DDBJ Activities: Contribution to the Research in Information Biology

DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also collecting and releasing gene expression data at CIBEX (Center for Information Biology gene EXpression database; "http://cibex.nig.ac.jp/":http://cibex.nig.ac.jp/). Furthermore, DDBJ contributed to international annotation jamborees such as FANTOM (mouse), H-Inv (human), RAP (rice) and E. coli K12. DDBJ provides many services to the research in information biology or bioinformatics. They include Web-API for Biology (WABI) "http://www.xml.nig.ac.jp/":http://www.xml.nig.ac.jp/ and All-round Retrieval of Sequence and Annotation (ARSA) "http://arsa.ddbj.nig.ac.jp/":http://arsa.ddbj.nig.ac.jp/. These activities are presented with the perspective of DDBJ in the coming years

Microscopic characterization of the C–F bonds in fluorine–graphite intercalation compounds

The structures of fluorine–graphite intercalation compounds (F-GICs, C₂.₈F and C₃.₅F) have been analyzed by high-resolution transmission electron microscopy (TEM). Cross-sectional TEM images of the F-GICs indicate that the interlayer distance increases by insertion of fluorine with randomly buckled carbon layers. Such a structure can form by alternation in the bond angle at a carbon atom covalently bonded with fluorine. Electron energy loss spectroscopy combined with TEM indicates that the π-orbital network over the graphitic carbon layer reduces with fluorination. The C–F bond is essentially covalent

Phase transformation of mesoporous calcium carbonate by mechanical stirring

We report a simple strategy to synthesize vaterite/calcite mesoporous calcium carbonate through collisions and organization of colloidal particles accelerated by mechanical stirring. Mechanically stirring the precursor colloidal dispersion can control the calcium carbonate polymorphs

DDBJ launches a new archive database with analytical tools for next-generation sequence data

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has collected and released 1 701 110 entries/1 116 138 614 bases between July 2008 and June 2009. A few highlighted data releases from DDBJ were the complete genome sequence of an endosymbiont within protist cells in the termite gut and Cap Analysis Gene Expression tags for human and mouse deposited from the Functional Annotation of the Mammalian cDNA consortium. In this period, we started a novel user announcement service using Really Simple Syndication (RSS) to deliver a list of data released from DDBJ on a daily basis. Comprehensive visualization of a DDBJ release data was attempted by using a word cloud program. Moreover, a new archive for sequencing data from next-generation sequencers, the ‘DDBJ Read Archive’ (DRA), was launched. Concurrently, for read data registered in DRA, a semi-automatic annotation tool called the ‘DDBJ Read Annotation Pipeline’ was released as a preliminary step. The pipeline consists of two parts: basic analysis for reference genome mapping and de novo assembly and high-level analysis of structural and functional annotations. These new services will aid users’ research and provide easier access to DDBJ databases

Quadrupolar effect and rattling motion in heavy fermion superconductor PrOs_4Sb_{12}

The elastic properties of a filled skutterudite PrOs_4Sb_{12} with a heavy Fermion superconductivity at T_C=1.85 K have been investigated. The elastic softening of (C_{11}-C_{12})/2 and C_{44} with lowering temperature down to T_C indicates that the quadrupolar fluctuation due to the CEF state plays a role for the Cooper paring in superconducting phase of PrOs_4Sb_{12}. A Debye-type dispersion in the elastic constants around 30 K revealed a thermally activated Gamma_{23} rattling due to the off-center Pr-atom motion obeying tau=tau_{0}exp(E/k_{B}T) with an attempt time tau_0=8.8*10^{-11} sec and an activation energy E=168 K. It is remarkable that the charge fluctuation of the off-center motion with Gamma_{23} symmetry may mix with the quadrupolar fluctuation and enhance the elastic softening of (C_{11}-C_{12})/2 just above T_C.Comment: 5 pages, 4 figures, to be published to Phys. Rev.

NBRP databases: databases of biological resources in Japan

The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created and made available through the NBRP home page (http://www.nbrp.jp). The 30 independent databases have individual features which directly reflect the data maintained by each resource facility. The BRW is designed for users who need to search across several resources without moving from one database to another. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones and so on. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources

The ASTRO-H X-ray Observatory

The joint JAXA/NASA ASTRO-H mission is the sixth in a series of highly successful X-ray missions initiated by the Institute of Space and Astronautical Science (ISAS). ASTRO-H will investigate the physics of the high-energy universe via a suite of four instruments, covering a very wide energy range, from 0.3 keV to 600 keV. These instruments include a high-resolution, high-throughput spectrometer sensitive over 0.3-2 keV with high spectral resolution of Delta E < 7 eV, enabled by a micro-calorimeter array located in the focal plane of thin-foil X-ray optics; hard X-ray imaging spectrometers covering 5-80 keV, located in the focal plane of multilayer-coated, focusing hard X-ray mirrors; a wide-field imaging spectrometer sensitive over 0.4-12 keV, with an X-ray CCD camera in the focal plane of a soft X-ray telescope; and a non-focusing Compton-camera type soft gamma-ray detector, sensitive in the 40-600 keV band. The simultaneous broad bandpass, coupled with high spectral resolution, will enable the pursuit of a wide variety of important science themes.Comment: 22 pages, 17 figures, Proceedings of the SPIE Astronomical Instrumentation "Space Telescopes and Instrumentation 2012: Ultraviolet to Gamma Ray

The Quiescent Intracluster Medium in the Core of the Perseus Cluster

Clusters of galaxies are the most massive gravitationally-bound objects in the Universe and are still forming. They are thus important probes of cosmological parameters and a host of astrophysical processes. Knowledge of the dynamics of the pervasive hot gas, which dominates in mass over stars in a cluster, is a crucial missing ingredient. It can enable new insights into mechanical energy injection by the central supermassive black hole and the use of hydrostatic equilibrium for the determination of cluster masses. X-rays from the core of the Perseus cluster are emitted by the 50 million K diffuse hot plasma filling its gravitational potential well. The Active Galactic Nucleus of the central galaxy NGC1275 is pumping jetted energy into the surrounding intracluster medium, creating buoyant bubbles filled with relativistic plasma. These likely induce motions in the intracluster medium and heat the inner gas preventing runaway radiative cooling; a process known as Active Galactic Nucleus Feedback. Here we report on Hitomi X-ray observations of the Perseus cluster core, which reveal a remarkably quiescent atmosphere where the gas has a line-of-sight velocity dispersion of 164+/-10 km/s in a region 30-60 kpc from the central nucleus. A gradient in the line-of-sight velocity of 150+/-70 km/s is found across the 60 kpc image of the cluster core. Turbulent pressure support in the gas is 4% or less of the thermodynamic pressure, with large scale shear at most doubling that estimate. We infer that total cluster masses determined from hydrostatic equilibrium in the central regions need little correction for turbulent pressure.Comment: 31 pages, 11 Figs, published in Nature July