Biomedical subjects

M Suwa

Publications and source records attributed to M Suwa.

At least 37 records · Page 2Linked to original sources

PubMed2000

Identification of two polyketide synthase gene clusters on the linear plasmid pSLA2-L in Streptomyces rochei.

The 200kb linear plasmid pSLA2-L was suggested to be involved in the production of two macrolide antibiotics, lankamycin (Lm) and lankacidin (Lc), in Streptomyces rochei 7434AN4. Hybridization experiments with the polyketide synthase (PKS) genes for erythromycin and actinorhodin identified two eryAI-homologous regions and an actI-homologous region on pSLA2-L. The nucleotide sequence of a 3.6kb SacI fragment carrying one of the eryAI-homologs revealed that it codes for part of a large protein with four domains for ketoreductase, acyl carrier protein, ketosynthase, and acyltransferase. Gene disruption confirmed that the two eryAI-homologs are parts of a large type-I PKS gene cluster for Lm. A 4.8kb DNA carrying the actI-homologous region contains four open reading frames (ORF1-ORF4) as well as an additional ORF, i.e. ORF5, which might code for a thioesterase. Deletion of the ORF2-ORF4 region showed that it is not involved in the synthesis of Lm or Lc. Thus, it was confirmed that pSLA2-L contains two PKS gene clusters for Lm and an unknown type-II polyketide.

Amino Acid Sequence↗

PubMed2000

Myocardial integrated ultrasonic backscatter in patients with dilated cardiomyopathy: prediction of response to beta-blocker therapy.

BACKGROUND: Myocardial integrated backscatter (IB) imaging has been reported to be useful for ultrasonic tissue characterization and delineation of myocardial viability or fibrosis. beta-Blocker therapy has beneficial effects for patients with dilated cardiomyopathy (DCM), but there are no clear findings that indicate which patients with DCM will respond to this therapy. This study was performed to evaluate whether myocardial IB analysis can predict the response to beta-blocker therapy. METHODS AND RESULTS: We prospectively performed echocardiographic examination with IB analysis in 29 patients with DCM (20 men, 9 women) before starting bisoprolol therapy and in 15 normal subjects. Standard echocardiographic examination and IB analysis in the left ventricular wall in the 2-dimensional short-axis view were performed and the magnitude of cyclic variation (CV) of IB and calibrated myocardial IB intensity (subtracted pericardial) were obtained from the interventricular septum and the left ventricular posterior wall. Sixteen patients responded to bisoprolol therapy and 13 did not respond after 12 months of full-dose therapy. Calibrated myocardial IB intensity was lower in responders relative to nonresponders in both the interventricular septum (responders, -20.1 +/- 3.6 dB vs nonresponders, -9.8 +/- 5.1 dB, P <.0001; controls, -20.1 +/- 4.4 dB) and posterior wall (responders, -20.6 +/- 3.6 dB vs nonresponders, -14.6 +/- 4.2 dB, P =.0002; controls, -22.7 +/- 3.3 dB). Also, the lower the myocardial intensity in the interventricular septum or posterior wall, the better left ventricular systolic function improved after beta-blocker therapy. However, CV was lower in both DCM groups than in the controls, and CV in the interventricular septum was lower in nonresponders than in responders (responders, 4.0 +/- 4.1 dB vs nonresponders, -0.8 +/- 6. 1 dB, P <.02; controls, 8.3 +/- 2.4 dB). In addition, CV in the posterior wall showed no difference between the 2 DCM groups (responders, 5.6 +/- 1.3 dB vs nonresponders, 5.1 +/- 3.5 dB, P = not significant; controls, 9.6 +/- 2.5 dB). Also, the percent fibrosis on right ventricular endomyocardial biopsy specimens showed no distinctions between these 2 groups (responders, 25.1% +/- 16.1% vs nonresponders, 24.9% +/- 15.0%, P = not significant). CONCLUSIONS: These findings suggest that left ventricular myocardial IB data, especially IB intensity, provide useful information for predicting the response to beta-blocker therapy in patients with DCM. However, right ventricular endomyocardial biopsy findings do not appear to contribute to discriminating between the 2 groups.

Adrenergic beta-Antagonists↗

PubMed2000

Prediction of mean pulmonary wedge pressure using doppler pulmonary venous flow variables in hypertrophic cardiomyopathy.

We examined whether pulmonary venous flow variables, assessed by transthoracic Doppler echocardiography, could predict mean pulmonary wedge pressure in hypertrophic cardiomyopathy. Forty-four patients with no left ventricular systolic dysfunction (left ventricular fractional shortening > or =25%) were studied. Forty patients with systolic dysfunction (dilated cardiomyopathy group) served as control. Mitral and pulmonary venous flow velocity curves were recorded with the pulsed-Doppler method and were related to mean pulmonary wedge pressure obtained by right heart catheterization. In hypertrophic cardiomyopathy group, the systolic (r=-0.15, P=0.335) and diastolic (r=0.35, P=0.022) forward flow velocity were poorly related to mean pulmonary wedge pressure, whereas the velocity of atrial reversal (r=0.68, P<0.001) correlated well with mean pulmonary wedge pressure. In dilated cardiomyopathy group, the systolic (r=-0.51, P=0.001) and diastolic (r=0.60, P<0.001) forward flow velocity were strongly related to mean pulmonary wedge pressure. With the cut-off value set at the velocity of atrial reversal >30 cm/s in hypertrophic cardiomyopathy group, the sensitivity for predicting mean pulmonary wedge pressure >15 mmHg was 79% and the specificity was 73%. In conclusion, the atrial component of the pulmonary venous flow can be used to predict mean pulmonary wedge pressure in hypertrophic cardiomyopathy.

Adult↗

PubMed2000

Using the CATH domain database to assign structures and functions to the genome sequences.

The CATH database of protein structures contains approximately 18000 domains organized according to their (C)lass, (A)rchitecture, (T)opology and (H)omologous superfamily. Relationships between evolutionary related structures (homologues) within the database have been used to test the sensitivity of various sequence search methods in order to identify relatives in Genbank and other sequence databases. Subsequent application of the most sensitive and efficient algorithms, gapped blast and the profile based method, Position Specific Iterated Basic Local Alignment Tool (PSI-BLAST), could be used to assign structural data to between 22 and 36 % of microbial genomes in order to improve functional annotation and enhance understanding of biological mechanism. However, on a cautionary note, an analysis of functional conservation within fold groups and homologous superfamilies in the CATH database, revealed that whilst function was conserved in nearly 55% of enzyme families, function had diverged considerably, in some highly populated families. In these families, functional properties should be inherited far more cautiously and the probable effects of substitutions in key functional residues carefully assessed.

Algorithms↗

PubMed2000

Epidermoid cyst of the penis: a case report and review of the literature.

Penile cysts are uncommon. A case of a 7-year-old boy with an epidermoid cyst of the penis is reported. He had an asymptomatic, slowly growing soft mass in the frenulum of the penis. Excision of the mass was performed, and the diagnosis was epidermoid cyst of the penis. No recurrence has been noted within the year since excision. To our knowledge, there have been no previous reports of malignancy developing in cystic disease of the penis. In such cases, clinicians should attempt more appropriate management, involving either watchful observation or complete excision of the cyst, by considering the embryogenesis and nature of the disease.

Child↗

PubMed2000

Integrated backscatter assessment of left atrial spontaneous echo contrast in chronic nonvalvular atrial fibrillation: relation with clinical and echocardiographic parameters.

Integrated backscatter (IB) provides the quantitative assessment of left atrial spontaneous echo contrast (SEC). The IB intensity of the left atrial cavity relative to the left ventricular cavity is related to atrial thrombus in patients with atrial fibrillation (AF) or sinus rhythm. However, little is known about the relation between the quantitative SEC value of the left atrial cavity and variables implying thromboembolism in nonvalvular AF. To examine this relation, we performed transesophageal echo-cardiography with IB analysis in 65 patients with chronic nonvalvular AF. The quantitative SEC value of the left atrial cavity was defined as the difference between atrial IB intensity and ventricular IB intensity (corrected IB intensity). The corrected IB intensity was correlated with the left atrial dimension (r = 0.25, P =.049), the left atrial appendage velocity (r = -0.41, P <.001), and the duration of AF (r = 0.23, P =. 023). The corrected IB intensity was higher in patients who had a history of hypertension (3.2 +/- 2.2 dB versus 2.0 +/- 1.6 dB, P =. 018), SEC (3.9 +/- 1.9 dB versus 1.4 +/- 1.1 dB, P =.002), and left atrial thrombus (4.5 +/- 2.7 dB versus 2.2 +/- 1.7 dB, P <.001) when compared with those who did not have these abnormalities. The corrected IB intensity was significantly lower in patients with significant mitral regurgitation than in those without it (1.1 +/- 1. 2 dB versus 2.7 +/- 2.0 dB, P =.036). When the cutoff value of the corrected IB intensity was set at >/=2.0 dB, the sensitivity for left atrial thrombus was 78% and the specificity was 55%. In patients with chronic nonvalvular AF, the quantitative SEC value of the left atrial cavity depends on the duration of AF as well as the left atrial dimension and appendage velocity. Although IB may be capable of identifying patients with higher risk of cardiogenic embolism, a large-scale prospective study is needed to actually establish this.

Adult↗

PubMed2000

Identification of hepatic tamoxifen-DNA adducts in mice: alpha-(N(2)-deoxyguanosinyl)tamoxifen and alpha-(N(2)-deoxyguanosinyl)tamoxifen N-oxide.

Tamoxifen-DNA adducts detected in the liver of mice treated with tamoxifen have not yet been identified. In the present study a new type of tamoxifen-DNA adduct, four stereoisomers of alpha-(N:(2)-deoxyguanosinyl)tamoxifen N:-oxide 3'-monophosphate (dG(3'P)-N:(2)-TAM N:-oxide) were prepared as standard DNA adducts by reacting 2'-deoxyguanosine 3'-monophosphate with trans-alpha-acetoxytamoxifen N:-oxide in addition to four stereoisomers of alpha-(N:(2)-deoxyguano- sinyl)tamoxifen 3'-monophosphate (dG(3'P)-N:(2)-TAM) that was reported previously. Liquid chromatography-electrospray ionization-mass spectrometry of the reaction products gave the most abundant ion at m/z 731 ([M - H](-)), which corresponded to dG(3'P)-N:(2)-TAM N:-oxide. The modified products digested by alkaline phosphatase corresponded to the isomers of dG-N:(2)-TAM N:-oxide whose structures were identified previously by mass spectrometry and nuclear magnetic resonance. Using these standard markers, we analyzed the hepatic DNA adducts of female DBA/2 mice treated with tamoxifen at a dosage of 120 mg/kg/day for 7 days by (32)P-post-labeling coupled with an HPLC/radioactive detector. Mixtures of eight isomers of dG(3'P)-N:(2)-TAM and dG(3'P)-N:(2)-TAM N-oxide were separated into six peaks, since each of the cis epimers were not separated under the present HPLC conditions. Nine adducts were detected in all liver samples of mice. An epimer of trans-dG(3'P)-N:(2)-TAM was detected as the principal DNA adduct at a level of 29.0 adducts/10(8) nucleotides, which accounted for 53.3% of the total tamoxifen-DNA adducts. Lesser amounts of cis-dG(3'P)-N:(2)-TAM (2.8%) were also observed. An epimer of the trans-dG(3'P)-N:(2)-TAM N:-oxide (3.9 adducts/10(8) nucleotides) was detected as the third biggest adduct (7.2% of the total). The cis-dG(3'P)-N:(2)-TAM N:-oxide (0.4 adducts/10(8) nucleotides) accounted for 0.7% of the total. Thus, dG(3'P)-N:(2)-TAM and dG(3'P)-N:(2)-TAM N:-oxide were identified in tamoxifen-treated mouse liver.

Animals↗

PubMed2000

A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle.

We developed a method of predicting the tertiary structures of seven transmembrane helical proteins in triangle lattice models, assuming that the configuration of helices is stabilized by polar interactions. Triangle lattice models having 12 or 11 nearest neighbor pairs were used as general templates of a seven-helix system, then the orientation angles of all helices were varied at intervals of 15 degrees. The polar interaction energy for all possible positions of each helix was estimated using the calculated polar indices of transmembrane helices. An automated system was constructed and applied to bacteriorhodopsin, a typical membrane protein with seven transmembrane helices. The predicted optimal and actual structures were similar. The top 100 predicted helical configurations indicated that the helix-triangle, CFG, occurred at the highest frequency. In fact, this helix-triangle of bacteriorhodopsin forms an active proton-pumping site, suggesting that the present method can identify functionally important helices in membrane proteins. The possibility of studying the structure change of bacteriorhodopsin during the functional process by this method is discussed, and may serve to explain the experimental structures of photointermediate states.

Algorithms↗

PubMed2000

Prostaglandin E2 predominantly induces production of hepatocyte growth factor/scatter factor in human dental pulp in acute inflammation.

Hepatocyte growth factor (HGF), which is also known as the scatter factor, is a broad-spectrum and multifunctional cytokine, mediates epithelial-mesenchyme interaction, and is shown to be involved in the development and regeneration of various tissues, including tooth. Here, we report that HGF was present in adult human dental pulps, and its levels increased during acute inflammation of the tissue. Levels of HGF mRNA in dental pulps also increased with inflammation, as determined by reverse-transcription/polymerase chain-reaction. The production of HGF in fibroblasts from dental pulps in culture was dose-dependently stimulated by inflammatory cytokines such as interleukin (IL)-1alpha and tumor necrosis factor (TNF)-alpha, and by prostaglandin (PG) E2, as determined by an enzyme-linked immunosorbent assay. We also showed that indomethacin did not affect the increase in HGF production by the cells with IL-1alpha, TNF-alpha, and PGE2. The levels of HGF mRNA in the cells were simultaneously increased by these stimulants, as determined by Northern blotting. Since the production of PGs is known to increase at the beginning of inflammation, PGE2 may be involved in the regeneration of dental pulps by the induction of HGF expression after inflammation.

Adolescent↗

PubMed2000

Prognostic value of left atrial appendage function in patients with dilated cardiomyopathy.

The purpose of the present study was to determine whether parameters of left atrial appendage (LAA) function, assessed by transesophageal echocardiography (TEE), could predict the clinical outcome in patients with dilated cardiomyopathy (DCM). Fifty-five patients (20 had ischemic cardiomyopathy; mean age, 56+/-14 years) who underwent TEE to evaluate LAA function from 1992 to 1996 were studied. After a mean follow-up period of 34+/-13 months, 16 patients died; the cause was cardiac in 14 and noncardiac in 2. Patients who died of cardiac cause had a lower LAA emptying velocity than survivors (38+/-18 vs 54+/-18 cm/s, p=0.01). There were, however, no significant differences between survivors and nonsurvivors with regard to the maximal LAA area (4.3+/-1.3 vs 4.5+/-0.9 cm2, p=0.55), minimal LAA area (2.4+/-1.1 vs 2.9+1.1 cm2, p=0.13), and LAA ejection fraction (46+/-16 vs 36+/-18%, p=0.05). On the Cox proportional hazards model analysis, LAA emptying velocity <50 cm/s (chi-square 5.9, p=0.02), LAA ejection fraction <43% (chi-square 5.6, p=0.02), female gender (chi-square 5.2, p=0.02), pulmonary artery wedge pressure > or =14 mmHg (chi-square 4.8, p=0.03), E/A ratio > or =1.3 (chi-square 4.6, p=0.03), deceleration time <148 ms (chi-square 4.6, p=0.03), and cardiothoracic ratio > or =54% (chi-square 4.3, p=0.04) were significantly related to cardiac death. The stepwise multivariate analysis revealed that LAA emptying velocity (chi-square 6.1, p=0.01) and gender (chi-square 5.4, p=0.02) were the independent predictors for outcome. In conclusion, the parameters of LAA function may be useful predictors of the clinical outcome in patients with DCM.

Adult↗

PubMed2000

[Medical treatment for cardiomyopathies].

Newer drug therapy for patients with cardiomyopathies has been introduced with standard one. Beta-blocker therapy improves the prognosis in patients with ischemic and non-ischemic DCM and even in asymptomatic ones with LV dysfunction. The combined therapy of ACE inhibitor and angiotensin II receptor blocker, the intermittent intravenous infusion of inotropic agents and the supplement of phosphodiesterase inhibitor on induction of beta-blocker therapy also elucidate the effectiveness in DCM patients.

Adrenergic beta-Antagonists↗

PubMed2000

An integrated analysis and database system for full-length cDNA.

Annotation and database system of full-length cDNA sequences was developed. As the components of the system, ORF annotation system, functional annotation system based on database search results, mapping annotation system, and integrated retrieval and display system were developed. In the ORF annotation system integrated analyses using conventional tools are performed and useful retrieval interface using motif list are introduced. In the functional annotation system based on database search results, a new method that characterizes a given unknown cDNA was developed by using a profile of similarity level over words appearing in sequence database entries. In the mapping annotation system, we linked by similarity searches full-length cDNA sequences with database DNA sequences that are already mapped on chromosomes. By using these links, full-length cDNAs can be retrieved by the retrieval condition of physical mapping information. Genetic disease information mapped on the physical mapping site can also be displayed by this system. Furthermore, we constructed an integrated database system for these analyzed data, and thus enabled annotation and selection of full-length cDNAs from points of both gene function and mapping information.

Chromosome Mapping↗

PubMed1999

Influence of warfarin therapy on left atrial spontaneous echo contrast in nonvalvular atrial fibrillation.

To examine whether warfarin therapy had any influence on left atrial spontaneous echo contrast, we performed serial transesophageal echocardiography with integrated backscatter analysis in 12 patients with non-valvular atrial fibrillation. We found that the integrated backscatter intensity of the left atrial cavity did not change after 1 to 2 months of warfarin therapy, and concluded that this therapy does not influence spontaneous echo contrast.

Aged↗

PubMed1999

Tamoxifen-DNA adducts formed by alpha-acetoxytamoxifen N-oxide.

DNA adduct formation is assumed to be a major carcinogenic event, leading to the development of endometrial cancer in breast cancer patients taking tamoxifen and healthy women enrolled in a tamoxifen chemopreventive trial. To determine whether DNA adducts were formed by tamoxifen, trans- and cis-alpha-acetoxytamoxifen N-oxides were synthesized as model-activated forms via major tamoxifen metabolites, tamoxifen N-oxide and alpha-hydroxytamoxifen N-oxide. When alpha-acetoxytamoxifen N-oxide was reacted with human DNA, at least three DNA adducts were detected by (32)P-postlabeling coupled with HPLC. The total amount of DNA adducts formed by trans-alpha-hydroxytamoxifen N-oxide was 1.5-fold higher than that formed by the cis form. Both trans- and cis-alpha-acetoxytamoxifen N-oxide reacted with 2'-deoxyguanosine, resulting in the formation of three adducts (fr-1, fr-2-1, and fr-2-2). These products were studied using mass spectroscopy and proton magnetic resonance spectroscopy. fr-1 was identified as a mixture of the epimers of trans-alpha-(N(2)-deoxyguanosinyl)tamoxifen N-oxide. fr-2-1 and fr-2-2 were determined to be epimers of cis-alpha-(N(2)-deoxyguanosinyl)tamoxifen N-oxide.

Acetylation↗

PubMed1999

Muscle fibre number is a possible determinant of muscle fibre composition in rats.

The purpose of the present study was to investigate whether the muscle fibre composition is related to the number of muscle fibres. To resolve this issue, we developed fast-twitch fibre dominant rats (FFDR) by selective breeding and compared the findings to those of control rats (CR) obtained by random breeding. Percentage of type I fibres of the deep portion of gastrocnemius (DG), soleus (SOL), vastus intermedius (VI), adductor longus (AL), and biceps brachii (BB) muscles in FFDR were lower than CR. Percentage of type IIB fibres in DG, VI and AL and percentage of type IIA fibres of SOL in FFDR were higher than CR. However, fibre composition of plantaris (PLAN), extensor digitorum longus (EDL), rectus abdominis (RA), diaphragm (DIA), and palmaris longus (PL) muscles in FFDR were identical with CR. Total fibre numbers on the cross-sectional area in SOL, PLAN, EDL, AL and PL were counted. Numbers of type I fibres of all those muscles in FFDR were not different from CR. Numbers of type IIA fibres of SOL and AL and of type IIB fibres of AL in FFDR were greater than CR, but there were no significant differences in the number of type IIA or type IIB fibres of PLAN, EDL or PL between the two groups. Based on these observations, it is suggested that there are pleiotropic and muscle-specific effects on muscle fibre composition. In addition, the number of type II fibres is a possible determinant of muscle fibre composition.

Animals↗

PubMed1999

Combining sensitive database searches with multiple intermediates to detect distant homologues.

Using data from the CATH structure classification, we have assessed the blastp, fasta, smith-waterman and gapped-blast algorithms, developed a portable normalization scheme and identified safe thresholds for database searching. Of the four methods assessed, fasta, smith-waterman and gapped-blast perform similarly, whereas the sensitivity of blastp was much lower. Introduction of an intermediate sequence search substantially improved the results. When tested on a set of relationships that could not be identified by blastp, intermediate sequences were able to find double the number of relationships identified by the smith-waterman algorithm alone. However, we found that the benefit of using intermediates varied considerably between each family and depended not only on the number of available sequences, but also their diversity. In an attempt to increase sensitivity further, a multiple intermediate sequence search (MISS) procedure was developed. When assessed on 1906 cases from a wide range of homologous families that could not be detected by the previous approaches, MISS was able to identify 241 additional relationships. MISS uses the full extent of sequence diversity to detect additional relationships, but does not consider any structure-specific information. For this reason, it is more generally applicable than fold recognition and threading methods, which require a library of known structures.

Computer Simulation↗

PubMed1999

Genome analysis: Assigning protein coding regions to three-dimensional structures.

We describe the results of a procedure for maximizing the number of sequences that can be reliably linked to a protein of known three-dimensional structure. Unlike other methods, which try to increase sensitivity through the use of fold recognition software, we only use conventional sequence alignment tools, but apply them in a manner that significantly increases the number of relationships detected. We analyzed 11 genomes and found that, depending on the genome, between 23 and 32% of the ORFs had significant matches to proteins of known structure. In all cases, the aligned region consisted of either >100 residues or >50% of the smaller sequence. Slightly higher percentages could be attained if smaller motifs were also included. This is significantly higher than most previously reported methods, even those that have a fold-recognition component. We survey the biochemical and structural characteristics of the most frequently occurring proteins, and discuss the extent to which alignment methods can realistically assign function to gene products.

Algorithms↗

PubMed1999

Dual-chamber pacing in hypertrophic obstructive cardiomyopathy: a comparison of acute and chronic effects.

This study describes the acute and chronic effects of dual-chamber (DDD) pacing in 14 consecutive patients with hypertrophic obstructive cardiomyopathy (HOCM), whose symptoms were refractory to drug therapy. Although left ventricular (LV) outflow tract pressure gradients diminished from 106+/-47 to 62+/-33 mm Hg (p<0.001) by temporary pacing, the residual pressure gradients were >30 mm Hg in the majority of those with concomitant reductions in cardiac output. The DDD pacing was judged as insufficient by the acute study in the majority of patients. A dual-chamber pacemaker was, however, implanted in 11 patients, and the chronic pacing effects were evaluated. All symptoms (syncope, fainting, palpitation and dyspnea) subsided within 1 month. Left ventricular outflow tract pressure gradients diminished from 99+/-56 to 21+/-13 mm Hg (p<0.004) at 1 week after, and to 17+/-12 mm Hg (p<0.002) at 1 year after the implantation, as measured by Doppler echocardiography. Echocardiogram showed disappearance of the systolic anterior motion of the mitral valve, and significant regression of the septal hypertrophy (from 18.5+/-4.3 to 15.7+/-4.1 mm, p<0.04). There was no significant correlation between the acute and chronic pacing effects in the reduction of the pressure gradients or symptomatic improvement. These results suggest that DDD pacemaker implantation is an effective treatment without any serious risks for patients with drug-refractory HOCM. The chronic-pacing effect in the reduction of the pressure gradient, the regression of hypertrophy and symptomatic improvement cannot be predicted by the assessment of temporary DDD pacing.

Adult↗