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Journal Articles

Oxidation of silicon carbide in steam studied by laser heating

Pham, V. H.; Nagae, Yuji; Kurata, Masaki; Furumoto, Kenichiro*; Sato, Hisaki*; Ishibashi, Ryo*; Yamashita, Shinichiro

Proceedings of International Nuclear Fuel Cycle Conference / Light Water Reactor Fuel Performance Conference (Global/Top Fuel 2019) (USB Flash Drive), p.670 - 674, 2019/09

Journal Articles

Improving the corrosion resistance of silicon carbide for fuel in BWR environments by using a metal coating

Ishibashi, Ryo*; Tanabe, Shigetada*; Kondo, Takao*; Yamashita, Shinichiro; Nagase, Fumihisa

Proceedings of 2017 Water Reactor Fuel Performance Meeting (WRFPM 2017) (USB Flash Drive), 10 Pages, 2017/09

For improving the corrosion resistance of silicon carbide (SiC) in boiling-water-reactor environments, corrosion-resistant coatings on SiC were evaluated. Due to its hydrogen-generation rate and reaction heat being lower than those of conventional Zircaloy, SiC is expected to be an appropriate material for accident-tolerant fuels. However, there are still many critical issues with the practical application of SiC fuel cladding and fuel channel boxes, one of which is hydrothermal corrosion. Silicon carbide is chemically stable, but silicon oxide formed by oxidation of SiC dissolves in high temperature water. Although the rate of SiC dissolution is very small, the dissolution must be suppressed to comply with regulations for dissolved silica concentration in reactor coolant. In this study, the corrosion behavior of candidate coatings for SiC substrates were evaluated before and after exposure to unirradiated high-purity-water environments.

Journal Articles

Nucleoside diphosphate kinase from psychrophilic ${it Pseudoalteromonas}$ sp. AS-131 isolated from Antarctic Ocean

Yonezawa, Yasushi*; Nagayama, Aiko*; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arai, Shigeki; Kuroki, Ryota; Watanabe, Keiichi*; Arakawa, Tsutomu*; Tokunaga, Masao*

Protein Journal, 34(4), p.275 - 283, 2015/08

 Times Cited Count:4 Percentile:13.25(Biochemistry & Molecular Biology)

Nucleoside diphosphate kinase isolated from psychrophilic ${it Pseudoalteromonas}$ sp. AS-131 (ASNDK) was expressed in ${it Escherichia coli}$ and purified to homogeneity. Comparing to mesophilic NDK isolated from ${it Pseudomonas aeruginosa}$, ASNDK exhibited highly elevated thermolability: (1) ${it E. coli}$ expression at 37$$^{circ}$$C as a denatured insoluble form, and (2) 30$$^{circ}$$C lower optimum temperature of enzymatic activity. The subunit structure of ASNDK was suggested to be dimer, as in NDKs isolated from moderate halophiles.

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:6 Percentile:49.63(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

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium ${it Halomonas}$ sp.593

Arai, Shigeki; Yonezawa, Yasushi*; Ishibashi, Matsujiro*; Matsumoto, Fumiko*; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Acta Crystallographica Section D, 70(3), p.811 - 820, 2014/03

 Times Cited Count:9 Percentile:58.39(Biochemical Research Methods)

In order to clarify the structural basis of halophilic characteristics of an alkaline phosphatase derived from the moderate halophile ${it Halomonas}$ sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1${AA}$ resolution by X-ray crystallography. Structural properties of surface negative charge and core hydrophobicity are shown to be intermediate between halophile and non-halophile characteristics, and may explain the unique functional adaptation to a wide-range of salt concentration.

JAEA Reports

Mizunami Underground Research Laboratory Project, Annual report for fiscal year 2012

Hama, Katsuhiro; Mikake, Shinichiro; Nishio, Kazuhisa; Matsuoka, Toshiyuki; Ishibashi, Masayuki; Sasao, Eiji; Hikima, Ryoichi*; Tanno, Takeo*; Sanada, Hiroyuki; Onoe, Hironori; et al.

JAEA-Review 2013-050, 114 Pages, 2014/02

JAEA-Review-2013-050.pdf:19.95MB

Japan Atomic Energy Agency (JAEA) at Tono Geoscience Center (TGC) is pursuing a geoscientific research and development project namely the Mizunami Underground Research Laboratory (MIU) Project in crystalline rock environment in order to construct scientific and technological basis for geological disposal of High-level Radioactive Waste (HLW). The MIU Project has three overlapping phases: Surface-based Investigation phase (Phase I), Construction phase (Phase II), and Operation phase (Phase III). The MIU Project has been ongoing the Phase II and the Phase III in fiscal year 2012. This report presents the results of the investigations, construction and collaboration studies in fiscal year 2012, as a part of the Phase II and Phase III based on the MIU Master Plan updated in 2010.

JAEA Reports

Mizunami Underground Research Laboratory Project, Annual report for fiscal year 2011

Kunimaru, Takanori; Mikake, Shinichiro; Nishio, Kazuhisa; Tsuruta, Tadahiko; Matsuoka, Toshiyuki; Ishibashi, Masayuki; Sasao, Eiji; Hikima, Ryoichi; Tanno, Takeo; Sanada, Hiroyuki; et al.

JAEA-Review 2013-018, 169 Pages, 2013/09

JAEA-Review-2013-018.pdf:15.71MB

Japan Atomic Energy Agency (JAEA) at Tono Geoscience Center (TGC) is pursuing a geoscientific research and development project namely the Mizunami Underground Research Laboratory (MIU) Project in crystalline rock environment in order to construct scientific and technological basis for geological disposal of High-level Radioactive Waste (HLW). The MIU Project has three overlapping phases: Surface-based Investigation phase (Phase I), Construction phase (Phase II), and Operation phase (Phase III). The MIU Project has been ongoing the Phase II and the Phase III in 2011 fiscal year. This report shows the results of the investigation, construction and collaboration studies in fiscal year 2011, as a part of the Phase II and Phase III based on the MIU Master Plan updated in 2010.

Journal Articles

Reduction of salt-requirement of halophilic nucleoside diphosphate kinase by engineering S-S bond

Ishibashi, Matsujiro*; Uchino, Manami*; Arai, Shigeki; Kuroki, Ryota; Arakawa, Tsutomu*; Tokunaga, Masao*

Archives of Biochemistry and Biophysics, 525(1), p.47 - 52, 2012/09

 Times Cited Count:7 Percentile:23.13(Biochemistry & Molecular Biology)

Nucleoside diphosphate kinase (HsNDK) from Halobacterium salinarum requires salt at high concentrations for folding. A D148C mutant, in which Asp148 was replaced with Cys, was designed to enhance stability and folding in low salt solution by S-S bond. It showed increased thermal stability by about 10$$^{circ}$$C in 0.2 M NaCl over the wild type HsNDK. It refolded from heat-denaturation even in 0.1 M NaCl, while the wild type required 2 M NaCl to achieve the same level of activity recovery. This enhanced refolding is due to the three S-S bonds between two basic dimeric units in the hexameric HsNDK structure. Moreover, salt concentration dependency of heat-denaturation process and refolding process of the wild type and D148C mutant HsNDKs were investigated by the circular dichroism and native-PAGE analysis.

JAEA Reports

Mizunami Underground Research Laboratory Project, Plan for fiscal year 2012

Kunimaru, Takanori; Mikake, Shinichiro; Nishio, Kazuhisa; Tsuruta, Tadahiko; Matsuoka, Toshiyuki; Ishibashi, Masayuki; Kuboshima, Koji; Takeuchi, Ryuji; Mizuno, Takashi; Sato, Toshinori; et al.

JAEA-Review 2012-028, 31 Pages, 2012/08

JAEA-Review-2012-028.pdf:3.86MB

Japan Atomic Energy Agency (JAEA) at Tono Geoscience Center (TGC) is pursuing a geoscientific research and development project namely the Mizunami Underground Research Laboratory (MIU) project in crystalline rock environment in order to construct scientific and technological basis for geological disposal of High-level Radioactive Waste (HLW). The MIU project is planned in three overlapping phases; Surface-based Investigation Phase (Phase I), Construction Phase (Phase II) and Operation Phase (Phase III). Currently, the project is under the Construction Phase and the Operation Phase. This document introduces the research and development activities planned for 2012 fiscal year based on the MIU Master Plan updated in 2010, construction plan and research collaboration plan, etc.

JAEA Reports

Mizunami Underground Research Laboratory Project, Annual report for fiscal year 2010

Kunimaru, Takanori; Mikake, Shinichiro; Nishio, Kazuhisa; Tsuruta, Tadahiko; Matsuoka, Toshiyuki; Ishibashi, Masayuki; Ueno, Takashi; Tokuyasu, Shingo; Daimaru, Shuji; Takeuchi, Ryuji; et al.

JAEA-Review 2012-020, 178 Pages, 2012/06

JAEA-Review-2012-020.pdf:33.16MB

Japan Atomic Energy Agency (JAEA) at Tono Geoscience Center (TGC) is pursuing a geoscientific research and development project namely the Mizunami Underground Research Laboratory (MIU) Project in crystalline rock environment in order to construct scientific and technological basis for geological disposal of High-level Radioactive Waste (HLW). The MIU Project has three overlapping phases: Surface-based Investigation phase (Phase I), Construction phase (Phase II), and Operation phase (Phase III). The MIU Project has been ongoing the Phase II. And Phase III started in 2010 fiscal year. This report shows the results of the investigation, construction and collaboration studies in fiscal year 2010, as a part of the Phase II based on the MIU Master Plan updated in 2002.

Journal Articles

Direct evidence of generation and accumulation of $$beta$$-sheet-rich prion protein in scrapie-infected neuroblastoma cells with human IgG1 antibody specific for $$beta$$-form prion protein

Kubota, Toshiya*; Hamazoe, Yuta*; Hashiguchi, Shuhei*; Ishibashi, Daisuke*; Akasaka, Kazuyuki*; Nishida, Noriyuki*; Katamine, Shigeru*; Sakaguchi, Suehiro*; Kuroki, Ryota; Nakashima, Toshihiro*; et al.

Journal of Biological Chemistry, 287(17), p.14023 - 14039, 2012/04

 Times Cited Count:5 Percentile:12.98(Biochemistry & Molecular Biology)

We prepared $$beta$$-sheet-rich recombinant full-length prion protein ($$beta$$-form PrP) (Jackson, G. S., Hosszu, L. L., Power, A., Hill, A. F., Kenney, J., Saibil, H., Craven, C. J., Waltho, J. P., Clarke, A. R., and Collinge, J. (1999) Science 283, 1935-1937). Using this $$beta$$-form PrP and a human single chain Fv-displaying phage library, we have established a human IgG1 antibody specific to $$beta$$-form but not $$alpha$$-form PrP, PRB7 IgG. When prion-infected ScN2a cells were cultured with PRB7 IgG, they generated and accumulated PRB7-binding granules in the cytoplasm with time, consequently becoming apoptotic cells bearing very large PRB7-bound aggregates. The SAF32 antibody recognizing the N-terminal octarepeat region of full-length PrP stained distinct granules in these cells as determined by confocal laser microscopy observation. When the accumulation of proteinase K-resistant PrP was examined in prion-infected ScN2a cells cultured in the presence of PRB7 IgG or SAF32, it was strongly inhibited by SAF32 but not at all by PRB7 IgG. Thus, we demonstrated direct evidence of the generation and accumulation of $$beta$$-sheet-rich PrP in ScN2a cells de novo. These results suggest first that PRB7-bound PrP is not responsible for the accumulation of $$beta$$-form PrP aggregates, which are rather an end product resulting in the triggering of apoptotic cell death, and second that SAF32-bound PrP lacking the PRB7-recognizing $$beta$$-form may represent so-called PrPSc with prion propagation activity. PRB7 is the first human antibody specific to $$beta$$-form PrP and has become a powerful tool for the characterization of the biochemical nature of prion and its pathology.

Journal Articles

A Structural mechanism for dimeric to tetrameric oligomer conversion in ${it Halomonas}$ sp. nucleoside diphosphate kinase

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Protein Science, 21(4), p.498 - 510, 2012/04

 Times Cited Count:15 Percentile:40.18(Biochemistry & Molecular Biology)

In order to clarify the oligomer state of nucleoside diphosphate kinase (NDK) from moderately halophilic ${it Halomonas}$ sp. 593 (HaNDK), the crystal structure of HaNDK was determined by X-ray crystallography. The crystal structures of the wild-type HaNDK and the mutant HaNDK (E134A) showed a dimer and a tetramer, respectively. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Journal Articles

Residue 134 determines the dimer-tetramer assembly of nucleoside diphosphate kinase from moderately halophilic bacteria

Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arisaka, Fimio*; Arai, Shigeki; Kuroki, Ryota; Arakawa, Tsutomu*; Tokunaga, Masao*

FEBS Letters, 582(7), p.1049 - 1054, 2008/04

 Times Cited Count:17 Percentile:42.48(Biochemistry & Molecular Biology)

${it Halomonas}$ nucleoside diphosphate kinase (HaNDK) forms a dimeric assembly and ${it Pseudomonas}$ NDK (PaNDK) forms a tetrameric assembly. The mutation of Glu134 to Ala in HaNDK resulted in conversion of the native dimeric structure to the tetramer assembly. Conversely, the mutation of Ala134 to Glu in PaNDK leads to conversion from tetramer to dimer assembly, indicating that a single amino acid substitution at position 134 results in an alteration of the oligomeric structure of NDK. Modeling structure of HaNDK and PaNDK, based on the crystal structure of ${it Myxococcus}$ NDK, suggested sufficient repulsion by Glu134 to disrupt dimer-dimer interaction to form tetramer.

Journal Articles

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Proceedings of the National Academy of Sciences of the United States of America, 103(9), p.3135 - 3140, 2006/02

 Times Cited Count:86 Percentile:83.84(Multidisciplinary Sciences)

A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF), and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8${AA}$ resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry via a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different to that between human GCSF and the CRH domain of mouse GCSF-R, but similar to that of the interleukin-6 (IL-6)/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.

Journal Articles

Crystallization of a 2:2 complex of Granulocyte-Colony Stimulating Factor (GCSF) with the ligand-binding region of the GCSF receptor

Honjo, Eijiro; Tamada, Taro; Maeda, Yoshitake*; Koshiba, Takumi*; Matsukura, Yasuko*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Acta Crystallographica Section F, 61(8), p.788 - 790, 2005/08

 Times Cited Count:7 Percentile:56.45(Biochemical Research Methods)

Granulocyte colony-stimulating factor (GCSF) receptor receives signals for regulating the proliferation and differentiation of the precursor cells of granulocytes. The complex composed of two GCSFs and two GCSF receptors was crystallized. The crystal of the complex was grown in 1.0 M sodium formate and 0.1 M sodium acetate (pH4.6). It belongs to the space group ${it P}$4$$_{1}$$2$$_{1}$$2 (or its enantiomorph ${it P}$4$$_{3}$$2$$_{1}$$2) with unit cell dimensions of ${it a}$ = ${it b}$ = 110.1 ${AA}$, ${it c}$ = 331.8 ${AA}$. However, the diffraction data from the crystal beyond 5 ${AA}$ resolution could not be collected. Since the heterogeneity of GCSF receptor seems to interrupt growth of good quality crystals, the GCSF receptor was fractionated by achromatography. Crystals of GCSF/fractionated GCSF receptor complex were grown as a new crystal form in 0.2 M ammonium phosphate. The new crystal diffracts beyond 3.0 ${AA}$ resolution and belongs to space group ${it P}$3$$_{1}$$21 (or its enantiomorph ${it P}$3$$_{2}$$21) with unit-cell parameters ${it a}$ = ${it b}$ = 134.8, ${it c}$ = 105.7 ${AA}$.

Oral presentation

Homodimeric crossover structure of the human GCSF-receptor signaling complex

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

We have succeeded in crystallization of 2:2 complex between human granulocyte colony-stimulating factor (hGCSF) and the Ig-like and CRH domains of human GCSF-R (hGCSF-R) and determined its tertiary structure by X-ray crystallography at 2.8 ${AA}$ resolution. The signaling 2:2 complex is formed via cross-over interactions between the Ig-like domain of hGCSF-R and the neighboring hGCSF, forming a two-fold axis of crystallographic symmetry. This conformation is quite different from that of the heterogeneous mGCSF-R complex, and more closely resembles the 2:2:2 active assembly of human interleukin-6 (IL-6), human IL-6 $$alpha$$-receptor and human gp130 (which is a shared signal transducing receptor for several cytokines), and the 2:2 assembly of viral IL-6 and human gp130. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.

Oral presentation

Residue 134 determines the dimer-tetramer assembly of nucleoside diphosphate kinase from moderately halophilic bacteria

Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arisaka, Fimio*; Arai, Shigeki; Kuroki, Ryota; Yamaguchi, Rui*; Arakawa, Tsutomu*; Tokunaga, Masao*

no journal, , 

no abstracts in English

Oral presentation

Positron production by laser-Compton $$gamma$$-rays and application to material study

Toyokawa, Hiroyuki*; Hirade, Tetsuya; Tomota, Yo*; Ishibashi, Toshihiro*; Sugaya, Satoshi*; Suzuki, Ryoichi*

no journal, , 

The brittleness of materials might be affected by defects, dislocations and impurities. However it is not well understood. Clarifying these problems is very important to make reliable models for estimating the degradation of materials for atomic energy. Injecting high energy photons with more than 1.02 MeV to materials can produce electron/positron pairs. Collimated MeV-energy-$$gamma$$-rays with several mm diameters can produce needle shaped positron distribution. By use of the produced positrons, it is possible to make 3D views of defect distribution or cross section of electro/positron pair production at deeper region of materials. This method is expected to be applied for measurements in atmosphere or high-temperature/high-pressure environments. We succeeded to obtain CT images of the transmission view and electron/positron pair production cross section of reinforcing bars in concrete by use of 5 mm diameter 9.1 MeV $$gamma$$-rays. We also measured S-parameters for defects in metal samples.

Oral presentation

Ologomeric structure of nucleoside diphosphate kinase from Halomonas sp. 593 (HaNDK)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. We determined the crystal structure of E134A mutant NDK from Halomonas sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the Myxococcus NDK tetramer and Type II seen in the E.coli NDK tetramer, appeared in the asymmetric unit. Change in the assembly form may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Oral presentation

Oligomeric structure of nucleoside diphosphate kinase from Halomonas sp.593 (HaNDK)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. We determined the crystal structure of E134A mutant NDK from ${it Halomonas}$ sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the ${it Myxococcus}$ NDK tetramer and Type II seen in the ${it E.coli}$ NDK tetramer, appeared in the asymmetric unit. Change in the assembly form may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

40 (Records 1-20 displayed on this page)