Biomedical subjects

J Oda

Publications and source records attributed to J Oda.

At least 55 records · Page 3Linked to original sources

PubMed1996

[Natural history of cloudy zone of pulmonary adenocarcinoma on HRCT].

Seven pulmonary adenocarcinomas with cloudy zone (CZ), which was defined as a lower density zone in the pulmonary lesion than pulmonary vessels in the surrounding normal lung on high resolution computed tomography (HRCT), were followed up for at least 3 months. There were three tumors with homogeneous CZ, one of which showed no change when rescanned after three months, the others showed enlargement with or without replacement by high density areas on rescanned images obtained after more than one year. Two tumors containing some high density areas on the initial scans showed slight decreases in size on rescanned images obtained after 1 to 3 months. However, on rescanned images obtained after more than 1 year and 9 months, these tumors also showed enlargement of CZ. Pathologically, CZs corresponded to well-differentiated adenocarcinoma of the bronchioloalveolar type with no or mild interstitial change, whereas high density areas mainly corresponded to papillary adenocarcinoma with severe interstitial fibrosis. In conclusion, long-term careful follow-up of CZ is necessary to detect enlargement or the appearance of high density. Unchanged CZ in short-term follow-up should be considered a finding suggestive of malignancy.

Adenocarcinoma, Papillary↗

PubMed1996

[MR imaging of hepatocellular carcinoma following microwave coagulation therapy].

MRI was performed in 13 patients who had microwave coagulation therapy (MCT) for hepatocellular carcinoma. Six of them underwent surgery after MRI. The area (including tumor) treated by MCT showed low to high intensity on T1WI, and low to isointensity on T2WI. No enhancement was obtained on dynamic MRI. Histologically, this area was supposed to be coagulation necrosis. On T1WI, only tumor showed high intensity within the MCT area in 8 patients, and nearly uniform intensity was observed in 5 patients. Histologically, residual cell nuclei were observed in the former, and nearly uniform coagulation necrosis in the latter. The marginal part of the MCT area exhibited low intensity on T1WI, and high intensity on T2WI. Strong enhancement was obtained on dynamic MRI, and histologically, granulation tissue was noted. In the hepatic parenchyma around the MCT area, a ring-or wedge-shaped high intensity part was observed in 7 patients on T2WI, and that part was enhanced on dynamic MRI. This finding was considered to reflect changes such as hepatic hyperperfusion. In terms of the capability of visualizing residual tumor after MCT, MRI was superior to CT. Furthermore, a clear distinction was seen between the MCT area and non-MCT area on T2WI and dynamic MRI. Thus, MRI was useful in the determination of additional therapy.

Aged↗

PubMed1995

Concurrent radiotherapy and chemotherapy with protracted continuous infusion of 5-fluorouracil in inoperable esophageal squamous cell carcinoma.

PURPOSE: The feasibility of a concurrent chemoradiotherapeutic protocol for patients with inoperable esophageal squamous cell carcinoma was tested. METHODS AND MATERIALS: Concurrent chemoradiotherapy using protracted low-dose continuous infusions of five-fluorouracil (5-FU; 250-300 mg/m2/24 h) and standard external beam irradiation was given to 28 patients with inoperable esophageal squamous cell carcinoma between November 1991 and June 1993. RESULTS: For 25 patients receiving a total dose of > or = 60 Gy and concurrent 5-FU infusion for more than 5 weeks, the complete response rate was 52%. Local progression-free rate in this chemoradiotherapy group was significantly higher than the historical controls treated by radiotherapy alone (p < 0.05). A multivariate analysis revealed the treatment scheme (concomitant chemoradiotherapy vs. radiotherapy alone) to be a significant factor in local control (p < 0.01). Swallowing pain (39%), anorexia (39%), and nausea (32%) were the most frequent early reactions. Serious late radiation complications have not been observed. CONCLUSION: The concurrent chemoradiotherapy using protracted low-dose continuous infusion of 5-FU and standard radiotherapy is an effective and safe method to obtain a local control in inoperable esophageal squamous cell carcinoma.

Aged↗

PubMed1995

Searching for common sequence patterns among distantly related proteins.

We have developed a program Gap Allowing Pattern Explorer (GAPE) to extract amino acid sequence motifs conserved among distantly related proteins. The GAPE program is designed to allow gaps in the sequences. First, this program generates all possible amino acid patterns comprising up to five amino acids. Sequences containing the amino acid residues in the same order as a generated pattern are selected as subsequences, where the differences in the distances between two consecutive amino acids are ignored. Next, the motifs are extracted from the subsequences under conditions in which all four distances between the five amino acids are fixed. At this stage, motifs with gaps in their subsequence are also found by relaxing one of the four fixed distances. The statistical significance for a motif obtained is calculated based on the amino acid composition of the sequences under consideration. When the GAPE program was applied to 59 pyridoxal-phosphate-related sequences and 64 ATP (AMP-forming)-related sequences, motifs extracted with a low expectation of occurrence contained some of the amino acid residues chemically proved to be involved in the ligand recognition.

Adenosine Triphosphate↗

PubMed1995

Site-directed mutagenesis of glutathione synthetase from Escherichia coli B: mapping of the gamma-L-glutamyl-L-cysteine-binding site.

Lys18, Arg86, Asn283, Ser286, Thr288 and Glu292 of glutathione synthetase from Escherichia coli B are presumed to be highly concerned with the substrate, gamma-L-glutamyl-L-cysteine (gamma-Glu-Cys), binding by X-ray crystallography and affinity labeling studies. Using site-directed mutagenesis, we investigated functional roles of those residues for gamma-Glu-Cys binding. The mutant enzymes of Arg86 and Asn283 altered their kinetic parameters, especially the Michaelis constants of gamma-Glu-Cys. In the case of Asn283, the residue is not likely to have an essential role in gamma-Glu-Cys binding but its side chain would extend to make a van der Waals contact with bound gamma-Glu-Cys. Chemical modification of a cysteine residue with 5,5'-dithiobis(2-nitrobenzoate) (DTNB) showed Arg86 would not only be much responsible for gamma-Glu-Cys binding but would also have a role in maintaining the structural integrity of the enzyme. The other mutant enzymes showed little defect in their kinetic parameters of gamma-Glu-Cys.

Base Sequence↗

PubMed1995

[High-resolution CT findings of Pneumocystis carinii pneumonia].

High resolution CT (HRCT) was performed on 7 patients with pneumocystis carinii pneumonia (PCP). Six cases were proven bacteriologically by bronchoalveolar lavage; one case was proven by autopsy. Three patients were re-scanned after specific treatment and symptomatic relief. All the CT scans were abnormal, usually showing bilateral diffuse ground-glass opacity, through which the pulmonary vessels remained visible. Chest X-ray, on the other hand, showed a normal pattern in one patient. Other changes such as air space consolidation (in 4 cases) and thickening of peripheral pulmona vessels (in 2 cases) were also seen. Air space consolidation was found in three cases with mixed infection (cytomegalovirus pneumonia in 2 cases, aspergillosis in one case). No patient showed significant mediastinal or hilar lymph node enlargement, pleural effusion or cystic pulmonary change. HRCT findings such as ground-glass opacity and air space consolidation were shown to disappear in some cases of PCP after specific treatment. HRCT is useful to evaluate the sequential pulmonary changes after the specific therapy.

Adult↗

PubMed1994

[Embolization of varicocele with ethanol].

Embolization with ethanol was performed in 40 varicocele patients to prevent recurrence due to collateral formation. A prescribed amount of ethanol (0.5-4 ml) was injected slowly into the testicular vein with the catheter tip as close as possible to the inguinal region. Embolization with stainless steel coils was also performed in 15 of the 40 patients. Immediately after embolization, three varicoceles were reduced in size, and 37 disappeared. Recurrence was recognized in only two patients. These patients were embolized at a proximal site above lumbar vertebra IV. Spermatic data have improved for 13 patients but not for one azoospermatic patient. Serious complications were recognized in only one patient, who received an injection of 15 ml ethanol in one dose. Therefore, we conclude that embolization with ethanol is an useful treatment for varicocele.

Adolescent↗

PubMed1994

Flexible loop that is novel catalytic machinery in a ligase. Atomic structure and function of the loopless glutathione synthetase.

The catalytic mechanism of glutathione synthetase is proposed to proceed via phosphorylation of the dipeptide substrate to yield an acyl phosphate intermediate; this intermediate is subsequently attacked by glycine, followed by loss of inorganic phosphate, leading to glutathione formation. A flexible loop (Ile226-Gly242) in Escherichia coli B glutathione synthetase is proposed to stabilize the acyl phosphate intermediate by preventing its decomposition by hydrolysis with water [Tanaka, T., Kato, H., Nishioka, T., & Oda, J. (1992) Biochemistry 31, 2259-2265; Tanaka, T., Yamaguchi, H., Kato, H., Nishioka, T., Katsube, Y., & Oda, J. (1993) Biochemistry 32, 12398-12404]. To investigate the function of the loop in the E. coli enzyme definitely, a loopless mutant in which the loop (Ile226-Arg241) was replaced with three residues of glycine was constructed. The crystal structure of the loopless mutant enzyme was essentially identical with that of the wild-type enzyme. Kinetic measurements showed that the replacement of the loop led to increases in the Km values, especially for the glycine, and a 930-fold decrease in the k0 value. Hence, the loopless mutant was 3 x 10(4) less active in terms of its specificity constant (k0/Km) for glycine than the wild-type enzyme. Moreover, the loopless mutant showed gamma-L-glutamyl-L-cysteine-dependent ATP hydrolase activity to almost the same extent as its glutathione synthetase activity. These studies support the fact that the loop enhances the recognition of glycine as well as stabilizes the acyl phosphate intermediate so that the intermediate rapidly reacts with glycine.

Amino Acid Sequence↗

PubMed1994

Characterization of a catalytic antibody for stereoselective ester hydrolysis--a catalytic residue and mode of product inhibition.

A catalytic antibody which catalyzes stereoselective ester hydrolysis was characterized, and the role of a catalytic Arg residue is discussed in terms of product inhibition. A monoclonal antibody 1C7 generated against the phosphonate 1 was highly stereoselective for (R)-isomer in hydrolyzing racemic ester 2. However, the reaction was almost stoichiometric due to strong inhibition by the product acid 3. One Arg residue in the antibody combining site was essential to the catalysis, and the same Arg was expected to play a dominant role in product inhibition by charge interaction with the negatively charged product acid. Indeed, the antibody experienced much less product inhibition with the hydrolysis of a carbonate ester 7, which yields a neutral alcohol 8 devoid of a negative charge, and exhibited at least 100 turnovers without any loss of activity. In addition, high stereoselectivity for (R)-isomer was still retained. The amino acid sequence and computer modeling of the variable domain of 1C7 suggested that Arg97 in the complementarity-determining region (CDR) of heavy chain was the putative catalytic residue.

Amino Acid Sequence↗

PubMed1994

[A case of mesenteric panniculitis: comparing the findings of 67Ga scintigraphy with pathological results].

We report a case of mesenteric panniculitis where we compared the findings of 67Ga-citrate (Ga) scintigraphy with pathological results. The patients, a 75-year-old man, was hospitalized for examination of low abdominal mass. After hospitalization he developed high CRP levels. A Ba enema revealed serrated intestinal walls and a thick fat density, the margins of which were distinct, as judged from abdominal CT scans. Therefore we suspected a mesenteric panniculitis. Since the patient did not improve under conservative treatment for three months, surgery was performed a day after Ga scintigraphy which showed the abnormal uptake in the abdominal mass, which was removed. The radioactivity of several tissue slices from the resected specimen containing the affected part which had been described inflammatory in the pathological examination showed very high radioactivity. This disease is usually diagnosed from the typical findings of Ba enema and CT scan. But, when an extraordinary abdominal accumulation presents, one should think of performing a Ga scan as an additional diagnostic parameter.

Aged↗

PubMed1994

[Evaluation of renal function by factor analysis using 99mTc-MAG3].

The kinetics of 99mTc-mercapto-acetyltriglycine (MAG3), a new renal scintigraphic agent, was studied by factor analysis in patients with chronic renal disorders, and its application to assessment of the renal function was evaluated. Data were collected for 30 minutes from immediately after intravenous injection of MAG3 at 370 MBq, the first pass image and serial renal scintigrams were obtained, and factor analysis was attempted simultaneously. Since most of MAG3 is excreted via the kidney during the first pass, factor analysis was performed. Two factors reflecting renal parenchymal components and pelvic components could be separated in 8 (Cre < or = 2.9 mg/dl) of 10 patients, and they corresponded with respective segmental renograms. In the remaining 2 (Cre > or = 3.0 mg/dl), separation was impossible by 2-factor analysis, and 3-factor analysis was needed. Factor analysis is considered to allow objective evaluation of renal function without setting the ROI.

Adult↗

PubMed1993

Flexibility impaired by mutations revealed the multifunctional roles of the loop in glutathione synthetase.

The loop from Ile-226 to Arg-241 in the glutathione synthetase (GSHase) from Escherichia coli B is rich in glycine and alanine and too flexible to take a fixed conformation [Yamaguchi, H., Kato, H., Hata, Y., Nishioka, T., Kimura, A., Oda, J., & Katsube, Y. (1993) J. Mol. Biol. 229, 1083-1100; Tanaka, T., Kato, H., Nishioka, T., & Oda, J. (1992) Biochemistry 31, 2259-2265]. To restrict the flexibility, three residues in the loop, Pro-227, Gly-229, and Gly-240, were replaced with alanine and valine residues. Variability in conformations of the mutant loops and shifts in the distribution of conformers between the open and closed states were assessed by steady-state kinetics, X-ray crystallographic structure analysis, and proteolysis with arginyl endopeptidase. Mutant enzymes replaced with a valine residue at the basal positions of the loop (P227V, G240V, and P227V/G240V) were identical with the wild-type enzyme in their crystal structures, except the loop region. The mutant loops retained apparent conformational variability, so as to take the open and closed states and to protect the acyl phosphate intermediate from the decomposition uncoupled from glutathione synthesis, but lost the catalytic activity; Kmapp values for glycine and gamma-Glu-Cys were sensitive to the mutations and drastically increased, and the k0app value was fatally reduced in the P227V/G240V mutant enzyme. The present results suggest that adjustability of the loop to the closed state is required for the recognition of the substrates, gamma-Glu-Cys and glycine, and for the chemical interactions with the bound substrates.

Amino Acid Sequence↗

PubMed1993

Lipase from Pseudomonas aeruginosa. Production in Escherichia coli and activation in vitro with a protein from the downstream gene.

The lipase gene from Pseudomonas aeruginosa TE3285 is followed by another gene, lipB. The lipase gene was expressed in Escherichia coli BL21(DE3)pLysS using the T7 RNA polymerase expression system. The mature lipase was accumulated as inclusion bodies at 42% of the total cell proteins. The inclusion bodies were solubilized with 8 M urea, but lipase activity was not detected in the solubilized preparation containing 85% lipase protein even after removing urea by dialysis. The lipB gene, positioned downstream of the lipase gene and thought to be necessary for the expression of the lipase gene, was expressed in Escherichia coli JM109 as a fusion with the glutathione transferase gene from Schistosoma japonicum. The fusion protein was partially purified on glutathione-agarose beads to 36% purity. Incubated with the fusion protein at a molar ratio of 1:1 at 4 degrees C for 24 h, the solubilized lipase showed lipase activity of about a tenth that of the purified lipase prepared from Pseudomonas aeruginosa TE3285. Magnesium ions and ATP were not essential but increased the activation. When the fusion protein was treated with thrombin to release the glutathione transferase part, it retained its activity. The lipase activation with lipB protein probably proceeds to form a 1:1 complex with the inactive, solubilized lipase protein but by a different mode from known chaperones.

Adenosine Triphosphate↗

PubMed1993

Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 A resolution.

Glutathione synthetase (gamma-L-glutamyl-L-cysteine: glycine ligase (ADP-forming) EC 6.3.2.3: GSHase) catalyzes the synthesis of glutathione from gamma-L-glutamyl-L-cysteine and Gly in the presence of ATP. The enzyme from Escherichia coli is a tetramer with four identical subunits of 316 amino acid residues. The crystal structure of the enzyme has been determined by isomorphous replacement and refined to a 2.0 A resolution. Two regions, Gly164 to Gly167 and Ile226 to Arg241, are invisible on the electron density map. The refined model of the subunit includes 296 amino acid residues and 107 solvent molecules. The crystallographic R-factor is 18.6% for 17.914 reflections with F > 3 sigma between 6.0 A and 2.0 A. The structure consists of three domains: the N-terminal, central, and C-terminal domains. In the tetrameric molecule, two subunits that are in close contact form a tight dimer, two tight dimers forming a tetramer with two solvent regions. The ATP molecule is located in the cleft between the central and C-terminal domains. The ATP binding site is surrounded by two sets of the structural motif that belong to those respective domains. Each motif consists of an anti-parallel beta-sheet and a glycine-rich loop.

Adenosine Triphosphate↗

PubMed1993

Use of adenosine (5')polyphospho(5')pyridoxals to study the substrate-binding region of glutathione synthetase from Escherichia coli B.

Adenosine(5')polyphospho(5')pyridoxals (APn-PLs, n = 2, 3, 4) were examined for affinity labeling of glutathione synthetase (EC 6.3.2.3) from Escherichia coli B. When the enzyme was incubated with an APn-PL or pyridoxal phosphate in the presence of Mg2+ and then reduced with sodium borohydride, it was most rapidly inactivated by AP4-PL. AP4-PL had a high affinity to the enzyme. The dissociation constant of AP4-PL in the inactivation process was 23 microM. The enzyme was almost completely protected from inactivation by addition of either ATP or gamma-glutamylcysteine. Complete inactivation corresponded to the incorporation of 1 mol of AP4-PL/mol of subunit of the tetrameric enzyme. Proteolytic digestion and sequence analysis of the AP4-PL-labeled enzyme revealed that only Lys-18 was modified. In contrast, the less efficient AP3-PL was found attached to Lys-17, Lys-18, Lys-144, and Lys-148. In the three-dimensional structure of the enzyme, Lys-18 is located close to the putative gamma-glutamylcysteine-binding site, but Lys-17, Lys-144, and Lys-148 are in the mouth of the inner-solvent region, at the bottom of which is the active-site cleft. Furthermore, difference Fourier analysis with the AP4-PL-soaked crystal of the enzyme showed that the adenosine moiety of the bound AP4-PL was in the crevice, which is the ATP-binding site of the enzyme. These results demonstrate the bivalent binding of AP4-PL lying across the gamma-glutamylcysteine- and ATP-binding sites.

Adenine Nucleotides↗

PubMed1993

Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database.

Recently we have constructed a database--the Enzyme-Reaction Database--which links a chemical structure to amino acid sequences of enzymes that recognize the chemical structure as their ligand. The total number of enzymes registered in the database is 1103 with 6668 NBRF-PIR entry codes and 1756 chemical compounds. The chemical structures and chemical names for 842 compounds are registered in the Chemical-Structure Database on the MACCS system. For each enzyme, the sequences were divided into clusters, and multiply aligned in each cluster to extract a conserved sequence. A total of 158,781 five-residue-long fragments were constructed from 433 conserved sequences and compared among different clusters of different enzymes. One of these motifs shared by different enzymes was S-G-G-L-D. The motif was conserved in both argininosuccinate synthase (EC 6.3.4.5) and asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4). This result showed that the database was useful for the analysis of the relationship between chemical structures and amino acid sequence motifs.

Algorithms↗

PubMed1993

SPECT imaging in a case of primary respiratory tract amyloidosis.

SPECT findings in a very rare case of primary amyloidosis localized in the laryngotracheobronchial area are reported. SPECT using Tc-99m PYP revealed widespread uptake in the larynx and the entire tracheobronchial tree up to the subsegmental divisions; the areas corresponded to diffuse thickening and calcification of the walls on CT. SPECT using Ga-67 citrate also showed marked uptake in the same area, consistent with the findings shown by SPECT using Tc-99m PYP.

Adult↗

PubMed1993

Fibroma of tendon sheath with ulceration.

We describe a 44-year-old man with fibroma of tendon sheath. The tumor originated in the foot and developed an ulcer during its course. It was totally excised, and the defect was reconstructed by full-thickness skin graft. The patient has been free of any recurrence during the follow-up period of one year. Fibroma of tendon sheath rarely occurs in the foot, and, to our best knowledge, this condition with ulceration is the first case reported.

Adult↗