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Kondo A, Takenaka Y, Fujiwara A, Takahashi S, Kitade-Miyayama M, Morifuji M, Kawashima M, Ishiguro N. Changes in the composition of molecular species of covalently bound and free ceramides [EOS], and their correlation with disease severity in atopic dermatitis. Exp Dermatol 2024; 33:e15025. [PMID: 38450766 DOI: 10.1111/exd.15025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 03/08/2024]
Abstract
Ceramides are major constituents of stratum corneum (SC) intercellular lipids involved in skin barrier function. The ratio of molecular species of ceramides and their correlation with disease severity was examined in patients with atopic dermatitis (AD). Thirty-eight patients with AD and 32 healthy controls (HCs) were assessed for transepidermal water loss, SC collection and clinical assessment. The ceramide content of different molecular species in the samples was quantified using high-performance liquid chromatography coupled with tandem mass spectrometry. Unsaturated acyl chains of both covalently bound and free ceramides [EOS] were higher in AD lesional skin than those in AD non-lesional or normal HC skin. The proportion of unsaturated acyl chains (C30:1, C32:1 and C34:1) was higher than other ceramide molecular species among covalently bound and free ceramides [EOS] in patients with AD. The proportion of unsaturated acyl chains in covalently bound ceramides was positively correlated with transepidermal water loss (r = 0.600) when considering the total number of non-lesional and lesional skin. Additionally, thymus and activation-regulated chemokine (TARC) showed a positive correlation with unsaturated acyl chains proportion in AD non-lesional (r = 0.676) and lesional (r = 0.503) skin. Our study is the first to show the increase in unsaturated acyl chains of both covalently bound and free ceramides [EOS] in lesional and non-lesional skin in AD for each molecular species. This increase is associated with dryness and impaired barrier function, which correlates with TARC levels, a marker for the degree of type 2 inflammation. We speculate that type 2 inflammation exacerbation leads to abnormal epidermal lipid metabolism in the skin of patients with AD.
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Affiliation(s)
- A Kondo
- Department of Dermatology, Tokyo Women's Medical University, Shinjuku-ku, Japan
| | - Y Takenaka
- Department of Dermatology, Tokyo Women's Medical University, Shinjuku-ku, Japan
| | - A Fujiwara
- Food Microbiology and Function Research Labs, Meiji Co., Ltd., Hachioji-city, Japan
| | - S Takahashi
- Food Microbiology and Function Research Labs, Meiji Co., Ltd., Hachioji-city, Japan
| | - M Kitade-Miyayama
- Food Microbiology and Function Research Labs, Meiji Co., Ltd., Hachioji-city, Japan
| | - M Morifuji
- Food Microbiology and Function Research Labs, Meiji Co., Ltd., Hachioji-city, Japan
| | - M Kawashima
- Tokyo Women's Medical University, Shinjuku-ku, Japan
| | - N Ishiguro
- Department of Dermatology, Tokyo Women's Medical University, Shinjuku-ku, Japan
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2
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Ohga H, Shibata K, Sakanoue R, Ogawa T, Kitano H, Kai S, Ohta K, Nagano N, Nagasako T, Uchida S, Sakuma T, Yamamoto T, Kim S, Tashiro K, Kuhara S, Gen K, Fujiwara A, Kazeto Y, Kobayashi T, Matsuyama M. Development of a chub mackerel with less-aggressive fry stage by genome editing of arginine vasotocin receptor V1a2. Sci Rep 2023; 13:3190. [PMID: 36823281 PMCID: PMC9950132 DOI: 10.1038/s41598-023-30259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Genome editing is a technology that can remarkably accelerate crop and animal breeding via artificial induction of desired traits with high accuracy. This study aimed to develop a chub mackerel variety with reduced aggression using an experimental system that enables efficient egg collection and genome editing. Sexual maturation and control of spawning season and time were technologically facilitated by controlling the photoperiod and water temperature of the rearing tank. In addition, appropriate low-temperature treatment conditions for delaying cleavage, shape of the glass capillary, and injection site were examined in detail in order to develop an efficient and robust microinjection system for the study. An arginine vasotocin receptor V1a2 (V1a2) knockout (KO) strain of chub mackerel was developed in order to reduce the frequency of cannibalistic behavior at the fry stage. Video data analysis using bioimage informatics quantified the frequency of aggressive behavior, indicating a significant 46% reduction (P = 0.0229) in the frequency of cannibalistic behavior than in wild type. Furthermore, in the V1a2 KO strain, the frequency of collisions with the wall and oxygen consumption also decreased. Overall, the manageable and calm phenotype reported here can potentially contribute to the development of a stable and sustainable marine product.
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Affiliation(s)
- Hirofumi Ohga
- grid.177174.30000 0001 2242 4849Aqua-Bioresource Innovation Center (ABRIC) Karatsu Satellite, Faculty of Agriculture, Kyushu University, Saga, 847-0132 Japan
| | - Koki Shibata
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Ryo Sakanoue
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Takuma Ogawa
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Hajime Kitano
- grid.410851.90000 0004 1764 1824Fishery Third Group, Marine Fisheries Research and Development Center, Japan Fisheries Research and Education Agency (FRA), Kanagawa, 221-8529 Japan
| | - Satoshi Kai
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Kohei Ohta
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Naoki Nagano
- grid.410849.00000 0001 0657 3887Laboratory of Aquaculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192 Japan
| | - Tomoya Nagasako
- grid.177174.30000 0001 2242 4849Human Interface Laboratory, Factory of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395 Japan
| | - Seiichi Uchida
- grid.177174.30000 0001 2242 4849Human Interface Laboratory, Factory of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395 Japan
| | - Tetsushi Sakuma
- grid.257022.00000 0000 8711 3200Molecular Genetics Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526 Japan
| | - Takashi Yamamoto
- grid.257022.00000 0000 8711 3200Molecular Genetics Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526 Japan
| | - Sangwan Kim
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Koichiro Gen
- Planning and Coordination Department, Fisheries Technology Institute, FRA, Nagasaki, 851-2213 Japan
| | - Atushi Fujiwara
- grid.410851.90000 0004 1764 1824Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, FRA, Mie, 516-0193 Japan
| | - Yukinori Kazeto
- Fisheries Technology Institute, Minamiizu Field Station, FRA, Shizuoka, 415-0156 Japan
| | - Takanori Kobayashi
- grid.410851.90000 0004 1764 1824Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, FRA, Kanagawa, 236-8648 Japan
| | - Michiya Matsuyama
- ABRIC, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan.
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Nishimura T, Fujimoto H, Fujiwara T, Ito K, Fujiwara A, Yuda H, Itani H, D'Alessandro-Gabazza C, Gabazza E, Kobayashi T. 1535P Efficacy and safety of amrubicin after treatment with immune checkpoint inhibitor combined with chemotherapy in extensive-stage small cell carcinoma: MiSSION1. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Li S, Coffinier Y, Lagadec C, Cleri F, Nishiguchi K, Fujiwara A, Fujii T, Kim SH, Clément N. Redox-labelled electrochemical aptasensors with nanosupported cancer cells. Biosens Bioelectron 2022; 216:114643. [PMID: 36030742 DOI: 10.1016/j.bios.2022.114643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022]
Abstract
The transfer of redox-labelled bioelectrochemical sensors from proteins to cells is not straightforward because of the cell downward force issue on the surface of the sensors. In this paper, 20-nm-thick nanopillars are introduced to overcome this issue, in a well-controlled manner. We show on both molecular dynamics simulations and experiments that suspending cells a few nanometers above an electrode surface enables redox-labelled tethered DNA aptamer probes to move freely, while remaining at an interaction distance from a target membrane protein, i. e. epithelial cell adhesion molecule (EpCAM), which is typically overexpressed in cancer cells. By this nanopillar configuration, the interaction of aptamer with cancer cells is clearly observable, with 13 cells as the lower limit of detection. Nanoconfinement induced by the gap between the electrode surface and the cell membrane appears to improve the limit of detection and to lower the melting temperature of DNA aptamer hairpins, offering an additional degree of freedom to optimize molecular recognition mechanisms. This novel nanosupported electrochemical DNA cell sensor scheme including Brownian-fluctuating redox species opens new opportunities for the design of all-electrical sensors using redox-labelled probes.
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Affiliation(s)
- S Li
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
| | - Y Coffinier
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - C Lagadec
- Univ. Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - F Cleri
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - T Fujii
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - S-H Kim
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - N Clément
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
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5
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Jonan S, Hamouda N, Fujiwara A, Iwata K, Fujita T, Kato S, Amagase K. Alleviative effects of glutamate against chemotherapeutic agent-induced intestinal mucositis. J Physiol Pharmacol 2022; 73. [PMID: 36696244 DOI: 10.26402/jpp.2022.4.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
5-Fluorouracil (5-FU) is one of the most widely used chemotherapeutic agents; however, it often causes intestinal mucositis with severe diarrhea. An efficient treatment strategy to reduce this side effect is lacking. Glutamate (Glu), a nonessential amino acid, is the most important energy source in the small intestine and has been shown to maintain intestinal morphology, barrier function, and antioxidative capacity. However, the effects of Glu on intestinal mucositis induced by chemotherapeutic agents have not been explored. This study aimed to demonstrate the alleviative effects of Glu on 5-FU-induced intestinal mucositis. Mucositis was induced in C57B/6N mice by intraperitoneal injection of 5-FU (50 mg/kg) for 6 days and assessed by histological and physiological analyses. Glu (500 or 1000 mg/kg) was orally administered as a pretreatment twice daily for 7 days before the initial treatment of 5-FU. Cellular proliferation and apoptosis were assessed using Ki-67 immunostaining and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, respectively. Furthermore, fluorescein isothiocyanate-dextran infiltration was assessed to measure intestinal permeability. In vitro experiments using rat intestinal epithelial cells (IEC-6 cells) were performed to clarify the effect of Glu on 5-FU-induced barrier dysfunction. Glu alleviated 5-FU-induced intestinal mucositis by reducing villi shortening, enhancing cell proliferation, and suppressing apoptosis. It also alleviated the 5-FU-induced increased intestinal permeability. In vitro studies revealed significantly increased trans-epithelial electrical resistance (TEER) in Glu-pretreated IEC-6 cells compared to that in 5-FU-treated and control cells. In conclusion, the findings of this study provide evidence for the potential of Glu to protect against 5-FU-induced intestinal mucositis in patients with cancer.
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Affiliation(s)
- S Jonan
- Laboratory of Pharmacology and Pharmacotherapeutics, Graduate School of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - N Hamouda
- Laboratory of Pharmacology and Pharmacotherapeutics, Graduate School of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - A Fujiwara
- Laboratory of Pharmacology and Pharmacotherapeutics, Graduate School of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - K Iwata
- Department of Pharmacology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - T Fujita
- Laboratory of Molecular Pharmacokinetics, College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - S Kato
- Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
| | - K Amagase
- Laboratory of Pharmacology and Pharmacotherapeutics, Graduate School of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan.
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6
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Nakamura Y, Higuchi K, Kumon K, Yasuike M, Takashi T, Gen K, Fujiwara A. Prediction of the Sex-Associated Genomic Region in Tunas ( Thunnus Fishes). Int J Genomics 2021; 2021:7226353. [PMID: 34957293 PMCID: PMC8693018 DOI: 10.1155/2021/7226353] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 11/17/2022] Open
Abstract
Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.
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Affiliation(s)
- Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Kentaro Higuchi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Kazunori Kumon
- Amami Field Station, Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 955-5 Hyousakiyamahara, Setouchi, Kagoshima 894-2414, Japan
| | - Motoshige Yasuike
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Toshinori Takashi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Koichiro Gen
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Atushi Fujiwara
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japan
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Shi YZ, Yoshida T, Fujiwara A, Nishiki I. Characterization of lsa(D), a Novel Gene Responsible for Resistance to Lincosamides, Streptogramins A, and Pleuromutilins in Fish Pathogenic Lactococcus garvieae Serotype II. Microb Drug Resist 2021; 27:301-310. [PMID: 32706619 DOI: 10.1089/mdr.2020.0218] [Citation(s) in RCA: 3] [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] [Indexed: 11/13/2022] Open
Abstract
Aims: Fish pathogenic Lactococcus garvieae serotype II has been isolated from cultured fish species in Japan. This study aimed to investigate the molecular mechanisms of lincomycin (LCM)-resistant L. garvieae serotype II and assess the molecular basis for lincosamides-streptogramins A-pleuromutilins (LSAP)-resistant phenotype. Results: We identified a novel lsa(D)-encoded 497-aa ATP-binding cassette F (ABC-F) protein in the LSAP-resistant strains. Amino acid identities of 41.25-54.73% were obtained between the deduced amino acids from Lsa(D) and other Lsa-type ABC-F proteins. Furthermore, comparative analysis revealed that the allele of lsa(D) with single point mutation at 233 aa position (TGG → TAG; tryptophan→premature termination codon [PTC]) in LSAP-sensitive strains. The minimum inhibitory concentrations of antimicrobials against the lsa(D) complementary strain and lsa(D)-disrupted mutant confirmed that lsa(D) conferred the LSAP-resistant phenotype. The reverse transcription-polymerase chain reaction could not detect the noncoding region of lsa(D) allelic variant in the LSAP-sensitive strains. Additionally, the PTC (TAG) in LCM-sensitive strains was replaced by TGG, CAG, or TAT in the laboratory-induced revertant mutants. Conclusions: The novel lsa(D) conferred the LSAP-resistant phenotype in clinically LCM-resistant L. garvieae serotype II strains. However, the allele of lsa(D) gene containing the PTC was found in L. garvieae serotype II, resulting in the LSAP-susceptible phenotype.
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Affiliation(s)
- Yin-Ze Shi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | | | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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Higuchi K, Kazeto Y, Ozaki Y, Yamaguchi T, Shimada Y, Ina Y, Soma S, Sakakura Y, Goto R, Matsubara T, Nishiki I, Iwasaki Y, Yasuike M, Nakamura Y, Matsuura A, Masuma S, Sakuma T, Yamamoto T, Masaoka T, Kobayashi T, Fujiwara A, Gen K. Author Correction: Targeted mutagenesis of the ryanodine receptor by Platinum TALENs causes slow swimming behaviour in Pacific bluefin tuna (Thunnus orientalis). Sci Rep 2020; 10:9351. [PMID: 32493909 PMCID: PMC7270151 DOI: 10.1038/s41598-020-65964-4] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Kentaro Higuchi
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, 851-2213, Japan.
| | - Yukinori Kazeto
- Kamiura Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, 879-2602, Japan
| | - Yuichi Ozaki
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, 519-0423, Japan
| | - Toshiya Yamaguchi
- Kamiura Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, 879-2602, Japan
| | - Yukinori Shimada
- Kamiura Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, 879-2602, Japan
| | - Yoshiaki Ina
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, 851-2213, Japan
| | - Satoshi Soma
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, 851-2213, Japan
| | - Yoshitaka Sakakura
- Organization for Marine Science and Technology, Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Rie Goto
- Nishiura Station, South Ehime Fisheries Research Center, Ehime University, Minamiuwa, Ehime, 798-4206, Japan
| | - Takahiro Matsubara
- Nishiura Station, South Ehime Fisheries Research Center, Ehime University, Minamiuwa, Ehime, 798-4206, Japan
| | - Issei Nishiki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuki Iwasaki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Aiko Matsuura
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Shukei Masuma
- Aquaculture Research Institute, Kindai University, Nishimuro, Wakayama, 649-2211, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsuji Masaoka
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, 519-0423, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 220-6115, Japan
| | - Atushi Fujiwara
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 220-6115, Japan
| | - Koichiro Gen
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, 851-2213, Japan
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9
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Matsuyama T, Takano T, Nishiki I, Fujiwara A, Kiryu I, Iinada M, Sakai T, Terashima S, Matsuura Y, Isowa K, Nakayasu C. Author Correction: A novel Asfarvirus-like virus identified as a potential cause of mass mortality of abalone. Sci Rep 2020; 10:8378. [PMID: 32409725 PMCID: PMC7225169 DOI: 10.1038/s41598-020-65515-x] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Tomomasa Matsuyama
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan.
| | - Tomokazu Takano
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | - Issei Nishiki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Research Center for Bioinformatics and Biosciences, Yokohama, Kanagawa, 2368648, Japan
| | - Atushi Fujiwara
- Japan Fisheries Research and Education Agency, Minato Mirai, Nishi-ku, Yokohama, Kanagawa, 2206115, Japan
| | - Ikunari Kiryu
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Diagnosis and Training Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | - Mari Iinada
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Diagnosis and Training Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | - Takamitsu Sakai
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | - Sachiko Terashima
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | - Yuta Matsuura
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
| | | | - Chihaya Nakayasu
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Research Center for Fish Diseases, Minami-Ise, Mie, 516-0193, Japan
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Kawato Y, Istiqomah I, Gaafar AY, Hanaoka M, Ishimaru K, Yasuike M, Nishiki I, Nakamura Y, Fujiwara A, Nakai T. A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages. Arch Virol 2019; 165:303-311. [PMID: 31786689 DOI: 10.1007/s00705-019-04485-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/26/2019] [Indexed: 01/21/2023]
Abstract
A novel jumbo bacteriophage (myovirus) is described. The lytic phage of Tenacibaculum maritimum, which is the etiological agent of tenacibaculosis in a variety of farmed marine fish worldwide, was plaque-isolated from seawater around a fish aquaculture field in Japan. The phage had an isometric head 110-120 nm in diameter, from which several 50- to 100-nm-long flexible fiber-like appendages emanate, and a 150-nm-long rigid contractile tail. The full genomes of the two representative phages (PTm1 and PTm5) were 224,680 and 226,876 bp long, respectively, both with 29.7% GC content, and the number of predicted open reading frames (ORFs) was 308 and 306, respectively. The average nucleotide sequence identity between PTm1 and PTm5 was 99.95%, indicating they are quite similar to each other. A genetic relationship was found in 15.0-16.6% of the predicted ORFs among the T. maritimum phages PTm1 and PTm5, the Tenacibaculum spp. phage pT24, and the Sphingomonas paucimobilis phage PAU. Phylogenetic analysis based on the terminase large subunit genes revealed that these four phages (PTm1, PTm5, pT24 and PAU) are more closely related than the other 10 jumbo myoviruses that have similar genome sizes. Transmission electron microscopy observations suggest that the head fibers of the T. maritimum phage function as tentacles to search and recognize the host cell surface to facilitate infection.
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Affiliation(s)
- Yasuhiko Kawato
- Nansei Main Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, Japan
| | - Indah Istiqomah
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Fisheries, Faculty of Agriculture, Gadjah Mada University, Yogyakarta, Indonesia
| | - Alkhateib Y Gaafar
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Veterinary Research Division, National Research Centre, Cairo, Egypt
| | - Makoto Hanaoka
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Katsuya Ishimaru
- Aquaculture Research Institute, Kindai University, Wakayama, Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.
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11
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Nagai S, Chen H, Kawakami Y, Yamamoto K, Sildever S, Kanno N, Oikawa H, Yasuike M, Nakamura Y, Hongo Y, Fujiwara A, Kobayashi T, Gojobori T. Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique. Harmful Algae 2019; 89:101660. [PMID: 31672234 DOI: 10.1016/j.hal.2019.101660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/10/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012-2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan.
| | - Hungyen Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, -12-17 Kandaizumicho, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 2926-1 Tanigawa, Misaki, Sen-Nan, Osaka, 599-0311, Japan
| | - Sirje Sildever
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuki Hongo
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
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12
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Hoai TD, Nishiki I, Fujiwara A, Yoshida T, Nakai T. Comparative genomic analysis of three lytic Lactococcus garvieae phages, novel phages with genome architecture linking the 936 phage species of Lactococcus lactis. Mar Genomics 2019; 48:100696. [PMID: 31301990 DOI: 10.1016/j.margen.2019.100696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/21/2019] [Accepted: 06/16/2019] [Indexed: 12/31/2022]
Abstract
To date, a number of bacteriophages that infect Lactococcus garvieae isolated from marine fish have been identified. However, the evolutionary insight between L. garvieae phages and other viral community have not yet been immersedly investigated. In this study, completed genomic sequence of phage PLgY-30 was obtained, a comparative analysis of three lytic phages, which have been using for phage typing and treatment of L. garvieae infecting marine fish, is conducted. The results revealed that the genomes of lytic phages specific for L. garvieae isolated from diseased marine fish share a high level of homology and almost all proteins are conserved. At genome level, no similarity was detected for either PLgY-30 or PLgY-16, while PLgW-1 shares only very limited homology (1%) with other sequences in Genbank database. In addition, the function of only 35% of ORFs in the PLgY-30 phage genomes could be predicted, demonstrating that it is novel phage. At protein level, lytic phage proteins shared a significant similarity to various proteins of global phage species isolated from dairy fermentation facilities that utilize L. lactis as a primary starter culture, called the 936 phage group. Genome organization and architecture of three lytic phages are also similar to that of the 936 phage group. To our knowledge, this is the first time lytic bacteriophages infecting L. garvieae from marine fish were characterized to genome level.
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Affiliation(s)
- Truong Dinh Hoai
- Faculty of Agriculture, University of Miyazaki, Gakuen kibanadai nishi 1-1, Miyazaki 889-2192, Japan; Faculty of Fisheries, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama 236-8648, Japan.
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama 236-8648, Japan
| | - Terutoyo Yoshida
- Faculty of Agriculture, University of Miyazaki, Gakuen kibanadai nishi 1-1, Miyazaki 889-2192, Japan
| | - Toshihiro Nakai
- Laboratory of Fish Pathology, Faculty of Applied Biological Science, Hiroshima University, Higashihiroshima 739-8528, Japan
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13
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Nishiki I, Yoshida T, Fujiwara A. Complete genome sequence and characterization of virulence genes in Lancefield group C Streptococcus dysgalactiae isolated from farmed amberjack (Seriola dumerili). Microbiol Immunol 2019; 63:243-250. [PMID: 31136000 DOI: 10.1111/1348-0421.12716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/19/2023]
Abstract
Lancefield group C Streptococcus dysgalactiae causes infections in farmed fish. Here, the genome of S. dysgalactiae strain kdys0611, isolated from farmed amberjack (Seriola dumerili) was sequenced. The complete genome sequence of kdys0611 consists of a single chromosome and five plasmids. The chromosome is 2,142,780 bp long and has a GC content of 40%. It possesses 2061 coding sequences and 67 tRNA and 6 rRNA operons. One clustered regularly interspaced short palindromic repeat, 125 insertion sequences, and four predicted prophage elements were identified. Phylogenetic analysis based on 126 core genes suggested that the kdys0611 strain is more closely related to S. dysgalactiae subsp. dysgalactiae than to S. dysgalactiae subsp. equisimilis. The genome of kdys0611 harbors 87 genes with sequence similarity to putative virulence-associated genes identified in other bacteria, of which 57 exhibit amino acid identity (>52%) to genes of the S. dysgalactiae subsp. equisimilis GGS124 human clinical isolate. Four putative virulence genes, emm5 (FGCSD_0256), spg_2 (FGCSD_1961), skc (FGCSD_1012), and cna (FGCSD_0159), in kdys0611 did not show significant homology with any deposited S. dysgalactiae genes. The chromosomal sequence of kdys0611 has been deposited in GenBank under Accession No. AP018726. This is the first report of the complete genome sequence of S. dysgalactiae isolated from fish.
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Affiliation(s)
- Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | | | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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14
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Miyoshi T, Umekawa T, Hosoda H, Asada T, Fujiwara A, Kurosaki KI, Shiraishi I, Nakai M, Nishimura K, Miyazato M, Kangawa K, Ikeda T, Yoshimatsu J, Minamino N. Plasma natriuretic peptide levels in fetuses with congenital heart defect and/or arrhythmia. Ultrasound Obstet Gynecol 2018; 52:609-616. [PMID: 29024133 DOI: 10.1002/uog.18925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/19/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE Diagnosing fetal heart failure remains challenging because it is difficult to know how well the fetal myocardium will perform as loading conditions change. In adult cardiology, natriuretic peptides (NPs) are established markers of heart failure. However, the number of studies investigating NP levels in fetuses is quite limited. The aim of this study was to evaluate the significance of plasma NP levels in the assessment of heart failure in fetuses with a congenital heart defect (CHD) and/or arrhythmia. METHODS This was a prospective observational study conducted at a tertiary pediatric cardiac center. A total of 129 singletons with CHD and/or arrhythmia and 127 controls were analyzed between 2012 and 2015. Umbilical cord plasma atrial NP, brain NP and N-terminal pro-brain NP levels at birth were compared with ultrasonography findings indicating fetal heart failure, such as cardiovascular profile (CVP) score and morphological characteristics. RESULTS Fetuses with CHD and/or arrhythmia had higher NP levels than did controls (P < 0.01). NP levels of fetuses with CHD and/or arrhythmia were correlated inversely with CVP score (P for trend < 0.01). No differences in NP levels were found in fetuses with CHD and/or arrhythmia and a CVP score of ≥ 8 in comparison to controls. Multivariate analysis showed that a CVP score of ≤ 5, tachy- or bradyarrhythmia at birth, preterm birth and umbilical artery pH < 7.15 were associated independently with high NP levels (P < 0.01). Among fetuses with a CVP score of ≤ 7, abnormal venous Doppler sonography findings were significantly more common and more severe in fetuses with tachy- or bradyarrhythmia than in those with CHD, and those with tachy- or bradyarrhythmia had higher NP levels than did those with CHD (P = 0.01). Fetuses with right-heart defect and moderate or severe tricuspid valve regurgitation had significantly higher NP levels than did fetuses with other types of CHD (P < 0.01). CONCLUSIONS Plasma NP levels in fetuses with CHD and/or arrhythmia are correlated with the severity of fetal heart failure. Elevated NP levels are attributed mainly to an increase in central venous pressure secondary to arrhythmia or atrioventricular valve regurgitation due to CHD, rather than to the morphological abnormality itself. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- T Miyoshi
- Department of Perinatology and Gynecology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - T Umekawa
- Department of Obstetrics and Gynecology, Mie University, Tsu, Japan
| | - H Hosoda
- Department of Regenerative Medicine and Tissue Engineering, National Cerebral and Cardiovascular Center, Suita, Japan
| | - T Asada
- Laboratory of Clinical Chemistry, National Cerebral and Cardiovascular Center, Suita, Japan
| | - A Fujiwara
- Laboratory of Clinical Chemistry, National Cerebral and Cardiovascular Center, Suita, Japan
| | - K I Kurosaki
- Department of Pediatric Cardiology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - I Shiraishi
- Department of Pediatric Cardiology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - M Nakai
- Department of Statistics and Data Analysis, Center for Cerebral and Cardiovascular Disease Information, National Cerebral and Cardiovascular Center, Suita, Japan
| | - K Nishimura
- Department of Statistics and Data Analysis, Center for Cerebral and Cardiovascular Disease Information, National Cerebral and Cardiovascular Center, Suita, Japan
| | - M Miyazato
- Department of Biochemistry, National Cerebral and Cardiovascular Center, Suita, Japan
| | - K Kangawa
- Department of Biochemistry, National Cerebral and Cardiovascular Center, Suita, Japan
| | - T Ikeda
- Department of Obstetrics and Gynecology, Mie University, Tsu, Japan
| | - J Yoshimatsu
- Department of Perinatology and Gynecology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - N Minamino
- Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Japan
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15
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Yasuike M, Iwasaki Y, Nishiki I, Nakamura Y, Matsuura A, Yoshida K, Noda T, Andoh T, Fujiwara A. The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract. DNA Res 2018; 25:547-560. [PMID: 30329019 PMCID: PMC6191305 DOI: 10.1093/dnares/dsy024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93.3%) were functionally annotated. Given our lack of knowledge of the yellowtail digestive system, and using the annotated draft genome as a reference, we conducted an RNA-Seq analysis of its three digestive organs (stomach, intestine and rectum). The RNA-Seq results highlighted the importance of certain genes in encoding proteolytic enzymes necessary for digestion and absorption in the yellowtail gastrointestinal tract, and this finding will accelerate development of formulated feeds for this species. Since this study offers comprehensive annotation of predicted protein-coding genes, it has potential broad application to our understanding of yellowtail biology and aquaculture.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazunori Yoshida
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tsutomu Noda
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tadashi Andoh
- Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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16
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Endo T, Sekino M, Fujiwara A, Sogabe A. Development and characterization of 19 novel microsatellite markers in the Pacific seaweed pipefish Syngnathus schlegeli using next-generation sequencing. Mol Biol Rep 2018; 45:2831-2834. [PMID: 30242666 DOI: 10.1007/s11033-018-4396-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
Abstract
Syngnathids (pipefishes, seahorses and seadragons) are vulnerable to human-mediated habitat perturbation. The Pacific seaweed pipefish Syngnathus schlegeli has a large distribution in the northwestern Pacific, where deterioration, loss and fragmentation of its seagrass habitat are occurring through coastal development. So far, few studies have been conducted to access the genetic structure and conservation status of S. schlegeli because of the low number of genetic markers currently described. Nineteen polymorphic microsatellite markers were developed for S. schlegeli using next-generation sequencing, and characterized in 32 individuals. The mean number of alleles was 14, with 2-28 alleles per locus. The estimates of observed heterozygosity (HO) and expected heterozygosity (HE) varied depending on the locus, ranging from 0.063 to 1.000, and from 0.062 to 0.969, respectively. Seventeen of the 19 microsatellites conformed to Hardy-Weinberg equilibrium. These new microsatellite markers should provide a wealth of information for studies on conservation genetics and the behavioral ecology of S. schlegeli.
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Affiliation(s)
- Takehiro Endo
- Graduate School of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
| | - Masashi Sekino
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atsushi Sogabe
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
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17
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Nomura K, Fujiwara A, Iwasaki Y, Nishiki I, Matsuura A, Ozaki A, Sudo R, Tanaka H. Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica). PLoS One 2018; 13:e0201784. [PMID: 30157280 PMCID: PMC6114518 DOI: 10.1371/journal.pone.0201784] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 07/23/2018] [Indexed: 01/31/2023] Open
Abstract
The Japanese eel (Anguilla japonica) is among the most important aquaculture fish species in Eastern Asia. The present study aimed to identify the genetic parameters underlying body size and the timing at metamorphosis from leptocephali to glass eels in captive-bred Japanese eels, with the intent to foster sustainable development. Larvae from a partly factorial cross (14 sires × 11 dams) were reared until the point of metamorphosis into glass eels. In these organisms, we observed moderate heritability and mild genetic correlations among traits related to body size (h2 = 0.16–0.33) and timing at metamorphosis (h2 = 0.36–0.41). In an F1 full-sib family, quantitative trait loci (QTL) mapping for these traits identified one significant (genome-wide P < 0.05) and five suggestive QTLs (chromosome-wide P < 0.05). These results suggest that in the Japanese eel, metamorphic traits exhibit a polygenic genetic structure comprising many QTLs with small effects. In addition, we updated the genetic linkage map for the Japanese eel and integrated it with our newly constructed de novo genome assembly. The information and tools generated from this study will contribute to the development of freshwater eel genetics and genomics.
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Affiliation(s)
- Kazuharu Nomura
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
- * E-mail:
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Ryusuke Sudo
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Hideki Tanaka
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
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18
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Nishiki I, Minami T, Murakami A, Hoai TD, Fujiwara A. Multilocus sequence analysis of Vibrionaceae isolated from farmed amberjack and the development of a multiplex PCR assay for the detection of pathogenic species. J Fish Dis 2018; 41:1295-1301. [PMID: 29882274 DOI: 10.1111/jfd.12823] [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] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Since 2011, high mortality rates and symptoms consistent with vibriosis have been observed in farmed amberjack (Seriola dumerili) in Japan. To identify 41 strains isolated from diseased amberjack, a multilocus sequence analysis using nine concatenated genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) was conducted. Twenty-seven strains were identified as Vibrio harveyi, suggesting an epidemic of V. harveyi infection in amberjack farms. Other strains were identified as Vibrio anguillarum, Vibrio owensii and Photobacterium damselae subsp. damselae. To develop an efficient diagnostic method for vibriosis in amberjack, a multiplex PCR system was developed to identify V. anguillarum, V. harveyi and P. damselae subsp. damselae. The method successfully discriminated between these three bacterial species, with amplification products of 350 bp for V. anguillarum, 545 bp for V. harveyi and 887 bp for P. damselae subsp. damselae and can be used for diagnosis in aquaculture farms.
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Affiliation(s)
- Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Takayuki Minami
- Miyazaki Prefectural Fisheries Research Institute, Miyazaki, Japan
| | - Ayana Murakami
- Advanced Technology Development Center, Kyoritsu Seiyaku Corporation, Tsukuba, Japan
| | - Truong Dinh Hoai
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Faculty of Fisheries, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
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Matsubara K, Iwasaki Y, Nishiki I, Nomura K, Fujiwara A. Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing. PLoS One 2018; 13:e0197040. [PMID: 29738551 PMCID: PMC5940218 DOI: 10.1371/journal.pone.0197040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/17/2017] [Accepted: 04/25/2018] [Indexed: 11/18/2022] Open
Abstract
Japanese eel (Anguilla japonica) constitutes one of the most important food fish in Japan; accordingly, genome sequencing and linkage mapping have been conducted for the purpose of artificial cultivation. In the next stage, integration of genomic sequences within linkage groups (LG) is required to construct higher-resolution genetic markers for quantitative trait loci mapping and selective breeding of beneficial traits in farming. In order to identify LG1-linked scaffolds from the draft genome assembly (323,776 scaffolds) reported previously, we attempted to isolate chromosomes corresponding to LG1 by flow sorting and subsequent analyses. Initially, single chromosomes were randomly collected by chromosome sorting and subjected to whole-genome amplification (WGA). A total of 60 WGA samples were screened by PCR with primers for a known LG1-linked scaffold, and five positive WGA samples were sequenced by next-generation sequencing (NGS). Following reference mapping analysis of the NGS reads, four of the five WGA samples were found to be enriched by LG1-linked sequences. These samples were cytogenetically assigned to chromosome 5 by fluorescence in situ hybridization. Using blastn searches with 82,081 contigs constructed from the NGS reads of the four WGA samples as queries, 2323 scaffolds were identified as putative LG1-linked scaffolds from the draft genome assembly. The total length of the putative LG1-linked scaffolds was 99.0 Mb, comparable to the estimated DNA amounts of chromosome 5 (91.1 Mb). These results suggest that the methodology developed herein is applicable to isolate specific chromosome DNAs and integrate unanchored scaffold sequences onto a particular LG and chromosome even in teleost fishes, in which isolation of specific chromosomes by flow sorting is generally difficult owing to similar morphologies, sizes, and GC-contents among chromosomes in the genome. The putative LG1-linked scaffolds of Japanese eel contain a total of 6833 short tandem repeats which will be available for higher-resolution linkage mapping.
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Affiliation(s)
- Kazumi Matsubara
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazuharu Nomura
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail:
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Matsuyama T, Sano N, Takano T, Sakai T, Yasuike M, Fujiwara A, Kawato Y, Kurita J, Yoshida K, Shimada Y, Nakayasu C. Antibody profiling using a recombinant protein–based multiplex ELISA array accelerates recombinant vaccine development: Case study on red sea bream iridovirus as a reverse vaccinology model. Vaccine 2018; 36:2643-2649. [DOI: 10.1016/j.vaccine.2018.03.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/14/2018] [Accepted: 03/22/2018] [Indexed: 01/10/2023]
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Sivakumarasamy R, Hartkamp R, Siboulet B, Dufrêche JF, Nishiguchi K, Fujiwara A, Clément N. Selective layer-free blood serum ionogram based on ion-specific interactions with a nanotransistor. Nat Mater 2018; 17:464-470. [PMID: 29403057 DOI: 10.1038/s41563-017-0016-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
Despite being ubiquitous in the fields of chemistry and biology, the ion-specific effects of electrolytes pose major challenges for researchers. A lack of understanding about ion-specific surface interactions has hampered the development and application of materials for (bio-)chemical sensor applications. Here, we show that scaling a silicon nanotransistor sensor down to ~25 nm provides a unique opportunity to understand and exploit ion-specific surface interactions, yielding a surface that is highly sensitive to cations and inert to pH. The unprecedented sensitivity of these devices to Na+ and divalent ions can be attributed to an overscreening effect via molecular dynamics. The surface potential of multi-ion solutions is well described by the sum of the electrochemical potentials of each cation, enabling selective measurements of a target ion concentration without requiring a selective organic layer. We use these features to construct a blood serum ionogram for Na+, K+, Ca2+ and Mg2+, in an important step towards the development of a versatile, durable and mobile chemical or blood diagnostic tool.
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Affiliation(s)
- R Sivakumarasamy
- Institute of Electronics, Microelectronics, and Nanotechnology, CNRS, University of Lille, Villeneuve d'Ascq, France
| | - R Hartkamp
- Process and Energy Department, Delft University of Technology, Delft, the Netherlands
| | - B Siboulet
- Institut de Chimie Separative de Marcoule ICSM, ICSM, CEA, CNRS, ENSCM, Montpellier University, Marcoule, Bagnols-sur-Ceze, France
| | - J-F Dufrêche
- Institut de Chimie Separative de Marcoule ICSM, ICSM, CEA, CNRS, ENSCM, Montpellier University, Marcoule, Bagnols-sur-Ceze, France
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Japan
| | - N Clément
- Institute of Electronics, Microelectronics, and Nanotechnology, CNRS, University of Lille, Villeneuve d'Ascq, France.
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Japan.
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Fujiwara A, Shintani Y, Funaki S, Kawamura T, Kanzaki R, Fukui E, Minami M, Okumura M. P1.02-068 Effects of Pirfenidone Targeting EMT and Tumor-Stroma Interaction as Novel Treatment for Non-Small Cell Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. Zoological Lett 2017; 3:18. [PMID: 29075512 PMCID: PMC5645911 DOI: 10.1186/s40851-017-0079-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. RESULTS In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. CONCLUSIONS Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.
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Affiliation(s)
- Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Seinen Chow
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Kenji Saitoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
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Matsuyama T, Yasuike M, Fujiwara A, Nakamura Y, Takano T, Takeuchi T, Satoh N, Adachi Y, Tsuchihashi Y, Aoki H, Odawara K, Iwanaga S, Kurita J, Kamaishi T, Nakayasu C. A Spirochaete is suggested as the causative agent of Akoya oyster disease by metagenomic analysis. PLoS One 2017; 12:e0182280. [PMID: 28771537 PMCID: PMC5542438 DOI: 10.1371/journal.pone.0182280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 03/26/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Mass mortality that is acompanied by reddish browning of the soft tissues has been occurring in cultured pearl oyster, Pinctada fucata martensii. The disease is called Akoya oyster disease (AOD). Although spreading pattern of the disease and transmission experiments suggest that the disease is infectious, the causative agent has not yet been identified. We used shotgun and 16S rRNA-based metagenomic analysis to identify genes that are present specifically in affected oysters. The genes found only in diseased oysters were mostly bacterial origin, suggesting that the causative agent was a bacterial pathogen. This hypothesis was supported by the inhibition of AOD development in naïve oysters injected with the hemolymph of diseased animals followed immediately with penicillin bath-administration. Further analyses of the hemolymph and mantle specifically and universally detected genes of bacteria that belong to phylum Spirochaetes in diseased pearl oysters but not in healthy oysters. By in situ hybridization or immunostaining, a Brachyspira-like bacterium was observed in the smears of hemolymph from affected oysters, but not from healthy oysters. Phylogenetic analysis using 16S rRNA sequences showed that the presumptive causative bacterium was outside of but most closely related to family Brachyspiraceae. We propose ‘Candidatus Maribrachyspira akoyae’ gen. nov, sp nov., for this bacterium.
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Affiliation(s)
- Tomomasa Matsuyama
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise, Mie, Japan
- * E-mail:
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Tomokazu Takano
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise, Mie, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yoshikazu Adachi
- Department of Biological production science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | | | - Hideo Aoki
- Mie Prefecture Fisheries Research Institute, Shima, Mie, Japan
| | - Kazushi Odawara
- Ehime Prefecture Fisheries Research Center, Uwajima, Ehime, Japan
| | - Shunsuke Iwanaga
- Nagasaki Prefectural Institute of Fisheries, Nagasaki, Nagasaki, Japan
| | - Jun Kurita
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise, Mie, Japan
| | - Takashi Kamaishi
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise, Mie, Japan
| | - Chihaya Nakayasu
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-Ise, Mie, Japan
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Shimada M, Imano H, Fujiwara A, Hashimoto T, Kato R, Ijiri Y, Izumi Y, Yoshiyama M, Hayashi T. P5147Direct factor Xa inhibition prevents cardiac remodeling induced by intermittent hypoxia through PAR-1/2 dual signaling pathway. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx493.p5147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
1. The E3 ubiquitin protein ligase 1 (WWP1) gene, the mutation of which causes muscular dystrophy in chickens, is expressed not only in the pectoral muscle, but also in a number of tissues such as the kidney. Therefore, this study examined some parameters related to kidney function in muscular dystrophic (MD) chickens. 2. Plasma osmolality, Na+ and K+ concentrations, aldosterone levels, and the expression of aquaporin (AQP) 2, AQP3, and α subunits of the amiloride-sensitive epithelial sodium channel (αENaC) were analysed in the kidneys of 5-week-old MD chickens and White Leghorn (WL) chickens under physiological conditions or after one day of water deprivation. 3. Plasma osmolality, Na+ concentrations, and plasma aldosterone levels were significantly higher in MD chickens than in WL chickens. αENaC mRNA expression levels were lower in MD chickens than in WL chickens. AQP2 and AQP3 mRNA expression levels were similar in the two strains of chickens. 4. Plasma osmolality correlated with aldosterone levels and AQP2 and αENaC mRNA levels in WL chickens. In MD chickens, plasma osmolality correlated with AQP2 mRNA levels, but not with plasma aldosterone or αENaC mRNA levels. 5. These results suggest that neither water reabsorption nor the expression of AQP2 and AQP3 is impaired in MD chickens and that a WWP1 gene mutation may or may not directly induce an abnormality in Na+-reabsorption in the kidneys of MD chickens, potentially through αENaC.
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Affiliation(s)
- N Saito
- a Laboratory of Animal Physiology, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan.,b Avian Bioresource Research Center, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - H Hirayama
- a Laboratory of Animal Physiology, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - K Yoshimura
- a Laboratory of Animal Physiology, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Y Atsumi
- b Avian Bioresource Research Center, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - M Mizutani
- b Avian Bioresource Research Center, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - K Kinoshita
- b Avian Bioresource Research Center, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - A Fujiwara
- c Laboratory Animal Research Station , Nippon Institute for Biological Science , Hokuto , Japan
| | - T Namikawa
- b Avian Bioresource Research Center, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
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Trasobares J, Rech J, Jonckheere T, Martin T, Aleveque O, Levillain E, Diez-Cabanes V, Olivier Y, Cornil J, Nys JP, Sivakumarasamy R, Smaali K, Leclere P, Fujiwara A, Théron D, Vuillaume D, Clément N. Estimation of π-π Electronic Couplings from Current Measurements. Nano Lett 2017; 17:3215-3224. [PMID: 28358215 DOI: 10.1021/acs.nanolett.7b00804] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The π-π interactions between organic molecules are among the most important parameters for optimizing the transport and optical properties of organic transistors, light-emitting diodes, and (bio-) molecular devices. Despite substantial theoretical progress, direct experimental measurement of the π-π electronic coupling energy parameter t has remained an old challenge due to molecular structural variability and the large number of parameters that affect the charge transport. Here, we propose a study of π-π interactions from electrochemical and current measurements on a large array of ferrocene-thiolated gold nanocrystals. We confirm the theoretical prediction that t can be assessed from a statistical analysis of current histograms. The extracted value of t ≈35 meV is in the expected range based on our density functional theory analysis. Furthermore, the t distribution is not necessarily Gaussian and could be used as an ultrasensitive technique to assess intermolecular distance fluctuation at the subangström level. The present work establishes a direct bridge between quantum chemistry, electrochemistry, organic electronics, and mesoscopic physics, all of which were used to discuss results and perspectives in a quantitative manner.
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Affiliation(s)
- J Trasobares
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - J Rech
- Aix Marseille University, Universite de Toulon, CNRS, CPT , 163 Avenue de Luminy, 13288 Marseille cedex 9, France
| | - T Jonckheere
- Aix Marseille University, Universite de Toulon, CNRS, CPT , 163 Avenue de Luminy, 13288 Marseille cedex 9, France
| | - T Martin
- Aix Marseille University, Universite de Toulon, CNRS, CPT , 163 Avenue de Luminy, 13288 Marseille cedex 9, France
| | - O Aleveque
- Université d'Angers, CNRS UMR 6200, Laboratoire MOLTECH-Anjou , 2 bd Lavoisier, 49045 Angers cedex, France
| | - E Levillain
- Université d'Angers, CNRS UMR 6200, Laboratoire MOLTECH-Anjou , 2 bd Lavoisier, 49045 Angers cedex, France
| | - V Diez-Cabanes
- Laboratory for Chemistry of Novel Materials, University of Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - Y Olivier
- Laboratory for Chemistry of Novel Materials, University of Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - J Cornil
- Laboratory for Chemistry of Novel Materials, University of Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - J P Nys
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - R Sivakumarasamy
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - K Smaali
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - P Leclere
- Laboratory for Chemistry of Novel Materials, University of Mons , Place du Parc 20, B-7000 Mons, Belgium
| | - A Fujiwara
- NTT Basic Research Laboratories, 3-1, Morinosato Wakamiya, Atsugi-shi, kanagawa 243-0198, Japan
| | - D Théron
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - D Vuillaume
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
| | - N Clément
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, University of Lille , Avenue Poincaré, BP60069, 59652, Villeneuve d'Ascq France
- NTT Basic Research Laboratories, 3-1, Morinosato Wakamiya, Atsugi-shi, kanagawa 243-0198, Japan
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Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 2017; 12:e0173198. [PMID: 28257489 PMCID: PMC5336288 DOI: 10.1371/journal.pone.0173198] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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] [Received: 11/18/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Yoshiko Shimahara
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan
| | - Takashi Kamaishi
- Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | | | - Satoshi Nagai
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masaya Katoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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Fujiwara A, Tokura K, Tome W, Kitai N. Multidirectional lip-closing force in adult females after short-term lip training. J Oral Rehabil 2016; 43:833-839. [DOI: 10.1111/joor.12430] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 11/30/2022]
Affiliation(s)
- A. Fujiwara
- Department of Orthodontics; School of Dentistry; Asahi University; Hozumi Gifu Japan
| | - K. Tokura
- Department of Orthodontics; School of Dentistry; Asahi University; Hozumi Gifu Japan
| | - W. Tome
- Department of Orthodontics; School of Dentistry; Asahi University; Hozumi Gifu Japan
| | - N. Kitai
- Department of Orthodontics; School of Dentistry; Asahi University; Hozumi Gifu Japan
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Fujiwara A, Komasawa N, Kido H, Kusaka Y, Minami T. Abstract PR538. Anesth Analg 2016. [DOI: 10.1213/01.ane.0000492921.03184.c0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yasuda G, Fujiwara A, Saka S, Hirawa N. SUN-P239: Effects of L-HISTIDINE Supplement on Treatment of Renal Anemia using Erythropoiesis-Stimulating Agents in Patients with Advanced Chronic Kidney Disease. Clin Nutr 2016. [DOI: 10.1016/s0261-5614(16)30582-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Fujiwara A, Komasawa N, Kido H, Kusaka Y, Minami T. Comparison of high and low pillow heights for tracheal tube intubation with the Pentax-AWS Airwayscope ® : a prospective randomized clinical trial. Br J Anaesth 2016; 117:132-3. [DOI: 10.1093/bja/aew158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nakamura Y, Yasuike M, Nishiki I, Iwasaki Y, Fujiwara A, Kawato Y, Nakai T, Nagai S, Kobayashi T, Gojobori T, Ototake M. V-GAP: Viral genome assembly pipeline. Gene 2016; 576:676-80. [DOI: 10.1016/j.gene.2015.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Uchino T, Nakamura Y, Sekino M, Kai W, Fujiwara A, Yasuike M, Sugaya T, Fukuda H, Sano M, Sakamoto T. Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.72010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ito K, Saiki H, Sakaguchi T, Hayashi K, Nishii Y, Watanabe F, Hataji O, Okano T, Naito M, Ibata H, Fujiwara A, Yoshida M, Itani H, Tanigawa M, Kobayashi H. 457P Background of patients (pts) with ALK rearranged (ALK+) non-small-cell lung cancer (NSCLC), and efficacy and safety of ALK inhibitors (ALK-Is) in actual clinical practice: Multicenter retrospective study. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv532.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yasuike M, Fujiwara A, Nakamura Y, Iwasaki Y, Nishiki I, Sugaya T, Shimizu A, Sano M, Kobayashi T, Ototake M. A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis. Gene 2015; 576:603-9. [PMID: 26477480 DOI: 10.1016/j.gene.2015.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
| | - Atushi Fujiwara
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoji Nakamura
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yuki Iwasaki
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Issei Nishiki
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Takuma Sugaya
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Akio Shimizu
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Motohiko Sano
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Takanori Kobayashi
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Mitsuru Ototake
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
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Tanabe AS, Nagai S, Hida K, Yasuike M, Fujiwara A, Nakamura Y, Takano Y, Katakura S. Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community. Mol Ecol Resour 2015; 16:402-14. [PMID: 26309223 DOI: 10.1111/1755-0998.12459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 08/05/2015] [Accepted: 08/21/2015] [Indexed: 11/27/2022]
Abstract
The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.
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Affiliation(s)
- Akifumi S Tanabe
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Satoshi Nagai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Kohsuke Hida
- AXIOHELIX Co. Ltd., 5-11 Kakozaki, Nihonbashi, Chuouku, Tokyo, 103-0015, Japan
| | - Motoshige Yasuike
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoshihito Takano
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Seiji Katakura
- City of Mombetsu, Kaiyo-koryukan, Kaiyo-koen, Mombetsu, Hokkaido, 094-0031, Japan
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Kato G, Takano T, Nishiki I, Kai W, Yasuike M, Nakamura Y, Fujiwara A, Sakai T, Matsuyama T, Nakayasu C. Expressed sequence tag analyses of three leukocyte subpopulations in ayu Plecoglossus altivelis altivelis, separated by monoclonal antibodies. Mar Genomics 2015; 23:123-32. [PMID: 26122836 DOI: 10.1016/j.margen.2015.06.011] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/20/2015] [Accepted: 06/22/2015] [Indexed: 11/25/2022]
Abstract
Ayu Plecoglossus altivelis altivelis are one of the most economically important fish for freshwater aquaculture in Japan. We conducted expressed sequence tag analyses of three leukocyte subpopulations, thrombocytes, neutrophils, and B lymphocytes in ayu using a next generation sequencer. The sequencing and de novo assembly yielded 22,494, 22,733, and 16,505 contigs from the thrombocyte, neutrophil, and B lymphocyte cDNA libraries, respectively. Pathways involving endocytosis, phagosomes, and lysosomes, were found in all three cDNA libraries using pathway analysis. The thrombocyte cDNA library contained 2894 unique sequences, including CXC chemokine receptor 4 and MHC class II. Cytokine and cytokine receptor genes such as interleukin (IL)-1β, IL-8, IL-1 receptor (IL-1R), IL-8RA, and IL-8RB were found among the 3056 unique sequences of the neutrophil cDNA library. Typical B lymphocyte related genes such as B cell linker protein, immunoglobulin (Ig) M, IgD and transforming growth factor β were found in the 1590 unique sequences of the B lymphocyte cDNA library. In summary, a large number of immune-related genes were identified from the three leukocyte cDNA libraries. Our results represent a valuable sequence resource for understanding the immune system function in ayu.
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Affiliation(s)
- Goshi Kato
- Tamaki Laboratory, National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruda, Tamaki, Mie 519-0423, Japan
| | - Tomokazu Takano
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minami-Ise, Mie 516-0193, Japan.
| | - Issei Nishiki
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Wataru Kai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Motoshige Yasuike
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoji Nakamura
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Atushi Fujiwara
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Takamitsu Sakai
- Tamaki Laboratory, National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruda, Tamaki, Mie 519-0423, Japan
| | - Tomomasa Matsuyama
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minami-Ise, Mie 516-0193, Japan
| | - Chihaya Nakayasu
- Tamaki Laboratory, National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruda, Tamaki, Mie 519-0423, Japan
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Renard VT, Piot BA, Waintal X, Fleury G, Cooper D, Niida Y, Tregurtha D, Fujiwara A, Hirayama Y, Takashina K. Valley polarization assisted spin polarization in two dimensions. Nat Commun 2015; 6:7230. [PMID: 26027889 PMCID: PMC4458877 DOI: 10.1038/ncomms8230] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 07/15/2014] [Accepted: 04/20/2015] [Indexed: 11/15/2022] Open
Abstract
Valleytronics is rapidly emerging as an exciting area of basic and applied research. In two-dimensional systems, valley polarization can dramatically modify physical properties through electron-electron interactions as demonstrated by such phenomena as the fractional quantum Hall effect and the metal-insulator transition. Here, we address the electrons' spin alignment in a magnetic field in silicon-on-insulator quantum wells under valley polarization. In stark contrast to expectations from a non-interacting model, we show experimentally that less magnetic field can be required to fully spin polarize a valley-polarized system than a valley-degenerate one. Furthermore, we show that these observations are quantitatively described by parameter-free ab initio quantum Monte Carlo simulations. We interpret the results as a manifestation of the greater stability of the spin- and valley-degenerate system against ferromagnetic instability and Wigner crystalization, which in turn suggests the existence of a new strongly correlated electron liquid at low electron densities.
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Affiliation(s)
- V. T. Renard
- Université Grenoble Alpes/CEA, INAC-SPSMS, F-38000, Grenoble, France
| | - B. A. Piot
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UJF-UPS-INSA-EMFL, 38042, Grenoble, France
| | - X. Waintal
- Université Grenoble Alpes/CEA, INAC-SPSMS, F-38000, Grenoble, France
| | - G. Fleury
- Service de Physique de l'État Condensé, DSM/IRAMIS/SPEC, CNRS UMR 3680 CEA Saclay, 91191 Gif sur Yvette, France
| | - D. Cooper
- Université Grenoble Alpes/CEA Leti Minatec campus, F-38054, Grenoble, France
| | - Y. Niida
- Graduate School of Science, Tohoku University, 6-3 Aramakiaza Aoba, Aobaku, Sendai, 980-8578, Japan
| | - D. Tregurtha
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - A. Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa, 243-0198, Japan
| | - Y. Hirayama
- Graduate School of Science, Tohoku University, 6-3 Aramakiaza Aoba, Aobaku, Sendai, 980-8578, Japan
| | - K. Takashina
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
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Mahboob I, Perrissin N, Nishiguchi K, Hatanaka D, Okazaki Y, Fujiwara A, Yamaguchi H. Dispersive and dissipative coupling in a micromechanical resonator embedded with a nanomechanical resonator. Nano Lett 2015; 15:2312-2317. [PMID: 25751406 DOI: 10.1021/nl5044264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A micromechanical resonator embedded with a nanomechanical resonator is developed whose dynamics can be captured by the coupled-Van der Pol-Duffing equations. Activating the nanomechanical resonator can dispersively shift the micromechanical resonance by more than 100 times its bandwidth and concurrently increase its energy dissipation rate to the point where it can even be deactivated. The coupled-Van der Pol-Duffing equations also suggest the possibility of self-oscillations. In the limit of strong excitation for the nanomechanical resonator, the dissipation in the micromechanical resonator can not only be reduced, resulting in a quality factor of >3× 10(6), it can even be eliminated entirely resulting in the micromechanical resonator spontaneously vibrating.
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Affiliation(s)
- I Mahboob
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - N Perrissin
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - D Hatanaka
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Y Okazaki
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - H Yamaguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
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Tadano R, Nunome M, Mizutani M, Kawahara-Miki R, Fujiwara A, Takahashi S, Kawashima T, Nirasawa K, Ono T, Kono T, Matsuda Y. Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing. Anim Genet 2014; 45:881-4. [PMID: 25287074 DOI: 10.1111/age.12227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2014] [Indexed: 11/29/2022]
Abstract
Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.
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Affiliation(s)
- R Tadano
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
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Kai W, Nomura K, Fujiwara A, Nakamura Y, Yasuike M, Ojima N, Masaoka T, Ozaki A, Kazeto Y, Gen K, Nagao J, Tanaka H, Kobayashi T, Ototake M. A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 2014; 15:233. [PMID: 24669946 PMCID: PMC3986909 DOI: 10.1186/1471-2164-15-233] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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: 11/21/2013] [Accepted: 03/17/2014] [Indexed: 12/30/2022] Open
Abstract
Background Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. Results We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. Conclusions The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.
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Affiliation(s)
| | | | - Atushi Fujiwara
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama-shi, Kanagawa 236-8648, Japan.
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Mahboob I, Mounaix M, Nishiguchi K, Fujiwara A, Yamaguchi H. A multimode electromechanical parametric resonator array. Sci Rep 2014; 4:4448. [PMID: 24658349 PMCID: PMC3963032 DOI: 10.1038/srep04448] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [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: 01/23/2014] [Accepted: 03/07/2014] [Indexed: 11/09/2022] Open
Abstract
Electromechanical resonators have emerged as a versatile platform in which detectors with unprecedented sensitivities and quantum mechanics in a macroscopic context can be developed. These schemes invariably utilise a single resonator but increasingly the concept of an array of electromechanical resonators is promising a wealth of new possibilities. In spite of this, experimental realisations of such arrays have remained scarce due to the formidable challenges involved in their fabrication. In a variation to this approach, we identify 75 harmonic vibration modes in a single electromechanical resonator of which 7 can also be parametrically excited. The parametrically resonating modes exhibit vibrations with only 2 oscillation phases which are used to build a binary information array. We exploit this array to execute a mechanical byte memory, a shift-register and a controlled-NOT gate thus vividly illustrating the availability and functionality of an electromechanical resonator array by simply utilising higher order vibration modes.
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Affiliation(s)
- I. Mahboob
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - M. Mounaix
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - K. Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - A. Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - H. Yamaguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
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Clément N, Nishiguchi K, Dufreche JF, Guerin D, Fujiwara A, Vuillaume D. Water electrolysis and energy harvesting with zero-dimensional ion-sensitive field-effect transistors. Nano Lett 2013; 13:3903-3908. [PMID: 23879333 DOI: 10.1021/nl4019879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The relationship of the gas bubble size to the size distribution critically influences the effectiveness of electrochemical processes. Several optical and acoustical techniques have been used to characterize the size and emission frequency of bubbles. Here, we used zero-dimensional (0D) ion-sensitive field-effect transistors (ISFETs) buried under a microbath to detect the emission of individual bubbles electrically and to generate statistics on the bubble emission time. The bubble size was evaluated via a simple model of the electrolytic current. We suggest that energy lost during water electrolysis could be used to generate electric pulses at an optimal efficiency with an array of 0D ISFETs.
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Affiliation(s)
- N Clément
- Institute of Electronics, Microelectronics and Nanotechnology, CNRS, Villeneuve d'Ascq, France.
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Clotet S, Soler MJ, Rebull M, Pascual J, Riera M, Kucher AG, Parastaeva MM, Beresneva ON, Ivanova GT, Zaraysky MI, Artemeva AV, Kaukov IG, Smirnov AV, Roszkowska-Chojecka M, Walkowska A, Gawrys O, Olszynski K, Kompanowska-Jezierska E, Walkowska A, Roszkowska-Chojecka M, Gawrys O, Baranowska I, Kompanowska-Jezierska EM, Roszkowska-Chojecka MM, Dobrowolski L, Badzynska B, Olszynski KH, Lipkowski AW, Sadowski J, Kobayashi Y, Hirawa N, Okuyama Y, Fujita M, Fujiwara A, Saka S, Yatsu K, Toya Y, Yasuda G, Umemura S, Oliveira-Sales EB, Maquigussa E, Semedo P, Pereira LG, Camara NOS, Bergamaschi CT, Campos RR, Boim MA, Potenza MA, Sirolli V, Addabbo F, Di Pietro N, Amoroso L, Pipino C, Pandolfi A, Montagnani M, Bonomini M, Quiroz YJ, Rivero M, Yaguas K, Moran L, Rodriguez-Iturbe B, Lee J, Heo NJ, Kim S, Joo KW, Han JS, Rapp W, Raab S, Sprecher U, Funk J, Apfel CM, Conde-Knape K, Qin Y, Mou L, Li X, Li X, Ilatovskaya ME, Andreev-Andrievsky AA, Pozdnev VF, Iliyn AV, Medvedeva NA, Malyszko J, Koc-Zorawska E, Zbroch E, Malyszko JS, Zorawski M, Mysliwiec M, Wakui H, Tamura K, Masuda SI, Tsurumi-Ikeya Y, Fujita M, Kanaoka T, Fujikawa T, Suzuki S, Kobayashi Y, Yabana M, Toya Y, Umemura S, Iimuro S, Imai E, Matsuo S, Watanabe T, Nitta K, Akizawa T, Makino H, Ohashi Y, Hishida A. Hypertension - experimental models. Nephrol Dial Transplant 2013. [DOI: 10.1093/ndt/gft128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tsuji T, Uruga T, Nitta K, Kawamura N, Mizumaki M, Suzuki M, Sekizawa O, Ishiguro N, Tada M, Ohashi H, Yamazaki H, Yumoto H, Koyama T, Senba Y, Takeuchi T, Terada Y, Nariyama N, Takeshita K, Fujiwara A, Goto S, Yamamoto M, Takata M, Ishikawa T. Development of Fast Scanning Microscopic XAFS Measurement System. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/430/1/012019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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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Fujiwara A, Kobayashi T, Kazato Y, Yayoshi N, Fujita M. Efficacy of hypofractionated radiotherapy for nasal tumours in 38 dogs (2005-2008). J Small Anim Pract 2013; 54:80-6. [PMID: 23373834 DOI: 10.1111/jsap.12024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To evaluate the efficacy of hypofractionated radiotherapy for canine nasal tumours, including the improvement in clinical signs, rate of complications and assessment of prognostic factors. METHODS Medical records of 38 dogs with malignant nasal tumours were reviewed, and those treated with a weekly schedule of hypofractionated radiotherapy were included in the study. Acute and late side effects were defined as complications noted either within 1 month or after 6 months of irradiation, respectively. Progression-free interval and overall survival were calculated using the Kaplan-Meier method. Log-rank test and Cox proportional hazard model were also performed. RESULTS Clinical signs improved in 30 of 36 dogs. Acute complications were seen in 28 of 36 dogs and were considered manageable. Late complications were observed in 17 of 30 dogs that survived 6 months or longer, but severe side effects were not observed. The median progression-free interval and overall survival was 245 days (95% CI: 127-512 days) and 512 days (95% CI: 203-820 days), respectively. Age, breed and presence of dyspnoea were negatively correlated with overall survival. CLINICAL SIGNIFICANCE These results suggest that hypofractionated radiotherapy could be a viable option for the treatment of nasal tumours in dogs that are not candidates for conventional multi-fractionated radiotherapy.
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Affiliation(s)
- A Fujiwara
- Department of Veterinary Radiology, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
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Abstract
An electromechanical resonator harboring an atomlike spectrum of discrete mechanical vibrations, namely, phonon modes, has been developed. A purely mechanical three-mode system becomes available in the electromechanical atom in which the energy difference of the two higher modes is resonant with a long-lived lower mode. Our measurements reveal that even an incoherent input into the higher mode results in coherent emission in the lower mode that exhibits all the hallmarks of phonon lasing in a process that is reminiscent of Brillouin lasing.
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Affiliation(s)
- I Mahboob
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
| | - H Yamaguchi
- NTT Basic Research Laboratories, NTT Corporation, Atsugi-shi, Kanagawa 243-0198, Japan
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Sakai K, Okada Y, Kitaoka S, Tsurumi J, Ohishi Y, Fujiwara A, Takimiya K, Takeya J. Anomalous pressure effect in heteroacene organic field-effect transistors. Phys Rev Lett 2013; 110:096603. [PMID: 23496736 DOI: 10.1103/physrevlett.110.096603] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/17/2012] [Indexed: 06/01/2023]
Abstract
Anomalous pressure dependent conductivity is revealed for heteroacene organic field-effect transistors of dinaphtho[2, 3-b:2', 3'-f]thieno[3, 2-b]thiophene single crystals in the direction of a and b crystallographic axes. In contrast to the normal characteristics of a monotonic increase in mobility μ with the application of external hydrostatic pressure P in conductors, we found that the present organic semiconductor devices exhibit nonmonotonic and gigantic pressure dependence including an even negative pressure coefficient dμ/dP. In combination with a structural analysis based on x-ray diffraction experiments under pressure, it is suggested that on-site molecular orientation and displacement peculiar in heteroacene molecules are responsible for the anomalous pressure effect.
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Affiliation(s)
- K Sakai
- ISIR, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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Yamaguchi K, Tsushima K, Kurita N, Fujiwara A, Soeda S, Yamaguchi A, Sugiyama S, Togashi Y, Kono Y, Kasagi S, Setoguchi Y. Clinical characteristics classified by the serum KL-6 level in patients with organizing pneumonia. Sarcoidosis Vasc Diffuse Lung Dis 2013; 30:43-51. [PMID: 24003534] [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: 06/02/2023]
Abstract
BACKGROUND The serum Krebs von der Lungen-6 (KL-6) level is a useful marker correlated with the severity of various interstitial lung diseases. There have been few reports about the clinical characteristics of organizing pneumonia (OP) associated with the serum KL-6 levels. OBJECTIVE This study was performed to determine whether the serum KL-6 levels can help determine the optimal treatment for OP. DESIGNS Patients diagnosed with OP by clinical, radiological and histopathological findings were retrospectively reviewed. The OP patients were classified into two groups based on their serum KL-6 levels: normal KL-6 and high KL-6 groups. The two groups were compared with regard to their clinical and radiological data and therapeutic response one month after the start of treatment. RESULTS The clinical records of twenty-two patients diagnosed with OP were reviewed. The serum KL-6 level was elevated in 11 of the 22 patients. There were no obvious differences in the clinical data between the two groups, although patients in the normal KL-6 group tended to have a fever. There were no significant differences in the chest X-ray (CXR) score or computed tomography (CT) score between the two groups. The CXR scores were correlated with the serum KL-6 levels. At 1 month after the diagnosis, 11 patients who needed treatment with prednisolone were included in the high KL-6 group. CONCLUSIONS Patients with normal KL-6 levels showed lower CXR and CT scores. The serum KL-6 level on admission is a useful marker to judge the need for corticosteroid treatment in OP patients.
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Affiliation(s)
- K Yamaguchi
- Department of Pulmonary Medicine, Tokyo Medical University,Tokyo, Japan
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