Biomedical subjects

Kentaro Yano

Publications and source records attributed to Kentaro Yano.

8 recordsLinked to original sources

PubMed2006

Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice.

Microstructural changes such as insertions and deletions (=indels) are a major driving force in the evolution of non-coding DNA sequences. To better understand the mechanisms by which indel mutations arise, as well as the molecular evolution of non-coding regions, the number and pattern of indels and nucleotide substitutions were compared in the whole chloroplast genomes. Comparisons were made for a total of over 38 kb non-coding DNA sequences from 126 intergenic regions in two data sets representing species with different divergence times: sugarcane and maize and Oryza sativa var. indica and japonica. The main findings of this study are: (i) Approximately half of all indels are single nucleotide indels. This observation agrees with previous studies in various organisms. (ii) The distribution and number of indels was different between two data sets, and different patterns were observed for tandem repeat and non-repeat indels. (iii) Distribution pattern of tandem repeat indels showed statistically significant bias towards A/T-rich. (iv) The rate of indel mutation was estimated to be approximately 0.8 +/- 0.04 x 10(-9) per site per year, which was similar to previous estimates in other organisms. (v) The frequencies of nucleotide substitutions and indels were significantly lower in inverted repeat (IR).

Conserved Sequence↗

PubMed2006

Dramatic amplification of a rice transposable element during recent domestication.

Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature inverted-repeat transposable element (mPing) has amplified from approximately 50 to approximately 1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPingelements in strains that already have > 1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice.

Base Sequence↗

PubMed2006

A new method for gene discovery in large-scale microarray data.

Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure to discover whole sets of genes related to a quantitative trait of interest, which is generally controlled by several loci that make various contributions. Here, we describe a high-throughput gene discovery method based on correspondence analysis with a new index for expression ratios [arctan (1/ratio)] and three artificial marker genes. This method allows us to quickly analyze the whole microarray dataset and discover up-/down-regulated genes related to a trait of interest. We employed an example dataset to show the theoretical advantage of this method. We then used the method to identify 88 cancer-related genes from a published microarray data from patients with breast cancer. This method also allows us to predict the phenotype of a given sample from the gene expression profile. This method can be easily performed and the result is also visible in 3D viewing software that we have developed.

Breast Neoplasms↗

PubMed2005

Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars.

Laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom has attracted attention as a host for functional genomics research. In this study, we generated 35,824 expressed sequence tags (ESTs) from leaves and fruits of Micro-Tom. The ESTs comprised 10,287 unigenes (5007 contigs and 5280 singletons), including 1858 novel tomato unigenes. Of the 18 unigenes that shared strong homology with tobacco chloroplast genome sequences, one unigene was likely derived from polyadenylated transcripts of the atpH gene. Interestingly, ESTs for vacuolar invertase, pectate lyase and alcohol acyl transferase were underrepresented in the Micro-Tom data set. From all of the ESTs, we mined 2039 candidate single nucleotide polymorphisms (SNPs) and 121 candidate insertions and deletions (indels) based on homology with four tomato inbred lines, E6203, R11-13, Rio Grande PtoR and R11-12, and a wild relative, L. pennellii TA56, for which sequence data was publicly available with more than 5000 entries. Direct genome sequencing of several SNP or indel sites in Micro-Tom and L. esculentum E6203 suggested that more than 69% of the candidate sites were truly polymorphic, making them useful for the preparation of DNA markers.

DNA, Complementary↗

PubMed2004

An electrochemical device for the assay of the interaction between a dioxin receptor and its various ligands.

Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the toxic and biological effects of a variety of chemicals. Although a significant amount of information is available with respect to the planar aromatic hydrocarbon AhR ligands, information on the actual spectrum of chemical structures that can bind to and activate the AhR is insufficient. In order to determine the binding affinities of chemicals to the human AhR (hAhR), we constructed an electrochemical system which carries the hAhR ligand-binding domain on the electrode surface. The recombinant hAhR ligand-binding domain that was expressed in Escherichia coli using a T7 expression system was immobilized on a gold electrode. The specificity of this biosensor based on a ligand-receptor interaction was comparable to other in vitro screening methods. The receptor-modified electrode can rapidly detect the binding of ligands to hAhR. The electrochemical measurement can be carried out within just 5 min. This electrochemical screening system is rapid, low in cost, and adaptable to high-throughput applications without sacrificing either sensitivity or selectivity.

Electrochemistry↗

PubMed2003

Piezo electric sensor for endocrine-disrupting chemicals using receptor-co-factor interaction.

In vitro screening assays are useful techniques for the determination of receptor-mediated activities in environmental samples. In order to define whether environmental chemicals act as an agonist or antagonist to the human estrogen receptor (hER), we have constructed a biosensor based on ligand-inducible interactions between hER and relative proteins on a quartz crystal microbalance (QCM). The his-tagged proteins, which were expressed in E. coli by recombinant DNA technology, were immobilized on an Au-electrode with Ni(II)-mediated chemisorption using the histidine tag and thiol-modified iminodiacetic acid. The resonance-frequency change of the protein-modified electrode was caused by association or dissociation with the hER relative proteins on the surface in the presence of estrogen. These results suggest that this sensor is applicable as a large-scale screening tool for estrogenic compounds.

Biosensing Techniques↗

PubMed2003

Protein-immobilized electrode for rapid and convenient sensing of thyroid hormone receptor-ligand interaction.

The recombinant human thyroid hormone receptor (TR) was expressed as an in-frame fusion with ten consecutive histidine residues using a bacterial system; then the receptor was immobilized on an Au-electrode with Ni(II)-mediated chemisorption using the histidine tag and thiol-modified nitrilotriacetic acid. The receptor-modified electrode could rapidly detect ligand binding to hTR without any separation procedures, and showed a good response in a concentration-dependent manner. The sensitivity of this biosensor based on ligand-receptor interactions was comparable to those of conventional competitive ligand binding assays using radio-labeled ligands. Our results strongly suggest that our new biosensor can be applied to the identification of new ligands for hTR.

Biosensing Techniques↗

PubMed2002

Thermodynamic quantities of surface formation of aqueous electrolyte solutions. V. Aqueous solutions of aliphatic amino acids.

The surface tension of aqueous solutions of glycine, L-alanine, L-valine, and L-leucine has been observed using the drop volume method as a function of temperature and concentration. The L-leucine molecules form an adsorbed film, while glycine affects the water surface in accordance with simple salts which dissociate into cations and anions completely. The surface tension data have been analyzed in view of K. Motomura's thermodynamic treatment (J. Colloid Interface Sci.64, 348 (1978)), and the thermodynamic quantities relevant to the surface have been shown systematically.

Adsorption↗