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Arita M, Pulverer B, Uemura T, Sakuma C, Hayashi S. Publishing in the Open Access and Open Science era. Genes Cells 2024; 29:275-281. [PMID: 38351723 DOI: 10.1111/gtc.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.
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Affiliation(s)
| | | | - Tadashi Uemura
- Graduate School of Biostudies, Center for Living Systems Information Science (CeLiSIS), Kyoto University, Kyoto, Japan
| | - Chisako Sakuma
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeo Hayashi
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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2
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Ara T, Kodama Y, Tokimatsu T, Fukuda A, Kosuge T, Mashima J, Tanizawa Y, Tanjo T, Ogasawara O, Fujisawa T, Nakamura Y, Arita M. DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata. Nucleic Acids Res 2024; 52:D67-D71. [PMID: 37971299 PMCID: PMC10767850 DOI: 10.1093/nar/gkad1046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/21/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.
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Affiliation(s)
- Takeshi Ara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Toshiaki Tokimatsu
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asami Fukuda
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehide Kosuge
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tomoya Tanjo
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Iwata T, Kousa T, Nishioka Y, Ohwada K, Sumida K, Annese E, Kakoki M, Kuroda K, Iwasawa H, Arita M, Kumar S, Kimura A, Miyamoto K, Okuda T. Laser-based angle-resolved photoemission spectroscopy with micrometer spatial resolution and detection of three-dimensional spin vector. Sci Rep 2024; 14:127. [PMID: 38177136 PMCID: PMC10766951 DOI: 10.1038/s41598-023-47719-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024] Open
Abstract
We have developed a state-of-the-art apparatus for laser-based spin- and angle-resolved photoemission spectroscopy with micrometer spatial resolution (µ-SARPES). This equipment is realized by the combination of a high-resolution photoelectron spectrometer, a 6 eV laser with high photon flux that is focused down to a few micrometers, a high-precision sample stage control system, and a double very-low-energy-electron-diffraction spin detector. The setup achieves an energy resolution of 1.5 (5.5) meV without (with) the spin detection mode, compatible with a spatial resolution better than 10 µm. This enables us to probe both spatially-resolved electronic structures and vector information of spin polarization in three dimensions. The performance of µ-SARPES apparatus is demonstrated by presenting ARPES and SARPES results from topological insulators and Au photolithography patterns on a Si (001) substrate.
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Affiliation(s)
- Takuma Iwata
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, Higashi-hiroshima, 739-8526, Japan
| | - T Kousa
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Y Nishioka
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - K Ohwada
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - K Sumida
- Materials Sciences Research Center, Japan Atomic Energy Agency, Sayo-gun, Hyogo, 679-5148, Japan
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
| | - E Annese
- Brazilian Center for Research in Physics, Rua Dr. Xavier Sigaud 150, Rio de Janeiro, RJ, 22290-180, Brazil
| | - M Kakoki
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Kenta Kuroda
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, Higashi-hiroshima, 739-8526, Japan.
| | - H Iwasawa
- Institute for Advanced Synchrotron Light Source, National Institutes for Quantum Science and Technology, Sendai, 980-8579, Japan
- Synchrotron Radiation Research Center, National Institutes for Quantum Science and Technology, Hyogo, 679-5148, Japan
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
| | - M Arita
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
| | - S Kumar
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
| | - A Kimura
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, Higashi-hiroshima, 739-8526, Japan
| | - K Miyamoto
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
| | - T Okuda
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, 739-0046, Japan
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Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit III R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O’Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications. Microb Genom 2023; 9:001145. [PMID: 38085797 PMCID: PMC10763499 DOI: 10.1099/mgen.0.001145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.
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Affiliation(s)
- Ruth E. Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Masanori Arita
- DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan
| | - Duncan MacCannell
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Finlay Maguire
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Canada
| | | | - Andrew J. Page
- Quadram Institute Bioscience, Norwich, Norfolk, UK
- Theiagen Genomics LLC, Highlands Ranch, CO, USA
| | | | - Muhammad Ibtisam Nasar
- Department of Biology, College of Science, United Arab Emirates University- Al Ain, Abu Dhabi, UAE
| | - Paul Oluniyi
- Chan Zuckerberg Biohub Network, San Francisco, CA, USA
| | - Andrea D. Tyler
- Science Technology Cores and Services, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amogelang R. Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer L. Guthrie
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Idowu Olawoye
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Colman O’Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami JI, Abe T, Arita M. SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes Genet Syst 2023; 98:221-237. [PMID: 37839865 DOI: 10.1266/ggs.23-00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.
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Affiliation(s)
- So Nakagawa
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Molecular Life Science, Tokai University School of Medicine
- Micro/Nano Technology Center, Tokai University
- Institute of Medical Sciences, Tokai University
| | | | | | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
| | - Rise Oyachi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Junko S Takeuchi
- Center for Clinical Sciences, National Center for Global Health and Medicine
| | | | - Satomi Asano
- Department of Informatics, National Institute of Genetics
| | - Momoka Komatsu
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Jun-Ichi Onami
- Research Center for Open Science and Data Platform, National Institute of Informatics
| | - Takashi Abe
- Bioinformation and DDBJ Center, National Institute of Genetics
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
- RIKEN Center for Sustainable Resource Science
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Koshimizu S, Masuda S, Shibata A, Ishii T, Shirasu K, Hoshino A, Arita M. Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum. DNA Res 2023; 30:dsad019. [PMID: 37691489 PMCID: PMC10558197 DOI: 10.1093/dnares/dsad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023] Open
Abstract
Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.
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Affiliation(s)
- Shizuka Koshimizu
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
| | - Sachiko Masuda
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Arisa Shibata
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori 680-001, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Atsushi Hoshino
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
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Koistinen V, Kärkkäinen O, Keski-Rahkonen P, Tsugawa H, Scalbert A, Arita M, Wishart D, Hanhineva K. Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature. Nat Metab 2023; 5:351-354. [PMID: 36890347 DOI: 10.1038/s42255-023-00757-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Affiliation(s)
- Ville Koistinen
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland.
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland.
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | | | - Hiroshi Tsugawa
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Masanori Arita
- National Institute of Genetics, Mishima, Japan
- RIKEN, Yokohama, Japan
| | | | - Kati Hanhineva
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species. Plants (Basel) 2023; 12:930. [PMID: 36840278 PMCID: PMC9966718 DOI: 10.3390/plants12040930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Zakaria D, Matsuda S, Iida T, Hayashi T, Arita M. Genome Analysis Identifies a Novel Type III Secretion System (T3SS) Category in Vibrio Species. Microorganisms 2023; 11:microorganisms11020290. [PMID: 36838254 PMCID: PMC9967039 DOI: 10.3390/microorganisms11020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
The nanomachine referred to as the type III secretion system (T3SS) is used by many Gram-negative pathogens or symbionts to inject their effector proteins into host cells to promote their infections or symbioses. Among the genera possessing T3SS is Vibrio, which consists of diverse species of Gammaproteobacteria including human pathogenic species and inhabits aquatic environments. We describe the genetic overview of the T3SS gene clusters in Vibrio through a phylogenetic analysis from 48 bacterial strains and a gene order analysis of the two previously known categories in Vibrio (T3SS1 and T3SS2). Through this analysis we identified a new T3SS category (named T3SS3) that shares similar core and related proteins (effectors, translocons, and chaperones) with the Ssa-Esc family of T3SSs in Salmonella, Shewanella, and Sodalis. The high similarity between T3SS3 and the Ssa-Esc family suggests a possibility of genetic exchange among marine bacteria with similar habitats.
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Affiliation(s)
- Douaa Zakaria
- Department of Genetics, SOKENDAI University, Mishima 411-8540, Japan
| | - Shigeaki Matsuda
- Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Tetsuya Iida
- Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Tetsuya Hayashi
- Department of Basic Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masanori Arita
- Department of Genetics, SOKENDAI University, Mishima 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-55-981-9449
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10
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab 2022; 4:1086-1088. [PMID: 35934691 DOI: 10.1038/s42255-022-00628-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - John A Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Maria Fedorova
- Center for Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | | | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Todd W Mitchell
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Dominik Schwudke
- Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Candice Z Ulmer
- Office of Public Health Science, Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Robert Ahrends
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
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11
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Mitochondrial genome of Garcinia mangostana L. variety Mesta. Sci Rep 2022; 12:9480. [PMID: 35676406 PMCID: PMC9177603 DOI: 10.1038/s41598-022-13706-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/26/2022] [Indexed: 11/27/2022] Open
Abstract
Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis using both maximum likelihood and Bayesian analysis methods showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.,Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | | | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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12
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Kusada H, Arita M, Tohno M, Tamaki H. Bile Salt Hydrolase Degrades β-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri. Front Microbiol 2022; 13:858263. [PMID: 35733973 PMCID: PMC9207391 DOI: 10.3389/fmicb.2022.858263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Bile salt hydrolase (BSH) is a well-characterized probiotic enzyme associated with bile detoxification and colonization of lactic acid bacteria in the human gastrointestinal tract. Here, we isolated a putative BSH (LpBSH) from the probiotic bacterium Lactobacillus paragasseri JCM 5343T and demonstrated its bifunctional activity that allows it to degrade not only bile salts but also the antibiotic (penicillin). Although antibiotic resistance and bile detoxification have been separately recognized as different microbial functions, our findings suggest that bifunctional BSHs simultaneously confer ecological advantages to host gut bacteria to improve their survival in the mammalian intestine by attaining a high resistance to bile salts and β-lactams. Strain JCM 5343T showed resistance to both bile salts and β-lactam antibiotics, suggesting that LpBSH may be involved in this multi-resistance of the strain. We further verified that such bifunctional enzymes were broadly distributed among the phylogeny, suggesting that the bifunctionality may be conserved in other BSHs of gut bacteria. This study revealed the physiological role and phylogenetic diversity of bifunctional enzymes degrading bile salts and β-lactams in gut bacteria. Furthermore, our findings suggest that the hitherto-overlooked penicillin-degrading activity of penicillin acylase could be a potential new target for the probiotic function of gut bacteria.
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Affiliation(s)
- Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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13
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Li Z, Zhao C, Dong L, Huan Y, Yoshimoto M, Zhu Y, Tada I, Wang X, Zhao S, Zhang F, Li L, Arita M. Comprehensive Metabolomic Comparison of Five Cereal Vinegars Using Non-Targeted and Chemical Isotope Labeling LC-MS Analysis. Metabolites 2022; 12:metabo12050427. [PMID: 35629931 PMCID: PMC9144210 DOI: 10.3390/metabo12050427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
Vinegar is used as an acidic condiment and preservative worldwide. In Asia, various black vinegars are made from different combinations of grains, such as Sichuan bran vinegar (SBV), Shanxi aged vinegar (SAV), Zhenjiang aromatic vinegar (ZAV), and Fujian Monascus vinegar (FMV) in China and Ehime black vinegar in Japan (JBV). Understanding the chemical compositions of different vinegars can provide information about nutritional values and the quality of the taste. This study investigated the vinegar metabolome using a combination of GC-MS, conventional LC-MS, and chemical isotope labeling LC-MS. Different types of vinegar contained different metabolites and concentrations. Amino acids and organic acids were found to be the main components. Tetrahydroharman-3-carboxylic acid and harmalan were identified first in vinegar. Various diketopiperazines and linear dipeptides contributing to different taste effects were also detected first in vinegar. Dipeptides, 3-phenyllactic acid, and tyrosine were found to be potential metabolic markers for differentiating vinegars. The differently expressed pathway between Chinese and Japanese vinegar was tryptophan metabolism, while the main difference within Chinese vinegars was aminoacyl-tRNA biosynthesis metabolism. These results not only give insights into the metabolites in famous types of cereal vinegar but also provide valuable knowledge for making vinegar with desirable health characteristics.
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Affiliation(s)
- Zhihua Li
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.Z.); (L.D.); (Y.Z.); (F.Z.)
- Correspondence: (Z.L.); (L.L.); (M.A.)
| | - Chi Zhao
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.Z.); (L.D.); (Y.Z.); (F.Z.)
| | - Ling Dong
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.Z.); (L.D.); (Y.Z.); (F.Z.)
| | - Yu Huan
- China Application Service Center, SCIEX Analytical Instrument Trading Co., Shanghai 200335, China;
| | - Miwa Yoshimoto
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan; (M.Y.); (I.T.)
| | - Yongqing Zhu
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.Z.); (L.D.); (Y.Z.); (F.Z.)
| | - Ipputa Tada
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan; (M.Y.); (I.T.)
| | - Xiaohang Wang
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.W.); (S.Z.)
| | - Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.W.); (S.Z.)
| | - Fengju Zhang
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.Z.); (L.D.); (Y.Z.); (F.Z.)
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.W.); (S.Z.)
- Correspondence: (Z.L.); (L.L.); (M.A.)
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Japan; (M.Y.); (I.T.)
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Correspondence: (Z.L.); (L.L.); (M.A.)
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14
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Katano K, Yamamoto T, Arita M, Kawamata S. iPSC: DIFFERENTIATION POTENTIAL OF INDUCED PLURIPOTENT STEM CELLS CAN BE ALTERED BY CULTURE CONDITIONS. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Yamamoto T, Arita M, Kawamura H, Suzuki T, Margetts D, Kubo T, Kawamata S. Mesenchymal Stem/Stromal Cells: DETERMINATION OF CRITICAL QUALITY ATTRIBUTES OF MESENCHYMAL STEM CELL BY DEFINING CRITICAL PROCESS PARAMETERS AND EFFICACY OF THE PRODUCT. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Fukushima A, Takahashi M, Nagasaki H, Aono Y, Kobayashi M, Kusano M, Saito K, Kobayashi N, Arita M. Development of RIKEN Plant Metabolome MetaDatabase. Plant Cell Physiol 2022; 63:433-440. [PMID: 34918130 PMCID: PMC8917833 DOI: 10.1093/pcp/pcab173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The advancement of metabolomics in terms of techniques for measuring small molecules has enabled the rapid detection and quantification of numerous cellular metabolites. Metabolomic data provide new opportunities to gain a deeper understanding of plant metabolism that can improve the health of both plants and humans that consume them. Although major public repositories for general metabolomic data have been established, the community still has shortcomings related to data sharing, especially in terms of data reanalysis, reusability and reproducibility. To address these issues, we developed the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM, http://metabobank.riken.jp/pmm/db/plantMetabolomics), which stores mass spectrometry-based (e.g. gas chromatography-MS-based) metabolite profiling data of plants together with their detailed, structured experimental metadata, including sampling and experimental procedures. Our metadata are described as Linked Open Data based on the Resource Description Framework using standardized and controlled vocabularies, such as the Metabolomics Standards Initiative Ontology, which are to be integrated with various life and biomedical science data using the World Wide Web. RIKEN PMM implements intuitive and interactive operations for plant metabolome data, including raw data (netCDF format), mass spectra (NIST MSP format) and metabolite annotations. The feature is suitable not only for biologists who are interested in metabolomic phenotypes, but also for researchers who would like to investigate life science in general through plant metabolomic approaches.
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Affiliation(s)
| | - Mikiko Takahashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | | | - Yusuke Aono
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Kobayashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyako Kusano
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Faculty of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuki Saito
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Norio Kobayashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Data Knowledge Organization Unit, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masanori Arita
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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17
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Siriwach R, Matsuzaki J, Saito T, Nishimura H, Isozaki M, Isoyama Y, Sato M, Arita M, Akaho S, Higashide T, Yano K, Hirai MY. Assessment of Greenhouse Tomato Anthesis Rate Through Metabolomics Using LASSO Regularized Linear Regression Model. Front Mol Biosci 2022; 9:839051. [PMID: 35300116 PMCID: PMC8923526 DOI: 10.3389/fmolb.2022.839051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
While the high year-round production of tomatoes has been facilitated by solar greenhouse cultivation, these yields readily fluctuate in response to changing environmental conditions. Mathematic modeling has been applied to forecast phenotypes of tomatoes using environmental measurements (e.g., temperature) as indirect parameters. In this study, metabolome data, as direct parameters reflecting plant internal status, were used to construct a predictive model of the anthesis rate of greenhouse tomatoes. Metabolome data were obtained from tomato leaves and used as variables for linear regression with the least absolute shrinkage and selection operator (LASSO) for prediction. The constructed model accurately predicted the anthesis rate, with an R2 value of 0.85. Twenty-nine of the 161 metabolites were selected as candidate markers. The selected metabolites were further validated for their association with anthesis rates using the different metabolome datasets. To assess the importance of the selected metabolites in cultivation, the relationships between the metabolites and cultivation conditions were analyzed via correspondence analysis. Trigonelline, whose content did not exhibit a diurnal rhythm, displayed major contributions to the cultivation, and is thus a potential metabolic marker for predicting the anthesis rate. This study demonstrates that machine learning can be applied to metabolome data to identify metabolites indicative of agricultural traits.
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Affiliation(s)
| | - Jun Matsuzaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takeshi Saito
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Japan
| | | | - Masahide Isozaki
- Mie Prefecture Agricultural Research Institute, Matsusaka, Japan
| | - Yosuke Isoyama
- Mie Prefecture Agricultural Research Institute, Matsusaka, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- National Institute of Genetics, Mishima, Japan
| | - Shotaro Akaho
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | | | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Masami Yokota Hirai,
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18
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Kusada H, Arita M, Tohno M, Tamaki H. Isolation of a Highly Thermostable Bile Salt Hydrolase With Broad Substrate Specificity From Lactobacillus paragasseri. Front Microbiol 2022; 13:810872. [PMID: 35250928 PMCID: PMC8893165 DOI: 10.3389/fmicb.2022.810872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Bile salt hydrolase (BSH) enzymes produced by intestinal Lactobacillus species have been recognized as major targets for probiotic studies owing to their weight-loss and cholesterol-lowering effects. In this study, we isolated a highly thermostable BSH with broad substrate specificity, designed as LapBSH (BSH from a probiotic bacterium, Lactobacillus paragasseri JCM 5343 T ). The recombinant LapBSH protein clearly hydrolyzed 12 different substrates, including primary/secondary, major/minor, and taurine/glycine-conjugated bile salts in mammalian digestive tracts. Intriguingly, LapBSH further displayed a highly thermostable ability among all characterized BSH enzymes. Indeed, this enzyme retained above 80% of its optimum BSH activity even after 6 h of incubation at 50-90°C. LapBSH also exerted a functionally stable activity and maintained above 85% of its original activity after pre-heating at 85°C for 2 h. Therefore, LapBSH is a very unique probiotic enzyme with broad substrate specificity and high thermostability. The strain itself, JCM 5343T, was also found to exhibit high heat-resistance ability and could form colonies even after exposure to 85°C for 2 h. As thermostable enzyme/bacterium offers industrial and biotechnological advantages in terms of its productivity and stability improvements, both thermostable LapBSH and thermotolerant L. paragasseri JCM 5343T could be promising candidates for future probiotic research.
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Affiliation(s)
- Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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19
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Ideta S, Johnston S, Yoshida T, Tanaka K, Mori M, Anzai H, Ino A, Arita M, Namatame H, Taniguchi M, Ishida S, Takashima K, Kojima KM, Devereaux TP, Uchida S, Fujimori A. Hybridization of Bogoliubov Quasiparticles between Adjacent CuO_{2} Layers in the Triple-Layer Cuprate Bi_{2}Sr_{2}Ca_{2}Cu_{3}O_{10+δ} Studied by Angle-Resolved Photoemission Spectroscopy. Phys Rev Lett 2021; 127:217004. [PMID: 34860085 DOI: 10.1103/physrevlett.127.217004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 07/08/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Hybridization of Bogoliubov quasiparticles (BQPs) between the CuO_{2} layers in the triple-layer cuprate high-temperature superconductor Bi_{2}Sr_{2}Cu_{2}Cu_{3}O_{10+δ} is studied by angle-resolved photoemission spectroscopy (ARPES). In the superconducting state, an anticrossing gap opens between the outer- and inner-BQP bands, which we attribute primarily to interlayer single-particle hopping with possible contributions from interlayer Cooper pairing. We find that the d-wave superconducting gap of both BQP bands smoothly develops with momentum without an abrupt jump in contrast to a previous ARPES study. Hybridization between the BQPs also gradually increases in going from the off nodal to the antinodal region, which is explained by the momentum dependence of the interlayer single-particle hopping. As possible mechanisms for the enhancement of the superconducting transition temperature, the hybridization between the BQPs as well as the combination of phonon modes of the triple CuO_{2} layers and spin fluctuations represented by a four-well model are discussed.
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Affiliation(s)
- S Ideta
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- UVSOR-III Synchrotron, Institute for Molecular Science, Okazaki 444-8585, Japan
| | - S Johnston
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - T Yoshida
- Department of Human and Environmental studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - K Tanaka
- UVSOR-III Synchrotron, Institute for Molecular Science, Okazaki 444-8585, Japan
| | - M Mori
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - H Anzai
- Graduate School of Engineering, Osaka Prefecture University, Sakai 599-8531, Japan
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - A Ino
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
- Department of Education and Creation Engineering, Kurume Institute of Technology, Fukuoka 2286-66, Japan
| | - M Arita
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - H Namatame
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - M Taniguchi
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - S Ishida
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan
| | - K Takashima
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - K M Kojima
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- J-PARC Center and Institute of Materials Structure Science, KEK, Tsukuba, Ibaraki 305-0801, Japan
- Centre for Molecular and Materials Science, TRIUMF, 4004 Vancouver, Canada
| | - T P Devereaux
- Geballe Laboratory for Advanced Materials, Stanford University, Stanford, California 94305, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Laboratory and Stanford University, Menlo Park, California 94025, USA
- Department of Materials Science and Engineering Stanford University, Stanford, California 94305, USA
| | - S Uchida
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568, Japan
| | - A Fujimori
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Applied Physics, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
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20
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Takenaka S, Kawashima T, Arita M. A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria. FEMS Microbiol Lett 2021; 368:6360976. [PMID: 34468734 PMCID: PMC8440127 DOI: 10.1093/femsle/fnab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.
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Affiliation(s)
- Shinkuro Takenaka
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kawashima
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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21
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Nishidono Y, Niwa K, Kitajima A, Watanabe S, Tezuka Y, Arita M, Takabayashi J, Tanaka K. α-Linolenic acid in Papilio machaon larvae regurgitant induces a defensive response in Apiaceae. Phytochemistry 2021; 188:112796. [PMID: 34052696 DOI: 10.1016/j.phytochem.2021.112796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/14/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Papilio machaon hippocrates C. Felder et R. Felder, 1864 (Papilionidae) larvae are pests of plants of the family Apiaceae. It is unclear whether Apiaceae plants show induced defensive responses against P. machaon hippocrates larvae, and if so, how these responses are induced. Comparison of the fatty acid (FA) composition of the leaves of host plants and the regurgitant of P. machaon hippocrates larvae by LC-MS revealed a great increase in α-linolenic acid (α-LA) in the regurgitant compared with the FAs contained in the leaves. However, specific FA amino acid conjugates, known as elicitor compounds, such as volicitin, were not detected. Sterile host plants (Saposhnikovia divaricata (Turcz.) Schischk., Apiaceae) were treated with α-LA to mimic the damage made by P. machaon hippocrates larvae. After α-LA treatment to leaves, induced defensive reactions, i.e., release of volatile compounds such as α- and β-pinene and camphene (possible induced indirect defense) and the accumulation of specialized metabolites such as (R)-falcarinol and bergapten (possible induced direct defense) were observed. These findings highlight the role of α-LA in the interaction between P. machaon hippocrates larvae and Apiaceae host plants.
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Affiliation(s)
- Yuto Nishidono
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Kotaro Niwa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Aoi Kitajima
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Shiro Watanabe
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
| | - Yasuhiro Tezuka
- Faculty of Pharmaceutical Sciences, Hokuriku University, Ho-3 Kanagawa-machi, Kanazawa, Ishikawa, 920-1181, Japan.
| | - Masanori Arita
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Junji Takabayashi
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan.
| | - Ken Tanaka
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
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22
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E. Kawaguchi, Miyai N, Zhang Y, Hattori S, Uematsu Y, Utsumi M, Takeshita T, Arita M. The association of arterial stiffness with muscle mass reduction and low muscle strength in community-dwelling elderly individuals: The Wakayama study. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Noureen M, Kawashima T, Arita M. Genetic Markers of Genome Rearrangements in Helicobacter pylori. Microorganisms 2021; 9:621. [PMID: 33802974 PMCID: PMC8002640 DOI: 10.3390/microorganisms9030621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Helicobacter pylori exhibits a diverse genomic structure with high mutation and recombination rates. Various genetic elements function as drivers of this genomic diversity including genome rearrangements. Identifying the association of these elements with rearrangements can pave the way to understand its genome evolution. We analyzed the order of orthologous genes among 72 publicly available complete genomes to identify large genome rearrangements, and rearrangement breakpoints were compared with the positions of insertion sequences, genomic islands, and restriction modification genes. Comparison of the shared inversions revealed the conserved genomic elements across strains from different geographical locations. Some were region-specific and others were global, indicating that highly shared rearrangements and their markers were more ancestral than strain-or region-specific ones. The locations of genomic islands were an important factor for the occurrence of the rearrangements. Comparative genomics helps to evaluate the conservation of various elements contributing to the diversity across genomes.
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Affiliation(s)
- Mehwish Noureen
- Department of Genetics, SOKENDAI University, Yata 1111, Mishima 411-8540, Shizuoka, Japan;
| | - Takeshi Kawashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima 411-8540, Shizuoka, Japan;
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima 411-8540, Shizuoka, Japan;
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan
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24
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Maeno S, Nishimura H, Tanizawa Y, Dicks L, Arita M, Endo A. Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group. BMC Microbiol 2021; 21:41. [PMID: 33563209 PMCID: PMC7871557 DOI: 10.1186/s12866-021-02101-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/20/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fructophilic lactic acid bacteria (FLAB) found in D-fructose rich niches prefer D-fructose over D-glucose as a growth substrate. They need electron acceptors for growth on D-glucose. The organisms share carbohydrate metabolic properties. Fructobacillus spp., Apilactobacillus kunkeei, and Apilactobacillus apinorum are members of this unique group. Here we studied the fructophilic characteristics of recently described species Apilactobacillus micheneri, Apilactobacillus quenuiae, and Apilactobacillus timberlakei. RESULTS The three species prefer D-fructose over D-glucose and only metabolize D-glucose in the presence of electron acceptors. The genomic characteristics of the three species, i.e. small genomes and thus a low number of coding DNA sequences, few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, are characteristic of FLAB. The three species thus are novel members of FLAB. Reduction of genes involved in carbohydrate transport and metabolism in accordance with reduction of genome size were the common characteristics of the family Lactobacillaceae, but FLAB markedly reduced the gene numbers more than other species in the family. Pan-genome analysis of genes involved in metabolism displayed a lack of specific carbohydrate metabolic pathways in FLAB, leading to a unique cluster separation. CONCLUSIONS The present study expanded FLAB group. Fructose-rich environments have induced similar evolution in phylogenetically distant FLAB species. These are examples of convergent evolution of LAB.
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Affiliation(s)
- Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Hiroya Nishimura
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Leon Dicks
- Department of Microbiology, University of Stellenbosch, Matieland, Stellenbosch, 7602, South Africa
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
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25
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Arita M, Karsch-Mizrachi I, Cochrane G. The international nucleotide sequence database collaboration. Nucleic Acids Res 2021; 49:D121-D124. [PMID: 33166387 PMCID: PMC7778961 DOI: 10.1093/nar/gkaa967] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been the core infrastructure for collecting and providing nucleotide sequence data and metadata for >30 years. Three partner organizations, the DNA Data Bank of Japan (DDBJ) at the National Institute of Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have been collaboratively maintaining the INSDC for the benefit of not only science but all types of community worldwide.
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Affiliation(s)
- Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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26
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Modesto M, Satti M, Watanabe K, Huang CH, Liou JS, Tamura T, Saito S, Mori K, Huang L, Sandri C, Spiezio C, Sgorbati B, Scarafile D, Cammà C, Ancora M, Patavino C, Arita M, Mattarelli P. Bifidobacteria in two-toed sloths ( Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov. Int J Syst Evol Microbiol 2021; 70:6115-6125. [PMID: 33052806 DOI: 10.1099/ijsem.0.004506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6T), whereas the type strain of Bifidobacterium dentium DSM 20436T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6T combined with phenotypic analyses clearly revealed that the strain BRDM 6T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6T=NBRC 114053T=BCRC 81222T) is proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Barbara Sgorbati
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Massimo Ancora
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Claudio Patavino
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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27
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Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P. Corrigendum to Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of Bifidobacterium vespertilionis sp. nov. and Bifidobacterium rousetti sp. nov. [Syst. Appl. Microbiol. 42 (2019) 126017]. Syst Appl Microbiol 2020; 44:126169. [PMID: 33279871 DOI: 10.1016/j.syapm.2020.126169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan; Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Universita'Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Universita'Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Piero Sciavilla
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | | | | | - Giorgia Perpetuini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Bonetti
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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28
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Ueda K, Kashiba A, Ooue C, Kimura A, Takeshita T, Arita M. Effects of a home blood pressure monitoring by mobile phone-based and health service (continuous antihypertensive treatment) in mild hypertension : The wakayama health promotion study. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Tada I, Chaleckis R, Tsugawa H, Meister I, Zhang P, Lazarinis N, Dahlén B, Wheelock CE, Arita M. Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies. Anal Chem 2020; 92:11310-11317. [PMID: 32648737 DOI: 10.1021/acs.analchem.0c01980] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Data-independent acquisition mass spectrometry (DIA-MS) is essential for information-rich spectral annotations in untargeted metabolomics. However, the acquired MS2 spectra are highly complex, posing significant annotation challenges. We have developed a correlation-based deconvolution (CorrDec) method that uses ion abundance correlations in multisample studies using DIA-MS as an update of our MS-DIAL software. CorrDec is based on the assumption that peak intensities of precursor and fragment ions correlate across samples and exploits this quantitative information to deconvolute complex DIA spectra. CorrDec clearly improved deconvolution of the original MS-DIAL deconvolution method (MS2Dec) in a dilution series of chemical standards and a 224-sample urinary metabolomics study. The primary advantage of CorrDec over MS2Dec is the ability to discriminate coeluting low-abundance compounds. CorrDec requires the measurement of multiple samples to successfully deconvolute DIA spectra; however, our randomized assessment demonstrated that CorrDec can contribute to studies with as few as 10 unique samples. The presented methodology improves compound annotation and identification in multisample studies and will be useful for applications in large cohort studies.
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Affiliation(s)
- Ipputa Tada
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Romanas Chaleckis
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan.,Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 171-77, Sweden
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 240-0045, Japan.,RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 240-0045, Japan
| | - Isabel Meister
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan.,Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 171-77, Sweden
| | - Pei Zhang
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan.,Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 171-77, Sweden
| | - Nikolaos Lazarinis
- Division of Respiratory Medicine and Allergy, Department of Medicine, Karolinska University Hospital Huddinge, Stockholm, 141-86, Sweden
| | - Barbro Dahlén
- Division of Respiratory Medicine and Allergy, Department of Medicine, Karolinska University Hospital Huddinge, Stockholm, 141-86, Sweden
| | - Craig E Wheelock
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan.,Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 171-77, Sweden
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 240-0045, Japan.,National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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30
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Modesto M, Satti M, Watanabe K, Scarafile D, Huang CH, Liou JS, Tamura T, Saito S, Watanabe M, Mori K, Huang L, Sandri C, Spiezio C, Arita M, Mattarelli P. Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov. Syst Appl Microbiol 2020; 43:126111. [PMID: 32847786 DOI: 10.1016/j.syapm.2020.126111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Three bifidobacterial Gram-stain-positive, non-spore forming and fructose-6-phosphate phosphoketolase-positive strains, SMA1T, SMB2 and SMA15T were isolated from the faeces of two adult males of the squirrel monkey (Saimiri sciureus). On the basis of 16S rRNA gene sequence similarities, the type strain of Bifidobacterium primatium DSM 100687T (99.3%; similarity) was the closest neighbour to strains SMA1T and SMB2, whereas the type strain of Bifidobacterium stellenboschense DSM 23968T (96.5%) was the closest neighbour to strain SMA15T. The average nucleotide identity (ANI) values of SMA1T and SAM15T with the closely related type strains were 93.7% and 88.1%, respectively. The in silico DNA‒DNA hybridization values with the closest neighbours were 53.1% and 36.9%, respectively. GC contents of strains SMA1T and SMA15T were 63.6 and 66.4 mol%, respectively. Based on the phylogenetic, genotypic and phenotypic data obtained, the strains SMA1T and SMA15T clearly represent two novel taxa within the genus Bifidobacterium for which the names Bifidobacterium saimiriisciurei sp. nov. (type strain SMA1T = BCRC 81223T = NBRC 114049T = DSM 106020T) and Bifidobacterium platyrrhinorum sp. nov. (type strain SMA15T = BCRC 81224T = NBRC 114051T = DSM 106029T) are proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mizuki Watanabe
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Masanori Arita
- RIKEN Centerfor Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 2230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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Jamil IN, Remali J, Azizan KA, Nor Muhammad NA, Arita M, Goh HH, Aizat WM. Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology. Front Plant Sci 2020; 11:944. [PMID: 32754171 PMCID: PMC7371031 DOI: 10.3389/fpls.2020.00944] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 05/03/2023]
Abstract
Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.
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Affiliation(s)
- Ili Nadhirah Jamil
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Juwairiah Remali
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kamalrul Azlan Azizan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Masanori Arita
- Bioinformation & DDBJ Center, National Institute of Genetics (NIG), Mishima, Japan
- Metabolome Informatics Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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Kuroda K, Arai Y, Rezaei N, Kunisada S, Sakuragi S, Alaei M, Kinoshita Y, Bareille C, Noguchi R, Nakayama M, Akebi S, Sakano M, Kawaguchi K, Arita M, Ideta S, Tanaka K, Kitazawa H, Okazaki K, Tokunaga M, Haga Y, Shin S, Suzuki HS, Arita R, Kondo T. Devil's staircase transition of the electronic structures in CeSb. Nat Commun 2020; 11:2888. [PMID: 32514054 PMCID: PMC7280508 DOI: 10.1038/s41467-020-16707-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/15/2020] [Indexed: 12/02/2022] Open
Abstract
Solids with competing interactions often undergo complex phase transitions with a variety of long-periodic modulations. Among such transition, devil's staircase is the most complex phenomenon, and for it, CeSb is the most famous material, where a number of the distinct phases with long-periodic magnetostructures sequentially appear below the Néel temperature. An evolution of the low-energy electronic structure going through the devil's staircase is of special interest, which has, however, been elusive so far despite 40 years of intense research. Here, we use bulk-sensitive angle-resolved photoemission spectroscopy and reveal the devil's staircase transition of the electronic structures. The magnetic reconstruction dramatically alters the band dispersions at each transition. Moreover, we find that the well-defined band picture largely collapses around the Fermi energy under the long-periodic modulation of the transitional phase, while it recovers at the transition into the lowest-temperature ground state. Our data provide the first direct evidence for a significant reorganization of the electronic structures and spectral functions occurring during the devil's staircase.
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Affiliation(s)
- Kenta Kuroda
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan.
| | - Y Arai
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - N Rezaei
- Department of Physics, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - S Kunisada
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - S Sakuragi
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - M Alaei
- Department of Physics, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Y Kinoshita
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - C Bareille
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - R Noguchi
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - M Nakayama
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - S Akebi
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - M Sakano
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
- Department of Applied Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - K Kawaguchi
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - M Arita
- Hiroshima Synchrotron Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - S Ideta
- UVSOR Facility, Institute for Molecular Science, Okazaki, 444-8585, Japan
| | - K Tanaka
- UVSOR Facility, Institute for Molecular Science, Okazaki, 444-8585, Japan
| | - H Kitazawa
- National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, 305-0047, Japan
| | - K Okazaki
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - M Tokunaga
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - Y Haga
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
| | - S Shin
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - H S Suzuki
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - R Arita
- Department of Applied Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takeshi Kondo
- ISSP, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
- Trans-scale Quantum Science Institute, University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Kawamata S, Yamamoto T, Arita M, Suzuki K, Kawamura H, Suzuki T, Margettes D. Determination of critical quality attributes of mesenchymal stem cell by defining critical process parameters and efficacy of the product. Cytotherapy 2020. [DOI: 10.1016/j.jcyt.2020.04.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ohbuchi K, Sakurai N, Kitagawa H, Sato M, Suzuki H, Kushida H, Nishi A, Yamamoto M, Hanazaki K, Arita M. Differential annotation of converted metabolites (DAC-Met): Exploration of Maoto (Ma-huang-tang)-derived metabolites in plasma using high-resolution mass spectrometry. Metabolomics 2020; 16:63. [PMID: 32335721 PMCID: PMC7183508 DOI: 10.1007/s11306-020-01681-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/15/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Traditional herbal medicine (THM) contains a vast number of natural compounds with varying degrees of pharmacological activity. To elucidate the mode of action, comprehensive metabolite profiling in the plasma before and after administration of THM is essential. OBJECTIVE The aim of this study was to explore and identify/annotate converted metabolites after administration of THM in humans. METHODS We performed untargeted metabolome analysis of human plasma collected before and after administration of maoto (ma-huang-tang), a traditional Japanese Kampo medicine. Maoto-derived metabolites were then selected and annotated following the DAC-Met strategy, which is an annotation method that uses mass differences of major metabolic reactions among the detected peaks and a differential network analysis. RESULTS About 80% of maoto-derived components were found to be converted forms. Following DAC-Met, the structures of 15 previously unidentified metabolites were determined, and five of these were later confirmed with authentic standards. Using published literature, we also reconstructed the metabolic pathway of maoto components in humans. A kinetic time-course analysis revealed their diverse kinetic profiles. CONCLUSION The results demonstrated that time-resolved comprehensive metabolite profiling in plasma using the DAC-Met strategy is highly useful for elucidating the complex nature of THM.
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Affiliation(s)
- Katsuya Ohbuchi
- Tsumura Kampo Research Laboratories, Tsumura & CO, Ibaraki, 300-1192, Japan.
| | - Nozomu Sakurai
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Hiroyuki Kitagawa
- Department of Surgery, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Masaru Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Hirotaka Kushida
- Tsumura Kampo Research Laboratories, Tsumura & CO, Ibaraki, 300-1192, Japan
| | - Akinori Nishi
- Tsumura Kampo Research Laboratories, Tsumura & CO, Ibaraki, 300-1192, Japan
| | - Masahiro Yamamoto
- Tsumura Kampo Research Laboratories, Tsumura & CO, Ibaraki, 300-1192, Japan
| | - Kazuhiro Hanazaki
- Department of Surgery, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
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Kaminuma E, Baba Y, Mochizuki M, Matsumoto H, Ozaki H, Okayama T, Kato T, Oki S, Fujisawa T, Nakamura Y, Arita M, Ogasawara O, Kashima H, Takagi T. DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences. Genes Genet Syst 2020; 95:43-50. [PMID: 32213716 DOI: 10.1266/ggs.19-00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generation sequencers has raised the interest of researchers. However, finding research collaborators with knowledge of machine learning techniques is difficult for many experimental life scientists. One solution to this problem is to utilise the power of crowdsourcing. In this report, we describe how we investigated the potential of crowdsourced modelling for a life science task by conducting a machine learning competition, the DNA Data Bank of Japan (DDBJ) Data Analysis Challenge. In the challenge, participants predicted chromatin feature annotations from DNA sequences with competing models. The challenge engaged 38 participants, with a cumulative total of 360 model submissions. The performance of the top model resulted in an area under the curve (AUC) score of 0.95. Over the course of the competition, the overall performance of the submitted models improved by an AUC score of 0.30 from the first submitted model. Furthermore, the 1st- and 2nd-ranking models utilised external data such as genomic location and gene annotation information with specific domain knowledge. The effect of incorporating this domain knowledge led to improvements of approximately 5%-9%, as measured by the AUC scores. This report suggests that machine learning competitions will lead to the development of highly accurate machine learning models for use by experimental scientists unfamiliar with the complexities of data science.
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Affiliation(s)
- Eli Kaminuma
- Center for Information Biology, National Institute of Genetics
| | - Yukino Baba
- Graduate School of Informatics, Kyoto University
| | | | - Hirotaka Matsumoto
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research
| | - Haruka Ozaki
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research
| | | | - Takuya Kato
- Graduate School of Information Science and Technology, The University of Tokyo
| | - Shinya Oki
- Graduate School of Medical Sciences, Kyushu University
| | | | | | - Masanori Arita
- Center for Information Biology, National Institute of Genetics
| | - Osamu Ogasawara
- Center for Information Biology, National Institute of Genetics
| | | | - Toshihisa Takagi
- Center for Information Biology, National Institute of Genetics.,Graduate School of Science, The University of Tokyo
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Tanizawa Y, Kobayashi H, Nomura M, Sakamoto M, Arita M, Nakamura Y, Ohkuma M, Tohno M. Lactobacillus buchneri subsp. silagei subsp. nov., isolated from rice grain silage. Int J Syst Evol Microbiol 2020; 70:3111-3116. [PMID: 32250236 DOI: 10.1099/ijsem.0.004138] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacteria, designated strains SG162T and NK01, were isolated from Japanese rice grain silage and total mixed ration silage, respectively. They were initially identified as Lactobacillus buchneri based on the 16S rRNA gene sequence similarities. However, the two strains were separated into a distinct clade from L. buchneri DSM 20057T (=JCM 1115T) through whole-genome sequence-based characterization, forming an infraspecific subgroup together with strains CD034 and S42, whose genomic sequences were available in the public sequence database. Strains within the subgroup shared 99.4-99.7 % average nucleotide identity (ANI) and 97.5-99.0 % digital DNA-DNA hybridization (dDDH) with each other, albeit 96.9-97.0 % ANI and 76.0-76.6 % dDDH against DSM 20057T. Strains SG162T and NK01 could utilize more substrates as sole carbon sources than DSM 20057T, potentially owing to the abundance of genes involved in carbon metabolism, especially the Entner-Doudoroff pathway. The inability of γ-aminobutyric acid (GABA) production was evidenced by the lack of glutamate decarboxylase and glutamate/GABA antiporter genes in the new subgroup strains. Strain SG162T grew at 10-45 °C (optimum, 30 °C), pH 3.5-8.0, and 0-8 % (w/v) NaCl. Its genomic DNA G+C content was 44.1 mol%. The predominant fatty acids were C16 : 0, C19 : 0 cyclo ω8c, and summed feature 8. On the basis of the polyphasic characterization findings, strains SG162T and NK01 represent a novel subspecies of L. buchneri, for which the name Lactobacillus buchneri subsp. silagei subsp. nov. is proposed. The type strain is SG162T (=JCM 32599T=DSM 107969T), and strains CD034 and S42 are also transferred to L. buchneri subsp. silagei.
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Affiliation(s)
- Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Masaru Nomura
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0901, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
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Ito S, Arita M, Haruyama J, Feng B, Chen WC, Namatame H, Taniguchi M, Cheng CM, Bian G, Tang SJ, Chiang TC, Sugino O, Komori F, Matsuda I. Surface-state Coulomb repulsion accelerates a metal-insulator transition in topological semimetal nanofilms. Sci Adv 2020; 6:eaaz5015. [PMID: 32219169 PMCID: PMC7083614 DOI: 10.1126/sciadv.aaz5015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
The emergence of quantization at the nanoscale, the quantum size effect (QSE), allows flexible control of matter and is a rich source of advanced functionalities. A QSE-induced transition into an insulating phase in semimetallic nanofilms was predicted for bismuth a half-century ago and has regained new interest with regard to its surface states exhibiting nontrivial electronic topology. Here, we reveal an unexpected mechanism of the transition by high-resolution angle-resolved photoelectron spectroscopy combined with theoretical calculations. Anomalous evolution and degeneracy of quantized energy levels indicate that increased Coulomb repulsion from the surface states deforms a quantum confinement potential with decreasing thickness. The potential deformation strongly modulates spatial distributions of quantized wave functions, which leads to acceleration of the transition beyond the original QSE picture. This discovery establishes a complete picture of the long-discussed transition and highlights a new class of size effects dominating nanoscale transport in systems with metallic surface states.
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Affiliation(s)
- S. Ito
- Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwa, Chiba, Japan
| | - M. Arita
- Hiroshima Synchrotron Radiation Center (HSRC), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - J. Haruyama
- Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwa, Chiba, Japan
| | - B. Feng
- Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - W.-C. Chen
- Department of Physics and Astronomy, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - H. Namatame
- Hiroshima Synchrotron Radiation Center (HSRC), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - M. Taniguchi
- Hiroshima Synchrotron Radiation Center (HSRC), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - C.-M. Cheng
- National Synchrotron Radiation Research Center (NSRRC), Hsinchu, Taiwan, Republic of China
| | - G. Bian
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
| | - S.-J. Tang
- Department of Physics and Astronomy, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- National Synchrotron Radiation Research Center (NSRRC), Hsinchu, Taiwan, Republic of China
| | - T.-C. Chiang
- Department of Physics and Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - O. Sugino
- Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwa, Chiba, Japan
| | - F. Komori
- Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwa, Chiba, Japan
| | - I. Matsuda
- Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwa, Chiba, Japan
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Buyo M, Takahashi S, Iwahara A, Tsuji T, Yamada S, Hattori S, Uematsu Y, Arita M, Ukai S. Metabolic Syndrome and Cognitive Function: Cross-Sectional Study on Community-Dwelling Non-Demented Older Adults in Japan. J Nutr Health Aging 2020; 24:878-882. [PMID: 33009539 DOI: 10.1007/s12603-020-1412-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM This is a cross-sectional study of relation between metabolic syndrome and cognitive function in community-dwelling non-demented older adults in Japan. We examine the effect of metabolic syndrome and its components on global cognitive function. We also aim to clarify differences of specific cognitive domains between the subjects with and without metabolic syndrome. METHODS We studied 2150 subjects aged between 60 and 90 years whose scores on mini mental state examination (MMSE) were over 23 points. We analyzed difference in MMSE scores between the subjects with and without metabolic syndrome. Logistic regression analysis was performed with MMSE score as the dependent variable and metabolic syndrome components as the independent variable adjusted with age. We also examined differences in attention, logical memory, and verbal and category fluency between the subjects with and without metabolic syndrome. RESULTS MMSE scores were not significantly different between subjects with and without metabolic syndrome. In logistic regression analysis, the score of MMSE was significantly negatively associated with triglycerides in males and significantly negatively associated with abdominal circumference in females. Subjects with metabolic syndrome showed significantly lower performance of attention tasks compared to subjects without metabolic syndrome. CONCLUSIONS Our results suggest that in community-dwelling non-demented Japanese older adults, attention but not global cognitive function may be impaired by metabolic syndrome. Inverted association between some components of metabolic syndrome and global cognitive function indicate necessity of further studies on the relation between undernutrition and cognitive function.
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Affiliation(s)
- M Buyo
- Momoko Buyo CNS MSN RN, Department of Neuropsychiatry, Wakayama Medical University, 811-1, Kimiidera, Wakayama, 641-0012 Japan, Telephone: +81-73-441-0759, Fax: +81-73-441-0769, E-mail:
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Abstract
Background Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment. Results We have developed a method to identify genome rearrangements by comparing almost-conserved genes among closely related strains. Orthologous gene clusters, rather than the gene sequences, are used to align the gene order so that comparison of large number of genomes becomes easier. Comparison of 72 Helicobacter pylori strains revealed shared as well as strain-specific reversals, some of which were found in different geographical locations. Conclusion Degree of genome rearrangements increases with time. Therefore, gene orders can be used to study the evolutionary relationship among species and strains. Multiple genome comparison helps to identify the strain-specific as well as shared reversals. Identification of the time course of rearrangements can provide insights into evolutionary events.
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Affiliation(s)
- Mehwish Noureen
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Ipputa Tada
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Takeshi Kawashima
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan. .,RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
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40
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Hu Y, Chen X, Peng ST, Lane C, Matzelle M, Sun ZL, Hashimoto M, Lu DH, Schwier EF, Arita M, Wu T, Markiewicz RS, Shimada K, Chen XH, Shen ZX, Bansil A, Wilson SD, He JF. Spectroscopic Evidence for Electron-Boson Coupling in Electron-Doped Sr_{2}IrO_{4}. Phys Rev Lett 2019; 123:216402. [PMID: 31809181 DOI: 10.1103/physrevlett.123.216402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Indexed: 06/10/2023]
Abstract
The pseudogap, d-wave superconductivity and electron-boson coupling are three intertwined key ingredients in the phase diagram of the cuprates. Sr_{2}IrO_{4} is a 5d-electron counterpart of the cuprates in which both the pseudogap and a d-wave instability have been observed. Here, we report spectroscopic evidence for the presence of the third key player in electron-doped Sr_{2}IrO_{4}: electron-boson coupling. A kink in nodal dispersion is observed with an energy scale of ∼50 meV. The strength of the kink changes with doping, but the energy scale remains the same. These results provide the first noncuprate platform for exploring the relationship between the pseudogap, d-wave instability, and electron-boson coupling in doped Mott insulators.
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Affiliation(s)
- Yong Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiang Chen
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - S-T Peng
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - C Lane
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - M Matzelle
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Z-L Sun
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - M Hashimoto
- Stanford Synchrotron Radiation Lightsource and Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D-H Lu
- Stanford Synchrotron Radiation Lightsource and Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - E F Schwier
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima 739-0046, Japan
| | - M Arita
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima 739-0046, Japan
| | - T Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - R S Markiewicz
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - K Shimada
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima 739-0046, Japan
| | - X-H Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Z-X Shen
- Stanford Synchrotron Radiation Lightsource and Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Geballe Laboratory for Advanced Materials, Departments of Physics and Applied Physics, Stanford University, Stanford, California 94305, USA
| | - A Bansil
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - S D Wilson
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - J-F He
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Physics and CAS Key Laboratory of Strongly-coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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41
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Tada I, Tsugawa H, Meister I, Zhang P, Shu R, Katsumi R, Wheelock CE, Arita M, Chaleckis R. Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics. Metabolites 2019; 9:E251. [PMID: 31717785 PMCID: PMC6918128 DOI: 10.3390/metabo9110251] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/17/2022] Open
Abstract
Accurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupled to mass spectrometry (LC-MS) methods across laboratories. Here, we illustrate how the combination of MS2 spectra, accurate mass, and retention time can improve the confidence of annotation and provide techniques to create a reliable library for all ion fragmentation (AIF) data with a focus on the characterization of the retention time. The resulting spectral library incorporates information on adducts and in-source fragmentation in AIF data, while noise peaks are effectively minimized through multiple deconvolution processes. We also report the development of the Mass Spectral LIbrary MAnager (MS-LIMA) tool to accelerate library sharing and transfer across laboratories. This library construction strategy improves the confidence in annotation for AIF data in LC-MS-based metabolomics and will facilitate the sharing of retention time and mass spectral data in the metabolomics community.
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Affiliation(s)
- Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Kanagawa, Yokohama 230-0045, Japan
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama 230-0045, Japan
| | - Isabel Meister
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
| | - Pei Zhang
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
| | - Rie Shu
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
| | - Riho Katsumi
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
| | - Craig E. Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Kanagawa, Yokohama 230-0045, Japan
- Center for Information Biology, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Romanas Chaleckis
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Gunma 371-8510, Japan
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Modesto M, Satti M, Watanabe K, Sciavilla P, Felis GE, Sandri C, Spiezio C, Arita M, Mattarelli P. Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada). Int J Syst Evol Microbiol 2019; 69:3041-3048. [DOI: 10.1099/ijsem.0.003584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan ROC
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan ROC
| | - Piero Sciavilla
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | | | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park (Bussolengo), Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park (Bussolengo), Verona, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI University, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Italy
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Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P. Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov. Syst Appl Microbiol 2019; 42:126017. [PMID: 31585749 DOI: 10.1016/j.syapm.2019.126017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022]
Abstract
Fifteen bifidobacterial strains were obtained from faeces of Rousettus aegyptiacus; after grouping them by RAPD PCR only eight were selected and characterized. Analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dna G) genes revealed that these eight strains were classified into five clusters: Cluster I (RST 8 and RST 16T), Cluster II (RST 9T and RST 27), Cluster III (RST 7 and RST 11), Cluster IV (RST 19), Cluster V (RST 17) were closest to Bifidobacterium avesanii DSM 100685T (96.3%), Bifidobacterium callitrichos DSM 23973T (99.2% and 99.7%), Bifidobacterium tissieri DSM 100201T (99.7 and 99.2%), Bifidobacterium reuteri DSM 23975 T (98.9%) and Bifidobacterium myosotis DSM 100196T (99.3%), respectively. Strains in Cluster I and strain RST 9 in Cluster II could not be placed within any recognized species while the other ones were identified as known species. The average nucleotide identity values between two novel strains, RST 16T and RST 9T and their closest relatives were lower than 79% and 89%, respectively. In silico DNA-DNA hybridization values for those closest relatives were 32.5 and 42.1%, respectively. Phenotypic and genotypic tests demonstrated that strains in Cluster I and RST 9T in Cluster II represent two novel species for which the names Bifidobacterium vespertilionis sp. nov. (RST 16T=BCRC 81138T=NBRC 113380T=DSM 106025T ; RST 8=BCRC 81135=NBRC 113377) and Bifidobacterium rousetti sp. nov. (RST 9T=BCRC 81136T=NBRC 113378T=DSM 106027T) are proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan; Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Piero Sciavilla
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | | | | | - Giorgia Perpetuini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Bonetti
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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Kashiba A, Ueda K, Uematsu Y, Utsumi M, Miyai N, Arita M. Blood Pressure-Variation By Room Temperature In Home Pressure Among Metabolic Syndrome Using Home Blood Pressure Web-Based Monitoring. Atherosclerosis 2019. [DOI: 10.1016/j.atherosclerosis.2019.06.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Sato M, Arita M, Kawashima T. Uncovering Ecdysozoa-specific Sphingomyelin Synthase by Phylogenetic Analysis of Metazoan Sequences. Zoolog Sci 2019; 36:316-321. [PMID: 34664902 DOI: 10.2108/zs180168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/01/2019] [Indexed: 11/17/2022]
Abstract
Sphingomyelin (SM) is a membrane phospholipid that is widely distributed in Metazoa; it is the major constituent of myelin sheaths in vertebrates. In mammals, two genes (SMS1 and SMS2) are responsible for its synthesis. No SM-producing genes have been clearly identified in insects and crustaceans (Ecdysozoa) despite the presence of a myelin sheath-like structure in shrimps. Since the rapid transmission of electrical signals requires the use of an insulating material in the nerve, it is possible that the convergent evolution of enzymes to synthesize the insulating compounds for the nervous system also occurred in animals other than vertebrates. Our exhaustive phylogenetic search for metazoan SM synthase identified an Ecdysozoa-specific SM synthase candidate, SMSe, which is absent in Drosophila and Lophotrochozoa. All Ecdysozoa lack the homolog of myelin basic- and proteolipid proteins present in mammals. We propose an evolutionary path of SM synthase and discuss the origin of the myelin structure in Metazoa.
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Affiliation(s)
- Mitsuharu Sato
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan,
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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46
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Liebisch G, Ahrends R, Arita M, Arita M, Bowden JA, Ejsing CS, Griffiths WJ, Holčapek M, Köfeler H, Mitchell TW, Wenk MR, Ekroos K. Lipidomics needs more standardization. Nat Metab 2019; 1:745-747. [PMID: 32694765 DOI: 10.1038/s42255-019-0094-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Tsugawa H, Satoh A, Uchino H, Cajka T, Arita M, Arita M. Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics. Metabolites 2019; 9:metabo9060119. [PMID: 31238512 PMCID: PMC6630716 DOI: 10.3390/metabo9060119] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022] Open
Abstract
Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine algal species, resulting in the annotation of 1437 lipids achieving a 40% increase in annotation compared to the previous results. Specifically, diacylglyceryl-carboxyhydroxy-methylcholine (DGCC) in Pavlova lutheri and Pleurochrysis carterae, glucuronosyldiacylglycerol (GlcADG) in Euglena gracilis, and P. carterae, phosphatidylmethanol (PMeOH) in E. gracilis, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in Chlorella variabilis were newly characterized with the enriched lipid spectral databases. Moreover, we integrated the data from untargeted and targeted analyses from data independent tandem mass spectrometry (DIA-MS/MS) acquisition, specifically the sequential window acquisition of all theoretical fragment-ion MS/MS (SWATH-MS/MS) spectra, to increase the lipidomic annotation coverage. After the creation of a global library of precursor and diagnostic ions of lipids by the MS-DIAL untargeted analysis, the co-eluted DIA-MS/MS spectra were resolved in MRMPROBS targeted analysis by tracing the specific product ions involved in acyl chain compositions. Our results indicated that the metabolite quantifications based on DIA-MS/MS chromatograms were somewhat inferior to the MS1-centric quantifications, while the annotation coverage outperformed those of the untargeted analysis of the data dependent and DIA-MS/MS data. Consequently, integrated analyses of untargeted and targeted approaches are necessary to extract the maximum amount of metabolome information, and our results showcase the value of data repositories for the discovery of novel insights in lipid biology.
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Affiliation(s)
- Hiroshi Tsugawa
- Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
- Laboratory for metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
| | - Aya Satoh
- Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
| | - Haruki Uchino
- Laboratory for metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo 105-8512, Japan.
| | - Tomas Cajka
- Department of Metabolomics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
- Department of Translational Metabolism, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Makoto Arita
- Laboratory for metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo 105-8512, Japan.
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
| | - Masanori Arita
- Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
- National Institute of Genetics, Mishima 411-8540, Japan.
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Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Cammà C, Michelini S, Sgorbati B, Mattarelli P. Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2019; 69:2477-2485. [PMID: 31180316 DOI: 10.1099/ijsem.0.003518] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel Bifidobacterium strain, MRM 9.3T, was isolated from a faecal sample of a baby common marmoset (Callithrixjacchus). Cells were Gram-stain-positive, non-motile, non-sporulating, non-haemolytic, facultatively anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, clpC, dnaJ and dnaG genes) and the core genomes revealed that strain MRM 9.3T exhibited phylogenetic relatedness to Bifidobacterium myosotis DSM 100196T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B.ifidobacterium myosotis DSM 100196T (95.6 %). The average nucleotide identity, amino acid average identity and in silico DNA-DNA hybridization values between MRM 9.3T and DSM 100196T were 79.9, 72.1 and 28.5 %, respectively. Phenotypic and genotypic features clearly showed that the strain MRM 9.3T represents a novel species, for which the name Bifidobacterium jacchi sp. nov. is proposed. The type strain is MRM 9.3T (=DSM 103362T =JCM 31788T).
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC.,Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Masanori Arita
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologiepark 94, 9052 Zwijnaarde, Belgium
| | - Piero Sciavilla
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Claudio Patavino
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Samanta Michelini
- Department of Agricultural and Food Sciences, University of Bologna, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
| | - Barbara Sgorbati
- Department of Agricultural and Food Sciences, University of Bologna, Italy.,School of Pharmacy, Biotechnology and Sport Science, 40100 Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Italy
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Tsugawa H, Nakabayashi R, Mori T, Yamada Y, Takahashi M, Rai A, Sugiyama R, Yamamoto H, Nakaya T, Yamazaki M, Kooke R, Bac-Molenaar JA, Oztolan-Erol N, Keurentjes JJB, Arita M, Saito K. A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nat Methods 2019; 16:295-298. [PMID: 30923379 DOI: 10.1038/s41592-019-0358-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/19/2019] [Indexed: 12/24/2022]
Abstract
We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13C-labeled and non-labeled plants and LC-MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.
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Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan. .,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yutaka Yamada
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | | | - Taiki Nakaya
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Rik Kooke
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Nihal Oztolan-Erol
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,National Institute of Genetics, Mishima, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan. .,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
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Abstract
Isolation of lactic acid bacteria (LAB) is the first and crucial step to study possible roles of LAB in the environment, especially in food fermentation. This is also important to use the organisms for further application. LAB are diverse bacterial group and have diverse growth characteristics. Culture condition of LAB is thus varied, and selection of a suitable culture medium is essential for the purposes. Identification is also an important step, since certain desirable and undesirable characteristics are shared within species. Identification was classically carried out by phenotypic characteristics but is usually performed by DNA sequence-based approaches. 16S rRNA gene sequencing is generally used for identification, and sequencing of housekeeping genes is used when needed. In addition, identification based on whole-genome sequence similarities is becoming common. Here we describe isolation and identification of LAB briefly.
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Affiliation(s)
- Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan.
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka Prefecture, Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka Prefecture, Japan
- RIKEN, Center for Sustainable Resource Science, Kanagawa, Japan
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