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Biomedical subjects

Takashi Abe

Publications and source records attributed to Takashi Abe.

At least 19 recordsLinked to original sources
PubMed2006

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

Bacteria↗
PubMed2006

Electrodeposition of anchored polypyrrole film on microelectrodes and stimulation of cultured cardiac myocytes.

The electrically conducting polymer polypyrrole (PPy) was electrochemically deposited onto Pt microelectrodes on a polyimide (PI) substrate. Pre-modification of the PI surface with a self-assembled monolayer of octadecyltrichlorosilane-induced anisotropic lateral growth of PPy along the PI surface and enhanced adhesive strength of the PPy film. The lateral growth of PPy film around the electrode anchored the whole film to the substrate. External stimulation of cultured cardiac myocytes was carried out using the PPy-coated microelectrode. The myocytes on the microelectrode substrate were electrically conjugated to form a sheet, and showed synchronized beating upon stimulation. The threshold charge for effective stimulation of a 0.8 cm(2) sheet of myocytes was around 0.2 microC, roughly corresponding to a membrane depolarization of 250 mV.

Animals↗
PubMed2006

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.

Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

Databases, Nucleic Acid↗
PubMed2006

DDBJ working on evaluation and classification of bacterial genes in INSDC.

DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) newly collected and released 12,927,184 entries or 13,787,688,598 bases in the period from July 2005 to June 2006. The released data contain honeybee expressed sequence tags (ESTs), re-examined and re-annotated complete genome data of Escherichia coli K-12 W3110, medaka WGS and human MGA. We also systematically evaluated and classified the genes in the complete bacterial genomes submitted to the International Nucleotide Sequence Database Collaboration (INSDC, http://insdc.org) that is composed of DDBJ, EMBL Bank and GenBank. The examination and classification selected 557,000 genes as reliable ones among all the bacterial genes predicted by us.

Animals↗
PubMed2006

Development of nonexercise prediction models of maximal oxygen uptake in healthy Japanese young men.

The present study developed nonexercise models for predicting maximal oxygen uptake (VO2max) using skeletal muscle (SM) mass and cardiac dimensions and to investigate the validity of these equations in healthy Japanese young men. Sixty healthy Japanese men were randomly separated into two groups: 40 in the development group and 20 in the validation group. VO2max during treadmill running was measured using an automated breath-by-breath mass spectrometry system. Left ventricular internal dimensions at end-diastole (LVIDD) and at end-systole (LVIDS) were measured using M-mode ultrasound with a 2.5 MHz transducer. Stroke volume (SV) was calculated based on the Pombo rule. SM mass was predicted by B-mode ultrasound muscle thickness. Correlations were observed between VO2max and predicted thigh (r = 0.74, P < 0.001) and lower leg SM mass (r = 0.55, P < 0.001). Furthermore, there were correlations between VO2max and LVIDD (r = 0.74, P < 0.001) and SV (r = 0.72, P < 0.001). Stepwise regression analysis was applied to thigh SM mass and SV for prediction of VO2max in the development group, and these parameters were closely correlated with absolute measured VO2max (R2 = 0.72, P < 0.001) by multiple regression analysis. When the VO2max prediction equations were applied to the validation group, significant correlations were also observed between the measured and predicted VO2max (R2 = 0.83, P < 0.001). These results suggested that nonexercise prediction of VO2max using thigh SM mass and cardiac dimension is a valid method to predict VO2max in young Japanese adults.

Adult↗
PubMed2006

Inhibition of HIV-1 replication by vesicular stomatitis virus envelope glycoprotein pseudotyped baculovirus vector-transduced ribozyme in mammalian cells.

The baculovirus has recently emerged as a promising vector for in vivo gene therapy. To investigate its potential as a delivery vector for an anti-virus ribozyme targeting HIV-1, we constructed recombinant baculovirus vectors bearing a ribozyme-synthesizing cassette driven by the tRNA(i)(Met) promoter with enhanced transduction efficiency by displaying vesicular stomatitis virus glycoprotein (VSV-G) on the viral envelope. Transduction of HeLa CD4(+) cells with a recombinant baculovirus delivering the HIV-1 U5 gene-specific ribozyme dramatically suppressed HIV-1 expression in this cell line. The VSV-G pseudotyped baculovirus vector-transduced ribozyme potently inhibited HIV-1 replication compared to a recombinant baculovirus vector-transduced ribozyme lacking VSV-G. The use of a baculovirus vector might be beneficial for application in gene therapy.

Baculoviridae↗
PubMed2006

G-InforBIO: integrated system for microbial genomics.

BACKGROUND: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs. RESULTS: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses. CONCLUSION: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

Algorithms↗
PubMed2006

Synthesis, structure, and bonding of stable dialkylsilaketenimines.

Stable (N-aryl)- and (N-alkyl)dialkylsilaketenimines R2SiCNR' [R = 1,1,4,4-tetrakis(trimethylsilyl)butane-1,4-diyl, R' = 2,6-diisopropylphenyl (2a) and 1-adamantyl (2b)] were synthesized as blue and red crystals by the reactions of isolable dialkylsilylene 3 with 2,6-diisopropylphenyl isocyanide and 1-adamantyl isocyanide. X-ray single-crystal analysis disclosed that molecular structures of 2a and 2b were close to each other and were characterized to be allenic rather than zwitterionic or a silylene-isocyanide complex. The bonding characteristics of silaketenimines are found to be affected strongly by the substituents on silicon and nitrogen atoms. Remarkable red-shift of the pi(Si=C) --> pi*(C=N) band of 2a [lambdamax/nm (epsilon) 647(156)] compared with that of 2b [465 nm (109)] is ascribed to lowering of the pi*(C=N) orbital level due to significant interaction between pi*(C=N) and pi*(N-aryl) orbitals.

Journal Article↗
PubMed2006

Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.

A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets or sequence alignments. We first constructed SOMs for tetranucleotide frequencies in 210,000 5 kb sequence fragments obtained from 1502 prokaryotes for which at least 10 kb of genomic sequence has been deposited in public DNA databases. The sequences could be classified primarily according to phylogenetic groups without information regarding the species. We used the SOM method to classify sequence fragments derived from environmental samples of the Sargasso Sea and of an acidophilic biofilm growing in acid mine drainage. Phylogenetic diversity of the environmental sequences was effectively visualized on a single map. Sequences that were derived from a single genome but cloned independently could be reassociated in silico. G + C% has been used for a long period as a fundamental parameter for phylogenetic classification of microbes, but the G + C% is apparently too simple a parameter to differentiate a wide variety of known species. Oligonucleotide frequency can be used to distinguish the species because oligonucleotide frequencies vary significantly among their genomes.

Algorithms↗
PubMed2006

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

Congresses as Topic↗
PubMed2006

Smoking, drinking, sleeping habits, and other lifestyle factors and the risk of systemic lupus erythematosus in Japanese females: findings from the KYSS study.

Many risk factors have been proposed for systemic lupus erythematosus (SLE). However, there is little information about the relationship between lifestyles and SLE in Japan. Two case control studies were conducted in Kyushu, southern Japan, and in Hokkaido, northern Japan, to examine the relationship between lifestyles and development of SLE in females. The participants were 78 patients and 329 controls in Kyushu and 35 patients and 188 controls in Hokkaido. Smoking was associated with an increased risk of SLE after adjusting for age in both regions. However, in Hokkaido, this association between smoking and SLE did not reach statistical significance after adjusting for alcohol drinking. The present study suggests that smoking may increase the risk of SLE among Japanese females.

Adolescent↗
PubMed2006

[A case of primary pulmonary MALT lymphoma with diffuse micronodules and anemia].

A 52-year-old woman presented with low grade fever and fatigue. She had diffuse micronodules in both lung fields on chest X-ray. Chest CT showed diffuse multiple small nodules. Laboratory examination revealed high values for C-reactive protein, together with anemia and polyclonal hyper-immunoglobulinemia and an elevated interleukin-6 level. Although we suspected multicentric Castleman's disease, thoracoscopic lung biopsy revealed primary pulmonary MALT lymphoma by immunohistochemical analysis of tissue specimens. After COP and rituximab therapy, partial remission was obtained.

Anemia↗
PubMed2005

Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes.

Novel tools are needed for comprehensive comparisons of interspecies characteristics of massive amounts of genomic sequences currently available. An unsupervised neural network algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM, on the basis of batch-learning SOM, for genome informatics making the learning process and resulting map independent of the order of data input. We generated the SOMs for tri- and tetranucleotide frequencies in 10- and 100-kb sequence fragments from 38 eukaryotes for which almost complete genome sequences are available. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in the genomic sequences, permitting species-specific classification of the sequences without any information regarding the species. We also generated the SOM for tetranucleotide frequencies in 1-kb sequence fragments from the human genome and found sequences for four functional categories (5' and 3' UTRs, CDSs and introns) were classified primarily according to the categories. Because the classification and visualization power is very high, SOM is an efficient and powerful tool for extracting a wide range of genome information.

3' Untranslated Regions↗
PubMed2005

Muscle size and strength are increased following walk training with restricted venous blood flow from the leg muscle, Kaatsu-walk training.

Previous studies have shown that low-intensity resistance training with restricted muscular venous blood flow (Kaatsu) causes muscle hypertrophy and strength gain. To investigate the effects of daily physical activity combined with Kaatsu, we examined the acute and chronic effects of walk training with and without Kaatsu on MRI-measured muscle size and maximum dynamic (one repetition maximum) and isometric strength, along with blood hormonal parameters. Nine men performed Kaatsu-walk training, and nine men performed walk training alone (control-walk). Training was conducted two times a day, 6 days/wk, for 3 wk using five sets of 2-min bouts (treadmill speed at 50 m/min), with a 1-min rest between bouts. Mean oxygen uptake during Kaatsu-walk and control-walk exercise was 19.5 (SD 3.6) and 17.2 % (SD 3.1) of treadmill-determined maximum oxygen uptake, respectively. Serum growth hormone was elevated (P < 0.01) after acute Kaatsu-walk exercise but not in control-walk exercise. MRI-measured thigh muscle cross-sectional area and muscle volume increased by 4-7%, and one repetition maximum and maximum isometric strength increased by 8-10% in the Kaatsu-walk group. There was no change in muscle size and dynamic and isometric strength in the control-walk group. Indicators of muscle damage (creatine kinase and myoglobin) and resting anabolic hormones did not change in both groups. The results suggest that the combination of leg muscle blood flow restriction with slow-walk training induces muscle hypertrophy and strength gain, despite the minimal level of exercise intensity. Kaatsu-walk training may be a potentially useful method for promoting muscle hypertrophy, covering a wide range of the population, including the frail and elderly.

Adult↗
PubMed2005

Prediction and validation of total and regional skeletal muscle mass by ultrasound in Japanese adults.

The present study was performed to develop regression-based prediction equations for skeletal muscle (SM) mass by ultrasound and to investigate the validity of these equations in Japanese adults. Seventy-two Japanese men (n=38) and women (n=34) aged 18-61 years participated in this study and were randomly separated into two groups: the model development group (n=48) and the validation group (n=24). The total and regional SM mass were measured using magnetic resonance imaging (MRI) 1.5 T-scanners with spin-echo sequence. Contiguous transverse images (about 150 slices) with a slice thickness of 1 cm were obtained from the first cervical vertebra to the ankle joints. The volume of SM was calculated from the summation of digitized cross-sectional area. The SM volume was converted into mass units (kg) by an assumed SM density of 1.04 kg l(-1). The muscle thickness (MTH) was measured by B-mode ultrasound (5 MHz scanning head) at nine sites on the anatomical SM belly. Strong correlations were observed between the site-matched SM mass (total, arm, trunk body, thigh, and lower leg) by MRI measurement and the MTH x height (in m) in the model development group (r=0.83-0.96 in men, r=0.53-0.91 in women, P<0.05). When the SM mass prediction equations were applied to the validation group, significant correlations were also observed between the MRI-measured and predicted SM mass (P<0.05). The predicted total SM mass for the validation group was 19.6 (6.5) kg and was not significantly different from the MRI-measured SM mass of 20.2 (6.5) kg. Bland-Altman analysis did not indicate a bias in prediction of the total SM mass for the validation group (r=0.00, NS). These results suggested that ultrasound-derived prediction equations are a valid method to predict SM mass and an alternative to MRI measurement in healthy Japanese adults.

Adolescent↗
PubMed2005

A missing allene of heavy Group 14 elements: 2-germadisilaallene.

The first stable 2-germadisilaallene was synthesized by the reduction of a 2 ratio 1 mixture of a stable dialkylsilylene and dichlorogermylene-dioxane complex with KC8; the 2-germadisilaallene showed dynamic disorder similar to the corresponding trisilaallene in the solid state.

Alkadienes↗
PubMed2005

Shape effect of hot droplets on fragmentation.

Fragmentation dynamics and the shape effect of initial hot droplets on it are investigated by using a classical molecular dynamics method. As the initial conditions for the fragmentation simulation, small hot droplets in the supercritical phase, with the number of particles N less than approximately 10(3), are considered. It is revealed that, in the process of the fragmentation, the largest cluster approaches a certain quasistable state corresponding to the so-called triple point. It is also revealed that the initial shape of the hot droplets has a significant effect on the cluster distribution generated after fragmentation; i.e., the more prolate the initial shape, the more markedly the size of the largest cluster decreases and the number of small clusters increases. The shape effect diminishes with an increasing number of particles in the initial hot droplet and could be negligible for large hot droplets, of the number of particles N more than approximately 10(3).

Journal Article↗