Updated on 2022/10/03

写真b

 
HANAI Ryo
 
*Items subject to periodic update by Rikkyo University (The rest are reprinted from information registered on researchmap.)
Affiliation*
College of Science Department of Life Science
Graduate School of Science Field of Study: Life Science
Graduate School of Science Field of Study: Life Science
Title*
Professor
Degree
Master of Science ( The University of Tokyo ) / PhD ( The University of Tokyo )
Contact information
Mail Address
Research Theme*
  • 分子構造生物物理学。タンパク質・核酸の分子構造と機能の相関およびその細胞中における役割の解明を目標とする。特に、DNAタンパク質複合体を対象とし、生物物理学・分子生物学・生化学の諸手法を組み合わせて研究している。

  • Research Interests
  • 生化学

  • 生物物理化学

  • 生体高分子学

  • 分子生物学

  • Molecular Biophysics

  • Campus Career*
    • 4 2008 - Present 
      College of Science   Department of Life Science   Professor
    • 4 2008 - Present 
      Graduate School of Science   Field of Study: Life Science   Professor
    • 4 2008 - Present 
      Graduate School of Science   Field of Study: Life Science   Professor
    • 4 2007 - 3 2008 
      College of Science   Department of Life Science   Associate Professor
    • 4 2002 - 3 2007 
      College of Science   Department of Life Science   Associate Professor (as old post name)
    • 4 1998 - 3 2002 
      College of Science   Department of Chemistry   Associate Professor (as old post name)
    • 4 1996 - 3 1998 
      College of Science   Department of Chemistry   Lecturer
     

    Research Areas

    • Life Science / Biophysics

    • Life Science / Structural biochemistry

    • Life Science / Molecular biology

    Research History

    • 4 2008 - Present 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Professor

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    • 4 2007 - 3 2008 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Associate Professor

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    • 4 2002 - 3 2007 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Associate Professor (as old post name)

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    • 4 1998 - 3 2002 
      RIKKYO UNIVERSITY   College of Science Department of Chemistry   Associate Professor (as old post name)

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    • 4 1996 - 3 1998 
      RIKKYO UNIVERSITY   College of Science Department of Chemistry   Lecturer

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    • 9 1989 - 3 1996 
      Harvard University

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    • 4 1989 - 8 1989 
      The University of Tokyo   Faculty of Science

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    Education

    • - 3 1989 
      The University of Tokyo   Graduate School, Division of Science

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      Country: Japan

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    • - 3 1984 
      The University of Tokyo   Faculty of Science

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      Country: Japan

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    Papers

    • Chemical and Genetic Diversity of Ligularia kanaitzensis in the Hengduan Mountains Area. Chemical Relationship with L. subspicata

      Ryo Hanai, Yasuko Okamoto, Takuya Hashida, Kosuzu Shiojiri, Ayumi Ohsaki, Yoshinori Saito, Motoo Tori, Xun Gong, Chiaki Kuroda

      Chemistry & Biodiversity18 ( 11 )   11 2021

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      Publishing type:Research paper (scientific journal)   Publisher:Wiley  

      Root chemicals and the sequences of the internal transcribed spacers (ITSs) were analyzed for 9 Ligularia kanaitzensis and 3 L. subspicata samples collected in northwestern Yunnan and southwestern Sichuan, China. Subspicatins A and C were isolated from two L. kanaitzensis samples. Introgression of genes responsible for these compounds from L. subspicata was suggested by their strong connection with L. subspicata/L. lamarum and the geographical proximity of the samples to L. subspicata. DNA analysis of a set of 27 L. kanaitzensis samples including those analyzed previously showed that they belong to two clades, designated A and B. Together with the presence/absence of furanoeremophilane, the 27 samples were sorted into three groups: clade A/furan, clade B/furan, and clade B/non-furan. The ancestral plant presumably belonged to clade B/non-furan, because furanoeremophilanes are biosynthesized from eremophilan-8-ones. 1β-Angeloyloxyfukinone, a likely intermediate between fukinone and subspicatin C, was isolated for the first time. This finding allowed us to propose plausible biosynthetic pathways of subspicatins A and C.

      DOI: 10.1002/cbdv.202100444

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    • Diversity in Eremophilane Components of Ligularia dictyoneura in Yunnan and Sichuan Provinces of China

      Ryo Hanai, Shizuka Watanabe, Mika Matsushima, Hajime Nagano, Chiaki Kuroda, Xun Gong

      Natural Product Communications14 ( 11 )   11 2019

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:{SAGE} Publications  

      <jats:p> The chemical composition of 3 samples of Ligularia dictyoneura was studied. Nine furanoeremophilanes 1 to 9 and bakkenolide A (10) were isolated, among which compound 6 was a new furanoeremophilane-15,6-olide. These results, together with our previous results on 20 L. dictyoneura samples, show that furanoeremophilane is the major compound in the peripheries of the plant’s distribution area, while eremophilan-8-one, in the center. DNA analysis suggests that a furanoeremophilane producer in the center, an exception, is introgressed; namely, the ability to produce furanoeremophilane in the sample may have its origin in some other plant. </jats:p>

      DOI: 10.1177/1934578x19878935

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    • Chemical Composition of Intergeneric Hybrids Between Ligularia and Cremanthodium Collected in Sichuan Province of China

      Yasuko Okamoto, Arisa Fukui, Takuya Hashida, Kosuzu Shiojiri, Chiaki Kuroda, Motoo Tori, Xun Gong, Ryo Hanai

      Natural Product Communications14 ( 11 )   11 2019

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:{SAGE} Publications  

      <jats:p> Two intergeneric hybrids between Ligularia nelumbifolia and Cremanthodium stenoglossum were examined with respect to the chemical composition of root extracts and the sequences of neutral DNA regions. The DNA data showed that the direction of hybridization was different between the individuals. Eremophilane sesquiterpenes were found in both hybrids and deduced to have come from their Cremanthodium parents, because sesquiterpenes were detected in C. stenoglossum but not in L. nelumbifolia. </jats:p>

      DOI: 10.1177/1934578x19878931

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    • Diversity of Furanoeremophilane Composition in Ligularia tongolensis

      Yasuko Okamoto, Yumi Nakadozono, Kosuzu Shiojiri, Sayaka Suehiro, Yoshinori Saito, Yosuke Matsuo, Takashi Tanaka, Chiaki Kuroda, Motoo Tori, Xun Gong, Ryo Hanai

      Natural Product Communications14 ( 10 )   10 2019

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:{SAGE} Publications  

      <jats:p> The composition of root chemicals was studied for 7 samples of Ligularia tongolensis collected in Yunnan and Sichuan Provinces of China. The structures of 2 new 3β-angeloyloxy-6β-acyloxyfuranoeremophilan-15-oic acids were determined. It was found that the plant harbors chemical diversity in the acyloxy groups in 3,6-bis(acyloxy)eremophilan-15-oic acids. The presence of a 3-methylpentanoate moiety at C-3 appears geographically differentiated to a degree. Consistent with this low diversity, results of DNA analysis indicated little genetic differentiation, although introgression was inferred for one of the samples. </jats:p>

      DOI: 10.1177/1934578x19878937

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    • Chemical and Genetic Identity of Ligularia tsangchanensis and L. muliensis. Isolation of a Cacalol Precursor from a Hybrid of L. tsangchanensis and L. vellerea

      Chiaki Kuroda, Taketo Itoh, Yurika Suzuki, Yuko Suzuki, Yasuko Okamoto, Motoo Tori, Ryo Hanai, Xun Gong

      Natural Product Communications13 ( 4 )   4 2018

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:{SAGE} Publications  

      <jats:p> The chemical composition and the DNA sequence of an evolutionarily neutral region were studied for three samples of L. tsangchanensis, three samples of L. muliensis, and one sample of a hybrid between L. tsangchanensis and L. vellerea. L. tsangchanensis and L. muliensis were indistinguishable in the chemical composition and the ITS sequence, supporting a recent taxonomic study that merged the two species into L. tsangchanensis. Cacalol (1) was isolated as the most major component from both L. tsangchanensis and L. muliensis, while 6-acetoxy-9-oxofuranoeremophilane (10), a putative cacalol precursor, was isolated from the hybrid. </jats:p>

      DOI: 10.1177/1934578x1801300402

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    • Chemical and genetic identity of Ligularia tsangchanensis and L. muliensis. Peer-reviewed

      Chiaki Kuroda 他

      Nat. Prod. Commun.14 ( 1 ) 389 - 392   1 2018

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    • Eremophilanes from ligularia hookeri collected in China and structural revision of 3β-acyloxyfuranoeremophilan-15,6-olide

      Yoshinori Saito, Yuko Shiosaki, Miho Fujiwara, Kanako Mihara, Hiromi Nakamizo, Kanako Otose, Yasuko Okamoto, Katsuyuki Nakashima, Ryo Hanai, Chiaki Kuroda, Xun Gong, Yosuke Matsuo, Takashi Tanaka, Motoo Tori

      Chemical and Pharmaceutical Bulletin66 ( 6 ) 668 - 673   2018

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Pharmaceutical Society of Japan  

      Chemical constituents of Ligularia hookeri (Asteraceae) collected in Yunnan and Sichuan Provinces in China were examined for the first time. Seven furanoeremophilanes, five of which were new, as well as known bisabolane- and eudesmane-type sesquiterpenoids, were isolated. Spectroscopic evidence indicates that the previously reported 3β-(2′-methylpropenoyloxy)furanoeremophilan-15,6β-olide should be revised to 3β-(2′-methylpropenoyloxy)furanoeremophilan-15,6α-olide.

      DOI: 10.1248/cpb.c18-00191

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    • Terpenoids and Phenylpropanoids in Ligularia duciformis, L. kongkalingensis, L. nelumbifolia, and L. limprichtii Peer-reviewed

      Chiaki Kuroda, Ryohei Kobayashi, Ayumi Nagata, Yumi Nakadozono, Taketo Itoh, Yasuko Okamoto, Motoo Tori, Ryo Hanai, Xun Gong

      Molecules22 ( 12 ) 2062   1 12 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

      The diversity in root chemicals and evolutionally neutral DNA regions in the complex of Ligularia duciformis, L. kongkalingensis, and L. nelumbifolia (the d/k/n complex) was studied using eight samples collected in central and northern Sichuan Province of China. Cacalol (14) and epicacalone (15), rearranged eremophilanes, were isolated from the complex for the first time. Two new phenylpropanoids were also obtained. Seven of the eight samples produced phenylpropanoids and the other produced lupeol alone. Two of the seven samples also produced furanoeremophilanes or their derivatives and one produced oplopanes. The geographical distribution of the sesquiterpene-producing populations suggests that the production of sesquiterpenes evolved independently in separate regions. L. limprichtii collected in northern Sichuan was also analyzed and its chemical composition and the sequence of internal transcribed spacers (ITSs) in the ribosomal RNA gene cluster were found to be similar to that in the d/k/n complex and L. yunnanensis, which are morphologically similar.

      DOI: 10.3390/molecules22122062

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    • Chemical Diversity in Ligularia oligonema Peer-reviewed

      Chiaki Kuroda, Kou Inagaki, Yasuko Okamoto, Motoo Tori, Ryo Hanai, Hiroka Yamada, Hajime Nagano, Xun Gong

      NATURAL PRODUCT COMMUNICATIONS12 ( 8 ) 1161 - 1164   8 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The chemical composition of a sample of the title species collected in Pianma, Lushui County, Yunnan Province of China, was examined. Two 3,6,10 oxygenated and two 3,6-oxygenated furanoeremophilanes were isolated. Structures of two new compounds were elucidated. The 3,6-oxygenated furanoeremophilanes were not detected in a sample of the same species previously collected in Laojunshan, Jianchuan County, Yunnan, indicating chemical diversity in the species.

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    • Intra-specific diversity of the chemical composition of Ligularia lamarum in the Hengduan Mountains, China: The structures of four new eremophilanes and a new seco-eremophilane Peer-reviewed

      Yoshinori Saito, Motoki Hidaka, Akane Fukuda, Yasuko Okamoto, Katsuyuki Nakashima, Motoo Tori, Ryo Hanai, Xun Gong, Eiji Watanabe, Chiaki Kuroda

      PHYTOCHEMISTRY LETTERS20   139 - 145   6 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

      Chemical compositions and internal transcribed spacer (ITS) sequences of five samples of Ligularia lamarum collected in Sichuan Province, China, were analyzed. Fourteen compounds, including four new eremophilanes and one new seco-eremophilane, were isolated and their structures were elucidated by spectroscopic methods. Intra-specific diversity in the chemical composition was found to be higher than previously known. The result of DNA analysis suggested that one of the samples was introgressed, although its chemical composition was typical of L. lamarum.

      DOI: 10.1016/j.phytol.2017.04.026

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    • Chemical and Genetic Study of two Ligularia Hybrids in Shangrila County, Yunnan Province, China Peer-reviewed

      Rye Hanai, Sayako Tanabe, Nao Aoyama, Yasuko Okamoto, Motoo Tori, Ningning Zhang, Xun Gong, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS11 ( 8 ) 1057 - 1060   8 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The composition of root chemicals was examined for samples of L. cyathiceps x L. duciformis, L. duciformis x L. yunnanensis, and L. yunnanensis. Various furanoeremophilanes were isolated from a sample of L. cyathiceps x L. duciformis and found to be very similar to those isolated from L. cyathiceps. Lupeol and docosyl ferulate were isolated from L. yunnanensis, L. duciformis, and L. duciformis x L. yunnanensis.

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    • Three New Eremophilanes from a Ligularia Hybrid Collected in China Peer-reviewed

      Yoshinori Saito, Yuriko Takashima, Yasuko Okamoto, Xun Gong, Ryo Hanai, Chiaki Kuroda, Motoo Tori

      NATURAL PRODUCT COMMUNICATIONS11 ( 7 ) 901 - 904   7 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Three New Eremophilanes from a Ligularia Hybrid Collected in China

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    • Chemical constituents in hybrids of Ligularia tongolensis and L. cymbulifera: chemical introgression in L. tongolensis. Peer-reviewed

      Shimizu, A, Hanai, R. 他

      Chem. Biodiv.13 ( 7 ) 837 - 844   6 2016

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    • Chemical Constituents of Ligularia wilsoniana Collected in Chongqing, China Peer-reviewed

      Yasuko Okamota, Mizuho Taniguchi, Katsuyuki Nakashima, Xun Gong, Ryo Hanai, Chiaki Kuroda, Motoo Tori

      NATURAL PRODUCT COMMUNICATIONS11 ( 2 ) 149 - 152   2 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The chemical constituents of Ligularia wilsoniana were studied for the first time, using four samples collected in Chongqing City, China. Two new compounds, 6 beta-(2',3'-Lepoxy-2'-methylpropanoyloxy)-1 beta,10 beta-epoxyfuranoeremophilane and 11 alpha H-6 beta-(2'-hydroxymethylacryloyloxy)-1 beta,10 beta;7 beta,8 beta-diepoxyeremophilanolide, as well as eight known compounds, were isolated from one of the samples, while three to four known furanoeremophilanes were isolated from the other three samples. No compound was common to the two classes of the samples, demonstrating the presence of at least two chemotypes of this species.

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    • Diversity in Chemical Constituents of Ligularia longihastata Collected in China Peer-reviewed

      Yasuko Okamoto, Mizuho Taniguchi, Kaori Terada, Katsuyuki Nakashima, Xun Gong, Ryo Hanai, Motoo Tori, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS11 ( 2 ) 145 - 148   2 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Root constituents of Ligularia longihastata were examined for the first time. Fourteen eremophilane sesquiterpenes, including two new eremophilanes identified as 3a-isobutyroyloxy-7 beta H-eremophila-9,11-dien-8-one and 3 beta-angeloyloxy-1 beta,10 beta-epoxyfuranoeremophilan-9-one, and three eudesmanes were isolated. From samples collected in Baiyu County, Sichuan Province, furanoeremophilane derivatives were isolated, while various eremophilan-8-ones were isolated from samples collected in Kangding County, Sichuan. The results suggest chemical diversity in the species.

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    • Chemical Lineages of Ligularia fischeri Peer-reviewed

      Chiaki Kuroda, Chiemi Shibayama, Kyosuke Inoue, Yasuko Okamoto, Motoo Tori, Yoshinori Saito, Ryo Hanai, Xun Gong

      NATURAL PRODUCT COMMUNICATIONS11 ( 2 ) 139 - 143   2 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Six Ligularia fischeri samples, two from Sichuan (samples 1 and 2) and four from Chongqing (samples 3-6), were examined for root chemicals and the DNA sequence of the internal transcribed spacers of the ribosomal RNA gene. Samples 2 and 3 contained benzofurans. The isolation of benzofurans shows that the chemical diversity in L. fischeri is higher than previously reported. Samples 1, 4, 5, and 6 contained eremophilanes. However, the compounds were different between sample 1 and samples 4-6, indicating variation within eremophilane producers. DNA data indicated that introgression could be a mechanism of benzofuran production in sample 2 and that sample 1 and samples 4-6 were genetically separate.

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    • Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis Peer-reviewed

      Genki Akanuma, Yuka Kazo, Kazumi Tagami, Hirona Hiraoka, Koichi Yano, Shota Suzuki, Ryo Hanai, Hideaki Nanamiya, Yasuyuki Kato-Yamada, Fujio Kawamura

      Microbiology (United Kingdom)162 ( 3 ) 448 - 458   1 2 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:Microbiology Society  

      Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, Δhpf mutant cells grew slower than WT cells. This observed lag in growth of Δhpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions.

      DOI: 10.1099/mic.0.000234

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    • Chemical and Genetic Diversity of Ligularia hodgsonii in China

      Chiaki Kuroda, Kou Inagaki, Xun Chao, Kyosuke Inoue, Yasuko Okamoto, Motoo Tori, Xun Gong, Ryo Hanai

      NATURAL PRODUCT COMMUNICATIONS10 ( 6 ) 823 - 826   6 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Ligularia hodgsonii was found to be diverse in China. Furanoeremophilanes were isolated from samples collected in Yunnan Province, while such compounds were absent from samples from Sichuan, Gansu, and Chongqing. DNA sequencing showed that the Yunnan samples were also genetically distinct. gamma-Humulene and a new bisabolane sesquiterpene were isolated.

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    • New roles of DNA and SopB in polymerization of SopA of Escherichia coli F plasmid Peer-reviewed

      Ryo Hanai, Yui Arai

      JOURNAL OF BIOCHEMISTRY157 ( 6 ) 459 - 466   6 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

      Active equi-paritioning of the F plasmid is achieved by its sopABC gene. SopA binds to the sopAB promoter region and SopB binds to sopC. SopA also polymerizes in the presence of ATP and Mg(II), which is stimulated by SopB. Non-specific DNA is known to inhibit SopA polymerization and disassemble SopA polymer. This study followed kinetics of polymerization and de-polymerization of SopA by turbidity measurement and found new effects by DNA and SopB. Plasmid DNA, at low concentrations, shortened the lag (nucleation) phase of SopA polymerization and also caused an initial 'burst' of turbidity. Results with two non-specific 20-bp DNAs indicated sequence/length dependence of these effects. sopAB operator DNA only showed inhibition of SopA polymerization. Results of turbidity decrease of pre-formed SopA polymer in the presence of ethylenediaminetetraacetic acid showed that SopB also accelerates disassembly of the SopA polymer. The steady-state level of turbidity in the presence of SopB and plasmid DNA indicated synergy between SopB and DNA in the disassembly. SopB protein showed no effect on SopA polymerization, when SopB was specifically bound to DNA. This result and others with truncation mutants of SopB suggested that a proper configuration of the domains of SopB is important for SopA-SopB interactions.

      DOI: 10.1093/jb/mvv003

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    • Chemotypes of Ligularia vellerea, its Hybrids, and L. melanothyrsa Peer-reviewed

      Anna Shimizu, Kyosuke Inoue, Mayu Ichihara, Ryo Hanai, Yoshinori Saito, Yasuko Okamoto, Motoo Tori, Xun Gong, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS10 ( 1 ) 9 - 12   1 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Ligztlaria vellerea and L. melanothyrsa have been found to share chemical characteristics based on geography. In one chemotype (Shangrila type), the major components were either 15-oxygenated furanoeremophilanes or eremophilanolides; and in another (Luguhu type), either 1-angeloyloxyfuranoeremophilanes or corresponding lactones. The two L. vellerea samples were found to have experienced hybridization with either L. cyathiceps or L. kanaitzensis; however, compounds typical of L. vellerea alone were isolated from them.

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    • Defect in the Formation of 70S Ribosomes Caused by Lack of Ribosomal Protein L34 Can Be Suppressed by Magnesium Peer-reviewed

      Genki Akanuma, Ako Kobayashi, Shota Suzuki, Fujio Kawamura, Yuh Shiwa, Satoru Watanabe, Hirofumi Yoshikawa, Ryo Hanai, Morio Ishizuka

      JOURNAL OF BACTERIOLOGY196 ( 22 ) 3820 - 3830   11 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC MICROBIOLOGY  

      To elucidate the biological functions of the ribosomal protein L34, which is encoded by the rpmH gene, the rpmH deletion mutant of Bacillus subtilis and two suppressor mutants were characterized. Although the Delta rpmH mutant exhibited a severe slow-growth phenotype, additional mutations in the yhdP or mgtE gene restored the growth rate of the Delta rpmH strain. Either the disruption of yhdP, which is thought to be involved in the efflux of Mg2+, or overexpression of mgtE, which plays a major role in the import of Mg2+, could suppress defects in both the formation of the 70S ribosome and growth caused by the absence of L34. Interestingly, the Mg2+ content was lower in the Delta rpmH cells than in the wild type, and the Mg2+ content in the Delta rpmH cells was restored by either the disruption of yhdP or overexpression of mgtE. In vitro experiments on subunit association demonstrated that 50S subunits that lacked L34 could form 70S ribosomes only at a high concentration of Mg2+. These results showed that L34 is required for efficient 70S ribosome formation and that L34 function can be restored partially by Mg2+. In addition, the Mg2+ content was consistently lower in mutants that contained significantly reduced amounts of the 70S ribosome, such as the Delta rplA (L1) and Delta rplW (L23) strains and mutant strains with a reduced number of copies of the rrn operon. Thus, the results indicated that the cellular Mg2+ content is influenced by the amount of 70S ribosomes.

      DOI: 10.1128/JB.01896-14

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    • Chemical and Genetic Studies on Hybrid of Ligularia subspicata and Ligularia cyathiceps Collected in Yunnan Province of China Peer-reviewed

      Anna Shimizu, Shizuka Watanabe, Ryo Hanai, Yasuko Okamoto, Motoo Tori, Xun Gong, Chiaki Kuroda

      CHEMISTRY & BIODIVERSITY11 ( 9 ) 1438 - 1448   9 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

      Two morphologically ambiguous Ligularia samples (samples A and B), and samples with morphology of Ligularia subspicata (sample C), Ligularia lamarum (sample D), or Ligularia cyathiceps (sample E), were collected at Tianchi Pond, Shangrila County, Yunnan Province, China. Analysis of the nucleotide sequence of the internal transcribed spacers (ITSs) in the nuclear ribosomal RNA gene cluster indicated that not only sample B but also sample D was a hybrid of L. cyathiceps and L. lamarum/ L. subspicata. Although the morphology of sample A suggested that it was also a hybrid, the ITS sequence of sample Awas that of L. cyathiceps. Twenty compounds were isolated from the five samples, and the structures of two new compounds 7 and 14 were determined. Furanoeremophilanes typical of L. lamarum/ L. subspicata were detected not only in samples C and D, but also in samples A and B. These results indicate that the ability to produce root chemicals can spread through introgression.

      DOI: 10.1002/cbdv.201400133

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    • Chemical and genetic similarity and diversity of Ligularia anoleuca and L. fischeri collected in the Hengduan Mountains of China Peer-reviewed

      Anna Shimizu, Yurika Suzuki, Ryo Hanai, Yasuko Okamoto, Motoo Tori, Xun Gong, Chiaki Kuroda

      PHYTOCHEMISTRY102   137 - 144   6 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      The sesquiterpenoid composition in the root and the DNA sequences of evolutionarily neutral regions were studied in Ligularia anoleuca and Ligularia fischeri (Asteraceae) collected in the Sichuan Province of China. LC-MS analysis showed that L anoleuca populations from different localities had different chemical compositions. However, the isolated compounds were similar to each other, indicating that the differences in chemical composition were not large. The DNA analysis suggested that the two species were indistinguishable. Seventeen furanoeremophilanes and an eremophilane acetal were isolated. (C) 2014 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.phytochem.2014.03.019

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    • The First Isolation of Furanoeremophilane from Ligularia nelumbifolia

      Hiroshi Hirota, Yurie Horiguchi, Satoru Kawaii, Ryo Hanai, Xun Gong, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS9 ( 3 ) 325 - 327   3 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      Ligularol (1), a furanoeremophilane, was isolated together with eremophil-1(10)-en-11-ol (2) from one of eight collected samples of Ligularia nelumbifolia and L. kongkalingensis, a closely related species. It is proposed that the ability to produce the furanoeremophilane has been acquired through hybridization.

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    • Chemical and genetic diversity of Cremanthodium lineare Peer-reviewed

      Yoshinori Saito, Mayu Ichihara, Koji Takiguchi, Yui Tanio, Yasuko Okamoto, Ryo Hanai, Chiaki Kuroda, Takayuki Kawahara, Xun Gong, Motoo Tori

      PHYTOCHEMISTRY96   184 - 190   12 2013

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      Chemical constituents and evolutionally neutral DNA sequences of six samples of Cremanthodium lineare Maxim., collected in the Sichuan Province of China, were studied. Three samples produced furanoeremophilanes and the other three, eremophilan-8-ones. The chemotypes were found to be correlated with DNA sequence types, suggesting that the chemical diversity observed has a genetic origin. Production of furanoeremophilanes by a Cremanthodium species suggests an evolutionary relationship between Cremanthodium and Ligularia species, and possibly to related genera. (C) 2013 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.phytochem.2013.08.009

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    • R-loop formation in trans at an AGGAG repeat Peer-reviewed

      Kazuya Toriumi, Takuma Tsukahara, Ryo Hanai

      Journal of Nucleic Acids2013   2013

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      Formation of RNA-DNA hybrid, or R-loop, was studied in vitro by transcribing an AGGAG repeat with T7 RNA polymerase. When ribonuclease T1 was present, R-loop formation in cis was diminished, indicating that the transcript was separated from the template and reassociated with it. The transcript was found to form an R-loop in trans with DNA comprising the AGGAG repeat, when the DNA was supercoiled. Results of chemical modification indicated that the duplex opened at the AGGAG repeat under negative supercoiling. © 2013 Kazuya Toriumi et al.

      DOI: 10.1155/2013/629218

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    • Chemical and genetic diversity of Ligularia virgaurea collected in northern Sichuan and adjacent areas of China. Isolation of 13 new compounds Peer-reviewed

      Yoshinori Saito, Yuriko Takashima, Aya Kamada, Yurika Suzuki, Midori Suenaga, Yasuko Okamoto, Yoichi Matsunaga, Ryo Hanai, Takayuki Kawahara, Xun Gong, Motoo Tori, Chiaki Kuroda

      TETRAHEDRON68 ( 48 ) 10011 - 10029   12 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      Root chemicals and DNA sequences were analyzed for Ligularia virgaurea collected in the northern Sichuan Province and adjacent areas of China. Thirty-eight samples were found to contain five chemotypes, two known and three new ones. From samples of the new chemotypes, 13 new compounds were isolated, including 3 sesquiterpene dimers and some rearranged eremophilanes. The DNA sequences suggested that the chemotype differentiation had a genetic origin. (C) 2012 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.tet.2012.09.042

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    • Expression of a small (p)ppGpp synthetase, YwaC, in the (p)ppGpp(0) mutant of Bacillus subtilis triggers YvyD-dependent dimerization of ribosome Peer-reviewed

      Kazumi Tagami, Hideaki Nanamiya, Yuka Kazo, Marie Maehashi, Shota Suzuki, Eri Namba, Masahiro Hoshiya, Ryo Hanai, Yuzuru Tozawa, Takuya Morimoto, Naotake Ogasawara, Yasushi Kageyama, Katsutoshi Ara, Katsuya Ozaki, Masaki Yoshida, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, Yoshiaki Ohashi, Fujio Kawamura

      MICROBIOLOGYOPEN1 ( 2 ) 115 - 134   6 2012

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      To elucidate the biological functions of small (p)ppGpp synthetases YjbM and YwaC of Bacillus subtilis, we constructed RIK1059 and RIK1066 strains carrying isopropyl-beta-D-thiogalactopyranoside (IPTG) inducible yjbM and ywaC genes, respectively, in the Delta relA Delta yjbM Delta ywaC triple mutant background. While the uninduced and IPTG-induced RIK1059 cells grew similarly in LB medium, the growth of RIK1066 cells was arrested following the addition of IPTG during the early exponential growth phase. Induction of YwaC expression by IPTG also severely decreased the intracellular GTP level and drastically altered the transcriptional profile in RIK1066 cells. Sucrose density gradient centrifugation analysis of the ribosomal fractions prepared from the IPTG-induced RIK1066 cells revealed three peaks corresponding to 30S, 50S, and 70S ribosome particles, and also an extra peak. Electron microscope studies revealed that the extra peak fraction contained dimers of 70S ribosomes, which were similar to the Escherichia coli 100S ribosomes. Proteomic analysis revealed that the 70S dimer contained an extra protein, YvyD, in addition to those found in the 70S ribosome. Accordingly, strain resulting from the disruption of the yvyD gene in the RIK1066 cells was unable to form 70S dimers following IPTG induction, indicating that YvyD is required for the formation of these dimers in B. subtilis.

      DOI: 10.1002/mbo3.16

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    • Expression of a small (p)ppGpp synthetase, YwaC, in the (p)ppGpp(0) mutant of Bacillus subtilis triggers YvyD-dependent dimerization of ribosome Peer-reviewed

      Kazumi Tagami, Hideaki Nanamiya, Yuka Kazo, Marie Maehashi, Shota Suzuki, Eri Namba, Masahiro Hoshiya, Ryo Hanai, Yuzuru Tozawa, Takuya Morimoto, Naotake Ogasawara, Yasushi Kageyama, Katsutoshi Ara, Katsuya Ozaki, Masaki Yoshida, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, Yoshiaki Ohashi, Fujio Kawamura

      MICROBIOLOGYOPEN1 ( 2 ) 115 - 134   6 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

      To elucidate the biological functions of small (p)ppGpp synthetases YjbM and YwaC of Bacillus subtilis, we constructed RIK1059 and RIK1066 strains carrying isopropyl-beta-D-thiogalactopyranoside (IPTG) inducible yjbM and ywaC genes, respectively, in the Delta relA Delta yjbM Delta ywaC triple mutant background. While the uninduced and IPTG-induced RIK1059 cells grew similarly in LB medium, the growth of RIK1066 cells was arrested following the addition of IPTG during the early exponential growth phase. Induction of YwaC expression by IPTG also severely decreased the intracellular GTP level and drastically altered the transcriptional profile in RIK1066 cells. Sucrose density gradient centrifugation analysis of the ribosomal fractions prepared from the IPTG-induced RIK1066 cells revealed three peaks corresponding to 30S, 50S, and 70S ribosome particles, and also an extra peak. Electron microscope studies revealed that the extra peak fraction contained dimers of 70S ribosomes, which were similar to the Escherichia coli 100S ribosomes. Proteomic analysis revealed that the 70S dimer contained an extra protein, YvyD, in addition to those found in the 70S ribosome. Accordingly, strain resulting from the disruption of the yvyD gene in the RIK1066 cells was unable to form 70S dimers following IPTG induction, indicating that YvyD is required for the formation of these dimers in B. subtilis.

      DOI: 10.1002/mbo3.16

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    • Chemical and Genetic Study of Ligularia duciformis and Related Species in Sichuan and Yunnan Provinces of China Peer-reviewed

      Hajime Nagano, Ryo Hanai, Hiroka Yamada, Mika Matsushima, Yui Miura, Takanori Hoya, Masaaki Ozawa, Miho Fujiwara, Hikari Kodama, Atsushi Torihata, Hiroyuki Onuki, Yoko Nezu, Satoru Kawai, Mizue Yamazaki, Hiroshi Hirota, Yoshinori Saito, Motoo Tori, Ayumi Ohsaki, Xun Gong, Chiaki Kuroda

      CHEMISTRY & BIODIVERSITY9 ( 4 ) 789 - 805   4 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

      The chemical constituents of the root extracts and the evolutionarily neutral DNA base sequences were studied for 28 samples of Ligularia duciformis, L. kongkalingensis, and L. nelumbifolia collected in Sichuan and Yunnan Provinces of China. The samples could be classified into four chemotypes (14). Sesquiterpenoids having eremophilane and oplopane skeletons were isolated from two (Chemotype 1) and three (Chemotype 2) samples, respectively. Two new oplopane derivatives were isolated and their structures were determined. In 18 samples, phenylpropenoids were the major components (Chemotype 3). In five samples, neither phenylpropenoids nor sesquiterpenoids were found (Chemotype 4). Despite this large chemical variety, no correlation was found between the chemotype and the morphological criteria of species identification. The analysis of the evolutionarily neutral DNA regions also indicated that the samples were not separated into distinct clades and that introgression was extensive.

      DOI: 10.1002/cbdv.201100240

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    • Four New Bisabolane-type Sesquiterpenes from Ligularia lankongensis Peer-reviewed

      Hiroshi Hirota, Yurie Horiguchi, Satoru Kawaii, Chiaki Kuroda, Ryo Hanai, Xun Gong

      NATURAL PRODUCT COMMUNICATIONS7 ( 4 ) 451 - 454   4 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The chemical constituents of the roots of two Ligularia lankongensis samples collected in Yunnan and Sichuan Provinces, China, were investigated, together with the DNA sequence of the atpB-rbcL and ITS regions. Four new highly oxygenated bisabolane-type sesquiterpenes (1 - 4) were obtained. Intraspecific diversity in the DNA sequence was found to be limited.

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    • Complex Diversity in Ligularia kanaitzensis Peer-reviewed

      Anna Shimizu, Yurika Suzuki, Atsushi Torihata, Ryo Hanai, Yoshinori Saito, Motoo Tori, Xun Gong, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS7 ( 4 ) 431 - 434   4 2012

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      Two samples of Ligularia kanaitzensis collected in the Shizhongshan Mountain region of Yunnan Province, as well as one sample collected in Sichuan Province, were analyzed with regard to root constituents and neutral DNA sequences. The two Shizhongshan samples were found to be different from each other and from other samples analyzed previously, indicating that the intra-specific diversity in the species was highly complex.

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    • Four New Bisabolane-type Sesquiterpenes from Ligularia lankongensis Peer-reviewed

      Hiroshi Hirota, Yurie Horiguchi, Satoru Kawaii, Chiaki Kuroda, Ryo Hanai, Xun Gong

      NATURAL PRODUCT COMMUNICATIONS7 ( 4 ) 451 - 454   4 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The chemical constituents of the roots of two Ligularia lankongensis samples collected in Yunnan and Sichuan Provinces, China, were investigated, together with the DNA sequence of the atpB-rbcL and ITS regions. Four new highly oxygenated bisabolane-type sesquiterpenes (1 - 4) were obtained. Intraspecific diversity in the DNA sequence was found to be limited.

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    • Chemical constituents of ligularia nelumbifolia and l. subspicata hybrid collected in shangrila county, yunnan province of china Peer-reviewed

      Ryo Hanai, Hiroka Yamada, Yurika Suzuki, Hajime Nagano, Takayuki Kawahara, Jiao-Jun Yu, Xun Gong, Chiaki Kuroda

      Natural Product Communications7 ( 12 ) 1565 - 1568   2012

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      Four Ligularia individuals possessing morphological characters of both L. nelumbifolia and L. subspicata were discovered in Shangrila County, Yunnan Province, China. DNA sequencing showed that the specimens were hybrids of the two species and their maternal parent was L. subspicata. The chemical composition of the root extract was examined for three of them as well as L. nelumbifolia and L. subspicata collected sympatrically. Nelumol was isolated from L. nelumbifolia, and furanoeremophilanes from L. subspicata. While nelumol and furanoeremophilanes were detected in two of the hybrid samples, only furanoeremophilanes were detected in the others.

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    • Overlapping chemical and genetic diversity in Ligularia lamarum and Ligularia subspicata. Isolation of ten new eremophilanes and a new seco-bakkane compound. Peer-reviewed

      Saito et

      Tetrahedron67   2220 - 2231   2 2011

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    • Mode of DNA binding by SopA protein of Escherichia coli F plasmid Peer-reviewed

      Masahiko Komai, Masafumi Umino, Ryo Hanai

      JOURNAL OF BIOCHEMISTRY149 ( 4 ) 455 - 461   2011

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

      The binding of SopA to the promoter region of its own gene, in which four copies of SopA's recognition sequence, 5'-CTTTGC-3', are arrayed asymmetrically, was examined in vitro. Titration using electrophoretic mobility shift assay showed that the stoichiometry of SopA protomers to the promoter-region DNA is 4 and that the binding is highly co-operative. The co-operativity was corroborated by EMSA and DNase I footprinting for a number of mutant DNA fragments in which 5'-CTTTGC-3' was changed to 5'-CTTACG-3'. EMSA in the style of circular permutation showed that SopA bends DNA. Mutation at either outermost binding site had a different effect on DNA bending by SopA, reflecting the asymmetry in the arrangement of the binding sites, for which the results of DNase I footprinting were in agreement. Gel filtration chromatography and analytical ultracentrifugation of free SopA showed that the protein can exist as a monomer and oligomers in the absence of ATP. Hence, the results indicate that the co-operativity in SopA's DNA binding is based on its intrinsic protein-protein interaction modified by DNA interaction.

      DOI: 10.1093/jb/mvq151

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    • Direct MS Measurement of the Extract of Ligularia virgaurea collected in Yunnan and Sichuan Provinces of China Peer-reviewed

      Yasuko Okamoto, Yoshinori Saito, Chiaki Kuroda, Ryo Hanai, Xun Gong, Motoo Tori

      PHYTOCHEMICAL ANALYSIS21 ( 6 ) 513 - 523   11 2010

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:JOHN WILEY & SONS LTD  

      Introduction - There are numerous Ligularia species in the eastern Qinghai-Tibet Plateau and adjacent areas. L. virgaurea has been used as a traditional folk medicine for the treatment of stomachache and nausea.
      Objective - To analyse chemical constituents of L. virgaurea, grown in Yunnan and Sichuan provinces of China.
      Methodology - The direct MS measurement of the crude extract of plant samples was used for grouping of this species. As the main compounds were available in pure form, the main peaks were analysed by LCMS.
      Results - An easy and speedy method of analysis using MS spectra was developed. On the basis of the findings, L. virgaurea could be divided into two groups. The genetic studies also supported this grouping. Type 1 mainly includes virgaurenones and virgaurenolides. The MS of type 2 is quite different because it includes mainly ligularol and its congeners. Both MS were easily distinguished.
      Conclusion - The crude extracts of 11 L. virgaurea samples already collected in recent years were analysed and it was possible to identify them as type 1 or 2. This method was applied to three samples collected in 2009 to successfully classify them as either type 1 or 2. Copyright (C) 2010 John Wiley & Sons, Ltd.

      DOI: 10.1002/pca.1219

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    • Two New Furanoeremophilane Sesquiterpenoids from Ligularia oligonema Peer-reviewed

      Hajime Nagano, Mika Matsushima, Hiroka Yamada, Ryo Hanai, Xun Gong, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS5 ( 1 ) 1 - 4   1 2010

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      From the roots of Ligularia oligonema and an unidentified sample of Ligularia collected in Yunnan Province of China, two new sesquiterpenoids, 3 beta-acetoxy-6 beta-(2-methylbutyryloxy)furanoereinophilan-10 beta-ol and 3 beta-acetoxy-6 beta-isobutyryloxyfuranoeremophilan-10 beta-ol, were isolated. DNA sequencing showed that the unidentified sample was likely to be L. oligonema. In addition, the DNA data suggested that the chemical evolution among L. oligonema and related Ligularia species is rather complex.

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    • Chemical and Genetic Study of Ligularia anoleuca and L. veitchiana in Yunnan and Sichuan Provinces of China Peer-reviewed

      Hajime Nagano, Midori Kanda, Hiroka Yamada, Ryo Hanai, Xun Gong, Chiaki Kuroda

      HELVETICA CHIMICA ACTA93 ( 10 ) 1945 - 1952   2010

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

      Chemical and genetic study of Ligularia anoleuca and L. veitchiana, which belong to section Ligularia, series Speciosae, was carried out. From L. anoleuca samples, collected in Yunnan and Sichuan Provinces of China, a new compound, furanoeremophil-1(10)-en-6 alpha-ol, was isolated together with known 6 beta-{[2-(hydroxymethyl)prop-2-enoyl]oxy}furanoeremophil-1(10)-ene and 1 beta,10 beta-epoxy-6 beta-{[2-(hydroxymethyl)prop-2-enoyl]oxy}furanoeremophilane. From L. veitchiana samples, collected in Yunnan Province, euparin, 2-isopropenyl-5,6-dimethoxybenzofuran, and 6-hydroxy-3 beta-methoxytrementone were isolated. DNA Sequencing of the internal transcribed spacers of the ribosomal RNA gene showed that the two species are not particularly close despite morphological similarities, in agreement with the chemical results.

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    • Chemical and Genetic Study of Ligularia cyathiceps in Yunnan Province of China Peer-reviewed

      Hajime Nagano, Atsushi Torihata, Mika Matsushima, Ryo Hanai, Yoshinori Saito, Makiko Baba, Yui Tanio, Yasuko Okamoto, Yuriko Takashima, Mayu Ichihara, Xun Gong, Chiaki Kuroda, Motoo Tori

      HELVETICA CHIMICA ACTA92 ( 10 ) 2071 - 2081   2009

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      Root chemicals and evolutionarily neutral DNA regions in L. cyathiceps samples collected in the Zhongdian (Shangrila) County of Yunnan, P. R. China, were examined. Twenty compounds were isolated, including three new ones, 1 beta,10 beta-epoxy-6 beta-(propionyloxy)furanoeremophilan-9-one (6), 1 beta,10 beta-epoxy-8 alpha-ethoxyeremophila-6,11-diene (14), and 11 alpha H-6 beta-isobutyryloxy-1 beta,10 beta,7 beta,8 beta-diepoxyeremophilan-12,8 alpha-olide (15). The chemical diversity was found to be limited, with cacalol (1) and 6(acyloxy)furanoeremophilan-9-ones (4 and/or5) being major components in all the samples. The nuclear ribosomal RNA gene was also found to harbor little variation, although two distinct sequence types were found for the plastid atp B-rbcL intergenic region.

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    • Chemical and Genetic Differentiation of Ligularia hodgsonii in Japan and China Peer-reviewed

      Atsushi Torihata, Xun Chao, Chiaki Kuroda, Ryo Hanai, Hiroshi Hirota, Xun Gong

      CHEMISTRY & BIODIVERSITY6 ( 12 ) 2184 - 2191   2009

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

      The chemical composition of the root extract and neutral base sequences of L. hodgsonii samples collected in Japan and China were examined. From the Japanese and the Chinese samples, 6 beta-(angeloyloxy)furanoeremophilan-15-oic acid (2) and 3 beta-acetoxy-6 beta-[(2-methyl butanoyl)oxy]furaneremophilan-10 beta-ol (3) were isolated as the major component, respectively. The sequence of the internal transcribed spacers (ITSs) of the ribosomal RNA gene was different in the Japanese and the Chinese samples. In contrast to the significant genetic difference, chemical diversity was limited to the positions of O-functionalities on the furanoeremophilane skeleton, supporting our hypothesis that the production of furanocremophilanes is ecologically advantageous,

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    • Isolation of new eremophilane-type sesquiterpenoids, subspicatins A-D and subspicatolide from Ligularia subspicata, and chemical and genetic diversity of the species Peer-reviewed

      Motoo Tori, Yasuko Okamoto, Kana Tachikawa, Kanako Mihara, Aki Watanabe, Misato Sakaoku, Shigeru Takaoka, Masami Tanaka, Xun Gong, Chiaki Kuroda, Masato Hattori, Ryo Hanai

      TETRAHEDRON64 ( 38 ) 9136 - 9142   9 2008

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      New C-1 oxidized eremophilane-type sesquiterpenoids, subspicatins A, B, C, and D, and subspicatolide, were isolated from the root of Ligularia subspicata and their structures were established by spectroscopic and X-ray analyses. Subspicatins A and B were the major components. The species were found to be diverse both in the composition of the root chemicals and in the nucleotide sequences of the internal transcribed spacers (ITS) of the ribosomal RNA gene and the atpB-rbcL intergenic region, but the difference among the samples was not distinct but continuous. (C) 2008 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.tet.2008.06.077

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    • Chemical and genetic diversity of Ligularia vellerea in Yunnan Province of China. Peer-reviewed

      Tori M, Nakamizo H, Mihara K, Sato M, Okamoto Y, Nakashima K, Tanaka M, Saito Y, Sono M, Gong X, Shen Y, Hanai R, Kuroda C

      Phytochemistry69 ( 5 ) 1158 - 1165   5 2008

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    • Diversity of Ligularia kanaitzensis in sesquiterpenoid composition and neutral DNA sequences Peer-reviewed

      Motoo Tori, Aki Watanabe, Sachie Matsuo, Yasuko Okamoto, Kana Tachikawa, Shigeru Takaoka, Xun Gong, Chiaki Kuroda, Ryo Hanai

      TETRAHEDRON64 ( 19 ) 4486 - 4495   5 2008

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      Twenty-six eremophilane-type sesquiterpenoids, including six new compounds, were isolated from the title species. One of the new compounds, kanaitzensol, suggested the presence of an enzyme for the conversion of eremophil-7(11)-en-8-one derivative to furanoeremophilanes. The plant was collected at 15 locations in Yunnan Province of China and found to be diverse with respect to its sesquiterpenoid composition. DNA sequencing also revealed a large intraspecific diversity of the plant. (c) 2008 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.tet.2008.02.036

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    • Chemical constituents and diversity of Ligularia lankongensis in Yunnan Province of China Peer-reviewed

      Hiroyuki Onuki, Mizue Yamazaki, Anri Nakamura, Ryo Hanai, Chiaki Kuroda, Xun Gong, Yuemao Shen, Hiroshi Hirota

      JOURNAL OF NATURAL PRODUCTS71 ( 4 ) 520 - 524   4 2008

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

      The chemical constituents of the roots of Ligularia lankongensis collected at seven different places in Yunnan Province, China, were investigated together with the DNA sequence of the atpB-rbcL intergenic region. All the samples contained a new, highly oxygenated bisabolane-type sesquiterpene (1). Four other oxygenated bisabolanes (2 and the new 3, 4, and 5) were also obtained. Intraspecific diversity was observed in the composition of the compounds, but not in the DNA sequence.

      DOI: 10.1021/np070195p

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    • Chemical constituents of Ligularia franchetiana collected in Yunnan Province of China. Peer-reviewed

      Tori M, Tanio Y, Okamoto Y, Saito Y, Gong X, Kuroda C, Hanai R

      Heterocycles75   2029 - 2034   1 1 2008

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    • Chemical and genetic diversity of Ligularia dictyoneura in northwestern Yunnan Province of China. Peer-reviewed

      Nagano, Iwazaki, Matsushima, Sato, Gong, Shen, Hirota, Kuroda, Hanai

      Chemistry & Biodiversity4   2874 - 2888   4 2007

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    • New oplopane-type sesquiterpenoids from Ligularia duciformis Peer-reviewed

      Motoo Tori, Miho Fujiwara, Yasuko Okamoto, Masami Tanaka, Xun Gong, Yuemao Shen, Ryo Hanai, Chiaki Kuroda

      NATURAL PRODUCT COMMUNICATIONS2 ( 4 ) 357 - 360   2007

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURAL PRODUCTS INC  

      The chemical constituents of the root of Ligularia duciformis, collected in Yunnan Province of China, was studied and two new oplopane-type sesquiterpenoids were isolated, whose structures were determined on the basis of spectroscopic evidence. Quite recently, oplopane-type compounds were found in Ligularia narynensis, and this is the second example to isolate oplopane-type sesquiterpenoids from Ligularia plants.

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    • Chemical and genetic differentiation of Ligularia tsangchanensis in Yunnan and Sichuan Provinces of China Peer-reviewed

      Atsushi Torihata, Ryo Hanai, Xun Gong, Yuemao Shen, Chiaki Kuroda

      CHEMISTRY & BIODIVERSITY4 ( 3 ) 500 - 507   2007

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

      The intraspecific diversity in L. tsangchanensis collected in the Chinese Provinces Yunnan and southwestern Sichuan was studied by chemical and genetic approaches. ne samples collected in Yunnan were found to contain cacalol (1) as the sole major component, while samples from Sichuan contained 7 alpha- and 7 beta-eremophila-9,11-dien-8-one (5 and 6) as well as the 3 alpha-angeloyloxy derivative 7 as major components. In addition, the sequences of the internal transcribed spacers (ITSs) of the ribosomal RNA gene indicated that the Yunnan and the Sichuan samples constitute separate clades. These results demonstrate that L. tsangchanensis in Yunnan and Sichuan are distinct.

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    • Chemical and genetic diversity of Ligularia latihastata and Ligularia villosa in Yunnan Province of China Peer-reviewed

      Chiaki Kuroda, Kota Kiuchi, Atsushi Torihata, Koichiro Takeshita, Xun Gong, Yuernao Shen, Hiroshi Hirota, Hiroyuki Onuki, Ryo Hanai

      CHEMISTRY & BIODIVERSITY4 ( 9 ) 2210 - 2217   2007

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

      ne chemical constituents of the root extracts and the nucleotide sequences of the atpB-rbcL intergenic region of Ligularia latihastata and L. villosa, collected in northwestern Yunnan Province, were studied. In the twelve collected samples of L. latihastata, two major benzofurans. 5,6-dimethoxy-2-(1-methylethenyl)-1-benzofuran (1) and euparin (2) were detected as major components. The minor compound (2R*,3S*)-5-acetyl-2,3-dihydro-6-hydroxy-2-(1-methylethenyl)-1-benzofuran-3-yl (2Z)-2[(acetoxy)methyl]but-2-enoate (4) was found to be susceptible to artifact formation upon extraction with EtOH. The intra-specific diversity in chemical composition of the samples was small, but the diversity in the atpB-rbcL sequence was fairly large. Compounds 1 and 2 were also found in the three collected samples of L. villosa, indicating that the two species are chemically close to each other, in agreement with morphological taxonomy

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    • Chemical constituents of Ligularia virgaurea and its diversity in southwestern Sichuan of China Peer-reviewed

      M Tori, K Honda, H Nakamizo, Y Okamoto, M Sakaoku, S Takaoka, Gong, X, YM Shen, C Kuroda, R Hanai

      TETRAHEDRON62 ( 20 ) 4988 - 4995   5 2006

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      Chemical constituents of root extract and the nucleotide sequences of the atpB-rbcL intergenic region and the internal transcribed spacers (ITSs) of the ribosomal RNA gene were studied for Ligularia virgaurea var. virgaurea collected in southwestern Sichuan Province of China. Eleven samples were collected. Four of them were found to contain four new furanoeremophilanes, virgaurenones A-D, as well as a new cremophilanolide, virgaurenolide A. The other samples contained different furanoeremophilanes and their derivatives including nor-type of compounds, two of which were new. Diversity was found to be present in the nucleotide sequences as well. The chemical composition was found to be correlated with the ITS variation but not with the geographic distribution of the samples. (c) 2006 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.tet.2006.02.078

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    • Chemical and genetic differentiation of Ligularia pleurocaulis in northwestern Yunnan and southwestern Sichuan Provinces of China Peer-reviewed

      H Nagano, Y Iwazaki, Gong, X, YM Shen, C Kuroda, R Hanai

      BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN79 ( 2 ) 300 - 304   2 2006

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CHEMICAL SOC JAPAN  

      Intra-specific diversity of Ligularia pleurocaulis was examined from both chemical and genetic aspects, using furanoeremophilanes as the chemical index and the nucleotide sequences in the atpB-rbcL and the ITS1 regions as the genetic index. Four samples of L. pleurocaulis were collected in northwestern Yunnan, and six in southwestern Sichuan. From the ethanol extracts of the roots of all of the samples, four compounds, 6 beta-angeloyloxy- and 6 beta-tigloyloxy-furanoeremophil-1(10)-enes, and 6 beta-angeloyloxy- and 6 beta-tigloyloxy-furanoeremophil-1(10)-en-3 beta-ols were isolated. Further, 3 beta-angeloyloxyfuranoeremophil-1(10)-en-6 beta-ol and furanoligularenone were isolated from the Yunnan and the Sichuan samples, respectively. Two variants were found for the atpB-rbcL sequence. Base multiplicity in the ITSI region was observed at only a few positions in the Yunnan samples, whereas it was observed at about 10 positions for the Sichuan samples. These results show that L. pleurocaulis is diverse, both chemically and genetically, and that plants in northwestern Yunnan and those in southwestern Sichuan can be distinguished by their chemical and genetic indexes.

      DOI: 10.1246/bcsj.79.300

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    • Chemical and genetic study of Ligularia tongolensis, Ligularia cymbulifera, and Ligularia atroviolacea in the Hengduan Mountains of China Peer-reviewed

      R Hanai, Gong, X, M Tori, S Kondo, K Otose, Y Okamoto, T Nishihama, A Murota, Y Shen, SG Wu, C Kuroda

      BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN78 ( 7 ) 1302 - 1308   7 2005

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CHEMICAL SOC JAPAN  

      Three Ligularia species (L. tongolensis, L. cymbulifera, and L. atroviolacea) were examined with respect to the chemical composition and nucleotide sequence. Furanoeremophilanes were found to be produced in the root of all samples of the three species collected in northwest Yunnan and southwest Sichuan. Eight furanoeremophilanes were identified, two of which were new. Most of the identified furanoeremophilanes were oxygenated at 3, 6, and 15-positions. The nucleotide sequence of the atpB-rbcL intergenic region was found to be essentially the same in the three species. These similarities imply that the three Ligularia species, all belonging to the section Corymbosae, are close to one another. The intra-specific diversity in the two widely distributed species in the Hengduan Mountains area, L. tongolensis and L. cymbulifera, were in contrast. Four out of 19 L. tongolensis samples contained a strongly Ehrlich-positive compound besides a number of positive compounds, and five variants of the atpB-rbcL sequence were found in these samples. In contrast, no variation was observed in 13 L. cymbulifera samples with respect to the furanoeremophilane composition or the atpB-rbcL sequence. The lack of diversity in L. cymbulifera probably resulted from the uniformity of its habitat.

      DOI: 10.1246/bcsj.78.1302

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    • Intracellular localization and domain organization of human TRIM41 proteins Peer-reviewed

      M Tanaka, Y Fukuda, K Mashima, R Hanai

      MOLECULAR BIOLOGY REPORTS32 ( 2 ) 87 - 93   6 2005

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER  

      A human gene previously identified as a partial cDNA homologous to the gene of RET. finger protein was characterized. Northern hybridization detected three messages of 3.3, 4.2, and 7.5 kb. The coding sequences of the more abundant of the three messages, the 4.2 and the 3.3 kb, were determined. The former encodes a 630 amino acid protein ( TRIM41&alpha;) and the latter a 518 amino acid protein ( TRIM41&beta;). Green. fluorescent protein ( GFP) fusions of full- length TRIM41&alpha; and TRIM41&beta; were both observed as speckles in the cytoplasm and the nucleus. The result was corroborated by Western analysis of cellular fractions. Results with GFP fusions of various segments of the TRIM41 proteins indicated that the nuclear transport of the proteins is mediated by an N- terminal segment common to both isoforms, but independent of a classical nuclear localization signal sequence.

      DOI: 10.1007/s11033-004-6613-2

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    • Chemical and genetic diversity of some Ligularia species (Compositae) in northwestern Yunnan and southwestern Sichuan of China.

      Kuroda C, Hanai R, Gong X, Shen Y, Tori M

      J. Fudan Univ.44   742 - 743   1 1 2005

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    • Characterization of two isoforms of a human DnaJ homologue, HSJ2 Peer-reviewed

      R Hanai, K Mashima

      MOLECULAR BIOLOGY REPORTS30 ( 3 ) 149 - 153   9 2003

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:KLUWER ACADEMIC PUBL  

      Two cDNA forms were characterized for a human dnaJ homologue, HSJ2. Nucleotide sequencing showed that the gene product HSJ2 was longer than previously reported, extending its homology to other human DnaJ paralogues, and that the two cDNAs encoded two proteins as a result of alternative splicing. The products were 326 amino acids (designated as HSJ2a) and 241 amino acids (HSJ2b) in length, sharing the N-terminal 231 amino acids including the DnaJ homology region. When fused to green fluorescent protein and expressed in HeLa cells, HSJ2a was found to be localized to the nucleus, indicating that HSJ2a is a nuclear co-chaperone. HSJ2b, however, was observed throughout the cell, consistent with the elimination of a putative nuclear localization signal sequence as a result of the alternative splicing.

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    • Isolation and characterization of novel F-plasmid sopB mutants defective in gene silencing Peer-reviewed

      Y Kubo, SK Kim, R Hanai

      MOLECULAR GENETICS AND GENOMICS266 ( 5 ) 806 - 812   1 2002

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER-VERLAG  

      The product of the sopB gene on the Escherichia coli F-plasmid has been shown to silence genes in the vicinity of its binding region, sopC, when overexpressed. We searched for mutants defective in SopB-dependent silencing by screening for a plasmid incompatibility phenotype, in order to examine the relationship between gene silencing and the intracellular localization of SopB, as revealed by a green fluorescent protein (GFP)-SopB fusion. Nine new mutants were isolated. One of them, in which leucine 92 is replaced by proline, was completely compatible with a sopC-carrying plasmid and was defective in other silencing activities. When expressed as a GFP fusion protein, the L92P mutant was found to be uniformly distributed in the cell. This implies a link between silencing and SopB localization, supporting the view that a high local concentration of SopB drives nonspecific DNA binding in segments of the plasmid adjacent to sopC. Despite the lack of apparent localization of GFP fluorescence, the mutant protein, like the wild-type SopB, was found mostly in the inner membrane fraction, indicating that the association with the inner membrane was retained.

      DOI: 10.1007/s00438-001-0597-6

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    • M phase-specific association of human topoisomerase III beta with chromosomes Peer-reviewed

      M Kobayashi, R Hanai

      BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS287 ( 1 ) 282 - 287   9 2001

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS INC  

      Two isoforms, 1 and 2, of human DNA topoisomerase III beta were expressed in HeLa cells as a fusion protein to the C-terminus of green fluorescent protein (GFP). The fusion protein of the isoform 1 was found to be localized to the nucleus, and to be associated with chromosomes during metaphase and anaphase. As yeast top3 mutants are known to exhibit phenotypes indicative of defective chromosome segregation, the result suggests that the isoform I of the human enzyme may also be involved in chromosome segregation. Two-hybrid screening for interaction partners of the isoform identified three candidate genes: CENP-F, a gene encoding a centromere protein and two genes of no known function, one of which was novel. The GFP fusion of the isoform 2 was found in the cytoplasm, indicating the nuclear localization signal sequence in the isoform I is in the C-terminal part that is different between the two isoforms. (C) 2001 Academic Press.

      DOI: 10.1006/bbrc.2001.5580

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    • Characterization of recombinant human DNA topoisomerase III alpha activity expressed in yeast Peer-reviewed

      N Hotoda, R Hanai

      JOURNAL OF BIOCHEMISTRY127 ( 6 ) 1109 - 1113   6 2000

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

      Recombinant human DNA topoisomerase III alpha was expressed in mutant yeast cells devoid of both topoisomerases I and III, and the gene product was partially purified. The activity of the protein in supercoil removal was found to be limited and also biphasic: in the first phase it processively changed the linking-number of hypernegatively supercoiled DNA, but only to the superhelicity of a regular negative supercoil; in the second phase the enzyme relaxed the DNA further, but only slightly and slowly. The optimal solution conditions for the enzyme activity were found to be physiological, The assay results with a truncation mutant showed that the C-terminal 334 amino acids are unnecessary for the activity, suggesting that this region, and perhaps the entire protein, is involved in a function other than supercoil removal.

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    • On the experimental distinction between ssbs and dsbs in circular DNA Peer-reviewed

      R Hanai, M Yazu, K Hieda

      INTERNATIONAL JOURNAL OF RADIATION BIOLOGY73 ( 5 ) 475 - 479   5 1998

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:TAYLOR & FRANCIS LTD  

      Purpose: To determine directly the minimal distance between two ssbs on complementary strands in circular DNA that are not observed as a dsb by electrophoresis.
      Materials and methods: 3.2kbp DNAs with cohesive overhangs of various lengths were systematically generated by a newly devised method and electrophoresed in agarose slabs.
      Results: At 4 degrees C, 3.2kbp DNA with cohesive overhangs larger than 6 bp migrated as circular DNA. The minimal overhang size for the DNA to migrate as circular DNA was larger at 25 degrees C. Whether the DNA migrated as a circular or a linear molecule depended also on the nucleotide sequence of its overhangs, most notably at the minimal size.
      Conclusions: The minimal distance obtained in the present study agrees with the smaller values of previous indirect estimates. The dependence of the distance on experimental conditions suggests feasibility of obtaining the stagger-size distribution of radiation-induced dsbs.

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    • Human TOP3: A single-copy gene encoding DNA topoisomerase III Peer-reviewed

      R Hanai, PR Caron, JC Wang

      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA93 ( 8 ) 3653 - 3657   4 1996

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATL ACAD SCIENCES  

      A human cDNA encoding a protein homologous to the Escherichia coli DNA topoisomerase I subfamily of enzymes has been identified through cloning and sequencing, Expressing the cloned human cDNA in yeast Delta top1 cells lacking endogenous DNA topoisomerase I yielded an activity in cell extracts that specifically reduces the number of supercoils in a highly negatively supercoiled DNA, On the basis of these results, the human gene containing the cDNA sequence has been denoted TOP3, and the protein it encodes has been denoted DNA topoisomerase III. Screening of a panel of human-rodent somatic hybrids and fluorescence in situ hybridization of cloned TOP3 genomic DNA to metaphase chromosomes indicate that human TOP3 is a single-copy gene located at chromosome 17p11.2-12.

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    • Molecular dissection of a protein SopB essential for Escherichia coli F plasmid partition Peer-reviewed

      Ryo Hanai, Ruiping Liu, Piero Benedetti, Paul R. Caron, A. Simon Lynch, James C. Wang

      Journal of Biological Chemistry271 ( 29 ) 17469 - 17475   1996

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      Biochemical and genetic experiments were carried out to deduce the structural and functional domains of SopB protein involved in the equipartition of F plasmid. The protein is dimeric. Proteolytic and chemical footprinting studies support earlier genetic analyses that the binding of SopB to specific sites within the F plasmid sopC locus involves mainly the C- terminal region. In vivo, the expression of a high level of SopB protein is known to repress sopC-linked genes. This silencing activity is shown to be unaffected by the deletion of 35 N-terminal residues, but abolished when 71 or more were removed from the N terminus. An excess of SopB protein does not extend its in vitro binding outside sopC, implicating participation of a host factor(s) in SopB-mediated gene silencing. A data base search identified a number of SopB homologues, including both chromosomally encoded bacterial proteins and phage- and plasmid-encoded proteins known to be involved in partition. Sequence homology is limited to the N-terminal half, suggesting that the N-terminal regions of these proteins are conserved to interact with a conserved cellular structure(s), whereas the C-terminal regions have diverged to bind different nucleotide sequences.

      DOI: 10.1074/jbc.271.29.17469

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    • PROTEIN FOOTPRINTING BY THE COMBINED USE OF REVERSIBLE AND IRREVERSIBLE LYSINE MODIFICATIONS Peer-reviewed

      R HANAI, JC WANG

      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA91 ( 25 ) 11904 - 11908   12 1994

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      A two-step lysine-modification procedure has been devised to chemically footprint protein surfaces involved in macromolecular interactions. A protein tagged at one particular end, in the free state or in a complex, is first treated lightly with a reversible lysine-modifying reagent, The protein is then unfolded and treated extensively with an irreversible lysine reagent to block those lysines that did not react previously; next, the first lysine modification is reversed, and a lysine-specific endoproteinase is used to cleave the tagged polypeptide at the deblocked lysines. Separation of the proteolytic products by size and identification of the tagged fragments map the positions of these lysines. In this procedure, the reversible lysine reagent serves as the chemical footprinting agent, as cleavage of the polypeptide ensues only at the sites of reaction with this reagent. Lysines involved in macromolecular contacts are identified from differences in proteolytic patterns of the tagged protein when the first lysine modification is done with the protein in the free form and in a complex. Application of the method to vaccinia virus topoisomerase identifies a number of lysines that are involved in its binding to DNA.

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    • CRYSTAL-STRUCTURE OF THE AMINO-TERMINAL FRAGMENT OF VACCINIA VIRUS-DNA TOPOISOMERASE-I AT 1.6-ANGSTROM RESOLUTION Peer-reviewed

      A SHARMA, R HANAI, A MONDRAGON

      STRUCTURE2 ( 8 ) 767 - 777   8 1994

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CURRENT BIOLOGY LTD  

      Background: Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin.
      Results: The crystal structure of a 9 kDa amino-terminal fragment of vaccinia virus DNA topoisomerase I has been determined at 1.6 Angstrom resolution. The fragment forms a five-stranded, antiparallel beta-sheet with two shore alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure.
      Conclusions: This is the first atomic structure of any region of a eukaryotic-like DNA topoisomerase I, It has provided insights into the structural bases of the phenotypes of some single-site mutants of the intact topoisomerase. The structure has enabled us to study the interactions within a well-folded protein fragment and the camptothecin resistance of the viral topoisomerase.

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    • THE MECHANISM OF SEQUENCE-SPECIFIC DNA CLEAVAGE AND STRAND TRANSFER BY PHI-X174 GENE-A-ASTERISK PROTEIN Peer-reviewed

      R HANAI, JC WANG

      JOURNAL OF BIOLOGICAL CHEMISTRY268 ( 32 ) 23830 - 23836   11 1993

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

      We have examined the biological role and catalytic function of two juxtaposed tyrosyl residues in the bacteriophage phiX174 gene A protein, Tyr-343 and Tyr-347, which have been implicated in the catalysis of sequence-specific DNA strand transfer. Site-directed mutagenesis changing either tyrosine to phenylalanine abolishes phage viability. The biochemical basis of this inviability was studied using purified A* protein containing the carboxyl-terminal 341 amino acids of the A protein, as well as purified A* protein with a Y343F or Y347F mutation. All three proteins can cleave the phiX174 replication origin and perform strand transfer between oligodeoxy-nucleotides bearing the recognition sequence of the A protein; however, both Tyr-343 and Tyr-347 appear to be required for coordinated DNA strand transfer by a single A* protein molecule. The chirality of a phosphorothioate group at the site of strand transfer in the DNA was found to be retained following the strand-transfer reaction, which argues against transfer of Tyr-343-linked DNA to Tyr-347 on the same protein molecule or vice versa. These results support the current model of gene A protein function in which the two tyrosines of a single protein molecule alternate in catalyzing DNA strand transfer at the viral replication origin.

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    • Phenomenological theory of GC/AT pressure on DNA base composition Peer-reviewed

      Wada A, Suyama A, Hanai R

      J. Mol. Evol.32 ( 5 ) 374 - 378   5 1990

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    • DOUBLET PREFERENCE AND GENE EVOLUTION Peer-reviewed

      R HANAI, A WADA

      JOURNAL OF MOLECULAR EVOLUTION30 ( 2 ) 109 - 115   1990

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER VERLAG  

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    • NOVEL 3RD-LETTER BIAS IN ESCHERICHIA-COLI CODONS REVEALED BY RIGOROUS TREATMENT OF CODING CONSTRAINTS Peer-reviewed

      R HANAI, A WADA

      JOURNAL OF MOLECULAR BIOLOGY207 ( 4 ) 655 - 660   6 1989

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS LTD  

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    • CHARACTERISTIC FEATURES OF THERMAL-STABILITY MAP OF DNA IN ESCHERICIA-COLI AND EUKARYOTIC GENES Peer-reviewed

      R HANAI, A SUYAMA, A WADA

      JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS6 ( 1 ) 51 - 62   8 1988

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ADENINE PRESS INC  

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    • THE EFFECTS OF GUANINE AND CYTOSINE VARIATION ON DINUCLEOTIDE FREQUENCY AND AMINO-ACID COMPOSITION IN THE HUMAN GENOME Peer-reviewed

      R HANAI, A WADA

      JOURNAL OF MOLECULAR EVOLUTION27 ( 4 ) 321 - 325   1988

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    • VESTIGES OF LOST INTRONS IN THE THERMAL-STABILITY MAP OF DNA Peer-reviewed

      R HANAI, A SUYAMA, A WADA

      FEBS LETTERS226 ( 2 ) 247 - 249   1 1988

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

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    • ANALYSIS OF THE CIS-TRANS ISOMERIZATION KINETICS OF L-ALANYL-L-PROLINE BY THE ELUTION-BAND RELAXATION METHOD Peer-reviewed

      R HANAI, A WADA

      JOURNAL OF CHROMATOGRAPHY394 ( 2 ) 273 - 278   5 1987

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

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    • ELUTION-BAND RELAXATION METHOD - A METHOD TO ANALYZE ISOMERIZATION KINETICS BY HPLC AND APPLICATION TO PROTEIN DENATURATION-RENATURATION Peer-reviewed

      R HANAI, S ENDO, A WADA

      BIOPHYSICAL CHEMISTRY25 ( 1 ) 27 - 36   11 1986

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

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    Misc.

    • 中国横断山脈に生育するLigularia属の生産するフラノエレモフィラン化合物の多様性 Invited Peer-reviewed

      黒田 智明, 花井 亮, 通 元夫, 岡本 育子, 齋藤 義紀, 永野 肇, 大崎 愛弓, 廣田 洋, 河原 孝行, 龔 洵

      有機合成化学72 ( 6 ) 717 - 725   6 2014

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

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    • Diversity of Furanoeremophilanes in Major Ligularia Species in the Hengduan Mountains

      Chiaki Kuroda, Ryo Hanai, Hajime Nagano, Motoo Tori, Xun Gong

      NATURAL PRODUCT COMMUNICATIONS7 ( 4 ) 539 - 548   4 2012

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      Language:English   Publishing type:Book review, literature introduction, etc.   Publisher:NATURAL PRODUCTS INC  

      The chemical and genetic diversity of Ligularia species in the Hengduan Mountains area of China is reviewed. A hypothesis that the production of furanoeremophilanes is ecologically advantageous is proposed.

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    • 中国横断山脈でオーミックスペースを齧る

      花井 亮, 黒田 智明, 通 元夫

      生物物理52 ( 1 ) 36 - 37   1 2012

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)   Publisher:日本生物物理学会  

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    • Diversity of Ligularia (Asteraceae)

      Kuroda C, Hanai R, Tori M, Nagano H, Nishihama T, Gong X, Shen Y

      Chemical Education54   490 - 491   1 1 2006

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)   Publisher:The Chemical Society of Japan  

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    • Two-dimensional agarose-gel electrophoresis of DNA topoisomers.

      Hanai R, Roca J

      Methods Mol. Biol.94   19 - 27   1 1 1999

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      Language:English   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:Humana Press  

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    • Topoisomerase III and genome stability

      Hanai R

      Cell Technology16 ( 11 ) 1583 - 1587   11 1997

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:Shujunsha  

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    • Protein Footprinting

      Hanai R

      Protein, Nucleic Acid, Enzyme41 ( 7 ) 929 - 933   7 1996

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:Kyoritsu Press  

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    • Characteristic features of protein codidng regions in DNA - From the viewpoint of thermal stability map -

      Hanai R, Wada A, Suyama A

      Biophysics28 ( 2 ) 1 - 4   1 2 1988

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      Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)   Publisher:The Biophysical Society of Japan  

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    • 1p-BF-2 HPLCによる異性化反応の速度論的研究(生体物理)

      花井 亮, 猿渡 茂, 和田 昭允

      年会講演予稿集41 ( 3 ) 390 - 390   29 3 1986

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      Language:Japanese   Publisher:一般社団法人日本物理学会  

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    Books and Other Publications

    • Encyclopedia of Molecular Biology

      Hanai R( Role: Sole author)

      John Wiley & Sons  1 1999 

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      Language:English Book type:Dictionary, encyclopedia

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    Professional Memberships

    Research Projects

    • 中国雲南省におけるキク科リグラリア属植物の化学的遺伝的多様性 (代表者:黒田智明)

      日本学術振興会  科学研究費助成事業 

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      4 2004 - 3 2007

      Grant type:Competitive

      中国雲南省産のキク科リグラリア植物のテルペノイドとDNAの多様性の研究

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    • 中国西蔵省における植物の高地適応機構の生物・化学的解析 (代表者:堀内昭)

      日本学術振興会  科学研究費助成事業 

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      4 1999 - 3 2002

      Grant type:Competitive

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    • Fプラズミド分配遺伝子産物SopA・SopBとDNAの高次複合体の構造生物学

      日本学術振興会  科学研究費助成事業 

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      4 1999 - 3 2001

      Grant type:Competitive

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    • ヒトDNAトポイソメラーゼIIIの機能

      立教大学  立教大学研究奨励助成金 

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      4 1998 - 3 1999

      Grant type:Competitive

      個人研究

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    • FプラズミドSopB蛋白質を核とする多要素DNA蛋白質複合体の構造生物学

      日本学術振興会  科学研究費助成事業 

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      4 1997 - 3 1999

      Grant type:Competitive

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    • Fプラスミド分配におけるタンパク質-DNA相互作用

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      Grant type:Competitive

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    • ローリングサークル複製におけるトランスエステリフィケーション

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      Grant type:Competitive

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    • キク科植物の化学的遺伝的多様性

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      Grant type:Competitive

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