Hydrogeochemical evolution of confined groundwater in Northeastern Osaka basin, Japan

Thesis (Ph. D. in Science)--University of Tsukuba, (A), no. 2868, 2002.3.25Includes bibliographical reference

Surface tension measurement of glass melts by the maximum bubble pressure method

The maximum bubble pressure method was used to obtain accurate surface tension measurements. The dependence of apparent surface tension value on bubble growth time was measured for times from several to longer than a thousand seconds. The static surface tension value was obtained by extrapolating bubble growth time to infinity. The dynamic surface tension, which is familiar in colloids, could not be directly obtained because of the high viscosity of glass melt. The effects of capillary tip material and shape were also examined. This method is applicable to melts with viscosity less than 10^3.5 dPa s. The reproducibility in the measurement was within a few percent

Bayesian Approach to Find a Long-Term Trend in Erratic Polarization Variations Observed in Blazars

We developed a method to separate a long-term trend from observed temporal variations of polarization in blazars using a Bayesian approach. The temporal variation of the polarization vector is apparently erratic in most blazars, while several objects occasionally exhibited systematic variations, for example, an increase of the polarization degree associated with a flare of the total flux. We assume that the observed polarization vector is a superposition of distinct two components, a long-term trend and a short-term variation component responsible for short flares. Our Bayesian model estimates the long-term trend which satisfies the condition that the total flux correlates with the polarized flux of the short-term component. We demonstrate that assumed long-term polarization components are successfully separated by the Bayesian model for artificial data. We applied this method to photopolarimetric data of OJ 287, S5 0716+714, and S2 0109+224. Simple and systematic long-term trends were obtained in OJ 287 and S2 0109+224, while no such a trend was identified in S5 0716+714. We propose that the apparently erratic variations of polarization in OJ 287 and S2 0109+224 are due to the presence of the long-term polarization component. The behavior of polarization in S5 0716+714 during our observation period implies the presence of a number of polarization components having a quite short time-scale of variations.Comment: 12 pages, 7 figures, accepted for publication in PAS

Difference in NaCl tolerance of membrane-bound 5′-nucleotidases purified from deep-sea and brackish water Shewanella species

Shewanella species are widely distributed in sea, brackish, and fresh water areas, growing psychrophilically or mesophilically, and piezophilically or piezo-sensitively. Here, membrane-bound 5′-nucleotidases (NTases) from deep-sea Shewanella violacea and brackish water Shewanella amazonensis were examined from the aspect of NaCl tolerance in order to gain an insight into protein stability against salt. Both NTases were single polypeptides with molecular masses of ~59 kDa, as determined on mass spectroscopy. They similarly required 10 mM MgCl2 for their activities, and they exhibited the same pH dependency and substrate specificity for 5′-nucleotides. However, S. violacea 5′-nucleotidase (SVNTase) was active enough in the presence of 2.5 M NaCl, whereas S. amazonensis 5′-nucleotidase (SANTase) exhibited significantly reduced activity with the same concentration of the salt. Although SVNTase and SANTase exhibited high sequence identity (69.7%), differences in the ratio of acidic to basic amino acid residues and the number of potential salt bridges maybe being responsible for the difference in the protein stability against salt. 5′-Nucleotidases from these Shewanella species will provide useful information regarding NaCl tolerance, which may be fundamental for understanding bacterial adaptation to growth environments.This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan [No. 26240045], a grant from the Japan Society for the Promotion of Science [No. 25-1446], and The Salt Science Research Foundation [No. 1655]

Photopolarimetric Monitoring of Blazars in the Optical and Near-Infrared Bands with the Kanata Telescope. I. Correlations between Flux, Color, and Polarization

We report on the correlation between the flux, color and polarization variations on time scales of days--months in blazars, and discuss their universal aspects. We performed monitoring of 42 blazars in the optical and near-infrared bands from 2008 to 2010 using TRISPEC attached to the "Kanata" 1.5-m telescope. We found that 28 blazars exhibited "bluer-when-brighter" trends in their whole or a part of time-series data sets. This corresponds to 88% of objects that were observed for >10 days. Thus, our observation unambiguously confirmed that the "bluer-when-brighter" trend is common in the emission from blazar jets. This trend was apparently generated by a variation component with a constant and relatively blue color and an underlying red component. Prominent short-term flares on time scales of days--weeks tended to exhibit a spectral hysteresis; their rising phases were bluer than their decay phases around the flare maxima. In contrast to the strong flux--color correlation, the correlation of the flux and polarization degree was relatively weak; only 10 objects showed significant positive correlations. Rotations of polarization were detected only in three objects: PKS 1510-089, 3C 454.3, and PKS 1749+096, and possibly in S5 0716+714. We also investigated the dependence of the degree of variability on the luminosity and the synchrotron peak frequency, \nu_peak. As a result, we found that lower luminosity and higher \nu_peak objects had smaller variations in their amplitudes both in the flux, color, and polarization degree. Our observation suggests the presence of several distinct emitting sources, which have different variation time-scales, colors, and polarizations. We propose that the energy injection by, for example, internal shocks in relativistic shells is a major factor for blazar variations on time scales of both days and months.Comment: 39 pages, accepted for publication in PAS

Large-Scale RNA Interference Screening in Mammalian Cells Identifies Novel Regulators of Mutant Huntingtin Aggregation

In polyglutamine (polyQ) diseases including Huntington's disease (HD), mutant proteins containing expanded polyQ stretch form aggregates in neurons. Genetic or RNAi screenings in yeast, C. elegans or Drosophila have identified multiple genes modifying polyQ aggregation, a few of which are confirmed effective in mammals. However, the overall molecular mechanism underlying polyQ protein aggregation in mammalian cells still remains obscure. We here perform RNAi screening in mouse neuro2a cells to identify mammalian modifiers for aggregation of mutant huntingtin, a causative protein of HD. By systematic cell transfection and automated cell image analysis, we screen ∼12000 shRNA clones and identify 111 shRNAs that either suppress or enhance mutant huntingtin aggregation, without altering its gene expression. Classification of the shRNA-targets suggests that genes with various cellular functions such as gene transcription and protein phosphorylation are involved in modifying the aggregation. Subsequent analysis suggests that, in addition to the aggregation-modifiers sensitive to proteasome inhibition, some of them, such as a transcription factor Tcf20, and kinases Csnk1d and Pik3c2a, are insensitive to it. As for Tcf20, which contains polyQ stretches at N-terminus, its binding to mutant huntingtin aggregates is observed in neuro2a cells and in HD model mouse neurons. Notably, except Pik3c2a, the rest of the modifiers identified here are novel. Thus, our first large-scale RNAi screening in mammalian system identifies previously undescribed genetic players that regulate mutant huntingtin aggregation by several, possibly mammalian-specific mechanisms

Optimization of salt concentration in PEG-based crystallization solutions

Optimal salt concentration in a PEG-based crystallization solution is important for successful crystal growth and can be predicted prior to performing crystallization experiments

Comprehensive Dipeptide Analysis Revealed Cancer-Specific Profile in the Liver of Patients with Hepatocellular Carcinoma and Hepatitis

As the physical properties and functionality of dipeptides differ from those of amino acids, they have attracted attention in metabolomics; however, their functions in vivo have not been clarified in detail. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, and its major cause is chronic hepatitis. This study was conducted to explore tumor-specific dipeptide characteristics by performing comprehensive dipeptide analysis in the tumor and surrounding nontumor tissue of patients with HCC. Dipeptides were analyzed by liquid chromatography tandem mass spectrometry and capillary electrophoresis tandem mass spectrometry. Principal component analysis using 236 detected dipeptides showed differences in the dipeptide profiles between nontumor and tumor tissues; however, no clear difference was observed in etiological comparison. In addition, the N- and C-terminal amino acid compositions of the detected dipeptides significantly differed, suggesting the substrate specificity of enzyme proteins, such as peptidase. Furthermore, hepatitis-derived HCC may show a characteristic dipeptide profile even before tumor formation. These results provide insight into HCC pathogenesis and may help identify novel biomarkers for diagnosis

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Thermophilic Hydrogenophilus thermoluteolus cytochrome c0 (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c0 (AVCP), which has a homo-dimeric structure and ligand-binding ability. To understand the thermal stability mechanism and ligand-binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo-dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 A ° . In the PHCP structure, six specific residues appeared to strengthen the heme-related and subunit–subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit–subunit interactions were more severely destabilized than ones having altered heme-related interactions. The PHCP structure further revealed a ligand-binding channel and a penta-coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme-related and subunit–subunit interactions with conservation of the ligand-binding ability.This work was performed under the Cooperative Research Program of the “Network Joint Research Center for Materials and Devices”