University of Tsukuba

About: University of Tsukuba is a education organization based out in Tsukuba, Ibaraki, Japan. It is known for research contribution in the topics: Population & Gene. The organization has 36352 authors who have published 79483 publications receiving 1934752 citations. The organization is also known as: Tsukuba daigaku & Tsukuba University.

The Stellar Abundances for Galactic Archeology (SAGA) Database - Compilation of the Characteristics of Known Extremely Metal-Poor Stars

Abstract: We describe the construction of a database of extremely metal-poor (EMP) stars in the Galactic halo whose elemental abundances have been determined. Our database contains detailed elemental abundances, reported equivalent widths, atmospheric parameters, photometry, and binarity status, compiled from papers in the recent literature that report studies of EMP halo stars with [Fe/H] < -2.5. The compilation procedures for this database have been designed to assemble the data effectively from electronic tables available from online journals. We have also developed a data retrieval system that enables data searches by various criteria, and permits the user to explore relationships between the stored variables graphically. Currently, our sample includes 1212 unique stars (many of which are studied by more than one group) with more than 15000 individual reported elemental abundances, covering all of the relevant papers published by December 2007. We discuss the global characteristics of the present database, as revealed by the EMP stars observed to date. For stars with [Fe/H] < -2.5, the number of giants with reported abundances is larger than that of dwarfs by a factor of two. The fraction of carbon-rich stars (among the sample for which the carbon abundance is reported) amount to ~30 % for [Fe/H] < -2.5. We find that known binaries exhibit different distributions of orbital period, according to whether they are giants or dwarfs, and also as a function of metallicity, although the total sample of such stars is still quite small.

p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria

Abstract: PINK1 and Parkin were first identified as the causal genes responsible for familial forms of early-onset Parkinson’s disease (PD), a prevalent neurodegenerative disorder. PINK1 encodes a mitochondrial serine/threonine protein kinase, whereas Parkin encodes an ubiquitin-protein ligase. PINK1 and Parkin cooperate to maintain mitochondrial integrity; however, the detailed molecular mechanism of how Parkin-catalyzed ubiquitylation results in mitochondrial integrity remains an enigma. In this study, we show that Parkin-catalyzed K63-linked polyubiquitylation of depolarized mitochondria resulted in ubiquitylated mitochondria being transported along microtubules to cluster in the perinuclear region, which was interfered by pathogenic mutations of Parkin. In addition, p62/SQSTM1 (hereafter referred to as p62) was recruited to depolarized mitochondria after Parkin-directed ubiquitylation. Intriguingly, deletion of p62 in mouse embryonic fibroblasts resulted in a gross loss of mitochondrial perinuclear clustering but did not hinder mitochondrial degradation. Thus, p62 is required for ubiquitylation-dependent clustering of damaged mitochondria, which resembles p62-mediated ‘aggresome’ formation of misfolded/unfolded proteins after ubiquitylation.

Photocatalytic Overall Water Splitting Promoted by Two Different Cocatalysts for Hydrogen and Oxygen Evolution under Visible Light

Abstract: Overall water splitting using a particulate photocatalyst and solar energy has attracted significant attention as a potential means of large-scale H2 production from renewable resources without carbon dioxide emission. 2] The reaction occurs in three steps: 1) the photocatalyst absorbs photon energy greater than the band-gap energy of the material and generates photoexcited electron–hole pairs in the bulk, 2) the photoexcited carriers separate and migrate to the surface without recombination, and 3) adsorbed species are reduced and oxidized by the photogenerated electrons and holes to produce H2 and O2, respectively. The first two steps are strongly dependent on the structural and electronic properties of the photocatalyst, while the third step is promoted by an additional catalyst (called cocatalyst). Therefore, it is important to develop a photocatalyst and a cocatalyst in harmony. Recently, our group has focused on active sites for H2 evolution on the surface of a photocatalyst, because most photocatalysts lack surface H2 evolution sites. [2b] Using a solid solution of GaN and ZnO (abbreviated GaN:ZnO hereafter) that can harvest visible photons up to ca. 500 nm, chromium-containing transition-metal oxides or noble-metal/ chromia (core/shell) nanoparticles (NPs) have been shown to function as H2 evolution cocatalysts, resulting in efficient water splitting under visible light. Meanwhile, also several sulfides were proposed as efficient catalysts for H2 evolution, and the role of H2 evolution cocatalysts has been explored by spectroscopic and electrochemical techniques. It would be natural to expect that loading both H2 and O2 evolution cocatalysts onto the same photocatalyst would improve water-splitting activity, compared to photocatalysts modified with either an H2 or O2 evolution cocatalyst. [8] It is easy to imagine how these two different cocatalysts would separately facilitate H2 and O2 evolution, thereby promoting overall water splitting in harmony. Unfortunately, no successful and reliable example of this has been reported since the initial reports on photocatalytic water splitting in the 1980s. The actual demonstration of the concept remains a major challenge. Herein, we show a proof-of-concept using GaN:ZnO loaded with Rh/Cr2O3 (core/shell) and Mn3O4 NPs as H2 and O2 evolution promoters, respectively, under irradiation with visible light (l> 420 nm). First, Mn oxide was introduced onto GaN:ZnO, prepared by our previous method, as O2 evolution cocatalyst. Some Mn oxides have been reported to act as O2 evolution promoters, and it is well known that a Mn complex is the O2 evolution center in the photosynthesis of green plants. MnO NPs with a mean size of (9.2 0.4) nm (Figure S1 in the Supporting Information) were adsorbed onto GaN:ZnO. It was revealed by UV/vis spectroscopy that the introduced MnO NPs (ca. 1.0 wt %) were almost quantitatively anchored on the GaN:ZnO surface, based on the change in the absorption band of the MnO NPs (Figure S2 in the Supporting Information). The as-prepared MnO/GaN:ZnO sample was then calcined in air at 673 K for 3 h to remove organic residues. Separate experiments with thermogravimetry, differential thermal analysis (TG-DTA), and X-ray diffraction (XRD) showed that the organic ligands stabilizing the MnO NPs were completely burned off by calcination in air at 673 K, and that calcination of dried MnO NP powder under the above conditions resulted in phase transformation of the MnO into Mn3O4 (Figure S3 in the Supporting Information). Transmission electron microscopy (TEM) observation revealed that the particle size of the Mn oxide was maintained, even after calcination (Figure S1 in the Supporting Information). Thus, GaN:ZnO particles were successfully decorated with Mn3O4 NPs which were expected to act as water oxidation cocatalysts. Because GaN:ZnO is an n-type semiconductor, it is possible to monitor the photooxidation reaction occurring on its surface using an electrochemical technique. Under [*] Dr. K. Maeda, A. Xiong, N. Sakamoto, Dr. T. Hisatomi, Prof. Dr. K. Domen Department of Chemical System Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan) Fax: (+ 81)3-5841-8838 E-mail: domen@chemsys.t.u-tokyo.ac.jp Homepage: http://www.domen.t.u-tokyo.ac.jp/

First-principles study of edge states of H-terminated graphitic ribbons

Abstract: The existence of the edge states of single-layered H-terminated graphitic ribbons predicted by Nakada et al. [Phys. Rev. B 54, 17 954 (1996)] has been confirmed by first-principles calculations within the framework of the local-density approximation and the pseudopotentials. The edge states in cases of stacked ribbons have also been examined, and it has been found that the existence of the edge states is dependent on the stacking manner. This phenomenon can be understood from the electronic structures of $\mathrm{AA}$- and $\mathrm{AB}$-stacked bulk graphite.

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

Abstract: Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1 (EF-1), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate’s clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.