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Abe C, Shimatani K, Tsumura K, Takaguchi K, Nakayama Y, Hayashi T, Mori C, Suzuki N. Impact of COVID-19 on the mental health of primary schoolchildren during the later phase of the pandemic: A case report of an 18-month longitudinal survey in a Japanese primary school. Public Health Pract (Oxf) 2024; 7:100471. [PMID: 38328526 PMCID: PMC10847696 DOI: 10.1016/j.puhip.2024.100471] [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: 09/15/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
Background Drastic changes such as school closures and stay-at-home measures due to the global COVID-19 pandemic, may have long-term negative effects on children's mental health; however, longitudinal studies after 2021 are limited. This study aimed to observe the long-term effects of the COVID-19 pandemic on children's mental health by exploring changes in their mental health over a period of 18 months. Study design We conducted a longitudinal study at Chiba Prefecture in Japan, focusing on schoolchildren's mental health changes. Methods Data were obtained from the Strengths and Difficulties Questionnaire (SDQ) questionnaire conducted at single primary school three times from October 2021 to March 2023 which and included 183 participants. This study adopted a linear-mixed model to evaluate changes in children's SDQ scores, with sex and grade as the independent variables, and participants as a random effect. Results Regarding changes in SDQ scores, there were no significant changes in the total difficulty scores or in each subscale; Emotional Symptoms, Conduct Problems, Hyperactivity/Inattention, Peer Problems, and Prosocial Behavior. There was no statistically significant interaction between changes in SDQ scores and sex. Conclusions This report indicates that the impact of the COVID-19 pandemic on the mental health of Japanese primary schoolchildren was negligible in the later phase of the pandemic. However, the impact may differ from country to country owing to factors such as social restrictions during the COVID-19 pandemic.
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Affiliation(s)
- C. Abe
- Department of Architecture, Division of Creative Engineering, Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - K. Shimatani
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - K. Tsumura
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - K. Takaguchi
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - Y. Nakayama
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - T. Hayashi
- Department of Architecture and Urban Science, Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
| | - C. Mori
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba, 260-8670, Japan
| | - N. Suzuki
- Center for Preventive Medical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522, Japan
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Horiguchi G, Oyama R, Akabane T, Suzuki N, Katoh E, Mizokami Y, Noguchi K, Hirotsu N. Cooperation of an external carbonic anhydrase and HCO3- transporter supports underwater photosynthesis in submerged leaves of the amphibious plant Hygrophila difformis. Ann Bot 2024; 133:287-304. [PMID: 37832038 PMCID: PMC11005787 DOI: 10.1093/aob/mcad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND AIMS HCO3- can be a major carbon resource for photosynthesis in underwater environments. Here we investigate the underlying mechanism of uptake and membrane transport of HCO3- in submerged leaves of Hygrophila difformis, a heterophyllous amphibious plant. To characterize these mechanisms, we evaluated the sensitivity of underwater photosynthesis to an external carbonic anhydrase (CA) inhibitor and an anion exchanger protein inhibitor, and we attempted to identify components of the mechanism of HCO3- utilization. METHODS We evaluated the effects of the external CA inhibitor and anion exchanger protein inhibitor on the NaHCO3 response of photosynthetic O2 evolution in submerged leaves of H. difformis. Furthermore, we performed a comparative transcriptomic analysis between terrestrial and submerged leaves. KEY RESULTS Photosynthesis in the submerged leaves was decreased by both the external CA inhibitor and anion exchanger protein inhibitor, but no additive effect was observed. Among upregulated genes in submerged leaves, two α-CAs, Hdα-CA1 and Hdα-CA2, and one β-carbonic anhydrase, Hdβ-CA1, were detected. Based on their putative amino acid sequences, the α-CAs are predicted to be localized in the apoplastic region. Recombinant Hdα-CA1 and Hdβ-CA1 showed dominant CO2 hydration activity over HCO3- dehydration activity. CONCLUSIONS We propose that the use of HCO3- for photosynthesis in submerged leaves of H. difformis is driven by the cooperation between an external CA, Hdα-CA1, and an unidentified HCO3- transporter.
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Affiliation(s)
- Genki Horiguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
- Japan Society for the Promotion of Science, Chiyoda, Tokyo, Japan
| | - Ryoma Oyama
- Faculty of Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Etsuko Katoh
- Faculty of Food and Nutritional Sciences Life Sciences, Toyo University, Itakura, Gunma, Japan
| | - Yusuke Mizokami
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ko Noguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Naoki Hirotsu
- Faculty of Life Sciences, Toyo University, Itakura, Gunma, Japan
- Graduate School of Life Sciences, Toyo University, Itakura, Gunma, Japan
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3
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Chiba S, Suzuki N, Velasco L, Ayllón MA, Lee-Marzano SY, Sun L, Sabanadzovic S, Turina M. ICTV Virus Taxonomy Profile: Fusariviridae 2024. J Gen Virol 2024; 105:001973. [PMID: 38619867 PMCID: PMC11094367 DOI: 10.1099/jgv.0.001973] [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: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/16/2024] Open
Abstract
Fusariviridae is a family of mono-segmented, positive-sense RNA viruses with genome sizes of 5.9-10.7 kb. Most genomic RNAs are bicistronic, but exceptions have up to four predicted ORFs. In bicistronic genomes, the 5'-proximal ORF codes for a single protein with both RNA-directed RNA polymerase (RdRP) and RNA helicase (Hel) domains; little is known about the protein encoded by the second ORF. Fusarivirids do not appear to form virions. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Fusariviridae, which is available at ictv.global/report/fusariviridae.
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Affiliation(s)
- Sotaro Chiba
- Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0861, Japan
| | | | - Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Centro de Málaga, 29140 Malaga, Spain
| | | | | | - Liying Sun
- Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, PR China
| | | | - Massimo Turina
- Institute for Sustainable Plant Protection-CNR, Torino 10135, Italy
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4
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Akabane T, Suzuki N, Ikeda K, Yonezawa T, Nagatoishi S, Matsumura H, Yoshizawa T, Tsuchiya W, Kamino S, Tsumoto K, Ishimaru K, Katoh E, Hirotsu N. THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring. Sci Rep 2024; 14:6778. [PMID: 38514802 PMCID: PMC10958001 DOI: 10.1038/s41598-024-57506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance (19F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.
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Affiliation(s)
- Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuyoshi Ikeda
- Medicinal Chemistry Data Intelligence Unit, Drug Development Data Intelligence Platform Group, Medical Sciences Innovation Hub Program (MIH), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Satoru Nagatoishi
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Wataru Tsuchiya
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Satoshi Kamino
- CRYO SHIP Incorporated, 1-266-3, Sakuragi-cho, Omiya-ku, Saitama, Saitama, 330-0854, Japan
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Etsuko Katoh
- Department of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
| | - Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
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Ji L, Zhang Z, Liu S, Zhao L, Li Q, Xiao B, Suzuki N, Burks DJ, Azad RK, Xie G. The OsTIL1 lipocalin protects cell membranes from reactive oxygen species damage and maintains the 18:3-containing glycerolipid biosynthesis under cold stress in rice. Plant J 2024; 117:72-91. [PMID: 37753661 DOI: 10.1111/tpj.16470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023]
Abstract
Lipocalins constitute a conserved protein family that binds to and transports a variety of lipids while fatty acid desaturases (FADs) are required for maintaining the cell membrane fluidity under cold stress. Nevertheless, it remains unclear whether plant lipocalins promote FADs for the cell membrane integrity under cold stress. Here, we identified the role of OsTIL1 lipocalin in FADs-mediated glycerolipid remodeling under cold stress. Overexpression and CRISPR/Cas9 mediated gene edition experiments demonstrated that OsTIL1 positively regulated cold stress tolerance by protecting the cell membrane integrity from reactive oxygen species damage and enhancing the activities of peroxidase and ascorbate peroxidase, which was confirmed by combined cold stress with a membrane rigidifier dimethyl sulfoxide or a H2 O2 scavenger dimethyl thiourea. OsTIL1 overexpression induced higher 18:3 content, and higher 18:3/18:2 and (18:2 + 18:3)/18:1 ratios than the wild type under cold stress whereas the gene edition mutant showed the opposite. Furthermore, the lipidomic analysis showed that OsTIL1 overexpression led to higher contents of 18:3-mediated glycerolipids, including galactolipids (monoglactosyldiacylglycerol and digalactosyldiacylglycerol) and phospholipids (phosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol) under cold stress. RNA-seq and enzyme linked immunosorbent assay analyses indicated that OsTIL1 overexpression enhanced the transcription and enzyme abundance of four ω-3 FADs (OsFAD3-1/3-2, 7, and 8) under cold stress. These results reveal an important role of OsTIL1 in maintaining the cell membrane integrity from oxidative damage under cold stress, providing a good candidate gene for improving cold tolerance in rice.
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Affiliation(s)
- Lingxiao Ji
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengfeng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Shuang Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liyan Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Benze Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - David J Burks
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, USA
- Department of Mathematics, University of North Texas, Denton, Texas, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, USA
- Department of Mathematics, University of North Texas, Denton, Texas, 76203, USA
| | - Guosheng Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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6
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Suzuki N, Ikeda Y, Oomori G, Yamada S, Okuda T, Minami S. Gastrointestinal: Type 2 autoimmune pancreatitis diagnosed with endoscopic ultrasound-guided fine needle biopsy. J Gastroenterol Hepatol 2023. [PMID: 38159080 DOI: 10.1111/jgh.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Affiliation(s)
- N Suzuki
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
| | - Y Ikeda
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
| | - G Oomori
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
| | - S Yamada
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
| | - T Okuda
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
| | - S Minami
- Department of Gastroenterology, Oji General Hospital, Tomakomai, Hokkaido, Japan
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7
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Iida E, Kuriyama K, Tabara M, Takeda A, Suzuki N, Moriyama H, Fukuhara T. Structural features of T-DNA that induce transcriptional gene silencing during agroinfiltration. Plant Biotechnol (Tokyo) 2023; 40:289-299. [PMID: 38434119 PMCID: PMC10905568 DOI: 10.5511/plantbiotechnology.23.0719a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 03/05/2024]
Abstract
Agrobacterium tumefaciens (Rhizobium radiobacter) is used for the transient expression of foreign genes by the agroinfiltration method, but the introduction of foreign genes often induces transcriptional and/or post-transcriptional gene silencing (TGS and/or PTGS). In this study, we characterized the structural features of T-DNA that induce TGS during agroinfiltration. When A. tumefaciens cells harboring an empty T-DNA plasmid containing the cauliflower mosaic virus (CaMV) 35S promoter were infiltrated into the leaves of Nicotiana benthamiana line 16c with a GFP gene over-expressed under the control of the same promoter, no small interfering RNAs (siRNAs) were derived from the GFP sequence. However, siRNAs derived from the CaMV 35S promoter were detected, indicating that TGS against the GFP gene was induced. When the GFP gene was inserted into the T-DNA plasmid, PTGS against the GFP gene was induced whereas TGS against the CaMV 35S promoter was suppressed. We also showed the importance of terminator sequences in T-DNA for gene silencing. Therefore, depending on the combination of promoter, terminator and coding sequences on T-DNA and the host nuclear genome, either or both TGS and/or PTGS could be induced by agroinfiltration. Furthermore, we showed the possible involvement of three siRNA-producing Dicers (DCL2, DCL3 and DCL4) in the induction of TGS by the co-agroinfiltration method. Especially, DCL2 was probably the most important among them in the initial step of TGS induction. These results are valuable for controlling gene expression by agroinfiltration.
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Affiliation(s)
- Emi Iida
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Atsushi Takeda
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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8
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Igarashi K, Takei N, Hori T, Yamamoto M, Sohma H, Suzuki N, Tsutsumi H, Kawasaki Y, Kokai Y. Corrigendum to 'CCL8 deficiency in the host abrogates early mortality of acute graft-versus-host disease in mice with dysregulated IL-6 expression' [Experimental Hematology 2022; 106: 47-57]. Exp Hematol 2023; 127:70. [PMID: 37690017 DOI: 10.1016/j.exphem.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Affiliation(s)
- Keita Igarashi
- Department of Biomedical Engineering, Research Institute of Frontier Medicine; Department of Pediatrics, Sapporo Medical University School of Medicine.
| | - Norio Takei
- Department of Biomedical Engineering, Research Institute of Frontier Medicine; Institute for Animal Experimentation, Faculty of Medicine, Hokkaido University, N15W7, Kita-ku, Sapporo 060-8638, Japan
| | - Tsukasa Hori
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Hitoshi Sohma
- Department of Educational Development, Center for Medical Education, Sapporo Medical University, S1W16, Chuo-ku, Sapporo 060-8543, Japan
| | | | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Yasuo Kokai
- Department of Biomedical Engineering, Research Institute of Frontier Medicine
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9
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Sato Y, Shahi S, Telengech P, Hisano S, Cornejo C, Rigling D, Kondo H, Suzuki N. Corrigendum to 'A new tetra-segmented splipalmivirus with divided RdRP domains from Cryphonectria naterciae, a fungus found on chestnut and cork oak trees in Europe' [Virus Research 291 (2021) 198221]. Virus Res 2023; 337:199228. [PMID: 37798193 PMCID: PMC10590685 DOI: 10.1016/j.virusres.2023.199228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Carolina Cornejo
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:269. [PMID: 37804442 DOI: 10.1007/s00705-023-05880-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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11
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Sato Y, Suzuki N. Continued mycovirus discovery expanding our understanding of virus lifestyles, symptom expression, and host defense. Curr Opin Microbiol 2023; 75:102337. [PMID: 37343415 DOI: 10.1016/j.mib.2023.102337] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
High-throughput sequencing technologies have greatly expanded the RNA virome in general and have led to an exponential increase in new fungal viruses, also known as mycoviruses. Mycoviruses are omnipresent in fungi and usually induce symptomless infections. Some mycoviruses infecting fungi pathogenic to plants, insects, and mammals are known to modify host virulence positively and negatively and attract particular interests. In addition, fungal viruses continue to provide intriguing research materials and themes that lead to discoveries of peculiar viruses as infectious entities and insights into virus evolution and diversity. In this review, we outline the diversity and neolifestyle of recently discovered fungal RNA viruses, and phenotypic alterations induced by them. Furthermore, we discuss recent advances in research regarding the fungal antiviral defense and viral counterdefense, which are closely associated with host phenotype alterations. We hope that this article will enhance understanding of the interesting and growing fungal virology field.
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Affiliation(s)
- Yukiyo Sato
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chu-ou, Kurashiki, Okayama 710-0046, Japan.
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12
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Cornejo C, Otani T, Suzuki N, Beenken L. Cryphonectria carpinicola discovered in Japan: first report of the sexual state on Carpinus tree. MYCOSCIENCE 2023; 64:123-127. [PMID: 37936945 PMCID: PMC10627740 DOI: 10.47371/mycosci.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 11/09/2023]
Abstract
Cryphonectria carpinicola is an ascomycetous fungus that has been regularly found in its asexual form on European hornbeam (Carpinus betulus) in Europe over the past two decades. Here we describe the discovery of C. carpinicola in Japan and report for the first time its sexual state on Carpinus species. No symptomatic trees were observed, but stromata were found saprotrophically on broken branches of Carpinus species on the forest floor. The sexual structures of C. carpinicola resembled that of other Cryphonectria species and strongly resembled those of the closely related species C. radicalis. A phylogenetic tree based on the internal transcribed spacer sequences showed monophyly for the Japanese and European isolates of C. carpinicola. Further studies on the distribution and host range of C. carpinicola in Japan and on the life history strategies of this fungus are needed.
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Affiliation(s)
- Carolina Cornejo
- Swiss Federal
Research Institute WSL, Forest Health and Biotic
Interactions
| | - Tatsuya Otani
- Shikoku
Research Center, Forestry and Forest Products Research
Institute
| | - Nobuhiro Suzuki
- Institute of
Plant Science and Resources, Okayama University
| | - Ludwig Beenken
- Swiss Federal
Research Institute WSL, Forest Health and Biotic
Interactions
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13
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Motoo I, Ando T, Hamashima T, Kajiura S, Sakumura M, Ueda Y, Murayama A, Ogawa K, Tsukada K, Ueda A, Suzuki N, Nakada N, Nakashima K, Hosokawa A, Yasuda I. Liver metastasis affects progression pattern during immune checkpoint inhibitors monotherapy in gastric cancer. Front Oncol 2023; 13:1193533. [PMID: 37790758 PMCID: PMC10542891 DOI: 10.3389/fonc.2023.1193533] [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: 03/25/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction The efficacy of immune checkpoint inhibitors (ICIs) is heterogeneous at each metastatic site, and tumor progression pattern is associated with survival; however, it remains unclear in gastric cancer (GC). Therefore, we aimed to clarify the progression pattern in response to ICIs in patients with GC, and we analyzed its mechanism focusing on the intratumoral immune cells. Methods Patients who received ICIs were retrospectively classified into non-systemic and systemic progression groups based on their radiological assessments. Moreover, the best percentage change in target lesions from each organ was compared. Results Among 148 patients, the non-systemic progression group showed a significant improvement in overall survival (OS) compared with the systemic progression group (median, 5.6 months vs. 3.3 months; HR, 0.53; 95%CI, 0.32-0.89; p = 0.012). Poor performance status (HR, 1.73, 95%CI, 1.00-2.87) and systemic progression (HR, 3.09, 95%CI, 1.95-4.82) were associated with OS. Of all metastatic sites, the liver showed the poorest percentage change, and liver metastasis (OR, 2.99, 95%CI, 1.04-8.58) was associated with systemic progression. Hence, intratumoral CD8+ T-cell density was lower in patients with liver metastasis than in those without liver metastasis after ICIs, although the density of CD4+ T-cells (Th1, Th17, and Treg) and CD163+ cells (TAM) were not significantly different. Conclusion The new progression pattern was associated with OS in GC. Liver metastasis may be a predictive factor of systemic progression during ICIs by regulating intratumoral CD8+ T-cells.
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Affiliation(s)
- Iori Motoo
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | | | - Shinya Kajiura
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Miho Sakumura
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Yuko Ueda
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Aiko Murayama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Kohei Ogawa
- Department of Gastroenterology, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Kenichiro Tsukada
- Department of Gastroenterology, Kouseiren Takaoka Hospital, Takaoka, Japan
| | - Akira Ueda
- Department of Medical Oncology, Toyama Red Cross Hospital, Toyama, Japan
| | - Nobuhiro Suzuki
- Department of Gastroenterology, Jouetsu Sogo Hospital, Jouetsu, Japan
| | - Naokatsu Nakada
- Department of Gastroenterology, Itoigawa Sogo Hospital, Itoigawa, Japan
| | - Koji Nakashima
- Department of Clinical Oncology, University of Miyazaki Hospital, Miyazaki, Japan
| | - Ayumu Hosokawa
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
- Department of Clinical Oncology, University of Miyazaki Hospital, Miyazaki, Japan
| | - Ichiro Yasuda
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
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14
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Sato Y, Hisano S, Suzuki N. Exploration of the yadokari/yadonushi nature of YkV3 and RnMBV3 in the original host and a model filamentous fungus. Virus Res 2023; 334:199155. [PMID: 37356581 PMCID: PMC10410583 DOI: 10.1016/j.virusres.2023.199155] [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: 04/19/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
The yadokari/yadonushi nature is a recently discovered virus lifestyle; "yadokari" refers to the ability of capsidless positive-sense (+) RNA viruses (yadokariviruses) to utilize the capsids of phylogenetically distant double-stranded RNA (dsRNA) viruses possibly as the replication site, while "yadonushi" refers to the ability of dsRNA viruses to provide capsids to yadokariviruses. This virus-virus interaction, however, has been only studied with limited pathosystems. Here, we established a new study model with a capsidless (+)RNA yadokarivirus YkV3 (family Yadokariviridae) and its capsid donor RnMBV3 (family Megabirnaviridae) in the original host fungus Rosellinia necatrix and a model filamentous fungal host Cryphonectria parasitica. YkV3 has a simple genome structure with one open reading frame of 4305 nucleotides encoding a single polyprotein with an RNA-dependent RNA polymerase and a 2A-like self-cleavage peptide domain. Reverse genetics of YkV3 in R. necatrix showed that YkV3 tolerates a nucleotide substitution in the extreme 5'-terminus. The insertion of two termination codons immediately downstream of the 2A-like cleavage site abolished YkV3 viability, suggesting the importance of the C-terminal portion of the polyprotein of unknown function. Transfection of RnMBV3 and YkV3 into an RNA silencing-deficient mutant Δdcl2 of C. parasitica showed the replication competency of both viruses. Comparison between the wild-type and Δdcl2 strains of C. parasitica in virus accumulation suggested that RnMBV3 and YkV3 are susceptible to RNA silencing in C. parasitica. Taken together, we have established a platform to further explore the yadokari/yadonushi nature using genetically manipulable host fungal and virus strains.
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Affiliation(s)
- Yukiyo Sato
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sakae Hisano
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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15
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Kaimori R, Iwakawa H, Suzuki N, Aokawa M, Tashiro H, Terata K, Watanabe H. Asymmetric remodeling between the left and right atria in patients with advanced interatrial block and atrial fibrillation. J Electrocardiol 2023; 80:63-68. [PMID: 37257248 DOI: 10.1016/j.jelectrocard.2023.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Advanced interatrial block (A-IAB) on electrocardiography (ECG) represents the conduction delay between the left and right atria. We investigated the association of A-IAB with left and right atrial (LA/RA) remodeling in patients with atrial fibrillation (AF). METHODS We enrolled 74 patients who underwent ECG, cardiac computed tomography (CCT), and echocardiography during sinus rhythm before catheter ablation of AF. A-IAB was defined as P-wave duration ≥120 ms with a biphasic morphology in leads III and aVF or notched morphology in lead II. We compared the maximum and minimum LA/RA volume indices (max and min LAV/RAVI), LA/RA expansion index (LAEI/RAEI), and total, passive, and active LA/RA emptying fraction (LAEF/RAEF) between patients with and without A-IAB. RESULTS Of the 74 patients (mean age, 64.3 ± 9.6 years), 35 (47%) showed A-IAB. Patients with A-IAB had a significantly higher likelihood of hypertension and left ventricular diastolic dysfunction than those without. Patients with A-IAB had significantly larger max (69.2 [60.7-79.7]mL/m2 vs. 60.9 [50.4-68.3]mL/m2, P < 0.01) and min (44.0 [37.2-52.1]mL/m2 vs. 34.1 [29.2-43.5]mL/m2, P < 0.01) LAVI than those without. The max and min RAVI were not significantly different between groups. LAEI (55.1 [48.2-78.5]% vs. 72.1 [57.8-84.8]%, P < 0.05), total LAEF (35.5 [32.5-44.0]% vs. 41.9 [36.6-45.9]%, P < 0.05), and passive LAEF (12.2 [10.0-14.4]% vs. 15.5 [11.2-19.6]%, P < 0.05) were significantly lower in patients with A-IAB than without. CONCLUSIONS A-IAB was associated with LA, but not RA enlargement, in patients with AF. A-IAB may indicate LA functional remodeling in the reservoir and conduit phases.
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Affiliation(s)
- Ryota Kaimori
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Hidehiro Iwakawa
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Nobuhiro Suzuki
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Mako Aokawa
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Haruwo Tashiro
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Ken Terata
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroyuki Watanabe
- Department of Cardiovascular Medicine, Akita University Graduate School of Medicine, Akita, Japan.
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16
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Kose E, Nakagawa S, Niki K, Hashizume J, Kawazoe T, Suzuki N, Uchida M, Takase H. Pharmacist Interventions for Adverse Drug Reactions in Palliative Care: A Multicentre Pilot Study. Pharmazie 2023; 78:141-149. [PMID: 37592417 DOI: 10.1691/ph.2023.3554] [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: 08/19/2023]
Abstract
This study aimed to investigate adverse reactions to medications administered during palliative care and compare the responses of Board-Certified Pharmacists in Palliative Pharmacy (BCPPP) and non-BCPPP professionals. Methods: This multicentre prospective survey included hospital and community pharmacists who are members of the Japanese Society for Pharmaceutical Palliative Care and Sciences. Study participants included patients who experienced new drug reactions during the study period and responded to the requested survey items. The follow-up period for each eligible patient began on the day the pharmacists initiated the intervention and ended at discharge, death, or after one month of intervention. The primary endpoint was the impact of pharmacist intervention on adverse drug reactions. The pharmacists included in the study evaluated the severity of adverse drug reactions to assess the effect of their intervention using an integrated palliative care outcome scale before and after the intervention. Key findings: During the survey period, 79 adverse drug reaction intervention reports from 69 patients were obtained from 54 pharmacists (28 certified and 26 non-certified). The response rate was 1.62% (54/3,343). The management of palliative pharmacotherapy side effects by BCPPP and non-BCPPP significantly improved the patients' activities of daily living (P < 0.001). The BCPPP group intervened for significantly more patients with adverse drug reactions and overall adverse drug reactions than the non-BCPPP group (P < 0.023 and P < 0.013, respectively). Conclusion: BCPPP interventions can improve symptom management.
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Affiliation(s)
- E Kose
- Department of Pharmacy; These authors contributed equally to this work
| | - S Nakagawa
- Department of Clinical Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee; These authors contributed equally to this work; Corresponding author: Sari Nakagawa, Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe-shi, Hyogo 650-8586, Japan,
| | - K Niki
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University; Department of Clinical Pharmacy Research and Education; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - J Hashizume
- Graduate School of Pharmaceutical Sciences, Osaka University; Department of Hospital Pharmacy
| | - T Kawazoe
- Nagasaki University Hospital; Department of Clinical Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - N Suzuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University; Department of Pharmacy
| | - M Uchida
- National Hospital Organization Sendai Medical Center; Department of Education and Research Center for Pharmacy Practice; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - H Takase
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts; Department of Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
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17
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:175. [PMID: 37296227 PMCID: PMC10861154 DOI: 10.1007/s00705-023-05797-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
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Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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18
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Raco M, Jung T, Horta Jung M, Chi NM, Botella L, Suzuki N. Sequence and phylogenetic analysis of a novel alphaendornavirus, the first virus described from the oomycete plant pathogen Phytophthora heveae. Arch Virol 2023; 168:158. [PMID: 37166518 PMCID: PMC10175314 DOI: 10.1007/s00705-023-05786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Here, we report the discovery and complete genome sequence of a novel virus, designated as "Phytophthora heveae alphaendornavirus 1" (PhAEV1), from a single isolate of the plant pathogenic oomycete Phytophthora heveae (kingdom Stramenipila) isolated from a tropical evergreen lowland rainforest in northern Vietnam. PhAEV1 was detected by both cellulose affinity chromatography of dsRNA and high-throughput sequencing of total RNA, and its presence and sequence were confirmed by RT-PCR and Sanger sequencing. The PhAEV1 genome, 12,820 nucleotides (nt) in length, was predicted to encode a single large polyprotein with the catalytic core domain of viral (superfamily 1) RNA helicase (HEL, amino acid [aa] positions 1,287-1,531), glycosyltransferase (GT, aa positions ca. 2,800-3,125), and RNA-directed RNA polymerase (RdRp, aa positions 3,875-4,112). PhAEV1 is the most similar to Phytophthora cactorum alphaendornavirus 3, sharing 39.4% and 39.1% nt and aa sequence identity, respectively. In addition to the first 5'-terminal AUG codon, three additional in-frame methionine codons were found in close proximity (nt 14-16, 96-98, and 176-178), suggesting potential additional translation initiation sites. Conserved RdRp motifs (A-E) similar to those detected in related endornaviruses were identified in PhAEV1, as well as in several previously described alphaendornaviruses from other Phytophthora species in which these motifs had not been identified previously. Phylogenetic analysis showed that PhAEV1 clusters with members of the genus Alphaendornavirus in the family Endornaviridae and is basal to two other alphaendornaviruses described from another oomycete, Phytophthora cactorum. PhAEV1 is the first virus reported in P. heveae.
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Grants
- CZ.02.1.01/0.0/0.0/15_003/0000453 European Regional Development Fund, project Phytophthora Research Centre
- LDF_VP_2021047 Specific University Research Fund of the Faculty of Forestry and Wood Technology, Mendel University in Brno
- KAKENHI 21H05035 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 21K18222 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16H06436 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16H06429 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- 16K21723 Grants in Aid for the Scientific Research (S), Research on the Innovative Areas, and Grants in Aid for JSPS, from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
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Affiliation(s)
- Milica Raco
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00.
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Marilia Horta Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Nguyen Minh Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, 10000, Vietnam
| | - Leticia Botella
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic, Zemědělská 3, 613 00
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 7100046, Japan, Chuo 2-20-1
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19
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Siddell SG, Smith DB, Adriaenssens E, Alfenas-Zerbini P, Dutilh BE, Garcia ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Mushegian AR, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). J Gen Virol 2023; 104. [PMID: 37141106 DOI: 10.1099/jgv.0.001840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.
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Affiliation(s)
- Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University of Bristol, Bristol, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Maria Laura Garcia
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Buenos Aires, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, USA
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, SS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, Genetics Graduate Interdisciplinary Program, Cancer Biology Graduate Interdisciplinary Program and University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium and Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Abstract
Hypoviridae is a family of capsidless viruses with positive-sense RNA genomes of 7.3-18.3 kb that possess either a single large open reading frame (ORF) or two ORFs. The ORFs appear to be translated from genomic RNA by non-canonical mechanisms, i.e. internal ribosome entry site- and stop/restart translation. This family includes the genera Alphahypovirus, Betahypovirus, Gammahypovirus, Deltahypovirus, Epsilonhypovirus, Zetahypovirus, Thetahypovirus and Etahypovirus. Hypovirids have been detected in ascomycetous and basidiomycetous filamentous fungi and are considered to replicate in host, Golgi apparatus-derived, lipid vesicles that contain virus dsRNA as the replicative form. Some hypovirids induce hypovirulence to host fungi, while others do not. This is a summary of the ICTV report on the family Hypoviridae, which is available at www.ictv.global/report/hypoviridae.
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Affiliation(s)
- Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0861, Japan
| | - Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Centro de Málaga, Almería, 290140 Malaga, Spain
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid Campus de Montegancedo Pozuelo de Alarcón, Madrid 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, ETSI. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28040, Spain
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Shin-Yi Lee-Marzano
- Department of Agriculture, Agricultural Research Service, Application Technology Research Unit, Toledo, OH 43606, USA
| | - Lying Sun
- College of Plant Protection, Northwest A&F University, Taicheng Road 3#, Yangling, Shaanxi, 712100, PR China
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection-CNR, Torino 10135, Italy
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Kondo H, Sugahara H, Fujita M, Hyodo K, Andika IB, Hisano H, Suzuki N. Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan. Pathogens 2023; 12:pathogens12030358. [PMID: 36986280 PMCID: PMC10053543 DOI: 10.3390/pathogens12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
- Correspondence: ; Tel./Fax: +81-(86)-434-1232
| | - Hitomi Sugahara
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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22
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Wang H, Salaipeth L, Miyazaki N, Suzuki N, Okamoto K. Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture. PLoS Pathog 2023; 19:e1011162. [PMID: 36848381 PMCID: PMC9997902 DOI: 10.1371/journal.ppat.1011162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/09/2023] [Accepted: 01/25/2023] [Indexed: 03/01/2023] Open
Abstract
Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.
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Affiliation(s)
- Han Wang
- The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Lakha Salaipeth
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Naoyuki Miyazaki
- Life Science Center of Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (NM); (NS); (KO)
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
- * E-mail: (NM); (NS); (KO)
| | - Kenta Okamoto
- The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail: (NM); (NS); (KO)
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23
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Oshita T, Sim J, Anee TI, Kiyono H, Nozu C, Suzuki N. Attenuation of negative effects caused by a combination of heat and cadmium stress in Arabidopsis thaliana deficient in jasmonic acid synthesis. J Plant Physiol 2023; 281:153915. [PMID: 36680838 DOI: 10.1016/j.jplph.2023.153915] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Due to recent global warming, heat stress can simultaneously occur with cadmium (Cd) stress in regions suffering from metal pollution. In this study, we investigated the effects of heat, Cd and their combination on the growth and physiological characteristics of Arabidopsis thaliana. Arabidopsis plants were more susceptible to a combination of heat and Cd stress than to each stress applied individually, although the accumulation of Cd in shoots was comparable between plants subjected to Cd stress and the combined stress. Plants subjected to this stress combination showed a dramatic reduction in the accumulation of the photosynthetic reaction center proteins in photosystem II as well as a tendency toward enhanced lipid peroxidation, suggesting that the negative effects of a combination of heat and Cd stresses might be caused by oxidative damage accompanied by damage to the photosynthetic apparatus. Interestingly, aos and lox3 mutants deficient in jasmonic acid (JA) synthesis showed attenuation of the negative effects caused by a combination of heat and Cd stresses on the growth and maximum quantum efficiency of photosystem II. The roles of JA might be altered when heat stress is combined with Cd stress, despite its significance in the tolerance of plants to Cd stress when individually applied, which has been shown in previous studies.
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Affiliation(s)
- Tomoki Oshita
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan
| | - Joongeun Sim
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan
| | - Taufika Islam Anee
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan; Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Hanako Kiyono
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan
| | - Chihiro Nozu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan
| | - Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda, 102-8554, Tokyo, Japan.
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24
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Takahashi T, Suzuki N, Ishii R, Toyoda S, Shibata M, Azuma Y, Kurose Y. Egg laying performance and egg quality with Paracoccus carotinifaciens supplementation containing high astaxanthin levels. Br Poult Sci 2023; 64:47-55. [PMID: 36129068 DOI: 10.1080/00071668.2022.2126933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. This study assessed 1) the effects of Paracoccus carotinifaciens supplementation containing high astaxanthin levels on egg production performance and quality, 2) dynamics of carotenoids levels in the egg yolk and 3) taste of astaxanthin-rich egg yolk.2. Laying hens were fed diets containing different levels of P. carotinifaciens-derived astaxanthin (ASX; 0, 2, 4, 8, or 16 ppm) for 28 d (experiment 1) or a diet containing 16 ppm astaxanthin for 28 d followed by a 0 ppm astaxanthin diet for 28 days (experiment 2).3. Production performance, egg quality and egg yolk carotenoid levels were examined in experiment 1 (Ex1) and the dynamics of egg yolk carotenoid levels and egg yolk taste in experiment 2 (Ex2).4. ASX supplementation did not affect production performance or egg quality. ASX levels in the egg yolk became saturated after seven days of 16 ppm supplementation and decreased to less than one-tenth of the saturated levels seven days after supplementation cessation. Supplementation with 16 ppm ASX for 28 d did not affect egg yolk taste.5. Supplementation resulted in the production of ASX-rich eggs for a brief period without affecting production performance, egg quality or taste. Understanding the time taken for the incorporation of ASX into egg yolks is beneficial for value-added egg production and may help in minimising supplementation costs.
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Affiliation(s)
- T Takahashi
- Laboratory of Animal Metabolism and Function, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - N Suzuki
- Research and Development Department, Kanematsu Agritech Co. Ltd, Koshigaya, Saitama, Japan
| | - R Ishii
- Laboratory of Animal Metabolism and Function, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - S Toyoda
- Laboratory of Animal Metabolism and Function, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - M Shibata
- Laboratory of Animal Metabolism and Function, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Y Azuma
- Laboratory of Animal and Human Nutritional Physiology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Y Kurose
- Laboratory of Animal Metabolism and Function, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
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25
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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Sato Y, Shahi S, Telengech P, Hisano S, Cornejo C, Rigling D, Kondo H, Suzuki N. Corrigendum to 'A new tetra-segmented splipalmivirus with divided RdRP domains from Cryphonectria naterciae, a fungus found on chestnut and cork oak trees in Europe' [Virus Research 307 (2022) 198606]. Virus Res 2023; 324:199013. [PMID: 36584542 DOI: 10.1016/j.virusres.2022.199013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Carolina Cornejo
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Pallas V, Serio FD, Suzuki N. The simplest RNA replicons, viroids: A tribute to Ricardo Flores. Virus Res 2023; 323:198996. [PMID: 36334616 PMCID: PMC10194228 DOI: 10.1016/j.virusres.2022.198996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vicente Pallas
- IBMCP, Consejo Superior de Investigaciones Cientificas-Universitat Politècnica de Valencia, Av. De los Naranjos s/n Ed. 8E CPI, Valencia 46020, Spain..
| | - Francesco Di Serio
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, Bari 70126, Italy
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0047, Japan
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Sato Y, Das S, Velasco L, Turina M, Osaki H, Kotta-Loizou I, Coutts RHA, Kondo H, Sabanadzovic S, Suzuki N. ICTV Virus Taxonomy Profile: Yadokariviridae 2023. J Gen Virol 2023; 104. [PMID: 36748548 DOI: 10.1099/jgv.0.001826] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The family Yadokariviridae, with the genera Alphayadokarivirus and Betayadokarivirus, includes capsidless non-segmented positive-sense (+) RNA viruses that hijack capsids from phylogenetically distant double-stranded RNA viruses. Yadokarivirids likely replicate inside the hijacked heterocapsids using their own RNA-directed RNA polymerase, mimicking dsRNA viruses despite their phylogenetic placement in a (+) RNA virus lineage. Yadokarivirids can have negative or positive impacts on their host fungi, through interactions with the capsid donor dsRNA viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Yadokariviridae, which is available at ictv.global/report/yadokariviridae.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
- Present address: Institute for Plant Sciences, University of Cologne, Cologne 50674, Germany
| | - Subha Das
- Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria, Centro de Málaga, Almería, 290140 Malaga, Spain
| | - Massimo Turina
- Institute for Sustainable Plant Protection-CNR, Torino 10135, Italy
| | - Hideki Osaki
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba 305-8666, Japan
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762, USA
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
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Sato Y, Turina M, Chiba S, Okada R, Bhatti MF, Kotta-Loizou I, Coutts RHA, Kondo H, Sabanadzovic S, Suzuki N, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Hadakaviridae 2023. J Gen Virol 2023; 104. [PMID: 36748490 DOI: 10.1099/jgv.0.001820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The family Hadakaviridae, including the genus Hadakavirus, accommodates capsidless viruses with a 10- or 11-segmented positive-sense (+) RNA genome. Currently known hosts are ascomycetous filamentous fungi. Although phylogenetically related to polymycovirids with a segmented double-stranded RNA genome and certain encapsidated picorna-like viruses, hadakavirids are distinct in their lack of a capsid ('hadaka' means naked in Japanese) and their consequent inability to be pelleted by conventional ultracentrifugation; they show ribonuclease susceptibility in host tissue homogenates. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Hadakaviridae, which is available at ictv.global/report/hadakaviridae.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.,Present address: Institute for Plant Sciences, University of Cologne, Cologne 50674, Germany
| | - Massimo Turina
- Institute for Sustainable Plant Protection-CNR, Torino 10135, Italy
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-0861, Japan
| | - Ryo Okada
- Horticultural Research Institute, Ibaraki Agricultural Center, Kasama 319-0292, Japan
| | - Muhammad F Bhatti
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, 44000 Islamabad, Pakistan
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
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Khan HA, Kondo H, Shahi S, Bhatti MF, Suzuki N. Identification of novel totiviruses from the ascomycetous fungus Geotrichum candidum. Arch Virol 2022; 167:2833-2838. [PMID: 36271949 DOI: 10.1007/s00705-022-05611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022]
Abstract
Mycoviruses are widely distributed across the kingdom Fungi, including ascomycetous yeast strains of the class Saccharomycetes. Geotrichum candidum is an important fungal pathogen belonging to Saccharomycetes and has a diverse host range. Here, we report the characterization of four new classical totiviruses from two distinct Geotrichum candidum strains from Pakistan. The four identified viruses were tentatively named "Geotrichum candidum totivirus 1, 2, 3a, and 3b" (GcTV1-3b). The complete dsRNA genomes of the identified totiviruses are 4621, 4592, 4576, and 4576 bp in length, respectively. All totivirus genomes have two open reading frames, encoding a capsid protein (CP) and an RNA-dependent RNA polymerase (RdRP), respectively. The downstream RdRP domain is assumed to be expressed as a CP-RdRP fusion product via -1 frameshifting mediated by a heptameric slippery site. Sequence comparisons and phylogenetic analysis showed that each of the discovered viruses belongs to a new species of the genus Totivirus in the family Totiviridae, with GcTV1 and GcTV3 (a and b strains) clustering in one subgroup and GcTV2 in another subgroup.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan.
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Arch Virol 2022; 167:2429-2440. [PMID: 35999326 PMCID: PMC10088433 DOI: 10.1007/s00705-022-05516-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit,, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and TransplantationClinical and Epidemiological VirologyInstitute for the Future, Rega Institute for Medical Research, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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Matthijnssens J, Attoui H, Bányai K, Brussaard CPD, Danthi P, del Vas M, Dermody TS, Duncan R, Fāng Q, Johne R, Mertens PPC, Mohd Jaafar F, Patton JT, Sasaya T, Suzuki N, Wei T. ICTV Virus Taxonomy Profile: Spinareoviridae 2022. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Spinareoviridae is a large family of icosahedral viruses that are usually regarded as non-enveloped with segmented (9–12 linear segments) dsRNA genomes of 23–29 kbp. Spinareovirids have a broad host range, infecting animals, fungi and plants. Some have important pathogenic potential for humans (e.g. Colorado tick fever virus), livestock (e.g. avian orthoreoviruses), fish (e.g. aquareoviruses) and plants (e.g. rice ragged stunt virus and rice black streaked dwarf virus). This is a summary of the ICTV Report on the family Spinareoviridae, which is available at ictv.global/report/spinareoviridae.
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Affiliation(s)
| | - Houssam Attoui
- National Institute for Agricultural Research (INRA), Maisons Alfort, France
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Budapest, H-1143, Hungary
| | - Corina P. D. Brussaard
- NIOZ Royal Netherlands Institute for Sea Research & University of Utrecht, Texel, The Netherlands
| | | | - Mariana del Vas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Buenos Aires, Argentina
| | - Terence S. Dermody
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Roy Duncan
- Dalhousie University, Halifax, Nova Scotia, Canada
| | - Qín Fāng
- Wuhan Institute of Virology, Wuhan, PR China
| | - Reimar Johne
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | | | | | - Takahide Sasaya
- National Agriculture and Food Research Organization, Fukuyama, Japan
| | | | - Taiyun Wei
- Fujian Agriculture and Forestry University, Fuzhou, PR China
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Woopen H, Sehouli J, Davis A, Lee Y, Cohen P, Ferrero A, Gleeson N, Jhingran A, Kajimoto Y, Mayadev J, Barretina-Ginesta M, Sundar S, Suzuki N, van Dorst E, Joly F. Erratum to “GCIG-Consensus guideline for long-term survivorship in gynecologic cancer: A position paper from the Gynecologic Cancer InterGroup (GCIG) symptom benefit committee” [Cancer Treatm. Rev. 107 (2022) 102396]. Cancer Treat Rev 2022; 109:102431. [DOI: 10.1016/j.ctrv.2022.102431] [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: 11/26/2022]
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Suzuki N, Ikeda Y, Ono M, Ohmori G, Maeda M. Gastrointestinal: Immune-related sclerosing cholangitis with pembrolizumab: Imaging and histological features. J Gastroenterol Hepatol 2022; 37:1652. [PMID: 35226968 DOI: 10.1111/jgh.15797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/12/2022] [Indexed: 12/09/2022]
Affiliation(s)
- N Suzuki
- Department of Gastroenterology, Steel Memorial Muroran Hospital, Muroran, Japan
| | - Y Ikeda
- Department of Gastroenterology, Steel Memorial Muroran Hospital, Muroran, Japan
| | - M Ono
- Department of Gastroenterology, Steel Memorial Muroran Hospital, Muroran, Japan
| | - G Ohmori
- Department of Gastroenterology, Steel Memorial Muroran Hospital, Muroran, Japan
| | - M Maeda
- Department of Gastroenterology, Steel Memorial Muroran Hospital, Muroran, Japan
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Abstract
High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses with unique genome structures and even neo-lifestyles. Examples in the former category include splipalmiviruses and ambiviruses. Splipalmiviruses, related to yeast narnaviruses, have multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode the RNA-dependent RNA polymerase motifs, the hallmark of RNA viruses (members of the kingdom Orthornavirae). Ambiviruses appear to have an undivided ssRNA genome of 3∼5 kb with two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has two fully overlapping ORFs on both strands of a genomic segment that span more than 90% of the genome size. New virus lifestyles exhibited by mycoviruses include the yado-kari/yado-nushi nature characterized by the partnership between the (+)ssRNA yadokarivirus and an unrelated dsRNA virus (donor of the capsid for the former) and the hadaka nature of capsidless 10-11 segmented (+)ssRNA accessible by RNase in infected mycelial homogenates. Furthermore, dsRNA polymycoviruses with phylogenetic affinity to (+)ssRNA animal caliciviruses have been shown to be infectious as dsRNA-protein complexes or deproteinized naked dsRNA. Many previous phylogenetic gaps have been filled by recently discovered fungal and other viruses, which haveprovided interesting evolutionary insights. Phylogenetic analyses and the discovery of natural and experimental cross-kingdom infections suggest that horizontal virus transfer may have occurred and continue to occur between fungi and other kingdoms.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Leticia Botella
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University, Brno, Czech Republic
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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Das S, Hisano S, Eusebio-Cope A, Kondo H, Suzuki N. A Transfectable Fusagravirus from a Japanese Strain of Cryphonectria carpinicola with Spherical Particles. Viruses 2022; 14:v14081722. [PMID: 36016344 PMCID: PMC9413294 DOI: 10.3390/v14081722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 02/05/2023] Open
Abstract
A novel dsRNA virus (Cryphonectria carpinicola fusagravirus 1, CcFGV1), isolated from a Japanese strain (JS13) of Cryphonectria carpinicola, was thoroughly characterized. The biological comparison of a set of isogenic CcFGV1-infected and -free (JS13VF) strains indicated asymptomatic infection by CcFGV1. The sequence analysis showed that the virus has a two open reading frame (ORF) genome of 9.6 kbp with the RNA-directed RNA polymerase domain encoded by ORF2. The N-terminal sequencing and peptide mass fingerprinting showed an N-terminally processed or degraded product (150 kDa) of the 5′-proximal ORF1-encoded protein (1462 amino acids) to make up the CcFGV1 spherical particles of ~40 nm in diameter. Interestingly, a portion of CcFGV1 dsRNA co-fractionated with a host protein of 70 kDa. The purified CcFGV1 particles were used to transfect protoplasts of JS13VF as well as the standard strain of an experimental model filamentous fungal host Cryphonectria parasitica. CcFGV1 was confirmed to be associated with asymptomatic infection of both fungi. RNA silencing was shown to target the virus in C. parasitica, resulting in reduced CcFGV1 accumulation by comparing the CcFGV1 content between RNA silencing-competent and -deficient strains. These results indicate the transfectability of spherical particles of a fusagravirus associated with asymptomatic infection.
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Khan HA, Telengech P, Kondo H, Bhatti MF, Suzuki N. Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan. Front Cell Infect Microbiol 2022; 12:913619. [PMID: 35846770 PMCID: PMC9277117 DOI: 10.3389/fcimb.2022.913619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/23/2022] Open
Abstract
Diplodia seriata in the family Botryosphaeriaceae is a cosmopolitan phytopathogenic fungus and is responsible for causing cankers, fruit rot and leaf spots on economically important plants. In this study, we characterized the virome of a single Pakistani strain (L3) of D. seriata. Several viral-like contig sequences were obtained via a previously conducted next-generation sequencing analysis. Multiple infection of the L3 strain by eight RNA mycoviruses was confirmed through RT-PCR using total RNA samples extracted from this strain; the entire genomes were determined via Sanger sequencing of RT-PCR and RACE clones. A BLAST search and phylogenetic analyses indicated that these eight mycoviruses belong to seven different viral families. Four identified mycoviruses belong to double-stranded RNA viral families, including Polymycoviridae, Chrysoviridae, Totiviridae and Partitiviridae, and the remaining four identified mycoviruses belong to single-stranded RNA viral families, i.e., Botourmiaviridae, and two previously proposed families “Ambiguiviridae” and “Splipalmiviridae”. Of the eight, five mycoviruses appear to represent new virus species. A morphological comparison of L3 and partially cured strain L3ht1 suggested that one or more of the three viruses belonging to Polymycoviridae, “Splipalmiviridae” and “Ambiguiviridae” are involved in the irregular colony phenotype of L3. To our knowledge, this is the first report of diverse virome characterization from D. seriata.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- *Correspondence: Muhammad Faraz Bhatti, ; Nobuhiro Suzuki,
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- *Correspondence: Muhammad Faraz Bhatti, ; Nobuhiro Suzuki,
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Tsuge S, Fujii H, Tamai M, Mizushima I, Yoshida M, Suzuki N, Takahashi Y, Takeji A, Horita S, Fujisawa Y, Matsunaga T, Zoshima T, Nishioka R, Nuka H, Hara S, Tani Y, Suzuki Y, Ito K, Yamada K, Nakazaki S, Kawakami A, Kawano M. POS1339 FACTORS RELATED TO SERUM IgG4 ELEVATION AND DEVELOPMENT OF IgG4-RELATED DISEASE: DATA FROM RESIDENT EXAMINATION. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundElevated serum IgG4 levels are one of the characteristic findings in immunoglobulin G4 (IgG4)-related disease (IgG4-RD). Serum IgG4 levels have an impact to a certain extent on the diagnosis of IgG4-RD although there are some issues in their sensitivity and specificity. In the reports from Japan, China, USA, and Europe, elevated serum IgG4 levels were reported to be observed in 83-97% of patients with IgG4-RD [1-5]. In the past investigations of hospital patients, some studies reported that 10-15% of hospital patients with elevated serum IgG4 levels had IgG4-RD [6,7]. However, in general adults with no symptom, investigations of prevalence of elevated serum IgG4 levels and/or IgG4-RD have rarely been conducted.ObjectivesThis study aimed to investigate the frequency of serum IgG4 elevation in the general Japanese population and its associated factors using data from resident examinations.MethodsWe measured the serum IgG4 levels in 1,204 residents who underwent a general medical examination in Ishikawa prefecture, Japan. Logistic regression analysis was used to search for factors related to elevated serum IgG4 levels. Secondary examinations were conducted for participants in whom elevation was identified.ResultsThe mean serum IgG4 level was 44 mg/dL, and elevated serum IgG4 levels were observed in 42 patients (3.5%). Univariate logistic regression analyses showed that male sex, older age, lower estimated glomerular filtration rates based on cystatin C (eGFR-CysC), serum high-density lipoprotein cholesterol levels, and higher hemoglobin A1c (HbA1c) levels were associated with elevated serum IgG4 levels. Subgroup analyses in men showed that older age, lower eGFR-CysC levels, and higher serum HbA1c levels were associated with elevated serum IgG4 levels. In contrast, the analyses in women found no significant factors. One of the 10 residents who underwent secondary examinations was diagnosed with possible IgG4-related retroperitoneal fibrosis.ConclusionIn the general population, elevated serum IgG4 levels are more common in elderly men, which is similar to the epidemiological features of IgG4-RD.References[1]Inoue D, et al. IgG4-related disease: dataset of 235 consecutive patients. Medicine (Baltimore). 2015;94(15):e680.[2]Yamada K, et al. New clues to the nature of immunoglobulin G4-related disease: a retrospective Japanese multicenter study of baseline clinical features of 334 cases. Arthritis Res Ther. 2017;19(1):262[3]Culver EL, et al. Elevated serum IgG4 levels in diagnosis, treatment response, organ involvement, and relapse in a prospective IgG4-related disease UK cohort. Am J Gastroenterol 2016;111:733–43.[4]Lin W, et al. Clinical characteristics of immunoglobulin G4-related disease: a prospective study of 118 Chinese patients. Rheumatology (Oxford). 2015;54(11):1982–90.[5]Carruthers MN, et al. The diagnostic utility of serum IgG4 concentrations in IgG4-related disease. Ann Rheum Dis 2015;74:14-18.[6]James Yun, et al. Poor positive predictive value of serum immunoglobulin G4 concentrations in the diagnosis of immunoglobulin G4-related sclerosing disease. Asia Pac Allergy. 2014 Jul;4(3):172-176.[7]Taiwo N Ngwa, et al. Sreum immunoglobulin G4 level is a poor predictor of immunoglobulin G4–related disease. Pancreas. 2014 Jul;43(5):704-7.Disclosure of InterestsNone declared
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Suzuki N, Cintra FF, Cintra ML, Maciel MG, Amstalden E, Teixeira F, Kubba F. "A case of vanishing bone disease complicated by chylothorax- diagnosis and treatment". JRSM Open 2022; 13:20542704221103912. [PMID: 35774987 PMCID: PMC9237928 DOI: 10.1177/20542704221103912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A 16-year old girl with Gorham-Stout disease is presented. She had progressive replacement of the bones of her left arm and shoulder girdle by fibroadipose tissue and numerous proliferated, non-neoplastic, lymphatic channels. The clinico-pathologic features of this condition are discussed, as are its possible complications and available therapeutic modalities.
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Affiliation(s)
- N Suzuki
- Department of Dermatology, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - F F Cintra
- Department of Orthopedics, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - M L Cintra
- Department of Pathology, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - M G Maciel
- Department of Dermatology, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Emi Amstalden
- Department of Pathology, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - F Teixeira
- Department of Pathology, Medical Sciences School, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - F Kubba
- Department of Pathology, London Northwest University Healthcare NHS Trust, UK
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Yamauchi M, Ono A, Amioka K, Fujii Y, Uchikawa S, Fujino H, Nakahara T, Murakami E, Okamoto W, Kawaoka T, Miki D, Tsuge M, Imamura M, Nelson H, Kato Y, Kimura M, Suzuki N, Aikata H, Chayama K. P-141 Lenvatinib activates potential anti-tumor immunity by increasing infiltration of immune cells and interferon response in tumor microenvironment of advanced hepatocellular carcinoma. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.231] [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: 11/01/2022] Open
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Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ, Adriaenssens EM, Alfenas-Zerbini P, Dutilh BE, García ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Differentiating between viruses and virus species by writing their names correctly. Arch Virol 2022; 167:1231-1234. [PMID: 35043230 PMCID: PMC9020231 DOI: 10.1007/s00705-021-05323-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the results of the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021, a standard two-part "binomial nomenclature" is now the norm for naming virus species. Adoption of the new nomenclature is still in its infancy; thus, it is timely to reiterate the distinction between "virus" and "virus species" and to provide guidelines for naming and writing them correctly.
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Affiliation(s)
| | - Stuart G. Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL 35294-2170, USA
| | | | | | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena 07743, Germany,Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris 75015, France
| | - Jens H. Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000 Leuven, Belgium,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ 85287-4701, USA
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Takahashi Y, Ishida H, Imamura T, Tamefusa K, Suenobu S, Usami I, Yumura-Yagi K, Hasegawa D, Nishimura S, Suzuki N, Hashii Y, Deguchi T, Moriya-Saito A, Kosaka Y, Kato K, Kobayashi R, Kawasaki H, Hori H, Sato A, Kudo T, Nakahata T, Oda M, Hara J, Horibe K. JACLS ALL-02 SR protocol reduced-intensity chemotherapy produces excellent outcomes in patients with low-risk childhood acute lymphoblastic leukemia. Int J Hematol 2022; 115:890-897. [PMID: 35258855 DOI: 10.1007/s12185-022-03315-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 10/18/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. As overall cure rates of childhood ALL have improved, reduction of overall treatment intensity while still ensuring excellent outcomes is imperative for low-risk patients. We report the outcomes of patients treated following the standard-risk protocol from the prospective Japan Association of Childhood Leukemia Study (JACLS) ALL-02 study, which was conducted between 2002 and 2008 for patients with newly diagnosed ALL aged 1-18 years. Of 1138 patients with B-cell precursor ALL, 388 (34.1%) were allocated to this protocol. Excellent outcomes were achieved despite the overall treatment intensity being lower than that of most contemporary protocols: 4 years event-free survival (EFS) was 92.3% and 4 years overall survival 98.2%. Patients with high hyperdiploidy (HHD) involving triple trisomy (trisomy of chromosomes 4, 10, and 17) or ETV6-RUNX1 had even better outcomes (4 years EFS 97.6% and 100%, respectively). Unique characteristics of this protocol include a selection of low-risk patients with a low initial WBC count and good early treatment response and reduction of cumulative doses of chemotherapeutic agents while maintaining dose density. In Japan, we are currently investigating the feasibility of this protocol while incorporating minimal residual disease into the patient stratification strategy.
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Affiliation(s)
- Yoshihiro Takahashi
- Department of Pediatrics, Aomori Prefectural Central Hospital, Aomori, Japan
| | - Hisashi Ishida
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, 465, Kajiichou, Hirokouji Kawaramachidori, Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Kosuke Tamefusa
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Souichi Suenobu
- Division of General Pediatrics and Emergency Medicine, Department of Pediatrics, Oita University Faculty of Medicine, Oita, Japan
| | - Ikuya Usami
- Department of Pediatric Hematology and Oncology, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan
| | | | - Daiichiro Hasegawa
- Department of Hematology/Oncology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | | | - Nobuhiro Suzuki
- Department of Pediatrics, Hokkaido Medical Center for Child Health and Rehabilitation, Sapporo, Japan
| | - Yoshiko Hashii
- Department of Pediatrics, Osaka University, Suita, Japan
| | - Takao Deguchi
- Department of Pediatrics, Mie University, Tsu, Japan
| | - Akiko Moriya-Saito
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yoshiyuki Kosaka
- Department of Hematology/Oncology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Koji Kato
- Department of Hematology Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Hirohide Kawasaki
- Department of Pediatrics, Kansai Medical University, Hirakata, Japan
| | - Hiroki Hori
- Department of Pediatrics, Mie University, Tsu, Japan
| | - Atsushi Sato
- Department of Hematology/Oncology, Miyagi Children's Hospital, Sendai, Japan
| | - Toru Kudo
- Saiseikai Nishiotaru Hospital, Otaru, Japan
| | - Tatsutoshi Nakahata
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Megumi Oda
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Junichi Hara
- Department of Pediatric Hematology/Oncology, Osaka City General Hospital, Osaka, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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Telengech P, Shahi S, Kondo H, Suzuki N. A novel deltapartitivirus from red clover. Arch Virol 2022; 167:1201-1204. [PMID: 35246731 DOI: 10.1007/s00705-022-05372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/28/2022]
Abstract
The family Partitiviridae has five genera, among which is the genus Deltapartitivirus. We report here the complete genome sequence of a deltapartitivirus from red clover, termed "red clover cryptic virus 3" (RCCV3). RCCV3 has a bisegmented double-stranded (ds) RNA genome. dsRNA1 and dsRNA2 are 1580 and 1589 nucleotides (nt) in length and are predicted to encode an RNA-directed RNA polymerase (RdRP) and a capsid protein (CP), respectively. The RCCV3 RdRP shares the highest sequence identity with the RdRP of a previously reported deltapartitivirus, Medicago sativa deltapartitivirus 1 (MsDPV1) (76.5%), while the RCCV3 CP shows 50% sequence identity to the CP of MsDPV1. RdRP- and CP-based phylogenetic trees place RCCV3 into a clade of deltapartitiviruses. The sequence and phylogenetic analyses clearly indicate that RCCV3 represents a new species in the genus Deltapartitivirus. RCCV3 was detectable in all three tested cultivars of red clover.
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Affiliation(s)
- Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Khan HA, Sato Y, Kondo H, Jamal A, Bhatti MF, Suzuki N. A novel victorivirus from the phytopathogenic fungus Neofusicoccum parvum. Arch Virol 2022; 167:923-929. [PMID: 35112205 DOI: 10.1007/s00705-021-05304-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 11/02/2022]
Abstract
Neofusicoccum parvum is an important plant-pathogenic ascomycetous fungus that causes trunk diseases in a variety of plants. A limited number of reports on mycoviruses from this fungus are available. Here, we report the characterization of a novel victorivirus, Neofusicoccum parvum victorivirus 3 (NpVV3). An agarose gel dsRNA profile of a Pakistani strain of N. parvum, NFN, showed a band of ~5 kbp that was not detectable in Japanese strains of N. parvum. Taking a high-throughput and Sanger sequencing approach, the complete genome sequence of NpVV3 was determined to be 5226 bp in length with two open reading frames (ORF1 and ORF2) that encode a capsid protein (CP) and an RNA-dependent RNA polymerase (RdRP). The RdRP appears to be translated by a stop/restart mechanism facilitated by the junction sequence AUGucUGA, as is found in some other victoriviruses. BLASTp searches showed that NpVV3 CP and RdRP share the highest amino acid sequence identity (80.5% and 72.4%, respectively) with the corresponding proteins of NpVV1 isolated from a French strain of N. parvum. However, NpVV3 was found to be different from NpVV1 in its terminal sequences and the stop/restart facilitator sequence. NpVV3 particles ~35 nm in diameter were partially purified and used to infect an antiviral-RNA-silencing-deficient strain (∆dcl2) of an experimental ascomycetous fungal host, Cryphonectria parasitica. NpVV3 showed symptomless infection in the new host strain.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Igarashi K, Hori T, Yamamoto M, Sohma H, Suzuki N, Tsutsumi H, Kawasaki Y, Kokai Y. CCL8 deficiency in the host abrogates early mortality of acute graft-versus-host disease in mice with dysregulated IL-6 expression. Exp Hematol 2022; 106:47-57. [PMID: 34808257 DOI: 10.1016/j.exphem.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022]
Abstract
Although allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for diverse malignant and nonmalignant diseases, acute graft-versus-host disease (aGVHD) is strongly linked to mortality caused by HSCT. We previously reported that CC chemokine ligand 8 (CCL8) is closely correlated to aGVHD mortality in both humans and mice. To study the role of CCL8 in aGVHD, CCL8 knockout (CCL8-/-) mice were transplanted with fully allogeneic marrow grafts. These mice exhibited a significant reduction in mortality (90.0% vs. 23.4% survival for CCL8-/- vs. wild-type recipients at day 28, p < 0.0001). As a result, apparent prolonged median survival from 9 days in wild-type mice to 45 days in CCL8-/- mice was observed. Acute GVHD pathology and liver dysfunction in CCL8-/- mice were significantly attenuated compared with those in wild-type mice. In association with the reduced mortality, a surge of plasma interleukin (IL)-6 was observed in CCL8-/- recipients with allogeneic marrow, which was significantly increased compared with wild-type mice that received allografts. Donor T-cell expansion and plasma levels of interferon-γ and TNF-α during aGVHD were similar in both types of mice. Collectively, these findings indicate that CCL8 plays a major role in aGVHD pathogenesis with possible involvement of an IL-6 signaling cascade.
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Affiliation(s)
- Keita Igarashi
- Department of Biomedical Engineering, Research Institute of Frontier Medicine; Department of Pediatrics, Sapporo Medical University School of Medicine.
| | - Tsukasa Hori
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Hitoshi Sohma
- Department of Educational Development, Center for Medical Education, Sapporo Medical University, Sapporo, Japan
| | | | - Hiroyuki Tsutsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Yukihiko Kawasaki
- Department of Pediatrics, Sapporo Medical University School of Medicine
| | - Yasuo Kokai
- Department of Biomedical Engineering, Research Institute of Frontier Medicine
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Motoo I, Ando T, Kajiura S, Ogawa K, Tsukada K, Ueda A, Suzuki N, Nakada N, Nakashima K, Hosokawa A, Yasuda I. Lesion-level response to immune checkpoint inhibitor in patients with advanced gastric cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
311 Background: The efficacy of anti-PD-1 monotherapy has been reported to be heterogeneous in each metastatic location in non-small cell lung cancer. Therefore, we analyzed the response of target lesions in each organ and the association between pattern of progression and survival in patients with gastric cancer (GC). Methods: We performed retrospective analysis, which include 148 patients with GC who received nivolumab or pembrolizumab treatment between 2017 and 2021 at eight institutions in Japan. Response rate (RR), progression free survival (PFS), and overall survival (OS) were evaluated in total patients. The percent change of target lesions of each organs was measured by CT using RECIST, and their best percent changes were compared. In the GC patients with best response of progression disease (PD), the association between pattern of progression and survival was analyzed. Systemic progression was defined as PD in two or more lesions including target or non-target lesions, and non-systemic progression was defined as PD in only one lesion. Results: Among 148 patients, the RR, median PFS, and median OS were 11.6%, 1.6 months (95%CI, 1.4-1.9), and 4.4 months (95%CI, 3.6-6.6), respectively. A total of 293 lesions from 112 patients with target lesions were examined. The median best percent change of lymph node (n = 76), liver (n = 62), peritoneum (n = 19) and lung (n = 8) was +2.3%, +27%, +12%, +8.5%, respectively. Liver had significantly the lowest responses compared with lymph node and peritoneum (p < 0.0001 and p = 0.016). The median OS in non-systemic and systemic progression group was 5.6 months (95%CI, 3.6-8.8) and 3.3 months (95%CI, 1.9-3.6) and survival of patients with non-systemic progression showed significantly longer than that of systemic progression (p = 0.012). According to univariate and multivariate analysis, poor performance status (PS) (HR 1.73, 95%CI, 1.00-2.87) and systemic progression (HR 3.09, 95%CI, 1.95-4.82) were associated with OS in total patients. Additionally, liver metastasis (OR 2.99, 95%CI, 1.04-8.58) was identified as a baseline factor associated with systemic progression in the univariate and multivariate analysis. Conclusions: The efficacy of immune checkpoint inhibitor (ICI) is dependent on the metastatic location. Moreover, pattern of progression has been associated with overall survival. Liver metastasis might be a predictive factor of systemic progression in ICI treatment for GC.
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Affiliation(s)
| | - Takayuki Ando
- Third Department of Internal Medicine, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Shinya Kajiura
- Third Department of Internal Medicine, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Kohei Ogawa
- Toyama Prefectural Central Hospital, Toyama, Japan
| | | | - Akira Ueda
- Department of Oncology, Toyama Red Cross Hospital, Toyama, Japan
| | | | | | - Koji Nakashima
- Department of Clinical Oncology, University of Miyazaki Hospital, Miyazaki, Japan
| | | | - Ichiro Yasuda
- Third Department of Internal Medicine, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
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Sato Y, Shahi S, Telengech P, Hisano S, Cornejo C, Rigling D, Kondo H, Suzuki N. A new tetra-segmented splipalmivirus with divided RdRP domains from Cryphonectria naterciae, a fungus found on chestnut and cork oak trees in Europe. Virus Res 2022; 307:198606. [PMID: 34688782 DOI: 10.1016/j.virusres.2021.198606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/04/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 01/01/2023]
Abstract
Positive-sense (+), single-stranded (ss) RNA viruses with divided RNA-dependent RNA polymerase (RdRP) domains have been reported from diverse filamentous ascomycetes since 2020. These viruses are termed splipalmiviruses or polynarnaviruses and have been characterized largely at the sequence level, but ill-defined biologically. Cryphonectria naterciae, from which only one virus has been reported, is an ascomycetous fungus potentially plant-pathogenic to chestnut and oak trees. We molecularly characterized multiple viruses in a single Portuguese isolate (C0614) of C. naterciae, taking a metatranscriptomic and conventional double-stranded RNA approach. Among them are a novel splipalmivirus (Cryphonectria naterciae splipalmivirus 1, CnSpV1) and a novel fusagravirus (Cryphonectria naterciae fusagravirus 1, CnFGV1). This study focused on the former virus. CnSpV1 has a tetra-segmented, (+)ssRNA genome (RNA1 to RNA4). As observed for other splipalmiviruses reported in 2020 and 2021, the RdRP domain is separately encoded by RNA1 (motifs F, A and B) and RNA2 (motifs C and D). A hypothetical protein encoded by the 5'-proximal open reading frame of RNA3 shows similarity to a counterpart conserved in some splipalmiviruses. The other RNA3-encoded protein and RNA4-encoded protein show no similarity with known proteins in a blastp search. The tetra-segment nature was confirmed by the conserved terminal sequences of the four CnSpV1 segments (RNA1 to RNA4) and their 100% coexistence in over 100 single conidial isolates tested. The experimental introduction of CnSpV1 along with CnFGV1 into a virus free strain C0754 of C. naterciae vegetatively incompatible with C0614 resulted in no phenotypic alteration, suggesting asymptomatic infection. The protoplast fusion assay indicates a considerably narrow host range of CnSpV1, restricted to the species C. naterciae and C. carpinicola. This study contributes to better understanding of the molecular and biological properties of this unique group of viruses.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Carolina Cornejo
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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48
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Khan HA, Shamsi W, Jamal A, Javaied M, Sadiq M, Fatma T, Ahmed A, Arshad M, Waseem M, Babar S, Dogar MM, Virk N, Janjua HA, Kondo H, Suzuki N, Bhatti MF. Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1. J Gen Virol 2021; 102. [PMID: 34850675 DOI: 10.1099/jgv.0.001690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Wajeeha Shamsi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Memoona Javaied
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mashal Sadiq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Maleeha Arshad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mubashra Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Samra Babar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Midhat Mustafa Dogar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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49
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Katano K, Suzuki N. What are the key mechanisms that alter the morphology of stigmatic papillae in Arabidopsis thaliana? Plant Signal Behav 2021; 16:1980999. [PMID: 34549683 PMCID: PMC9208798 DOI: 10.1080/15592324.2021.1980999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 05/31/2023]
Abstract
Pollination is one of the critical processes that determines crop yield and quality. Thus, it is an urgent need to elucidate the mechanisms underlying pollination. Our previous research has revealed a novel phenomenon that pollen attachment to stigma caused stigma shrinkage, whereas failure of pollen attachment to stigma due to the environmental stress induced elongation of stigmatic papillae. However, little is known about the mechanisms of these morphological alterations in stigmatic papillae. Since the RLK-ROPGEF-ROP network is a common mechanism for the elongation of pollen tubes and root hairs, this network may be also involved in the elongation of papillae in the stigma. In this review, we will discuss the known mechanisms regulating pollen tube growth and root hair elongation and attempt to propose an elongation mechanism of stigmatic papillae. In addition, we will suggest that the degradation of F-actin by a significant increase in Ca2+ induced by the components of pollen coat might be a putative molecular mechanism of stigmatic papillae shrinkage during pollen adhesion.
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Affiliation(s)
- Kazuma Katano
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Chiyoda, Japan
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Chiyoda-ku, Tokyo, Japan
| | - Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Chiyoda-ku, Tokyo, Japan
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50
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Davison AJ, Dempsey DM, Dutilh BE, García ML, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Nibert ML, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Dooerslaer K, Vandamme AM, Varsani A, Zerbini FM. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol 2021; 166:2633-2648. [PMID: 34231026 DOI: 10.1007/s00705-021-05156-1] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Balázs Harrach
- Veterinary Medical Research Institute, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc-West, Beltsville, MD, 20705, USA
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany, Berlin, Germany
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, Surrey, UK
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Max L Nibert
- Department of Microbiology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Dooerslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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