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Journal Articles

Discovery of a selective Cs$$^{+}$$ binding site of a $$beta$$-lactamase from the halophile by anomalous X-ray diffraction

Arai, Shigeki; Shibazaki, Chie; Shimizu, Rumi; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Kyushu Shinkurotoronko Kenkyu Senta Nempo, 2014, p.17 - 19, 2016/03

no abstracts in English

Journal Articles

Draft genome sequence of ${it Methylobacterium}$ sp. ME121, isolated from soil as a mixed single colony with ${it Kaistia}$ sp. 32K

Fujinami, Shun*; Takeda, Kiyoko*; Onodera, Takefumi*; Sato, Katsuya; Shimizu, Tetsu*; Wakabayashi, Yu*; Narumi, Issey*; Nakamura, Akira*; Ito, Masahiro*

Genome Announcements (Internet), 3(5), p.e01005-15_1 - e01005-15_2, 2015/09

Journal Articles

Structure of a highly acidic $$beta$$-lactamase from the moderate halophile ${it Chromohalobacter}$ sp.560 and the discovery of a Cs$$^{+}$$-selective binding site

Arai, Shigeki; Yonezawa, Yasushi*; Okazaki, Nobuo*; Matsumoto, Fumiko*; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu*; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide*; et al.

Acta Crystallographica Section D, 71(3), p.541 - 554, 2015/03

 Times Cited Count:7 Percentile:50.91(Biochemical Research Methods)

The crystal structure of halophilic $$beta$$-lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr$$^{2+}$$ and Cs$$^{+}$$ ions were identified by anomalous X-ray diffraction. The location of one Cs$$^{+}$$ specific binding site was identified on HaBLA even in the presence of 9-fold molar excess of Na$$^{+}$$ (90 mM Na$$^{+}$$ /10 mM Cs$$^{+}$$). This Cs$$^{+}$$ binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs$$^{+}$$ by the cation-$$pi$$ interaction. The observation of a selective and high-affinity Cs$$^{+}$$ binding site provides important information that is useful for designing artificial Cs$$^{+}$$ binding sites useful in bioremediation of radioactive isotopes.

Journal Articles

Interaction of double-stranded DNA with polymerized PprA protein from ${it Deinococcus radiodurans}$

Adachi, Motoyasu; Hirayama, Hiroshi; Shimizu, Rumi; Sato, Katsuya; Narumi, Issey*; Kuroki, Ryota

Protein Science, 23(10), p.1349 - 1358, 2014/10

 Times Cited Count:9 Percentile:25.73(Biochemistry & Molecular Biology)

Pleiotropic protein promoting DNA repair A (PprA) is a key protein that facilitates the extreme radioresistance of ${it Deinococcus radiodurans}$. To clarify the role of PprA in the radioresistance mechanism, the interaction between recombinant PprA expressed in Escherichia coli with several double-stranded DNAs was investigated. In a gel-shift assay, the band shift of supercoiled pUC19 DNA caused by the binding of PprA showed a bimodal distribution, which was promoted by the addition of 1 mM Mg, Ca, or Sr ions. The dissociation constant of the PprA-supercoiled pUC19 DNA complex, calculated from the relative portions of shifted bands, was 0.6 $$mu$$M with a Hill coefficient of 3.3 in the presence of 1 mM Mg acetate. This indicates that at least 281 PprA molecules are required to saturate a supercoiled pUC19 DNA, which is consistent with the number of bound PprA molecules estimated by the UV absorption of the PprA-pUC19 complex purified by gel filtration. This saturation also suggests linear polymerization of PprA along the dsDNA. On the other hand, the bands of linear dsDNA and nicked circular dsDNA that eventually formed PprA complexes did not saturate, but created larger molecular complexes when the PprA concentration was greater than 1.3 $$mu$$M. This result implies that DNA-bound PprA aids association of the termini of damaged DNAs, which is regulated by the concentration of PprA.

Journal Articles

Molecular analysis of heavy ion induced mutations in budding yeast ${it S. cerevisiae}$

Matsuo, Yoichiro*; Izumi, Yoshinobu*; Hase, Yoshihiro; Sakamoto, Ayako; Nozawa, Shigeki; Narumi, Issey*; Shimizu, Kikuo*

JAEA-Review 2013-059, JAEA Takasaki Annual Report 2012, P. 112, 2014/03

Journal Articles

Simultaneous saccharification and fermentation from ionic liquid-pretreated biomass using ionic liquid-tolerant yeast mutant

Ninomiya, Kazuaki*; Omote, Sayuri*; Sato, Katsuya; Narumi, Issey*; Shimizu, Nobuaki*

JAEA-Review 2013-059, JAEA Takasaki Annual Report 2012, P. 115, 2014/03

Journal Articles

Creation and structure determination of an artificial protein with three complete sequence repeats

Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota; Blaber, M.

Journal of Synchrotron Radiation, 20(6), p.953 - 957, 2013/11

 Times Cited Count:2 Percentile:13.23(Instruments & Instrumentation)

Symfoil-4P is a ${it de novo}$ protein exhibiting the threefold symmetrical beta-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine-glycine sequences of Symfoil-4P are replaced with glutamine-glycine (Symfoil-QG) or serine-glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in ${it Eschericha coli}$ as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Symfoil-QG and II crystals gave 1.5 and 1.1${AA}$, resolution, respectively. The refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils.

Journal Articles

The Possible interplanetary transfer of microbes; Assessing the viability of ${it Deinococcus}$ spp. under the ISS environmental conditions for performing exposure experiments of microbes in the Tanpopo mission

Kawaguchi, Yuko*; Yang, Y.*; Kawashiri, Narutoshi*; Shiraishi, Keisuke*; Takasu, Masako*; Narumi, Issey*; Sato, Katsuya; Hashimoto, Hirofumi*; Nakagawa, Kazumichi*; Tanigawa, Yoshiaki*; et al.

Origins of Life and Evolution of Biospheres, 43(4-5), p.411 - 428, 2013/10

 Times Cited Count:40 Percentile:80.46(Biology)

Journal Articles

DNA damage evaluation system of the high-LET ion beam using the polymerase chain reaction

Matsuo, Yoichiro*; Izumi, Yoshinobu*; Hase, Yoshihiro; Sakamoto, Ayako; Nozawa, Shigeki; Narumi, Issei; Shimizu, Kikuo*

JAEA-Review 2012-046, JAEA Takasaki Annual Report 2011, P. 105, 2013/01

Journal Articles

FACS-based screening for yeast clone highly expressing cellulase

Ninomiya, Kazuaki*; Nomura, Tomoyo*; Sato, Katsuya; Narumi, Issei; Shimizu, Nobuaki*

JAEA-Review 2012-046, JAEA Takasaki Annual Report 2011, P. 108, 2013/01

Journal Articles

Fundamental study on molecular mechanism underlying repair of heavy-ion induced DNA damage in the ${it Saccharomyces cerevisiae}$

Matsuo, Yoichiro*; Izumi, Yoshinobu*; Hase, Yoshihiro; Sakamoto, Ayako; Nozawa, Shigeki; Narumi, Issei; Shimizu, Kikuo*

JAEA-Review 2011-043, JAEA Takasaki Annual Report 2010, P. 108, 2012/01

Journal Articles

Repeated FACS-based screening for yeast strain highly expressing cellulase

Ninomiya, Kazuaki*; Soda, Hiroshi*; Sato, Katsuya; Narumi, Issei; Shimizu, Nobuaki*

JAEA-Review 2011-043, JAEA Takasaki Annual Report 2010, P. 111, 2012/01

Journal Articles

FACS-based screening of yeast strain highly expressing cellulase

Ninomiya, Kazuaki*; Soda, Hiroshi*; Sato, Katsuya; Narumi, Issei; Shimizu, Nobuaki*

JAEA-Review 2010-065, JAEA Takasaki Annual Report 2009, P. 78, 2011/01

no abstracts in English

Journal Articles

Molecular analysis of carbon ion induced mutations in yeast ${it Saccharomyces cerevisiae}$ cells

Shimizu, Kikuo*; Matsuo, Yoichiro*; Izumi, Yoshinobu*; Hase, Yoshihiro; Nozawa, Shigeki; Sakamoto, Ayako; Narumi, Issei

JAEA-Review 2010-065, JAEA Takasaki Annual Report 2009, P. 79, 2011/01

Journal Articles

Molecular analysis of carbon ion induced mutations in the yeast ${it ogg1}$ and ${it msh2}$ mutants

Matsuo, Yoichiro*; Nishijima, Shigehiro*; Hase, Yoshihiro; Nozawa, Shigeki; Sakamoto, Ayako; Narumi, Issei; Shimizu, Kikuo*

JAEA-Review 2009-041, JAEA Takasaki Annual Report 2008, P. 75, 2009/12

no abstracts in English

Journal Articles

Deletion of minor enzyme activities of ${it Rhizomucor miehei}$ by heavy ion irradiation

Sakai, Kazuya*; Kobayashi, Hiroyuki*; Shimizu, Masatoshi*; Oshima, Akio*; Kato, Shigeaki*; Sato, Katsuya; Narumi, Issei

JAEA-Review 2008-055, JAEA Takasaki Annual Report 2007, P. 85, 2008/11

no abstracts in English

Journal Articles

Functional analysis of the low-fidelity DNA polymerase AtREV1

Takahashi, Shinya*; Nakagawa, Mayu; Tanaka, Atsushi; Narumi, Issei; Shimizu, Kikuo*; Sakamoto, Ayako

JAEA-Review 2008-055, JAEA Takasaki Annual Report 2007, P. 58, 2008/11

no abstracts in English

Journal Articles

Ion beam breeding of flower color variations in transgenic plants with multi-disease tolerance

Okamura, Masachika*; Shimizu, Akira*; Onishi, Noboru*; Hase, Yoshihiro; Yoshihara, Ryohei; Narumi, Issei

JAEA-Review 2008-055, JAEA Takasaki Annual Report 2007, P. 62, 2008/11

no abstracts in English

Journal Articles

Study on molecular mechanism of high-LET carbon ion beam induced mutations in ${it S. cerevisiae}$

Matsuo, Yoichiro*; Nishijima, Shigehiro*; Hase, Yoshihiro; Sakamoto, Ayako; Narumi, Issei; Shimizu, Kikuo*

JAEA-Review 2008-055, JAEA Takasaki Annual Report 2007, P. 60, 2008/11

no abstracts in English

Journal Articles

Ion beam breeding of flower color variations in transgenic plants with multi-disease tolerance

Okamura, Masachika*; Shimizu, Akira*; Watanabe, Satomi*; Hase, Yoshihiro; Narumi, Issei; Tanaka, Atsushi

JAEA-Review 2007-060, JAEA Takasaki Annual Report 2006, P. 82, 2008/03

no abstracts in English

68 (Records 1-20 displayed on this page)