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Journal Articles

A New Standard DNA Damage (SDD) data format

Schuemann, J.*; McNamara, A. L.*; Warmenhoven, J. W.*; Henthorn, N. T.*; Kirkby, K.*; Merchant, M. J.*; Ingram, S.*; Paganetti, H.*; Held, K. D.*; Ramos-Mendez, J.*; et al.

Radiation Research, 191(1), p.76 - 93, 2019/01

 Times Cited Count:34 Percentile:97.99(Biology)

We propose a new Standard DNA Damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modelling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.

Journal Articles

Redox behavior of Ce(IV)/Ce(III) in the presence of nitrilotriacetic acid; A Surrogate study for An(IV)/An(III) redox behavior

Suzuki, Yoshinori*; Nankawa, Takuya; Francis, A. J.*; Onuki, Toshihiko

Radiochimica Acta, 98(7), p.397 - 402, 2010/07

 Times Cited Count:17 Percentile:78.18(Chemistry, Inorganic & Nuclear)

no abstracts in English

Journal Articles

Association of actinides with microorganisms and clay; Implications for radionuclide migration from waste-repository sites

Onuki, Toshihiko; Kozai, Naofumi; Sakamoto, Fuminori; Ozaki, Takuo; Nankawa, Takuya; Suzuki, Yoshinori; Francis, A. J.*

Geomicrobiology Journal, 27(3), p.225 - 230, 2010/04

 Times Cited Count:15 Percentile:21.04(Environmental Sciences)

The recent research results on the interation of heavy-elements and microorganisms are shown. (1) Adsorption of Pu(IV), Th(IV) and Eu(III)-DFO complexes on bacteria, (2) Biodegradation of Eu(III) in the presence of malic acids.

Journal Articles

Modeling of the interaction of Pu(VI) with the mixture of microorganism and clay

Onuki, Toshihiko; Yoshida, Takahiro*; Ozaki, Takuo; Kozai, Naofumi; Sakamoto, Fuminori; Nankawa, Takuya; Suzuki, Yoshinori; Francis, A. J.*

Journal of Nuclear Science and Technology, 46(1), p.55 - 59, 2009/01

 Times Cited Count:8 Percentile:53.11(Nuclear Science & Technology)

Model analysis of the transformation of Pu(VI) in a mixture of a common soil bacterium, Bacillus subtilis, and kaolinite clay was carried out. When we assumed in the model analysis that reduction rate of Pu(V) to Pu(IV) was higher on B. subtilis than on kaolinite, the estimated fractions of Pu in the solution and in the mixture, oxidation states of Pu in the solution and in the mixture were in good agreement with the measured ones. On the contrary, assumption that reduction rate of Pu(V) to Pu(IV) was the same on kaolinite as on ${it B. subtilis}$ gave wrong prediction of Pu association with the mixture. These results strongly suggested the electron transfer from the bacteria to Pu(V) on the bacterial cell to be reduced to Pu(IV) during the accumulation of Pu(VI) to the mixture.

Journal Articles

Concurrent transformation of Ce(III) and formation of biogenic manganese oxides

Onuki, Toshihiko; Ozaki, Takuo; Kozai, Naofumi; Nankawa, Takuya; Sakamoto, Fuminori; Sakai, Takuro; Suzuki, Yoshinori; Francis, A. J.*

Chemical Geology, 253(1-2), p.23 - 29, 2008/07

 Times Cited Count:24 Percentile:54.78(Geochemistry & Geophysics)

We examined the changes in the chemical states of Ce(III) during the formation of manganese oxide occasioned by Mn(II)-oxidizing bacteria. The oxidation states of Ce and Mn then were measured by X-ray Absorption Near Edge Structure (XANES). We also determined the elemental distributions in the bacteria and precipitates by Scanning-Proton Induced X-ray Emission (S-PIXE). We found that the precipitation of Ce is preceded by its accumulation by the bacterium, followed by its oxidization to Ce(IV) by the Mn(III, IV)-containing precipitates that the bacteria generate.

Journal Articles

Sorption of U(VI) on the 4-mercaptopyridine self-assembled monolayer

Nankawa, Takuya; Suzuki, Yoshinori; Ozaki, Takuo; Francis, A. J.; Onuki, Toshihiko

Journal of Nuclear Science and Technology, 45(3), p.251 - 256, 2008/03

 Times Cited Count:3 Percentile:25.63(Nuclear Science & Technology)

Sorption of U(VI) on the 4-mercaptopyridine self-assembled-monolayer (4-PyS-SAM) on Au(111) was studied by cyclic voltammetry. Cyclic voltammograms (CV) of the 4-PyS-SAM working electrode was obtained by contact with 1 mM UO$$_{2}$$(NO$$_{3}$$)$$_{2}$$ solution, 1 mM UO$$_{2}$$(NO$$_{3}$$)$$_{2}$$ and 50 mM acetic acid solution, or 1 mM UO$$_{2}$$(NO$$_{3}$$)$$_{2}$$ and 50 mM oxalic acid solution for 6 h at pH 4. Reduction current of uranium(VI) to U(V) was detected in the CV. The CV of the U(VI) associated 4-PyS-SAM after transporting to U(VI) free 0.1 M NaClO4 solution showed that the reduction current was detected in the cases of UO$$_{2}$$(NO$$_{3}$$)$$_{2}$$ and U(VI)-acetate, but not in the case of U(VI)-oxalate solutions, indicating that U(VI) was adsorbed on the 4-PyS-SAM from the UO$$_{2}$$(NO$$_{3}$$)$$_{2}$$ and U(VI)-acetate solutions, but not from U(VI)-oxalate solution. These results suggests that stability of U(VI)-4-PyS-SAM is not so high that U(VI)-4-PyS-SAM cannot be formed in the presence of 50 mM oxalate.

Journal Articles

Protein expression of ${it Saccharomyces cerevisiae}$ in response to uranium exposure

Sakamoto, Fuminori; Nankawa, Takuya; Kozai, Naofumi; Fujii, Tsutomu*; Iefuji, Haruyuki*; Francis, A. J.; Onuki, Toshihiko

Journal of Nuclear and Radiochemical Sciences, 8(2), p.133 - 136, 2007/10

Protein expression of ${it Saccharomyces cerevisiae}$ grown in the medium containing $$^{238}$$U(VI) and $$^{233}$$U(VI) was examined by two-dimensional gel electrophoresis. ${it S. cerevisiae}$ of BY4743 was grown in medium containing $$^{238}$$U of 0, 2.0, and 5.0 $$times$$ 10$$^{-4}$$ M or $$^{233}$$U of 2.5 $$times$$ 10$$^{-6}$$ (radioactivity was higher by 350 times than 2.0 $$times$$ 10$$^{-4}$$ M $$^{238}$$U) and 5.0 $$times$$ 10$$^{-6}$$ M for 112 h at 30$$^{circ}$$C. The growths of the yeast grown in the above media were in the following order: control $$>$$ 2.5 $$times$$ 10$$^{-6}$$ M $$^{233}$$U $$>$$ 2.0 $$times$$ 10$$^{-4}$$ M $$^{238}$$U $$>$$ 5.0 $$times$$ 10$$^{-6}$$ M $$^{233}$$U $$>$$ 5.0 $$times$$ 10$$^{-4}$$ M $$^{238}$$U. This result indicated that not only radiological but also chemical effect of U reduced the growth of the yeast. The concentrations of U in the medium containing $$^{238}$$U or $$^{233}$$U decreased, suggesting U accumulation by the yeast cells. The 2-D gel electrophoresis analysis showed the appearance of several spots after exposure to $$^{238}$$U or to $$^{233}$$U but not in the control containing no uranium. These results show that the yeast cells exposed to U express several specific proteins.

Journal Articles

Microbial transformations of plutonium

Francis, A. J.; Dodge, C. J.*; Onuki, Toshihiko

Journal of Nuclear and Radiochemical Sciences, 8(2), p.121 - 126, 2007/10

We investigated the biotransformation of Pu(IV)-citrate by ${it Pseudomonas fluorescens}$ under aerobic conditions. Citric acid was rapidly metabolized by ${it P. fluorescens}$ resulting in the formation of Pu polymer. Addition of Pu(VI) to a mixture consisting of bacterial cells and kaolinite clay showed that the Pu was preferentially associated with bacterial cells as Pu(IV) and that Pu(VI) was reduced to Pu(V) and Pu(IV) only in the presence of bacteria.

Journal Articles

Electrochemical studies on uranium in the presence of organic acids

Suzuki, Yoshinori; Nankawa, Takuya; Ozaki, Takuo; Onuki, Toshihiko; Francis, A. J.*; Enokida, Yoichi*; Yamamoto, Ichiro*

Journal of Nuclear Science and Technology, 44(9), p.1227 - 1232, 2007/09

 Times Cited Count:13 Percentile:69.08(Nuclear Science & Technology)

We examined electrochemical redox reactions of UO$$_{2}$$$$^{2+}$$ in organic acid (oxalic, malonic, succinic, adipic, L-malic, and L-tartaric acids) solutions using cyclic voltammetry. A redox reaction of UO$$_{2}$$$$^{2+}$$/UO$$_{2}$$$$^{+}$$ and an oxidation reaction of U(IV) were observed. The peak potentials of the UO$$_{2}$$$$^{2+}$$ reduction showed a good linear relationship with the log of the stability constants of 1:1 UO$$_{2}$$$$^{2+}$$-organic complexes. We also revealed the redox reactions of UO$$_{2}$$$$^{2+}$$ in the presence of malonic or oxalic acids between pH 1 and 6.

Journal Articles

Chemical speciation and association of plutonium with bacteria, kaolinite clay, and their mixture

Onuki, Toshihiko; Yoshida, Takahiro*; Ozaki, Takuo; Kozai, Naofumi; Sakamoto, Fuminori; Nankawa, Takuya; Suzuki, Yoshinori*; Francis, A. J.

Environmental Science & Technology, 41(9), p.3134 - 3139, 2007/05

 Times Cited Count:28 Percentile:56.67(Engineering, Environmental)

We investigated the interactions of Pu(VI) with Bacillus subtilis, kaolinite clay, and a mixture of the two to determine and delineate the role of the microbes in regulating the environmental mobility of Pu. The amount of Pu sorbed by B. subtilis increased with time, but had not reached equilibrium in 48 h, whereas equilibrium was attained in kaolinite within 8 h. After 48 h, the oxidation state of Pu in the solutions exposed to B. subtilis and the mixture had changed to Pu(V), whereas the oxidation state of Pu associated with B. subtilis and the mixture was Pu(IV). In contrast, there was no change in the oxidation state of Pu in the solution or on kaolinite after exposure to Pu(VI). SEM-EDS analysis indicated that most of the Pu in the mixture was associated with B. subtilis. These results suggest that Pu(IV) is preferably sorbed to bacterial cells in the mixture, and that Pu(VI) is reduced to Pu(V) and Pu(IV).

Journal Articles

Effects of ionic strength on the coordination of Eu(III) and Cm(III) to a Gram-negative bacterium, Paracoccus denitrificans

Ozaki, Takuo; Kimura, Takaumi; Onuki, Toshihiko; Francis, A. J.

Radiochimica Acta, 94(9-11), p.715 - 721, 2006/11

 Times Cited Count:9 Percentile:56.05(Chemistry, Inorganic & Nuclear)

no abstracts in English

Journal Articles

Reduction behavior of uranium in the presence of citric acid

Suzuki, Yoshinori; Nankawa, Takuya; Yoshida, Takahiro*; Ozaki, Takuo; Onuki, Toshihiko; Francis, A. J.; Tsushima, Satoru*; Enokida, Yoichi*; Yamamoto, Ichiro*

Radiochimica Acta, 94(9-11), p.579 - 583, 2006/11

 Times Cited Count:20 Percentile:81.23(Chemistry, Inorganic & Nuclear)

We examined the reduction behavior of UO$$_{2}$$$$^{2+}$$ in citrate media at pH 2.0-7.0 by column electrodes. At pH 2.0, UO$$_{2}$$$$^{2+}$$ was reduced to U(IV) through a one-step reduction process, while it was reduced to U(IV) through a two-step reduction process at pH 3.0-5.0. The reduction potential of UO$$_{2}$$$$^{2+}$$ shifted to lower values with an increase in pH from 2.0 to 7.0. At pH 6.0 and 7.0, UO$$_{2}$$$$^{2+}$$ was not reduced to U(IV) completely at the electrode potential above -0.8 V. Ultraviolet-visible spectroscopy and speciation calculation of UO$$_{2}$$$$^{2+}$$ in citrate media indicated that uranium existed as a mainly UO$$_{2}$$$$^{2+}$$ at pH 2-3, and a predominant species at pH 3-5 was [(UO$$_{2}$$)$$_{2}$$Cit$$_{2}$$]$$^{2-}$$. At pH 5-7, polymeric complexes were present. These findings suggest that the reduction of UO$$_{2}$$$$^{2+}$$ is more difficult by polymerization of UO$$_{2}$$$$^{2+}$$ with citric acid at higher pHs.

Journal Articles

Association of europium(III), americium(III), and curium(III) with cellulose, chitin, and chitosan

Ozaki, Takuo; Kimura, Takaumi; Onuki, Toshihiko; Kirishima, Akira*; Yoshida, Takahiro*; Isobe, Hiroshi*; Francis, A. J.

Environmental Toxicology and Chemistry, 25(8), p.2051 - 2058, 2006/08

 Times Cited Count:7 Percentile:16.79(Environmental Sciences)

no abstracts in English

Journal Articles

Degradation of Eu(III)-malic acid complexes by $$Pseudomonas fluorescens$$

Nankawa, Takuya; Suzuki, Yoshinori*; Ozaki, Takuo; Onuki, Toshihiko; Francis, A. J.*

Journal of Alloys and Compounds, 408-412, p.1329 - 1333, 2006/02

 Times Cited Count:2 Percentile:23.4(Chemistry, Physical)

We studied the biodegradation of Eu(III)-malic acid complexes by $$Pseudomonas fluorescens$$. Ten milimolar Malic acid was degraded in the absence and in the presence of Eu(III) of 0.05, 0.1, and 0.2 mM. The degradation rate of malic acid increased with decreasing the ratios of Eu(III) to malic acid. These results suggest that the toxicity of Eu(III) can be masked through its complexation with malic acid. The degradation of malic acid was followed by the production of unidentified metabolites which were associated with Eu(III). One of the unidentified organic acids was analysed to be pyruvic acid. Our findings suggest that metabolites can influence the environmental behavior of Eu(III) by biologically transformed through subsequent complexation with Eu(III).

Journal Articles

Interactions of rare earth elements with bacteria and organic ligands

Ozaki, Takuo; Suzuki, Yoshinori*; Nankawa, Takuya; Yoshida, Takahiro; Onuki, Toshihiko; Kimura, Takaumi; Francis, A. J.*

Journal of Alloys and Compounds, 408-412, p.1334 - 1338, 2006/02

 Times Cited Count:41 Percentile:87.19(Chemistry, Physical)

We investigated the interactions of Eu(III) with the common soil bacterium Pseudomonas fluorescens and organic ligands, such as malic acid, citric acid, and a siderophore (DFO). Malic acid formed complexes with Eu(III), but degradation of malic acid was observed when the ratio of malic acid to Eu(III) was high. Citric acid formed a stoichiometric complex with Eu(III) that was not degraded by P. fluorescens. Adsorption of Eu(III) from the DFO complex occurred as a free ion dissociated from DFO and not as the Eu(III)-DFO complex. Time-resolved laser-induced fluorescence spectroscopy analysis showed that adsorption of Eu(III) on P. fluorescens was through a multidentate and predominantly inner-spherical coordination.

Journal Articles

Mechanisms of uranium mineralization by the yeast ${it saccharomyces cerevisiae}$

Onuki, Toshihiko; Ozaki, Takuo; Yoshida, Takahiro*; Sakamoto, Fuminori; Kozai, Naofumi; Wakai, Eiichi; Francis, A. J.; Iefuji, Haruyuki*

Geochimica et Cosmochimica Acta, 69(22), p.5307 - 5316, 2005/11

 Times Cited Count:45 Percentile:68.99(Geochemistry & Geophysics)

no abstracts in English

Journal Articles

Interactions of uranium with bacteria and kaolinite clay

Onuki, Toshihiko; Yoshida, Takahiro*; Ozaki, Takuo; Samadfam, M.*; Kozai, Naofumi; Yubuta, Kunio*; Mitsugashira, Toshiaki*; Kasama, Takeshi*; Francis, A. J.*

Chemical Geology, 220(3-4), p.237 - 243, 2005/08

 Times Cited Count:46 Percentile:70.65(Geochemistry & Geophysics)

no abstracts in English

Journal Articles

Effect of uranium (VI) on the growth of yeast and influence of metabolism of yeast on adsorption of U (VI)

Sakamoto, Fuminori; Onuki, Toshihiko; Kozai, Naofumi; Wakai, Eiichi; Fujii, Tsutomu*; Iefuji, Haruyuki*; Francis, A. J.

Journal of Nuclear and Radiochemical Sciences, 6(1), p.99 - 101, 2005/07

We have carried out the growth experiments of 3 strains of yeast in a medium containing uranium (VI) to elucidate the effect of U (VI) on the growth of microorganisms. Hansenula fabianii J640 grew in the liquid medium containing 0.1 mM U (VI) at lower rate than the control, but Saccharomyces cerevisiae did not grow under this condition. The H. fabianii J640 pre-cultured for 21 h in the liquid medium without U (VI) grew even after the exposure to 1 mM U (VI), but did not grow without pre-cultivation. For the pre-cultured H. fabianii J640, radioactivity of U in the medium was the same as the initial one for 110 h, and then gradually decreased. TEM-EDS analysis of H. fabianii J640 exposed to 1 mM U (VI) for 165 h showed accumulation of U (VI) on the cells. When H. fabianii J640 was not pre-cultured, radioactivity of U in the medium was lower than the initial one. These results indicated that U (VI) inhibits the growth of yeast, and that the adsorption of U (VI) by the cells depends on the metabolism of yeast.

Journal Articles

A Continuous flow system for in-situ XANES measurements of change in oxidation state of Ce(III) to Ce(IV)

Onuki, Toshihiko; Yoshida, Takahiro*; Nankawa, Takuya; Ozaki, Takuo; Kozai, Naofumi; Sakamoto, Fuminori; Suzuki, Yoshinori*; Francis, A. J.*

Journal of Nuclear and Radiochemical Sciences, 6(1), p.65 - 67, 2005/07

no abstracts in English

Journal Articles

Associations of Eu(III) with Gram-Negative Bacteria, $$Alcaligenes faecalis$$, $$Shewanella putrefaciens$$, and $$Paracoccus denitrificans$$

Ozaki, Takuo; Kimura, Takaumi; Onuki, Toshihiko; Francis, A. J.*

Journal of Nuclear and Radiochemical Sciences, 6(1), p.73 - 76, 2005/07

no abstracts in English

60 (Records 1-20 displayed on this page)