Biomedical subjects

N Miyajima

Publications and source records attributed to N Miyajima.

At least 37 records · Page 2Linked to original sources

PubMed1999

Il-1, EGF, and HGF suppress the antiviral activity of interferon in primary monkey hepatic parenchymal cells.

The purpose of this study was to elucidate the mechanism behind low efficacy of interferon therapy to hepatitis C virus infected patients by using primary monkey hepatic parenchymal cells as a surrogate of primary human liver cells. The effects of various cytokines on the antiviral activity of IFNs in the monkey hepatic cells were studied to search for physiological inhibitors. Interleukin-1 alpha, EGF, and HGF showed suppressive effects on the antiviral activity of IFN-alpha, -beta in primary monkey hepatic cells when examined by the yield reduction method using vesicular stomatitis virus (VSV). In contrast, 50 ng/ml of TNF and IL-6 had no suppressive effect on the IFN-induced antiviral state in the hepatic cells.

Animals↗

PubMed1998

Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

In this paper, we report the sequences of 100 cDNA clones newly determined from a set of size-fractionated human brain cDNA libraries and predict the coding sequences of the corresponding genes, named KIAA0819 to KIAA0918. These cDNA clones were selected on the basis of their coding potentials of large proteins (50 kDa and more) by using in vitro transcription/translation assays. The sequence data showed that the average sizes of the inserts and corresponding open reading frames are 4.4 kb and 2.5 kb (831 amino acid residues), respectively. Homology and motif/domain searches against the public databases indicated that the predicted coding sequences of 83 genes were similar to those of known genes, 59% of which (49 genes) were categorized as coding for proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. The chromosomal locations and the expression profiles of all the genes were also examined. For 54 clones including brain-specific ones, the mRNA levels were further examined among 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substantia nigra, subthalamic nucleus, and thalamus), spinal cord, and fetal brain.

Amino Acid Sequence↗

PubMed1998

Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones.

A total of 17 Pl and TAC clones each representing an assigned region of chromosome 5 were isolated from P1 and TAC genomic libraries of Arabidopsis thaliana Columbia, and their nucleotide sequences were determined. The length of the clones sequenced in this study summed up to 1,081,958 bp. As we have previously reported the sequence of 9,072,622 bp by analysis of 125 P1 and TAC clones, the total length of the sequences of chromosome 5 determined so far is now 10,154,580 bp. The sequences were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling. As a consequence, a total of 253 potential protein-coding genes with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also assigned using computer programs for exon prediction. The average density of the genes identified in this study was 1 gene per 4277 bp. Introns were observed in 74% of the potential protein genes, and the average number per gene and the average length of the introns were 4.3 and 168 bp, respectively. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1998

Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

In our series of projects for accumulating sequence information on the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0711 to KIAA0810. These cDNA clones were selected according to their coding potentials of large proteins (50 kDa and more) in vitro. The average sizes of the inserts and corresponding open reading frames were 4.3 kb and 2.6 kb (869 amino acid residues), respectively. Sequence analyses against the public databases indicated that the predicted coding sequences of 78 genes were similar to those of known genes, 64% of which (50 genes) were categorized as proteins functionally related to cell signaling/communication, cell structure/motility and nucleic acid management. As additional information concerning genes characterized in this study, the chromosomal locations of the clones were determined by using human-rodent hybrid panels and the expression profiles among 10 human tissues were examined by reverse transcription-coupled polymerase chain reaction which was substantially improved by enzyme-linked immunosorbent assay.

Brain Chemistry↗

PubMed1998

Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones.

Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Animals↗

PubMed1998

Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro.

As an extension of our cDNA analysis for deducing the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0611 to KIAA0710. In vitro transcription-coupled translation assay was applied as the first screening to select cDNA clones which produce proteins with apparent molecular mass of 50 kDa and over. One hundred unidentified cDNA clones thus selected were then subjected to sequencing of entire inserts. The average size of the inserts and corresponding open reading frames was 4.9 kb and 2.8 kb (922 amino acid residues), respectively. Computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes were similar to those of known genes, 62% of which (54 genes) were categorized as proteins related to cell signaling/communication, cell structure/motility and nucleic acid management. The expression profiles in 10 human tissues of all the clones characterized in this study were examined by reverse transcription-coupled polymerase chain reaction and the chromosomal locations of the clones were determined by using human-rodent hybrid panels.

Brain Chemistry↗

PubMed1998

Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones.

Nineteen P1 and TAC clones, which have been mapped on the fine physical map of the Arabidopsis thaliana chromosome 5, were sequenced according to the shotgun-based strategy, and their structural features were analysed. The total length of the regions sequenced in this study was 1,367,185 bp. Combining this with the regions covered by 90 P1 and TAC clones previously reported, the total length of chromosome 5 sequenced to date becomes 8,058,855 bp. On the basis of similarity search against protein and EST databases and gene modeling with computer programs, a total of 330 potential protein-coding regions were identified, bringing an average density of the genes to approximately one gene per 4.1 kb. Introns were identified in 81.0% of the potential protein genes for which the entire gene structure was predicted, with an average number per gene of 4.2 and an average length of the introns of 180 bp. The RNA-coding genes identified were 9 tRNA genes corresponding to 8 amino acid species and 2 genes for U2 nuclear RNA. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1998

Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones.

The nucleotide sequences of 21 P1 and TAC clones which have been precisely localized to the fine physical map of the Arabidopsis thaliana chromosome 5, were determined, and their sequence features were analyzed. The total length of the regions sequenced in this study were 1,381,565 bp, bringing the total length of the chromosome 5 sequences determined so far to 6,691,670 bp together with the regions of the 69 clones previously reported. By computer-aided analyses including similarity search against protein and EST databases and gene modeling with computer programs, a total of 337 potential protein-coding genes and/or gene segments were identified on the basis of similarity to the reported gene sequences. An average density of the genes and/or gene segments thus assigned was 1 gene/4,100 bp. Introns were identified in 76.7% of the potential protein genes for which the entire gene structure were predicted, and the average number per gene and the average length of the introns were 3.9 and 176 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:@www.kazusa.or.jp@arabi

Arabidopsis↗

PubMed1998

Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro.

As an extension of a series of projects for sequencing human cDNA clones derived from relatively long transcripts, we herein report the entire sequences of 100 newly determined cDNA clones with the potential of coding for large proteins in vitro. The cDNA clones were isolated from size-fractionated human brain cDNA libraries with insert sizes between 4.5 and 8.3 kb. The sequencing of these clones revealed that the average size of the cDNA inserts and of their open reading frames was 5.3 kb and 2.8 kb (930 amino acid residues), respectively. Homology search against public databases indicated that the predicted coding sequences of 86 clones exhibited significant similarities to known genes; 51 of them (59%) were related to those for cell signaling/communication, nucleic acid management, and cell structure/motility. All the clones characterized in this study are accompanied by their expression profiles in 14 human tissues examined by reverse transcription-coupled polymerase chain reaction and the chromosomal mapping data.

Amino Acid Sequence↗

PubMed1998

Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones.

Nineteen P1 and TAC clones, which have been precisely localized to the fine physical map of Arabidopsis thaliana chromosome 5, were newly sequenced, and their sequence features were analysed. The total length of the clones sequenced was 1,456,315 bp. Together with the previously reported sequences, the regions of chromosome 5 that have been sequenced to date is now 5,310,105 bp. When the sequences determined in this study were subjected to similarity search against protein and expressed sequence tag (EST) databases and analysis with computer programs for gene modeling, a total of 354 potential protein-coding genes and/or gene segments were identified. The average density of the assigned genes and/or gene segments was one gene per 4,114 bp. Introns were identified in 75% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 194 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (the Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1998

CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803.

CyanoBase (http://www.kazusa.or.jp/cyano/) is a database containing genomic information on the cyanobacterium Synechocystis sp. strain PCC6803. It furnishes an annotation to each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. Information on the genome can be directly accessed through three different menus: a clickable physical map of the genome, a gene classification list, and a keyword search menu, all of which are accessible from the main page of the database. The entry page for a gene annotation contains the following information: the location of the gene on the genome, the nucleotide and deduced amino acid sequence of the gene, the result of a similarity search, and the classification of the deduced gene product according to its function. This page has reverse-links to the local physical map and gene classification list so that relevant genes can be searched in terms of their location on the genome and their function. In addition, the main page of CyanoBase provides engines for similarity searches between a query sequence and the entire genome sequence and for keyword searches, in addition to numerous links to pages containing related information.

Bacterial Proteins↗

PubMed1998

Common bile duct stones: management strategies in the laparoscopic era.

We reviewed our experience with the treatment of common bile duct (CBD) stones in 70 patients by sequential endoscopic-laparoscopic management and single-stage laparoscopic treatment during the past 7 years. The advantages, disadvantages, and feasibility of the two procedures are discussed to elucidate therapeutic strategies for patients harboring gallbladder stones and associated choledocholithiasis. In 44 patients, sequential endoscopic-laparoscopic management was indicatedd, and was successful in 37 of them but, in seven patients endoscopic stone extraction could not be accomplished. Single-stage laparoscopic treatment was attempted in 26 patients. In practice, laparoscopic transcystic common duct exploration or choledochotomy may not always be feasible if the cystic duct or CBD are not dilated; there is a high risk of intraoperative CBD injury in such circumstances. Laparoscopic management was considered to be especially useful for the treatment of numerous, large or difficult stones, because stone removal could be succesfully performed without any injury to the papilla of Vater. This last issue is of particular importance in patients with dilated CBD, because insufficient opening of the ampulla of Vater made by endoscopic sphincterotomy (EST) may lead to stasis and reflux-related complications such as cholangitis and recurrent stones. We conclude that the most rational management of CBD stones should be decided according to the size of the CBD, which depends on the size, number, and location of stones. Patients with dilated CBD are indicated to under-go laparoscopic single-stage treatment and combined endoscopic-laparoscopic treatment may be best for patients with non-dilated CBD.

Adolescent↗

PubMed1998

[Regional lymph node metastasis in renal pelvic or ureteral cancer].

BACKGROUND: The objective of this study is to evaluate the frequency of regional lymph node metastasis, clinical outcomes and histopathological findings of renal pelvic or ureteral cancer with regional lymph node metastasis. PATIENTS AND METHODS: One hundred and sixty three patients with renal pelvic or ureteral cancer were treated in our hospital between 1961 and 1995. Eighty nine in 155 patients underwent lymph node dissection. Frequency of regional lymph node metastasis, clinical outcomes and histopathological findings of these 89 patients were investigated. Patient survival rates were determined by actuarial calculation using Kaplan-Meier method with log-rank test. RESULTS: The status of lymph node involvement was pN0 in 61 (68.5%), pN1 in 5 (5.6%), pN2 in 15(16.9%) and pN3 in 8 patients (9.0%). The 5-year survival rate was 78.8%, 12.5%, 20.0% and 0% for pN0 pN(+), pN1, pN2 and pN3 respectively. In 28 patients with regional lymph node metastasis, patients with distant metastasis were all dead within 1.2 years and the 3- or 5-yer survival rates of patients without distant metastasis were 31.4% and 15.7%. The difference between two groups were obvious (p < 0.01). The 3-year survival rate was 100%, 66.7%, 33.3% and 0% for pT1, pT2, pT3 and pT4 patients with M0 and pN(+) respectively. CONCLUSION: Our data suggested that conventional treatments were not effective for almost patients with regional lymph node metastasis. However in the patients with low grade, under pT3 and M0, pN1-2, the possibility of long time survival was shown.

Adult↗

PubMed1997

Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones.

A total of 17 P1 and TAC clones each containing a marker(s) specifically mapped on chromosome 5 were isolated from P1 and TAC libraries of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun-based strategy and precisely located on the physical map of chromosome 5. The total length of the clones sequenced in this study was 1,191,918 bp. As we have previously reported the sequence of 2,662,078 bp by analysis of 33 P1 clones, the total length of the sequences of chromosome 5 determined so far is now 3,853,996 bp. The sequences determined in this study were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling, and a total of 310 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also predicted by computer-aided analysis. An average density of the assigned genes and/or gene segments was 1 gene/3,845 bp. Introns were identified in 78% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 185 bp, respectively. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1997

Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro.

As a part of our project for accumulating sequence information of the coding regions of unidentified human genes, we herein report the sequence features of 78 new cDNA clones isolated from human brain cDNA libraries as those which may code for large proteins. The sequence data showed that the average size of the cDNA inserts and their open reading frames was 6.0 kb and 2.8 kb (925 amino acid residues), respectively, and these clones produced the corresponding sizes of protein products in an in vitro transcription/translation system. Homology search against the public databases indicated that the predicted coding sequences of 68 genes contained sequences similar to known genes, 69% of which (47 genes) were related to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of these genes in 14 different tissues have been analyzed by the reverse transcription-coupled polymerase chain reaction method, and 8 genes were found to be predominantly expressed in the brain.

Brain Chemistry↗

PubMed1997

Characterization of cDNA clones in size-fractionated cDNA libraries from human brain.

To evaluate the size-fractionated cDNA libraries of human brain previously constructed (O. O'hara et al. DNA Research, 4, 53-59, 1997), the occurrence of chimeric clones and the content of clones with coding potentiality were analyzed using the randomly sampled clones with insert sizes of 5 to 7 kb. When the chromosomal location of 30 clones was determined by the radiation-hybrid mapping method, the map positions assigned from the 3'- and 5'-end sequences separately were coincident for 29 clones, suggesting that the occurrence of chimeric clones is at most 1/30. Using 91 clones mapped to chromosome 1, the content of clones that have the potentiality coding for proteins larger than 100 amino acid residues was estimated to be approximately 50% (46 out of 91 clones) on the basis of nucleotide sequence analysis and coding potentiality assay in vitro. No significant open reading frames were detected in the remaining clones. Although the clones coding for short peptides may not have been included in the above estimation, the libraries constructed from the whole brain mRNA fraction appear to contain a considerable amount of clones corresponding to the 5'-truncated transcripts in an unprocessed form and/or those with long 3'-untranslated regions.

Animals↗

PubMed1997

Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones.

A total of 13 P1 clones, each containing a marker(s) specifically mapped on chromosome 5, were isolated from a P1 library of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun based strategy and precisely located on the physical map of chromosome 5. The total length of the sequenced regions was 1,044,062 bp. Since we have previously reported the sequence of 1,621,245 bp by analysis of 20 non-redundant P1 clones, the total length of the sequences of chromosome 5 determined so far reached 2,665,307 bp. The regions sequenced in this study were analysed by comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling; a total of 225 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit similarity to known genes were also predicted by computer-aided analysis. An average density of the genes and/or gene was 1 gene/4,640 bp. Introns were identified in approximately 84% of the potential genes, and the average number and length of the introns per gene were 5.3 and 184 bp, respectively. These sequence features are essentially identical to those for the previously sequenced regions. The transcription level of the predicted genes has been roughly monitored by counting the numbers of matched Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http:@www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1997

Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones.

A total of 20 P1 clones with an average insert size of 80 kb and each containing a marker(s) specifically mapped on chromosome 5 were isolated from a P1 library of the Arabidopsis thaliana genome, and their nucleotide sequences were determined according to a shotgun-based strategy and precisely located on the physical map of chromosome 5 separately constructed. The total length of the sequenced regions were summed up to 1,621,245 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 347 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit any similarity to known genes were also predicted. An average density of the genes and/or gene segments assigned so far as 1 gene/4,672 bp. Introns were identified in approximately 78% of the potential genes, and the average number and length of the introns per gene were 3.7 and 161 bp. The transcription level of the predicted genes was roughly monitored by counting the numbers of identified Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http:/(/)www.kazusa.or.jp/arabi/.

Arabidopsis↗