Biomedical subjects

O Gotoh

Publications and source records attributed to O Gotoh.

At least 55 records · Page 3Linked to original sources

PubMed1994

Further improvement in methods of group-to-group sequence alignment with generalized profile operations.

It has previously been shown that rigorous optimization of alignment between two groups of sequences in the sense of minimal sum of pairs (SP) score with a linear gap-weighting function can be achieved by an extended version of the dynamic programming algorithm. The major drawback of this algorithm was that the computation time grows in proportion to the product of the numbers (M and N) of sequences comprising the two groups. A new algorithm presented in this paper achieves the same rigorous alignment in a time complexity much less dependent on the sizes of the groups. Examinations with many groups of sequences indicated that the new algorithm runs faster than the earlier one when M x N > 6-10, approximately 10 times faster when M x N approximately 200, and > 100 times faster when M x N > 2500. This computational acceleration facilitates application of the algorithm to alignment of large groups, especially in the framework of iterative refinement strategies.

Algorithms↗

PubMed1994

Interindividual difference in expression of human Ah receptor and related P450 genes.

The genomic clones of human aryl hydrocarbon receptor (Ahr) and Ahr nuclear translocator (Arnt) were isolated, and the structures of exon-intron junctions of these genes were partially determined. Based on the sequence information, a quantitative RT-PCR analysis was developed, and the expression of these genes was studied in various human tissues. mRNAs for Ahr and Arnt were widely expressed in human tissues and abundantly in lung. Individual difference in expression levels of Ahr and Arnt mRNA was observed in liver, lung and blood. In order to examine whether expression levels of Ahr and Arnt were associated with those of CYP1A1, we studied the expression of these mRNAs in blood among 20 healthy subjects, taking account of individuals' cigarette smoking habits. We found that the expression levels of CYP1A1 appeared to associate with those of Ahr and Arnt mRNAs (P < 0.06), and also that the expression of Ahr and Arnt was influenced by cigarette smoking. The expression of human Ahr and Arnt is reported here for the first time, providing a quantitative RT-PCR analysis as a useful tool for further studies.

Adult↗

PubMed1993

Structural characterization of the gene encoding rat 25-hydroxyvitamin D3 24-hydroxylase.

The structural gene encoding 25-hydroxyvitamin D3 24-hydroxylase (P-450cc24) was isolated from the rat genomic DNA. It spans approximately 15 kb, is composed of 12 exons, and was demonstrated by Southern blot analysis to be present as a single copy. One major T residue was identified at the cap site, a putative TATA (ATAAATA) box was located at position -30, and a putative CCAAT box was at -58. Four possible vitamin D responsive elements that may be involved in regulation of 24-hydroxylase expression were found in the 5'-flanking region. Alignment with mitochondrial P-450 proteins showed that 7 out of 11 intron insertion sites of P-450cc24 gene occupied positions identical with those in the CYP11 family (P-450scc, P-450(11 beta)). The structure of the gene is discussed in relation to present knowledge about the mechanism of regulation of the 25-hydroxyvitamin D3 24-hydroxylase and calcium homeostasis.

Amino Acid Sequence↗

PubMed1993

Optimal alignment between groups of sequences and its application to multiple sequence alignment.

Four algorithms, A-D, were developed to align two groups of biological sequences. Algorithm A is equivalent to the conventional dynamic programming method widely used for aligning ordinary sequences, whereas algorithms B-D are designed to evaluate the cost for a deletion/insertion more accurately when internal gaps are present in either or both groups of sequences. Rigorous optimization of the 'sum of pairs' (SP) score is achieved by algorithm D, whose average performance is close to O(MNL2), where M and N are numbers of sequences included in the two groups and L is the mean length of the sequences. Algorithm B uses some approximations to cope with profile-based operations, whereas algorithm C is a simpler variant of algorithm D. These group-to-group alignment algorithms were applied to multiple sequence alignment with two iterative strategies: a progressive method based on a given binary tree and a randomized grouping--realignment method. The advantages and disadvantages of the four algorithms are discussed on the basis of the results of examinations of several protein families.

Algorithms↗

PubMed1993

[Acute aneurysm surgery and the Glasgow Coma Scale: relationship with 6-month outcome].

A series of 610 patients who had aneurysm surgery within 7 days of the hemorrhage were analyzed as to the relationship between the preoperative Glasgow Coma Scale (GCS) score and the outcome assessed by using the Glasgow Outcome Scale (GOS) at 6 months after surgery. The patient distribution in accordance with the GCS scores in descending order from 15 to 3 was as follows: 265, 109, 44, 24, 17, 20, 25, 15, 18, 12, 16, 23, and 22 cases, respectively. In general, the larger the GCS score, the better the outcome. Thus, the overall results proved to be significantly correlated with the GCS score prior to surgery (r = 0.608, P < 0.01). As for demarcation levels along the GCS axis in terms of the GOS, a significant difference in the outcome was observed at the level of GCS scores between 15 and 14 (P < 0.0001, Wilcoxon test). However, no borderlines were evident at any GCS levels other than 15/14. The problems of applying the GCS to the grading system of aneurysmal subarachnoid hemorrhage are discussed.

Adult↗

PubMed1993

[Vasospasm and its outcome after early surgery for ruptured cerebral aneurysms: changing pattern of its incidence and outcome during this 9-year period].

The occurrence and outcome of vasospasm (VS) were analyzed in 240 patients who had aneurysm surgery within 7 days of a hemorrhage during 9-year period (1981-89). Occurrence of VS was evaluated by the appearance of ischemic symptoms, (A) with or (B) without CT evidence of infarcts. The surgical outcome was assessed by the Glasgow Outcome Scale 6 months postoperatively. The results in the first and the latter halves of the period were compared. The overall incidence of VS (A+B) was 34.8% (A: 23.5%, B: 11.3%) and 33.6% (A: 15.2%, B: 18.4%) in the first and the latter halves, respectively. Thus, VS leading to infarction showed a tendency to decrease in the latter half of the period, though the overall incidence of VS itself was almost identical in both the first and second halves of the period. The results were also analyzed according to preoperative grading based on the Glasgow Coma Scale (GCS). The tendency toward decreased severity of VS in the latter term was most remarkable in patients with GCS total scores between 14 and 13. The decreased incidence of severe VS proved to be reflected in decreased mortality and in increased rate of good outcome in the latter half of the period. In order to confirm whether the results obtained in our clinic are universal, we applied the same analysis for control groups in four cooperative double-blind clinical trials performed during this period in Japan. The study again showed that the rate of infarction has decreased significantly over the decade, resulting in the improved surgical outcome.(ABSTRACT TRUNCATED AT 250 WORDS)

Cerebral Infarction↗

PubMed1993

[Vasospasm and its outcome after early surgery for ruptured cerebral aneurysms: relationship with the clinical grade based on the Glasgow Coma Scale].

Over a 9 year period, 270 patients who had early aneurysm surgery within 7 days after subarachnoid hemorrhage were analyzed regarding occurrence of vasospasm (VS) and its outcome. Occurrence of VS was recognized by ischemic neurological deterioration, with or without CT evidence of infarcts. Surgical outcome was assessed by the Glasgow Outcome Scale 6 months postoperatively. The results were correlated with age, aneurysm site, day of surgery, and preoperative clinical grade evaluated by the Glasgow Coma Scale (GCS). Thirty patients with the GCS sum score of less than 6 were excluded from the analysis of VS. Eighty two patients (34%) developed VS, of which 36 patients (15%) showed ischemic symptoms only, and 46 (19%) had infarct on CT. The incidence of symptomatic VS was 12% in GCS 15 group (117 patients), 23% in GCS 14-13 group (70 patients), and 11% in GCS 12-7 group (53 patients). That of VS with infarct was 14%, 23%, and 26% in GCS 15, GCS 14-13, and GCS 12-7 groups, respectively. Thus, there was a close correlation between the clinical grade based on the GCS and the incidence of VS, especially with infarct. The grade was also useful in predicting the surgical outcome. VS was more common in the older age group. The site of aneurysm or the day of surgery had no apparent influences on the incidence of VS or its outcome. Overall, the incidence of poor outcome due to VS proved to be 12%, which accounted for one-third of the cases in which there was poor outcome due to various causes.

Adult↗

PubMed1992

cDNA cloning and structure of mouse putative Ah receptor.

Mouse cDNA clones for a putative Ah receptor have been isolated from a cDNA library of mRNA from Hepa-1 cells by an oligonucleotide probe produced by PCR with a pair of primers which was synthesized according to the reported N-terminal sequence of 26 amino acids. The cDNA clones encode a polypeptide of 805 amino acids with a helix-loop-helix motif and with some similarity to a certain region designated PAS of Drosophila Per and Sim, and human Arnt protein. Cotransfection of an expression vector of the Ah receptor with a reporter plasmid pMC6.3k consisting of CYP1A1 promoter and CAT structural gene into CV-1 cells enhanced the CAT expression in response to added 3-methylcholanthrene.

Amino Acid Sequence↗

PubMed1992

Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences.

The substrate recognition regions in cytochrome P450 family 2 (CYP2) proteins were inferred by group-to-group alignment of CYP2 sequences and those of bacterial P450s, including Pseudomonas putida P450 101A (P450cam), whose substrate-binding residues have been definitely identified by x-ray crystallography of a substrate-bound form (Poulos T. L., Finzel, B. C., and Howard, A. J. (1987) J. Mol. Biol. 195, 687-700). The six putative substrate recognition sites, SRSs, thus identified are dispersively located along the primary structure and constitute about 16% of the total residues. All the reported point mutations and chimeric fragments that significantly affect the substrate specificities of the parental CYP2 enzymes fell within or overlapped some of the six SRSs. Analysis of nucleotide substitution patterns in closely related members in four subfamilies, CYP2A, 2B, 2C, and 2D, consistently indicated that the SRSs have accumulated more nonsynonymous (amino acid-changing) substitutions than the rest of the sequence. This observation supports the idea that diversification of duplicate genes of drug-metabolizing P450s occurs primarily in substrate recognition regions to cope with an increasing number of foreign compounds.

Amino Acid Sequence↗

PubMed1992

A second gene for the African green monkey poliovirus receptor that has no putative N-glycosylation site in the functional N-terminal immunoglobulin-like domain.

Using cDNA of the human poliovirus receptor (PVR) as a probe, two types of cDNA clones of the monkey homologs were isolated from a cDNA library prepared from an African green monkey kidney cell line. Either type of cDNA clone rendered mouse L cells permissive for poliovirus infection. Homologies of the amino acid sequences deduced from these cDNA sequences with that of human PVR were 90.2 and 86.4%, respectively. These two monkey PVRs were found to be encoded in two different loci of the genome. Evolutionary analysis suggested that duplication of the PVR gene in the monkey genome had occurred after the species differentiation between humans and monkeys. The NH2-terminal immunoglobulin-like domain, domain 1, of the second monkey PVR, which lacks a putative N-glycosylation site, mediated poliovirus infection. In addition, a human PVR mutant without N-glycosylation sites in domain 1 also promoted viral infection. These results suggest that domain 1 of the monkey receptor also harbors the binding site for poliovirus and that sugar moieties possibly attached to this domain of human PVR are dispensable for the virus-receptor interaction.

Amino Acid Sequence↗

PubMed1991

Nucleotide sequence of the unique nitrate/nitrite-inducible cytochrome P-450 cDNA from Fusarium oxysporum.

A cDNA clone for the nitrate/nitrite-inducible cytochrome P-450 (P-450) of the fungus Fusarium oxysporum (tentatively termed P-450dNIR) was isolated by an immunoscreening method. Sequence determination revealed a polypeptide of 403 amimo acid residues (Mr = 44,371), which was shown to contain the full-length sequence of the fungal P-450. The amino terminus region of the predicted sequence contained neither the signal-like, hydrophobic domain that is commonly observed in microsomal P-450s nor the tagging prosequence that is essential for localization of mitochondrial P-450s. Further, the sequence exhibited higher homologies against those of soluble bacterial P-450s, in particular P-450s of Streptomyces, rather than those of eukaryotic P-450s including yeast and fungal P-450s. These results are highly indicative that P-450dNIR is the first soluble P-450 derived from eukaryotic organisms. The unique features might be related to the novel function of P-450dNIR, which is involved in a dissimilatory reduction of nitrite by the fungus. P-450dNIR was classified into a new family, P-450LV, and the corresponding gene of the fungus was named CYP55.

Amino Acid Sequence↗

PubMed1991

Structural analysis of the gene encoding rat cholesterol alpha-hydroxylase, the key enzyme for bile acid biosynthesis.

The gene encoding cholesterol 7 alpha-hydroxylase (P450VIIA) was isolated from rat genomic DNA. The gene spanned about 11 kilobases and contained six exons. Blotting analysis of genomic DNA and complete matching of restriction maps of several isolated genomic clones indicated that there appeared to be only one gene in the rat genome. The putative transcription initiation site was present 61 base pairs upstream from the ATG codon. The typical TATA sequence and CCAAT promoter element were found at 24 and 47 base pairs upstream from the transcription initiation site, respectively. Alignment of several P450 proteins showed that the cholesterol 7 alpha-hydroxylase gene shared location of introns with none of the other P450 genes except for intron 5, which was in the same position as intron 10 of the gene encoding P450IVA1. The alignment also indicated that the distal helix of cholesterol 7 alpha-hydroxylase contained an asparagine in place of the well conserved threonine that is postulated to be involved in the O2 binding site. Unusual residues, Asn-126 and Thr-442, were also found at the sites where all other P450s have positively charged amino acids, which are considered to be involved in interaction with heme propionate. These replacements may be related to the unique function and unusual lability of the hydroxylase. Analysis of evolutionary distance between the cholesterol 7 alpha-hydroxylase gene and other known P450 genes indicated that yeast P450LIA is most closely related to P450VIIA. This finding suggests that the cholesterol 7 alpha-hydroxylase gene is an evolutionarily old P450 gene.

Amino Acid Sequence↗

PubMed1991

Xenobiotic responsive element in the 5'-upstream region of the human P-450c gene.

The nucleotide sequence of the 5'-upstream region up to about -4.1 kb of the human P-450c gene was determined. Two kinds of repetitive sequences were located; one was the Alu sequence which was inserted at three positions (-3127 to -3038, -3017 to -2770, and -2167 to -1851), and the other was the SINE-R element located just upstream of the most distal Alu sequences. The region other than the two repeated sequences showed an overall similarity of 70% to that of the rat P-450c gene. Survey of XRE or its homologues, responsible for the inducible expression of the rat P-450c gene, revealed eight XRE core sequences in this region of the human P-450c gene. Three of them were carried in the Alu sequences. A fusion gene which was constructed by ligating the upstream region of the human P-450c gene to the chloramphenicol acetyltransferase (CAT) gene expressed the CAT activity in response to the inducer, methylcholanthrene, when transfected into Hepa-1 cells. Stepwise decrease in CAT activity in three regions was observed as the 5'-upstream sequence containing XRE motifs was removed. However, the XRE core sequence in the Alu sequences seemed inactive, because elimination of the three elements in the Alu sequences did not affect the expressed CAT activity. In accordance with this observation, competition experiments using gel mobility shift assay showed that XRE core sequences in the Alu sequences could not compete with the XRE sequence for the inducer-bound receptor.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1991

Thalamic atrophy following cerebral infarction in the territory of the middle cerebral artery.

We investigated shrinkage of the ipsilateral thalamus following infarction in the territory of the middle cerebral artery in 33 patients who were admitted less than or equal to 2 days after the stroke and who were followed by computed tomography for greater than 1 year with no recurrences. The thalamic area was measured on the computed tomograms, and the ratio of the ipsilateral area to the contralateral area was calculated. All values were compared with values from the initial computed tomogram taken less than or equal to 2 days after the stroke. The values of the ratio on follow-up computed tomograms decreased gradually in 15 patients. In these cases, the area of the ipsilateral thalamus was significantly reduced after 1 year (p less than 0.01) and marked atrophy was observed. These results demonstrate the significance of remote changes over a long period of time after focal cerebral infarction.

Atrophy↗

PubMed1990

Structural and functional analysis of the human thymidylate synthase gene.

The complete nucleotide sequence of the human thymidylate synthase (TS) gene was determined. The biologically active unit spans about 16 kilobase pairs (kbp) and is composed of seven exons and six introns. The promoter region and the major transcriptional start sites were located within about 400 base pairs (bp) and 160-180 bp, respectively, upstream from the ATG initiation codon. A minigene consisting of a 5'-flanking sequence of about 4 kbp, a coding sequence of about 1.7 kpb was sufficient for cell cycle-dependent expression of TS when introduced into a TS-deficient mutant of rodent cells. The 5'-flanking region does not contain a "TATA," "CAAT," or the consensus sequence for Sp1 binding (GC box), whereas intron 1 contains three GC boxes. The gene is G + C-rich and the CpG-rich region extends from 5'-flanking region to intron 1. These sequence characteristics were compared with those of the mouse TS gene and other cell cycle-regulated genes.

Animals↗

PubMed1990

cDNA cloning of cytochrome P-450 related to P-450p-2 from the cDNA library of human placenta. Gene structure and expression.

We have isolated and analyzed cDNA (designated P-450HP cDNA) clones from a human placenta cDNA library, using the cDNA for rabbit pulmonary cytochrome P-450p-2, a prostaglandin omega-hydroxylase, as a hybridization probe. The cDNA obtained encoded a polypeptide comprising 511 amino acids with a calculated molecular mass of 58987 Da, and the amino acid sequence similarity with P-450p-2 and rat liver laurate omega-hydroxylase (P-450LA omega) was only about 50%. RNA blot analysis showed that the mRNA hybridizable with the human P-450HP cDNA was inducibly expressed 3-5-fold in rabbit small intestine and lung by gestation, but the expression remained constant in rabbit liver and kidney. This mode of expression was quite different from that of P-450p-2 and P-450LA omega. Interestingly, the mRNA hybridized with the cDNA of P-450HP was found to be expressed in all the human tumor tissues so far examined, in sharp contrast with the facts that almost all the other species of P-450s are known to disappear in the tumor tissues. Taken together, the deduced hemoprotein termed P-450HP dose not seem to be the human counterpart of rabbit P-450p-2 or rat P-450LA omega, and is presumably a new member of the P-450 family including P-450p-2 and P-450LA omega. Furthermore, the corresponding genomic DNA was also cloned and analyzed. The gene of P-450HP spanned 18.8 kb and was separated into 11 exons by 10 introns whose locations were completely different from those of P-450 genes so far determined.

Amino Acid Sequence↗

PubMed1990

Differentiation of restriction sites in ribosomal DNA in the genus Apodemus.

Southern blot analysis of ribosomal DNA (rDNA) from seven species of Apodemus was carried out in order to examine the genetic relationships between the species. Analysis of heterogeneity in rDNA spacers in A. sylvaticus, A. flavicollis, A. semotus, A. agrarius, A. argenteus, A. speciosus, and A. peninsulae, using 13 different restriction enzymes and cloned mouse rDNA probes, revealed that the families of rDNA in these species can be characterized by restriction maps which show the major constituents of rDNA repeating units (repetypes). Based on differences in the arrangement of restriction sites, sequence divergence among the different major repetypes was estimated. Among the seven species of Apodemus examined, the major repetypes of A. flavicollis and A. sylvaticus were the most closely related, having only 1.0% sequence divergence. These repetypes and those of the remaining five species differ substantially from one another, with 4.3-8.5% divergence.

Animals↗

PubMed1990

Speech perception and auditory P300 potentials after section of the posterior half of the truncus of the corpus callosum.

A 47 year old woman who underwent surgical section of the posterior half of the corpus callosum because of meningioma in the right lateral ventricle was studied from the aspects of speech perception and auditory evoked potentials. The pure tone audiometry showed normal hearing levels for both ears. The monosyllable perception test disclosed that the left ear had lower correct percent than the right ear. The dichotic listening test demonstrated remarkable extinction in response to verbal stimuli in the left ear. Auditory brainstem, middle latency and slow vertex responses were normal for both ears, without right and left difference. P300 event related potentials were recorded by three different pairs of stimuli: pure tone (1 KHz vs. 2 KHz), words (Aka vs. Kuro), and monosyllable (PA vs. BA). Both P300 for pure tone and word stimuli to each ear showed large positive potentials within 200-500 msec but P300 for monosyllable stimuli to each ear did not show obvious potentials within 200-500 msec. These results suggest that the posterior half of the truncus of the corpus callosum can be related to transfer of speech information between right and left hemispheres.

Acoustic Stimulation↗