Evaluation of the remaining spent extraction solvent in vermiculite after leaching tests via PIXE analysis

Arai, Yoichi; Watanabe, So; Hasegawa, Kenta; Okamura, Nobuo; Watanabe, Masayuki; Takeda, Keisuke*; Fukumoto, Hiroki*; Ago, Tomohiro*; Hagura, Naoto*; Tsukahara, Takehiko*

Nuclear Instruments and Methods in Physics Research B, 542, p.206 - 213, 2023/09

https://doi.org/10.1016/j.nimb.2023.07.003

Structure of a highly acidic -lactamase from the moderate halophile 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

https://doi.org/10.1107/S1399004714027734

The crystal structure of halophilic -lactamase from sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr 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- 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.

Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro; Honjo, Eijiro; Okazaki, Nobuo; Arai, Shigeki; Shoyama, Yoshinari; Kimura, Kaname*; Matsumura, Hiroyoshi*; et al.

Proceedings of the National Academy of Sciences of the United States of America, 106(12), p.4641 - 4646, 2009/03

https://doi.org/10.1073/pnas.0809400106

To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp25 and Asp125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9 resolution and X-ray crystallography at 1.4 resolution. The resulting structural data shows that the catalytic residue Asp25 is protonated and that Asp125 is deprotonated. The proton on Asp25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine group in KNI-272. The deprotonated Asp125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease; and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.

Chemical abundances in the secondary star of the black hole binary V4641 Sagittarii (SAX J1819.3-2525)

Sadakane, Kozo*; Arai, Akira*; Aoki, Wako*; Arimoto, Nobuo*; Hidai, Masahide*; Onishi, Takashi*; Tajitsu, Akito*; Beers, T. C.*; Iwamoto, Nobuyuki; Tominaga, Nozomu*; et al.

Publications of the Astronomical Society of Japan, 58(3), p.595 - 604, 2006/06

https://doi.org/10.1093/pasj/58.3.595

We report detailed spectroscopic studies performed for the secondary star in the black hole binary (micro-quasar) V4641 Sgr in order to examine its surface chemical composition and to see if its surface shows any signature of pollution by ejecta from a supernova explosion. We obtain abundances of 10 elements and find definite over-abundances of N (by 0.8 dex or more) and Na (by 0.8 dex) in V4641 Sgr. From line-by-line comparisons of eight other elements (C, O, Mg, Al, Si, Ti, Cr, Fe) between V4641 Sgr and the two normal late B-type stars, which have been reported to have solar abundances. An evolutionary model of a massive close binary system has been constructed to explain the abundances observed in V4641 Sgr. The model suggests that the BH forming supernova in this system was a dark one.

Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography

Niimura, Nobuo; Arai, Shigeki; Kurihara, Kazuo; Chatake, Toshiyuki*; Tanaka, Ichiro*; Bau, R.*

Cellular and Molecular Life Sciences, 63(3), p.285 - 300, 2006/02

https://doi.org/10.1007/s00018-005-5418-3

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins and DNA oligomers. Three different types of high resolution neutron diffractometers for biological macromolecules have been constructed in Japan, France and the U.S.A., and they have all been actively used in recent years to determine the crystal structures of numerous proteins. Examples include the detailed geometries of hydrogen bonds, information on H/D exchange in proteins, the unambiguous location of protons, the role of key hydrogen atoms in enzymatic activity and thermostability, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed in this article. Other important techniques, such as the optimization of growth of large single crystals using phase diagrams, the preparation of fully deuterated proteins, the introduction of cryogenic techniques to neutron protein crystallography, and the establishment of a "hydrogen and hydration in proteins" database, will also be described in this paper.

Hydrogen and hydration in proteins and nucleic acids; Neutron diffraction from bio-macromolecules at JAERI

Niimura, Nobuo; Arai, Shigeki; Kurihara, Kazuo; Chatake, Toshiyuki*; Tanaka, Ichiro*; Bau, R.*

Hydrogen- and Hydration-Sensitive Structural Biology, p.17 - 35, 2005/00

At the JAERI, we have constructed several high-resolution neutron diffractometers dedicated to biological macromolecules (called BIX-type diffractometers), which use a monochromatized neutron beam and a neutron imaging plate detector. In this paper, we review several interesting results regarding hydrogen positions and hydration in proteins, obtained using the two BIX-type diffractometers in JAERI. The general subject of neutron protein crystallography has been reviewed by several authors, and several selected topics have been discussed.

Research and development on accelerator-driven transmutation system at JAERI

Sasa, Toshinobu; Oigawa, Hiroyuki; Tsujimoto, Kazufumi; Nishihara, Kenji; Kikuchi, Kenji; Kurata, Yuji; Saito, Shigeru; Futakawa, Masatoshi; Umeno, Makoto*; Ouchi, Nobuo; et al.

Nuclear Engineering and Design, 230(1-3), p.209 - 222, 2004/05

https://doi.org/10.1016/j.nucengdes.2003.11.033

JAERI carries out research and development on accelerator-driven system (ADS) to transmute minor actinides and long-lived fission products. The system is composed of high intensity proton accelerator, lead-bismuth spallation target and lead-bismuth cooled subcritical core with nitride fuel. About 2,500 kg of minor actinide is loaded into the subcritical core. Annual transmutation amount using this system is 250 kg with 800MW of thermal output. A superconducting linear accelerator with the beam power of 30MW is connected to drive the subcritical core. Many research and development activities are under way and planned in the fields of subcritical core design, spallation target technology, lead-bismuth handling technology, accelerator development, and minor actinide fuel development. Especially, to study and evaluate the feasibility of the ADS from physics and engineering aspects, the Transmutation Experimental Facility (TEF) is proposed under a framework of the High-Intensity Proton Accelerator Project.

High efficiency indirect geometory crystal analyzer TOF spectrometer; DYANA dedicated to biology, planning in JSNS

Shibata, Kaoru; Tamura, Itaru; Soyama, Kazuhiko; Arai, Masatoshi; Middendorf, H. D.*; Niimura, Nobuo

Proceedings of ICANS-XVI, Volume 1, p.351 - 354, 2003/07

In this research report we describe the design of DYANA, a new neutron spectrometer dedicated for biology, biomaterials, and related soft-matter studies, which will be installed in the material and life science experimental facility project at the JAERI Tokai establishment. The DYANA spectrometer is an indirect-geometry crystal-analyzer instrument and its energy and momentum transfer range are from several 10eV to several meV and from 0.1 to several , respectively. These specifications will become possible to do the study of protein dynamics analysis.

Research and development on accelerator-driven transmutation system at JAERI

Sasa, Toshinobu; Oigawa, Hiroyuki; Tsujimoto, Kazufumi; Nishihara, Kenji; Kikuchi, Kenji; Kurata, Yuji; Saito, Shigeru; Futakawa, Masatoshi; Umeno, Makoto*; Ouchi, Nobuo; et al.

Proceedings of 11th International Conference on Nuclear Engineering (ICONE-11) (CD-ROM), 9 Pages, 2003/04

JAERI carries out research and development on accelerator-driven system (ADS) to transmute minor actinides and long-lived fission products in high-level radioactive waste. The system is composed of high intensity proton accelerator, lead-bismuth spallation target and lead-bismuth cooled subcritical core with nitride fuel. About 2500 kg of minor actinide is loaded into the subcritical core. Annual transmutation amount using this system is 250 kg with 800MW of thermal output. A superconducting linear accelerator with the beam power of 20 - 30MW is connected to drive the subcritical core. The nitride fuel without uranium, such as (Np, Am, Pu)N, is selected. The fuel irradiated in the ADS is reprocessed by pyrochemical process followed by the re-fabrication of the fuel. Many research and development activities are under way. Especially, to study and evaluate the feasibility of the ADS from physics and engineering aspects, the Transmutation Experimental Facility (TEF) is proposed under a framework of the High-Intensity Proton Accelerator Project.

Research and development on accelerator-driven system for transmutation of long-lived nuclear waste at JAERI

Oigawa, Hiroyuki; Sasa, Toshinobu; Takano, Hideki; Tsujimoto, Kazufumi; Nishihara, Kenji; Kikuchi, Kenji; Kurata, Yuji; Saito, Shigeru; Futakawa, Masatoshi; Umeno, Makoto*; et al.

Proceedings of 13th Pacific Basin Nuclear Conference (PBNC 2002) (CD-ROM), 8 Pages, 2002/10

To reduce the burden on the final disposal of the nuclear waste, the Acclelerator-Driven System (ADS) which can transmute minor actinides efficiently has been studied in JAERI. The proposed ADS design is an 800MWth subcritical core with lead-bismuth coolant and minor-actinide nitride fuel driven by a neutron source of a superconductivity linear accelerator with 30MW and a lead-bismuth spallation target. To realize the ADS, many research and development are under way in the fields of the accelerator, the spallation target and the nitride fuel. Moreover, a new experimental facility, the Transmutation Experimental Facility, is proposed under a framework of the High-Intensity Proton Accelerator Project to study the feasibility of the ADS from physics and engineering aspects.