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Biomedical subjects

N Miyajima

Publications and source records attributed to N Miyajima.

At least 55 records · Page 3Linked to original sources
PubMed1997

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

In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. The cDNA libraries used were the fractions with average insert sizes from 5.3 to 7.0 kb of the size-fractionated cDNA libraries from human brain. The randomly sampled clones were single-pass sequenced from both the ends to select clones that are not registered in the public database. Then their protein-coding potentialities were examined by an in vitro transcription/translation system, and the clones that generated proteins larger than 60 kDa were entirely sequenced. Each clone gave a distinct open reading frame (ORF), and the length of the ORF was roughly coincident with the approximate molecular mass of the in vitro product estimated from its mobility on SDS-polyacrylamide gel electrophoresis. The average size of the cDNA clones sequenced was 6.1 kb, and that of the ORFs corresponded to 1200 amino acid residues. By computer-assisted analysis of the sequences with DNA and protein-motif databases (GenBank and PROSITE databases), the functions of at least 73% of the gene products could be anticipated, and 88% of them (the products of 64 clones) were assigned to the functional categories of proteins relating to cell signaling/communication, nucleic acid managing, and cell structure/motility. The expression profiles in a variety of tissues and chromosomal locations of the sequenced clones have been determined. According to the expression spectra, approximately 11 genes appeared to be predominantly expressed in brain. Most of the remaining genes were categorized into one of the following classes: either the expression occurs in a limited number of tissues (31 genes) or the expression occurs ubiquitously in all but a few tissues (47 genes).

Blotting, Northern↗
PubMed1997

Transformation in Garnet from Orthorhombic Perovskite to LiNbO3 Phase on Release of Pressure

High-pressure in situ x-ray diffraction and transmission electron microscopy on quenched samples show that natural garnet transforms to orthorhombic perovskite (and minor coexisting phases) containing increasing amounts of aluminum with increasing pressure. This suggests that the perovskite is the dominant host mineral for aluminum in Earth's lower mantle. Orthorhombic perovskite is quenched from approximately 35 gigapascals but, because of the increased aluminum content, transforms to the LiNbO3 structure upon quenching from approximately 60 gigapascals.

Journal Article↗
PubMed1997

[Present state and problems of laparoscopic surgery for colon and rectal carcinoma].

Laparoscopic surgery has been indicated as a choice of treatment for colon and rectal carcinoma in many institutes. However, indication and techniques of laparoscopic surgery have not been fixed probably because curability of laparoscopic surgery has not proved clear. D1 lymphadenectomy for early cancer is easy because only dissection of the mesenterium is necessary. But D2 and D3 lymphadenectomy is not popular because it needs the clearance of the root of main artery of the tumor. We compared the postoperative recovery and curability of laparoscopic surgery with conventional operation. Curavility of the operation was similar among laparoscopic surgery and conventional operation. Thus laparoscopic surgery for colon and rectum can be indicated even in cases of advanced carcinoma. To spread laparoscopic surgery, post graduate education program is necessary to get consensus of indication and techniques of laparoscopic surgery.

Colonic Neoplasms↗
PubMed1996

Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain.

In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts, we newly determined the sequences of 80 clones, and predicted the coding sequences of the corresponding genes, named KIAA0201 to KIAA0280. Among the sequenced clones, 68 were obtained from human immature myeloid cell line KG-1 and 12 from human brain. The average size of the clones was 5.3 kb, and that of distinct ORFs in clones was 2.8 kb, corresponding to a protein of approximately 100 kDa. Computer search against the public databases indicated that the sequences of 22 genes were unrelated to any reported genes, while the remaining 58 genes carried sequences which show some similarities to known genes. Protein motifs that matched those in the PROSITE motif database were found in 25 genes and significant transmembrane domains were identified in 30 genes. Among the known genes to which significant similarity was shown, the genes that play key roles in regulation of developmental stages, apoptosis and cell-to-cell interaction were included. Taking into account of both the search data on sequence similarity and protein motifs, at least seven genes were considered to be related to transcriptional regulation and six genes to signal transduction. When the expression profiles of the cDNA clones were examined with different human tissues, about half of the clones from brain (5 of 11) showed significant tissue-specificity, while approximately 80% of the genes from KG-1 were expressed ubiquitously.

Amino Acid Sequence↗
PubMed1996

Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions.

The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.

Bacterial Proteins↗
PubMed1996

Amorphization of Serpentine at High Pressure and High Temperature

Pressure-induced amorphization of serpentine was observed at temperatures of 200° to 300°C and pressures of 14 to 27 gigapascals with a combination of a multianvil apparatus and synchrotron radiation. High-pressure phases then crystallized rapidly when the temperature was increased to 400°C. These results suggest that amorphization of serpentine is an unlikely mechanism for generating deep-focus earthquakes, as the temperatures of subducting slabs are significantly higher than those of the rapid crystallization regime.

Journal Article↗
PubMed1996

Nitric oxide induction by pertussis toxin in mouse spleen cells via gamma interferon.

We examined the major pathogenic substances of Bordetella pertussis for the ability to induce nitric oxide, and important biological function of macrophages, via gamma interferon in spleen cells. B. pertussis, which produces a variety of pathogenic substances, including pertussis toxin and filamentous hemagglutinin, causes a severe respiratory disease. Nitric oxide was detected in the culture fluid of spleen cells stimulated with pertussis toxin or its B oligomer but not in the culture fluid of spleen cells stimulated with the A protomer of pertussis toxin or with filamentous hemagglutinin. Incubation of the peritoneal exudate macrophages with pertussis toxin, B oligomer, A protomer, or filamentous hemagglutinin induced little nitric oxide, whereas incubation with gamma interferon induced a significant amount of nitric oxide. The induction of nitric oxide in spleen cells stimulated with pertussis toxin was completely inhibited by anti-gamma interferon antibody. The treatment of spleen cells with anti-Thy-1.2 antibody plus complement followed by stimulation with pertussis toxin decreased the secretion of gamma interferon and nitric oxide. These results suggest that gamma interferon from T lymphocytes stimulated with pertussis toxin induces nitric oxide.

Animals↗
PubMed1995

Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome.

The contiguous sequence of 1,003,450 bp spanning map positions 64% to 92% of the genome of Synechocystis sp. strain PCC6803 has been deduced. Computer analysis of the sequence predicts that this region contains at least 818 potential ORFs, in which 255 (31%) were either genes that had already been identified or their homologues, 84 (10%) were homologues to registered hypothetical genes, and 149 (18%) showed weak similarities to reported genes. The remaining 330 ORFs showed no apparent similarity to any reported genes or carried no significant protein motifs. The potential ORFs as a whole occupied 86% of the sequenced region, implying compact arrangement of genes in the genome. As to the structural RNA genes, one rRNA operon consisting of 5,028 bp and at least 11 species of tRNA genes were identified. It is noteworthy that 10 out of the 11 tRNA species showed significant sequence similarities to tRNAs reported in plant chloroplasts. As other notable unique sequences, three classes of IS-like elements each with characteristics typical of IS elements were identified, and a typical unit of WD(Trp-Asp)-repeats which have only been detected in the regulatory proteins of eukaryotes was identified within the large 5,079-bp ORF located at map position 69%.

Base Sequence↗
PubMed1995

Experience with laparoscopic double gallbladder removal.

Double gallbladder is a rare congenital anomaly and an encounter with it while performing cholecystectomy laparoscopically is a challenge to the laparoscopic surgeon. A 28-year-old man complaining of epigastric pain was evaluated at Teikyo University Hospital, Mizonokuchi, Japan. There were no abnormal laboratory findings. Ultrasonography revealed an acoustic shadow in each compartment without any inflammatory changes in the gallbladder. No lesions were endoscopically noted in the stomach. CT scan could not demonstrate the anomaly. ERCP revealed a duplication of the gallbladder shadow with a stone in each vesicle and also the confluence of two cystic ducts from both the gallbladders draining into the common bile duct (CBD). Laparoscopic cholecystectomy was performed successfully in this case. This paper presents this particular case because of double gallbladder's rarity in the literature and to emphasize the importance of preoperative cholangiographic evaluation for double gallbladder. The laparoscopic surgeon is given an idea of the meticulous dissection at the "hepatocystic triangle" due to the various other vascular and other congenital anomalies associated with it. An account of the classification of this congenital abnormality and its various types is also discussed here.

Adult↗
PubMed1995

Prevention of laparoscopic surgeon's thumb.

Laparoscopic surgery is being used in an increasing number of operations today. We have been performing various types of laparoscopic techniques in our department. A problem we sometimes have encountered involves a ring of pressure that develops around the surgeon's thumb at the end of the procedure, which is accompanied by an area of paresthesia in the distribution of the lateral digital nerve. We report our own experience and a small review of the literature.

Humans↗
PubMed1995

Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1.

We isolated full-length cDNA clones from size-fractionated cDNA libraries of human immature myeloid cell line KG-1, and the coding sequences of 40 genes were newly predicted. A computer search of the GenBank/EMBL databases indicated that the sequences of 14 genes were unrelated to any reported genes, while the remaining 26 genes carried some sequences with similarities to known genes. Significant transmembrane domains were identified in 17 genes, and protein motifs that matched those in the PROSITE motif database were identified in 11 genes. Northern hybridization analysis with 18 different cells and tissues demonstrated that 10 genes were apparently expressed in a cell-specific or tissue-specific manner. Among the genes predicted, half were isolated from the medium-sized cDNA library and the other half from the small-sized cDNA library, and their average sizes were 4 kb and 1.4 kb, respectively. As judged by Northern hybridization profiles, small-sized cDNAs appeared to be expressed more ubiquitously and abundantly in various tissues, compared with that of medium-sized cDNAs.

Cell Line↗
PubMed1995

[A case report of far advanced gastric cancer with multiple liver metastasis (H3) treated with transarterial intermittent chemotherapy and intradermal administration of low molecular lipopolysaccharide (LPSp) extracted from Pantoea agglomerans].

A case of far advanced gastric cancer with multiple liver metastasis (H3) was treated with transarterial intermittent chemotherapy (5-FU: 250 mg/week, Farmorubicin: 10 mg/4 weeks, MMC: 4 mg/2 weeks) and intradermal administration of low molecular lipopolysaccharide (LPSp) extracted from Pantoea agglomerans. The CT examination and endoscopy showed regression of the tumor and the patient was discharged from the hospital. LPSp was given at the concentration of 0.1 microgram initially, and the dose was gradually increased. Finally, the dose of LPSp was increased up to 70 micrograms. No serious side effect except fever was observed. The serum TNF-alpha levels were elevated and, histologically, CD 8(+) lymphocyte dominantly infiltrated around the tumor. These findings clearly indicated the immunological anticancer effect of LPSp. Intradermal administration of LPSp is a promising new adjuvant therapy to improve QOL without serious side effect.

Aged↗
PubMed1995

[Tissue concentration of 5-FU after intra-operative arterial infusion].

The aim of this study was to measure the tissue concentration of anti-cancer agents administered by arterial infusion. After the abdominal cavity was opened, 250 mg of 5-FU diluted in 20 ml saline was infused into the feeding artery in 16 patients with colonic cancer. After the affected lesion was resected, specimens were obtained at the tumor, at sites 5 and 10 cm from the center of the tumor, and at the adjacent nodes. The concentration of 5-FU was higher in the tumor and the adjacent lymph nodes than in the normal colon near the lesion. This suggests that 5-FU has a more favorable distribution profile in tumor tissue than in normal tissue. Patients with a high concentration of 5-FU in the tumor also demonstrated high levels in the other tissue. Blood flow volume and the length of time between the injection of 5-FU and harvest of the specimen may account for differences in the tissue concentration of the agent after administration of the same dose.

Colonic Neoplasms↗
PubMed1994

A defective non-LTR retrotransposon is dispersed throughout the genome of the silkworm, Bombyx mori.

The presence of long repetitive sequences is demonstrated in the genome of the silkworm, Bombyx mori. Members of this BMC1 family reveal several features typical of the L1 (long interspersed sequence one) family of mammals, except for species specific elements. The number of BMC1 elements is estimated to be approximately 3500 per haploid genome. Elements containing the full length unit of 5.1 kb are dispersed throughout the genome and their restriction sites are conserved, although most members are preferentially truncated to varying extents at their 5' ends. DNA sequencing indicates that this element contains six tandem repeats of 15 bp CpG-rich sequence in the 5' proximal region. It terminates with a 3' oligo(A) stretch, and is flanked at both ends by a 7-10 bp target sequence duplication. In addition, there is significant evidence for amino acid sequence homology with reverse transcriptase domains of other L1 families, especially F, Doc and Jockey of Drosophila melanogaster. No large open reading frame is present. The BMC1 element is suggested to be dispersed in the genome by a transposition mechanism involving RNA intermediates.

Amino Acid Sequence↗
PubMed1994

Characterization of cDNAs induced in meiotic prophase in lily microsporocytes.

To identify and analyze genes functioning during reproductive cell formation in higher plants, cDNAs harboring the messages induced in meiotic prophase were isolated and characterized. A cDNA library constructed from microsporocytes in meiotic prophase of Lilium longiflorum was screened with a subtraction probe specific to meiotic prophase. Clones selected were classified into 18 groups by cross hybridization and partial sequencing. Northern blot analysis revealed that the transcripts corresponding to the respective cDNA groups began accumulating at the early stages of meiosis and exhibited clone-specific profiles during meiosis and the spore formation process. The amino acid sequences of the predicted gene products showed similarity with known gene products, e.g. heat shock proteins, serine proteases in Bacillus, and RAD 51 gene product in yeast. Half of the putative gene products had hydrophobic N-terminal regions, suggesting that they may function as signal peptides.

Amino Acid Sequence↗
PubMed1994

Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1.

We established a protocol for the prediction of the coding sequences of unidentified human genes based on the double selection and sequence analysis of cDNA clones with inserts carrying unreported 5'-terminal sequences and with insert sizes corresponding to nearly full-length transcripts. By applying the protocol, cDNA clones with inserts longer than 2 kb were isolated from a cDNA library of human immature myeloid cell line KG-1, and the coding sequences of 40 new genes were predicted. A computer search of the sequences indicated that 20 genes contained sequences similar to known genes in the GenBank/EMBL databases. The sequences of the remaining 20 genes were entirely new, and characteristic protein motifs or domains were identified in 32 genes. Other sequence features noted were that the coding sequences of 23 genes were followed by relatively long stretches of 3'-untranslated sequences and that 5 genes contained repetitive sequences in their 3'-untranslated regions. The chromosomal location of these genes has been determined. By increasing the scale of the above analysis, the coding sequences of many unidentified genes can be predicted.

Base Sequence↗