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Biomedical subjects

Takashi Miyata

Publications and source records attributed to Takashi Miyata.

At least 19 recordsLinked to original sources

Functional development of Src tyrosine kinases during evolution from a unicellular ancestor to multicellular animals.

The Src family of tyrosine kinases play pivotal roles in regulating cellular functions characteristic of multicellular animals, including cell-cell interactions, cell-substrate adhesion, and cell migration. To investigate the functional alteration of Src kinases during evolution from a unicellular ancestor to multicellular animals, we characterized Src orthologs from the unicellular choanoflagellate Monosiga ovata and the primitive multicellular sponge Ephydatia fluviatilis. Here, we show that the src gene family and its C-terminal Src kinase (Csk)-mediated regulatory system already were established in the unicellular M. ovata and that unicellular Src has unique features relative to multicellular Src: It can be phosphorylated by Csk at the negative regulatory site but still exhibits substantial activity even in the phosphorylated form. Analyses of chimera molecules between M. ovata and E. fluviatilis Src orthologs reveal that structural alterations in the kinase domain are responsible for the unstable negative regulation of M. ovata Src. When expressed in vertebrate fibroblasts, M. ovata Src can induce cell transformation irrespective of the presence of Csk. These findings suggest that a structure of Src required for the stable Csk-mediated negative regulation still is immature in the unicellular M. ovata and that the development of stable negative regulation of Src may correlate with the evolution of multicellularity in animals.

Amino Acid Sequence↗

Tissue preferential expression of estrogen receptor gene in the marine snail, Thais clavigera.

Sex steroid hormones have been widely detected in molluscs, and experiments have shown the importance of sex steroids in sex determination, gonadal tissue maturation and gametogenesis. Nevertheless, the signaling pathways of sex steroids in invertebrates have not yet been elucidated. In order to gain insights into the mechanism of sex steroid signaling in molluscs, we have, therefore, tried to isolate molluscan estrogen receptors from the prosobranch mollusc Thais clavigera. Cerebral ganglia of T. clavigera (Mollusca, Gastropoda, Prosobranchia) were subjected to RNA extraction, and degenerate primers for amino acid sequences conserved in vertebrate estrogen receptors were designed. PCR amplification using cerebral RNA and degenerate primers followed by 5'- and 3'-RACE identified the cDNA encoding T. clavigera estrogen receptor 1 (tcER1). The deduced amino acid sequence showed 93% identity in the DNA-binding domain and 72% identity in the ligand binding domain when compared to Aplysia estrogen receptor. Reporter gene assay revealed that tcER1 is constitutively active and unresponsive to estrogen. Quantitative analysis of the tcER1 mRNA level demonstrated the preferential expression in the ovary. Furthermore, cerebral ganglia expressed tcER1 at a high level in the spring followed by subsequent enlargement of the ovary in later seasons. These results suggest importance of tcER1 in the seasonal development of reproductive organs in T. clavigera.

Amino Acid Sequence↗

Tumor marker-responsive behavior of gels prepared by biomolecular imprinting.

We report dynamic glycoprotein recognition of gels prepared by biomolecular imprinting using lectin and antibody molecules as ligands for tumor-specific marker glycoproteins. The glycoprotein-imprinted gels prepared with minute amounts of cross-linkers could dynamically recognize tumor-specific marker glycoproteins by lectin and antibody ligands and induce volume changes according to the glycoprotein concentration. The glycoprotein-imprinted gel shrank in response to a target glycoprotein but nonimprinted gel swelled a little. The glycoprotein-responsive shrinking of the imprinted gel was caused by formation of lectin-glycoprotein-antibody complexes that acted as reversible cross-linking points. Glycoprotein-imprinted gels only shrank when both lectin and antibody in the gels simultaneously recognized the saccharide and peptide chains of the target glycoprotein. As shrinking behavior of biomolecularly imprinted gels in response to glycoproteins enables the accurate detection and recognition of tumor-specific marker glycoproteins, they have many potential applications as smart devices in sensing systems and for molecular diagnostics.

Biomarkers, Tumor↗

No high-mass protostars in the silhouette young stellar object M17-SO1.

The birth of very massive stars is not well understood, in contrast to the formation process of low-mass stars like our Sun. It is not even clear that massive stars can form as single entities; rather, they might form through the mergers of smaller ones born in tight groups. The recent claim of the discovery of a massive protostar in M17 (a nearby giant ionized region) forming through the same mechanism as low-mass stars has therefore generated considerable interest. Here we show that this protostar has an intermediate mass of only 2.5 to 8 solar masses (M(o), contrary to the earlier claim of 20M(o) (ref. 8). The surrounding circumstellar envelope contains only 0.09M(o) and a much more extended local molecular cloud has 4-9M(o).

Journal Article↗

MAFFT version 5: improvement in accuracy of multiple sequence alignment.

The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of approximately 8 sequences with low similarity, the accuracy was improved (2-10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10(-5)-10(-20)) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.

Reproducibility of Results↗

Platelet-derived growth factor-BB (PDGF-BB) induces differentiation of bone marrow endothelial progenitor cell-derived cell line TR-BME2 into mural cells, and changes the phenotype.

Blood vessels are composed of endothelial cells (EC) and mural cells, and the interaction between EC and mural cells is essential for the development and maintenance of the vasculature. EC differentiate from bone marrow-derived endothelial progenitor cells (EPC). Recently, we established a conditionally immortalized bone marrow EPC-derived cell line, TR-BME2, and a brain capillary EC (BCEC) line, TR-BBB, from temperature-sensitive-SV40 T-antigen gene transgenic rats. To understand the function of EPC, it is important to analyze the difference between EPC and mature EC such as BCEC. In this study, we identified EPC-specific genes by means of subtractive hybridization between TR-BME2 and TR-BBB. There was no significant difference between TR-BME2 and TR-BBB in the mRNA level of annexin II, which is expressed in EC. In contrast, the mRNA level of smooth muscle cell (SMC) markers such as smooth muscle protein 22 (SM22), calvasculin, and platelet-derived growth factor (PDGF) receptor-beta, was higher in TR-BME2 than in TR-BBB. Moreover, the mRNA level of contractile SMC markers, such as smooth muscle alpha-actin and SM22, was increased in the absence of EC growth factors, such as vascular endothelial growth factor. The mRNA level of synthetic SMC markers, such as matrix Gla protein, was increased by the addition of PDGF-BB. The SMC derived from TR-BME2 showed an altered phenotype, from contractile-type to synthetic-type, when they were cultured in the absence of PDGF-BB. These results show that TR-BME2 cells have higher levels of SMC markers compared with mature EC, and can differentiate into contractile- or synthetic-type SMC.

AC133 Antigen↗

Isolation of Ef silicatein and Ef lectin as molecular markers for sclerocytes and cells involved in innate immunity in the freshwater sponge Ephydatia fluviatilis.

Sponges (phylum Porifera) have remarkable regenerative and reconstitutive abilities and represent evolutionarily the oldest metazoans. To investigate sponge stem cell differentiation, we have focused on the asexual reproductive system in the freshwater sponge Ephydatia fluviatilis. During germination, thousands of stem cells proliferate and differentiate to form a fully functional sponge. As an initial step of our investigation of stem cell (archeocyte) differentiation, we isolated molecular markers for two differentiated cell types: spicule-making sclerocyte cells, and cells involved in innate immunity. Sclerocyte lineage-specific Ef silicatein shares 45% to 62% identity with other sponge silicateins. As in situ hybridization of Ef silicatein specifically detects archeocytes possibly committed to sclerocytes, as well as sclerocytes with an immature or mature spicule, therefore covering all the developmental stages, we conclude that Ef silicatein is a suitable sclerocyte lineage marker. Ef lectin, a marker for the cell type involved in innate immunity, shares 59% to 65% identity with the marine sponge Suberites domuncula galactose-binding protein (Sd GBP) and horseshoe crab Tachypleus tridentatus tachylectin1/lectinL6. Since Sd GBP and tachylectin1 are known to bind to bacterial lipopolysaccharides and inhibit the growth of bacteria, Ef lectin may have a similar function and be expressed in a specialized type of cell involved in defense against invading bacteria. Ef lectin mRNA and protein are not expressed in early stages of development, but are detected in late stages. Therefore, Ef lectin may be specifically expressed in differentiating and/or differentiated cells. We suggest Ef lectin as a marker for cells that assume innate immunity in freshwater sponges.

Amino Acid Sequence↗

Improvement in the accuracy of multiple sequence alignment program MAFFT.

In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, both of which were released in 2004, in several benchmark tests. Here we report a recent extension of MAFFT that aims to improve the accuracy with as little cost of calculation time as possible. The extended version of MAFFT (v.5) has new iterative refinement options, G-INS-i and L-INS-i (collectively denoted as [GL]-INS-i in this report). These options use a new objective function combining the weighted sum-of-pairs (WSP) score and a score similar to COFFEE derived from all pairwise alignments. We discuss the improvement in accuracy brought by this extension, mainly using two benchmark tests released very recently, BAliBASE v.3 (for protein alignments) and BRAliBASE (for RNA alignments). According to BAliBASE v.3, the overall average accuracy of L-INS-i was higher than those of other methods successively released in 2004, although the difference among the most accurate methods (ProbCons, TCoffee v.2 and new options of MAFFT) was small. The advantage in accuracy of [GL]-INS-i became greater for the alignments consisting of approximately 50-100 sequences. By utilizing this feature of MAFFT, we also examined another possible approach to improve the accuracy by incorporating homolog information collected from database. The [GL]-INS-i options are applicable to aligning up to approximately 200 sequences, although not applicable to thousands of sequences because of time and space complexities.

Amino Acid Sequence↗

Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins.

The phylogenetic position of turtles is a currently controversial issue. Recent molecular studies rejected a traditional view that turtles are basal living reptiles (Hedges, S. B., and L. L. Poling. 1999. A molecular phylogeny. Science 83:998-1001; Kumazawa, Y., and M. Nishida. 1999. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink, statistical evidence for archosaurian affinity of turtles. Mol. Biol. Evol. 16:784-792). Instead, these studies grouped turtles with birds and crocodiles. The relationship among turtles, birds, and crocodiles remained unclear to date. To resolve this issue, we have cloned and sequenced two nuclear genes encoding the catalytic subunit of DNA polymerase alpha and glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide formyltransferase from amniotes and an amphibian. The amino acid sequences of these proteins were subjected to a phylogenetic analysis based on the maximum likelihood method. The resulting tree showed that turtles are the sister group to a monophyletic cluster of archosaurs (birds and crocodiles). All other possible tree topologies were significantly rejected.

Alligators and Crocodiles↗

An early extrasolar planetary system revealed by planetesimal belts in beta Pictoris.

beta Pictoris (beta Pic) is a main-sequence star with an edge-on dust disk that might represent a state of the early Solar System. The dust does not seem to be a remnant from the original protoplanetary disk, but rather is thought to have been generated from large bodies like planetesimals and/or comets. The history and composition of the parent bodies can therefore be revealed by determining the spatial distribution, grain size, composition and crystallinity of the dust through high-resolution mid-infrared observations. Here we report that the sub-micrometre amorphous silicate grains around beta Pic have peaks in their distribution around 6, 16 and 30 au (1 au is the Sun-Earth distance), whereas the crystalline and micrometre-sized amorphous silicate grains are concentrated in the disk centre. As sub-micrometre grains are blown quickly out from the system by radiation pressure from the central star, the peaks indicate the locations of ongoing dust replenishment, which originates from ring-like distributions of planetesimals or 'planetesimal belts'.

Journal Article↗

Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes.

BACKGROUND: Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates. RESULTS: We have cloned and sequenced seven nuclear DNA-coded genes from 13 vertebrate species. These sequences, together with sequences available from databases including 13 jawed vertebrates from eight major groups (cartilaginous fishes, bichir, chondrosteans, gar, bowfin, teleost fishes, lungfishes and tetrapods) and an outgroup (a cyclostome and a lancelet), have been subjected to phylogenetic analyses based on the maximum likelihood method. CONCLUSION: Cartilaginous fishes have been inferred to be basal to other jawed vertebrates, which is consistent with the generally accepted view. The minimum log-likelihood difference between the maximum likelihood tree and trees not supporting the basal position of cartilaginous fishes is 18.3 +/- 13.1. The hypothesis by Rasmussen and Arnason has been significantly rejected with the minimum log-likelihood difference of 123 +/- 23.3. Our tree has also shown that living holosteans, comprising bowfin and gar, form a monophyletic group which is the sister group to teleost fishes. This is consistent with a formerly prevalent view of vertebrate classification, although inconsistent with both of the current morphology-based and mitochondrial sequence-based trees. Furthermore, the bichir has been shown to be the basal ray-finned fish. Tetrapods and lungfish have formed a monophyletic cluster in the tree inferred from the concatenated alignment, being consistent with the currently prevalent view. It also remains possible that tetrapods are more closely related to ray-finned fishes than to lungfishes.

Animals↗

Counterion displacement in the molecular evolution of the rhodopsin family.

The counterion, a negatively charged amino acid residue that stabilizes a positive charge on the retinylidene chromophore, is essential for rhodopsin to receive visible light. The counterion in vertebrate rhodopsins, Glu113 in the third transmembrane helix, has an additional role as an intramolecular switch to activate G protein efficiently. Here we show on the basis of mutational analyses that Glu181 in the second extracellular loop acts as the counterion in invertebrate rhodopsins. Like invertebrate rhodopsins, UV-absorbing parapinopsin has a Glu181 counterion in its G protein-activating state. Its G protein activation efficiency is similar to that of the invertebrate rhodopsins, but significantly lower than that of bovine rhodopsin, with which it shares greater sequence identity. Thus an ancestral vertebrate rhodopsin probably acquired the Glu113 counterion, followed by structural optimization for efficient G protein activation during molecular evolution.

Amino Acids, Acidic↗

Preparation of reversibly glucose-responsive hydrogels by covalent immobilization of lectin in polymer networks having pendant glucose.

Glucose-responsive hydrogels were prepared by copolymerization of a monomer having a pendant glucose with modified lectin (concanavalin A (ConA)) having vinyl groups. Swelling behavior of ConA-copolymerized glucosyloxyethyl methacrylate (GEMA) hydrogels was discussed from the viewpoint of their synthetic condition and structures. The swelling ratio of the ConA-copolymerized GEMA hydrogels was strongly dependent on the glucose concentration in a buffer solution. As free glucose resulted in the dissociation of the complex between ConA and pendant glucose in the networks and the cross-linking density in the hydrogel decreased, the hydrogels swelled gradually in the presence of free glucose. Leak of ConA from the ConA-entrapment hydrogel and ConA-copolymerized hydrogel was examined in order to discuss the reversible changes of their glucose-responsive behavior. During swelling in the presence of free glucose, ConA leaked out of the ConA-entrapment GEMA hydrogel but did not out of the ConA-copolymerized GEMA hydrogel. As a result, the ConA-copolymerized GEMA hydrogel showed the reversible swelling changes in response to a stepwise change in the glucose concentration. This study revealed that covalent immobilization of ConA in the GEMA networks is very important for development of reversibly glucose-responsive hydrogels.

Biocompatible Materials↗

Synthesis and characterization of stimuli-sensitive hydrogels having a different length of ethylene glycol chains carrying phosphate groups: loading and release of lysozyme.

In order to prepare a polymer matrix capable of loading protein at high density, anionic hydrogels were synthesized by copolymerizing a monomer carrying a pendant phosphate group, methacryloyl-polyoxyethyl phosphate, with N-isopropylacrylamide and N,N'-methylene-bis-acrylamide, and the stumuli-sensitivity of hydrogels was characterized. The number of repeating ethylene glycol units in the phosphate carrying monomer was 1, 2, 5 or 8. Lysozyme bearing a positive net charge was immobilized in the hydrogel through formation of polyelectrolyte complex. It was shown that the amount of complexed lysozyme reached to 1.7 g/g dry gel, when high content of a phosphate-carrying monomer with 5 ethylene glycol units was incorporated into a hydrogel. It was further found that lysozyme complexed with phosphate-carrying network could be released by immersion of the lysozyme/hydrogel composite in a phosphate buffer solution of pH 7.4 owing to the pH-sensitivity of the hydorgel but no lysozyme was released at pH 1.4. The initial rate of lysozyme release was varied depending on the length of the ethylene glycol chains possessed by a network polymer and the content of the phosphate-carrying monomer unit. Lysozyme released from the phosphate-carrying hydrogel was proved to retain enzymatic activity at a level similar to the activity of lysozyme, which had been kept in buffer solution.

Ethylene Glycol↗

Markedly reduced evolutionary rates of transcription factors and cytoplasmic ribosomal RNAs and proteins in higher vertebrates and their evolutionary implications.

To reveal the relationship between organismal evolution and the molecular evolutionary rate, the temporal pattern of evolutionary rates were investigated for various genes during the course of deuterostome evolution. Deuterostome lineage leading to extant mammals was tentatively divided into two periods (the First and the Latter periods) by the time of divergence of bony fishes and mammals. For each of the First and the Latter period, evolutionary rates of 207 gene sets were calculated. In the Latter period, the evolutionary rate was significantly reduced in such informational genes as transcription factors and cytoplasmic ribosomal RNAs and proteins. In contrast, a variety of enzymes and mitochondrial ribosomal proteins evolve at nearly constant rate throughout the First and the Latter periods. The present result suggests that the increase of gene number by extensive gene duplications in the early evolution of vertebrates is responsible for the decrease of evolutionary rate.

Animals↗

A unifying model for functional difference and redundancy of presenilin-1 and -2 in cell apoptosis and differentiation.

Mutations in genes encoding the highly homologous proteins presenilin-1 and -2 (PS1 and PS2) are linked to the early onset of Alzheimer's disease (AD). Here, we report that polyclonal antibodies against Xenopus PSbeta (PS2), but not PSalpha (PS1), suppress the in vitro apoptotic activation of Xenopus egg extracts. To clarify the relationship between structural and functional differences in presenilins, we searched for presenilin homologues in various living sources, and found that presenilins were divided into three distinct groups, named alpha-, beta- and gamma-types, based on the size of the large hydrophilic loop (HL) regions as follows: HLalpha/HLbeta/HLgamma=4:3:6. No such size conservations were found in the N-terminal (NT) hydrophilic regions. Phylogenetic studies revealed that the presenilin genes were duplicated independently in different lineages of phyla/divisions, suggesting that there were functional requirements for and constraints on the generation and conservation of these HL sizes. On the basis of these findings, we propose a model postulating that both PS1 and PS2 can be differentiative or apoptotic when they are proteolytically processed within the HL regions or not, respectively, and PS1 may be more sensitive than PS2 to auto-proteolytic cleavage due to the larger size of the HL region of the former. Furthermore, the model assumes that C-terminal fragments (CTF) stabilized by phosphorylation may inhibit both the activities due to the dominant-negative effect. The model explains not only the functional redundancy but also apparently conflicting observations reported so far for PS1 and PS2.

Animals↗

A pilot study on antiplaque effects of mastic chewing gum in the oral cavity.

BACKGROUND: Chemical plaque control is a useful aid in mechanical oral hygiene, and various chemical agents have been evaluated as antiplaque agents. It has been shown that mastic chewing gum has antibacterial effects on Helicobacter pylori. In this study, the antiplaque effect of mastic chewing gum was investigated. METHODS: Twenty dental students who were both systemically and periodontally healthy participated in this study. The effects of mastic gum were assessed from 2 double-blinded, randomized studies. In the first trial, after mechanical toothbrushing, the inhibitory effect of mastic gum on bacteria in saliva following its use was compared to a placebo gum. Saliva samples were collected at the end of 1, 2, 3, and 4 hours; diluted; inoculated onto 10% horse blood chocolate agar plates; and cultured anaerobically at 37 degrees C for 48 hours. The total number of bacterial colonies on each plate was calculated (n = 20). In the second trial, the effects of mastic gum on de novo plaque formation on tooth surfaces and gingival inflammation were evaluated over a 7-day period without mechanical oral hygiene following random use of either mastic or placebo chewing gum. The degree of plaque accumulation and gingival inflammation were compared between the 2 groups (n = 10). RESULTS: The total number of bacterial colonies was significantly reduced during the 4 hours of chewing mastic gum compared to the placebo gum (P < 0.05, Student t test). The mastic group showed a significantly reduced plaque index (2.69 +/- 0.29 versus 3.15 +/- 0.24; P = 0.001, Student t test) and gingival index (0.44 +/- 0.15 versus 0.66 +/- 0.23, P = 0.021, Student t test) compared to the placebo group. CONCLUSION: These results suggest that mastic chewing gum is a useful antiplaque agent in reducing the bacterial growth in saliva and plaque formation on teeth.

Adult↗

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

Computer Simulation↗