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Biomedical subjects

T Kawabata

Publications and source records attributed to T Kawabata.

At least 37 records · Page 2Linked to original sources
PubMed2000

Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches.

Among the total of 274 orfs within bacteriophage T4, only half have been reasonably well characterized, and the functions of the rest have remained obscure. In order to predict the molecular functions of the orfs, a position-specific iterated (PSI)-BLAST search of bacteriophage T4 against the sequence database of known 3D structures was carried out. PSI-BLAST is one of the most powerful iterative sequence search methods using multiple sequence alignment, with the ability to detect many more proteins with distant homology than standard pairwise methods. The 3D structures of proteins are considered to be better preserved than the sequences, and the detected distantly homologous proteins are likely to possess highly similar 3D structures. Thirteen orfs of phage T4, whose homologues were not detected by standard pairwise methods, were found to have significantly homologous counterparts by this method. The plausibility of the results was confirmed by checking whether important residues at substrate/ligand-binding sites were conserved. Among them, two orfs, vs.1 and e.1, which are similar to Escherichia coli lytic enzyme and MutT protein, respectively, had not been studied previously. Also, gp rIIA, a rapid lysis protein, whose gene structure had been intensively studied during the development of molecular biology in the 1950s and yet whose molecular function remains unknown, has an N-terminal domain that is significantly similar to the N-terminal region of the heat shock protein Hsp90.

Amino Acid Sequence↗
PubMed2000

Memory of chirality in diastereoselective alpha-alkylation of isoleucine and allo-isoleucine derivatives.

[reaction: see text] alpha-Methylation of 3 gave 5 as a major product whereas 4 gave 6 predominantly, although both 3 and 4 have an (S)-chiral center at C(3). This indicates that chirality at C(2) in 3 and 4 was memorized in the corresponding intermediate enolates and the induced chirality made a major contribution in the stereochemical course of the reaction, while chirality at the adjacent chiral center C(3) had little effect.

Alkylation↗
PubMed2000

Gamow-teller strengths of the inverse beta transition 176Yb-->176Lu for spectroscopy of proton-proton and other sub-MeV solar neutrinos

Discrete Gamow-Teller (GT) transitions 176Yb-->176Lu at low excitation energies have been measured via the ( 3He,t) reaction at 450 MeV and at 0 degrees. For 176Yb, two low-lying states are observed, setting low thresholds Q(nu) = 301 and 445 keV for neutrino ( nu) capture. Capture rates estimated from the measured GT strengths, the simple two-state excitation structure, and the low Q(nu) in Yb-Lu indicate that Yb-based nu detectors are well suited for a direct measurement of the sub-MeV solar electron-neutrino ( nu(e)) spectrum including pp neutrinos.

Journal Article↗
PubMed2000

Protein structure comparison using the markov transition model of evolution.

A number of automatic protein structure comparison methods have been proposed; however, their similarity score functions are often decided by the researchers' intuition and trial-and-error, and not by theoretical background. We propose a novel theory to evaluate protein structure similarity, which is based on the Markov transition model of evolution. Our similarity score between structures i and j is defined as log P(j --> i)/P(i), where P(j --> i) is the probability that structure j changes to structure i during the evolutionary process, and P(i) is the probability that structure i appears by chance. This is a reasonable definition of structure similarity, especially for finding evolutionarily related (homologous) similarity. The probability P(j --> i) is estimated by the Markov transition model, which is similar to the Dayhoff's substitution model between amino acids. To estimate the parameters of the model, homologous protein structure pairs are collected using sequence similarity, and the numbers of structure transitions within the pairs are counted. Next these numbers are transformed to a transition probability matrix of the Markov transition. Transition probabilities for longer time are obtained by multiplying the probability matrix by itself several times. In this study, we generated three types of structure similarity scores: an environment score, a residue-residue distance score, and a secondary structure elements (SSE) score. Using these scores, we developed the structure comparison program, Matras (MArkovian TRAnsition of protein Structure). It employs a hierarchical alignment algorithm, in which a rough alignment is first obtained by SSEs, and then is improved with more detailed functions. We attempted an all-versus-all comparison of the SCOP database, and evaluated its ability to recognize a superfamily relationship, which was manually assigned to be homologous in the SCOP database. A comparison with the FSSP database shows that our program can recognize more homologous similarity than FSSP. We also discuss the reliability of our method, by studying the disagreement between structural classifications by Matras and SCOP.

Databases, Factual↗
PubMed2000

Videothoracoscopic surgery for thoracic neurogenic tumors: a 7-year experience.

While videothoracoscopic surgery has rapidly become accepted as an effective method of performing minimally invasive surgery, the advantages and feasibility of using this surgical technique for the treatment of neurogenic tumors of the thorax are not yet well defined. Between August 1992 and May 1999, 15 solitary thoracic neurogenic tumors were surgically excised using videothoracoscopic surgery in our hospital. The patients comprised six women and nine men, with a mean age of 38.1 years. The mean tumor size was 3.5 cm, with a range of 1.5-6.5 cm and included 12 schwannomas, 2 ganglioneuromas, and 1 neurofibroma. Among the 15 patients, 4 were treated using videothoracoscopic surgery plus minithoracotomy. The only complication associated with videothoracoscopic surgery was hoarseness which developed in one patient. Our experience indicates that videothoracoscopic surgery is a useful alternative to facilitate the excision of small thoracic neurogenic tumors.

Adolescent↗
PubMed2000

Endobronchial metastasis from renal cell carcinoma: report of a case.

A case of endobronchial metastasis from renal cell carcinoma developing 5 years after a right nephrectomy in a 63-year-old man is reported. Bronchoscopic examination performed after the patient presented with hemoptysis showed a polypoid tumor obstructing the entrance to the left upper bronchus. A snare was introduced through a bronchofiberscope to remove the endobronchial tumor, following which his atelectasis improved remarkably and his hemoptysis resolved. No side effects were observed. Electrosurgical snaring proved useful as palliative treatment to relieve bronchial obstruction due to an endobronchial metastasis in this patient.

Bronchial Neoplasms↗
PubMed2000

Lysosomal cysteine protease, cathepsin B, is targeted to lysosomes by the mannose 6-phosphate-independent pathway in rat hepatocytes: site-specific phosphorylation in oligosaccharides of the proregion.

Cathepsin B, a lysosomal cysteine protease, is synthesized as a glycoprotein with two N-linked oligosaccharide chains, one of which is in the propeptide region while the other is in the mature region. When cultured rat hepatocytes were labeled with [(32)P]phosphate, (32)P-labeled cathepsin B was immunoprecipitated only in the proform from cell lysates and medium. Either Endo H or alkaline phosphatase treatment of (32)P-labeled procathepsin B demonstrated the acquisition of a mannose 6-phosphate (Man 6-P) residue on high mannose type oligosaccharides. To identify the site of phosphorylation, immunoisolated (35)S- or (32)P-labeled procathepsin B was incubated with purified lysosomal cathepsin D, since cathepsin D cleaves 48 amino acid residues from the N-terminus of procathepsin B, in which one N-linked oligosaccharide chain was also included [Kawabata, T. et al. (1993) J. Biochem. 113, 389-394]. Treatment of intracellular (35)S-labeled procathepsin B with a molecular mass of 39-kDa with cathepsin D resulted in the production of the 31-kDa intermediate form, but the (32)P-label incorporated into procathepsin B disappeared after treatment with cathepsin D. These results indicate that the phosphorylation of procathepsin B is restricted to an oligosaccharide chain present in the propeptide region. Interestingly, cathepsin B sorting to lysosomes was not inhibited by NH(4)Cl treatment and about 90% of the intracellular procathepsin B initially phosphorylated was secreted into the medium without being dephosphorylated intracellularly, and did not bind significantly to cation-independent-Man 6-P receptor, suggesting the failure of Man 6-P-dependent transport of procathepsin B to lysosomes. Additionally, about 50% of the newly synthesized (35)S-labeled cathepsin B was retained in the cells in mature forms consisting of a 29-kDa single chain form and a 24-kDa two chain form, while part of the procathepsin B was associated with membranes in a Man 6-P-independent manner. Taken together, these results show that in rat hepatocytes, cathepsin B is targeted to lysosomes by an alternative mechanism(s) other than the Man 6-P-dependent pathway.

Ammonium Chloride↗
PubMed2000

Vasodilator responses of coronary conduit and resistance arteries to continuous nitroglycerin infusion in humans: a Doppler guide wire study.

To examine the responses of coronary conduit and resistance arteries to the continuous i.v. administration of nitroglycerin in 15 patients with atypical chest pain, we measured coronary blood flow velocity in the left anterior descending coronary artery using a Doppler guide wire and the lumen diameter and cross-sectional area by quantitative coronary angiography. Systolic flow, diastolic flow, total coronary flow, and coronary vascular resistance were calculated. Stepwise increases in dose of nitroglycerin resulted in significant dose-dependent decrease in mean aortic pressure (p < 0.01) and increase in lumen diameter (p < 0.05). After nitroglycerin administration of 0.5 microg/kg/min, systolic flow decreased significantly by 89.9+/-15.7% (p < 0.01), and diastolic flow increased significantly by 74.2+/-37.1% (p < 0.05). Total coronary flow did not change significantly with the various doses of nitroglycerin. However, coronary vascular resistance decreased significantly at concentrations greater than 0.5 microg/kg/min nitroglycerin. Continuous nitroglycerin infusion did not reduce either diastolic or total coronary blood flow despite a significant reduction in coronary perfusion pressure. These results indicate that subendocardial blood flow might be maintained during continuous i.v. infusion of nitroglycerin within the clinical dose range.

Angiography↗
PubMed2000

Generalized algorithm for the unified analysis and simultaneous evaluation of geometrical spin-redirection phase and Pancharatnam phase in a complex interferometric system.

To permit unified analysis and simultaneous evaluation of geometrical spin-redirection phase and Pancharatnam phase, the conventional 2 x 2 Jones matrix calculation is generalized and a new scheme of 3 x 3 matrix calculation is proposed. With the proposed algorithm one can trace the polarization state changes and the geometric phase shifts caused by beam propagation along an arbitrary optical path that involves both reflection and refraction at surfaces with Fresnel shift and birefringence.

Algorithms↗
PubMed2000

[Snacking behavior among elementary and junior high school students and its relationship to stress-coping].

The aim of the present study was to investigate current problems of snacking behavior and their relationship to stress coping among 1,486 fourth through ninth grade students from 10 elementary schools and six junior high schools. An anonymous self-completed questionnaire was utilized which included items about 1) selection of snack foods, which were classified into healthy, popular, complementary and western-style snacks, 2) problems of snacking behavior, which included external and emotional eating scores, and 3) stress coping scale. The stress coping scale contained two sub-scales; problem-focused and emotion-focused coping. The results were as follows: 1) Students who frequently went without breakfast did not select healthy foods, i.e., fruits and dairy products, but popular snacks, i.e., potato chips, pop corn and sweet beverage. 2) Both external and emotional eating scores increased by age in girls but was not apparent in boys. 3) Students who preferred either western-style or popular snacks showed higher score of external and emotional eating. 4) The score of problem-focused coping was positively correlated with preference for health snacks, but emotion-focused coping was positively correlated with external and emotional eating scores. The close relationship between snack food selection and problematic aspects of eating behavior suggests that modification of eating behavior is necessary to develop healthy snack habits in early adolescents. Also, it is interesting that snacking behavior is closely related to stress coping, which suggested the behavioral intervention for healthy eating habit should be included in development of stress-coping skills against various kinds of demands in life.

Adaptation, Psychological↗
PubMed1999

Increased uncoupling protein2 mRNA in white adipose tissue, and decrease in leptin, visceral fat, blood glucose, and cholesterol in KK-Ay mice fed with eicosapentaenoic and docosahexaenoic acids in addition to linolenic acid.

The effects of n-3 polyunsaturated fatty acids (n-3PUFA) on obesity and diabetes were examined using KK-Ay mice fed with perilla oil (P), soybean oil (S), or lard (L), and those containing 30% fish oil (PF, SF, or LF), containing eicosapentaenoic acid (EPA = 9.9%) and docosahexaenoic acid (DHA = 18.0%). Perilla oil contained the largest proportion of linolenic acid (LNA = 61.9%). Computerized tomography (CT) scans showed narrower areas of visceral fat in the abdominal cross sections of groups given fish oil (PF, SF, and LF) and lower leptin levels (p < 0.05-p < 0.001) compared with controls (P, S, and L), without significant changes in energy intake and body weight. The highest plasma n-3PUFA content (21.31 +/- 0.35%) was attained with PF. This group contained 2.6-fold more plasma DHA (p < 0.001), and expressed 2.7-fold more UCP2 mRNA in white adipose tissue (p < 0.01) than in the P group. The epididymal fat pad (p < 0.05) weighed less, and levels of blood glucose (p < 0.05) and total cholesterol (p < 0.01) were reduced in PF compared with P.

Adipose Tissue↗
PubMed1999

The Protein Mutant Database.

Currently the protein mutant database (PMD) contains over 81 000 mutants, including artificial as well as natural mutants of various proteins extracted from about 10 000 articles. We recently developed a powerful viewing and retrieving system (http://pmd.ddbj.nig.ac.jp), which is integrated with the sequence and tertiary structure databases. The system has the following features: (i) mutated sequences are displayed after being automatically generated from the information described in the entry together with the sequence data of wild-type proteins integrated. This is a convenient feature because it allows one to see the position of altered amino acids (shown in a different color) in the entire sequence of a wild-type protein; (ii) for those proteins whose 3D structures have been experimentally determined, a 3D structure is displayed to show mutation sites in a different color; (iii) a sequence homology search against PMD can be carried out with any query sequence; (iv) a summary of mutations of homologous sequences can be displayed, which shows all the mutations at a certain site of a protein, recorded throughout the PMD.

Amino Acid Sequence↗
PubMed1999

Cooperative approach for the protein fold recognition.

We, four independent predictors, organized a team and tackled blind protein structure predictions using fold recognition methods. We tried to assign the homologous or analogous folds in the protein structure database for a number of target sequences that showed no apparent sequence homology to the proteins of known folds. After primary analyses by conventional softwares, these sequences were threaded through the structural library using three different programs developed by ourselves, which employed different compatibility functions. Collecting the results of our individual analyses, and the available biological knowledge about the target, we held meetings and discussed all plausible structures for the target. For 25 target sequences, we submitted 56 models including NONE: This was the first time the fold was determined. At the time of the meeting (CASP3), 19 protein structures (21 domains) categorized as the threading targets were available. We succeeded in predicting eight out of 18 targets (20 domains) that we submitted; however, alignment accuracies were not satisfactory for some of the models. We often obtained correct answers even if some of us missed the right prediction; therefore it would appear that our threaders compensated each other. When all the information is managed effectively, the prediction gains more accuracy.

Algorithms↗
PubMed1999

Nasal and nasal-type natural killer/T-cell lymphoma.

Nasal and nasal-type natural killer (NK)/T-cell lymphomas follow an aggressive course and have a poor prognosis. Recent pathologic studies suggest that the disease is a malignant proliferation of NK cells, which often express CD56. An association with the Epstein-Barr virus has also been reported. Skin involvement occurred in each of the 3 patients studied. Radiation therapy provided some benefit to the patients in the early stages. Conventional chemotherapies were not effective. To overcome this multiple-drug resistance of the tumor cells, cyclosporine and high-dose chemotherapy was combined with peripheral-blood stem-cell transplantation. The average life span from the onset of the disease for our patients was 9.6 months. Further improvement in the management of nasal and nasal-type NK/T-cell lymphomas is necessary.

Adult↗