Search PubMed⌕ Search

Biomedical subjects

A Koga

Publications and source records attributed to A Koga.

At least 19 recordsLinked to original sources
PubMed2000

Quantum phase transitions in the shastry-sutherland model for SrCu2(BO3)(2)

We investigate quantum phase transitions in the frustrated antiferromagnetic Heisenberg model for SrCu2(BO3)(2) by using the series expansion method. It is found that a novel spin-gap phase, adiabatically connected to the plaquette-singlet phase, exists between the dimer and the magnetically ordered phases known thus far. When the ratio of the competing exchange couplings alpha( = J'/J) is varied, this spin-gap phase exhibits a first- (second-) order quantum phase transition to the dimer (the magnetically ordered) phase at the critical point alpha(c1) = 0.677(2) [ alpha(c2) = 0. 86(1)]. Our results shed light on some controversial arguments about the nature of quantum phase transitions in this model.

Journal Article↗
PubMed2000

Identification of a novel 70 kDa protein that binds to the core promoter element and is essential for ribosomal DNA transcription.

Mammalian ribosomal RNA genes (rDNA) are transcribed by RNA polymerase I and at least two auxiliary factors, UBF and SL1/TFID/TIF-IB. It has also been reported that an additional factor(s) is required to reconstitute efficient initiation of rDNA transcription in vitro, depending upon the procedures of chromatographic separation. In an attempt to elucidate the molecular identity of such yet uncertain activities, we have developed agarose gel shift and UV cross-linking assays to detect proteins directly bound to the core promoter region of murine rDNA. With these techniques, we identified a 70 kDa protein (p70) in the flow-through fraction of a phosphocellulose column (TFIA-fraction). Interestingly, the binding of p70 to the rDNA core promoter was observed only in the presence of the SL1-containing fraction. The probable human orthologue of p70 was also detected in HeLa cells. Consistent with the observation that p70 bound to the core promoter only in the presence of the TFIA- and SL1-fractions, alteration of DNase I footprint pattern over the core promoter element was demonstrated by cooperative action of the TFIA- and SL1-fractions. A reconstituted in vitro transcription assay with further purified p70 indicated that p70 was required for accurate initiation of rDNA transcription. These results indicate that the p70 identified recently by the current DNA-binding experiments represents a novel transcription factor in rDNA transcription.

DNA, Ribosomal↗
PubMed2000

Single-fiber analysis of mitochondrial A3243G mutation in four different phenotypes.

Five unrelated patients harboring the A3243G mutation in the mitochondrial DNA (mtDNA) but presenting with different clinical phenotype were studied for their percentage of mutation at the single muscle fiber levels. One patient had a clinically and pathologically defined Leigh syndrome (LS), two showed mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), another showed progressive external ophthalmoplegia (PEO), and the other showed mitochondrial diabetes mellitus (MDM). The mutation load was greater in the muscle from the patient with LS (92%), who showed more than 80% even in the non-ragged red fibers (RRF) and also presented the highest proportion of RRF. The patients with MELAS had lower mutation levels as well as a lower proportion of RRF, and these two parameters were even lower in the PEO and MDM patients. These results were consistent with the concept that differences in the mutation load and in the somatic distribution of the mutation among different cells and tissues are responsible for the differences in phenotypical expression of the disease.

Adenine↗
PubMed2000

Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element.

Tol2 is a transposable element of the terminal-inverted-repeat class, residing in the genome of the medaka fish Oryzias latipes. The genus Oryzias contains more than 10 species for which phylogenetic relationships have previously been estimated. To infer the history of Tol2 in this genus we performed genomic Southern blots and PCR analyses of 10 of the species. It was revealed that Tol2 occurs in 2 of the 10 species (O. curvinotus and O. latipes) and that the length and the restriction map structure of Tol2 are identical in the two cases. Further, sequencing analysis revealed an extremely low level of divergence compared with that in a nuclear gene. These results suggest recent incorporation of Tol2 into one or both of the two species, implying horizontal transfer of Tol2 from one species to the other or into them both from a common source.

Animals↗
PubMed2000

Detection of de novo insertion of the medaka fish transposable element Tol2.

Tol2 is a terminal-inverted-repeat transposable element of the medaka fish Oryzias latipes. It is a member of the hAT (hobo/Activator/Tam3) transposable element family that is distributed in a wide range of organisms. We here document direct evidence for de novo insertion of this element. A Tol2 clone marked with the bacterial tetracycline-resistance gene was microinjected into fertilized eggs together with a target plasmid, and the plasmid was recovered from embryos. The screening of plasmid molecules after transformation into Escherichia coli demonstrated transposition of tet into the plasmid and, by inference, precise insertion of Tol2 in medaka fish cells. De novo excision of Tol2 has previously been demonstrated. The present study provides direct evidence that the Tol2 element has the entire activity necessary for cut-and-paste transposition. Some elements of the mariner/Tc1 family, another widespread group, have already been applied to development of gene tagging systems in vertebrates. The Tol2 element of the hAT family, having different features from mariner/Tc1 family elements, also has potential as an alternative gene tagging tool in vertebrates.

Animals↗
PubMed2000

Chromosome mapping and expression of human tip49 family genes.

TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. At least, TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. In this study, we investigated the chromosome positions of this family of genes. Human tip49a and tip49b genes were mapped on 3q21 and 19q13.2, respectively. Consistent with the notion that tip49 family genes are essential for cell growth, Northern blot analysis demonstrated that both genes are expressed ubiquitously in human tissues. It is worthy of notice that the testes contained large amounts of the both transcripts. These results are consistent with our previous results from tissue distribution analysis for of TIP49 proteins.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1999

Amino acid sequence of a putative transposase protein of the medaka fish transposable element Tol2 deduced from mRNA nucleotide sequences.

Tol2 is a terminal-inverted repeat transposable element of the medaka fish Oryzias latipes. It is one of a few elements of this class so far demonstrated to be active in vertebrates, thus providing a unique tool for establishing a gene tagging system. For the purpose of identifying its transposase, we analyzed the structures of mRNAs originating from the Tol2 element. The results indicated that transcription of Tol2 is initiated at several sites, the four open reading frames in Tol2 roughly corresponding to exons, and that two main forms of mRNAs, covering exons 1-4 and exons 2-4, are present in medaka fish cells. One or both of these mRNAs are likely to encode a transposase, the amino acid sequence of which was deduced.

Amino Acid Sequence↗
PubMed1999

Homogeneity in the structure of the medaka fish transposable element Tol2.

The hAT family is a group of transposable elements of the terminal inverted repeat class, which includes Ac of maize, hobo of Drosophila and Tam3 of Antirrhinum (snapdragon). All the members of this family so far examined are known to comprise complete and defective copies, with a good correspondence to autonomous and non-autonomous elements, respectively. Internal deletion is the most common cause of defective copies. Tol2, a transposable element of the medaka fish Oryzias latipes, is a member of the hAT family. We examined, mainly by the genomic Southern blot analysis, variation in the structure of copies of this element, and revealed that there are few or no internally deleted copies. This situation is unusual in a member of the hAT family. Possible causes of this anomaly are discussed.

Animals↗
PubMed1999

Oculocutaneous albinism in the i6 mutant of the medaka fish is associated with a deletion in the tyrosinase gene.

Three mutant alleles (i1, i4, and i5) of the tyrosinase gene in the i locus of the medaka fish Oryzias latipes have hitherto been described, all being associated with transposable element insertion. We have recently identified another allele causing a complete albino phenotype in homozygous carriers and named it i6. Sequence comparison between the tyrosinase gene for the i6 allele (Tyr-i6) and the wild-type gene previously obtained (Tyr-i+) revealed three deletions of 8, 44, and 245 bp. The first two deletions reside in an intron and are differences in the number of tandem tetranucleotide repeats that are polymorphic even among wild-type genes, and, thus, not likely to be responsible for the i6 albino phenotype. The largest deletion spans over the last 180 bp of the second intron and the first 65 bp of the third exon. Because of this deletion, the Tyr-i6 gene lacks the branch point sequence and the acceptor site for the second intron, both being considered to be necessary for normal RNA splicing. Therefore, the 245-bp deletion is likely to be responsible for the albino phenotype. With a mutant gene of this type, unlike ones bearing transposable element insertions, the possibility of reversion mutations to the wild-type would be negligible. Therefore, fish having the i6/i6 genotype should serve as superior recipients for the tyrosinase gene in rescue experiments.

Albinism, Oculocutaneous↗
PubMed1998

Excision of the tol2 transposable element of the medaka fish, Oryzias latipes, in zebrafish, Danio rerio.

The Tol2 element is a transposable element in Oryzias latipes (the medaka fish) found in the tyrosinase gene locus of the tyrosinase-deficient mutant medaka fish and has been shown to be excised from the genome during medaka embryogenesis (Koga, A., Suzuki, M., Inagaki, H., Bessho, Y., Hori, H., 1996. Transposon element in fish. Nature 383, 30). It is, however, not known whether the Tol2 element is an autonomous element. To determine whether the cloned Tol2 element is an autonomous element and whether excision can occur also in the other fish species, the plasmid DNA harboring the Tol2 element was injected to fertilized eggs of zebrafish, Danio rerio, and the total DNA extracted from the embryos 9-10h after the injection was analyzed by PCR. When a plasmid with the full-length Tol2 element was used for the microinjection, in 39 out of 43 injected embryos, we found generation of short PCR products indicative of the loss of the Tol2 element from the injected plasmid. Ten of these cases were analyzed at the DNA sequence level, and nine of them showed either precise excision of the Tol2 element (three cases) or nearly precise excision of the element with the addition of a few nucleotides of the target duplication (six cases). When a deletion version of the Tol2 element that retained the terminal inverted repeats but lacked about one-fourth of the open reading frame-coding region was used for the microinjection, such short PCR products could not be amplified from any of the injected embryos (0 out of 30). Thus, the Tol2 element is capable of excision in zebrafish embryos, presumably dependent on a putative transposase encoded by the Tol2 element itself. This transient embryonic excision assay using zebrafish should be useful to analyze the structure and the function of the transposase and cis-elements necessary for excision. Also, this study implies the potential use of the Tol2 element in transgenesis and insertional mutagenesis in both zebrafish and the medaka fish.

Animals↗
PubMed1998

The tyrosinase gene from medakafish: transgenic expression rescues albino mutation.

We have determined the 9.8 kb genomic nucleotide sequence of the tyrosinase gene and its 5 upstream region from a teleost, medakafish (Oryzias latipes), and shown that the coding region is composed of five exons and four introns, spanning 4.7 kb. While the number and sizes of the exons were found to be similar to those of mammalian tyrosinase genes, however, the total size of the coding region (4.7 kb) was demonstrated to be less than one tenth those of mouse (ca. 70 kb) and human (> 70 kb) genes. Primer extension analysis revealed that the transcription initiation site starts with a long untranslated leader sequence (340 nucleotide long) from the AUG start codon. A characteristic CATGTG sequence known as a putative regulatory motif in melanocyte-specific genes was present in the 131st base upstream from the initiation site, while other typical regulatory elements such as the TATA-box or M-box common to terrestrial vertebrates were lacking. Transgenic experiments were carried out by microinjecting two kinds of plasmid clones into fertilized eggs of the albino i(l) mutant: one consisting of the genomic tyrosinase gene with the 10 kb 5 upstream region and the other the tyrosinase cDNA with the 3 kb 5 upstream region. The results showed that 53 and 45 of 114 and 118 transgenic eggs, respectively, developed normally beyond hatching and 15 and 10 exhibited a mosaic pattern of pigmentation. Despite the absence of typical regulatory elements like a TATA-box in both cases correct melanin pigmentation was obtained without ectopic expression. Thus, transgenic expression rescued from the albino-i(l) mutation, and the i locus of the medaka genome can be concluded to encode the tyrosinase gene.

Albinism↗
PubMed1998

An active Ac-like transposable element in teleost fish.

The i4/i4 genotype of the medakafish, Oryzias latipes, exhibits a quasi albino phenotype due to insertion of a novel transposable element, Tol2, into the tyrosinase gene. Tol2 is 4681 bp in length, has short inverted terminal repeats, and contains four ORFs with the potential to encode a transposase protein. Excision activity of the element has been detected by PCR analysis. Genomic Southern of the Tol2 element revealed that about 20 copies are present in the diploid genome. Dot-matrix comparisons of amino acid sequences of ORFs show relatively high similarity with transposases from Ac of maize, hobo of Drosophila, and Tam3 of snapdragon, which are all active transposable elements. Tol2 is thus concluded to be an active Ac-like transposable element probably encoding a transposase protein. It should therefore find application as a unique material for establishing a gene tagging system in fish.

Journal Article↗
PubMed1997

Fine structure of cholesterolosis in the human gallbladder and the mechanism of lipid accumulation.

Gallbladders with cholesterolosis removed surgically for cholelithiasis were studied by light and electron microscopy as well as by cytochemical methods to demonstrate the presence of free cholesterol in the epithelial cells. Lipid droplets were found not only in the submucosa, but also in the infranuclear cytoplasm of epithelial cells. These contained well developed mitochondria and an agranular endoplasmic reticulum. Macrophages were often present between the epithelial cells and the submucosa, and protruded numerous processes, which also contained well developed cell organelles, abundant lysosomes and lipid droplets. With the excessive lipid deposition, macrophages were filled with lipid droplets and became foam cells. In the epithelial cells, many reaction precipitates occurred after digitonin treatment and some of them were observed in the endoplasmic reticulum. It is suggested, therefore, that free cholesterol is absorbed by epithelial cells and thereafter becomes esterified in the endoplasmic reticulum and thus appears as lipid droplets. Lipid droplets synthesized in the epithelial cells may then be released into the intercellular space, and phagocytosed there by macrophages. It is thus suggested that macrophages filled with lipid droplets may become too large and rigid to pass through the endothelium of lymph vessels, and those large "foam cells" may cause the destruction of lymph vessels. Those sequential events should eventually advance the accumulation of foam cells in the submucosa.

Cholelithiasis↗
PubMed1997

Molecular cloning of a rat 49-kDa TBP-interacting protein (TIP49) that is highly homologous to the bacterial RuvB.

TBP as a central component in transcriptional regulation can form complexes with various regulatory factors. Using histidine-tagged TBP for affinity-purification of TBP-bound proteins, we isolated a 49-kD protein termed TBP-interacting protein 49 (TIP49) from rat liver nuclear extracts. We cloned the entire cDNA of TIP49 encoding a novel polypeptide of 456 amino acids, and thereafter established an FM3A cell line that constitutively expressed an epitope-tagged TBP. Immunoprecipitation analysis of the cell extracts indicated that TIP49 and TBP were present in an identical complex. Interestingly, the amino acid sequence of TIP49 exhibited high similarity to those sequences of the RuvB bacterial recombination factors which direct branch migration of the Holliday junction and contain the Walker A and B motifs responsible for ATP binding and ATP hydrolysis. These findings suggest that TIP49 is a putative ATP-dependent DNA helicase.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1997

Albinism due to transposable element insertion in fish.

The i locus of the medaka fish, Oryzias latipes, is responsible for tyrosinase expression, and several mutant alleles have been identified. The genotype i1/i1 exhibits a complete albino phenotype, having pale orange-red skin and red eyes. This mutant lacks in vivo tyrosinase activity. The genotype i4/i4, on the other hand, shows a quasi-albino phenotype with skin as bright as that of i1/i1 but with red-wine-colored eyes. At the light microscope level, reduced pigmentation is observed both in the skin and eyes of this mutant. The tyrosinase genes for the i1 and the i4 alleles were cloned and sequenced, and compared with that of the wild-type tyrosinase gene. The i1 allele was found to contain a 1.9-kb transposable element in the 1st exon, and the i4 allele was found to contain a 4.7-kb transposable element in the 5th exon. Both i1 and i4 are alleles that were found in a commercial breeding population. The insertion of a transposable element thus appears to constitute a natural cause of mutations that cause albinism in this organism.

Albinism↗
PubMed1997

[Continuous arterial infusion of low-dose cisplatin, 5-fluorouracil as adjuvant therapy in cytoreductive surgery for advanced hepatocellular carcinoma].

We investigated the effectiveness of continuous arterial infusion of low-dose CDDP, 5-FU for residual cancer after cytoreductive surgery for advanced hepatocellular carcinoma. Thirty-one patients with unresectable advanced hepatocellular carcinoma were classified into two groups by adjuvant therapy after reduction surgery: 1) Low-dose FP Group: 17 patients; continuous arterial infusion of low-dose CDDP, 5-FU via implanted port system; 2) Conventional group: 8 patients; Lipiodolization (6 cases) and transcatheter arterial embolization (2 cases). The five-year survival rate in the low-dose FP group was 34.8%, the efficacy was 64.7%, CR: 6 (35.3%); PR: 5; NC: 4; PD: 2. Thus, continuous arterial infusion of low-dose CDDP, 5-FU was effective as adjuvant therapy in cytoreductive surgery for advanced hepatocellular carcinoma.

Antineoplastic Combined Chemotherapy Protocols↗