Biomedical subjects
Publications and source records attributed to T Oshima.
Explore the source record for details and available documents.
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.
The basis of protein stability has been investigated by the structural comparison of themophilic enzymes with their mesophilic counterparts. A number of characteristics have been found that can contribute to the stabilization of thermophilic proteins, but no one is uniquely capable of imparting thermostability. The crystal structure of 3-isopropylmalate dehydrogenase (IPMDH) from the mesophiles Escherichia coli and Salmonella typhimurium have been determined by the method of molecular replacement using the known structure of the homologous Thermus thermophilus enzyme. The structure of the E. coli enzyme was refined at a resolution of 2.1 A to an R-factor of 17.3%, that of the S. typhimurium enzyme at 1.7 A resolution to an R-factor of 19.8%. The three structures were compared to elucidate the basis of the higher thermostability of the T. thermophilus enzyme. A mutant that created a cavity in the hydrophobic core of the thermophilic enzyme was designed to investigate the importance of packing density for thermostability. The structure of this mutant was analyzed. The main stabilizing features in the thermophilic enzyme are an increased number of salt bridges, additional hydrogen bonds, a proportionately larger and more hydrophobic subunit interface, shortened N and C termini and a larger number of proline residues. The mutation in the hydrophobic core of T. thermophilus IPMDH resulted in a cavity of 32 A3, but no significant effect on the activity and thermostability of the mutant was observed.
The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 A resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The "core fold" part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two alpha-helices near the clusters, and two sheets of two-stranded antiparallel beta-sheet (the terminal and central beta-sheets). The "N-terminal extension" part is mainly formed by a one-turn alpha-helix and a three-stranded antiparallel beta-sheet. The beta-sheet in the N-terminal extension is hydrogen-bonded with the terminal beta-sheet in the core fold to form a larger beta-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the beta-sheet in the N-terminal extension and the central beta-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.
The dicluster-type ferredoxins from the thermoacidophilic archaea such as Thermoplasma acidophilum and Sulfolobus sp. are known to contain an unusually long extension of unknown function in the N-terminal region. Recent x-ray structural analysis of the Sulfolobus ferredoxin has revealed the presence of a novel zinc center, which is coordinated by three histidine ligand residues in the N-terminal region and one aspartate in the ferredoxin core domain. We report here the quantitative metal analyses together with electron paramagnetic resonance and resonance Raman spectra of T. acidophilum ferredoxin, demonstrating the presence of a novel zinc center in addition to one [3Fe-4S] and one [4Fe-4S] cluster (Fe/Zn = 6.8 mol/mol). A phylogenetic tree constructed for several archaeal monocluster and dicluster type ferredoxins suggests that the zinc-containing ferredoxins of T. acidophilum and Sulfolobus sp. form an independent subgroup, which is more distantly related to the ferredoxins from the hyperthermophiles than those from the methanogenic archaea, indicating the existence of a novel group of ferredoxins, namely, a "zinc-containing ferredoxin family" in the thermoacidophilic archaea. Inspection of the N-terminal extension regions of the archaeal zinc-containing ferredoxins suggested strict conservation of three histidine and one aspartate residues as possible ligands to the novel zinc center.
3-isopropylmalate dehydrogenase (IPMDH) from Escherichia coli was overexpressed, purified and crystallized. The enzyme was characterized and compared to its thermophilic counterpart from Thermus thermophilus strain HB8. As in the thermophile enzyme, the activity of E. coli IPMDH was dependent on the divalent cations, Mg2+ or Mn2+, with Mn2+ being the preferred cation. Activity was also strongly influenced by KCl: 0.3 M were necessary for the optimal activity. At 40 degrees C the K(m) of E. coli IPMDH was 105 microM for IPM and 321 microM for NAD, the kcat was 69 s-1. The half denaturation temperature was 64 degrees C, which was 20 degrees C lower than that of the thermophile enzyme.
OBJECTIVE: To evaluate the diagnostic algorithms leading to minimal-access surgery in unilateral sinonasal disease without evidence of bone destruction. DESIGN: In selected patients, we assigned qualitative preoperative diagnoses by performing computed tomography (CT), magnetic resonance imaging (MRI), and endonasal endoscopic biopsy and prospectively analyzed the results for 3 years, from 1992 to 1995. PATIENTS: Of 278 untreated patients who complained of nasal and sinus-related symptoms and underwent CT examinations, 130 were found to have unilateral sinonasal abnormalities without detectable changes in the bone structure. RESULTS: Accurate preoperative diagnoses were made using CT in 75% of the patients with chronic sinusitis with or without nasal polyps and 85% of the patients with mucoceles. In the remaining patients, preoperative diagnoses for both diseases were made using MRI. All fungal and vascular diseases were accurately diagnosed using MRI alone. Although neither CT nor MRI were useful in the qualitative diagnosis of neoplasm, the presence of neoplastic conditions, except papilloma, was indicated by MRI. Using endonasal endoscopy, biopsy was an accurate diagnostic tool, with minimal tissue damage, in 88% of the neoplasms. CONCLUSIONS: In differentiating untreated unilateral sinonasal disease without evidence of bone destruction, we conclude that CT is the first modality of diagnostic imaging and MRI is more sensitive than CT in identifying fungal disease and angiofibroma. Furthermore, MRI is helpful when neoplasm is indicated, but it is not an accurate diagnostic tool. The endonasal endoscopic approach for obtaining pathologic specimens is a qualitative diagnostic tool in the diagnosis of sinonasal neoplasm.
The GC-rich leuB gene (coding for 3-isopropylmalate dehydrogenase) of Thermus thermophilus is scarcely expressed in Escherichia coli, unless a leader open reading frame (ORF) is provided. We conducted experiments on nonexpressible plasmids and obtained a modified plasmid showing greatly enhanced expression: the degree of expression from the plasmid was higher than that from any other plasmid so far constructed. Sequence analysis of the plasmid showed that a 258-bp leader ORF overlapped with the initiation codon of leuB was newly formed as a consequence of the insertion of a 0.5-kb BamHI fragment derived from the E. coli chromosome. The degree of expression from the plasmid was further improved by shortening the leader ORF to 36 bp without changing the overlapping portion, and the flanking sequence between the promoter and the leader ORF was removed. The expression in E. coli of the pfk1 gene (coding for phosphofructokinase) of T. thermophilus was improved by the construction of a structure similar to that which enhanced the expression of the leuB gene. Based on the results, a practical method for the overexpression of GC-rich genes in E. coli is proposed.
BACKGROUND: Whether endoscopic sinus surgery (ESS) restores the mucociliary clearance of the maxillary sinus needs further evaluation. METHODS: We evaluated the mucociliary clearance of the maxillary sinus by using a radionuclide technique in 12 patients with chronic sinusitis (sinusitis group) and in six patients who had undergone ESS 6 to 14 months after the surgery (post-ESS group). The mucosal cilia taken from the maxillary sinus in 12 patients with sinusitis before and after ESS (paired experiments) were examined by light and electron microscopy. RESULTS: The radionuclide placed endoscopically in the maxillary sinus in eight patients immediately after ESS maintained 81.2 +/- 16.3% of its radioactivity after 30 minutes. This result was consistent with results in four patients with untreated chronic sinusitis in whom the radionuclide had been instilled by antral puncture (86.9% +/- 3.5%). On the other hand, in six patients in the post-ESS group the radionucleotide maintained only 25.9% +/- 11.6% of its radioactivity, demonstrating statistically significant differences from those of both the sinusitis group without ESS (p < 0.005) and the group 4 days after ESS (p < 0.005). The absence of the cilia in the sinusitis condition was recognized in 35.5% +/- 12.1% (n = 12) of the epithelial cells. On the other hand, the absence of cilia was significantly (p < 0.01) reduced to 5.3% +/- 3.7% of the epithelial cells in the post-ESS condition. Electron microscopic observation also revealed abnormal cilia in the sinusitis condition, whereas the mucosal cilia were regularly arranged in the post-ESS condition. CONCLUSIONS: The mucociliary clearance of the maxillary sinus disturbed by chronic inflammation was restored by ESS, indicating the clinical effectiveness of ESS for the treatment of chronic sinusitis.
Voltage-dependent chloride (ClC) channels have not yet been identified in the cochlea. In this study, an approach utilizing the reverse transcription-polymerase chain reaction (RT-PCR) was devised to clone the cDNA of ClC channels. PCR was performed using degenerate primers corresponding to two highly conserved regions of the ClC channels. By Southern hybridization and sequencing studies, the sequences corresponding to ClC-2 and ClC-3 were found in the cochlear lateral wall, while ClC-1 was not detected. These results suggest that ClC-2 and ClC-3 might be involved in Cl- transport in the cochlear lateral wall.
Recent advances in molecular biology have been applied to inner ear research. Loop diuretic ototoxicity has been suggested, but not proven, to share a common mechanism with diuretic effects on renal tubules. The discovery of the molecular nature of the Na-K-2Cl cotransporter in the cochlea provided a better understanding of loop diuretic ototoxicity. In this review, we describe clinical reports of loop diuretic ototoxicity and other information obtained by physiological, biochemical and morphological investigations related to the mechanism sensitive to loop diuretics. Based on recent evidence for the molecular nature of the Na-K-2Cl cotransporter expressed in the mammalian cochlea, the underlying mechanisms of ototoxicity induced by loop diuretics are described.
Insertion/deletion (I/D) polymorphism of the angiotensin converting enzyme (ACE) gene has been shown to be a determinant for serum ACE level and a marker for several cardiovascular diseases. We investigated whether the ACE gene can predict the therapeutic efficacy of ACE inhibitors in essential hypertensive patients. The response of blood pressure and plasma renin activity (PRA) 1 h after 50 mg captopril administration were evaluated in 82 inpatients with untreated essential hypertension (42 men, 40 women; mean age +/- SD: 52 +/- 13 years; range: 27 to 79 years) in relation to ACE genotypes. There were no differences in age, gender, blood pressure, and PRA in the basal conditions, among essential hypertensive patients with the II, ID, and DD genotypes (n = 36, 34, and 12, respectively). The acute responses of PRA and blood pressure to an ACE inhibitor were similar in the three groups. The blood pressure response was negatively correlated with baseline PRA (r = 0.497). These data suggest that PRA but not the I/D polymorphism of the ACE gene is a useful predictor of the short-term antihypertensive effects of ACE inhibitors.
1. We evaluated the effects of the dietary restriction of sodium chloride on blood pressure and systemic calcium metabolism in 19 in-patients with essential hypertension (11 men and 8 women, mean age 49.9 +/- 12.1 years). 2. All patients received a high-sodium diet (250 mmol/day) for 1 week, followed by a low-sodium diet (10 mmol/day) for another week. Intake of potassium (100 mmol/day) and of calcium (15 mmol/day) were kept constant throughout the study. 3. Sodium restriction significantly reduced the mean blood pressure (from 114.0 +/- 1.9 to 105.0 +/- 13.7 mmHg, P < 0.01). Urinary calcium excretion was significantly reduced (from 5.1 +/- 2.4 to 2.2 +/- 1.0 mmol/day, P < 0.01). 4. The change in mean blood pressure after sodium restriction was not correlated with a change in any parameter of calcium metabolism [whole blood ionized calcium, plasma intact parathyroid hormone, or 1,25-(OH)2 vitamin D3]. 5. Plasma renin activity during a regular sodium diet, an index of renin status, was significantly and inversely correlated with the change in blood pressure during sodium restriction, but not with any change in the parameters of calcium metabolism. 6. We conclude that sodium restriction reduces blood pressure and decreases urinary calcium excretion. However, we observed no significant role of extracellular calcium concentration or of calciotropic hormone concentration in the mechanism of sodium sensitivity.
The substrate-binding sites of NADP-dependent isocitrate dehydrogenase and NAD-dependent 3-isopropylmalate dehydrogenase from Thermus thermophilus were analyzed by site-directed mutagenesis. Ser97 and Asn99 of isocitrate dehydrogenase were identified to be involved in the isocitrate recognition. In 3-isopropylmalate dehydrogenase, the corresponding residues, Leu90 and Leu91, appear to recognize the substrate by forming a hydrophobic pocket. Double mutation of Asp78 and Glu87 revealed that negative charge of these residues plays a crucial role in discriminating isopropylmalate from isocitrate.
A mutant plasmid with elevated expression efficiency of GC-rich Thermus thermophilus leuB gene was screened in Escherichia coli. A wild-type plasmid pHB2 carrying T. thermophilus leuB gene was introduced into leuB-deficient E. coli C600 cells. During successive cultures of the transformant in leucine-free medium, the original plasmid was spontaneously replaced by a mutant plasmid. The expression efficiency of the leuB gene on the mutant plasmid was 4.8-fold higher than that of the wild-type plasmid. Sequencing of the mutant plasmid revealed that the open reading frame (ORF1) in front of the leuB gene was shortened from 822 to 306 bp. Several expression vectors were constructed to investigate the effect of the length of ORF1, and the optimal length for the expression of the following leuB gene was determined. It was also shown that the stop codon of ORF1 should be overlapped with the initiation codon of leuB gene for the highest efficiency.
The structure of a thermostable Ala172Leu mutant, designated A172L, of 3-isopropylmalate dehydrogenase from Thermus thermophilus was determined. The crystal belongs to space group P2(1), with cell parameters a = 55.5 A, b = 88.1 A, c = 72.0 A and beta = 100.9 degrees. There is one dimer in each asymmetric unit. The final R factor is 17.8% with 69 water molecules at 2.35 A resolution. The mutation is located at the interface between domains and the C alpha trace of the mutant structure deviates from that of the native structure by as much as 1.7 A, while the structure of each domain barely changes. The mutant enzyme has a more closed conformation compared with the wild-type enzyme as a result of the replacement of Ala with Leu at residue 172. These structural variations were found independent of the crystal packing, because the structure of wild type was the same in crystals obtained in different precipitants. The hinge regions for the movement of domains are located around the active cleft of the enzyme, an observation that implies that the mobility of domains around the hinge is indispensable for the activity of the enzyme. The larger side chain at the mutated site contributed to the thermostability of the mutant protein by enhancing the local packing of side chains, and also by shifting the backbone of the opposing domain.
To determine the key position for the unusual stability of isopropylmalate dehydrogenase from extreme thermophiles (Thermus thermophilus and T. aquaticus), sequence comparisons were carried out. As a result, a motif which is characteristic to the thermophilic dehydrogenases was found between two highly conserved stretches. The sequence motif was introduced into a mesophilic (Escherichia coli) isopropylmalate dehydrogenase, one by one. Contrary to our expectation, introduction of the whole motif led the mesophilic enzyme to be more unstable whereas substitution of only one amino acid residue in the motif thermostabilized the enzyme. From the 3D structure of the enzyme, a mechanism for the thermostabilization is speculated.
Endothelial and epithelial adhesion molecules are important in the recruitment of leukocytes to inflammatory sites. To determine the relationship between recruited leukocytes and adhesion molecules in the paranasal sinus mucosa of nonallergic chronic sinusitis, we surgically obtained mucosa from 16 patients and identified the expression of intercellular adhesion molecules (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), E-selectin, and P-selectin by immunohistochemistry. Neutrophils were significantly dominant in the nasal discharge as compared with eosinophils. The degree of neutrophil infiltration in the paranasal sinus mucosa was prominent in both intraepithelial and subepithelial areas as compared with the lamina propria. In each tissue site, the degree of infiltration of neutrophils was similar to that of eosinophils. These findings suggest that the tissue neutrophils actively and rapidly migrated into the lumen. All the adhesion molecules except VCAM-1 were expressed in the vascular endothelial cells. On the other hand, the surface epithelial cells showed the expression of only ICAM-1. The expression of ICAM-1 on the endothelial cells correlated with the degree of neutrophil infiltration in the mucosa The eosinophil infiltration was not dependent on any adhesion molecules examined here. It was concluded that ICAM-1 expression in the mucosa may be involved in neutrophil recruitment and may contribute to the establishment of the inflammatory cell distribution in the paranasal sinus of nonallergic chronic sinusitis.