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Biomedical subjects

K Mizobuchi

Publications and source records attributed to K Mizobuchi.

At least 37 records · Page 2Linked to original sources
PubMed1998

An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIalpha plasmid ColIb-P9.

Translation initiation of the repZ gene encoding the replication initiator of plasmid ColIb-P9 is not only negatively regulated by the action of the antisense Inc RNA encoded in the leader region, but is also coupled to the translation and termination of a transcribed leader sequence, repY, a positive regulatory element for repZ gene expression. This translational coupling depends on base pairing between two complementary sequences, 5'-rGGCG-3' and 5'-rCGCC-3', which are located upstream of and in the middle of repY, respectively, and have the potential to form a pseudoknot with the stem-loop structure I. Another stem-loop called structure III near the 3'-end of repY sequesters both the 5'-rCGCC-3' sequence and the repZ ribosome-binding site. Here we show that the RepZ mRNA leader sequence synthesized in vitro indeed contains several stem-loop structures including structures I and III, but not the pseudoknot. However, disruption of structure III, without changing the repZ ribosome-binding site, by means of base substitution and deletion induces base pairing between the two short complementary sequences distantly separated, resulting in the formation of a pseudoknot. When the pseudoknot is allowed to form in vivo due to the same mutations, a maximum level of repZ expression is obtained comparable to one observed in the absence of Inc RNA. These results strengthen our previously proposed model that the pseudoknot induced by the translation and termination of the repY reading frame functions as the molecular switch for translational initiation of the repZ gene.

Bacterial Proteins↗
PubMed1998

Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5'-rUUGGCG-3' motif in the loop sequence.

The sequence 5'-rUUGGCG-3' is conserved within the loop regions of antisense RNAs or their targets involved in replication of various prokaryotic plasmids. In IncIalpha plasmid ColIb-P9, the partially base paired 21-nucleotide loop of a stem-loop called structure I within RepZ mRNA contains this hexanucleotide sequence, and comprises the target site for the antisense Inc RNA. In this report, we find that the base pairing interaction at the 5'-rGGC-3' sequence in the hexanucleotide motif is important for interaction between Inc RNA and structure I. In addition, the 21-base loop domain of structure I is folded tighter than predicted, with the hexanucleotide sequence at the top. The second U residue in the sequence is favored for Inc RNA binding in a base-specific manner. On the other hand, the upper domain of the Inc RNA stem-loop is loosely structured, and maintaining the loop sequence single-stranded is important for the intermolecular interaction. Based on these results, we propose that a structural feature in the loop I domain, conferred probably by the conserved 5'-rUUGGCG-3' sequence, favors binding to a complementary, single-stranded RNA. This model also explains how the RepZ mRNA pseudoknot, described in the accompanying paper (Asano, K., and Mizobuchi, K. (1998) J. Biol. Chem. 273, 11815-11825) is formed specifically with structure I. A possible conformation adopted by the 5'-rUUGGCG-3' loop sequence is discussed.

Bacterial Proteins↗
PubMed1998

[Swyer-James syndrome with pneumothorax].

We report a case of Swyer-James syndrome with pneumothorax. A 20 year-old man was admitted to our hospital with dyspnea. Right pneumothorax was diagnosed by chest X-ray. He had a history of current pneumonia in childhood. After improvement of the pneumothorax, chest X-ray revealed hyperlucency of the right upper lung. Chest-CT revealed a low attenuation area and a cystic space in the right upper lobe. Xenon-133 clearance was delayed in ventilation scintigraphy. Bronchography showed cylindrical bronchiectasis in the proximal bronchi and poor filling of the peripheral bronchi in the right upper lobe. Pulmonary angiography showed a small right upper pulmonary artery. Swyer-James syndrome was diagnosed. The pneumothorax was probably caused by weakness of the cystic spaces.

Adult↗
PubMed1997

Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features.

The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We analyzed its sequence features and found that this region contained at least 894 potential open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any other genes. A homology search of the ORFs also identified several new gene clusters. Those include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a cluster of five genes coding for the homologues of degradation enzymes for aromatic hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.

Base Sequence↗
PubMed1997

[Effect of imipenem/cilastatin combined with vancomycin for MRSA infection].

Therapeutic efficacy of the combined regimen, imipenem/cilastatin (IPM/CS) plus vancomycin (VCM), was examined in a total of 13 patients infected with MRSA (10 patients with pneumonia, 2 with sepsis and 1 with urinary tract infection). Based on the results of determination of FIC indices, in vitro combined effects were synergistic in 4 strains and additive in 3 strains. There was, however, no apparent correlation between the in vitro combined effect in terms of FIC index and clinical outcome. No side effects or abnormal laboratory findings were observed. The average daily doses of IPM/CS and VCM were 1.2 g and 1.25 g and the average administration periods were 17.5 and 14.9 days, respectively. The present results suggested that simultaneous use of IPM/CS and VCM at the standard doses could yield an enhancement of both bacteriological and clinical efficacies in treatment of the patients with MRSA infection.

Adult↗
PubMed1997

[Usefulness and early detection of acute exacerbation by peak expiratory flow rate in the management of asthma].

The monitoring of peak expiratory flow (PEF) and maintenance of a symptom diary have been proposed as means to monitor asthma severity. This study assessed via longitudinal analysis, the usefulness and limitation of daily PEF monitoring (amplitude percent mean) as an index for asthma severity, and the usefulness of recording daily intake of beta-agonists as a measure of symptom severity. Nine subjects with moderate to severe asthma were treated with inhaled beclomethasone dipropionate (BDP). Sustained-release theophylline and oral corticosteroids supplemented inhaled BDP according to both individual symptom prevalence and PEF measurements. The patients kept records four times daily of their PEF and asthmatic symptoms (cough, sputum and number of attacks), from the beginning to the end of treatment. They also recorded the daily frequency of beta-agonist inhalation (as needed for symptomatic relief). Minimum daily PEF (expressed as percent best) correlated significantly with symptom scores: cough (r = -0.69), sputum (r = -0.69) and attack (r = -0.69). Minimum PEF correlated strongly with the daily frequency of beta agonist inhalation (r = 0.76). Each symptom score and the daily frequency of beta-agonist inhalation was zero when the minimum PEF was approximately 80%. We evaluated the correlation between minimum PEF and daily PEF variability in all data (r = -0.72): for a minimum PEF > or = 20% (r = -0.72), a minimum PEF > or = 30% (r = -0.77), a minimum PEF > or = 40% (r = -0.82) and a minimum PEF > or = 50% (r = -0.80). We determined the correlation between minimum PEFs of > or = 35 to 45% in 1% increments and daily PEF variability in relation to the severity of asthma. With a minimum PEF > or = 40%, the strongest correlation was demonstrated between minimum PEF and daily PEF variability. Daily PEF variability was a reliable indicator for the management of asthma when the PEF > or = 40%. When the minimum PEF was 80%, daily PEF variability was approximately 10%. When the minimum PEF was 40%, daily PEF variability was 46%, and the daily frequency of beta-agonist inhalation was 2.6. We concluded that, 1) The target values of minimum PEF and daily PEF variability are 80% and 10% respectively in the treatment of asthmatic patients, 2) The daily frequency of beta-agonist inhalation is recommended as an indicator for the severity of asthmatic symptoms, and 3) Daily PEF variability in combination with the daily frequency of beta-agonist inhalation is very useful in the management and early detection of acute asthma.

Adolescent↗
PubMed1996

A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map.

The 569,750 base pair sequence corresponding to the 28.0-40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. This region includes the replication terminus region and contained at least 549 potential open reading frames. Among them, 160 (29%) were previously reported, 174 (32%) were homologous to other known genes, 102 (18%) were identical or similar to hypothetical genes registered in databases, and the remaining 113 (21%) did not show a significant similarity to any other gene. Of interest was the finding of a large number of genes and gene clusters in and near the replication termination region which had been thought to be genetically silent. Those included a cluster of genes for fatty acid beta-oxidation, the third copy of the pot (spermidine/putrescine transport system) gene cluster, the second dpp (dipeptide transport system) operon, the second dsm (anaerobic dimethyl sulfoxide reductase) operon, a cluster of fim (fimbrial) genes and a DNA helicase-like gene with a high molecular weight. In addition, we found the dnaC- and dnaT-like genes in the cryptic prophage, Rac, and a number of genes originated probably from plasmids.

Chromosome Mapping↗
PubMed1996

A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.

The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this region contained at least 466 potential open reading frames, of which 187 (40%) were previously reported, 105 (23%) were homologous to other known genes, 103 (22%) were identical or similar to hypothetical genes registered in databases, and the remaining 71 (15%) did not show a significant similarity to any other gene. At the 45.2-46.0 min region, we found a very large cluster of about 30 genes, whose functions are involved in the biosynthesis of polysaccharides as the components of outer membranes. In addition, we identified a new asn-tRNA gene, designated asnW, between the asnT and asnU genes and a new lysogenic phage attachment site as the cis-element.

Attachment Sites, Microbiological↗
PubMed1996

A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map.

The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 681 potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%) are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical genes registered in databases, and the remaining 118 (17%) do not show a significant similarity to any other gene. In this region, we assigned a cluster of cit genes encoding multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes encoding integrase, excisionase and repressor in the e14 genetic element. In addition, a new valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B and -C, were found.

DNA, Bacterial↗
PubMed1996

[An elderly case of squamous cell lung cancer showing partial response by daily administration of oral etoposide].

We report an elderly case of squamous cell lung cancer showing partial response by daily administration of oral etoposide. The 86-year-old man had been diagnosed as squamous cell lung cancer (Stage II, T2N1M0) in September 1992. He had received no active treatment, because he was too old and had pulmonary emphysema. Dyspnea became gradually worse due to complete atelectasis of right lung in December 1994. After treatment with oral etoposide (50 mg/day) for 10 days, atelectasis was reduced and a partial response was obtained. No severe side effect except leukopenia was noted.

Administration, Oral↗
PubMed1996

[Optimal time of the day for measuring peak expiratory flow rates in patients with asthma].

Regular measurement of peak expiratory flow rate (PEF) has been recommended as an aid in the management of asthma, but the time of the day when PEF should be measured remains unclear. We therefore sought to determine the optimal time for measuring PEF in untreated patients with mild to moderate asthma. PEF was measured in 11 patients four times daily: on waking, around noon, in the evening, and at bedtime. Significant (p < 0.05) rhythms were detected by single cosinor analysis in all patients. Analysis by the population mean cosinor method showed that the mesor was 381 +/- 120 l/m, the amplitude was 52 +/- 21 l/m, and the acrophase was at 16:28 +/- 0:55. These data indicate that, in general, PEF is lowest at 4:30 a.m. and highest at 4:30 p.m. in patients with mild to moderate asthma. We conclude that PEF should be measured early in the morning and at 4:30 p.m. in such patients.

Adolescent↗
PubMed1995

Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.

BACKGROUND: The purine repressor (PurR) regulates genes that encode enzymes for purine biosynthesis. PurR has a two domain structure with an N-terminal DNA-binding domain (DBD) and a C-terminal corepressor-binding domain (CBD). The three dimensional structure of a ternary complex of PurR bound to both corepressor and a specific DNA sequence has recently been determined by X-ray crystallography. RESULTS: We have determined the solution structure of the PurR DBD by NMR. It contains three helices, with the first and second helices forming a helix-turn-helix motif. The tertiary structure of the three helices is very similar to that of the corresponding region in the ternary complex. The structure of the hinge helical region, however, which makes specific base contacts in the minor groove of DNA, is disordered in the DNA-free form. CONCLUSION: The stable formation of PurR hinge helices requires PurR dimerization, which brings the hinge regions proximal to each other. The dimerization of the hinge helices is likely to be controlled by the CBD dimerization interface, but is induced by specific-DNA binding.

Amino Acid Sequence↗
PubMed1995

A transcription terminator signal necessary for plasmid ColIb-P9 replication.

Replication of the IncI alpha plasmid ColIb-P9 requires the repZ gene, which encodes an essential, unstable initiator protein termed RepZ. Although many functional features of the ColIb-P9 replicon resemble those of structurally unrelated IncFII plasmids R1 and NR1, the role of transcription of repZ towards the replication origin is poorly understood. Using a series of deletion and substitution mutants of the ColIb-P9 replicon, we found that RepZ prefers to act in cis and that a spacer sequence between repZ and the origin is required for replication. This spacer element, referred to as CIS, retained strong transcription terminator activity. Efficient transcription terminators, whether Rho-dependent or -independent, were capable of replacing CIS function for in vivo replication; ColIb-P9 replicated better as transcription terminated more efficiently within CIS. When the CIS element was substituted for by a strong Rho-dependent terminator, such as lambda tR1 or E. coli trp t', in vivo replication of these recombinant replicons became dependent on the Rho factor, in contrast to the authentic ColIb-P9 replicon.

Bacterial Proteins↗