Bank Japan Research Articles

Comparison of Unrelated Cord Blood Transplantation and HLA-Mismatched Unrelated Bone Marrow Transplantation for Adults with Leukemia

Recent advances in unrelated cord blood transplantation (UCBT) and high-resolution typing of human leukocyte antigen (HLA) from an unrelated donor have increased choices in alternative donor/stem cell source selection. We assessed HLA-mismatched locus-specific comparison of the outcomes of 351 single-unit UCB and 1,028 unrelated bone marrow (UBM) adult recipients 16 years old or older at the time of transplantation who received first stem cell transplantation with myeloablative conditioning for acute leukemia or myelodysplastic syndromes. With adjusted analyses, HLA 0 to 2 mismatched UCBT showed similar overall mortality (relative risk [RR] = 0.85, 95% confidence interval [CI], 0.68-1.06; P = .149) compared with that of single-HLA-DRB1-mismatched UBMT. UCBT showed inferior neutrophil recovery (RR = 0.50, 95% CI, 0.42-0.60; P < .001), lower risk of acute graft-versus-host disease (RR = 0.55, 95% CI, 0.42-0.72; P < .001), and lower risk of transplantation-related mortality (RR = 0.68, 95% CI, 0.50-0.92; P = .011) compared with single-HLA-DRB1-mismatched UBMT. No significant difference was observed for risk of relapse (RR = 1.28, 95% CI, 0.93-1.76; P = .125). HLA 0 to 2 antigen-mismatched UCBT is a reasonable second alternative donor/stem cell source with a survival outcome similar to that of single-HLA-DRB1-mismatched or other 7 of 8 UBMT.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University

Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB.Database URL: http://www.pdbj.org/

Comparative Structural Biology of Eubacterial and Archaeal Oligosaccharyltransferases

Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. In the bacterium Campylobacter jejuni, a single-subunit membrane protein, PglB, catalyzes N-glycosylation. We report the 2.8 A resolution crystal structure of the C-terminal globular domain of PglB and its comparison with the previously determined structure from the archaeon Pyrococcus AglB. The two distantly related oligosaccharyltransferases share unexpected structural similarity beyond that expected from the sequence comparison. The common architecture of the putative catalytic sites revealed a new catalytic motif in PglB. Site-directed mutagenesis analyses confirmed the contribution of this motif to the catalytic function. Bacterial PglB and archaeal AglB constitute a protein family of the catalytic subunit of OST along with STT3 from eukaryotes. A structure-aided multiple sequence alignment of the STT3/PglB/AglB protein family revealed three types of OST catalytic centers. This novel classification will provide a useful framework for understanding the enzymatic properties of the OST enzymes from Eukarya, Archaea, and Bacteria.

Development of Protein Structure Databases and their Applications to Functional Annotation

We manage the Protein Data Bank Japan (PDBj), curating, editing and distributing protein structural data, as a member of the worldwide Protein Data Bank (wwPDB) and currently process about 25-30% of all deposited data in the world [1]. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies [2, 3]: a Java-based molecular graphics viewer, jV; an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; identification of sequence and structural neighbours; a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects [4].

Protein structure databases with new web services for structural biology and biomedical research

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.

A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules

The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.

1P481 Real-time Structure Based Queries at the Protein Data Bank japan(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS &amp; BSJ 2006)

1P481 Real-time Structure Based Queries at the Protein Data Bank japan(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS &amp; BSJ 2006)

ＰＤＢｊの国際協力による登録作業と品質管理，ユーザサービス

ＰＤＢｊの国際協力による登録作業と品質管理，ユーザサービス

Price deflation and consumption: central bank policy and Japan’s economic and financial stagnation

In this paper we review the major causes of Japan’s economic and financial stagnation during the past decade, considering in particular how past policies of the Bank of Japan have generated the current deflationary environment. This paper does not attribute Japan’s economic and financial distress entirely to Bank of Japan policy nor does it fail to recognize the shift in policy starting March 2001 when the Bank shifted toward a policy of “quantitative easing” that generated a significant increase in the growth of high powered money by late 2002. The paper argues the Bank’s deflationary policies starting in the mid-1990s up to late 2002 exacerbated the distress and it remains to be seen whether the new policy will reverse deflationary expectations. We consider the economic effects of the deflation, and in particular we argue for a link between expected deflation when nominal interest rates approach their lower bound and a decline in consumption. We find some initial evidence for this hypothesis using both a simple two-period model with a simulation and estimates of consumption functions for both the United States and Japan. Reinflation is thus a necessary, though not a sufficient condition for Japanese economic recovery.

Book Reviews

Book reviewed in this articles: The Emerging Asia‐Pacific Era and the Regional Cooperation towards the Year 2000. Sustainable development Economic Policies for Sustainable Development. Edited by the Asian Development Bank Japan's economic outlook Japan's Growing External Assets: A Medium for Regional Growth? Edited by Susumu Awanohara. China's rural reforms China's Rural Industry: Structure, Development, and Reform. Edited by William A. Byrd and Lin Qingsong. Economics in the South Pacific Oceanic Economic Handbook. Edited by Euromonitor Malaysia's economy Growth and Ethnic Inequality: Malaysia's New Economic Policy. By Just Faaland, J. R. Parkinson and Rais Saniman. Malaysia's economy The Malaysian Economy: Spatial Perspectives. By George Cho. Malaysian challenge The Malaysian Economic Challenge in the 1990s: Transformation for Growth By Fong Chan Onn. Comparative study of capitalism Capitalism in Contrasting Cultures. Edited by Steward R. Glegg and S. Gordon Redding assisted by Monica Cartner. Philippine agrarian reform Toward an Alternative Land Reform Paradigm. By Y. Hayami, M. A. Quisumbing and L. Adriano. Global economy The New Global Economy and the Developing Countries: Essays in International Economics and Development. By G. K. Helleiner. China's wool industry The Wool Industry in China: Some Chinese Perspectives. Edited by John W. Longworth. China's technology strategy Industrialization and technological development in China. By Nobuo Mayuyama. Repeating Asian NICs success Trade, Finance and Developing Countries: Strategies and Constraints in the 1990s. By Sheila Page. China's forestry Forests and Forestry in China. By S. D. Richardson. Political economy in foreign policy The Political Economy of Singapore's Industrialization: National State and International Capital. By Garry Rodan. Political economy in foreign policy The Political Economy of Foreign Policy in Southeast Asia. Edited by David Wurfel and Bruce Burton. The Taiwan miracle The Foreign Factor, Studies in Economic, Social and Political Change: The Republic of China. By Chi schive. Korea's economic development The Rise of the Korean Economy. By Byung‐Nak Song. Multilateral trade negotiations Services in Asia and the Pacific: Selected Papers, Volume One.