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Biomedical subjects

A Ogiwara

Publications and source records attributed to A Ogiwara.

16 recordsLinked to original sources
PubMed1998

DBGET/LinkDB: an integrated database retrieval system.

The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese GenomeNet service. DBGET is used to search and extract entries from a wide range of molecular biology databases, while LinkDB is used to search and compute links between entries in different databases. DBGET/LinkDB is designed to be a network distributed database system with an open architecture, which is suitable for incorporating local databases or establishing a specialized server environment. It also has an advantage of simple architecture allowing rapid daily updates of all the major databases. The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools, such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. In addition to factual links between database entries, LinkDB is being extended to included similarity links and biological links toward computerization of logical reasoning processes.

Databases, Factual↗
PubMed1997

The complete genome sequence of the gram-positive bacterium Bacillus subtilis.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Bacillus subtilis↗
PubMed1996

Construction of a normalized directionally cloned cDNA library from adult heart and analysis of 3040 clones by partial sequencing.

Large-scale sequencing of clones from cDNA libraries derived from specific tissues is a rapid and efficient way of discovering novel genes expressed in those tissues. However, because the heart is continually contracting and relaxing, it strongly expresses muscle-contractile genes and/or mitochondrial genes, a bias that reduces the efficiency of this method. To improve the efficiency of identifying novel genes expressed in the heart, we constructed a normalized directionally cloned cDNA library from adult heart and partially sequenced 3040 clones. Comparisons of these sequence data with known DNA sequences in the database revealed that 57.1% of the clones matched human genes already known, 23.4% were identical or almost identical to human expressed sequence tags (ESTs), 14.2% bore no significant homology to any sequences in the database, and 1.2% represented repetitive sequences. The remaining 4.1% showed some homology with known genes, and Northern blot analysis of several clones in this category revealed that most of them were expressed mainly in the heart and skeletal muscle. After redundancy was excluded, the 3040 clones accounted for 1395 distinctive ESTs, 446 of which exhibited no match to any known sequence. Our results suggest that our normalized library is less redundant than standard libraries and is a useful resource for cataloging genes expressed in the heart.

Adult↗
PubMed1996

Construction and analysis of a profile library characterizing groups of structurally known proteins.

A new sequence motif library StrProf was constructed characterizing the groups of related proteins in the PDB three-dimensional structure database. For a representative member of each protein family, which was identified by cross-referencing the PDB with the PIR superfamily classification, a group of related sequences was collected by the BLAST search against the nonredundant protein sequence database. For every group, the motifs were identified automatically according to the criteria of conservation and uniqueness of pentapeptide patterns and with a dual dynamic programming algorithm. In the StrProf library, motifs are represented by profile matrices rather than consensus patterns to allow more flexible search capabilities. Another dynamic programming algorithm was then developed to search this motif library. When the computationally derived StrProf was compared with PROSITE, which is a manually derived motif library in the best consensus pattern representation, the numbers of identified patterns were comparable. StrProf missed about one third of the PROSITE motifs, but there were also new motifs lacking in PROSITE. The new library was incorporated in SMART (Sequence Motif Analysis and Retrieval Tool), a computer tool designed to help search and annotate biologically important sites in an unknown protein sequence. The client program is available free of charge through the Internet.

Algorithms↗
PubMed1996

Is outer arm dynein intermediate chain 1 multifunctional?

The outer arm dynein of sea urchin sperm axoneme contains three intermediate chains (IC1, IC2, and IC3; M(r) 128,000, 98,000, and 74,000, respectively). IC2 and IC3 are members of the WD family; the WD motif is responsible for a protein-protein interaction. We describe here the molecular cloning of IC1. IC1 has a unique primary structure, the N-terminal part is homologous to the sequence of thioredoxin, the middle part consists of three repetitive sequences homologous to the sequence of nucleoside diphosphate kinase, and the C-terminal part contains a high proportion of negatively charged glutamic acid residues. Thus, IC1 is a novel dynein intermediate chain distinct from IC2 and IC3 and may be a multifunctional protein. The thioredoxin-related part of IC1 is more closely related to those of two redox-active Chlamydomonas light chains than thioredoxin. Antibodies were prepared against the N-terminal and middle domains of IC1 expressed as His-tagged proteins in bacteria. These antibodies cross-reacted with some dynein polypeptides (potential homologues of IC1) from distantly related species. We propose here that the three intermediate chains are the basic core units of sperm outer arm dynein because of their ubiquitous existence. The recombinant thioredoxin-related part of IC1 and outer arm dyneins from sea urchin and distantly related species were specifically bound to and eluted from a phenylarsine oxide affinity column with 2-mercaptoethanol, indicating that they contain vicinal dithiols competent to undergo reversible oxidation/reduction.

Amino Acid Sequence↗
PubMed1995

Construction of YAC contigs at human chromosome 11q22.3-q23.1 region covering the Ataxia telangiectasia locus.

Ataxia telangiectasia (AT) is an autosomal recessive disease of unknown etiology associated with cerebellar ataxia, telangiectasia, immune dysfunction, higher cancer risk, genomic instability and hypersensitivity to ionizing radiation. The major AT loci, AT-A and AT-C, are shown to be closely linked at chromosome 11q22-q23. The most recent genetic linkage mapping and linkage disequilibrium analysis have localized the major AT loci to a sequence of approximately 850 kb between the markers D11S1819 and D11S1818. The isolation of yeast artificial chromosomes spanning the AT region is an essential step to identify the gene or genes responsible for the mutation(s). We isolated a total of 20 YAC clones from three independent YAC libraries, using sequence tagged sites mapped in the AT region as primers for PCR-based YAC screening. The PCR assay for the presence or absence of 16 different DNA markers allowed us to construct and to order four YAC contigs at the AT region. One of the contigs which consists of the 10 YAC clones, covers about 2 Mb of DNA at the boundary between Giemsa-positive band 11q22.3 and Giemsa-negative band 11q23.1 and includes the entire region of the major AT locus between D11S1819 and D11S1818. Thus, the YAC contigs will facilitate the positional cloning approach for searching transcribed sequences from the defined genomic region.

Ataxia Telangiectasia↗
PubMed1994

Gnome--an Internet-based sequence analysis tool.

Gnome (GenomeNet Open Mail-service Environment) is a sequence analysis tool that enables an end-user to make use of several Internet- (mainly e-mail) based services with an easy-to-use graphical user interface. Users can conduct homology and motif searches, and database-entry retrieval against the latest databases by emitting search requests to and receiving their results form a search-server by e-mail. The search results are viewed and managed efficiently with this system. The Macintosh and X (Motif) versions of the Gnome client and the UNIX version of the Gnome server are available to academic users free of charge.

Computer Communication Networks↗
PubMed1994

[Association of antiphospholipid antibodies with valvular heart disease in patients with systemic lupus erythematosus].

The purpose of this study was to evaluate the association of antiphospholipid antibodies with the valvular lesions in patients with systemic lupus erythematosus (SLE). Two-dimensional and color Doppler echocardiographic studies were performed in 65 patients with SLE. Antiphospholipid antibodies were assayed in each patient using two methods: anticardiolipin antibody and lupus anticoagulant. Valvular lesions were observed in 43 patients (66.2%). Mitral or aortic regurgitation (MR or AR) were recognized in 37 patients (56.9%). Moderate or severe MR were significantly associated with antiphospholipid antibodies (20.0%, p < 0.01) compared with patients without antiphospholipid antibodies (2%). Four of nine patients with moderate to severe AR or MR developed cerebral infarctions or digital infarctions. It is suggested that there may be a causal link between antiphospholipid antibodies and moderate to severe valvular lesions in SLE.

Adolescent↗
PubMed1993

Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database.

Recently we have constructed a database--the Enzyme-Reaction Database--which links a chemical structure to amino acid sequences of enzymes that recognize the chemical structure as their ligand. The total number of enzymes registered in the database is 1103 with 6668 NBRF-PIR entry codes and 1756 chemical compounds. The chemical structures and chemical names for 842 compounds are registered in the Chemical-Structure Database on the MACCS system. For each enzyme, the sequences were divided into clusters, and multiply aligned in each cluster to extract a conserved sequence. A total of 158,781 five-residue-long fragments were constructed from 433 conserved sequences and compared among different clusters of different enzymes. One of these motifs shared by different enzymes was S-G-G-L-D. The motif was conserved in both argininosuccinate synthase (EC 6.3.4.5) and asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4). This result showed that the database was useful for the analysis of the relationship between chemical structures and amino acid sequence motifs.

Algorithms↗
PubMed1993

Multiple sequence alignment by parallel simulated annealing.

We have developed simulated annealing algorithms to solve the problem of multiple sequence alignment. The algorithm was shown to give the optimal solution as confirmed by the rigorous dynamic programming algorithm for three-sequence alignment. To overcome long execution times for simulated annealing, we utilized a parallel computer. A sequential algorithm, a simple parallel algorithm and the temperature parallel algorithm were tested on a problem. The results were compared with the result obtained by a conventional tree-based algorithm where alignments were merged by two-way dynamic programming. Every annealing algorithm produced a better energy value than the conventional algorithm. The best energy value, which probably represents the optimal solution, was reached within a reasonable time by both of the parallel annealing algorithms. We consider the temperature parallel algorithm of simulated annealing to be the most suitable for finding the optimal multiple sequence alignment because the algorithm does not require any scheduling for optimization. The algorithm is also useful for refining multiple alignments obtained by other heuristic methods.

Algorithms↗
PubMed1992

Construction of a dictionary of sequence motifs that characterize groups of related proteins.

An automatic procedure is proposed to identify, from the protein sequence database, conserved amino acid patterns (or sequence motifs) that are exclusive to a group of functionally related proteins. This procedure is applied to the PIR database and a dictionary of sequence motifs that relate to specific superfamilies constructed. The motifs have a practical relevance in identifying the membership of specific superfamilies without the need to perform sequence database searches in 20% of newly determined sequences. The sequence motifs identified represent functionally important sites on protein molecules. When multiple blocks exist in a single motif they are often close together in the 3-D structure. Furthermore, occasionally these motif blocks were found to be split by introns when the correlation with exon structures was examined.

Amino Acid Sequence↗
PubMed1991

Myxoid leiomyosarcoma of the kidney accompanying ipsilateral ureteral transitional cell carcinoma. A case report with cytological, immunohistochemical and ultrastructural study.

The authors report a case of myxoid leiomyosarcoma of the kidney accompanying ipsilateral ureteral transitional cell carcinoma. A 74-year-old male patient complained of turbid urine and macroscopic hematuria. He also complained of left back pain, appetite loss and weight loss. Computed tomography revealed a large mass in the left retroperitoneum. Urine cytology disclosed two types of malignant cells, atypical spindle-shaped cells and transitional cell carcinoma. Left total nephro-ureterectomy was performed. The left kidney was occupied by a 6 x 4 x 4 cm, multinodular and mucinous tumor. A transitional cell carcinoma of the left ureter was also observed. The renal tumor was composed of atypical spindle-shaped cells in the mucinous stroma, which showed positive immunoreactivity for anti-muscle-specific actin and anti-desmin antibodies. The ultrastructural examination revealed intracytoplasmic microfilaments with dense bodies, pinocytotic vesicles and junctional structure. These findings were suggestive of the myogenic feature of the case. Urine cytology revealed a number of sarcoma cells in this case since the sarcoma cells markedly invaded the renal pelvis and were apt to separate individually in myxoid stroma. Simultaneous and ipsilateral double malignancies of the renal sarcoma and ureteral transitional cell carcinoma have never been reported in the literature.

Aged↗
PubMed1988

A model for rouleaux pattern formation of red blood cells.

Human red blood cells (RBCs) in a solution form rouleaux patterns under various conditions. The degree of rouleaux formation depends on, for example, the concentration and molecular weight of added large molecules. We present a two-dimensional discrete cellular space model in which an RBC is represented by a rectangle and differential adhesion is assumed among the longer (a-site), the shorter (b-site) sides of the rectangle and the solvent. The total sum of the adhesion energy is assumed to guide the step-by-step change of the model cell configuration and also define absolutely stable patterns. We compare the set of absolutely stable patterns and cell aggregate patterns for both actual and computer-simulated cases to obtain the basic validity of our framework. Then we proceed to assess the effects of added high polymers to the adhesion parameters. We first note that under suitable conditions, decrease in a-site-solvent affinity is necessary to have complex patterns rather than increase of a-a affinity. The hypothesis that addition of high polymers reduce the a-site-solvent affinity is concomitant with a newly proposed osmotic stress theory. The parameter fitting results for the experimental phase change curves can also be interpreted as supporting more the new theory than existing traditional explanations.

Cell Adhesion↗