Kanai, Akio

写真a

Affiliation

Graduate School of Media and Governance (Shonan Fujisawa)

Position

Professor

Related Websites

External Links
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  • Dr. Akio Kanai was born in Tokyo, Japan. He graduated from Waseda University in 1985, and obtained his PhD in molecular biology at the University of Tokyo in 1990. He finished postdoctoral training at the National Institutes of Health, USA (1990-1992), and he was appointed a researcher in the Tokyo Metropolitan Institute of Medical Science (1992-1996). He was a group leader for the Japan Science and Technology Corporation (JST), ERATO Project Group (1996-2001). He was an Associate Professor at the Institute for Advanced Biosciences, Keio University (2001-2006) and accepted a full professorship in April, 2006 (concurrently serves as a professor at the Faculty of Environment and Information Studies, Keio University). Since 2022, he is also a professor of Systems Biology Program, Graduate School of Media and Governance, Keio University. His major research fields include molecular cellular biology and gene regulation in a variety of organisms. His work in life sciences has led him to his present research into RNA-binding proteins and non-coding RNAs.

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Message from the Faculty Member 【 Display / hide 】

  • We have been carrying out research mainly related to the molecular biology and molecular evolution of RNAs in a manner that combines bioinformatics and experimental biology. One of our representative studies is the systematic discovery of functional RNAs. For example, through the analysis of experimentally collected mouse full-length cDNA clones, we showed for the first time that a large amount of long noncoding RNAs exist in mammals (Genome Res. 2003, in collaboration with RIKEN). Subsequently, we have discovered and reported new molecular species of small RNAs in E. coli (BMC Genomics 2011) and microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp) (RNA 2015), at the genome level. We also reported that artificially synthesized small RNAs can inhibit the growth of E. coli (RNA Biol. 2017). Furthermore, we systematized the evolution of group II introns in prokaryotes, known as one of the genes that move across the genome (Front. Microbiol. 2022). In addition to these findings, we also contributed to the discovery of various disrupted transfer RNA (tRNA) genes and tRNA-like genes since 2006 (Mol. Biol. Evol. 2008; PNAS. 2009; Nucleic Acids Res. 2012; Mol. Biol. Evol. 2016). We have also reported on the characteristics of a group of enzymes involved in the regulation of RNA molecules and their molecular evolution (RNA 2009; Nucleic Acids Res. 2011; Genome Biol. Evol. 2019; J. Mol. Evol. 2023). Recently, we reported that the ribosomes of a tiny group of bacteria called CPR bacteria are small (RNA 2022) and analyzed the rRNA introns of this group of bacteria (J. Bact. 2024).

    Due to my dual role as a professor at the Institute for Advanced Biosciences, and the Faculty of Environment and Information Studies, I have been particularly mindful of the concepts of "Environment" and "Information" in shaping the direction of my research over the past decade. When I speak of the "Environment," I specifically refer to habitats where life can barely survive, with a particular focus on extreme environments. On the other hand, "Information" is self-evident; it pertains to genetic information. In essence, by examining gene expression in situations critical to cells, we strive to gain a deeper understanding of the essence of "Life." (Appl. Environ. Microbiol. 2024; ISME J. 2024).

    Education of undergraduate and graduate students:
    The goal of our RNA research group is to create human resources who can think for themselves. This needs to be learned properly during the student years. In extreme terms, it does not matter who you learn the experimental techniques from, as long as you can learn them correctly. What is important is to be able to think properly about what to study, what to do when in trouble, and how to develop. In other words, it is important for you to be able to develop your research without being bound by the themes of your student days.

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Profile Summary 【 Display / hide 】

  • It has been 65 years since the flow of genetic information (central dogma) from DNA to RNA to protein was proposed. Although this concept remains unchanged as the basic axis, it has been required to be modified with the discovery of reverse transcriptases in the 1970s and RNA enzymes (ribozymes) in the 1980s. Furthermore, with the discovery of so many non-coding RNAs in the 21st century, the function of the RNA molecules themselves in central dogma has become impossible to ignore. This project focuses on functional RNAs, RNA-binding proteins, and RNA-related enzymes involved in gene regulations, and aims to elucidate new regulatory mechanisms mediated by RNAs. Furthermore, based on the findings obtained through these studies, we will discuss the origin of life, evolution, and the basic regulatory mechanisms of genes.

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Career 【 Display / hide 】

  • 2022.04
    -
    Present

    Professor, Graduate School of Media and Governance, Keio University, Systems Biology Program

  • 2006.04
    -
    Present

    Professor, Institute for Advanced Biosciences, Keio University

  • 2001.04
    -
    2006.03

    Associate Professor, Institute for Advanced Biosciences, Keio University

  • 1996.04
    -
    2001.03

    Group Leader, ERATO Project, Japan Science and Technology Agency (JST)

  • 1992.11
    -
    1996.03

    Researcher, Tokyo Metropolitan Institute of Medical Science, Japan

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Academic Background 【 Display / hide 】

  • 1987.04
    -
    1990.03

    The University of Tokyo, Graduate School, Division of Pharmaceutical Scienc, Life Science

    Graduate School, Completed, Doctoral course

  • 1985.04
    -
    1987.03

    Waseda University, Graduate School, Division of Science and Engineering, Physics and Applied Physics

    Graduate School, Completed, Master's course

  • 1981.04
    -
    1985.03

    Waseda University, Faculty of Education, Biology

    University, Graduated

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Academic Degrees 【 Display / hide 】

  • Ph. D., The University of Tokyo, Coursework, 1990.03

    Structural and expression analysis of gene clusters for Sarcotoxin I and II, antibacterial proteins of flesh fly, Sarcophaga peregrina

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Research Areas 【 Display / hide 】

  • Life Science / Molecular biology (RNA molecular biology)

  • Life Science / Genome biology (Gene evolution)

  • Life Science / Evolutionary biology (Molecular evolution)

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Research Keywords 【 Display / hide 】

  • Archaea, Bacteria, RNA viruses

  • Systems biology, Synthetic biology, Genome biology

  • Non-codingRNA, transfer RNA, ribosomal RNA, RNA-related enzymes

  • RNA processing, pre-tRNA-splicing, RNA ligase, Ribonuclease

  • Genetic code, Molecular evolution

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Research Themes 【 Display / hide 】

  • (1) RNA-Binding Proteins & RNA-Related Enzymes, (2) Non-coding RNAs, (3) Origin of Life, (4) Molecular Evolution, (5) Microbiomes of Extreme Environments, (6) Systems Biology of Gene Regulation, (7) Evolution of RNA viruses, 

    2001
    -
    Present

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Books 【 Display / hide 】

  • RNAの科学 ―時代を拓く生体分子― (in Japanese)

    Akio Kanai (Ed.), Asakura Publishing Co., Ltd., 2024.06,  Page： 288

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    RNAは，DNAやタンパク質と並んで生命現象を司る基本的な生体分子である。近年，従来知られていた以上に生体内で重要な役割を数多く担っていることが明らかにされつつある。さらに創薬やワクチンなどへの応用も注目を集めている。RNAの基本的なはたらきから最近の知見まで，全体像を俯瞰できる一冊。オールカラー。

  • Molecular Biology 15 Lectures [Basic Edition] in Japanese

    Akio Kanai (Higashinakagawa, T., Kuwayama, S., and Kawamura, A. Ed.), Ohmsha, 2024.10,  Page： 394

    Scope: Lecture 8: RNA functions I Regulation of translation/ Lecture 9: RNA functions II Importance of functional RNAs,  Contact page： 169-210

    　View Summary

    本書は、「学生にとってわかりやすい」かつ「教師にとって使いやすい」ことを基本方針とした、分子生物学の新しいテキストです。分子生物学の基本（基礎的事項）を、多数の図表を用いて、わかりやすくまとめています。また、「基礎的な内容を重視」「入門者にも理解できる丁寧な記述」「詳しすぎない」「適度な分量」等、教科書・参考書に求められるニーズを踏まえた構成としました。

  • Hadean Bioscience (in Japanese)

    Maruyama, S., Ebisuzaki, T., Kanai, A., Kurokawa, K., Asakura Publishing Co., Ltd., 2022.10,  Page： 483

    Scope: Chapter 2: Introduction to biology for the study of the origin of life/ Chapter 10: History and cutting edge of artificial life ,  Contact page： 25-66/ 373-394

  • Study of Corrosion and Degradation of the Objects in the Nuclear Reactor by Microorganisms, JAEA-Review 2021-048

    Kanai, A., Warashina, T., Koma, Y., Nishimura, A., Hinai, H., and Shagimardanova, E., Japan Atomic Energy Agency, 2022.01,  Page： 190

  • 遺伝学の百科事典 継承と多様性の源

    金井昭夫 (公益財団法人 遺伝学普及会 日本遺伝学会 編), 丸善出版, 2022.01,  Page： 690

    Scope: DNA・RNA,  Contact page： 84-85

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Papers 【 Display / hide 】

  • An internal loop region is responsible for inherent target specificity of bacterial Cold-shock proteins

    Hasegawa, S., Inose, R., Igarashi, M., Tsurumaki, M., Saito, M., Yanagisawa, T., Kanai, A., and Morita, T.

    RNA (Cold Spring Harbor Laboratory Press)  31 ( 1 ) 67 - 85 2025.01

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  13558382

    　View Summary

    Cold shock proteins (Csps), of around 70 amino acids, share a protein fold for the cold shock domain (CSD) that contains RNA binding motifs, RNP1 and RNP2, and constitute one family of bacterial RNA-binding proteins. Despite similar amino acid composition, Csps have been shown to individually possess inherent specific functions. Here we identify the molecular differences in Csps that allow selective recognition of RNA targets. Using chimeras and mutants of Escherichia coli CspD and CspA, we demonstrate that Lys43-Ala44 in an internal loop of CspD and the N-terminal portion with Lys4 of CspA are important for determining their target specificities. Pull-down assays suggest these distinct specificities reflect differences in the ability to act on the target RNAs rather than differences in binding to the RNA targets. A phylogenetic tree constructed from 1,573 Csps reveals that the Csps containing Lys-Ala in the loop form a monophyletic clade, and the members in this clade are shown to have target specificities similar to E. coli CspD. The phylogenetic tree also finds a small cluster of Csps containing Lys-Glu in the loop, and these exhibit different specificity than E. coli CspD. Examination of this difference suggests a role of the loop of CspD type proteins in recognition of specific targets. Additionally, each identified type of Csp shows a different distribution pattern among bacteria. Our findings provide a basis for subclassification of Csps based on target RNA specificity, which will be useful for understanding of the functional specialization of Csps.

  • Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences

    Tsurumaki, M., Sato, A., Saito, M., and Kanai, A.

    Journal of Bacteriology (American Society for Microbiology)  206 ( 7 ) e0007424 2024.07

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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    ABSTRACT
    The Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of Candidatus (Ca.) Saccharibacteria and the 16S rRNA genes of Ca. Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI from Ca. Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs.

    IMPORTANCE
    Insertion sequences (ISs) in rRNA genes are relatively limited and infrequent in most bacterial phyla. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.

  • Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station

    Warashina T, Sato A, Hinai H, Shaikhutdinov N, Shagimardanova E, Mori H, Tamaki S, Saito M, Sanada Y, Sasaki Y, Shimada K, Dotsuta Y, Kitagaki T, Maruyama S, Gusev O, Narumi I, Kurokawa K, Morita T, Ebisuzaki T, Nishimura A, Koma Y, Kanai A.

    Applied Enviromental Microbiology (American Society for Microbiology)  90 ( 4 ) e0211323 2024.04

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted,  ISSN  00992240

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    A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 × 10exp9 Bq 137Cs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus Limnobacter, a thiosulfate-oxidizing bacterium. γ-Irradiation tests on Limnobacter thiooxidans, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus Brevirhabdus, a manganese-oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, ~70% of identified genera were associated with metal corrosion. Latent environment allocation-an analytical technique that estimates habitat distributions and co-detection analyses-revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts.

  • Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea

    Takamiya H, Kouduka M, Kato S, Suga H, Oura M, Yokoyama T, Suzuki M, Mori M, Kanai A, Suzuki Y.

    ISME J. (Oxford University Press)  18 ( 1 ) wrae207 2024.11

    Research paper (scientific journal), Accepted,  ISSN  17517362

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    Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.

  • Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei

    Motofumi Saito, Rerina Inose, Asako Sato, Masaru Tomita, Haruo Suzuki & Akio Kanai

    Journal of Molecular Evolution (Springer Nature)  91 ( 5 ) 669 - 686 2023.10

    Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted,  ISSN  00222844

    　View Summary

    The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5′ end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species to classify the diverse Clp1 family proteins. The average number of Clp1 family proteins in eukaryotes was 2.3 ± 1.0, and most representative species had both Clp1 and Nol9/Grc3 proteins, suggesting that the Clp1 and Nol9/Grc3 groups were already formed in the eukaryotic ancestor by gene duplication. We also detected an average of 4.1 ± 0.4 Clp1 family proteins in members of the protist phylum Euglenozoa. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. As in this example, N-terminal and C-terminal domain replacement also contributed to the diversification of the Clp1 family proteins in other eukaryotic species. Our analysis also revealed that the Clp1 family proteins in humans and plants diversified through isoforms created by alternative splicing.

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Papers, etc., Registered in KOARA 【 Display / hide 】

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Reviews, Commentaries, etc. 【 Display / hide 】

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Research Projects of Competitive Funds, etc. 【 Display / hide 】

  • 微生物生態系による原子炉内物体の腐食・変質に関する評価研究

    2019.10
    -
    2020.12

    文部科学省, 英知を結集した原子力科学技術・人材育成事業 国際協力型廃炉研究プログラム（廃炉加速化研究プログラム）, Elena Shagimardanova, Research grant, Principal investigator

    　View Summary

    高放射能環境でも一部の微生物は繁殖する。また、高放射能に繰り返し曝されることにより、放射能耐性を獲得する。福島第一原子力発電所（1F）事故では、定常的に微生物を含んだ地下水が流れ込んでおり、その内部に微生物群集が形作られている可能性が高い。このことから、1F敷地内外の地下水や放射能汚染水のメタゲノム解析により、それらの微生物群集の実態（生物種の群集構造と発現遺伝子プロファイル）を明らかにする。微生物群集の代謝反応経路を推定することにより、微生物生態系の原子炉内構造物に対する影響を調べ、微生物により燃料デブリや構造材（コンクリート、鉄材など）の腐食・変性が促進される可能性を検討する。それらを基に、微生物群集の制御に関する指針を提案するとともに、定常的な生物環境モニタリングのための拠点形成を進める。

  • 多様性を有するRNAキナーゼの進化情報解析とその情報に基づいた酵素機能の改変

    2017.04
    -
    2020.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Principal investigator

  • Identification and biochemical characterization of RNA ligases in archaea

    2010.04
    -
    2012.03

    日本学術振興会, 科研費　, Akio Kanai, 基盤研究(B), Principal investigator

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Awards 【 Display / hide 】

  • 「平成29年度『科研費』審査委員」表彰

    金井昭夫, 2017.09, 独立行政法人 日本学術振興会

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    科学研究費助成事業の審査に関し、有意義な審査意見を付したことによる

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Courses Taught 【 Display / hide 】

  • SPECIAL RESEARCH PROJECT B

    2025

  • SEMINAR B

    2025

  • MASTER SEMINAR

    2025

  • INDEPENDENT RESEARCH

    2025

  • GRADUATION PROJECT 2

    2025

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Courses Previously Taught 【 Display / hide 】

  • ADVANCED MOLECULAR AND CELLULAR BIOLOGY

    Keio University

    2018.04
    -
    2019.03
    , 

    Autumn Semester

  • ADVANCED RESEARCH (SYSTEMS BIOLOGY)

    Keio University

    2018.04
    -
    2019.03
    , 

    Autumn Semester

  • GENOMIC MOLECULAR BIOLOGY 2

    Keio University

    2018.04
    -
    2019.03
    , 

    Autumn Semester

  • CONCEPTUAL FRAMEWORK (SYSTEMS BIOLOGY)

    Keio University

    2018.04
    -
    2019.03
    , 

    Spring Semester

  • GENOMIC MOLECULAR BIOLOGY 1

    Keio University

    2018.04
    -
    2019.03
    , 

    Spring Semester, Lecture

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Memberships in Academic Societies 【 Display / hide 】

  • RNA Society, 

    1999
    -
    Present

  • American Association for the Advancement of Science (AAAS), 

    2001
    -
    Present

  • American Society for Microbiology (ASM), 

    2013.10
    -
    Present

  • RNA Society of Japan (2021 Annual Meeting Organizer) , 

    2012.04
    -
    Present

  • Molecular Biology Society of Japan (MBSJ) , 

    1990
    -
    Present

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Committee Experiences 【 Display / hide 】

  • 2020.05
    -
    Present

    Visiting professor, Yamaguchi University Graduate School of Medicine

  • 2010.10
    -
    2024.12

    Frontiers in Genetics (RNA), Editorial Board – Associate Editor

  • 2010.08
    -
    2023.04

    PLOS ONE, Editorial Board - Academic Editor

  • 2010.06
    -
    2024.02

    Frontiers in Microbiology (Virology), Editorial Board - Review Editor

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