Toxicogenomics using yeast DNA microarrays.

Development of genomics and bioinformatics enable us to analyze the global gene expression profiles of cells by DNA microarray. Changes in gene expression patterns indicate changes in its physiological conditions. Following the exposure of an organism or cell to toxic chemicals or other environmental stresses, the global genetic responses can be expeditiously and easily analyzed.

Microbiota during fermentation of chum salmon (Oncorhynchus keta) sauce mash inoculated with halotolerant microbial starters: analyses using the plate count method and PCR-denaturing gradient gel electrophoresis (DGGE).

Nine different combinations of mugi koji (barley steamed and molded with Aspergillus oryzae) and halotolerant microorganisms (HTMs), Zygosaccharomyces rouxii, Candida versatilis, and Tetragenococcus halophilus, were inoculated into chum salmon sauce mash under a non-aseptic condition used in industrial fish sauce production and fermented at 35 +/- 2.5 degrees C for 84 days to elucidate the microbial dynamics (i.e.

Effect of halotolerant starter microorganisms on chemical characteristics of fermented chum salmon (Oncorhynchus keta) sauce.

Chum salmon sauce mash was inoculated with barley koji (barley steamed and molded with Aspergillus oryzae ) and halotolerant microorganisms (HTMs), Zygosaccharomyces rouxii , Candida versatilis , and Tetragenococcus halophilus , in nine different combinations under non-aseptic conditions similar to the industrial fish sauce production and fermented at 35 +/- 2.5 degrees C for 84 days. The changes in the chemical components, color, and sensory properties during fermentation were investigated.

DNA microarray analysis suggests that zinc pyrithione causes iron starvation to the yeast Saccharomyces cerevisiae.

Zinc pyrithione has been used in anti-dandruff shampoos and in anti-fouling paint on ships. However, little is known of its mode of action. We characterized the effects of sub-lethal concentrations of zinc pyrithione (Zpt) on Saccharomyces cerevisiae using DNA microarrays.

Toxicity of methanol and formaldehyde towards Saccharomyces cerevisiae as assessed by DNA microarray analysis.

To assess the toxicity of the C1 compounds methanol and formaldehyde, gene expression profiles of treated baker's yeast were analyzed using DNA microarrays. Among approximately 6,000 open reading frames (ORFs), 314 were repressed and 375 were induced in response to methanol. The gene process category "energy" comprised the greatest number of induced genes while "protein synthesis" comprised the greatest number of repressed genes.

Mechanisms of copper toxicity in Saccharomyces cerevisiae determined by microarray analysis.

The effect of the heavy metal copper on the expression of a wide spectrum of genes was analyzed by using a DNA microarray. The gene expression profile of baker's yeast Saccharomyces cerevisiae grown in a medium containing a sublethal concentration of cupric sulfate was compared with that of yeast grown in a normal medium. Among approximately 6000 yeast ORFs, 143 ORFs were induced more than twofold to resist copper toxicity after exposure to copper.

Heat treatment of scallop adductor muscle using superheated steam.

Scallop (Patinopecten yessoensis) adductor muscles were heated using superheated steam (150 and 200 degrees C), boiling (98 degrees C), and normal steaming (95 degrees C). The amounts of amino acids, water-soluble peptides, and nucleotides, expressed as extractive nitrogen in scallop products, are very important elements of quality and taste. After 15-min heating of scallop muscles with normal steaming and boiling, respective losses of 50% and 64% of the extractive nitrogen were observed.

Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study.

The Japanese scallop (Mizuhopecten yessoensis) is one of the main fishery products in Japan, but with the expansion of culture operations of the Japanese scallop, various problems have been encountered including high mortality, poor growth, poor seed production, and so on. Moreover, there is concern that many years of cultivation may have affected the genetic structure of the scallop population. To approach these problems and concerns, we developed microsatellite markers as a molecular tool for population genetic studies.

Genetic structure of Japanese scallop population in Hokkaido, analyzed by mitochondrial haplotype distribution.

To examine the genetic structure of Japanese scallop populations (Mizuhopecten yessoensis) in Hokkaido prefecture, Japan, and compare it with those in the Aomori prefecture, we applied a method for lineage analysis based on sequence variation in a mitochondrial DNA segment (NcR2). After showing that there was a low probability of doubly uniparental inheritance of mitochondrial DNA in the scallop, we sequenced the NcR2 regions of 914 individuals from 15 populations (13 in Hokkaido and 2 in Aomori). In total, 103 different haplotypes were detected.

Molecular characterization of a mitochondrial DNA segment from the Japanese scallop (Patinopecten yessoensis): demonstration of a region showing sequence polymorphism in the population.

A 1.3-kb mitochondrial DNA segment from the Japanese scallop Patinopecten yessoensis was cloned and sequenced. This segment contained the transfer RNA(Met) gene and partial sequences of 2 ribosomal RNA genes, together with 2 separate noncoding regions (designated NcR1 and NcR2).

Stimulated accumulation of lectin mRNA and stress response in Helianthus tuberosus callus by methyl jasmonate.

Callus from Helianthus tuberosus expresses a mannose-specific lectin (HTA). The level of HTA mRNA significantly increased one hour after treatment of the callus with 20 mg/l methyl jasmonate. Following this, fragmentation of the callus DNA at regular intervals was observed together with strong self-fluorescence emission in the callus cells.

Cloning, sequencing, and heterologous expression of a cellobiohydrolase cDNA from the basidiomycete Corticium rolfsii.

From a Corticium rolfsii cDNA library, a clone homologous to other fungal cellobiohydrolase (CBH1) genes was isolated using the polymerase chain reaction. In the nucleotide sequence, one 1.6 kb long open reading frame coding for a polypeptide of 530 amino acid residues was detected which showed 64% identity with CBH1 of Phanerochaete chrysosporium.

Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces.

New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (Escherichia coli positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with RsaI plus BfaI or with BslI.

Alpha-glucosidase inhibitory activity of a 70% methanol extract from ezoishige (Pelvetia babingtonii de Toni) and its effect on the elevation of blood glucose level in rats.

The 70% methanol extract from ezoishige (Pelvetia babingtonii de Toni) inhibited the rat-intestinal alpha-glucosidase, sucrase and maltase activities, with IC50 values of 2.24 and 2.84 mg/ml.

Modulation of gene expression in transgenic mouse hearts overexpressing calsequestrin.

Calsequestrin (CSQ) is the major Ca2+ binding protein of the cardiac sarcoplasmic reticulum (SR). Transgenic mice overexpressing CSQ at the age of 7 weeks exhibit concentric cardiac hypertrophy, and by 13 weeks the condition progresses to dilated cardiomyopathy. The present study used a differential display analysis to identify genes whose expressions are modulated in the CSQ-overexpressing mouse hearts to provide information on the mechanism of transition from concentric cardiac hypertrophy to failure.

Improving effect of feeding with a phosphorylated guar gum hydrolysate on calcium absorption impaired by ovariectomy in rats.

We have previously reported that a phosphorylated guar gum hydrolysate (P-GGH) promoted calcium absorption and the accumulation of bone calcium in rats. We now investigate the effect of P-GGH (50 g/kg of diet) on the intestinal calcium absorption and bones of ovariectomized (OVX) rats in comparison with sham-operated rats over a six-week ingestion period. The apparent calcium absorption was decreased by aging and ovariectomy in the rats fed on the control and GGH diets (50 g/kg of diet), but not in the rats fed on the P-GGH diet.

Cloning and sequence analysis of cDNA coding for a lectin from Helianthus tuberosus callus and its jasmonate-induced expression.

Two lectins (designated as HTA I and HTA II) that seemed to be isolectins were found in Helianthus tuberosus callus. cDNA encoding HTA I was isolated from a ZAP Express expression library by immunoselection by using the anti-HTA antiserum. The sequence of this cDNA consisted of 432 bp nucleotides coding for a polypeptide of 143 amino acid residues (Mr, 15,314).

Purification and characterization of two lectins from calllus of Helianthus tuberosus.

Two lectins were purified from Helianthus tuberosus callus by maltose affinity chromatography and subsequent preparative electrophoresis. The lectins were designated HTA I and HTA II and their molecular masses were about 34 kDa by gel-filtration chromatography. A single band of 17 kDa and bands of 17 kDa and 18 kDa were detected after SDS-PAGE of HTA I and HTA II, respectively, indicating that HTA I is a homodimer while HTA II is a heterodimer.