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sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formationUeno, Akio*; Tamazawa, Satoshi*; Tamamura, Shuji*; Murakami, Takuma*; Kiyama, Tamotsu*; Inomata, Hidenori*; Amano, Yuki; Miyakawa, Kazuya; Tamaki, Hideyuki*; Naganuma, Takeshi*; et al.
International Journal of Systematic and Evolutionary Microbiology, 71(2), p.004683_1 - 004683_10, 2021/02
Times Cited Count：8 Percentile：62.07(Microbiology)A novel mesophilic sulfate-reducing bacterium, designated strain HN2
, was isolated from groundwater sampled from the subsurface Miocene Wakkanai Formation located in Horonobe, Hokkaido, Japan. The cells were Gram-negative rods, with motility conferred by a single polar flagellum. The isolate expressed desulfoviridin, but no catalase or oxidase activities was detected. Strain HN2 grew in a temperature range of 5-43 
C (optimum, 35 C) and in a pH range of 6.5-7.5 (optimum, pH 7.0-7.3). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe
, and manganese oxide as electron acceptors, but not elemental sulfur, nitrite, or nitrate. The bacterium showed very weak growth with sulfite as the electron acceptor. The strain fermented pyruvate and cysteine in the absence of sulfate, but not malate or succinate. The bacterium did not require NaCl, but tolerated up to 4% NaCl (w/v). Strain HN2 did not require vitamins. The G+C content of the genomic DNA was 56.66 mol%. A 16S rRNA gene sequence analysis showed that the closest recognized relative of strain HN2 is 
JS1 (97.0% similarity). The average nucleotide identity (ANI) value between strain HN2 and D. 
JS1 was 79.8%. Based on the phenotypic and molecular genetic evidence, the isolate is assigned to the new species sp. nov. The type strain is HN2 (=DSM 101010 =NBRC 112213).
Tamamura, Shuji*; Miyakawa, Kazuya; Aramaki, Noritaka*; Igarashi, Toshifumi*; Kaneko, Katsuhiko*
Groundwater, 56(1), p.118 - 130, 2018/01
Groundwater saturated with gas forms bubble under atmospheric pressure, bothering most authorized methods to determine in-situ dissolved gas concentrations. To circumvent this problem, a simple theory to quantify effect of 
[bar]) of a gas component "
" (e.g., CH
, CO
and H) in equilibrium with in-situ dissolved concentration (
[mol L 
]) was related to partial pressure of the 
[bar]) emerged from groundwater in the form: 
= 
+ 
(k' /(
k' 
)), where [bar] is groundwater pressure difference before and after the 
" The k
' and k
' corresponds to the Henry's constant [bar L mol] of (k) and (k), respectively, except for k
', which is pH-dependent function. Dissolved CH concentrations were successfully estimated by the model within the error of 
4.0% from the direct measurements by the sealed sampler method. Similar TIC concentration in the groundwater before and after the rm bubble formation was consistent with the model prediction. The wide application of the model is suggested without selecting sampling locations.
Nara, Yoshitaka*; Cho, S. H.*; Yoshizaki, Takaya*; Kaneko, Katsuhiko*; Sato, Toshinori*; Nakama, Shigeo; Matsui, Hiroya
International Journal of the JCRM (Internet), 7(1), p.1 - 9, 2011/01
This study presents a back analysis based on three-dimensional finite element analysis in order to estimate the regional stress fields and the elastic moduli of a rock mass simultaneously from in situ measurements. In order to improve the accuracy of the estimation of three-dimensional stress field, heterogeneities in a rock mass consisting of geological layers with different elastic properties was considered. Back analysis was applied to determine the regional stresses for a broad field study that includes Tono Mine, the Shobasama Site and the Mizunami Underground Research Laboratory (MIU) Construction Site.
Mizuta, Yoshiaki*; Kaneko, Katsuhiko*; Matsuki, Koji*; Sugawara, Katsuhiko*; Sudo, Shigeaki*; Hirano, Toru; Tanno, Takeo; Matsui, Hiroya
JAEA-Research 2010-011, 35 Pages, 2010/06
JAEA-Research-2010-011.pdf:4.42MB
The best way to know the initial stress clearly is to measure it in the location where a tunnel will be excavated. However, it is difficult to measure a large number of the initial stresses, budgetary considerations notwithstanding, because of the large scale of underground structures like a radioactive waste disposal facility. Therefore we developed a method for determination of initial stress for arbitrary points from limited results of initial stress measurements. This report is a summary of the contract work about this development. At first, we made local scale numerical models of the Tono area. Using these models, we determined the regional stress state from limited initial stress measurements results. Then we applied the regional stress state to boundary conditions of other numerical models and estimated initial stress at arbitrary points. The result is an estimated initial stress that matched the original stress measurement results from the first analytical results.
Ishikawa, Masumi*; Kaneko, Satoru*; Kitayama, Kazumi*; Ishiguro, Katsuhiko*; Ueda, Hiroyoshi*; Wakasugi, Keiichiro*; Shinohara, Nobuo; Okumura, Keisuke; Chino, Masamichi; Moriya Noriyasu*
Nihon Genshiryoku Gakkai Wabun Rombunshi, 8(4), p.304 - 312, 2009/12
Since quality control issues for vitrified waste are defined mainly with the focus on the transport and storage of the waste rather than the long-term safety of geological disposal, they do not cover inventories of long-lived nuclides which are of most interest in the safety assessment of geological disposal. Therefore we suggest a flow chart for assessment of inventories of long-lived nuclides in the vitrified waste focusing on measured value. We started a programme to examine the applicability as well as to improve reliability of nuclide generation/decay code and nuclear data library using liquid waste from spent fuel with clear irradiation history. To solve the issue of quality control for vitrified waste, comprehensive study is needed in aspects not only of geological disposal field but also of operation of nuclear power plant, reprocessing of spent fuel and vitrification of liquid waste. This study is a pioneering study to integrate them.
Yamasaki, Chisato*; Murakami, Katsuhiko*; Fujii, Yasuyuki*; Sato, Yoshiharu*; Harada, Erimi*; Takeda, Junichi*; Taniya, Takayuki*; Sakate, Ryuichi*; Kikugawa, Shingo*; Shimada, Makoto*; et al.
Nucleic Acids Research, 36(Database), p.D793 - D799, 2008/01
Times Cited Count：51 Percentile：71.25(Biochemistry & Molecular Biology)Here we report the new features and improvements in our latest release of the H-Invitational Database, a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of fulllength cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 protein-coding and 642 non-protein-coding loci; 858 transcribed loci overlapped with predicted pseudogenes.
Mizuta, Yoshiaki*; Kaneko, Katsuhiko*; Matsuki, Koji*; Sugawara, Katsuhiko*; Sudo, Shigeaki*
JNC TJ7400 2004-011, 125 Pages, 2004/02
JNC-TJ7400-2004-011.pdf:11.26MB
In the fiscal year of 2003, our committee achieved the following work items during the contract period, from September 3rd, 2003 to February 13th, 2004. The more accurate numerical data with respect to the geological / geometrical conditions including the fault were provided from Tono Geoscience Center and the numerical models by Finite Element Method (FEM), Finite Difference Method (FDM) and Boundary Element Method (BEM) were built taking those strata data into account. For small region modeling by FEM, these layers models, Shoumasama model and Tohnou-Shoumasama model, as well as Thounou Mine model, were constructed, and each strain state at the far field boundary was determined. In order to get better agreement in local stress states with the measured values, a far field strain state was determined to the modified model in which material properties of upper granite and lower granite are different. In intermediate region modeling by FDM, actual strata data was taken into account, whereas strata boundary was assumed to be horizontal in former modeling, and far field stress field was analyzed. Intermediate region modeling by BEM was also carried out and field stress state was determined. In wide region modeling by FEM, the fault was built in the model and fault slip was taken into account, and evaluation of strain state at the far field boundary was carried out for inhomogeneous rock including fault. It was proposed to output three-dimensional distribution of the maximum shear stress coefficients in order to advance three-dimensional modeling. It will make clear effect of shape, scale and property of the fault on stress state characteristic. This report describes minutely the results of the studies mentional above.
Mizuta, Yoshiaki*; Kaneko, Katsuhiko*; Matsuki, Koji*; Sugawara, Katsuhiko*; Sudo, Shigeaki*
JNC TJ7400 2003-004, 70 Pages, 2003/02
JNC-TJ7400-2003-004.pdf:3.29MB
In the fiscal year of 2002, our committee achieved the following work items during the contract period, from August 28th, 2002 to February 7th, 2003. Confirm mutual understanding with respect to the geological / geometrical data provided from Tono Geoscience Center and exchange procedure for taking those into each numerical models. The numerical models by Finite Element Method and Finite Difference Method were built taking strata data into account. A problem accompanying to back analysis for inhomogeneous modeling was brought up. A new 3D Boundary Element Method Code in which integrations to calculate the influence coefficients are carried out analytically and thus, the solutions with high accuracy can be given faster. Three examples of determination procedures, wide region model by FEM, small region model by FEM and intermediate region model by FDM were introduced. This is the report as the results of the studies mentioned above.
Sato, Toshinori; Chen, Y.*; Nishiyama, Takashi*; Kaneko, Katsuhiko*
31st International Geological Congress, 0 Pages, 2000/00
None
Sato, Toshinori; *; Chen, Y.*; Nishiyama, Takashi*; Kaneko, Katsuhiko*
Shigen To Sozai, 116(8), p.656 - 661, 2000/00
None
Noguchi, Yoshifumi*; Iwasaki, Hiroshi*; Kaneko, Katsuhiko*; Koike, Katsuaki*
Joho Chishitsu, 4(2), p.45 - 57, 1993/00
Nakama, Shigeo; Sato, Toshinori; Kaneko, Katsuhiko*; Matsuki, Koji*; Sugawara, Katsuhiko*; Mizuta, Yoshiaki*
no journal, ,
no abstracts in English
Nakabayashi, Ryo*; Elakneswaran, Y.*; Chino, Daisuke*; Sato, Tsutomu*; Yoneda, Tetsuro*; Oda, Chie; Kaneko, Katsuhiko*
no journal, ,
Flow-through dissolution experiment was carried out using compacted bentonite with hyperalkaline solutions. In-situ observation of bentonite during the experiment was concocted by using X-CT analysis. Time-dependence of secondary minerals formation inside the compacted bentonite during the experiment was analysed and quantified based on the observation. Geochemical modeling using a 1D reactive transport code was able to reproduct time-dependence of space-distribution of minerals in the bentonite and Si, Al concentrations in the output solutions.
Nakabayashi, Ryo*; Elakneswaran, Y.*; Chino, Daisuke*; Sato, Tsutomu*; Yoneda, Tetsuro*; Oda, Chie; Kaneko, Katsuhiko*
no journal, ,
Flow-through dissolution experiment of compacted purified bentonite with highly alkaline solution was carried out in order to quantitatively understand the bentonite-cement interaction. A combined analysis with XRD and in situ-observation by using X-ray CT method were applied. A geochemical model simulation of the experiment considering kinetics of montmorillonite (the main component of bentonite) dissolution was carried out. From output of the simulation, it was found that (1) dissolution rate of montmorillonite in compacted system were slower than that in suspension system, (2) slowering rate resulted in invisible change in dry density of montmorillonite in the simulation, which was consistent with the experimental result, and (3) the reason for slowring rate could likely to be attributed to the constraint of reactive surface area of montmorillonite and the effect of saturation degree of powewater.
Nakabayashi, Ryo*; Elakneswaran, Y.*; Sato, Tsutomu*; Oda, Chie; Yoneda, Tetsuro*; Kaneko, Katsuhiko*
no journal, ,
The objective of this study is to develop a microstructural analysis method by X-ray CT to track the alteration process arising from bentonite and hyperalkaline fluid interactions as a function of time and to use these data to underpin a geochemical model of the alteration process. Advective alteration experiment of bentonite was performed at 80 C (pH = 13.5 at 25 C) for 180 days and in-situ analysis by X-ray CT during the experiment was conducted. The geochemical reactive transport code PHREEQC was used to simulate the results of the experiments. Consequently, the formation of secondary minerals (analcime) in the bentonite could be confirmed by X-ray CT at different times and quantified by X-ray CT images analysis. The predicted time-dependency of volume of analcime by a geochemical reactive transport model became consistent with the results obtained by X-ray CT analysis, and the concentration of dissolved Si and Al in the output solution could be replicated.
Nakabayashi, Ryo*; Elakneswaran, Y.*; Sato, Tsutomu*; Otake, Tsubasa*; Oda, Chie; Yoneda, Tetsuro*; Kaneko, Katsuhiko*
no journal, ,
The current study developed developed an in situ microstructural analysis method using X-ray CT to track bentonite/hyperalkaline fluid interactions. An advective alteration experiment was conducted by reacting a compacted bentonite (0.3 Mg/m
) with a 0.3M NaOH solution at 80C for 180 days. No significant dissolution of montmorillonite in the bentonite was observed using X-ray CT, although the formation of secondary minerals could be quantified by X-ray CT. A geochemical modeling using the dissolution rate of montmorillonite obtained in a dispersed system did not fit the experimental data, but could provide a satisfactory match to that by changes to the reactive surface area and the inclusion of an empirical term to account for the saturation state of montmorillonite. This implies that there is difference in effective reactive surface area and effect of the saturation state on the dissolution rate between dispersed and compacted systems.
Fujii, Kazumi*; Iwanami, Masaru*; Ishioka, Shinichi*; Kaneko, Tetsuji*; Tanaka, Norihiko*; Kawaharada, Yoshiyuki*; Yokoyama, Yutaka*; Umehara, Ryuji*; Kato, Chiaki; Ueno, Fumiyoshi; et al.
no journal, ,
no abstracts in English
Kaneko, Tetsuji*; Tanaka, Norihiko*; Kawaharada, Yoshiyuki*; Fujii, Kazumi*; Iwanami, Masaru*; Ishioka, Shinichi*; Yokoyama, Yutaka*; Umehara, Ryuji*; Kato, Chiaki; Ueno, Fumiyoshi; et al.
no journal, ,
no abstracts in English
-ray irradiation on inhibition of steel corrosion in diluted sea waterSato, Tomonori; Kato, Chiaki; Motooka, Takafumi; Ueno, Fumiyoshi; Nakano, Junichi; Kaneko, Tetsuji*; Tanaka, Norihiko*; Kawaharada, Yoshiyuki*; Fujii, Kazumi*; Iwanami, Masaru*; et al.
no journal, ,
no abstracts in English
Yokoyama, Yutaka*; Umehara, Ryuji*; Tanaka, Norihiko*; Kawaharada, Yoshiyuki*; Kaneko, Tetsuji*; Fujii, Kazumi*; Iwanami, Masaru*; Ishioka, Shinichi*; Kato, Chiaki; Ueno, Fumiyoshi; et al.
no journal, ,
no abstracts in English
