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Rahmani N, Mani-Varnosfaderani A. Quality control, classification, and authentication of Iranian rice varieties using FT-IR spectroscopy and sparse chemometric methods. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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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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3
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Signal Deconvolution and Generative Topographic Mapping Regression for Solid-State NMR of Multi-Component Materials. Int J Mol Sci 2021; 22:ijms22031086. [PMID: 33499371 PMCID: PMC7865946 DOI: 10.3390/ijms22031086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 01/19/2023] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy provides information on native structures and the dynamics for predicting and designing the physical properties of multi-component solid materials. However, such an analysis is difficult because of the broad and overlapping spectra of these materials. Therefore, signal deconvolution and prediction are great challenges for their ssNMR analysis. We examined signal deconvolution methods using a short-time Fourier transform (STFT) and a non-negative tensor/matrix factorization (NTF, NMF), and methods for predicting NMR signals and physical properties using generative topographic mapping regression (GTMR). We demonstrated the applications for macromolecular samples involved in cellulose degradation, plastics, and microalgae such as Euglena gracilis. During cellulose degradation, 13C cross-polarization (CP)-magic angle spinning spectra were separated into signals of cellulose, proteins, and lipids by STFT and NTF. GTMR accurately predicted cellulose degradation for catabolic products such as acetate and CO2. Using these methods, the 1H anisotropic spectrum of poly-ε-caprolactone was separated into the signals of crystalline and amorphous solids. Forward prediction and inverse prediction of GTMR were used to compute STFT-processed NMR signals from the physical properties of polylactic acid. These signal deconvolution and prediction methods for ssNMR spectra of macromolecules can resolve the problem of overlapping spectra and support macromolecular characterization and material design.
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4
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Comparative effect of ionic liquids pretreatment on thermogravimetric kinetics of crude oil palm biomass for possible sustainable exploitation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Saito Y, Tsuchida H, Matsumoto T, Makita Y, Kawashima M, Kikuchi J, Matsui M. Screening of fungi for decomposition of lignin-derived products from Japanese cedar. J Biosci Bioeng 2018; 126:573-579. [DOI: 10.1016/j.jbiosc.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/23/2018] [Accepted: 05/04/2018] [Indexed: 11/24/2022]
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6
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Yiin CL, Yusup S, Quitain AT, Uemura Y, Sasaki M, Kida T. Thermogravimetric analysis and kinetic modeling of low-transition-temperature mixtures pretreated oil palm empty fruit bunch for possible maximum yield of pyrolysis oil. BIORESOURCE TECHNOLOGY 2018; 255:189-197. [PMID: 29414166 DOI: 10.1016/j.biortech.2018.01.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/25/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
The impacts of low-transition-temperature mixtures (LTTMs) pretreatment on thermal decomposition and kinetics of empty fruit bunch (EFB) were investigated by thermogravimetric analysis. EFB was pretreated with the LTTMs under different duration of pretreatment which enabled various degrees of alteration to their structure. The TG-DTG curves showed that LTTMs pretreatment on EFB shifted the temperature and rate of decomposition to higher values. The EFB pretreated with sucrose and choline chloride-based LTTMs had attained the highest mass loss of volatile matter (78.69% and 75.71%) after 18 h of pretreatment. For monosodium glutamate-based LTTMs, the 24 h pretreated EFB had achieved the maximum mass loss (76.1%). Based on the Coats-Redfern integral method, the LTTMs pretreatment led to an increase in activation energy of the thermal decomposition of EFB from 80.00 to 82.82-94.80 kJ/mol. The activation energy was mainly affected by the demineralization and alteration in cellulose crystallinity after LTTMs pretreatment.
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Affiliation(s)
- Chung Loong Yiin
- Biomass Processing Cluster, Centre for Biofuel and Biochemical Research, Institute for Sustainable Living, Chemical Engineering Department, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak, Malaysia
| | - Suzana Yusup
- Biomass Processing Cluster, Centre for Biofuel and Biochemical Research, Institute for Sustainable Living, Chemical Engineering Department, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak, Malaysia.
| | - Armando T Quitain
- Department of Applied Chemistry and Biochemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan; International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yoshimitsu Uemura
- Biomass Processing Cluster, Centre for Biofuel and Biochemical Research, Institute for Sustainable Living, Chemical Engineering Department, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak, Malaysia
| | - Mitsuru Sasaki
- Institute of Pulsed Power Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Tetsuya Kida
- Department of Applied Chemistry and Biochemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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7
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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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8
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Okubo-Kurihara E, Ohtani M, Kurihara Y, Kakegawa K, Kobayashi M, Nagata N, Komatsu T, Kikuchi J, Cutler S, Demura T, Matsui M. Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium. Sci Rep 2016; 6:34602. [PMID: 27694977 PMCID: PMC5046155 DOI: 10.1038/srep34602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/15/2016] [Indexed: 11/25/2022] Open
Abstract
The cell wall is one major determinant of plant cell morphology, and is an attractive bioresource. Here, we report a novel strategy to modify plant cell wall property by small molecules. Lasalocid sodium (LS) was isolated by chemical screening to identify molecules that affect the cell morphology of tobacco BY-2 cells. LS treatment led to an increase in cell wall thickness, whilst the quantity and sugar composition of the cell wall remained unchanged in BY-2 cells. The chemical also disordered the cellular arrangement of hypocotyls of Arabidopsis plants, resulting in a decrease in hypocotyl length. LS treatment enhanced enzymatic saccharification efficiency in both BY-2 cells and Arabidopsis plants. Microarray analysis on Arabidopsis showed that exposure to LS upregulated type III peroxidase genes, of which some are involved in lignin biogenesis, and jasmonic acid response genes, and phloroglucinol staining supported the activation of lignification by the LS treatment. As jasmonic acid-mediated lignification is a typical reaction to cell wall damage, it is possible that LS induces cell wall loosening, which can trigger cell wall damage response. Thus, LS is a unique chemical for modification of cell wall and morphology through changes in cell wall architecture.
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Affiliation(s)
- Emiko Okubo-Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Misato Ohtani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yukio Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Koichi Kakegawa
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305–8687, Japan
| | - Megumi Kobayashi
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Takanori Komatsu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Sean Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, 5451 Boyce Hall, Riverside, CA 92521, USA
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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9
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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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10
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Shiokawa Y, Misawa T, Date Y, Kikuchi J. Application of Market Basket Analysis for the Visualization of Transaction Data Based on Human Lifestyle and Spectroscopic Measurements. Anal Chem 2016; 88:2714-9. [PMID: 26824632 DOI: 10.1021/acs.analchem.5b04182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With the innovation of high-throughput metabolic profiling methods such as nuclear magnetic resonance (NMR), data mining techniques that can reveal valuable information from substantial data sets are constantly desired in this field. In particular, for the analytical assessment of various human lifestyles, advanced computational methods are ultimately needed. In this study, we applied market basket analysis, which is generally applied in social sciences such as marketing, and used transaction data derived from dietary intake information and urinary chemical data generated using NMR and inductively coupled plasma optical emission spectrometry measurements. The analysis revealed several relationships, such as fish diets with high trimethylamine N-oxide excretion and N-methylnicotinamide excreted at higher levels in the morning and produced from a protein that was consumed one day prior. Therefore, market basket analysis can be applied to metabolic profiling to effectively understand the relationships between metabolites and lifestyle.
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Affiliation(s)
- Yuka Shiokawa
- Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - 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
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11
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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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12
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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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13
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Teramura H, Sasaki K, Oshima T, Aikawa S, Matsuda F, Okamoto M, Shirai T, Kawaguchi H, Ogino C, Yamasaki M, Kikuchi J, Kondo A. Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR. PLoS One 2015; 10:e0128417. [PMID: 26083431 PMCID: PMC4470627 DOI: 10.1371/journal.pone.0128417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45-0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = -0.95 to -0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate.
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Affiliation(s)
- Hiroshi Teramura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Kengo Sasaki
- Organization of Advanced Science and Technology, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Tomoko Oshima
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Shimpei Aikawa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, Japan
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Mami Okamoto
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo, Japan
| | - Tomokazu Shirai
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo, Japan
| | - Jun Kikuchi
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehirocho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan
- RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- * E-mail:
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14
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Polenova T, Gupta R, Goldbourt A. Magic angle spinning NMR spectroscopy: a versatile technique for structural and dynamic analysis of solid-phase systems. Anal Chem 2015; 87:5458-69. [PMID: 25794311 PMCID: PMC4890703 DOI: 10.1021/ac504288u] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Magic Angle Spinning (MAS) NMR spectroscopy is a powerful method for analysis of a broad range of systems, including inorganic materials, pharmaceuticals, and biomacromolecules. The recent developments in MAS NMR instrumentation and methodologies opened new vistas to atomic-level characterization of a plethora of chemical environments previously inaccessible to analysis, with unprecedented sensitivity and resolution.
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Affiliation(s)
- Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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15
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Komatsu T, Kobayashi T, Hatanaka M, Kikuchi J. Profiling planktonic biomass using element-specific, multicomponent nuclear magnetic resonance spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7056-62. [PMID: 25973714 DOI: 10.1021/acs.est.5b00837] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Planktonic metabolism plays crucial roles in Earth's elemental cycles. Chemical speciation as well as elemental stoichiometry is important for advancing our understanding of planktonic roles in biogeochemical cycles. In this study, a multicomponent solid-state nuclear magnetic resonance (NMR) approach is proposed for chemical speciation of cellular components, using several advanced NMR techniques. Measurements by ssNMR were performed on (13)C and (15)N-labeled Euglena gracilis, a flagellated protist. 3D dipolar-assisted rotational resonance, double-cross-polarization (1)H-(13)C correlation spectroscopy, and (1)H-(13)C solid-state heteronuclear single quantum correlation spectroscopy successively allowed characterization of cellular components. These techniques were then applied to E. gracilis cultured in high and low ammonium media to demonstrate the power of this method for profiling and comparing cellular components. Cellular NMR spectra indicated that ammonium induced both paramylon degradation and amination. Arginine was stored as a nitrogen reserve and ammonium replaced by arginine catabolism via the arginine dihydrolase pathway. (15)N and (31)P cellular ssNMR indicated arginine and polyphosphate accumulation in E. gracilis, respectively. This chemical speciation technique will contribute to environmental research by providing detailed information on environmental chemical properties.
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Affiliation(s)
- Takanori Komatsu
- †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
| | - Toshiya Kobayashi
- ‡Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Minoru Hatanaka
- §Bruker Biospin K. K., 3-9, Moriya-cho, Kanagawa-ku, Yokohama, 221-0022, 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 and School of Agricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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16
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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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17
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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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18
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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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19
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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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20
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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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21
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Yamazawa A, Iikura T, Morioka Y, Shino A, Ogata Y, Date Y, Kikuchi J. Cellulose digestion and metabolism induced biocatalytic transitions in anaerobic microbial ecosystems. Metabolites 2013; 4:36-52. [PMID: 24958386 PMCID: PMC4018678 DOI: 10.3390/metabo4010036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 01/07/2023] Open
Abstract
Anaerobic digestion of highly polymerized biomass by microbial communities present in diverse microbial ecosystems is an indispensable metabolic process for biogeochemical cycling in nature and for industrial activities required to maintain a sustainable society. Therefore, the evaluation of the complicated microbial metabolomics presents a significant challenge. We here describe a comprehensive strategy for characterizing the degradation of highly crystallized bacterial cellulose (BC) that is accompanied by metabolite production for identifying the responsible biocatalysts, including microorganisms and their metabolic functions. To this end, we employed two-dimensional solid- and one-dimensional solution-state nuclear magnetic resonance (NMR) profiling combined with a metagenomic approach using stable isotope labeling. The key components of biocatalytic reactions determined using a metagenomic approach were correlated with cellulose degradation and metabolic products. The results indicate that BC degradation was mediated by cellulases that contain carbohydrate-binding modules and that belong to structural type A. The degradation reactions induced the metabolic dynamics of the microbial community and produced organic compounds, such as acetic acid and propionic acid, mainly metabolized by clostridial species. This combinatorial, functional and structural metagenomic approach is useful for the comprehensive characterization of biomass degradation, metabolic dynamics and their key components in diverse ecosystems.
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Affiliation(s)
- Akira Yamazawa
- Research Planning and Management Group, Kajima Technical Research Institute, Kajima Corporation, 2-19-1 Tobitakyu, Chofu, Tokyo 182-0036, Japan.
| | - Tomohiro Iikura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yusuke Morioka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Amiu Shino
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yoshiyuki Ogata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, Japan.
| | - Yasuhiro Date
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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22
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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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