Bank Japan Research Articles

A genome-wide association study identifies a possible role for cannabinoid signalling in the pathogenesis of diabetic kidney disease

Diabetic kidney disease (DKD), also known as diabetic nephropathy, is the leading cause of renal impairment and end-stage renal disease. Patients with diabetes are at risk for DKD because of poor control of their blood glucose, as well as nonmodifiable risk factors including age, ethnicity, and genetics. This genome-wide association study (GWAS) was conducted for the first time in the Emirati population to investigate possible genetic factors associated with the development and progression of DKD. We included data on 7,921,925 single nucleotide polymorphism (SNPs) in 258 cases of type 2 diabetes mellitus (T2DM) who developed DKD and 938 control subjects with T2DM who did not develop DKD. GWAS suggestive results (P < 1 × 10–5) were further replicated using summary statistics from three cohorts with T2DM-induced DKD (Bio Bank Japan data, UK Biobank, and FinnGen Project data) and T1DM-induced DKD (UK-ROI cohort data from Belfast, UK). When conducting a multiple linear regression model for gene-set analyses, the CNR2 gene demonstrated genome-wide significance at 1.46 × 10–6. SNPs in CNR2 gene, encodes cannabinoid receptor 2 or CB2, were replicated in Japanese samples with the leading SNP rs2501391 showing a Pcombined = 9.3 × 10–7, and odds ratio = 0.67 in association with DKD associated with T2DM, but not with T1DM, without any significant association with T2DM itself. The allele frequencies of our cohort and those of the replication cohorts were in most cases markedly different. In addition, we replicated the association between rs1564939 in the GLRA3 gene and DKD in T2DM (P = 0.016, odds ratio = 0.54 per allele C). Our findings suggest evidence that cannabinoid signalling may be involved in the development of DKD through CB2, which is expressed in different kidney regions and known to be involved in insulin resistance, inflammation, and the development of kidney fibrosis.

Three-dimensional Structure Databases of Biological Macromolecules.

Databases of three-dimensional structures of proteins (and their associated molecules) provide: (a) Curated repositories of coordinates of experimentally determined structures, including extensive metadata; for instance information about provenance, details about data collection and interpretation, and validation of results. (b) Information-retrieval tools to allow searching to identify entries of interest and provide access to them. (c) Links among databases, especially to databases of amino-acid and genetic sequences, and of protein function; and links to software for analysis of amino-acid sequence and protein structure, and for structure prediction. (d) Collections of predicted three-dimensional structures of proteins. These will become more and more important after the breakthrough in structure prediction achieved by AlphaFold2. The single global archive of experimentally determined biomacromolecular structures is the Protein Data Bank (PDB). It is managed by wwPDB, a consortium of five partner institutions: the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), the Protein Data Bank Japan (PDBj), the BioMagResBank (BMRB), and the Electron Microscopy Data Bank (EMDB). In addition to jointly managing the PDB repository, the individual wwPDB partners offer many tools for analysis of protein and nucleic acid structures and their complexes, including providing computer-graphic representations. Their collective and individual websites serve as hubs of the community of structural biologists, offering newsletters, reports from Task Forces, training courses, and "helpdesks," as well as links to external software.Many specialized projects are based on the information contained in the PDB. Especially important are SCOP, CATH, and ECOD, which present classifications of protein domains.

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.

Protein Data Bank Japan: 20 years and more as the Asian hub for 3D structure and the founding member of the wwPDB

Protein Data Bank Japan: 20 years and more as the Asian hub for 3D structure and the founding member of the wwPDB

Investigation and Analysis on the Function of Space Formation of Spur Dike for Around Shingen Bank Japan

The Shingen Bank is famous for its flood control in Japan. Spur dike is skilfully used in river management, which creates good conditions for the human activities. In this paper, using the representative of the river regulation buildings in the Shingen Bank as the object to analyze the space formation function of Spur dike and examine human activities at the water edge. Firstly, by analyzing the ecological function and utilization of Spur dike in river space, the relationship between the Spur dike and human activities is clarified. And then, the configuration method of spur dikes in the course of river management was put forward, which could provide reference for the management and landscape planning of the near natural rivers.

An Investigation on Human Activities in Shingen Bank Japan Centred on Spur Dike

River space is one of the precious open spaces that human beings can contact with nature. Respecting, complying with and protecting nature is the essence of river landscape construction. In the process of natural river construction, the spur dike is an indispensable element for the stability of river banks, the formation of natural environment of ecological system and human activities, and its various functions are widely recognized. In this study, the spur dike in the Shingen Bank is taken as the center to investigate the forms of riverside activities of residents on the spot, to understand the impression of residents on the river, and on this basis, to investigate the spatial structure characteristics along the river and its relationship with human activities, with a view to providing some help for future urban river and riverside space reconditioning.

The Protein Data Bank Archive.

Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu ). The PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving data standards and data validation for improving data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve data quality and accommodate new data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metadata for all experimentally determined atomic structures, experimental data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR)spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

Researches on the Improvement of the Bioactivity of TiO2 Deposits, Obtained by Magnetron Sputtering - DC

In this paper, layers of TiO2 were deposited, by magnetron sputtering, on a glass support. The parameters of the deposition process were kept constant except for the O2/(Ar + O2) ratio that varied on three levels. The physical and mechanical properties of the layers obtained were investigated by SEM optical microscopy, electronics, AFM and X-ray diffraction. The bioactivity of TiO2 surfaces was investigated by growing M3C3-E1 osteoblast cells produced by RIKEN Cell Bank (Japan) for a period of 5 days. The modification of the working environment in the enclosure determines both the phasic modification in the TiO2 film, respectively the amount of the anatase or rutile phase and the decrease of the average roughness of the film from 112.3nm to 56.7nm. The research has demonstrated that the finer layers with a high content of anatase promote the growth of M3C3-E1 cells.

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).

The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode‐Elastic server for normal mode analysis, a virtual reality system for the eF‐site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.

Abstract 925: Tumorigenesis of murine iPS cell is prevented by iron depletion with downregulation of stemness markers

Abstract Background: Iron plays a crucial role in the various metabolic pathways and it is essential for life. However excess of iron is known to cause cancer. There are many reports that iron depletion treatment indicates antitumor effect. Previously, we have confirmed that iron depletion treatment indicates antitumor effect against Cancer stem cell (CSC) model, miPS-LLCcm, which was converted from murine induced pluripotent stem cell (miPS cell) in Okayama university (Chen at el. PLOS ONE 2012), and also suppresses CSC markers. Many tumors contain phenotypically and functionally heterogenous cancer cells due to pluripotency of CSC. Although there are various theories about the origin of CSC, miPS has a pluripotency and regarded as the top of the hierarchy, it can be the candidate of the origin of CSC. miPS cell is known to form teratoma when inoculated into nude mouse because of its undifferentiated status. We hypothesized if we could suppress the stemness and tumorigenicity of miPS cell by iron depletion treatment, it can be applied to the therapy for CSC and undifferentiated status cancer cell. In this study, we investigated the stemness and tumorigenecity of miPS cell with iron depletion treatment. Methods: We used miPS cell(cell name : iPS-MEF-Ng-20D-17) purchased from Riken Cell Bank(Japan). Deferasirox (DFX), an popular commercial available oral iron chelator was used for iron depletion treatment. Western blot analysis was done to examine the expression of the stemness markers including Nanog, Oct3/4, Sox2, Klf4, c-Myc. Subcutaneous model of miPS cell and miPS cell treated with DFX (50μM) were used in vivo study. Tumors were harvested for immunohistochemistry. Results: Stemness markers of miPS cell were suppressed strongly by DFX in western blot analysis. DFX also suppressed the subcutaneous tumor growth. The average tumor volume of the control group was 665.3±430.8mm3 while that of the DFX treated group was 204.3±76.2 mm3(p&amp;lt;0.05) on day 20. Immunohistochemistry of the tumor revealed the suppression of the stemness markers in the DFX treated group compared with the control group. Citation Format: Yuki Katsura, Toshiaki Ohara, Hajime Kashima, Hiroaki Sato, Takuya Kato, Takayuki Ninomiya, Kazuhiro Noma, Yasuko Tomono, Hiroshi Tazawa, Shunsuke Kagawa, Yasuhiro Shirakawa, Toshiyoshi Fujiwara. Tumorigenesis of murine iPS cell is prevented by iron depletion with downregulation of stemness markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 925. doi:10.1158/1538-7445.AM2017-925

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), 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. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

Molmil: a molecular viewer for the PDB and beyond.

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user’s local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0155-1) contains supplementary material, which is available to authorized users.

New wwPDB validation pipelines for X-ray, NMR and 3DEM structures

The Protein Data Bank (PDB) is the single global archive of 3D biomacromolecular structure data. The archive is managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org) organisation through its partners, the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank Japan (PDBj), the Protein Data Bank in Europe and the Biological Magnetic Resonance Bank (BMRB). Analogously, the Electron Microscopy Data Bank (EMDB) is managed by the EMDataBank (emdatabank.org) organisation. A few years ago, realising the needs and opportunities to assess the quality of biomacromolecular structures deposited in the PDB, the wwPDB and EMDataBank partners established Validation Task Forces (VTFs) to advice them on up-to-date and community-agreed methods and standards to validate X-ray, NMR and 3DEM structures and data. All three VTFs have now published their recommendations (1, 2, 3) and these are getting implemented as validation-software pipelines . The pipelines are integrated in the new joint wwPDB deposition and annotation system (http://deposit.wwpdb.org/deposition/). In addition, stand-alone servers are provided to allow practising structural biologists to validate models prior to publication and deposition (http://wwpdb.org/validation-servers.html). The validation pipelines and the output they produce (human-readable PDF reports and machine-readable XML files) will be described.

Educational Outreach and User Training at the Worldwide Protein Data Bank

The Protein Data Bank (PDB) contains a wealth of structural and functional knowledge about proteins, RNA, DNA, and other macromolecules, and their assemblies and complexes with small molecules. The challenge faced by the providers of PDB data is to make this knowledge accessible to an increasingly large and diverse audience, ranging from expert structural biologists to non-specialist consumers of structural information. Educators, students, and general audiences will have their own specific interests and expectations from molecular structure data. For a general user, a 2D image of hemoglobin illustrates how a protein looks at a microscopic level. For high school students and educators, 3D models or computer graphics can show how one or a few specific proteins can assemble into an icosahedral virus. In contrast, PhD and post-doc level researchers require expert guidance on how to critically assess the quality of structural data, and in-depth training on the use of specialist tools and resources for the comparison and analysis of structures. The PDB archive is managed by members of the Worldwide Protein Data Bank (wwPDB): the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; rcsb.org), Protein Data Bank in Europe (PDBe; pdbe.org), Protein Data Bank Japan (PDBj), and BioMagResBank (BMRB, bmrb.wisc.edu). In addition to managing and distributing structural data, the wwPDB partners are engaged in numerous outreach initiatives and user training programs. These efforts are vital to ensuring that these uniquely valuable data can be effectively accessed and used by research scientists, students, and educators alike. This talk will describe on-going wwPDB outreach efforts and highlight exciting new initiatives at the RCSB PDB, PDBe and PDBj.

Modifications to the Protein Data Bank : A new PDB format, Data Deposition, and Validation Report(PDBj: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Modifications to the Protein Data Bank : A new PDB format, Data Deposition, and Validation Report(PDBj: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Browsing searching, and Comparing 3D electron microscopy data(PDBJ: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Browsing searching, and Comparing 3D electron microscopy data(PDBJ: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Tools for highly automated NMR analysis and applications using database(PDBj: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Tools for highly automated NMR analysis and applications using database(PDBj: Protein Data Bank Japan,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Activities of PDBj and wwPDB : A new PDB format, Data Deposition, Validation, and Data Integration(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Activities of PDBj and wwPDB : A new PDB format, Data Deposition, Validation, and Data Integration(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

PDBj-BMRB : Publishing NMR Spectroscopy Derived Data of BioMagResBank in Structured Data Formats, XML and RDF(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

PDBj-BMRB : Publishing NMR Spectroscopy Derived Data of BioMagResBank in Structured Data Formats, XML and RDF(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)