Shuichi Kawashima

Publications of Shuichi Kawashima

• Global classical solutions for partially dissipative hyperbolic system of balance laws

  Authors: Jiang Xu, Shuichi Kawashima

  02/2012;

  This work is concerned with ($N$-component) hyperbolic system of balance laws in arbitrary space dimensions. Under entropy dissipative assumption and the Shizuta-Kawashima algebraic condition, aThis work is concerned with ($N$-component) hyperbolic system of balance laws in arbitrary space dimensions. Under entropy dissipative assumption and the Shizuta-Kawashima algebraic condition, a general theory on the well-posedness of classical solutions in the framework of Chemin-Lerner's spaces with critical regularity is established. To do this, we first explore the functional space theory and develop an elementary fact that indicates the relation between homogeneous and inhomogeneous Chemin-Lerner's spaces. Then this fact allows to prove the local well-posedness for general data and global well-posedness for small data by using the Fourier frequency-localization argument. Finally, we apply the new existence theory to a specific fluid model-the compressible Euler equations with damping, and obtain the corresponding results in critical spaces.

• Global existence and asymptotic decay of solutions to the Non-isentropic Euler-Maxwell system

  Authors: Yuehong Feng, Shu Wang, Shuichi Kawashima

  02/2012;

  The non-isentropic compressible Euler-Maxwell system is investigated in $R^3$ in the present paper, and the $L^q$ time decay rate for the global smooth solution is established. It is shown that theThe non-isentropic compressible Euler-Maxwell system is investigated in $R^3$ in the present paper, and the $L^q$ time decay rate for the global smooth solution is established. It is shown that the density and temperature of electron converge to the equilibrium states at the same rate $(1+t)^{-11/4}$ in $L^q$ norm.

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii.

  Authors: Mihoko Imada, Shuichi Kawashima, Minoru Kanehisa, Tsutomu Takeuchi, Takashi Asai

  Parasitology international. 02/2010; 59(2):206-10.

  The Toxoplasma gondii genome project has revealed two putative isoforms (TgPGM-I and TgPGM-II) of alpha-phosphoglucomutase (EC 5.4.2.2). We obtained recombinant proteins of these isoforms from theThe Toxoplasma gondii genome project has revealed two putative isoforms (TgPGM-I and TgPGM-II) of alpha-phosphoglucomutase (EC 5.4.2.2). We obtained recombinant proteins of these isoforms from the Beverley strain of T. gondii and characterized their properties, particularly the kinetic properties of these isoforms. The specific activities of TgPGM-I and TgPGM-II for alpha-D-glucose 1-phosphate were 338+/-9 and 84+/-6micromol/min/mg protein, respectively, at 37 degrees C under optimal conditions. The Kcat and Km values of TgPGM-I were 398+/-11/s and 0.19+/-0.03mM and those for TgPGM-II were 93+/-7/s and 3.53+/-0.91mM, respectively, for alpha-d-glucose 1-phosphate. Magnesium ions were the most effective divalent cations for both the enzyme activities. The maximum activities of both the enzymes were obtained in the presence of more than 0.2mM alpha-D-glucose 1,6-bisphosphate. Although both enzymes were attached to the alpha-phosphohexomutase superfamily, amino acid sequence homology between TgPGM-I and TgPGM-II showed very low overall identity (25%). No alpha-phosphomannomutase (EC 5.4.2.8) activity was detected for either enzyme. The data indicated that TgPGM-I, but not TgPGM-II, may play an important role in alpha-D-glucose 6-phosphate production.

• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

  Authors: Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts [......] Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi

  Journal of biomedical semantics. 01/2010; 1(1):8.

  Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands forWeb services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

• Systems biology approaches and pathway tools for investigating cardiovascular disease.

  Authors: Craig E Wheelock, Asa M Wheelock, Shuichi Kawashima, Diego Diez, Minoru Kanehisa, Marjan van Erk, Robert Kleemann, Jesper Z Haeggström, Susumu Goto

  Molecular bioSystems. 07/2009; 5(6):588-602.

  Systems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism. One important aspect of systems biology approaches is toSystems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism. One important aspect of systems biology approaches is to identify the biological pathways or networks that connect the differing elements of a system, and examine how they evolve with temporal and environmental changes. The utility of this method becomes clear when applied to multifactorial diseases with complex etiologies, such as inflammatory-related diseases, herein exemplified by atherosclerosis. In this paper, the initial studies in this discipline are reviewed and examined within the context of the development of the field. In addition, several different software tools are briefly described and a novel application for the KEGG database suite called KegArray is presented. This tool is designed for mapping the results of high-throughput omics studies, including transcriptomics, proteomics and metabolomics data, onto interactive KEGG metabolic pathways. The utility of KegArray is demonstrated using a combined transcriptomics and lipidomics dataset from a published study designed to examine the potential of cholesterol in the diet to influence the inflammatory component in the development of atherosclerosis. These data were mapped onto the KEGG PATHWAY database, with a low cholesterol diet affecting 60 distinct biochemical pathways and a high cholesterol exposure affecting 76 biochemical pathways. A total of 77 pathways were differentially affected between low and high cholesterol diets. The KEGG pathways "Biosynthesis of unsaturated fatty acids" and "Sphingolipid metabolism" evidenced multiple changes in gene/lipid levels between low and high cholesterol treatment, and are discussed in detail. Taken together, this paper provides a brief introduction to systems biology and the applications of pathway mapping to the study of cardiovascular disease, as well as a summary of available tools. Current limitations and future visions of this emerging field are discussed, with the conclusion that combining knowledge from biological pathways and high-throughput omics data will move clinical medicine one step further to individualize medical diagnosis and treatment.

• Domain shuffling and the evolution of vertebrates.

  Authors: Takeshi Kawashima, Shuichi Kawashima, Chisaki Tanaka, Miho Murai, Masahiko Yoneda, Nicholas H Putnum, Daniel S Rokhsar, Minoru Kanehisa, Nori Satoh, Hiroshi Wada

  Genome research. 06/2009;

  The evolution of vertebrates was driven by a number of important events, including the development of cartilage, the immune system, and complicated craniofacial structures. Here we examine domainThe evolution of vertebrates was driven by a number of important events, including the development of cartilage, the immune system, and complicated craniofacial structures. Here we examine domain shuffling as an alternative mechanism for the contribution of novel genetic material required for vertebrate evolution. We mapped domain-shuffling events during the evolution of deuterostomes with a focus on how domain shuffling contributed to the evolution of vertebrate- and chordate-specific characteristics. We identified approximately 1,000 new domain pairs in the vertebrate lineage, including approximately 100 that were shared by all seven of the vertebrate species examined. Some of these pairs occur in the protein components of vertebrate-specific structures, such as cartilage and the inner ear, suggesting that domain shuffling made a marked contribution to the evolution of vertebrate-specific characteristics. The evolutionary history of the domain pairs is traceable; for example, the Xlink domain of aggrecan, one of the major components of cartilage, was originally utilized as a functional domain of a surface molecule of blood cells in protochordate ancestors, and it was recruited by the protein of the matrix component of cartilage in the vertebrate ancestor. We also identified genes that were created as a result of domain shuffling in ancestral chordates. Some of these are involved in the functions of chordate structures, such as the endostyle, Reissner's fiber of the neural tube, and the notochord. Our analyses shed new light on the evolutionary role of domain shuffling, especially in the evolution of vertebrates and chordates.

• Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.

  Authors: Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima, Eri Kibukawa, Kazushi Hiranuka, Masahide Sasaki, Sumio Sugano, Junichi Watanabe

  Nucleic acids research. 12/2008;

  Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In thisFull-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this update, the database has been expanded to contain the shogun sequencing for the entire sequences of 14 818 non-redundant full-length cDNA clones from six apicomplexa parasites and 6.8 million of transcription start sites (TSS), both of which had been produced by novel protocols using the oligo-capping method and the Illumina GA sequencer. The former should be the ultimate data for exact annotation of the expressed genes, while the latter should be useful for ultra-deep expression analysis. Furthermore, we have launched Full-Arthropods, a full-length cDNA database for arthropods of medical importance. Full-Arthropods contains 50 343 one-pass sequences, 10 399 shotgun complete sequences and 22.4 million TSS tags in anopheles mosquitoes that transmit malaria, tsetse flies that transmit trypanosomiasis and dust mites that cause allergic dermatitis and bronchial asthma. By providing the largest integrated full-length cDNA data resources in the apicomplexa parasites as well as their vectors, Full-Malaria/Parasites and Full-Arthropods should help combat parasitic diseases. Full-Malaria/Parasites and Full-Arthropods are accessible from http://fullmal.hgc.jp/.

• AAindex: amino acid index database, progress report 2008.

  Authors: Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, Minoru Kanehisa

  Nucleic acids research. 02/2008; 36(Database issue):D202-5.

  AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contactAAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid substitution matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/).

• KEGG for linking genomes to life and the environment.

  Authors: Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi

  Nucleic acids research. 02/2008; 36(Database issue):D480-4.

  KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linkingKEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

• VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

  Authors: Zhenjun Hu, David M Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M Stuart, Charles DeLisi

  Nucleic acids research. 08/2007; 35(Web Server issue):W625-32.

  With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and GeneWith the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile. Multiple experiments can be navigated or animated. Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions. Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data. Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG). Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu.

• EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG.

  Authors: Ali Masoudi-Nejad, Susumu Goto, Ruy Jauregui, Masumi Ito, Shuichi Kawashima, Yuki Moriya, Takashi R Endo, Minoru Kanehisa

  Plant physiology. 07/2007; 144(2):857-66.

  EGENES is a knowledge-based database for efficient analysis of plant expressed sequence tags (ESTs) that was recently added to the KEGG suite of databases. It links plant genomic information withEGENES is a knowledge-based database for efficient analysis of plant expressed sequence tags (ESTs) that was recently added to the KEGG suite of databases. It links plant genomic information with higher order functional information in a single database. It also provides gene indices for each genome. The genomic information in EGENES is a collection of EST contigs constructed from assembly of ESTs. Due to the extremely large genomes of plant species, the bulk collection of data such as ESTs is a quick way to capture a complete repertoire of genes expressed in an organism. Using ESTs for reconstructing metabolic pathways is a new expansion in KEGG and provides researchers with a new resource for species in which only EST sequences are available. Functional annotation in EGENES is a process of linking a set of genes/transcripts in each genome with a network of interacting molecules in the cell. EGENES is a multispecies, integrated resource consisting of genomic, chemical, and network information containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions. Using EGENES, genome-based pathway annotation and EST-based annotation can now be compared and mutually validated. The ultimate goals of EGENES will be to: bring new plant species into KEGG by clustering and annotating ESTs; abstract knowledge and principles from large-scale plant EST data; and improve computational prediction of systems of higher complexity. EGENES will be updated at least once a year. EGENES is publicly available and is accessible by the following link or by KEGG's navigation system (http://www.genome.jp/kegg-bin/create_kegg_menu?category=plants_egenes).

• Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis.

  Authors: Shinobu Okamoto, Yoshihiro Yamanishi, Shigeki Ehira, Shuichi Kawashima, Koichiro Tonomura, Minoru Kanehisa

  Proteomics. 04/2007; 7(6):900-9.

  Prediction of molecular interaction networks from large-scale datasets in genomics and other omics experiments is an important task in terms of both developing bioinformatics methods and solvingPrediction of molecular interaction networks from large-scale datasets in genomics and other omics experiments is an important task in terms of both developing bioinformatics methods and solving biological problems. We have applied a kernel-based network inference method for extracting functionally related genes to the response of nitrogen deprivation in cyanobacteria Anabaena sp. PCC 7120 integrating three heterogeneous datasets: microarray data, phylogenetic profiles, and gene orders on the chromosome. We obtained 1348 predicted genes that are somehow related to known genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While this dataset contained previously known genes related to the nitrogen deprivation condition, it also contained additional genes. Thus, we attempted to select any relevant genes using the constraints of Pfam domains and NtcA-binding sites. We found candidates of nitrogen metabolism-related genes, which are depicted as extensions of existing KEGG pathways. The prediction of functional relationships between proteins rather than functions of individual proteins will thus assist the discovery from the large-scale datasets.

• New amino acid indices based on residue network topology.

  Authors: Jian Huang, Shuichi Kawashima, Minoru Kanehisa

  Genome informatics. International Conference on Genome Informatics. 02/2007; 18:152-61.

  Amino acid indices are useful tools in bioinformatics. With the appearance of novel theory and technology, and the rapid increase of experimental data, building new indices to cope with new orAmino acid indices are useful tools in bioinformatics. With the appearance of novel theory and technology, and the rapid increase of experimental data, building new indices to cope with new or unsolved old problems is still necessary. In this study, residue networks are constructed from the PDB structures of 640 representative proteins based on the distance between Calpha atoms with an 8 A cutoff. All these networks show typical small world features. New amino acid indices, termed relative connectivity, clustering coefficient, closeness and betweenness, are derived from the corresponding topological parameters of amino acids in the residue networks. The 4 new network based indices are closely clustered together and related to hydrophobicity and beta propensity. When compared with related amino acid indices, the new indices show better or comparable performance in protein surface residue prediction. Relative connectivity is the best index and can reach a useful performance with an area under the curve about 0.75. It indicates that the network property based amino acid indices can be useful complements to the existing physicochemical property based amino acid indices.

• Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

  Authors: Shuichi Kawashima, Takeshi Kawashima, Nicholas H Putnam, Daniel S Rokhsar, Hiroshi Wada, Minoru Kanehisa

  Genome informatics. International Conference on Genome Informatics. 02/2007; 19:50-60.

  In the evolution of the eukaryotic genome, exon or domain shuffling has produced a variety of proteins. On the assumption that each fusion event between two independent protein-domains occurred onlyIn the evolution of the eukaryotic genome, exon or domain shuffling has produced a variety of proteins. On the assumption that each fusion event between two independent protein-domains occurred only once in the evolution of metazoans, we can roughly estimate when the fusion events were happened. For this purpose, we made phylogenetic profiles of pair-wise domain-combinations of metazoans. The phylogenetic profiles can be expected to reflect the protein evolution of metazoan. Interestingly, the phylogenetic tree of metazoans, derived from the profiles, supported the "Ecdysozoa hypothesis" that is one of the major hypotheses for metazoan evolution. Further, the phylogenetic profiles showed the candidates of genes that were required for each clade-specific features in metazoan evolution. We propose that comparative proteome analysis focusing on pair-wise domain-combinations is a useful strategy for researching the metazoan evolution. Additionally, we found that the extant ecdysozoans share only fourteen domain-combinations in our profiles. Such a small number of ecdysozoan-specific domain-combinations is consistent with the extensive gene-losses through the evolution of ecdysozoans.

• Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli.

  Authors: Shujiro Okuda, Shuichi Kawashima, Kazuo Kobayashi, Naotake Ogasawara, Minoru Kanehisa, Susumu Goto

  BMC genomics. 02/2007; 8:48.

  BACKGROUND: Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptionalBACKGROUND: Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation. RESULTS: We systematically analyzed the experimentally verified transcriptional units (TUs) in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP) belong to the same TU, sub-operon pairs (SOP) that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP) belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes. CONCLUSION: Complicated operon structures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes.

• Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic.

  Authors: Akiyasu C Yoshizawa, Shuichi Kawashima, Shujiro Okuda, Masashi Fujita, Masumi Itoh, Yuki Moriya, Masahiro Hattori, Minoru Kanehisa

  Traffic (Copenhagen, Denmark). 09/2006; 7(8):1104-18.

  The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and canThe SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been determined. We discovered by whole genome sequence analysis that sequence motifs (conserved sequences) in the SNARE motif domains for each protein group correspond to localization sites or transport pathways. We claim that these motifs reflect the specificity of the binding combinations of SNARE motif domains. Using these motifs, we could classify SNARE proteins from 48 organisms into their localization sites or transport pathways. The classification result shows that more than 10 SNARE subgroups are kingdom specific and that the SNARE paralogs involved in the plasma membrane-related transport pathways have developed greater variations in higher animals and higher plants than those involved in the endoplasmic reticulum-related transport pathways throughout eukaryotic evolution.

• EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.

  Authors: Ali Masoudi-Nejad, Koichiro Tonomura, Shuichi Kawashima, Yuki Moriya, Masanori Suzuki, Masumi Itoh, Minoru Kanehisa, Takashi Endo, Susumu Goto

  Nucleic acids research. 08/2006; 34(Web Server issue):W459-62.

  Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencingExpressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs. EGassembler (http://egassembler.hgc.jp/) is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community a unique all-in-one online application web service for large-scale ESTs and genomic DNA clustering and assembling. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways. The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers.

• Metabolite antigens and pathway incompatibility.

  Authors: Wataru Honda, Shuichi Kawashima, Minoru Kanehisa

  Genome informatics. International Conference on Genome Informatics. 02/2006; 17(1):184-94.

  Vgamma9Vdelta2 cells, which constitute a small portion of peripheral blood T-cells (approximately 5%), are known to be the biggest subset of human gammadelta T-cells ( approximately 70%) inVgamma9Vdelta2 cells, which constitute a small portion of peripheral blood T-cells (approximately 5%), are known to be the biggest subset of human gammadelta T-cells ( approximately 70%) in circulating blood. The Vgamma9Vdelta2 T-cells expressing Vgamma9Vdelta2 T-cell receptors have an ability to recognize non-peptide antigens directly or indirectly, for example, phosphorylated metabolites referred to as phosphoantigens, synthesized aminobisphosphonates used for therapeutic purpose such as pamidronate, and alkylamines. These chemical compounds recognized by Vgamma9Vdelta2 T-cells are produced by many prokaryotic and eukaryotic organisms. Previous works show that the phosphoantigens recognized by Vgamma9Vdelta2 T-cells are found as the intermediates in the pathogens' pathway producing IPP. In this paper, we show that the other compounds recognized by Vgamma9Vdelta2 T-cells are found on the pathogens' biosynthetic pathways leading to production of shared compounds with human. In addition, many compounds having high structural similarity with alkylamine antigens are also found only in pathogen's biosynthetic pathways or produced only by non-human enzymes.

• From genomics to chemical genomics: new developments in KEGG.

  Authors: Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, Mika Hirakawa

  Nucleic acids research. 02/2006; 34(Database issue):D354-7.

  The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with theThe increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.