Biomedical subjects

N Miyajima

Publications and source records attributed to N Miyajima.

At least 19 recordsLinked to original sources

PubMed2000

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.

Animals↗

PubMed2000

Isolation of a cDNA for a novel human RING finger protein gene, RNF18, by the virtual transcribed sequence (VTS) approach(1).

We have recently developed a novel database system, designated as the virtual transcribed sequence (VTS) which efficiently extracts many genes from public human genome databases, and tested the feasibility of this novel computational approach (N. Miyajima, C. Burge, T. Saito, Biochem. Biophys. Res. Commun. 272 (2000) 801; http://host45.maze.co.jp/vts/). In this study, using the VTS approach, we isolated a cDNA for a novel human gene with RING finger motif (C(3)HC(4)), which is not deposited in public EST databases. The isolated cDNA clone is 2163 bp in length, and contains an open reading frame of 452 amino acids. We designated the novel gene as RNF18. A database search showed that the RNF18 gene had the moderate similarity to SS-A/Ro52 protein, which is a ribonucleoprotein reactive with autoantibodies in patients with Sjögren's syndrome and systemic lupus erythematosus. Tissue distribution analyses by Northern blot and RT-PCR methods demonstrated that the RNF18 messenger RNA was preferentially expressed in testis. The exon-intron boundaries of RNF18 gene were determined by aligning the cDNA sequence with the corresponding genome sequence. The isolated cDNA consists of eight exons that span about 11 kb of the genome DNA. The precise chromosomal location of the RNF18 gene was determined by PCR-based radiation hybrid mapping, and the gene was located to centromere region of chromosome 11 between markers NIB1900 and D11S1350. Taken together, the VTS approach should provide a novel cDNA cloning strategy for isolating unidentified genes, which are not found even in EST databases but are detectable computationally.

Amino Acid Sequence↗

PubMed2000

Computational and experimental analysis identifies many novel human genes.

Because of advances in automation, human genomic sequences are being deposited in public databases at a dramatic rate. However, the process of detecting genes in these sequences is still something of an art. Here we describe the implementation and testing of a relatively straightforward computational approach, the Virtual Transcribed Sequence project, which analyzes their gene content using the gene prediction program GENSCAN (GENSCAN 1.0 1,2) in combination with similarity-based methods. This approach identifies many novel human genes not found even in EST databases.

Amino Acid Sequence↗

PubMed2000

Expression of m2 muscarinic acetylcholine receptor mRNA in primary culture of human prostate stromal cells.

The aim of this study was to investigate the expression of the muscarinic acetylcholine receptor (mAchR) subtypes mRNA in primary culture of human prostate stromal cells using the reverse transcription polymerase chain reaction (RT-PCR), RNA blotting and in situ hybridization (ISH). Using an explant method, we obtained a primary culture of prostate stromal cells from three patients with benign prostatic hypertrophy. Total RNA was extracted using the acid guanidinium method for cDNA synthesis. First-strand cDNA was then used for PCR with primers designed to amplify the fragments of each mAchR subtypes (m1-m5) cDNA sequence. The m2, m3 and m4 subtype expected bands were detected; in particular m2 transcripts was strongly detected in the stromal cell culture. Each of the PCR products were subcloned into the pGEM-T plasmid vector, sequenced and random primer labeled using 32P. Digoxigenin-labeled cRNA probes were synthesized by in vitro transcription. RNA blotting using a m2 muscarinic receptor cDNA probe revealed a 4.5 kb single transcript. However, m3 and m4 probes did not hybridize. Using in situ hybridization (ISH), m2 receptor mRNA signals were detected in several smooth muscle cells. The staining was predominantly localized to the perinuclear cytoplasm. The m3 and m4 probes did not hybridize. These results suggested that m2 receptor subtype plays a role in smooth muscle activity of the human prostate.

Blotting, Northern↗

PubMed2000

cDNA cloning of a human RAB26-related gene encoding a Ras-like GTP-binding protein on chromosome 16p13.3 region.

Members of the RAB protein family are important regulators of vesicular fusion and trafficking. A putative new member of the RAB family of genes was identified through a public database search, and its full-length cDNA was isolated from a human fetal brain cDNA library. The predicted protein product of the gene consists of 190 amino acid residues and has 87% identity with rat Rab26. Thus, we designated this gene as the human RAB26-related gene. Reverse transcription-coupled polymerase chain reaction (RT-PCR) demonstrated that the RAB26-related messenger RNA was predominantly expressed in adult and fetal brain. Furthermore, an RT-PCR experiment for brain subregions showed that the mRNA was highly expressed in the amygdala, cerebellum, caudate nucleus, and hippocampus. By PCR-based analysis with both a human/rodent monochromosomal hybrid cell panel and a radiation hybrid panel, the gene was mapped to the chromosome 16p13.3 region between markers WI-7742 and WI-3061. The RAB26-related gene consists of eight exons that span about 44kb of the genome DNA.

Amino Acid Sequence↗

PubMed2000

Comparative nucleotide sequence analyses of the entire genomes of B95a cell-isolated and vero cell-isolated measles viruses from the same patient.

Experimental infection of monkeys with the IC-B strain of measles virus (MV), which was isolated in marmoset B lymphoblastoid B95a cells from an acute measles patient, caused clinical signs typical for measles, while infection by the IC-V strain isolated in African green monkey kidney Vero cells from the same patient did not cause any clinical signs in infected monkeys. The IC-B strain replicated only in B95a cells, whereas the IC-V strain replicated in both B95a and Vero cells (3,6). To clarify which gene or mutation(s) was responsible for the difference in these phenotypes, the nucleotide sequences of the entire genomes of the IC-B and IC-V strains were determined. Comparative nucleotide sequence analyses revealed only two nucleotide differences, one in the P/V/C gene and the other in the M gene, predicting amino acid differences in the P, V and M proteins and a 19 amino acid deletion in the C protein of the IC-V strain. The truncation in the C protein was confirmed for the IC-V strain by immunoprecipitation using the C protein specific antiserum. No nucleotide difference was found in the envelope H gene. These results indicated that nucleotide difference(s) in the P/V/C or/and M gene, and not H gene, was responsible for the different cell tropism and pathogenicity of MV in this case.

Animals↗

PubMed2000

Suppression of interferon-induced antiviral activity in cells expressing hepatitis C virus proteins.

To elucidate the mechanism of the persistent nature of hepatitis C virus (HCV) infection, we examined whether the expression of HCV proteins affect the antiviral activity of interferon (IFN). Antiviral activity of IFN in HepG2 cells expressing all HCV (type 1b) proteins was much lower than vector control (VC) HepG2 cells when encephalomyocarditis virus (EMCV) was used as a challenge virus. Lesser sensitivity to IFN was also observed in cells expressing NS3, NS4, and NS5 and in cells expressing only NS5A. In contrast, HepG2 cells expressing core, E1, E2, NS2, and NS3 proteins were equally sensitive to IFN as VC cells. We then tested the antiviral activity by IFN in two human amnion-derived FL cell lines expressing NS5A from two different clones, one with an intact sequence of IFN sensitivity-determining region (ISDR) and the other with a mutated ISDR sequence. They were almost equally insensitive to IFN treatment when EMCV was challenged. HCV thus has functional protein(s), possibly NS5A, to suppress IFN-induced antiviral activity and plays an important role in virus-cell interaction and regulation of viral replication.

Antiviral Agents↗

PubMed2000

Recovery of pathogenic measles virus from cloned cDNA.

Reverse genetics technology so far established for measles virus (MeV) is based on the Edmonston strain, which was isolated several decades ago, has been passaged in nonlymphoid cell lines, and is no longer pathogenic in monkey models. On the other hand, MeVs isolated and passaged in the Epstein-Barr virus-transformed marmoset B-lymphoblastoid cell line B95a would retain their original pathogenicity (F. Kobune et al., J. Virol. 64:700-705, 1990). Here we have developed MeV reverse genetics systems based on the highly pathogenic IC-B strain isolated in B95a cells. Infectious viruses were successfully recovered from the cloned cDNA of IC-B strain by two different approaches. One was simple cotransfection of B95a cells, with three plasmids each encoding the nucleocapsid (N), phospho (P), or large (L) protein, respectively, and their expression was driven by the bacteriophage T7 RNA polymerase supplied by coinfecting recombinant vaccinia virus vTF7-3. The second approach was transfection with the L-encoding plasmid of a helper cell line constitutively expressing the MeV N and P proteins and the T7 polymerase (F. Radecke et al., EMBO J. 14:5773-5784, 1995) on which B95a cells were overlaid. Virus clones recovered by both methods possessed RNA genomes identical to that of the parental IC-B strain and were indistinguishable from the IC-B strain with respect to growth phenotypes in vitro and the clinical course and histopathology of experimentally infected cynomolgus monkeys. Thus, the systems developed here could be useful for studying viral gene functions in the context of the natural course of MeV pathogenesis.

Animals↗

PubMed2000

[A case of lung tumorlets with pulmonary carcinoid].

It has been postulated that differential pathological diagnosis of lung tumorlet from pulmonary carcinoid is very important to decide the therapeutic strategy, because both of them are pathologically consisted of similar type of cells originated from same cells. At the present, although lung tumorlet is considered to be a hyperplastic lesion of Kultschitzky cells which is located in the epithelial cell of the bronchial mucosa by stimuli such as hypoxia and inflammation, but it occasionally recognized in the normal lung and the concept that it is a subtype of carcnoid is also undeniable. In this paper, a case of lung tumorlet with minute pulmonary carcinoid suggesting a subtype of carcinoid operated upon in our department is presented. Although simple pulmonary resection is a method of choice for pulmonary carcinoid, but it is still controversial as to therapeutic strategy for the lung tumorlet, because it is a benign entity and not tumorous lesion. However pulmonary resection with a close subsequent followed-up study must be a best method of choice for the case with lung tumorlet includes a minute lesion of carcinoid seen in this particular case.

Carcinoid Tumor↗

PubMed1999

Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones.

In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential protein-coding genes in the 10,154,580 bp regions, which are covered by 142 P1 and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 P1 and TAC clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available on the database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Arabidopsis↗

PubMed1999

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

To extend our cDNA project for accumulating basic information on unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human adult and fetal brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA1019 to KIAA1118. The sequencing of these clones revealed that the average size of the inserts and corresponding open reading frames were 5.0 kb and 2.6 kb (880 amino acid residues), respectively. Database search of the predicted amino acid sequences classified 58 predicted gene products into the five functional categories, such as cell signaling/communication, cell structure/motility, nucleic acid management, protein management and cell division. It was also found that, for 34 gene products, homologues were detected in the databases, which were similar in sequence through almost the entire regions. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗

PubMed1999

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

As a part of our cDNA project for deducing the coding sequence of unidentified human genes, we 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 KIAA0919 to KIAA1018. The sequencing of these clones revealed that the average sizes of the inserts and corresponding open reading frames were 4.9 kb and 2.6 kb (882 amino acid residues), respectively. A computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes contained sequences similar to known genes, 53% of which (46 genes) were categorized as proteins relating to cell signaling/communication, cell structure/motility and nucleic acid management. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Animals↗

PubMed1999

Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803.

CyanoBase provides internet access to the complete genomic information of the cyanobacterium Synechocystis sp. strain PCC6803. CyanoBase contains annotations to each protein-coding gene, deduced from the entire nucleotide sequence of the genome, gene classification lists, keywords and similarity search engines. The present paper describes a recent extension of CyanoBase, named CyanoMutants. CyanoMutants is a repository database of mutant information on PCC6803. Each entry contains a dataset which describes a gene identifier, mutant information, and an address for correspondence. Two closely-linked databases, CyanoBase and CyanoMutants, connect information obtained from computational analysis to experimental analysis resulting in the clarification of the functions of hypothetical genes of the cyanobacterial genome. CyanoMutants can be accessed at http://www.kazusa.or. jp/cyano/mutants/

Computational Biology↗

PubMed1999

Cloning, tissue expression, and chromosomal assignment of human MRJ gene for a member of the DNAJ protein family.

The DnaJ protein family consists of proteins with a highly conserved amino acid stretch called the "J-domain". A cDNA clone encoding a new protein with a J-domain was isolated from a human fetal brain cDNA library. This new member of the DnaJ family of 241 amino acid residues showed 94% identity with mouse Mrj (accession number, AF035962) and 71% identity with mouse Msj-1 (accession number, U95607) along its entire sequence. Reverse transcription-coupled polymerase chain reaction (RT-PCR) analysis showed the messenger RNA was ubiquitously expressed in various human tissues. The chromosomal location of the gene was determined by PCR-based analyses with both a human/rodent monochromosomal hybrid cell panel and a radiation hybrid panel to map on chromosome 11q25 region.

Amino Acid Sequence↗

PubMed1999

[Outpatient chemotherapy with infusional 5-fluorouracil in advanced gastrointestinal cancer].

These studies were designed to evaluate the efficacy, toxicity, and resulting quality of life (QOL) of outpatient chemotherapy with infusional 5-FU for advanced gastrointestinal cancer. Schedule, sch. A: Treatment consisted of CI 5-FU 200 mg/m2/day, days 1-28, IVB Leucovorin 20 mg/m2 q week. Fifteen patients with advanced gastrointestinal cancer were treated to maintain the efficacy of prior inpatient chemotherapy. Twenty-one patients treated with adjuvant chemotherapy were added to evaluate toxicity and QOL. The mean time to progression (TTP) was 2.6 months. Grade 2 toxicities were seen, including mucositis (23%) and diarrhea (7%). Hand-foot syndrome was seen 60% of patients. The mean QOL score was 89.5 +/- 7.8. Sch.B: Treatment consisted of weekly 24 h infusion of 5-FU 2,600 mg/m2. 5-FU was administered using a Groshong catheter and Baxter infusor LV5 (5 ml/hr). Nine patients with advanced gastrointestinal cancer were treated. Twenty-one patients were treated with adjuvant chemotherapy. The mean TTP was 3.6 month. Grade 2 toxicities were seen, including leucocytopenia (7%), mucositis (3%), diarrhea (10%), and nausea and vomiting (10%). The mean QOL score was 82.6 +/- 10.7. In conclusion, both 5-FU schedules are feasible for outpatient chemotherapy for advanced gastrointestinal cancer.

Ambulatory Care↗

PubMed1999

[Laparoscopic surgery for early rectal carcinoma].

The indications, techniques, and results of laparoscopic surgery for early rectal carcinoma are described in detail. Laparoscopic surgery is indicated when a mucosal tumor is too large to perform endoscopic or transanal resection or the tumor invades the submucosal layer. When the tumor is located in the Rs or Ra region, surgery can be completed laparoscopically. After dissection of the mesenterium and lymphadenectomy are performed, the anal side of the rectum is divided using EndoGIA II. When the tumor is located in the Rb portion, it is impossible to resect the rectum intracorporeally. In this situation, aperi anal maneuver is essential. The rectal mucosa is circumferentially incised just above the dentate line and the internal anal sphincter is dissected. Dissection is advanced to the intersphincteric space. Dissection between the rectum and the levator ani muscle is completed, and the rectum is pulled through the anus. After the oral side of the rectum is divided, a J-pouch is mase and J-pouch-anal anastomosis is performed. Forty-seven patients with rectal carcinoma were operated upon laparoscopically. Postoperative recovery was better than that after open surgery. Serious intraoperative or postoperative complications have not been encountered in this series. In conclusion, laparoscopic surgery is thought to be the procedure of first choice for early rectal carcinoma.

Carcinoma↗

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↗