in estuarine ecosystem, yellowfin goby, urohaze-goby, and juvenile Japanese seabass sampled from Tsurumi River estuary, Japan. Multivariate analyses, including nuclear magnetic resonance-based metabolomics and inductively coupled plasma optical emission spectrometry-based ionomics approaches, revealed that the profiles were clustered according to differences among body tissues rather than differences in body size, sex, and species. The metabolic and mineral profiles of the muscle and fin tissues, respectively, suggest that these tissues are most appropriate for evaluating environmental perturbations. Such analyses will be highly useful in evaluating the environmental variation and diversity in aquatic ecosystems.
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Affiliation(s)
- Seiji Yoshida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- 1] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makiko Akama
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- 1] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [3] RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [4] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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Asakura T, Sakata K, Yoshida S, Date Y, Kikuchi J. Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches. PeerJ 2014; 2:e550. [PMID: 25374774 PMCID: PMC4217172 DOI: 10.7717/peerj.550] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/09/2014] [Indexed: 12/20/2022] Open
Abstract
An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.
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Affiliation(s)
- Taiga Asakura
- RIKEN Center for Sustainable Resource Science , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan ; Graduate School of Medical Life Science, Yokohama City University , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan
| | - Kenji Sakata
- RIKEN Center for Sustainable Resource Science , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan
| | - Seiji Yoshida
- RIKEN Center for Sustainable Resource Science , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan ; Graduate School of Medical Life Science, Yokohama City University , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan ; Graduate School of Medical Life Science, Yokohama City University , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan ; Graduate School of Medical Life Science, Yokohama City University , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan ; Graduate School of Bioagricultural Sciences, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, Aichi , Japan ; RIKEN Biomass Engineering Program , Suehirocho, Tsurumi-ku, Yokohama, Kanagawa , Japan
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33
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Ogawa DMO, Moriya S, Tsuboi Y, Date Y, Prieto-da-Silva ÁRB, Rádis-Baptista G, Yamane T, Kikuchi J. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses. PLoS One 2014; 9:e110723. [PMID: 25330259 PMCID: PMC4203823 DOI: 10.1371/journal.pone.0110723] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 09/24/2014] [Indexed: 12/11/2022] Open
Abstract
We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.
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Affiliation(s)
- Diogo M. O. Ogawa
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
| | - Shigeharu Moriya
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- RIKEN Antibiotics Laboratory, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Álvaro R. B. Prieto-da-Silva
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Genetics, Butantan Institute, Sao Paulo, SP, Brazil
| | - Gandhi Rádis-Baptista
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
| | - Tetsuo Yamane
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- Center of Biotechnology of Amazon, Manaus, AM, Brazil
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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Watanabe T, Shino A, Akashi K, Kikuchi J. Chemical profiling of Jatropha tissues under different torrefaction conditions: application to biomass waste recovery. PLoS One 2014; 9:e106893. [PMID: 25191879 PMCID: PMC4156417 DOI: 10.1371/journal.pone.0106893] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 08/10/2014] [Indexed: 12/17/2022] Open
Abstract
Gradual depletion of the world petroleum reserves and the impact of environmental pollution highlight the importance of developing alternative energy resources such as plant biomass. To address these issues, intensive research has focused on the plant Jatropha curcas, which serves as a rich source of biodiesel because of its high seed oil content. However, producing biodiesel from Jatropha generates large amounts of biomass waste that are difficult to use. Therefore, the objective of our research was to analyze the effects of different conditions of torrefaction on Jatropha biomass. Six different types of Jatropha tissues (seed coat, kernel, stem, xylem, bark, and leaf) were torrefied at four different temperature conditions (200°C, 250°C, 300°C, and 350°C), and changes in the metabolite composition of the torrefied products were determined by Fourier transform-infrared spectroscopy and nuclear magnetic resonance analyses. Cellulose was gradually converted to oligosaccharides in the temperature range of 200°C–300°C and completely degraded at 350°C. Hemicellulose residues showed different degradation patterns depending on the tissue, whereas glucuronoxylan efficiently decomposed between 300°C and 350°C. Heat-induced depolymerization of starch to maltodextrin started between 200°C and 250°C, and oligomer sugar structure degradation occurred at higher temperatures. Lignin degraded at each temperature, e.g., syringyl (S) degraded at lower temperatures than guaiacyl (G). Finally, the toxic compound phorbol ester degraded gradually starting at 235°C and efficiently just below 300°C. These results suggest that torrefaction is a feasible treatment for further processing of residual biomass to biorefinery stock or fertilizer.
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Affiliation(s)
- Taiji Watanabe
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Amiu Shino
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Kinya Akashi
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan; Biomass Engineering Program, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan; Graduate School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, Chikusa-ku, Nagoya-shi, Japan
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Cheng YF, Jin W, Mao SY, Zhu WY. Production of Citrate by Anaerobic Fungi in the Presence of Co-culture Methanogens as Revealed by (1)H NMR Spectrometry. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1416-23. [PMID: 25049725 PMCID: PMC4093067 DOI: 10.5713/ajas.2013.13134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/26/2013] [Accepted: 04/30/2013] [Indexed: 11/27/2022]
Abstract
The metabolomic profile of the anaerobic fungus Piromyces sp. F1, isolated from the rumen of goats, and how this is affected by the presence of naturally associated methanogens, was analyzed by nuclear magnetic resonance spectroscopy. The major metabolites in the fungal monoculture were formate, lactate, ethanol, acetate, succinate, sugars/amino acids and α-ketoglutarate, whereas the co-cultures of anaerobic fungi and associated methanogens produced citrate. This is the first report of citrate as a major metabolite of anaerobic fungi. Univariate analysis showed that the mean values of formate, lactate, ethanol, citrate, succinate and acetate in co-cultures were significantly higher than those in the fungal monoculture, while the mean values of glucose and α-ketoglutarate were significantly reduced in co-cultures. Unsupervised principal components analysis revealed separation of metabolite profiles of the fungal mono-culture and co-cultures. In conclusion, the novel finding of citrate as one of the major metabolites of anaerobic fungi associated with methanogens may suggest a new yet to be identified pathway exists in co-culture. Anaerobic fungal metabolism was shifted by associated methanogens, indicating that anaerobic fungi are important providers of substrates for methanogens in the rumen and thus play a key role in ruminal methanogenesis.
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Affiliation(s)
- Yan Fen Cheng
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wei Jin
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Sheng Yong Mao
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wei-Yun Zhu
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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36
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Guennec AL, Giraudeau P, Caldarelli S. Evaluation of Fast 2D NMR for Metabolomics. Anal Chem 2014; 86:5946-54. [DOI: 10.1021/ac500966e] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrien Le Guennec
- Centre de Recherche CNRS de Gif-sur-Yvette, Institut
de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie
Structurales, UPR 2301,
1, avenue de la Terrasse, 91198 Gif-sur-Yvette, France
- Université de Nantes, CNRS, CEISAM UMR 6230, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France
| | - Patrick Giraudeau
- Université de Nantes, CNRS, CEISAM UMR 6230, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France
| | - Stefano Caldarelli
- Centre de Recherche CNRS de Gif-sur-Yvette, Institut
de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie
Structurales, UPR 2301,
1, avenue de la Terrasse, 91198 Gif-sur-Yvette, France
- Aix Marseille Université, Centrale Marseille,
CNRS, iSm2 UMR 7313, 13397, Marseille, France
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37
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In vitro evaluation method for screening of candidate prebiotic foods. Food Chem 2014; 152:251-60. [DOI: 10.1016/j.foodchem.2013.11.126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 11/21/2022]
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38
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Ito K, Sakata K, Date Y, Kikuchi J. Integrated analysis of seaweed components during seasonal fluctuation by data mining across heterogeneous chemical measurements with network visualization. Anal Chem 2014; 86:1098-105. [PMID: 24401131 DOI: 10.1021/ac402869b] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biological information is intricately intertwined with several factors. Therefore, comprehensive analytical methods such as integrated data analysis, combining several data measurements, are required. In this study, we describe a method of data preprocessing that can perform comprehensively integrated analysis based on a variety of multimeasurement of organic and inorganic chemical data from Sargassum fusiforme and explore the concealed biological information by statistical analyses with integrated data. Chemical components including polar and semipolar metabolites, minerals, major elemental and isotopic ratio, and thermal decompositional data were measured as environmentally responsive biological data in the seasonal variation. The obtained spectral data of complex chemical components were preprocessed to isolate pure peaks by removing noise and separating overlapping signals using the multivariate curve resolution alternating least-squares method before integrated analyses. By the input of these preprocessed multimeasurement chemical data, principal component analysis and self-organizing maps of integrated data showed changes in the chemical compositions during the mature stage and identified trends in seasonal variation. Correlation network analysis revealed multiple relationships between organic and inorganic components. Moreover, in terms of the relationship between metal group and metabolites, the results of structural equation modeling suggest that the structure of alginic acid changes during the growth of S. fusiforme, which affects its metal binding ability. This integrated analytical approach using a variety of chemical data can be developed for practical applications to obtain new biochemical knowledge including genetic and environmental information.
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Affiliation(s)
- Kengo Ito
- Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
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Nagana Gowda G, Raftery D. Advances in NMR-Based Metabolomics. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00008-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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40
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Bingol K, Brüschweiler R. Multidimensional approaches to NMR-based metabolomics. Anal Chem 2013; 86:47-57. [PMID: 24195689 DOI: 10.1021/ac403520j] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210
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Mavel S, Nadal-Desbarats L, Blasco H, Bonnet-Brilhault F, Barthélémy C, Montigny F, Sarda P, Laumonnier F, Vourc′h P, Andres CR, Emond P. 1H–13C NMR-based urine metabolic profiling in autism spectrum disorders. Talanta 2013; 114:95-102. [DOI: 10.1016/j.talanta.2013.03.064] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/16/2013] [Accepted: 03/25/2013] [Indexed: 01/04/2023]
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42
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Solid-, solution-, and gas-state NMR monitoring of ¹³C-cellulose degradation in an anaerobic microbial ecosystem. Molecules 2013; 18:9021-33. [PMID: 23899835 PMCID: PMC6269877 DOI: 10.3390/molecules18089021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/10/2013] [Accepted: 07/19/2013] [Indexed: 12/22/2022] Open
Abstract
Anaerobic digestion of biomacromolecules in various microbial ecosystems is influenced by the variations in types, qualities, and quantities of chemical components. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for characterizing the degradation of solids to gases in anaerobic digestion processes. Here we describe a characterization strategy using NMR spectroscopy for targeting the input solid insoluble biomass, catabolized soluble metabolites, and produced gases. 13C-labeled cellulose produced by Gluconacetobacter xylinus was added as a substrate to stirred tank reactors and gradually degraded for 120 h. The time-course variations in structural heterogeneity of cellulose catabolism were determined using solid-state NMR, and soluble metabolites produced by cellulose degradation were monitored using solution-state NMR. In particular, cooperative changes between the solid NMR signal and 13C-13C/13C-12C isotopomers in the microbial degradation of 13C-cellulose were revealed by a correlation heat map. The triple phase NMR measurements demonstrated that cellulose was anaerobically degraded, fermented, and converted to methane gas from organic acids such as acetic acid and butyric acid.
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43
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Ogura T, Date Y, Kikuchi J. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota. PLoS One 2013; 8:e66919. [PMID: 23840554 PMCID: PMC3686774 DOI: 10.1371/journal.pone.0066919] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 05/10/2013] [Indexed: 02/01/2023] Open
Abstract
Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an "ECOMICS" web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.
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Affiliation(s)
- Tatsuki Ogura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yasuhiro Date
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- Biomass Engineering Program, RIKEN Research Cluster for Innovation, Wako, Saitama, Japan
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44
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An YJ, Xu WJ, Jin X, Wen H, Kim H, Lee J, Park S. Metabotyping of the C. elegans sir-2.1 mutant using in vivo labeling and (13)C-heteronuclear multidimensional NMR metabolomics. ACS Chem Biol 2012; 7:2012-8. [PMID: 23043523 DOI: 10.1021/cb3004226] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The roles of sir-2.1 in C. elegans lifespan extension have been subjects of recent public and academic debates. We applied an efficient workflow for in vivo(13)C-labeling of C. elegans and (13)C-heteronuclear NMR metabolomics to characterizing the metabolic phenotypes of the sir-2.1 mutant. Our method delivered sensitivity 2 orders of magnitude higher than that of the unlabeled approach, enabling 2D and 3D NMR experiments. Multivariate analysis of the NMR data showed distinct metabolic profiles of the mutant, represented by increases in glycolysis, nitrogen catabolism, and initial lipolysis. The metabolomic analysis defined the sir-2.1 mutant metabotype as the decoupling between enhanced catabolic pathways and ATP generation. We also suggest the relationship between the metabotypes, especially the branched chain amino acids, and the roles of sir-2.1 in the worm lifespan. Our results should contribute to solidifying the roles of sir-2.1, and the described workflow can be applied to studying many other proteins in metabolic perspectives.
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Affiliation(s)
- Yong Jin An
- Department of Biochemistry,
College of Medicine, Inha University, Incheon,
400-712, Korea
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45
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Date Y, Iikura T, Yamazawa A, Moriya S, Kikuchi J. Metabolic Sequences of Anaerobic Fermentation on Glucose-Based Feeding Substrates Based on Correlation Analyses of Microbial and Metabolite Profiling. J Proteome Res 2012; 11:5602-10. [DOI: 10.1021/pr3008682] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yasuhiro Date
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho,
Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Iikura
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Akira Yamazawa
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Research Planning and Management Group, Kajima Technical Research
Institute, KAJIMA Corporation, 2-19-1 Tobitakyu,
Chofu, Tokyo 182-0036, Japan
| | - Shigeharu Moriya
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- RIKEN Advanced Science Institute, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho,
Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural
Sciences, Nagoya University, 1 Furo-cho,
Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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46
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Mori T, Chikayama E, Tsuboi Y, Ishida N, Shisa N, Noritake Y, Moriya S, Kikuchi J. Exploring the conformational space of amorphous cellulose using NMR chemical shifts. Carbohydr Polym 2012; 90:1197-203. [PMID: 22939331 DOI: 10.1016/j.carbpol.2012.06.027] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 12/20/2022]
Abstract
(13)C-labeled amorphous cellulose and (13)C NMR chemical shifts by 2D (13)C-(13)C correlation spectroscopy were obtained in the regenerated solid-state from ionic liquids. On the basis of the assigned chemical shifts, combined with information from molecular dynamics and quantum chemistry computer simulations a twisted structure for amorphous cellulose is proposed exposing more hydrophilic surface than that of extended crystalline cellulose.
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Affiliation(s)
- Tetsuya Mori
- Biotechnology Laboratory, Toyota Central R&D Laboratories, Inc., 41-1, Nagakute 480-1192, Japan.
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47
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Date Y, Sakata K, Kikuchi J. Chemical profiling of complex biochemical mixtures from various seaweeds. Polym J 2012. [DOI: 10.1038/pj.2012.105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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48
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Goulitquer S, Potin P, Tonon T. Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. Mar Drugs 2012; 10:849-880. [PMID: 22690147 PMCID: PMC3366679 DOI: 10.3390/md10040849] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/13/2012] [Accepted: 03/21/2012] [Indexed: 01/01/2023] Open
Abstract
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 and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.
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Affiliation(s)
- Sophie Goulitquer
- Plate-forme MetaboMER, CNRS & UPMC, FR2424, Station Biologique, 29680 Roscoff, France
| | - Philippe Potin
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
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49
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Yamada H, Mizusawa K, Igarashi R, Tochio H, Shirakawa M, Tabata Y, Kimura Y, Kondo T, Aoyama Y, Sando S. Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug. ACS Chem Biol 2012; 7:535-42. [PMID: 22260358 DOI: 10.1021/cb2003972] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We report the application of one-dimensional triple-resonance NMR to metabolic analysis and thereon-based evaluation of drug activity. Doubly (13)C/(15)N-labeled uracil ([(15)N1,(13)C6]-uracil) was prepared. Its catabolic (degradative) conversion to [(13)C3,(15)N4]-β-alanine and inhibition thereof by gimeracil, a clinical co-drug used with the antitumor agent 5-fluorouracil, in mouse liver lysates were monitored specifically using one-dimensional triple-resonance ((1)H-{(13)C-(15)N}) NMR, but not double-resonance ((1)H-{(13)C}) NMR, in a ratiometric manner. The administration of labeled uracil to a mouse resulted in its non-selective distribution in various organs, with efficient catabolism to labeled β-alanine exclusively in the liver. The co-administration of gimeracil inhibited the catabolic conversion of uracil in the liver. In marked contrast to in vitro results, however, gimeracil had practically no effect on the level of uracil in the liver. The potentiality of triple-resonance NMR in the analysis of in vivo pharmaceutical activity of drugs targeting particular metabolic reactions is discussed.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | | | | - Yasuhiko Tabata
- Department of Biomaterials, Field
of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku,
Kyoto 606-8507, Japan
| | - Yu Kimura
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Teruyuki Kondo
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasuhiro Aoyama
- Department
of Molecular Chemistry
and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Shinsuke Sando
- INAMORI Frontier Research Center, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
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50
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Ogata Y, Chikayama E, Morioka Y, Everroad RC, Shino A, Matsushima A, Haruna H, Moriya S, Toyoda T, Kikuchi J. ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. PLoS One 2012; 7:e30263. [PMID: 22319563 PMCID: PMC3271069 DOI: 10.1371/journal.pone.0030263] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 12/12/2011] [Indexed: 01/05/2023] Open
Abstract
Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/.
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Affiliation(s)
| | - Eisuke Chikayama
- Plant Science Center, RIKEN, Yokohama, Kanagawa, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yusuke Morioka
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | | | - Amiu Shino
- Plant Science Center, RIKEN, Yokohama, Kanagawa, Japan
| | - Akihiro Matsushima
- Bioinformatics and Systems Engineering Division, RIKEN, Yokohama, Kanagawa, Japan
| | - Hideaki Haruna
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Shigeharu Moriya
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Advanced Science Institute, RIKEN, Wako, Saitama, Japan
| | - Tetsuro Toyoda
- Bioinformatics and Systems Engineering Division, RIKEN, Yokohama, Kanagawa, Japan
- Biomass Engineering Program, RIKEN Cluster for Innovation, Wako, Saitama, Japan
| | - Jun Kikuchi
- Plant Science Center, RIKEN, Yokohama, Kanagawa, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Biomass Engineering Program, RIKEN Cluster for Innovation, Wako, Saitama, Japan
- Graduate School of Bioagriculture Sciences, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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