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Biomedical subjects

Kosuke Tashiro

Publications and source records attributed to Kosuke Tashiro.

12 recordsLinked to original sources
PubMed2006

Gene expression profiling in common cormorant liver with an oligo array: assessing the potential toxic effects of environmental contaminants.

To establish a monitoring system for gene expression profiles related to chemical contamination in wild common cormorants (Phalacrocorax carbo), the present study constructed an oligo array designed from expressed sequence tag (EST) sequences of the cormorant liver, where 1061 unique oligonucleotides were spotted. Common cormorants were collected from Lake Biwa, Japan in May 2001 and 2002. With the use of this oligo array, gene expression profiles in the liver of individual specimens were evaluated. To determine the expression patterns of genes altered by environmental contaminants, relationships between concentrations of persistent organochlorines including polychlorinated dibenzo-p-dioxins, furans, polychlorinated biphenyls, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane and its metabolites (DDTs), hexachlorocyclohexane isomers (HCHs), chlordane compounds (CHLs), butyltins, and bisphenol A (BPA) and expression levels of each gene in the cormorant liver were examined using stepwise multiple regression analysis. The reliability of data obtained by the oligo array was further confirmed by quantifying the expression levels of certain genes using real-time RT-PCR. The 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic equivalent (TEQ) level was positively correlated with both cytochrome P4501A4 and 1A5 gene expression. In addition, the mRNA level of an antioxidant enzyme, Cu/Zn superoxide dismutase, was negatively correlated with hepatic total TEQ. Other antioxidant enzymes, glutathione peroxidase 3 and glutathione S-transferase class mu, were negatively correlated with HCHs and BPA levels, respectively. The mRNA expression level of a nonenzymatic antioxidant, haptoglobin, was negatively but not significantly correlated with CHLs. These results led to a hypothesis that wild cormorant population may suffer from oxidative stress due to chemically induced formation of reactive oxygen species and subsequent reduction of antioxidant resistance. Thus, the cormorant oligo array may be a useful monitoring tool to identify specific gene expression profiles altered by various environmental contaminants. Although further research is required to clarify a definitive cause-and-effect relationship, the current study provides valuable information on contaminant-responsive genes to predict potential effects on wildlife in a real environment.

Animals↗
PubMed2006

Identification of novel genes with prognostic value in childhood leukemia using cDNA microarray and quantitative RT-PCR.

The aim of this study was to identify genes distinctively expressed or suppressed in childhood leukemia with different prognoses, using cDNA microarray and quantitative reverse transcription-polymerase chain reaction (RT-PCR). The expression levels of the selected genes by cDNA microarray were quantified in primary leukemic blasts from 44 patients (acute lymphoblastic leukemia, 28; acute myelogenous leukemia (AML), 13; transient myeloproliferative disorder, 3). The expression levels of CDKN2C, CRADD, and IGFBP-2 genes were significantly associated with the event-free survival of the patients in AML. The present results suggest that a combination of cDNA microarray and quantitative RT-PCR may be useful to identify novel genes with prognostic value in childhood AML.

Adaptor Proteins, Signal Transducing↗
PubMed2006

ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes.

For a new pathogen to emerge, it must acquire both virulence genes and a system for responding to changes in environmental conditions. Starvation of nutrients or growth arrest induces the stringent response in Escherichia coli, via increased ppGpp. We found the adherence capacity of enterohaemorrhagic E. coli (EHEC) and gene expression in the locus of enterocyte effacement (LEE) were enhanced by a downshift in nutrients or by entry into the stationary growth phase, both of which increase the ppGpp concentration. The activation was dependent on relA and spoT, which encode enzymes for the synthesis and degradation of ppGpp, and on dksA, which encodes an RNA polymerase accessory protein required for the stringent response. Upon induction of RelA expression, LEE gene transcription was activated within 20 min, even without starvation. The expression of two LEE transcriptional regulators, Ler and Pch, was activated by ppGpp and essential for the enhancement of LEE gene expression. In addition, the ler and pch promoters were directly activated by ppGpp in an in vitro transcription system. These findings suggest that the regulation of virulence genes in EHEC is integrated with E. coli's stringent response system, through the regulation of virulence regulatory genes.

Adhesins, Bacterial↗
PubMed2006

Properties of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae.

We characterized a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae, TFL20, that has a mutation in the LEU4 gene. We monitored the concentration of extracellular i-AmOH and intracellular amino acids, and compared the ratios of gene expression in TFL20 with the wild-type strain, K30. We found that the LEU1, LEU2, and BAT1 genes were up-regulated in TFL20 for metabolism, and that TFL20 simultaneously produced as much i-AmOH and leucine as K30 does.

2-Isopropylmalate Synthase↗
PubMed2005

Association of the GTP-binding protein Gtr1p with Rpc19p, a shared subunit of RNA polymerase I and III in yeast Saccharomyces cerevisiae.

Yeast Gtr1p and its human homolog RRAG A belong to the Ras-like small G-protein superfamily and genetically interact with RCC1, a guanine nucleotide exchange factor for Ran GTPase. Little is known regarding the function of Gtr1p. We performed yeast two-hybrid screening using Gtr1p as the bait to find interacting proteins. Rpc19p, a shared subunit of RNA polymerases I and III, associated with Gtr1p. The association of Gtr1p with Rpc19p occurred in a GTP-form-specific manner. RRAG A associated with RPA16 (human Rpc19p homolog) in a GTP-form-specific manner, suggesting that the association is conserved during evolution. Ribosomal RNA and tRNA synthesis were reduced in the gtr1Delta strain expressing the GDP form of Gtr1p, but not the GTP form of Gtr1p. Gel-filtration studies revealed an accumulation of the smaller Rpc19p-containing complex, but not of A135, in the gtr1Delta strain. Here, we propose that Gtr1p is involved in RNA polymerase I and III assembly by its association with Rpc19p and could be a mediator that links growth regulatory signals with ribosome biogenesis.

DNA-Directed RNA Polymerases↗
PubMed2005

Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.

Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed prior to any data analysis. To remove these biases, many normalization methods are used by researchers. However, not all biases are eliminated from the microarray data because not all types of errors from experimental protocols are known. In this paper, we report an effective way of removing various types of biases by treating each microarray dataset independently to detect biases present in the dataset. After the biases contained in each dataset were identified, a combination of normalization methods specifically made for each dataset was applied to remove biases one at a time.

Algorithms↗
PubMed2005

Dual regulatory pathways integrating the RcsC-RcsD-RcsB signalling system control enterohaemorrhagic Escherichia coli pathogenicity.

Bacterial pathogenesis is strictly regulated in response to changes in environmental conditions. A His-Asp phosphorelay system consisting of a sensor kinase and response regulator is used by Gram-positive and Gram-negative bacteria to control gene expression in response to environmental stimuli. We screened His-Asp phosphorelay systems for their effect on virulence expression in enterohaemorrhagic Escherichia coli (EHEC), and found rcsD or rcsB overexpression enhanced locus for enterocyte effacement (LEE) gene transcription and adherence to Caco-2 cells through transcriptional activation of the ler regulatory gene. An EHEC-specific regulator GrvA, encoded by ECs1274, was required for ler transcription activation by RcsB. Furthermore, GrvA activated ler transcription in E. coli K12. Stimulation of the RcsDCB regulatory system by RcsF overexpression slightly increased EspB expression in the wild type but not the ECs1274 mutant. However, EspB expression in an rcsB deletion mutant increased compared with wild type, suggesting that RcsB negatively regulates LEE gene expression and that active RcsB protein is present under normal growth conditions. Deletion of pchA, which encodes a positive regulator for ler, abolished the effect of the rcsB deletion, suggesting that pchA mediated the negative RcsB effect. pchA transcript levels decreased when RcsB expression increased. Thus, LEE gene transcription may be regulated by RcsB through two oppositely regulated O157-specific regulators, PchA and GrvA.

Adaptation, Physiological↗
PubMed2005

Asp578 in LEU4p is one of the key residues for leucine feedback inhibition release in sake yeast.

We identified a new mutation, Asp578Tyr, in alpha-isopropylmalate synthase (a LEU4 gene product) that releases leucine feedback inhibition and causes hyperproduction of isoamyl alcohol (i-AmOH) in sake yeast. Spontaneous sake yeast mutants that express resistance to 5,5,5-trifluoro-DL-leucine (TFL) were isolated, and a mutant strain, TFL20, was characterized at the genetic and biochemical levels. An enzyme assay for alpha-isopropylmalate synthase showed that strain TFL20 was released from feedback inhibition by L-leucine. Furthermore, DNA sequencing of the LEU4 gene for a haploid of the mutant TFL20 revealed that aspartic acid in position 578 changes to tyrosine. A comparison of the three-dimensional structures of wild-type LEU4p and mutant LEU4D578Yp by the homology modeling method showed that Asp578 is important for leucine feedback inhibition. We conclude that the mutation from Asp to Tyr in 578 is a novel change causing release from leucine feedback inhibition.

2-Isopropylmalate Synthase↗
PubMed2003

Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries.

Gene regulatory networks elucidated from strategic, genome-wide experimental data can aid in the discovery of novel gene function information and expression regulation events from observation of transcriptional regulation among genes of known and unknown biological function. To create a reliable and comprehensive data set for the elucidation of transcription regulation networks, we conducted systematic genome-wide disruption expression experiments of yeast on 118 genes with known involvement in transcription regulation. We report several novel regulatory relationships between known transcription factors and other genes with previously unknown biological function discovered with this expression library. Here we report the downstream regulatory subnetworks for UME6 and MET28. The elucidated network topology among these genes demonstrates MET28's role as a nodal point between genes involved in cell division and those involved in DNA repair mechanisms.

Algorithms↗
PubMed2003

Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades.

We developed an extensive yeast gene expression library consisting of full-genome cDNA array data for over 500 yeast strains, each with a single-gene disruption. Using this data, combined with dose and time course expression experiments with the oral antifungal agent griseofulvin, whose exact molecular targets were previously unknown, we used Boolean and Bayesian network discovery techniques to determine the gene expression regulatory cascades affected directly by this drug. Using this method we identified CIK1 as an important affected target gene related to the functional phenotype induced by griseofulvin. Cellular functional analysis of griseofulvin showed similar tubulin-specific morphological effects on mitotic spindle formation to those of the drug, in agreement with the known function of CIK1p. Further, using the nonparametric, nonlinear Bayesian gene networks we were able to identify alternative ligand-dependant transcription factors and G protein homologues upstream of CIK1 that regulate CIK1 expression and might therefore serve as alternative molecular targets to induce the same molecular response as griseofulvin.

Bayes Theorem↗
PubMed2003

Response of genes associated with mitochondrial function to mild heat stress in yeast Saccharomyces cerevisiae.

The genome-wide expression pattern of budding yeast Saccharomyces cerevisiae in response to mild heat treatment in a non-fermentable carbon source was analyzed using DNA microarrays. Of 5,870 open reading frames (nuclear genome transcripts) examined, 104 genes were upregulated and 287 genes were downregulated upon shifting of the cells from 25 degrees C to 37 degrees C. Forty upregulated genes and 235 downregulated genes encoded localization-assigned proteins. Of 113 heat-repressible genes (excluding 122 heat-repressible ribosomal genes), 36 were mitochondria-related genes, whereas only 2 of 40 heat-inducible genes were mitochondria-related. In particular, 9 genes involved in the mitochondrial respiratory chain and 7 genes involved in mitochondrial protein translocation were significantly repressed, suggesting that mitochondrial respiratory function and biogenesis were downregulated. Consistent with these findings, the growth of yeast cells in a non-fermentable carbon source was repressed at 37 degrees C and the mitochondria isolated from heat-stressed cells exhibited compromised preprotein-import activity compared with those from unstressed cells. In contrast, many genes involved in glycolysis and the metabolic pathway to produce glutamate via the tricarboxylic acid cycle, which is essential for biosynthetic reactions, were upregulated. Yeast cells might downregulate mitochondrial function to circumvent heat-induced oxidative stress, upregulate stress-related genes, and remodel genes for metabolic pathways in response to mild heat stress: an adaptive response at the expense of cell growth.

Down-Regulation↗