Biomedical subjects

Yoichi Matsuda

Publications and source records attributed to Yoichi Matsuda.

At least 19 recordsLinked to original sources

PubMed2024

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Animals↗

PubMed2007

Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds.

To clarify the process of avian sex chromosome differentiation in palaeognathous birds, we performed molecular and cytogenetic characterization of W chromosome-specific repetitive DNA sequences for elegant crested tinamou (Eudromia elegans, Tinamiformes) and constructed comparative cytogenetic maps of the Z and W chromosomes with nine chicken Z-linked gene homologues for E. elegans and ostrich (Struthio camelus, Struthioniformes). A novel family of W-specific repetitive sequences isolated from E. elegans was found to be composed of guanine- and cytosine-rich 293-bp elements that were tandemly arrayed in the genome as satellite DNA. No nucleotide sequence homologies were found for the Struthioniformes and neognathous birds. The comparative cytogenetic maps of the Z and W chromosomes of E. elegans and S. camelus revealed that there are partial deletions in the proximal regions of the W chromosomes in the two species, and the W chromosome is more differentiated in E. elegans than in S. camelus. These results suggest that a deletion firstly occurred in the proximal region close to the centromere of the acrocentric proto-W chromosome and advanced toward the distal region. In E. elegans, the W-specific repeated sequence elements were amplified site-specifically after deletion of a large part of the W chromosome occurred.

Animals↗

PubMed2006

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes.

All snake species exhibit genetic sex determination with the ZZ/ZW type of sex chromosomes. To investigate the origin and evolution of snake sex chromosomes, we constructed, by FISH, a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 109 cDNA clones. Eleven of the 109 clones were localized to the Z chromosome. All human and chicken homologues of the snake Z-linked genes were located on autosomes, suggesting that the sex chromosomes of snakes, mammals, and birds were all derived from different autosomal pairs of the common ancestor. We mapped the 11 Z-linked genes of E. quadrivirgata to chromosomes of two other species, the Burmese python (Python molurus bivittatus) and the habu (Trimeresurus flavoviridis), to investigate the process of W chromosome differentiation. All and 3 of the 11 clones were localized to both the Z and W chromosomes in P. molurus and E. quadrivirgata, respectively, whereas no cDNA clones were mapped to the W chromosome in T. flavoviridis. Comparative mapping revealed that the sex chromosomes are only slightly differentiated in P. molurus, whereas they are fully differentiated in T. flavoviridis, and E. quadrivirgata is at a transitional stage of sex-chromosome differentiation. The differentiation of sex chromosomes was probably initiated from the distal region on the short arm of the protosex chromosome of the common ancestor, and then deletion and heterochromatization progressed on the sex-specific chromosome from the phylogenetically primitive boids to the more advanced viperids.

Animals↗

PubMed2006

A novel family of repetitive DNA sequences amplified site-specifically on the W chromosomes in Neognathous birds.

A novel family of repetitive DNA sequences was molecularly cloned from ApaI-digested genomic DNA of two Galliformes species, Japanese quail (Coturnix japonica) and guinea fowl (Numida meleagris), and characterized by chromosome in-situ hybridization and filter hybridization. Both the repeated sequence elements produced intensely painted signals on the W chromosomes, whereas they weakly hybridized to whole chromosomal regions as interspersed-type repetitive sequences. The repeated elements of the two species had high similarity of nucleotide sequences, and cross-hybridized to chromosomes of two other Galliformes species, chicken (Gallus gallus) and blue-breasted quail (Coturnix chinensis). The nucleotide sequences were conserved in three other orders of Neognathous birds, the Strigiformes, Gruiformes and Falconiformes, but not in Palaeognathous birds, the Struthioniformes and Tinamiformes, indicating that the repeated sequence elements were amplified on the W chromosomes in the lineage of Neognathous birds after the common ancestor diverged into the Palaeognathae and Neognathae. They are components of the W heterochromatin in Neognathous birds, and a good molecular cytogenetic marker for estimating the phylogenetic relationships and for clarifying the origin of the sex chromosome heterochromatin and the process of sex chromosome differentiation in birds.

Animals↗

PubMed2006

cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids.

Mammalian and avian genomes comprise several classes of chromosomal segments that vary dramatically in GC-content. Especially in chicken, microchromosomes exhibit a higher GC-content and a higher gene density than macrochromosomes. To understand the evolutionary history of the intra-genome GC heterogeneity in amniotes, it is necessary to examine the equivalence of this GC heterogeneity at the nucleotide level between these animals including reptiles, from which birds diverged. We isolated cDNAs for 39 protein-coding genes from the Chinese soft-shelled turtle, Pelodiscus sinensis, and performed chromosome mapping of 31 genes. The GC-content of exonic third positions (GC3) of P. sinensis genes showed a heterogeneous distribution, and exhibited a significant positive correlation with that of chicken and human orthologs, indicating that the last common ancestor of extant amniotes had already established a GC-compartmentalized genomic structure. Furthermore, chromosome mapping in P. sinensis revealed that microchromosomes tend to contain more GC-rich genes than GC-poor genes, as in chicken. These results illustrate two modes of genome evolution in amniotes: mammals elaborated the genomic configuration in which GC-rich and GC-poor regions coexist in individual chromosomes, whereas sauropsids (reptiles and birds) refined the chromosomal size-dependent GC compartmentalization in which GC-rich genomic fractions tend to be confined to microchromosomes.

Animals↗

PubMed2006

Isolation and Characterization of a Novel Human Radiosusceptibility Gene, NP95.

The murine nuclear protein Np95 has been shown to underlie resistance to ionizing radiation and other DNA insults or replication arrests in embryonic stem (ES) cells. Using the databases for expressed sequenced tags and a two-step PCR procedure, we isolated human NP95, the full-length human homologue of the murine Np95 cDNA, which consists of 4,327 bp with a single open reading frame (ORF) encoding a polypeptide of 793 amino acids and 73.3% homology to Np95. The ORF of human NP95 cDNA is identical to the UHRF1 (ubiquitin-like protein containing PHD and RING domain 1). The NP95 gene, assigned to 19p13.3, consists of 18 exons, spanning 60 kb. Several stable transformants from HEK293 and WI-38 cells that had been transfected with the antisense NP95 cDNA were, like the murine Np95-knockout ES cells, more sensitive to X rays, UV light and hydroxyurea than the corresponding parental cells. In HEK293 cells, the lack of NP95 did not affect the activities of topoisomerase IIalpha, whose expression had been demonstrated to be regulated by the inverted CCAAT box binding protein of 90 kDa (ICBP90) that closely resembles NP95 in amino acid sequence and in cDNA but differs greatly in genomic organization. These findings collectively indicate that the human NP95 gene is the functional orthologue of the murine Np95 gene.

Animals↗

PubMed2006

Promoter activity and chromosomal location of the Rana rugosa P450 aromatase (CYP19) gene.

Sex is determined genetically in amphibians, but is reversed occasionally by steroid hormones. The phenotypic sex of some amphibian species can be reversed from male to female by estrogens. Estrogens, which are synthesized from testosterone irreversibly by the enzyme P450 aromatase (CYP19), are essential for ovarian development in vertebrates. CYP19 expression is reportedly regulated by steroidogenic factor-1 (SF-1), also designated as Ad4BP, in fish and mammals. However, it is unknown if this is also the case in amphibians. Thus, to elucidate the role of SF-1 in CYP19 gene expression in the gonad of amphibians, it is necessary to isolate and characterize the promoter region of the CYP19 gene of amphibians. For this purpose, we first cloned the promoter region of CYP19 from genomic DNA fragments of the frog Rana rugosa. As a result, a potential binding site of SF-1 was found in the region. When a luciferase promoter assay in HEK 293 cells was carried out to examine the ability of SF-1 as a transcriptional regulator, we found that R. rugosa SF-1 stimulated the expression of the CYP19 gene of the tilapia Oreochromis niloticus, but not that of the frogs R. rugosa and Xenopus laevis. RT-PCR analysis revealed that CYP19 mRNA was expressed at a higher level in the indifferent gonads of females than in those of males. This was also true to SF-1 mRNA In addition, FISH analysis showed that the CYP19 gene was located on chromosome 3 of R. rugosa. Taken together, our data suggest that CYP19, an autosomal gene, is expressed in the undifferentiated gonads to an extent greater in females than in males, but its expression probably is not regulated by SF-1 alone. Another factor(s) may be required if SF-1 promotes the expression of the CYP19 gene in R. rugosa as it does in fish and mammals.

Animals↗

PubMed2006

[Perioperative management for laparoscopic repair of congenital duodenal atresia].

BACKGROUND: Laparoscopic surgery has been applied even to neonates. To examine the safety and efficacy of laparoscopic repair of neonatal congenital duodenal atresia, we compared the 5 laparoscopic cases with the 5 conventional surgical cases. METHODS: The charts were retrospectively reviewed to investigate the anesthetic management, perioperative status and complications in the most recent 5 cases each of laparoscopic and conventional surgeries. RESULTS: There was a tendency to avoid laparoscopic repair in the patients with congenital heart disease. There were no intraoperative complications in both groups. Laparoscopic group exhibited less blood loss but longer operation time. In the two out of five laparoscopic cases re-operation was required due to technical issues, and the group needed a longer period before starting enteral feeding and longer hospitalization. CONCLUSIONS: Up to this time, laparoscopic repair of congenital duodenal atresia exhibited few advantages over conventional open repair.

Anesthesia↗

PubMed2006

Genetic polymorphisms of human ABC transporter ABCG2: development of the standard method for functional validation of SNPs by using the Flp recombinase system.

The vector-mediated introduction of cDNA into mammalian cells by calcium phosphate co-precipitation or permeation with lipofectamine is widely used for the integration of cDNA into genomic DNA. However, integration of cDNA into the host's chromosomal DNA occurs randomly at unpredictable sites, and the number of integrated recombinant DNAs is not controllable. To investigate the effect of genetic polymorphisms of ABCG2 on the protein expression and the drug resistance profile, we developed the Flp-In method to integrate one single copy of ABCG2 variant-cDNA into FRT-tagged genomic DNA. More than 20 metaphase spreads were examined for both fluorescence in situ hybridization (FISH) mapping and multicolor-FISH analysis, and it has been revealed that ABCG2 cDNA was incorporated into the telomeric region of the short arm on one of chromosomes 12 in Flp-In-293 cells. Based on the currently available SNP data for human ABCG2, we have created a total of seven variants by site-directed mutagenesis and stably expressed them in Flp-In-293 cells. While mRNAs of those integrated ABCG2 variants and wild type were evenly expressed in Flp-In-293 cells, the protein expression levels of F208S and S441N variants were found to be markedly low. It is suggested that the protein instability due to enhanced degradation resulted in the low levels of their protein expression. Thus, the Flp recombinase system would provide a useful tool to validate the effect of nonsynonymous SNPs on the protein stability and post-translational modification of ABCG2.

ATP Binding Cassette Transporter, Subfamily G, Mem↗

PubMed2005

New families of site-specific repetitive DNA sequences that comprise constitutive heterochromatin of the Syrian hamster (Mesocricetus auratus, Cricetinae, Rodentia).

We molecularly cloned new families of site-specific repetitive DNA sequences from BglII- and EcoRI-digested genomic DNA of the Syrian hamster (Mesocricetus auratus, Cricetrinae, Rodentia) and characterized them by chromosome in situ hybridization and filter hybridization. They were classified into six different types of repetitive DNA sequence families according to chromosomal distribution and genome organization. The hybridization patterns of the sequences were consistent with the distribution of C-positive bands and/or Hoechst-stained heterochromatin. The centromeric major satellite DNA and sex chromosome-specific and telomeric region-specific repetitive sequences were conserved in the same genus (Mesocricetus) but divergent in different genera. The chromosome-2-specific sequence was conserved in two genera, Mesocricetus and Cricetulus, and a low copy number of repetitive sequences on the heterochromatic chromosome arms were conserved in the subfamily Cricetinae but not in the subfamily Calomyscinae. By contrast, the other type of repetitive sequences on the heterochromatic chromosome arms, which had sequence similarities to a LINE sequence of rodents, was conserved through the three subfamilies, Cricetinae, Calomyscinae and Murinae. The nucleotide divergence of the repetitive sequences of heterochromatin was well correlated with the phylogenetic relationships of the Cricetinae species, and each sequence has been independently amplified and diverged in the same genome.

Animals↗

PubMed2005

Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other.

The karyotypes of birds, turtles and snakes are characterized by two distinct chromosomal components, macrochromosomes and microchromosomes. This close karyological relationship between birds and reptiles has long been a topic of speculation among cytogeneticists and evolutionary biologists; however, there is scarcely any evidence for orthology at the molecular level. To define the conserved chromosome synteny among humans, chickens and reptiles and the process of genome evolution in the amniotes, we constructed comparative cytogenetic maps of the Chinese soft-shelled turtle (Pelodiscus sinensis) and the Japanese four-striped rat snake (Elaphe quadrivirgata) using cDNA clones of reptile functional genes. Homology between the turtle and chicken chromosomes is highly conserved, with the six largest chromosomes being almost equivalent to each other. On the other hand, homology to chicken chromosomes is lower in the snake than in the turtle. Turtle chromosome 6q and snake chromosome 2p represent conserved synteny with the chicken Z chromosome. These results suggest that the avian and turtle genomes have been well conserved during the evolution of the Arcosauria. The avian and snake sex Z chromosomes were derived from different autosomes in a common ancestor, indicating that the causative genes of sex determination may be different between birds and snakes.

Amino Acid Sequence↗

PubMed2005

Ssdp1 regulates head morphogenesis of mouse embryos by activating the Lim1-Ldb1 complex.

The transcriptional activity of LIM-homeodomain (LIM-HD) proteins is regulated by their interactions with various factors that bind to the LIM domain. We show that reduced expression of single-stranded DNA-binding protein 1 (Ssdp1), which encodes a co-factor of LIM domain interacting protein 1 (Ldb1), in the mouse mutant headshrinker (hsk) disrupts anterior head development by partially mimicking Lim1 mutants. Although the anterior visceral endoderm and the anterior definitive endoderm, which together comprise the head organizer, were able to form normally in Ssdp1(hsk/hsk) mutants, development of the prechordal plate was compromised. Head development is partially initiated in Ssdp1(hsk/hsk) mutants, but neuroectoderm tissue anterior to the midbrain-hindbrain boundary is lost, without a concomitant increase in apoptosis. Cell proliferation is globally reduced in Ssdp1(hsk/hsk) mutants, and approximately half also exhibit smaller body size, similar to the phenotype observed in Lim1 and Ldb1 mutants. We also show that Ssdp1 contains an activation domain and is able to enhance transcriptional activation through a Lim1-Ldb1 complex in transfected cells, and that Ssdp1 interacts genetically with Lim1 and Ldb1 in both head development and body growth. These results suggest that Ssdp1 regulates the development of late head organizer tissues and body growth by functioning as an essential activator component of a Lim1 complex through interaction with Ldb1.

Animals↗

PubMed2005

Disruption of mouse XAB2 gene involved in pre-mRNA splicing, transcription and transcription-coupled DNA repair results in preimplantation lethality.

The XAB2 protein (XPA-binding protein 2) with 15 tetratricopeptide repeat motifs has been isolated by virtue of its ability to interact with xeroderma pigmentosum group A (XPA) protein in the yeast two-hybrid system. It has been shown that XAB2 interacted with Cockayne syndrome groups A and B (CSA and CSB) proteins and RNA polymerase II, which are known to be involved in transcription-coupled repair (TCR) and transcription, and that the antibodies against XAB2 protein inhibited the recovery of RNA synthesis after UV irradiation and normal RNA synthesis when microinjected into living fibroblasts. These results have indicated that XAB2 is involved in TCR and transcription. In this report, to elucidate the function of XAB2 in vivo, two types of mutations were introduced into the XAB2 gene in mice: a deletion of the region encompassing the promoter and exons 1-4, and a deletion of the C-terminal 162 amino acids. Both types of XAB2-heterozygous mice appeared normal physiologically and behaviorally. However, XAB2-homozygotes were selectively absent among the newborn mice. A detailed analysis of embryos at different stages of development indicated that the XAB2-homozygous mutants could survive until the morula stage, but could not develop to the blastocyst stage. These results indicate that XAB2 has an essential function in mouse embryogenesis.

Animals↗

PubMed2005

A dioxin sensitive gene, mammalian WAPL, is implicated in spermatogenesis.

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is an endocrine disruptor that produces a variety of toxic effects. We have isolated a mouse homolog of the hWAPL gene, termed mouse WAPL (mWAPL), as a target of TCDD by cDNA representational difference analysis from mouse embryonic stem cells. A statistically significant increase in mWAPL expression was observed at 0.1 microM TCDD in AhR-/- mouse embryonic fibroblast cells. Interestingly, at 1 microM TCDD, mWAPL mRNA levels decreased in AhR+/+ cells, but further increased in AhR-/- cells. hWAPL and mWAPL were highly expressed only in testes among normal tissue samples, and we observed mWAPL localization in the synaptonemal complex of testicular chromosomes. In addition, mouse testes decreased the expression of mWAPL mRNA after a single intraperitoneal injection of TCDD. Thus, mammalian WAPL such as hWAPL and mWAPL may be involved in spermatogenesis and be target genes mediating the reproductive toxicity induced by TCDD.

Amino Acid Sequence↗

PubMed2005

Molecular and cytogenetic characterization of site-specific repetitive DNA sequences in the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae).

A novel family of repetitive DNA sequences that are components of constitutive heterochromatin were cloned from BglI-digested genomic DNA of the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae), and characterized by filter hybridization and chromosome in-situ hybridization. The BglI-family of repetitive sequences were classified into four types by their genome organization and chromosomal distribution as follows: the repeated sequences located on (1) two pairs of microchromosomes, (2) four pairs of microchromosomes,(3) about half the number of microchromosomes and (4) the interstitial region of the short arm of chromosome 2. The presence of microchromosome-specific repetitive sequences has also been reported in the Struthioniformes and Galliformes, suggesting that turtle chromosomes retain some similarity to the chromosome structure as well as the karyotypes of avian species.

Animals↗

PubMed2005

Cloning, expression and chromosomal assignment of human pleckstrin 2.

We report the isolation of human pleckstrin 2 cDNA. The cDNA contains a 1059 bp open reading frame encoding a polypeptide of 353 amino acid residues. The deduced amino acid sequence indicates that pleckstrin 2 contains two pleckstrin homology domains and a DEP (dishvelled, egl-10, and pleckstrin) domain and had a 95% identity with the sequence of mouse pleckstrin 2. Northern blot and a reverse transcription-coupled polymerase chain reaction analysis revealed that pleckstrin 2 mRNA is widely expressed in a variety of cell lines. The chromosomal location of the mouse pleckstrin 2 gene was on the D3 band of chromosome 12, as determined by fluorescence in situ hybridization and the human pleckstrin 2 gene was mapped to chromosome 14q24.1 by a bioinformatics analysis.

Amino Acid Sequence↗

PubMed2005

Molecular cloning, expression and chromosomal localization of mouse MM-1.

The protooncogene product Myc associates with many proteins. The isolation of the mouse MM-1; c-Myc binding protein (Myc-Modulator 1) cDNA is described. The cDNA contains a 462 bp open reading frame that encodes a polypeptide of 154 amino acid residues. The deduced amino acid sequence indicates that mouse MM-1 has a 99% identity with the sequence of human MM-1. The expression of mouse MM-1 mRNA was detected in the fetal liver, but its level was 3-fold higher than that in the normal adult liver, and was slightly increased after a partial hepatectomy. It is expressed widely in a variety of adult mouse tissues. Thus, MM-1 may play a role in liver development and growth. A bioinformatics analysis indicates that mouse MM-1 gene consists of 6 exons. Furthermore, the chromosomal location of the mouse MM-1 gene was on the F2-F3 band of chromosome 15, as determined by fluorescence in situ hybridization.

Amino Acid Sequence↗

PubMed2005

Molecular cytogenetic characterization of Ciona intestinalis chromosomes.

The compact genome of the ascidian Ciona intestinalis has been sequenced. Chromosome karyotype and mapping of the genome sequence information on each of the 14 pairs of chromosomes are essential for genome-wide studies of gene expression and function in this basal chordate. Although the small chromosome size (most pairs measuring less than 2 mum) complicates accurate chromosome pairing based on morphology alone, the present results suggest that 20 chromosomes are metacentric and 8 are submetacentric or subtelocentric, and two pairs of large chromosomes (#1 and #2) were defined. The characterization of chromosomes by FISH and staining with propidium iodide indicated that 18S/28S ribosomal gene repeats are present in the short arms of three pairs of chromosomes and that the short arms of these pairs show remarkable size polymorphism. In addition, each chromosome was characterized molecular cytogenetically by mapping representative BAC clones with FISH. The present study is therefore a first step in expanding the karyotype analysis and entire physical mapping of the genome sequence of Ciona intestinalis.

Animals↗