Works matching AU Nagata, Yuji

Results: 49

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering.

Published in:

Angewandte Chemie, 2010, v. 122, n. 35, p. 6247, doi. 10.1002/ange.201001753

By:

Prokop, Zbynek;
Sato, Yukari;
Brezovsky, Jan;
Mozga, Tomas;
Chaloupkova, Radka;
Koudelakova, Tana;
Jerabek, Petr;
Stepankova, Veronika;
Natsume, Ryo;
van Leeuwen, Jan G. E.;
Janssen, Dick B.;
Florian, Jan;
Nagata, Yuji;
Senda, Toshiya;
Damborsky, Jiri

Publication type:

Article

Properties and biotechnological applications of natural and engineered haloalkane dehalogenases.

Published in:

Applied Microbiology & Biotechnology, 2015, v. 99, n. 23, p. 9865, doi. 10.1007/s00253-015-6954-x

By:

Nagata, Yuji;
Ohtsubo, Yoshiyuki;
Tsuda, Masataka

Publication type:

Article

Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts.

Published in:

Applied Microbiology & Biotechnology, 2015, v. 99, n. 10, p. 4453, doi. 10.1007/s00253-014-6322-2

By:

Nagayama, Hirofumi;
Sugawara, Tomonori;
Endo, Ryo;
Ono, Akira;
Kato, Hiromi;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06.

Published in:

Applied Microbiology & Biotechnology, 2010, v. 86, n. 2, p. 567, doi. 10.1007/s00253-009-2278-z

By:

Matsushima, Ryoji;
Danno, Hiroko;
Uchida, Motoharu;
Ishihara, Kenji;
Suzuki, Toshiyuki;
Kaneniwa, Masaki;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Insertion sequence-based cassette PCR: cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA.

Published in:

Applied Microbiology & Biotechnology, 2008, v. 79, n. 4, p. 627, doi. 10.1007/s00253-008-1463-9

By:

Fuchu, Genki;
Ohtsubo, Yoshiyuki;
Ito, Michihiro;
Miyazaki, Ryo;
Ono, Akira;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis.

Published in:

Applied Microbiology & Biotechnology, 2007, v. 76, n. 4, p. 741, doi. 10.1007/s00253-007-1066-x

By:

Nagata, Yuji;
Endo, Ryo;
Ito, Michihiro;
Ohtsubo, Yoshiyuki;
Tsuda, Masataka

Publication type:

Article

Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches.

Published in:

Applied Microbiology & Biotechnology, 2007, v. 74, n. 2, p. 501, doi. 10.1007/s00253-006-0671-4

By:

Ono, Akira;
Miyazaki, Ryo;
Sota, Masahiro;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Strategies for bioremediation of polychlorinated biphenyls.

Published in:

Applied Microbiology & Biotechnology, 2004, v. 65, n. 3, p. 250, doi. 10.1007/s00253-004-1654-y

By:

Ohtsubo, Yoshiyuki;
Kudo, Toshiaki;
Tsuda, Masataka;
Nagata, Yuji

Publication type:

Article

Increase of secondary metabolites in sweet basil (Ocimum basilicum L.) leaves by exposure to N<sub>2</sub>O<sub>5</sub> with plasma technology.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-63508-8

By:

Tateishi, Rie;
Ogawa-Kishida, Natsumi;
Fujii, Nobuharu;
Nagata, Yuji;
Ohtsubo, Yoshiyuki;
Sasaki, Shota;
Takashima, Keisuke;
Kaneko, Toshiro;
Higashitani, Atsushi

Publication type:

Article

Possible involvement of zinc transporter ZIP13 in myogenic differentiation.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-56912-7

By:

Shoji, Masaki;
Ohashi, Takuto;
Nagase, Saki;
Yuri, Haato;
Ichihashi, Kenta;
Takagishi, Teruhisa;
Nagata, Yuji;
Nomura, Yuki;
Fukunaka, Ayako;
Kenjou, Sae;
Miyake, Hatsuna;
Hara, Takafumi;
Yoshigai, Emi;
Fujitani, Yoshio;
Sakurai, Hidetoshi;
dos Santos, Heloísa G.;
Fukada, Toshiyuki;
Kuzuhara, Takashi

Publication type:

Article

Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.01125

By:

Miyakoshi, Masatoshi;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Identification of a response regulator gene for catabolite control from a PCB-degrading β-proteobacteria, Acidovorax sp. KKS102.

Published in:

Molecular Microbiology, 2006, v. 60, n. 6, p. 1563, doi. 10.1111/j.1365-2958.2006.05197.x

By:

Ohtsubo, Yoshiyuki;
Goto, Hiroyuki;
Nagata, Yuji;
Kudo, Toshiaki;
Tsuda, Masataka

Publication type:

Article

Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria.

Published in:

Mobile DNA, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s13100-023-00295-5

By:

Idola, Desmila;
Mori, Hiroshi;
Nagata, Yuji;
Nonaka, Lisa;
Yano, Hirokazu

Publication type:

Article

Employment of the Human Estrogen Receptor β Ligand-Binding Domain and Co-Activator SRC1 Nuclear Receptor-Binding Domain for the Construction of a Yeast Two-Hybrid Detection System for Endocrine Disrupters1.

Published in:

Journal of Biochemistry, 2002, v. 131, n. 3, p. 399, doi. 10.1093/oxfordjournals.jbchem.a003115

By:

Lee, Haeng-Seog;
Miyauchi, Keisuke;
Nagata, Yuji;
Fukuda, Ryouichi;
Sasagawa, Shin-ichi;
Endoh, Hideki;
Kato, Shigeaki;
Horiuchi, Hiroyuki;
Takagi, Masamichi;
Ohta, Akinori

Publication type:

Article

Identification of protein fold and catalytic residues of γ-hexachlorocyclohexane dehydrochlorinase LinA.

Published in:

Proteins, 2001, v. 45, n. 4, p. 471, doi. 10.1002/prot.10007

By:

Nagata, Yuji;
Mori, Katsuki;
Takagi, Masamichi;
Murzin, Alexey G.;
Damborský, Jiří

Publication type:

Article

The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase Dat A from Agrobacterium tumefaciens C58.

Published in:

FEBS Journal, 2013, v. 280, n. 13, p. 3149, doi. 10.1111/febs.12238

By:

Hasan, Khomaini;
Gora, Artur;
Brezovsky, Jan;
Chaloupkova, Radka;
Moskalikova, Hana;
Fortova, Andrea;
Nagata, Yuji;
Damborsky, Jiri;
Prokop, Zbynek

Publication type:

Article

Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature.

Published in:

FEBS Journal, 2011, v. 278, n. 15, p. 2728, doi. 10.1111/j.1742-4658.2011.08203.x

By:

Chaloupkova, Radka;
Prokop, Zbynek;
Sato, Yukari;
Nagata, Yuji;
Damborsky, Jiri

Publication type:

Article

Properties and efficient scrap-and-build repairing of mechanically sheared 3' DNA ends.

Published in:

Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0660-7

By:

Ohtsubo, Yoshiyuki;
Sakai, Keiichiro;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids.

Published in:

Environmental Microbiology, 2012, v. 14, n. 11, p. 2946, doi. 10.1111/j.1462-2920.2012.02861.x

By:

Miyakoshi, Masatoshi;
Shintani, Masaki;
Inoue, Kei;
Terabayashi, Tsuguno;
Sai, Fumiya;
Ohkuma, Moriya;
Nojiri, Hideaki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Identification of Burkholderia multivorans ATCC 17616 genes induced in soil environment by in vivo expression technology.

Published in:

Environmental Microbiology, 2010, v. 12, n. 9, p. 2539, doi. 10.1111/j.1462-2920.2010.02227.x

By:

Nishiyama, Eri;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

STRUCTURE-SPECIFICITY RELATIONSHIPS FOR HALOALKANE DEHALOGENASES.

Published in:

Environmental Toxicology & Chemistry, 2001, v. 20, n. 12, p. 2681

By:

Damborský, Jiří;
Rorije, Emiel;
Jesenská, Andrea;
Nagata, Yuji;
Klopman, Gilles;
Peijnenburg, Willie J. G. M.

Publication type:

Article

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering.

Published in:

Angewandte Chemie International Edition, 2010, v. 49, n. 35, p. 6111, doi. 10.1002/anie.201001753

By:

Prokop, Zbynek;
Sato, Yukari;
Brezovsky, Jan;
Mozga, Tomas;
Chaloupkova, Radka;
Koudelakova, Tana;
Jerabek, Petr;
Stepankova, Veronika;
Natsume, Ryo;
van Leeuwen, Jan G. E.;
Janssen, Dick B.;
Florian, Jan;
Nagata, Yuji;
Senda, Toshiya;
Damborsky, Jiri

Publication type:

Article

Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA.

Published in:

BMC Biotechnology, 2024, v. 24, n. 1, p. 1, doi. 10.1186/s12896-024-00867-0

By:

Deng, Wenhao;
Takada, Yoshinobu;
Nanasato, Yoshihiko;
Kishida, Kouhei;
Stari, Leonardo;
Ohtsubo, Yoshiyuki;
Tabei, Yutaka;
Watanabe, Masao;
Nagata, Yuji

Publication type:

Article

Lessons from the genomes of lindane‐degrading sphingomonads.

Published in:

Environmental Microbiology Reports, 2019, v. 11, n. 5, p. 630, doi. 10.1111/1758-2229.12762

By:

Nagata, Yuji;
Kato, Hiromi;
Ohtsubo, Yoshiyuki;
Tsuda, Masataka

Publication type:

Article

Three distinct metabolic phases of polychlorinated biphenyls/biphenyl degrader Acidovorax sp. KKS102 in nutrient broth.

Published in:

Bioscience, Biotechnology & Biochemistry, 2024, v. 88, n. 3, p. 305, doi. 10.1093/bbb/zbad178

By:

Sakai, Keiichiro;
Kishida, Kouhei;
Matsumoto, Satoshi;
Nagata, Yuji;
Tsuda, Masataka;
Ohtsubo, Yoshiyuki

Publication type:

Article

Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA.

Published in:

Bioscience, Biotechnology & Biochemistry, 2024, v. 88, n. 1, p. 123, doi. 10.1093/bbb/zbad141

By:

Habibullah, Kafayat Olaide Yusuf;
Ren Ito;
Leonardo Stari;
Kouhei Kishida;
Yoshiyuki Ohtsubo;
Eiji Masai;
Masao Fukuda;
Keisuke Miyauchi;
Yuji Nagata

Publication type:

Article

Genome evolution related to γ-hexachlorocyclohexane metabolic function in the soil microbial population.

Published in:

Bioscience, Biotechnology & Biochemistry, 2022, v. 86, n. 6, p. 800, doi. 10.1093/bbb/zbac042

By:

Hiromi Kato;
Lijun Su;
Ayami Tanaka;
Honami Katsu;
Yoshiyuki Ohtsubo;
Shigeto Otsuka;
Keishi Senoo;
Yuji Nagata

Publication type:

Article

Algorisms used for in silico finishing of bacterial genomes based on short-read assemblage implemented in GenoFinisher, AceFileViewer, and ShortReadManager.

Published in:

Bioscience, Biotechnology & Biochemistry, 2022, v. 86, n. 6, p. 693, doi. 10.1093/bbb/zbac032

By:

Yoshiyuki Ohtsubo;
Yuu Hirose;
Yuji Nagata

Publication type:

Article

Establishment of plasmid vector and allelic exchange mutagenesis systems in a mycobacterial strain that is able to degrade polycyclic aromatic hydrocarbon.

Published in:

Bioscience, Biotechnology & Biochemistry, 2018, v. 82, n. 7, p. 1169, doi. 10.1080/09168451.2018.1445522

By:

Kishida, Kouhei;
Ogawa, Natsumi;
Ichihashi, Eikichi;
Kato, Hiromi;
Nagata, Yuji;
Ohtsubo, Yoshiyuki;
Tsuda, Masataka

Publication type:

Article

The lin Genes for γ-Hexachlorocyclohexane Degradation in Sphingornonas sp. MM-1 Proved to Be Dispersed across Multiple Plasmids.

Published in:

Bioscience, Biotechnology & Biochemistry, 2011, v. 75, n. 3, p. 466, doi. 10.1271/bbb.100652

By:

Tabata, Michiro;
Endo, Ryo;
Michihiro Ito;
Ohtsubo, Yoshiyuki;
Kumar, Ashwani;
Tsuda, Masataka;
Nagata, Yuji

Publication type:

Article

GenomeMatcher: A graphical user interface for DNA sequence comparison.

Published in:

2008

By:

Ohtsubo, Yoshiyuki;
Ikeda-Ohtsubo, Wakako;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Product Review

Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205.

Published in:

Archives of Microbiology, 2007, v. 188, n. 4, p. 313, doi. 10.1007/s00203-007-0251-8

By:

Ito, Michihiro;
Prokop, Zbyňek;
Klvaňa, Martin;
Otsubo, Yoshiyuki;
Tsuda, Masataka;
Damborský, Jiří;
Nagata, Yuji

Publication type:

Article

Clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis by Taq polymerase involves nick-translation.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-52095-3

By:

Ohtsubo, Yoshiyuki;
Kawahara, Syoutaro;
Nagata, Yuji

Publication type:

Article

Optimization of single strand DNA incorporation reaction by Moloney murine leukaemia virus reverse transcriptase.

Published in:

DNA Research, 2018, v. 25, n. 5, p. 477, doi. 10.1093/dnares/dsy018

By:

Ohtsubo, Yoshiyuki;
Sasaki, Haruna;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.

Published in:

DNA Research, 2016, v. 23, n. 6, p. 581, doi. 10.1093/dnares/dsw041

By:

Michiro Tabata;
Satoshi Ohhata;
Yuki Nikawadori;
Kouhei Kishida;
Takuya Sato;
Toru Kawasumi;
Hiromi Kato;
Yoshiyuki Ohtsubo;
Masataka Tsuda;
Yuji Nagata

Publication type:

Article

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance.

Published in:

DNA Research, 2015, v. 22, n. 6, p. 413, doi. 10.1093/dnares/dsv023

By:

Hiromi Kato;
Hiroshi Mori;
Fumito Maruyama;
Atsushi Toyoda;
Kenshiro Oshima;
Ryo Endo;
Genki Fuchu;
Masatoshi Miyakoshi;
Ayumi Dozono;
Yoshiyuki Ohtsubo;
Yuji Nagata;
Masahira Hattori;
Asao Fujiyama;
Ken Kurokawa;
Tsuda, Masataka

Publication type:

Article

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes.

Published in:

DNA Research, 2014, v. 21, n. 2, p. 217, doi. 10.1093/dnares/dst052

By:

Mori, Hiroshi;
Maruyama, Fumito;
Kato, Hiromi;
Toyoda, Atsushi;
Dozono, Ayumi;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Fujiyama, Asao;
Tsuda, Masataka;
Kurokawa, Ken

Publication type:

Article

Construction of Signature-tagged Mutant Library in Mesorhizobium loti as a Powerful Tool for Functional Genomics.

Published in:

DNA Research, 2008, v. 15, n. 5, p. 297, doi. 10.1093/dnares/dsn017

By:

Shimoda, Yoshikazu;
Mitsui, Hisayuki;
Kamimatsuse, Hiroko;
Minamisawa, Kiwamu;
Nishiyama, Eri;
Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka;
Shinpo, Sayaka;
Watanabe, Akiko;
Kohara, Mitsuyo;
Yamada, Manabu;
Nakamura, Yasukazu;
Tabata, Satoshi;
Sato, Shusei

Publication type:

Article

Growth Inhibition by Metabolites of γ-Hexachlorocyclohexane in Sphingobium japonicum UT26.

Published in:

Bioscience, Biotechnology & Biochemistry, 2006, v. 70, n. 4, p. 1029, doi. 10.1271/bbb.70.1029

By:

Endo, Ryo;
Ohtsubo, Yoshiyuki;
Tsuda, Masataka;
Nagata, Yuji

Publication type:

Article

Identification of Insertion Sequence from a γ-Hexachlorocyclohexane Degrading Bacterium, Sphingomonas paucimobilis UT26.

Published in:

Bioscience, Biotechnology & Biochemistry, 2005, v. 69, n. 1, p. 216, doi. 10.1271/bbb.69.216

By:

Miyauchi, Keisuke;
Fukuda, Masao;
Tsuda, Masataka;
Takagi, Masamichi;
Nagata, Yuji

Publication type:

Article

Long-term changes and effect of pterygium size on corneal topographic irregularity after recurrent pterygium surgery.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-65376-4

By:

Ono, Takashi;
Mori, Yosai;
Nejima, Ryohei;
Lee, Jinhee;
Abe, Kentaro;
Nagata, Yuji;
Iwasaki, Takuya;
Aihara, Makoto;
Miyata, Kazunori

Publication type:

Article

Microbial communities developing within bulk sediments under fish carcasses on a tidal flat.

Published in:

PLoS ONE, 2021, v. 16, n. 2, p. 1, doi. 10.1371/journal.pone.0247220

By:

Kawamoto, Yasutake;
Kato, Hiromi;
Nagata, Yuji;
Urabe, Jotaro

Publication type:

Article

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Published in:

Nature Chemical Biology, 2009, v. 5, n. 10, p. 727, doi. 10.1038/nchembio.205

By:

Pavlova, Martina;
Klvana, Martin;
Prokop, Zbynek;
Chaloupkova, Radka;
Banas, Pavel;
Otyepka, Michal;
Wade, Rebecca C.;
Tsuda, Masataka;
Nagata, Yuji;
Damborsky, Jiri

Publication type:

Article

Biodegradation of γ-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA.

Published in:

Plant Cell Reports, 2016, v. 35, n. 9, p. 1963, doi. 10.1007/s00299-016-2011-1

By:

Nanasato, Yoshihiko;
Namiki, Sayuri;
Oshima, Masao;
Moriuchi, Ryota;
Konagaya, Ken-ichi;
Seike, Nobuyasu;
Otani, Takashi;
Nagata, Yuji;
Tsuda, Masataka;
Tabei, Yutaka

Publication type:

Article

Special Issue: Microbial Degradation of Xenobiotics.

Published in:

2020

By:

Nagata, Yuji

Publication type:

Editorial

Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase.

Published in:

Scientific Reports, 2017, p. 41769, doi. 10.1038/srep41769

By:

Ohtsubo, Yoshiyuki;
Nagata, Yuji;
Tsuda, Masataka

Publication type:

Article

Electrochemical Oxidation of Benzylic Amines into the Corresponding Imines in the Presence of Catalytic Amounts of KI.

Published in:

Synthetic Communications, 2005, v. 35, n. 15, p. 1989, doi. 10.1081/SCC-200066648

By:

Okimoto, Mitsuhiro;
Takahashi, Yukio;
Numata, Kaori;
Nagata, Yuji;
Sasaki, Gaku

Publication type:

Article

One Pot Electrooxidative Conversion of Benzyl Type Alcohols into the Corresponding Methyl Carboxylates.

Published in:

Synthetic Communications, 2004, v. 34, n. 2, p. 281, doi. 10.1081/SCC-120027264

By:

Okimoto, Mitsuhiro;
Nagata, Yuji;
Sueda, Satoru;
Takahashi, Yukio

Publication type:

Article

One Pot Electrooxidative Conversion of Aromatic 1,2-Diketones into Methyl Carboxylates.

Published in:

Synthetic Communications, 2003, v. 33, n. 21, p. 3771, doi. 10.1081/SCC-120025186

By:

Okimoto, Mitsuhiro;
Nagata, Yuji;
Sueda, Satoru;
Takahashi, Yukio

Publication type:

Article