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Wakabayashi N, Kimura R, Kuwatani M, Matsui A, Ino N, Mitsuhashi T, Kishi K, Tsuneta S, Nakagawa J, Nishioka N, Sakamoto K, Kato F, Shimizu A, Hirano S, Kudo K. Gastrointestinal: Solid pseudopapillary neoplasm of the pancreas with high-grade malignant transformation. J Gastroenterol Hepatol 2024; 39:618-619. [PMID: 38224676 DOI: 10.1111/jgh.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Affiliation(s)
- N Wakabayashi
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - R Kimura
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - M Kuwatani
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Japan
| | - A Matsui
- Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - N Ino
- Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - T Mitsuhashi
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - K Kishi
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Japan
| | - S Tsuneta
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - J Nakagawa
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - N Nishioka
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - K Sakamoto
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - F Kato
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
| | - A Shimizu
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - S Hirano
- Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - K Kudo
- Department of Diagnostic and Interventional Radiology, Hokkaido University Hospital, Sapporo, Japan
- Department of Diagnostic Imaging, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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2
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Ito T, Kimura R, Wakamori H, Tanaka M, Tezuka A, Nagano AJ, Hamada Y, Kawamoto Y. Hybridization and its impact on the ontogenetic allometry of skulls in macaques. Evolution 2024; 78:284-299. [PMID: 37952211 DOI: 10.1093/evolut/qpad206] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (Macaca fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, that is, the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and nonadditive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.
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Affiliation(s)
- Tsuyoshi Ito
- The Kyoto University Museum, Kyoto University, Sakyo, Kyoto, Japan
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hikaru Wakamori
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Mikiko Tanaka
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Ayumi Tezuka
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yoshi Kawamoto
- School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
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3
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Koganebuchi K, Matsunami M, Imamura M, Kawai Y, Hitomi Y, Tokunaga K, Maeda S, Ishida H, Kimura R. Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data. J Hum Genet 2023; 68:759-767. [PMID: 37468573 PMCID: PMC10597838 DOI: 10.1038/s10038-023-01180-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/29/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023]
Abstract
The Ryukyu Islands are located in the southernmost part of the Japanese Archipelago and consist of several island groups. Each island group has its own history and culture, which differ from those of mainland Japan. People of the Ryukyu Islands are genetically subdivided; however, their detailed demographic history remains unclear. We report the results of a whole-genome sequencing analysis of a total of 50 Ryukyu islanders, focusing on genetic differentiation between Miyako and Okinawa islanders. We confirmed that Miyako and Okinawa islanders cluster differently in principal component analysis and ADMIXTURE analysis and that there is a population structure among Miyako islanders. The present study supports the hypothesis that population differentiation is primarily caused by genetic drift rather than by differences in the rate of migration from surrounding regions, such as the Japanese main islands or Taiwan. In addition, the genetic cline observed among Miyako and Okinawa islanders can be explained by recurrent migration beyond the bounds of these islands. Our analysis also suggested that the presence of multiple subpopulations during the Neolithic Ryukyu Jomon period is not crucial to explain the modern Ryukyu populations. However, the assumption of multiple subpopulations during the time of admixture with mainland Japanese is necessary to explain the modern Ryukyu populations. Our findings add insights that could help clarify the complex history of populations in the Ryukyu Islands.
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Affiliation(s)
- Kae Koganebuchi
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, 903-0215, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, 142-8501, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, 903-0215, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Mt. Olive Hospital, Naha, 903-0804, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan.
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4
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Liu X, Matsunami M, Horikoshi M, Ito S, Ishikawa Y, Suzuki K, Momozawa Y, Niida S, Kimura R, Ozaki K, Maeda S, Imamura M, Terao C. Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations. Mol Biol Evol 2023; 40:msad231. [PMID: 37903429 PMCID: PMC10615566 DOI: 10.1093/molbev/msad231] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20-150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.
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Affiliation(s)
- Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kunihiko Suzuki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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5
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Hayashi K, Tanaka Y, Tsuda T, Nomura A, Fujino N, Furusho H, Sakai N, Iwata Y, Usui S, Sakata K, Kato T, Tada H, Kusayama T, Usuda K, Kawashiri MA, Passman RS, Wada T, Yamagishi M, Takamura M, Fujino N, Nohara A, Kawashiri MA, Hayashi K, Sakata K, Yoshimuta T, Konno T, Funada A, Tada H, Nakanishi C, Hodatsu A, Mori M, Tsuda T, Teramoto R, Nagata Y, Nomura A, Shimojima M, Yoshida S, Yoshida T, Hachiya S, Tamura Y, Kashihara Y, Kobayashi T, Shibayama J, Inaba S, Matsubara T, Yasuda T, Miwa K, Inoue M, Fujita T, Yakuta Y, Aburao T, Matsui T, Higashi K, Koga T, Hikishima K, Namura M, Horita Y, Ikeda M, Terai H, Gamou T, Tama N, Kimura R, Tsujimoto D, Nakahashi T, Ueda K, Ino H, Higashikata T, Kaneda T, Takata M, Yamamoto R, Yoshikawa T, Ohira M, Suematsu T, Tagawa S, Inoue T, Okada H, Kita Y, Fujita C, Ukawa N, Inoguchi Y, Ito Y, Araki T, Oe K, Minamoto M, Yokawa J, Tanaka Y, Mori K, Taguchi T, Kaku B, Katsuda S, Hirase H, Haraki T, Fujioka K, Terada K, Ichise T, Maekawa N, Higashi M, Okeie K, Kiyama M, Ota M, Todo Y, Aoyama T, Yamaguchi M, Noji Y, Mabuchi T, Yagi M, Niwa S, Takashima Y, Murai K, Nishikawa T, Mizuno S, Ohsato K, Misawa K, Kokado H, Michishita I, Iwaki T, Nozue T, Katoh H, Nakashima K, Ito S, Yamagishi M. Correction: Characterization of baseline clinical factors associated with incident worsening kidney function in patients with non-valvular atrial fibrillation: the Hokuriku-Plus AF Registry. Heart Vessels 2023; 38:412. [PMID: 36508013 DOI: 10.1007/s00380-022-02218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kenshi Hayashi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.
| | - Yoshihiro Tanaka
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Center for Arrhythmia Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Toyonobu Tsuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Akihiro Nomura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Noboru Fujino
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hiroshi Furusho
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Department of Cardiology, Ishikawa Prefectural Central Hospital, 2-1, Kuratsuki-higashi, Kanazawa, Japan
| | - Norihiko Sakai
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Yasunori Iwata
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Soichiro Usui
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Kenji Sakata
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Takeshi Kato
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hayato Tada
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Takashi Kusayama
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Keisuke Usuda
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Masa-Aki Kawashiri
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Rod S Passman
- Center for Arrhythmia Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Takashi Wada
- Department of Nephrology and Laboratory Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, Japan
| | - Masakazu Yamagishi
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.,Osaka University of Human Sciences, Settsu, Osaka, Japan
| | - Masayuki Takamura
- Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
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Goto S, Kataoka K, Isa M, Nakamori K, Yoshida M, Murayama S, Arasaki A, Ishida H, Kimura R. Factors associated with bone thickness: Comparison of the cranium and humerus. PLoS One 2023; 18:e0283636. [PMID: 36989318 PMCID: PMC10057751 DOI: 10.1371/journal.pone.0283636] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Cortical bone thickness is important for the mechanical function of bone. Ontogeny, aging, sex, body size, hormone levels, diet, behavior, and genetics potentially cause variations in postcranial cortical robusticity. However, the factors associated with cranial cortical robusticity remain poorly understood. Few studies have examined cortical robusticity in both cranial and postcranial bones jointly. In the present study, we used computed tomography (CT) images to measure cortical bone thicknesses in the cranial vault and humeral diaphysis. This study clearly showed that females have a greater cranial vault thickness and greater age-related increase in cranial vault thickness than males. We found an age-related increase in the full thickness of the temporal cranial vault and the width of the humeral diaphysis, as well as an age-related decrease in the cortical thickness of the frontal cranial vault and the cortical thickness of the humeral diaphysis, suggesting that the mechanisms of bone modeling in cranial and long bones are similar. A positive correlation between cortical indices in the cranial vault and humeral diaphysis also suggested that common factors affect cortical robusticity. We also examined the association of polymorphisms in the WNT16 and TNFSF11 genes with bone thickness. However, no significant associations were observed. The present study provides fundamental knowledge about similarities and differences in the mechanisms of bone modeling between cranial and postcranial bones.
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Affiliation(s)
- Shimpei Goto
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
- Department of Oral and Maxillofacial Surgery, University of the Ryukyus Hospital, Nishihara, Nakagami, Okinawa, Japan
| | - Keiichi Kataoka
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
- Department of Oral and Maxillofacial Surgery, University of the Ryukyus Hospital, Nishihara, Nakagami, Okinawa, Japan
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
| | - Kenji Nakamori
- Department of Oral and Maxillofacial Surgery, Regional Independent Administrative Corporation Naha City Hospital, Naha, Okinawa, Japan
| | - Makoto Yoshida
- Department of Dentistry and Oral Surgery, Doujin Hospital, Urasoe, Okinawa, Japan
| | - Sadayuki Murayama
- Department of Radiology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
| | - Akira Arasaki
- Department of Oral and Maxillofacial Surgery, University of the Ryukyus Hospital, Nishihara, Nakagami, Okinawa, Japan
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Nakagami, Okinawa, Japan
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7
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Fujimoto S, Yaguchi H, Myosho T, Aoyama H, Sato Y, Kimura R. Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing. Sci Rep 2022; 12:19989. [PMID: 36411327 PMCID: PMC9678866 DOI: 10.1038/s41598-022-24498-7] [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: 08/18/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Cost-effective genotyping can be achieved by sequencing PCR amplicons. Short 3-10 base primers can arbitrarily amplify thousands of loci using only a few primers. To improve the sequencing efficiency of the multiple arbitrary amplicon sequencing (MAAS) approach, we designed new primers and examined their efficiency in sequencing and genotyping. To demonstrate the effectiveness of our method, we applied it to examining the population structure of the small freshwater fish, medaka (Oryzias latipes). We obtained 2987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. We also attempted to reconstruct the genetic backgrounds of a commercial orange mutant strain, Himedaka, which has caused a genetic disturbance in wild populations. Our admixture analysis focusing on Himedaka showed that at least two wild populations had genetically been contributed to the nuclear genome of this mutant strain. Our genotyping methods and results will be useful in quantitative assessments of genetic disturbance by this commercially available strain.
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Affiliation(s)
- Shingo Fujimoto
- grid.267625.20000 0001 0685 5104Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0125 Japan ,grid.267625.20000 0001 0685 5104Present Address: Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan ,grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan
| | - Hajime Yaguchi
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan ,grid.258777.80000 0001 2295 9421Present Address: Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Nishihara, Hyogo 669-1330 Japan
| | - Taijun Myosho
- grid.469280.10000 0000 9209 9298Laboratory of Molecular Reproductive Biology, Institute for Environmental Sciences, University of Shizuoka, Nishihara, 422-8526 Japan
| | - Hiroaki Aoyama
- grid.267625.20000 0001 0685 5104Center for Strategic and Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan ,grid.267625.20000 0001 0685 5104Research Planning Office, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan
| | - Yukuto Sato
- grid.267625.20000 0001 0685 5104Present Address: Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan ,grid.267625.20000 0001 0685 5104Center for Strategic and Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213 Japan
| | - Ryosuke Kimura
- grid.267625.20000 0001 0685 5104Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0125 Japan
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8
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Akita T, Oda Y, Kimura R, Nagai M, Tezuka A, Shimamura M, Washizu K, Oka JI, Yamashita C. Involvement of trigeminal axons in nose-to-brain delivery of glucagon-like peptide-2 derivative. J Control Release 2022; 351:573-580. [PMID: 36179766 DOI: 10.1016/j.jconrel.2022.09.047] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022]
Abstract
In our previous study, we created a glucagon-like peptide-2 (GLP-2) derivative with the functional sequence PAS-CPP to achieve efficient uptake by the respiratory epithelium and trigeminal nerve. By using octaarginine for cell penetrating peptides (CPP) and FFLIPKG, a reverse sequence of a part of the cathepsin D sequence for the penetration accelerating sequence (PAS), we found that the derivative was taken up by the cells through macropinocytosis and efficiently escaped from the endosomes and exited the cells. Moreover, it showed drug effects by intranasal (in.) administration at the same dose as intracerebroventricular (icv.) administration, which is direct drug administration into the brain. The purpose of this study was to elucidate the cause of the drug effect of in. administered PAS-CPP-GLP-2 at the same dose as that by icv. Administration. The present results suggested that although icv. Administered PAS-CPP-GLP-2 entered the cerebrospinal fluid, it barely penetrated the perivascular space of the brain, and therefore, only a small amount of the administered dose may have reached the site of action in the brain. In contrast, it was qualitatively suggested that in. administered PAS-CPP-GLP-2 migrates from the trigeminal nerve to the central nervous system via the principal sensory trigeminal nucleus and then through the trigeminal lemniscus. The present results show that nose-to-brain delivery by trigeminal axons, which is assumed to be a transcellular pathway, may be possible. As the drug can be delivered into the nerve, it is expected to be applied not only as a central delivery route but also for the treatment of neurological diseases.
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Affiliation(s)
- Tomomi Akita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yusuke Oda
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ryosuke Kimura
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mio Nagai
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayano Tezuka
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mizuki Shimamura
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kaho Washizu
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Jun-Ichiro Oka
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Chikamasa Yamashita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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9
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Takamatsu G, Yanagi K, Koganebuchi K, Yoshida F, Lee JS, Toyama K, Hattori K, Katagiri C, Kondo T, Kunugi H, Kimura R, Kaname T, Matsushita M. Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus. J Affect Disord 2022; 310:96-105. [PMID: 35504398 DOI: 10.1016/j.jad.2022.04.150] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high-impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci. METHODS We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects. RESULTS We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples. LIMITATIONS The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed. CONCLUSION The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.
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Affiliation(s)
- Gakuya Takamatsu
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Neuropsychiatry, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kae Koganebuchi
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fuyuko Yoshida
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Jun-Seok Lee
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kanako Toyama
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kotaro Hattori
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Chiaki Katagiri
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Synbiotics, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Tsuyoshi Kondo
- Department of Neuropsychiatry, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Psychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Masayuki Matsushita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
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10
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Montenegro J, Fujimoto S, Ansai S, Nagano AJ, Sato M, Maeda Y, Tanaka R, Masengi KWA, Kimura R, Kitano J, Yamahira K. Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish. Mol Ecol 2022; 31:3798-3811. [PMID: 35638236 DOI: 10.1111/mec.16555] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a non-brooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.
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Affiliation(s)
- Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.,Present address: Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masahiro Sato
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Yusuke Maeda
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | | | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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11
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Sato F, Wong CP, Furuya K, Kuzu C, Kimura R, Udo T, Honda H, Yang J. Anti-skin Aging Activities of Sideritis scardica and 3 Flavonoids With an Uncommon 8-Hydroxyl Moiety. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221094910] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The skin plays various crucial biological functions and gradually degenerates due to the process of skin aging. Hence, the development of new ingredients for delaying or even reversing skin aging is an essential subject that needs to be addressed. Our screening effort for anti-skin aging ingredients has led to the discovery that Sideritis scardica extract (SSE) possesses collagenase inhibition, advanced glycation end product (AGE) formation inhibition, antioxidative, and antiallergic activities, as well as ultraviolet B (UVB)-induced matrix metalloproteinase-1 (MMP-1) expression inhibition activity. However, the effect of S. scardica, commonly known as a mountain herb, on skin aging is unknown and needs additional study. Further studies on SSE have led to the isolation of 3 flavonoids with an uncommon 8-hydroxyl moiety, isoscutellarein (1), 4′- O-methylhypolaetin (2), and 4′- O-methylisoscutellarein (3). Biological evaluations also revealed that 1-3 possess SSE collagenase inhibition, AGE formation inhibition, antioxidative, and antiallergic activities, while 3 was identified to possess SSE UVB-induced MMP-1 expression inhibition activity. Moreover, the AGE formation inhibition activity and antiallergic activity of 1-3 were speculated to be derived from their antioxidative activity, while direct inhibition of the collagenase enzyme led to their observed collagenase inhibition activity. Regarding the inhibition activity of 1-3 on UVB-induced MMP-1 expression, further studies are necessary to reveal their possible mechanism of action. Collectively, the biological activities of SSE and the isolated flavonoids 1-3 highlight the potential of S. scardica to be further developed as an agent to delay or reverse skin aging.
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Affiliation(s)
- Fumiaki Sato
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | | | - Kaito Furuya
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | - Chikako Kuzu
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | - Ryosuke Kimura
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | - Tomoha Udo
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | - Haruno Honda
- Laboratory of Analytical Pathophysiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo, Japan
| | - Jinwei Yang
- Tokiwa Phytochemical Co. Ltd, Sakura, Chiba, Japan
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12
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Yamaguchi R, Matsudaira I, Takeuchi H, Imanishi T, Kimura R, Tomita H, Kawashima R, Taki Y. RELN rs7341475 associates with brain structure in japanese healthy females. Neuroscience 2022; 494:38-50. [DOI: 10.1016/j.neuroscience.2022.05.007] [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] [Received: 12/18/2021] [Revised: 04/06/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
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13
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Sato Y, Hermawan I, Kakita T, Okano S, Imai H, Nagai H, Kimura R, Yamashiro T, Kajita T, Toma C. Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan. PLoS Negl Trop Dis 2022; 16:e0010234. [PMID: 35358181 PMCID: PMC8970387 DOI: 10.1371/journal.pntd.0010234] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/05/2022] [Indexed: 01/10/2023] Open
Abstract
Background Leptospirosis, a zoonosis caused by species in the spirochete genus Leptospira, is endemic to the Yaeyama region in Okinawa, subtropical Japan. Species of the P1 subclade “virulent” group, within the genus Leptospira, are the main etiological agents of leptospirosis in Okinawa. However, their environmental persistence is poorly understood. This study used a combination of bacterial isolation and environmental DNA (eDNA) metabarcoding methods to understand the eco-epidemiology of leptospirosis in this endemic region. Findings Polymerase chain reaction (PCR) characterized twelve human clinical L. interrogans isolates belonging to the P1 subclade “virulent” subgroup and 11 environmental soil isolates of the P1subclade “low virulent” subgroup (genetically related to L. kmetyi, n = 1; L. alstonii, n = 4; L. barantonii, n = 6) from the Yaeyama region targeting four virulence-related genes (lipL32, ligA, ligB and lpxD1). Clinical isolates were PCR positive for at least three targeted genes, while all environmental isolates were positive only for lipL32. Analysis of infected renal epithelial cells with selected clinical and environmental strains, revealed the disassembly of cell-cell junctions for the Hebdomadis clinical strain serogroup. Comparison of leptospiral eDNA during winter and summer identified operational taxonomic units corresponding to the species isolated from soil samples (L. kmetyi and L. barantonii) and additional P2 subclade species (L. licerasiae, L. wolffii-related, among others) that were not detected by soil cultivation. Total Leptospira read counts were higher in summer than in winter and the analysis of leptospiral/animal eDNA relationship suggested Rattus spp. as a potential reservoir animal. Conclusion Our study demonstrated high environmental Leptospira diversity in the Yaeyama region, particularly during summer, when most of the leptospirosis cases are reported. In addition, several Leptospira species with pathogenic potential were identified that have not yet been reported in Yaeyama; however, the environmental persistence of P1 subclade species previously isolated from human clinical cases in this region was absent, suggesting the need of further methodology development and surveillance. Leptospirosis is a widespread bacterial zoonosis and one of the most important acute febrile infectious disease in tropical and subtropical regions, which is difficult to differentiate from other infectious diseases common in these regions. Leptospirosis is endemic to Okinawa prefecture, the southernmost prefecture of Japan, where the infection occurs mainly after recreational activities in rivers in the northern part of Okinawa Main Island and the Yaeyama region. This study combined several methods such as bacterial isolation from soil and environmental DNA metabarcoding from river water samples to understand the persistence of Leptospira outside the human host, leptospiral diversity in the environment, and their potential reservoir animals in the wild environment of the Yaeyama region. Although this study didn’t confirm the environmental persistence of Leptospira species previously isolated from clinical cases, several newly reported Leptospira species with pathogenic potential from the Yaeyama region suggested the need for continual surveillance to improve leptospirosis control and prevention in this region.
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Affiliation(s)
- Yukuto Sato
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
| | - Idam Hermawan
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsuya Kakita
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Uruma-shi, Okinawa, Japan
| | - Sho Okano
- Department of Biological Sciences, Okinawa Prefectural Institute of Health and Environment, Uruma-shi, Okinawa, Japan
| | - Hideyuki Imai
- Department of Chemistry, Biology and Marine Science; Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Hiroto Nagai
- Department of Chemistry, Biology and Marine Science; Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
- United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
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14
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Tanaka T, Ariya M, Ueda S, Kimura R, Hayakawa R, Suzuki H, Kuroishi K, Hamamura K, Oyaidu T, Moriki T. [Hemobilia due to ruptured superior pancreaticoduodenal pseudoaneurysm after chemoradiotherapy for pancreatic head cancer: an autopsy case report]. Nihon Shokakibyo Gakkai Zasshi 2022; 119:768-775. [PMID: 35944995 DOI: 10.11405/nisshoshi.119.768] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A 78-year-old man came to our department because of obstructive jaundice, and was diagnosed as pancreatic head cancer. He underwent chemoradiation therapy. A metal stent was inserted into the common bile duct and the patient was followed up on an outpatient basis. The patient visited our emergency department 46 days after stent insertion due to abdominal pain. The patient was diagnosed with ruptured pseudoaneurysm of the superior pancreaticoduodenal artery by angiography and treated with coil embolization. He died due to sudden deterioration the next day. Pathological autopsy revealed that the cause of the ruptured pseudoaneurysm appeared to be vasculopathy due to radiation therapy.
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Affiliation(s)
- Toshio Tanaka
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | - Minori Ariya
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | - Shunsuke Ueda
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | - Ryosuke Kimura
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | | | - Hiroki Suzuki
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | - Kengo Kuroishi
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
| | | | - Tatsuki Oyaidu
- Department of Gastroenterology, Shizuoka City Shizuoka Hospital
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15
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Takeuchi H, Kimura R, Tomita H, Taki Y, Kikuchi Y, Ono C, Yu Z, Matsudaira I, Nouchi R, Yokoyama R, Kotozaki Y, Nakagawa S, Hanawa S, Iizuka K, Sekiguchi A, Araki T, Miyauchi CM, Ikeda S, Sakaki K, Dos S Kawata KH, Nozawa T, Yokota S, Magistro D, Imanishi T, Kawashima R. Polygenic risk score for bipolar disorder associates with divergent thinking and brain structures in the prefrontal cortex. Hum Brain Mapp 2021; 42:6028-6037. [PMID: 34587347 PMCID: PMC8596941 DOI: 10.1002/hbm.25667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 04/08/2021] [Revised: 08/26/2021] [Accepted: 09/13/2021] [Indexed: 11/11/2022] Open
Abstract
It has been hypothesized that a higher genetic risk of bipolar disorder (BD) is associated with greater creativity. Given the clinical importance of bipolar disorder and the importance of creativity to human society and cultural development, it is essential to reveal their associations and the neural basis of the genetic risk of bipolar disorder to gain insight into its etiology. However, despite the previous demonstration of the associations of polygenic risk score (PRS) of BD and creative jobs, the associations of BD‐PRS and creativity measured by the divergent thinking (CMDT) and regional gray matter volume (rGMV) as well as regional white matter volume (rWMV) have not been investigated. Using psychological analyses and whole‐brain voxel‐by‐voxel analyses, we examined these potential associations in 1558 young, typically developing adult students. After adjusting for confounding variables and multiple comparisons, a greater BD‐PRS was associated with a greater total CMDT fluency score, and a significant relationship was found in fluency subscores. A greater BD‐PRS was also associated with lower total mood disturbance. Neuroimaging analyses revealed that the BD‐PRS was associated with greater rGMV in the right inferior frontal gyrus, which is a consistently affected area in BD, as well as a greater rWMV in the left middle frontal gyrus, which has been suggested to play a central role in the increased creativity associated with the risk of BD with creativity. These findings suggest a relationship between the genetic risk of BD and CMDT and prefrontal cortical structures among young educated individuals.
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Affiliation(s)
- Hikaru Takeuchi
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yasuyuki Taki
- Division of Medical Neuroimaging Analysis, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Radiology and Nuclear Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Chiaki Ono
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | | | - Rui Nouchi
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Creative Interdisciplinary Research Division, Frontier Research Institute for Interdisciplinary Science, Tohoku University, Sendai, Japan.,Human and Social Response Research Division, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | | | - Yuka Kotozaki
- Division of Clinical research, Medical-Industry Translational Research Center, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Seishu Nakagawa
- Department of Human Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Division of Psychiatry, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Sugiko Hanawa
- Department of Human Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kunio Iizuka
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Sekiguchi
- Division of Medical Neuroimaging Analysis, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | - Carlos Makoto Miyauchi
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Shigeyuki Ikeda
- Department of Ubiquitous Sensing, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kohei Sakaki
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | | | - Takayuki Nozawa
- Research Center Institute for the Earth Inclusive Sensing Empathizing with Silent Voices, Tokyo Institute of Technology, Tokyo, Japan
| | - Susumu Yokota
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
| | - Daniele Magistro
- Department of Sport Science, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Tadashi Imanishi
- Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Ryuta Kawashima
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Ubiquitous Sensing, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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16
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Robbeets M, Bouckaert R, Conte M, Savelyev A, Li T, An DI, Shinoda KI, Cui Y, Kawashima T, Kim G, Uchiyama J, Dolińska J, Oskolskaya S, Yamano KY, Seguchi N, Tomita H, Takamiya H, Kanzawa-Kiriyama H, Oota H, Ishida H, Kimura R, Sato T, Kim JH, Deng B, Bjørn R, Rhee S, Ahn KD, Gruntov I, Mazo O, Bentley JR, Fernandes R, Roberts P, Bausch IR, Gilaizeau L, Yoneda M, Kugai M, Bianco RA, Zhang F, Himmel M, Hudson MJ, Ning C. Triangulation supports agricultural spread of the Transeurasian languages. Nature 2021; 599:616-621. [PMID: 34759322 PMCID: PMC8612925 DOI: 10.1038/s41586-021-04108-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 02/18/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Abstract
The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.
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Affiliation(s)
- Martine Robbeets
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Remco Bouckaert
- Max Planck Institute for the Science of Human History, Jena, Germany
- Centre of Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Matthew Conte
- Department of Archaeology and Art History, Seoul National University, Seoul, South Korea
| | - Alexander Savelyev
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia
| | - Tao Li
- Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeology, Wuhan University, Wuhan, China
- Archaeological Institute for Yangtze Civilization (AIYC), Wuhan University, Wuhan, China
| | - Deog-Im An
- Department of Conservation of Cultural Heritage, Hanseo University, Seosan, Korea
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
- Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun, China
| | | | - Geonyoung Kim
- Department of Archaeology and Art History, Seoul National University, Seoul, South Korea
| | - Junzo Uchiyama
- Sainsbury Institute for the Study of Japanese Arts and Cultures, Norwich, UK
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
| | - Joanna Dolińska
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sofia Oskolskaya
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Linguistic Studies, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Ken-Yōjiro Yamano
- Research Center for Buried Cultural Properties, Kumamoto University, Kumamoto, Japan
| | - Noriko Seguchi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
- Department of Anthropology, The University of Montana, Missoula, MT, USA
| | - Hirotaka Tomita
- Hokkaido Government Board of Education, Sapporo, Japan
- Graduate School of Integrated Sciences of Global Society, Kyushu University, Fukuoka, Japan
| | - Hiroto Takamiya
- Research Center for the Pacific Islands, Kagoshima University, Kagoshima, Japan
| | | | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Jae-Hyun Kim
- Department of Archaeology and Art History, Donga University, Busan, South Korea
| | - Bingcong Deng
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Rasmus Bjørn
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Seongha Rhee
- Hankuk University of Foreign Studies, Seoul, South Korea
| | - Kyou-Dong Ahn
- Hankuk University of Foreign Studies, Seoul, South Korea
| | - Ilya Gruntov
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Olga Mazo
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - John R Bentley
- Department of World Languages and Cultures, Northern Illinois University, DeKalb, IL, USA
| | - Ricardo Fernandes
- Max Planck Institute for the Science of Human History, Jena, Germany
- Faculty of Arts, Masaryk University, Brno, Czech Republic
- School of Archaeology, University of Oxford, Oxford, UK
| | - Patrick Roberts
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ilona R Bausch
- Sainsbury Institute for the Study of Japanese Arts and Cultures, Norwich, UK
- Leiden University Institute of Area Studies, Leiden, The Netherlands
- Kokugakuin University Museum, Tokyo, Japan
| | - Linda Gilaizeau
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Mitsugu Kugai
- Miyakojima City Board of Education, Miyakojima, Japan
| | - Raffaela A Bianco
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Marie Himmel
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mark J Hudson
- Max Planck Institute for the Science of Human History, Jena, Germany.
- Institut d'Asie Orientale, ENS de Lyon, Lyon, France.
| | - Chao Ning
- Max Planck Institute for the Science of Human History, Jena, Germany.
- School of Archaeology and Museology, Peking University, Beijing, China.
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17
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Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J. Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. BMC Ecol Evol 2021; 21:179. [PMID: 34551727 PMCID: PMC8456657 DOI: 10.1186/s12862-021-01900-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01900-y.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-0015, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tsukasa Inaoka
- Department of Human Ecology, Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Yasuhiro Matsumura
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, 253-8550, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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18
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Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K. Species divergence and repeated ancient hybridization in a Sulawesian lake system. J Evol Biol 2021; 34:1767-1780. [PMID: 34532915 DOI: 10.1111/jeb.13932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/17/2020] [Accepted: 09/09/2021] [Indexed: 01/02/2023]
Abstract
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.
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Affiliation(s)
- Ixchel F Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | | | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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19
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Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda A, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda KI, Hanihara T, Weber A, Kato H, Ishida H. Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan. Genome Biol Evol 2021; 13:6355032. [PMID: 34410389 PMCID: PMC8449830 DOI: 10.1093/gbe/evab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Accepted: 08/15/2021] [Indexed: 12/18/2022] Open
Abstract
Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.
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Affiliation(s)
- Takehiro Sato
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.,Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | | | - Hiromi Matsumae
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kentaro K Shimizu
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Andrzej Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada.,Research Centre "Baikal Region", Irkutsk State University, Irkutsk, Russia.,Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA) - UMR 7269, Aix-Marseille Université, Aix-en-Provence, France
| | - Hirofumi Kato
- Centre for Ainu and Indigenous Studies, Hokkaido University, Sapporo, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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20
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Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, Kitano J. Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae). Biol Lett 2021; 17:20210212. [PMID: 34343438 DOI: 10.1098/rsbl.2021.0212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hajime Yaguchi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Takeshi Kon
- Center for Strategic Research Project, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Wakayama, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Ken Maeda
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hau D Tran
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Noriyuki Koizumi
- Strategic Planning Headquarters, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Shinsuke Morioka
- Fisheries Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | - L K C Yun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | | | - V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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21
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Matsunami M, Koganebuchi K, Imamura M, Ishida H, Kimura R, Maeda S. Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago. Mol Biol Evol 2021; 38:2045-2056. [PMID: 33432348 PMCID: PMC8097307 DOI: 10.1093/molbev/msab005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis on genome-wide single-nucleotide polymorphisms, genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 single-nucleotide polymorphisms to infer population history within the Miyako Islands, including Miyakojima, Irabu, and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 − 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about seven generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.
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Affiliation(s)
- Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Kae Koganebuchi
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara-Cho, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara-Cho, Japan
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22
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Akita T, Kimura R, Akaguma S, Nagai M, Nakao Y, Tsugane M, Suzuki H, Oka JI, Yamashita C. Usefulness of cell-penetrating peptides and penetration accelerating sequence for nose-to-brain delivery of glucagon-like peptide-2. J Control Release 2021; 335:575-583. [PMID: 34116136 DOI: 10.1016/j.jconrel.2021.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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] [Received: 03/01/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/19/2023]
Abstract
Neuropeptides are expected as therapeutic drug candidates for central nervous system (CNS) disorders. Intracerebroventricular (i.c.v.) administration of glucagon-like peptide-2 (GLP-2) has an antidepressant-like effect not only in depression model mice but also in treatment-resistant depression model mice. However, because i.c.v. administration is very invasive, research is progressing on brain delivery using intranasal administration as a non-invasive method. After intranasal administration of the drug, there are two routes to the brain. That of direct delivery from the paracellular route of olfactory epithelium to the brain via the olfactory bulb has been studied, and that of systemic absorption via the paracellular route of respiratory epithelium has been put to practical use. The high degree of vascularization and permeability of the nasal mucosa enables drug delivery via the paracellular route that leads to systemic delivery. Therefore, suppressing systemic absorption may increase drug delivery to brain, so we focused on the transcellular route. We created a GLP-2 derivative by adding cell-penetrating peptides (CPP) and penetration accelerating sequences (PAS), which are reported to provide efficient intracellular uptake, to GLP-2. However, to deliver GLP-2 by the transcellular route, GLP-2 must not only be taken up into cells but also move out of the cells. We investigated in vitro and in vivo function of PAS-CPP-GLP-2 to enable the translocation of GLP-2 directly from the nose to the brain. Derivatization of PAS-CPP-GLP-2 prevented its degradation. In the evaluation of intracellular dynamics, PAS-CPP-GLP-2 enhanced cellular uptake by macropinocytosis with CPP and promoted escape from endosomal vesicles by PAS. This study also showed that PAS-CPP-GLP-2 can move out of cells. Furthermore, only this PAS-CPP-GLP-2 showed an antidepression-like effect within 20 min of intranasal administration. Intranasal administered PAS-CPP-GLP-2 surprisingly showed the effect at the same dose with i.c.v. administration, but intravenous administered PAS-CPP-GLP-2 did not show the effect. These results suggested that PAS-CPP-GLP-2 can be efficiently delivered from the nose to the CNS and show a pharmacological effect, demonstrating the usefulness of PAS and CPP for nose-to-brain delivery of GLP-2.
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Affiliation(s)
- Tomomi Akita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ryosuke Kimura
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Saki Akaguma
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mio Nagai
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yusuke Nakao
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mamiko Tsugane
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Jun-Ichiro Oka
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Chikamasa Yamashita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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23
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Kataoka K, Fujita H, Isa M, Gotoh S, Arasaki A, Ishida H, Kimura R. The human EDAR 370V/A polymorphism affects tooth root morphology potentially through the modification of a reaction-diffusion system. Sci Rep 2021; 11:5143. [PMID: 33664401 PMCID: PMC7933414 DOI: 10.1038/s41598-021-84653-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Morphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR 370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between the EDAR polymorphism and tooth root traits by using computed tomography images and identified that the effects of the EDAR variant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction-diffusion system. The computational study suggested that the complicated effects of the EDAR polymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction-diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.
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Affiliation(s)
- Keiichi Kataoka
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hironori Fujita
- Astrobiology Center, National Institutes of Natural Sciences, Tokyo, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate School for Advanced Studies), Aichi, Japan
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Shimpei Gotoh
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Akira Arasaki
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan.
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24
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Sato Y, Tsurui‐Sato K, Katoh M, Kimura R, Tatsuta H, Tsuji K. Population genetic structure and evolution of Batesian mimicry in Papilio polytes from the Ryukyu Islands, Japan, analyzed by genotyping-by-sequencing. Ecol Evol 2021; 11:872-886. [PMID: 33520172 PMCID: PMC7820160 DOI: 10.1002/ece3.7092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/11/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 01/03/2023] Open
Abstract
Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby receiving protection from predators. In some species exhibiting Batesian mimicry, nonmimetic individuals coexist as polymorphism in the same population despite the benefits of mimicry. In a previous study, we proposed that the abundance of mimics is limited by that of the models, leading to polymorphic Batesian mimicry in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. We found that their mimic ratios (MRs), which varied among the Islands, were explained by the model abundance of each habitat, rather than isolation by distance or phylogenetic constraint based on the mitochondrial DNA (mtDNA) analysis. In the present study, this possibility was reexamined based on hundreds of nuclear single nucleotide polymorphisms (SNPs) of 93 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations show significant correlation with the geographic distances, which was not evident by the mtDNA-based analysis. A partial Mantel test controlling for the present SNP-based genetic distances revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection interacting with model species shaped and maintained the mimetic polymorphism. Taken together, our results support the possibility that predation pressure, not isolation by distance or other neutral factors, is a major driving force of evolution of the Batesian mimicry in P. polytes from the Ryukyus.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Kaori Tsurui‐Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Mitsuho Katoh
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Kimura
- Department of Human Biology and AnatomyGraduate School of MedicineUniversity of the RyukyusOkinawaJapan
| | - Haruki Tatsuta
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Kazuki Tsuji
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
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25
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Nishikawa M, Honda M, Kimura R, Kobayashi A, Yamaguchi Y, Hori S, Kobayashi H, Kawamura H, Nakayama Y, Todate Y, Takano Y, Yamaguchi H, Hamada K, Iketani S, Seto I, Izumi Y, Seto K. The effects of intensive oral care before surgery for gastric cancer patients. Oral Dis 2020; 27:1847-1853. [PMID: 33191579 DOI: 10.1111/odi.13722] [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: 07/16/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Oral function management has been recognized as important strategy for preventing postoperative complications. In this historical cohort study, we focused on the patients who planed gastrectomy, and investigated the appropriate duration and frequency of preoperative oral care to prevent complications after surgery. METHODS Patients who planed surgery for gastric cancer between 2012 and 2018 were enrolled. We defined intensive oral care (IOC) as initial intervention at least three weeks before surgery and follow-up intervention within a week before surgery. As the primary outcome, the incidence of postoperative infectious complications was compared between the IOC and non-intensive oral care groups. RESULTS A total of 576 patients were enrolled, including 66 with IOC. The incidence of infectious complications was 2/66 (3.0%) in the IOC group and 64/510 (12.5%) in the non-intensive oral care group. After adjusting for confounding factors, patients with IOC exposure had a lower chance of developing postoperative infectious complications (odds ratio; 0.217, 0.051-0.927). CONCLUSIONS Intensive oral care can help prevent postoperative infectious complications after gastrectomy. These findings suggest that appropriate preoperative oral care includes at least two interventions: three weeks or more before and within one week before surgery.
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Affiliation(s)
- Mao Nishikawa
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Michitaka Honda
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Ryosuke Kimura
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Ayaka Kobayashi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Yuji Yamaguchi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Soshi Hori
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Hiroshi Kobayashi
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Hidetaka Kawamura
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Yujiro Nakayama
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Yukitoshi Todate
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan.,Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Yoshinao Takano
- Department of Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Hisashi Yamaguchi
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hamada
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan
| | - Susumu Iketani
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Ichiro Seto
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Yuichi Izumi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
| | - Kanichi Seto
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Fukushima, Japan
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26
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Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun Biol 2020; 3:437. [PMID: 32843717 PMCID: PMC7447786 DOI: 10.1038/s42003-020-01162-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 08/31/2019] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia. Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.
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Affiliation(s)
- Takashi Gakuhari
- Center for Cultural Resource Studies, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Kitasato University School of Medicine, Sagamihara, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Simon Rasmussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ryan Schmidt
- Kitasato University School of Medicine, Sagamihara, Japan
| | - Souichiro Mizushima
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Toshiyuki Tsurumoto
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Tetsuaki Wakebe
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Hiromi Shitara
- Department of Archaeology, The University of Tokyo, Tokyo, Japan
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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27
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Gamage CD, Sato Y, Kimura R, Yamashiro T, Toma C. Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka. PLoS Negl Trop Dis 2020; 14:e0008437. [PMID: 32701971 PMCID: PMC7377381 DOI: 10.1371/journal.pntd.0008437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Leptospirosis is one of the most significant zoonoses across the world not only because of its impact on human and animal health but also because of the economic and social impact on agrarian communities. Leptospirosis is endemic in Sri Lanka where paddy farming activities, the use of draught animals in agriculture, and peridomestic animals in urban and rural areas play important roles in maintaining the infection cycle of pathogenic Leptospira, especially concerning animals as a potential reservoir. In this study, an environmental DNA (eDNA) metabarcoding methodology was applied in two different agro-ecological regions of Sri Lanka to understand the eco-epidemiology of leptospirosis. Methodology/Principal findings Irrigation water samples were collected in Kandy District (wet zone mid-country region 2) and Girandurukotte, Badulla District (intermediate zone low-country region 2); and analysed for the presence of pathogenic Leptospira, associated microbiome and the potential reservoir animals. Briefly, we generated PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. The analysis of eDNA showed different environmental microbiomes in both regions and a higher diversity of Leptospira species circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenic Leptospira species associated with clinical cases such as L. interrogans was higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species including Arcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenic Leptospira. Conclusions/Significance Leptospirosis has been considered to be endemic in wet regions, consistently, leptospiral sequences were detected strongly in Kandy. The great Leptospira species diversity in Kandy observed in this study shows that the etiological agents of leptospirosis in Sri Lanka might be underestimated. Furthermore, our eDNA metabarcoding can be used to discriminate bacterial and animal species diversity in different regions and to explore environmental microbiomes to identify other associated bacterial pathogens in the environment. Leptospirosis is a widespread bacterial zoonosis with increasing importance due to its vast range of reservoir hosts. Early symptoms are shared by other infectious diseases common in tropical and sub-tropical regions, where the real burden and risk factors need to be known. In Sri Lanka, leptospirosis is mostly an occupational disease associated with freshwater or animal exposure in agriculture communities. Thus, there is a need for understanding the epidemiology of leptospirosis in agrarian regions of the country for developing better prevention and intervention strategies. In this study, we applied an environmental DNA metabarcoding methodology to understand the environmental microbiome, potential reservoir animals and the Leptospira species circulating in two different agro-ecological regions of Sri Lanka: Kandy (wet region mid-country region 2) and Girandurukotte (intermediate region low-country region 2). It is known that pathogenic Leptospira are excreted through the urine of reservoir animals in the environment, where they can persist in humid conditions. Congruently, this study showed a higher detection of pathogenic Leptospira in the environment of Kandy where the environmental microbiome showed a higher diversity than Girandurukotte. Potential animal reservoirs were also detected in samples positive for pathogenic Leptospira, suggesting that environmental DNA metabarcoding can provide important information for management and intervention strategies to control leptospirosis.
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Affiliation(s)
- Chandika D. Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Kandy, Sri Lanka
| | - Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
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28
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Isshiki M, Naka I, Watanabe Y, Nishida N, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Eddie R, Ohtsuka R, Ohashi J. Admixture and natural selection shaped genomes of an Austronesian-speaking population in the Solomon Islands. Sci Rep 2020; 10:6872. [PMID: 32327716 PMCID: PMC7181741 DOI: 10.1038/s41598-020-62866-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/31/2019] [Accepted: 03/16/2020] [Indexed: 11/24/2022] Open
Abstract
People in the Solomon Islands today are considered to have derived from Asian- and Papuan-related ancestors. Papuan-related ancestors colonized Near Oceania about 47,000 years ago, and Asian-related ancestors were Austronesian (AN)-speaking population, called Lapita, who migrated from Southeast Asia about 3,500 years ago. These two ancestral populations admixed in Near Oceania before the expansion of Lapita people into Remote Oceania. To understand the impact of the admixture on the adaptation of AN-speaking Melanesians in Near Oceania, we performed the genome-wide single nucleotide polymorphism (SNP) analysis of 21 individuals from Munda, the main town of the New Georgia Islands in the western Solomon Islands. Population samples from Munda were genetically similar to other Solomon Island population samples. The analysis of genetic contribution from the two different ancestries to the Munda genome revealed significantly higher proportions of Asian- and Papuan-related ancestries in the region containing the annexin A1 (ANXA1) gene (Asian component > 82.6%) and in the human leukocyte antigen (HLA) class II region (Papuan component > 85.4%), respectively. These regions were suspected to have undergone natural selection since the time of admixture. Our results suggest that admixture had affected adaptation of AN-speaking Melanesians in the Solomon Islands.
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Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-8540, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ricky Eddie
- National Gizo Hospital, Ministry of Health and Medical Services, P.O. Box 36, Gizo, Solomon Islands
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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29
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Nishikawa M, Honda M, Kimura R, Kobayashi A, Yamaguchi Y, Hori S, Kobayashi H, Waragai M, Kawamura H, Nakayama Y, Todate Y, Takano Y, Yamaguchi H, Hamada K, Iketani S, Seto I, Izumi Y, Seto K. The bacterial association with oral cavity and intra-abdominal abscess after gastrectomy. PLoS One 2020; 15:e0242091. [PMID: 33166362 PMCID: PMC7652288 DOI: 10.1371/journal.pone.0242091] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Perioperative oral management has been reported to be effective for preventing postoperative infectious complications. In addition, severe periodontal disease was identified as the significant risk factor for complications after gastrointestinal surgery. We investigated the bacteriological association between the periodontal pocket, stomach mucosa and drainage fluid to determine whether oral bacteria directly cause intra-abdominal infection after gastrectomy. METHODS Patients who were scheduled to undergo surgery for gastric cancer were prospectively enrolled. We evaluated the similarity of bacterial strains in periodontal pocket, stomach mucosa and fluid from drainage tube. Gingival crevicular fluid and dental plaque were collected from the periodontal pocket and cultured to detect bacteria. Specimens from the resected stomach were collected and used for bacterial culturing. Drainage fluid from the abdominal cavity was also cultured. RESULTS All of 52 patients were enrolled. In the periodontal pocket, α-Streptococcus spp., Neisseria sp., and Prevotella sp. were mainly detected. Bacterial cultures in the stomach mucosa were positive in 26 cases. In 20 cases (76.9%), the detected strains were the same as those in the periodontal pocket. Six patients had the postoperative intra-abdominal infection after gastrectomy, and the same bacterial strains was detected in both of drainage fluid and periodontal pocket in two patients with severe periodontal disease. CONCLUSIONS We found the bacteriological association that same strain detected in periodontal pocket, stomach and in intra-abdominal drainage fluid after gastrectomy in patients with periodontal disease.
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Affiliation(s)
- Mao Nishikawa
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Michitaka Honda
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
- * E-mail:
| | - Ryosuke Kimura
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Ayaka Kobayashi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Yuji Yamaguchi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Soshi Hori
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Hiroshi Kobayashi
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Mitsuru Waragai
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Hidetaka Kawamura
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Yujiro Nakayama
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Yukitoshi Todate
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Yoshinao Takano
- Department of Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Hisashi Yamaguchi
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Koichi Hamada
- Department of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Susumu Iketani
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Ichiro Seto
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Yuichi Izumi
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
| | - Kanichi Seto
- Department of Oral and Maxillofacial Surgery, Southern TOHOKU General Hospital, Koriyama, Fukushima, Japan
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Yoshida K, Liu Q, Yasue R, Wada S, Kimura R, Konishi T, Ogasawara M. Versatile and Enantioselective Preparation of Planar-Chiral Metallocene-Fused 4-Dialkylaminopyridines and Their Application in Asymmetric Organocatalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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)
- Kazuhiro Yoshida
- Department of Chemistry, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Qiang Liu
- Department of Natural Science, Graduate School of Science and Technology and Research Cluster on ″Innovative Chemical Sensing″, Tokushima University, Tokushima 770-8506, Japan
- Graduate School of Life Science, Hokkaido University, Kita-ku, Sapporo 001-0021, Japan
| | - Risa Yasue
- Department of Chemistry, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Shiro Wada
- Department of Chemistry, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Ryosuke Kimura
- Department of Chemistry, Graduate School of Science, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takuma Konishi
- Department of Natural Science, Graduate School of Science and Technology and Research Cluster on ″Innovative Chemical Sensing″, Tokushima University, Tokushima 770-8506, Japan
| | - Masamichi Ogasawara
- Department of Natural Science, Graduate School of Science and Technology and Research Cluster on ″Innovative Chemical Sensing″, Tokushima University, Tokushima 770-8506, Japan
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31
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Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K. Evidence for sympatric speciation in a Wallacean ancient lake. Evolution 2019; 73:1898-1915. [DOI: 10.1111/evo.13821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Nobu Sutra
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Junko Kusumi
- Faculty of Social and Cultural StudiesKyushu University Fukuoka 819‐0395 Japan
| | - Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Shingo Fujimoto
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | | | | | - Atsushi Toyoda
- Comparative Genomics LaboratoryNational Institute of Genetics Mishima 411‐8540 Japan
| | | | - Ryosuke Kimura
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
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32
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A Masengi KW, Mandagi IF, Manu L, Silooy F, Labaro IL, Masengi AWR, Sebua N, Masengi EIKG, Pinontoan B, Hutabarat Y, Hukom F, Iwata M, Abe Y, Sato Y, Kimura R, Yamahira K. Study on existence of the fisheries resources abundance by using environmental deoxyribonucleic acid (e-DNA) approach at fishing grounds in the Sulawesi Sea, Indonesia. ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1757-899x/567/1/012026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Koganebuchi K, Kimura R. Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits. Ann Hum Biol 2019; 46:354-366. [PMID: 31116031 DOI: 10.1080/03014460.2019.1582699] [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] [Indexed: 02/06/2023]
Abstract
Context: The Ryukyu Islands stretch across a southwestern area of the Japanese Archipelago. Because of their unique geographical and historical backgrounds, Ryukyuans have their own genetic and phenotypic characteristics, which have been disclosed in previous anthropological and biomedical studies. Objective: The history, peopling and biomedical and genetic characteristics of Ryukyuans are reviewed and future research directions are discussed. Conclusion: Morphological and genetic studies have suggested the complex demographic history of Ryukyuans and their relationships with other Asian populations. Knowledge of population formation processes is important to understand the distribution of pathogens. In viral infectious diseases, some strains that may be associated with disease symptoms are specific to Ryukyuans. Dramatic changes in diet have played an important role among Ryukyuans in terms of increases in lifestyle-related diseases and mortality risks. To achieve a better understanding of pathogenic disease factors, further integration of findings regarding the genetic and biomedical characteristics of the Ryukyuans is needed.
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Affiliation(s)
- Kae Koganebuchi
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus , Okinawa , Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus , Okinawa , Japan
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34
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Tsurui‐Sato K, Sato Y, Kato E, Katoh M, Kimura R, Tatsuta H, Tsuji K. Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan. Ecol Evol 2019; 9:5991-6002. [PMID: 31161014 PMCID: PMC6540699 DOI: 10.1002/ece3.5182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/29/2019] [Indexed: 11/23/2022] Open
Abstract
Batesian mimicry is a well-studied adaptation for predation avoidance, in which a mimetic species resembles an unpalatable model species. Batesian mimicry can be under positive selection because of the protection gained against predators, due to resemblance to unpalatable model species. However, in some mimetic species, nonmimetic individuals are present in populations, despite the benefits of mimicry. The mechanism for evolution of such mimetic polymorphism remains an open question. Here, we address the hypothesis that the abundance of mimics is limited by that of the models, leading to mimetic polymorphism. In addition, other forces such as the effects of common ancestry and/or isolation by distance may explain this phenomenon. To investigate this question, we focused on the butterfly, Papilio polytes, that exhibits mimetic polymorphism on multiple islands of the Ryukyus, Japan, and performed field surveys and genetic analysis. We found that the mimic ratio of P. polytes was strongly correlated with the model abundance observed on each of the five islands, suggesting negative frequency-dependent selection is driving the evolution of polymorphism in P. polytes populations. Molecular phylogenetic analysis indicated that the southern island populations are the major source of genetic diversity, and the middle and northern island populations arose by relatively recent migration. This view was also supported by mismatch distribution and Tajima's D analyses, suggesting a recent population expansion on the middle and northern islands, and stable population persistence on the southern islands. The frequency of the mimetic forms within P. polytes populations is thus explained by variations in the model abundance rather than by population structure. Thus, we propose that predation pressure, rather than neutral forces, have shaped the Batesian mimicry polymorphism in P. polytes observed in the Ryukyus.
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Affiliation(s)
- Kaori Tsurui‐Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Yukuto Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Emi Kato
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
| | - Mitsuho Katoh
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of MedicineUniversity of the RyukyusOkinawaJapan
| | - Haruki Tatsuta
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Kazuki Tsuji
- Department of Agro‐Environmental Sciences, Faculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
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35
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Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C. Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Sci Rep 2019; 9:6575. [PMID: 31024059 PMCID: PMC6484013 DOI: 10.1038/s41598-019-42978-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 12/20/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Leptospires, which cause the zoonotic disease leptospirosis, persist in soil and aqueous environments. Several factors, including rainfall, the presence of reservoir animals, and various abiotic and biotic components interact to influence leptospiral survival, persistence, and pathogenicity in the environment. However, how these factors modulate the risk of infection is poorly understood. Here we developed an approach using environmental DNA (eDNA) metabarcoding for detecting the microbiome, vertebrates, and pathogenic Leptospira in aquatic samples. Specifically, we combined 4 sets of primers to generate PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. Using our method to analyze the eDNA of leptospirosis-endemic areas in northern Okinawa, Japan, we found that the microbiota in each river shifted over time. Operating taxonomic units corresponding to pathogenic L. alstonii, L. kmetyi, and L. interrogans were detected in association with 12 nonpathogenic bacterial species. In addition, the frequencies of 11 of these species correlated with the amount of rainfall. Furthermore, 10 vertebrate species, including Sus scrofa, Pteropus dasymallus, and Cynops ensicauda, showed high correlation with leptospiral eDNA detection. Our eDNA metabarcoding method is a powerful tool for understanding the environmental phase of Leptospira and predicting human infection risk.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.,Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, 2-746 Asahimachi-dori, Chuo-ku, Niigata, 951-8122, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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36
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Kimura R, Shibata M, Koeda S, Miyagawa A, Yamamura H, Mizuno T. Development of New Antimicrobial Agents from Cationic PG-Surfactants Containing Oligo-Lys Peptides. Bioconjug Chem 2018; 29:4072-4082. [DOI: 10.1021/acs.bioconjchem.8b00693] [Citation(s) in RCA: 8] [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: 12/20/2022]
Affiliation(s)
- Ryosuke Kimura
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Masahide Shibata
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Shuhei Koeda
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Atsushi Miyagawa
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Hatsuo Yamamura
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku, Nagoya, Aichi 466-8555, Japan
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Ohashi J, Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R. Association study of CREBRF missense variant (rs373863828:G > A; p.Arg457Gln) with levels of serum lipid profile in the Pacific populations. Ann Hum Biol 2018; 45:215-219. [PMID: 29877158 DOI: 10.1080/03014460.2018.1461928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 10/14/2022]
Abstract
BACKGROUND A missense variant (rs373863828:G > A; p.Arg457Gln) of the CREBRF gene is strongly associated with a higher body mass index (BMI; kg/m2) in Polynesian populations. This variant has also been reported to be associated with lower total cholesterol in Samoans. AIM The aim of this study is to examine the association of rs373863828:G > A with levels of serum lipids in four Pacific populations. METHODS A total of 613 adult subjects were recruited from Tonga (Polynesians) and the Solomon Islands (Melanesians and Micronesians). Multiple regression analyses adjusted for age and sex were performed to examine the association of rs373863828 with levels of serum lipids in each population. RESULTS A significant association of rs373863828:G > A with lower level of HDL-cholesterol was detected in the Tonga population (β = -3.32 and p-value = 0.030). The expected change in HDL-cholesterol with respect to a single copy of the rs373863828-A allele was 3.32 mg/dL. However, the association between rs373863828-A and lower levels of HDL-cholesterol was not significant after further adjustment for BMI in the Tonga population (β = -2.32 and p-value = 0.13). CONCLUSIONS The rs373863828-A allele may not directly affect the level of serum HDL-cholesterol independent of BMI. To confirm the present findings, association studies with large sample sizes and functional analyses are required.
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Affiliation(s)
- Jun Ohashi
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Izumi Naka
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Takuro Furusawa
- b Graduate School of Asian and African Area Studies , Kyoto University , Kyoto , Japan
| | - Ryosuke Kimura
- c Department of Human Biology and Anatomy, Graduate School of Medicine , University of the Ryukyus , Nishihara , Japan
| | - Kazumi Natsuhara
- d Faculty of Nursing , The Japanese Red Cross Akita College of Nursing , Akita , Japan
| | - Taro Yamauchi
- e Faculty of Health Science , Hokkaido University , Sapporo , Japan
| | - Minato Nakazawa
- f Graduate School of Health Sciences , Kobe University , Kobe , Japan
| | - Takafumi Ishida
- a Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo , Japan
| | - Tsukasa Inaoka
- g Department of Human Ecology, Faculty of Agriculture , Saga University , Saga , Japan
| | - Yasuhiro Matsumura
- h Faculty of Health and Nutrition , Bunkyo University , Chigasaki , Japan
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Adel M, Yamaguchi T, Tomita D, Kim YI, Takahashi M, Nakawaki T, Hikita Y, Haga S, Nadim M, Kawaguchi A, Isa M, El-Kenany W, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R. Association between the FGFR1 rs13317 single nucleotide polymorphism and orbitale-nasion depth based on cephalometric images. J Hum Genet 2018; 63:901-909. [PMID: 29872111 DOI: 10.1038/s10038-018-0471-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 11/09/2022]
Abstract
The fibroblast growth factor receptor 1 (FGFR1) gene plays an important role in craniofacial morphogenesis. In our previous study, an association between FGFR1 single nucleotide polymorphisms (SNPs) and craniofacial morphology was demonstrated in Japanese and Korean subjects. The present study aimed to evaluate the relationship between a common FGFR1 SNP (rs13317) with craniofacial morphology, increasing the number of measurements and examining Egyptian subjects (n = 191) in addition to the Japanese (n = 211) and Korean (n = 226) subjects. Genotyping for rs13317 was performed using the TaqMan assay, and its associations with 81 craniofacial measurements derived from lateral and posteroanterior cephalograms were analyzed by multiple regression analysis controlling sex and facial size. The results from each of the populations were then statistically combined. In the Egyptian subjects, rs13317 was significantly associated with the nasion-orbitale depth (P = 0.00040), and a suggestive association was also observed in the Japanese (P = 0.037) and Korean subjects (P = 0.045). The combined analysis revealed that only the nasion-orbitale depth showed a significant association (P = 0.000062) and that several measurements showed a suggestive association. Our results strongly indicate that rs13317 is associated with a smaller depth between the nasion and orbitale, representing a relative protrusion of the cheekbones and retrusion of the nasal root. A similar characteristic is also observed in individuals with Pfeiffer syndrome, which is caused by a dysfunctional FGFR1 mutation.
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Affiliation(s)
- Mohamed Adel
- Department of Orthodontics, Showa University, Tokyo, Japan.,Department of Orthodontics, Suez Canal University, Ismailia, Egypt
| | | | - Daisuke Tomita
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Yong-Il Kim
- Department of Orthodontics, Dental Research Institute, Pusan National University Dental Hospital, Yangsan, South Korea
| | | | | | - Yu Hikita
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Shugo Haga
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Mohamed Nadim
- Department of Orthodontics, Suez Canal University, Ismailia, Egypt
| | - Akira Kawaguchi
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Walid El-Kenany
- Department of Orthodontics, Alexandria University, Alexandria, Egypt
| | - Abbadi A El-Kadi
- Department of Orthodontics, Suez Canal University, Ismailia, Egypt
| | - Soo-Byung Park
- Department of Orthodontics, Dental Research Institute, Pusan National University Dental Hospital, Yangsan, South Korea
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Koutaro Maki
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
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Kimura R, Sugita K, Goto H, Yamamoto O. A small nodule on the auricle. Clin Exp Dermatol 2018; 44:203-205. [PMID: 29851135 DOI: 10.1111/ced.13636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2018] [Indexed: 11/27/2022]
Affiliation(s)
- R Kimura
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Tottori University, Faculty of Medicine, Yonago, Japan
| | - K Sugita
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Tottori University, Faculty of Medicine, Yonago, Japan
| | - H Goto
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Tottori University, Faculty of Medicine, Yonago, Japan
| | - O Yamamoto
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Tottori University, Faculty of Medicine, Yonago, Japan
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Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R. Growth hormone receptor gene is related to root length and tooth length in human teeth. Angle Orthod 2018; 88:575-581. [PMID: 29667468 DOI: 10.2319/092917-659.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To examine the relationship between tooth length and growth hormone receptor (GHR) gene variants in a healthy Japanese population. MATERIALS AND METHODS The subjects consisted of 193 Japanese adults (69 men, 124 women), aged 13 to 56 years. Genomic DNA was extracted from saliva and genotyped GHR rs6184 and rs6180 variants using the Taqman genotyping. Computed tomography (CT) images were acquired using a dental cone-beam CT scanner and reconstructed using open-source OsiriX medical image processing software. The maxillary (upper; U) and mandibular (lower, L) central incisors (1), lateral incisors (2), canines (3), first premolars (4), second premolars (5), first molars (6), and second premolars (7) were evaluated. Teeth were assessed for crown height (CH), root length (RL), overall tooth length (C+R), and crown to root ratio (C/R). The relationships between GHR variants and CH, RL, C+R, and C/R were statistically examined. RESULTS The GHR variant rs6184 was associated with the root lengths and tooth length for the upper and lower lateral incisors and upper canines (U2 RL; U3 RL, C+R; L2 RL [ P < .05]). CONCLUSIONS The results indicate that the GHR rs6184 variant is associated with tooth length and ratio dimensions in a Japanese cohort. Further studies utilizing a larger sample size are needed to confirm this finding.
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Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R. Relationship between tooth length and three-dimensional mandibular morphology. Angle Orthod 2018; 88:403-409. [PMID: 29664333 DOI: 10.2319/103017-734.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To clarify the relationship between tooth length and three-dimensional mandibular morphology in a healthy Japanese population. MATERIALS AND METHODS This study included 181 Japanese adults: 66 men and 115 women. Cone-beam computed tomography (CBCT) images were acquired with a dentofacial cone-beam x-ray CT scanner. Tooth length was measured with open-source OsiriX medical image processing software. Crown height and root length were measured in the maxillary and mandibular central incisors, lateral incisors, canines, first premolars, second premolars, first molars, and second molars. Based on these measurements, principal component (PC) analysis was performed. The following measurements were used to assess three-dimensional mandibular morphology: CD-GO, GO-GN, RCD-LCD, RGO-LGO, RCP-LCP, and the gonial angle. Stepwise multiple regression analysis was performed to examine the associations between three-dimensional mandibular morphology and the patterns of crown and root lengths using the mandibular measurements as explanatory variables and each PC as the dependent variable. RESULTS CD-GO was positively associated with PC1, which represented overall tooth length. RGO-LGO was positively associated with PC2, whereas GO-GN, RCP-LCP, and gonial angle were negatively associated with PC2, which was the axis denoting relatively longer root (+) vs higher crown (-). Being female was associated with PC3, which was the axis denoting relatively longer posterior tooth (+) vs anterior tooth (-). CONCLUSIONS The present clinical study effectively used CBCT images and PC analysis to reveal significant correlations between tooth length and mandibular morphology in a modern human population, confirming in part the statement that "large teeth necessitate large jaws."
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Issiki M, Naka I, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J. Mitochondrial DNA variations in Austronesian-speaking populations living in the New Georgia Islands, the Western Province of the Solomon Islands. J Hum Genet 2017; 63:101-104. [DOI: 10.1038/s10038-017-0372-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/11/2023]
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Takeuchi F, Katsuya T, Kimura R, Nabika T, Isomura M, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Liu X, Saw WY, Mamatyusupu D, Yang W, Xu S, Teo YY, Kato N. The fine-scale genetic structure and evolution of the Japanese population. PLoS One 2017; 12:e0185487. [PMID: 29091727 PMCID: PMC5665431 DOI: 10.1371/journal.pone.0185487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/13/2017] [Indexed: 11/21/2022] Open
Abstract
The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.
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Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Minoru Isomura
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Xuanyao Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | | | - Yik-Ying Teo
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
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Tomita D, Yamaguchi T, Nakawaki T, Hikita Y, Adel M, Kim YI, Haga S, Takahashi M, Kawaguchi A, Isa M, Park SB, Ishida H, Maki K, Kimura R. Interferon regulatory factor 6 variants affect nasolabial morphology in East Asian populations. Arch Oral Biol 2017; 85:142-147. [PMID: 29065370 DOI: 10.1016/j.archoralbio.2017.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 06/13/2017] [Revised: 09/23/2017] [Accepted: 10/07/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The interferon regulatory factor 6 gene (IRF6) is one of the most conspicuous genes among a large number of candidate risk genes for non-syndromic cleft lip with or without cleft palate, which is considered to be a multifactorial defect. Variants of IRF6 are also suggested to affect normal craniofacial variations, especially in the area of the nose and the upper lip. In the present study, we used lateral cephalograms to establish the relationship between IRF6 and sagittal nasolabial morphology in healthy East Asian subjects. DESIGN Genomic DNA was extracted from 215 Japanese and 226 Korean individuals, and genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs17389541, rs642961, rs2013162, rs2235371, and rs7802. These SNPs were tested by multiple regression analyses for their association with craniofacial measurements obtained from lateral cephalometrics. RESULTS We detected a significant association between the derived variants, rs2013162 and rs2235371 and the distances between a facial bone plane indicated by distance from Nasion and Point A (NA plane) to soft tissue landmarks; the Subalare (NA-Sbal) and the Subnasale (NA-Sn) in the sagittal plane. CONCLUSION Our results indicate that IRF6 variants play an important role in the normal range of variation in nasolabial soft-tissue morphology.
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Affiliation(s)
- Daisuke Tomita
- Department of Orthodontics, Showa University, Tokyo, Japan.
| | | | | | - Yu Hikita
- Department of Orthodontics, Showa University, Tokyo, Japan.
| | - Mohamed Adel
- Department of Orthodontics, Showa University, Tokyo, Japan.
| | - Yong-Il Kim
- Department of Orthodontics, Pusan National University, Pusan, South Korea.
| | - Shugo Haga
- Department of Orthodontics, Showa University, Tokyo, Japan.
| | | | - Akira Kawaguchi
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
| | - Soo-Byung Park
- Department of Orthodontics, Pusan National University, Pusan, South Korea.
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
| | - Koutaro Maki
- Department of Orthodontics, Showa University, Tokyo, Japan.
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
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Hayasaka K, Ishida H, Kimura R, Nishimaki T. Spatial relationships of the bronchial arteries to the left recurrent laryngeal nerve in the sub-aortic arch area. Surg Today 2017; 48:346-351. [PMID: 28948403 DOI: 10.1007/s00595-017-1593-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 05/23/2017] [Accepted: 09/12/2017] [Indexed: 01/30/2023]
Abstract
PURPOSE To safely perform lymphadenectomy in the sub-aortic arch area during esophagectomy for esophageal cancer, we investigated the spatial relationships between the bronchial arteries (BAs) and the left recurrent laryngeal nerve (LRLN). METHODS For this macro-anatomical study, 72 cadavers were used. RESULTS Of the 195 dissected BAs, 15 (7.7%) arteries ran dorsally across the LRLN. Such a running pattern of the BA was found in 15 (20.8%) of the 72 cadavers. Fourteen (93.3%) of the 15 arteries ran anteriorly along the left side of the esophagus, and 13 (86.7%) passed further to the lateral side of the left main bronchus to reach the ventral surface of the tracheobronchus; we named this running pattern "Type III". Of the 51 arteries with the Type III pattern, 25.5% ran across the dorsal side of the LRLN. CONCLUSION Approximately 20% of the cadavers had BAs running dorsally to the LRLN in the sub-aortic arch area. Most of these arteries had the Type III pattern. One-quarter of the BAs with the Type III pattern showed this running pattern. Care must be practiced to safely perform lymphadenectomy for esophageal cancer in patients with Type III BAs.
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Affiliation(s)
- Ken Hayasaka
- Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan.
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan
| | - Tadashi Nishimaki
- Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan
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Akiyama T, Katsumura T, Nakagome S, Lee SI, Joh K, Soejima H, Fujimoto K, Kimura R, Ishida H, Hanihara T, Yasukouchi A, Satta Y, Higuchi S, Oota H. An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression. PLoS One 2017. [PMID: 28650999 PMCID: PMC5484468 DOI: 10.1371/journal.pone.0178373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Humans show various responses to the environmental stimulus in individual levels as “physiological variations.” However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05). The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P < 0.05), and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.
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Affiliation(s)
- Tokiho Akiyama
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biosciences, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Takafumi Katsumura
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Shigeki Nakagome
- Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Sang-il Lee
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Science, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Science, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Kazuma Fujimoto
- Department of Internal Medicine, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | - Akira Yasukouchi
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Shigekazu Higuchi
- Department of Human Science, Faculty of Design, Kyushu University, Minami-ku Fukuoka, Japan
- * E-mail: (SH); (HO)
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
- * E-mail: (SH); (HO)
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Furusawa T, Naka I, Yamauchi T, Natsuhara K, Eddie R, Kimura R, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J. Polymorphisms associated with a tropical climate and root crop diet induce susceptibility to metabolic and cardiovascular diseases in Solomon Islands. PLoS One 2017; 12:e0172676. [PMID: 28253292 PMCID: PMC5333831 DOI: 10.1371/journal.pone.0172676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/08/2017] [Indexed: 01/19/2023] Open
Abstract
The people of the Solomon Islands represent an Austronesian (AN)-speaking population's adaptation to a humid tropical environment and subsistence of tuberous crops. Genome-wide association studies (GWASs) of other populations (e.g. the Human Genome Diversity Project [HGDP]) have suggested the existence of genotypes adaptive to ecoregion, diet, and subsistence, and that those genotypes are also associated with metabolic and cardiovascular diseases. Recently, the incidence of non-communicable diseases has been increasing in the Solomon Islands. In the present study, we explored the association of genotypes adaptive to a tropical environment and tuberous crop diet with metabolic and cardiovascular conditions in rural and urban AN-speaking Melanesian and Micronesian populations of the Solomon Islands. A total of 561 participants were genotyped for single nucleotide polymorphisms (SNPs) potentially associated with a tropical environment (rs174570 and rs2237892) and a tuberous crop diet (rs162036, rs185819, and rs2722425). The results showed that the allele frequencies of the Solomon Islands populations adopted patterns similar to those in populations from other hot, tropical areas with a tuberous crop diet in previous studies. Furthermore, rs162036, rs185819, rs2237892, and rs2722425 were all strongly associated with one or more metabolic and cardiovascular conditions. The derived allele of rs2722425 (i.e. rs2722425-G) was significantly associated with an elevated LDL level (P = 0.000264) even after the significance level was adjusted for multiple testing (i.e., α = 0.0005). Our results suggest that the inhabitants of the Solomon Islands exhibit the effects of the tropical environment and tuberous crop diet on their allele frequencies, and that their susceptibility to metabolic and cardiovascular diseases is therefore considered to be associated with their environment and diet.
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Affiliation(s)
- Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
| | - Izumi Naka
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Taro Yamauchi
- Graduate School of Health Sciences, Hokkaido University, Hokkaido, Japan
| | | | - Ricky Eddie
- National Gizo Hospital, Ministry of Health and Medical Services, Gizo, Solomon Islands
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Minato Nakazawa
- Department of International Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Takafumi Ishida
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Jun Ohashi
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Yamaguchi T, Hosomichi K, Yano K, Kim YI, Nakaoka H, Kimura R, Otsuka H, Nonaka N, Haga S, Takahashi M, Shirota T, Kikkawa Y, Yamada A, Kamijo R, Park SB, Nakamura M, Maki K, Inoue I. Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing. Hum Genome Var 2017; 4:17005. [PMID: 28265457 PMCID: PMC5321669 DOI: 10.1038/hgv.2017.5] [Citation(s) in RCA: 14] [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: 10/04/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
Tooth agenesis is described as the absence of one or more teeth. It is caused by a failure in tooth development and is one of the most common human developmental anomalies. We herein report genomic analyses of selective mandibular incisor agenesis (SMIA) using exome sequencing. Two Japanese families with SMIA were subjected to exome sequencing, and family with sequence similarity 65 member A (FAM65), nuclear factor of activated T-cells 3 (NFATC3) and cadherin-related 23 gene (CDH23) were detected. In the follow-up study, 51 Japanese and 32 Korean sporadic patients with SMIA were subjected to exome analyses, and 18 reported variants in PAX9, AXIN2, EDA, EDAR, WNT10A, BMP2 and GREM2 and 27 variants of FAM65, NFATC3 and CDH23 were found in 38 patients. Our comprehensive genetic study of SMIA will pave the way for a full understanding of the genetic etiology of SMIA and provide targets for treatment.
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Affiliation(s)
- Tetsutaro Yamaguchi
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan; Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | | | - Yong-Il Kim
- Department of Orthodontics, School of Dentistry, Pusan National University , Busan, South Korea
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics , Shizuoka, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus , Okinawa, Japan
| | - Hirotada Otsuka
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Naoko Nonaka
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Shugo Haga
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Masahiro Takahashi
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Tatsuo Shirota
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Showa University , Tokyo, Japan
| | - Yoshiaki Kikkawa
- Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science , Tokyo, Japan
| | - Atsushi Yamada
- Department of Biochemistry, School of Dentistry, Showa University , Tokyo, Japan
| | - Ryutaro Kamijo
- Department of Biochemistry, School of Dentistry, Showa University , Tokyo, Japan
| | - Soo-Byung Park
- Department of Orthodontics, School of Dentistry, Pusan National University , Busan, South Korea
| | - Masanori Nakamura
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry , Tokyo, Japan
| | - Koutaro Maki
- Department of Orthodontics, School of Dentistry, Showa University , Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics , Shizuoka, Japan
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Adel M, Yamaguchi T, Tomita D, Nakawaki T, Kim YI, Hikita Y, Haga S, Takahashi M, Nadim MA, Kawaguchi A, Isa M, El-Kenany WH, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R. Contribution of FGFR1 Variants to Craniofacial Variations in East Asians. PLoS One 2017; 12:e0170645. [PMID: 28129408 PMCID: PMC5271310 DOI: 10.1371/journal.pone.0170645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/29/2016] [Indexed: 11/29/2022] Open
Abstract
FGFR1 plays an important role in the development of the nervous system as well as the regulation of the skeletal development and bone homeostasis. Mutations in FGFR1 genes affect skull development, specifically suture and synchondrosis, resulting in craniosynostosis and facial abnormalities. We examined subjects with normal skull morphology for genetic polymorphisms that might be associated with normal craniofacial variations. Genomic DNA was obtained from 216 Japanese and 227 Korean subjects. Four FGFR1 SNPs, namely, rs881301, rs6996321, rs4647905, and rs13317, were genotyped. These SNPs were tested for association with craniofacial measurements obtained from lateral and posteroanterior cephalometries, in which principle component analysis was performed to compress the data of the craniofacial measurements. We observed that SNPs rs13317 and rs6996321 were correlated with the overall head size and midfacial development, indicating that FGFR1 SNPs played crucial roles in the normal variation of human craniofacial morphology. Subjects with the derived alleles of SNPs rs13317 and rs6996321 had a small face and a facial pattern associated with a retruded midface and relatively wide-set eyes. These facial features were similar to but were milder than those of individuals with Pfeiffer syndrome, which is caused by a dysfunctional mutation in FGFR1.
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Affiliation(s)
- Mohamed Adel
- Department of Orthodontics, Showa University, Tokyo, Japan
- Department of Orthodontics, Suez Canal University, Ismailia, Egypt
| | | | - Daisuke Tomita
- Department of Orthodontics, Showa University, Tokyo, Japan
| | | | - Yong-Il Kim
- Department of Orthodontics, Dental Research Institute, Pusan National University Dental Hospital, Yangsan, South Korea
| | - Yu Hikita
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Shugo Haga
- Department of Orthodontics, Showa University, Tokyo, Japan
| | | | - Mohamed A. Nadim
- Department of Orthodontics, Suez Canal University, Ismailia, Egypt
| | - Akira Kawaguchi
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | | | | | - Soo-Byung Park
- Department of Orthodontics, Dental Research Institute, Pusan National University Dental Hospital, Yangsan, South Korea
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Koutaro Maki
- Department of Orthodontics, Showa University, Tokyo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TNB, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY. Characterising private and shared signatures of positive selection in 37 Asian populations. Eur J Hum Genet 2017; 25:499-508. [PMID: 28098149 DOI: 10.1038/ejhg.2016.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Philip J Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Worachart Lert-Itthiporn
- Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanrutai Chin-Inmanu
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tran Nguyen Bich Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Katie Anders
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina
| | - Yeun-Jun Chung
- Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | | | - RickTwee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sarah J Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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