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Wei F, Ito K, Sakata K, Asakura T, Date Y, Kikuchi J. Fish ecotyping based on machine learning and inferred network analysis of chemical and physical properties. Sci Rep 2021; 11:3766. [PMID: 33580151 PMCID: PMC7881121 DOI: 10.1038/s41598-021-83194-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/27/2021] [Indexed: 01/13/2023] Open
Abstract
Functional diversity rather than species richness is critical for the understanding of ecological patterns and processes. This study aimed to develop novel integrated analytical strategies for the functional characterization of fish diversity based on the quantification, prediction and integration of the chemical and physical features in fish muscles. Machine learning models with an improved random forest algorithm applied on 1867 muscle nuclear magnetic resonance spectra belonging to 249 fish species successfully predicted the mobility patterns of fishes into four categories (migratory, territorial, rockfish, and demersal) with accuracies of 90.3-95.4%. Markov blanket-based feature selection method with an ecological-chemical-physical integrated network based on the Bayesian network inference algorithm highlighted the importance of nitrogen metabolism, which is critical for environmental adaptability of fishes in nutrient-rich environments, in the functional characterization of fish biodiversity. Our study provides valuable information and analytical strategies for fish home-range assessment on the basis of the chemical and physical characterization of fish muscle, which can serve as an ecological indicator for fish ecotyping and human impact monitoring.
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Affiliation(s)
- Feifei Wei
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan
| | - Kenji Sakata
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan
| | - Taiga Asakura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 235-0045, Japan. .,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, 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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Ito K, Tsuboi Y, Kikuchi J. Spatial molecular-dynamically ordered NMR spectroscopy of intact bodies and heterogeneous systems. Commun Chem 2020; 3:80. [PMID: 36703472 PMCID: PMC9814264 DOI: 10.1038/s42004-020-0330-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 05/29/2020] [Indexed: 01/29/2023] Open
Abstract
Noninvasive evaluation of the spatial distribution of chemical composition and diffusion behavior of materials is becoming possible by advanced nuclear magnetic resonance (NMR) pulse sequence editing. However, there is room for improvement in the spectral resolution and analytical method for application to heterogeneous samples. Here, we develop applications for comprehensively evaluating compounds and their dynamics in intact bodies and heterogeneous systems from NMR data, including spatial z-position, chemical shift, and diffusion or relaxation. This experiment is collectively named spatial molecular-dynamically ordered spectroscopy (SMOOSY). Pseudo-three-dimensional (3D) SMOOSY spectra of an intact shrimp and two heterogeneous systems are recorded to evaluate this methodology. Information about dynamics is mapped onto two-dimensional (2D) chemical shift imaging spectra using a pseudo-spectral imaging method with a processing tool named SMOOSY processor. Pseudo-2D SMOOSY spectral images can non-invasively assess the different dynamics of the compounds at each spatial z-position of the shrimp's body and two heterogeneous systems.
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Affiliation(s)
- Kengo Ito
- grid.7597.c0000000094465255RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.268441.d0000 0001 1033 6139Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yuuri Tsuboi
- grid.7597.c0000000094465255RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Jun Kikuchi
- grid.7597.c0000000094465255RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.268441.d0000 0001 1033 6139Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ,grid.27476.300000 0001 0943 978XGraduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810 Japan
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Koptyug IV. MRI of mass transport in porous media: drying and sorption processes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 65:1-65. [PMID: 22781314 DOI: 10.1016/j.pnmrs.2011.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 12/05/2011] [Indexed: 06/01/2023]
Affiliation(s)
- Igor V Koptyug
- International Tomography Center, SB RAS, 3A Institutskaya Str., Novosibirsk 630090, Russian Federation.
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