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Nobuyoshi Ishii

Publications and source records attributed to Nobuyoshi Ishii.

12 recordsLinked to original sources
PubMed2006

Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli.

Phosphoenolpyruvate inhibited Escherichia coli NADP-isocitrate dehydrogenase allosterically (Ki of 0.31 mM) and isocitrate lyase uncompetitively (Ki' of 0.893 mM). Phosphoenolpyruvate enhances the uncompetitive inhibition of isocitrate lyase by increasing isocitrate, which protects isocitrate dehydrogenase from the inhibition, and contributes to the control through the tricarboxylic acid cycle and glyoxylate shunt.

Escherichia coli↗
PubMed2006

Removal of technetium from solution by algal flagellate Euglena gracilis.

Based on limited data for the removal of radioactive (99)Tc by freshwater phytoplankton, it has been thought that phytoplankton are unsuitable for remediation of (99)Tc-contaminated waters. This work sought to verify the validity of this assumption by studying the removal of (99)TcO(4)(-) by freshwater and brackish water phytoplankton. The phytoplankton used were Euglena gracilis, Chlamydomonas pulsatilla, Chlorella vulgaris, and Spirulina platensis. Each of them was incubated for 63 d, and the removal of (99)Tc from solution was periodically determined. Significant removal of (99)Tc was observed only for E. gracilis, and the maximum removal was 70% of the total (99)Tc added. The killed cells of E. gracilis, however, removed hardly any (99)Tc. When E. gracilis cells were washed with fresh culture medium, only 13% of the total (99)Tc was desorbed. These results suggested that intracellular uptake of (99)Tc by E. gracilis occurred. These results are the first documented example of significant removal of (99)Tc by planktonic microalgae.

Animals↗
PubMed2005

The influence of paddy soil drying on Tc insolubilization by bacteria.

Tc insolubilization in four soils samples was compared by pre-incubating them in both dry and wet states, then measuring Tc concentrations in solution when the samples were saturated with an excess of water spiked with 99Tc. Soils pre-incubated in a dry state showed higher Tc insolubilization than soils incubated in a wet state. To clarify the difference in Tc insolubilization, Eh, bacterial abundances, and bacterial species compositions in the dry and wet ponding water samples were determined. For the wet ponding water samples, Eh values were forced to decrease, but no increase in Tc insolubilization was observed. The dry and wet ponding water samples had similar numbers of bacteria. However, denaturing gradient gel electrophoresis analysis revealed that they had different bacterial species compositions. These results suggested the difference in bacterial species compositions would account for the difference in Tc insolubilization.

Agriculture↗
PubMed2005

In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations.

The translation start site, immediately downstream from the start codon, is a dominant factor for gene expression in Escherichia coli. At present, no method exists to improve the expression level of cloned genes, since it remains difficult to find the best codon combination within the region. We determined the expression parameters that correspond to all sense codons within the first four codons using GFPuv which encodes a derivative of green fluorescent protein. Using a genetic algorithm (GA)-based computer program, these parameters were incorporated in a simple, static model for the prediction of translation efficiency, and optimized to the expression level for 137 randomly isolated GFPuv genes. The calculated initial translation index (ITI), also proven for the DsRed2 gene that encodes a red fluorescent protein, should provide a solution to overcome the gene expression problem in cloned genes whose expression is often inherently blocked at the translation process. The proposed method facilitates heterologous protein production in E. coli, the most commonly used host in biological and industrial fields.

Cloning, Molecular↗
PubMed2005

Gram-negative bacteria responsible for insoluble technetium formation and the fate of insoluble Tc in the water column above flooded paddy soil.

We studied the characteristic gram-stain of Tc insolubilizing bacteria using various antibiotics, and the fate of insoluble Tc in a water column above flooded paddy soil to clarify Tc behavior in paddy fields. The formation of insoluble Tc in water column samples was inhibited by the addition of antibiotics, especially reagents against gram-negative bacteria. For a sample without antibiotics, insoluble Tc formation increased with time, and the maximum amount of insoluble Tc was observed on day 4 of incubation with (95m)Tc. In contrast, concentrations of ferrous ion decreased with time. These results suggested that gram-negative bacteria were mainly responsible for insoluble Tc formation, and that these bacteria were able to transform soluble Tc to insoluble forms under oxidizing conditions.

Disasters↗
PubMed2004

Release of transforming plasmid DNA from actively growing genetically engineered Escherichia coli.

We studied the transforming ability of the extracellular plasmid DNA released from a genetically engineered Escherichia coli pEGFP and the culturing conditions for the release of transforming DNA. The transforming ability was evaluated by transformation of competent cells with filtrates of E. coli pEGFP cultures. The number of transformants increased with time when E. coli pEGFP cells grew exponentially in rich medium, but not in stationary phase or when inoculated in freshwater. These results suggested that crude extracellular plasmid DNA had transforming ability and this transforming DNA was mainly released by actively growing bacteria.

Colony Count, Microbial↗
PubMed2004

Toward large-scale modeling of the microbial cell for computer simulation.

In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these "omics" methods are the focus of intensive research activities. As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective. Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry. In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging. Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system developed in our laboratory is introduced. Finally, our strategy for building a "whole cell metabolism model", including the experimental approach, is presented.

Biotechnology↗
PubMed2004

Physicochemical forms of technetium in surface water covering paddy and upland fields.

The behavior of an element in the environment depends on its physicochemical form. Basic data for the behavior of technetium in an agricultural environment were obtained by determining the physicochemical forms of Tc in 28 surface water samples from paddy and upland fields. Most of the (95m)Tc was present as TcO(4)(-) in the samples. The relative amount of this chemical form was 72% on average. A significant amount of insoluble Tc (particles more than 0.2 microm in size), however, was found in some samples. The maximum amount of the insoluble Tc was 91%. Other forms were found in insignificant amounts. The amount of insoluble Tc was relatively high in paddy soil samples. Paddy soils, gley soils and gray lowland soils were particularly effective in the insolubilization of Tc. Among the soil characteristics studied, cation exchange capacity, anion exchange capacity, and active aluminum showed significant correlations with the relative amount of insoluble Tc. When microorganisms were eliminated from the surface water samples before the addition of (95m)TcO(4)(-), little insoluble Tc was found, suggesting that microorganisms cause the physicochemical transformation. These results showed that the physicochemical form of Tc changes from TcO(4)(-) to insoluble forms in surface water covering paddy fields. The insoluble forms would restrict the mobility of Tc in paddy fields.

Fresh Water↗
PubMed2004

Influence of microorganisms on the behavior of technetium and other elements in paddy soil surface water.

Insolubilization patterns of technetium (Tc) and other trace elements (Sc, Co, Zn, Se, Rb, Sr, Y, Nb, Ce, Pm, Gd, Lu, Hf, and Re) in surface water covering paddy fields were compared to gain insight into the behavior of Tc in an agricultural environment. The insolubilization of Tc, which did not pass through a 0.2-microm-pore-size filter, was mainly caused by bacteria. Among the 14 other elements investigated, Nb was insolubilized by bacteria and the amounts of insoluble Nb were positively correlated with those of Tc. Although Re is a chemical analog of Tc, no similarity was observed. These results suggest that Tc behaves similarly to Nb in the insolubilization in surface water covering paddy fields.

Bacteria↗
PubMed2003

Spatial memory impairment in OLETF rats without cholecystokinin - a receptor.

Cholecystokinin (CCK) is one of the most abundant neurotransmitter peptides in the brain. As Otsuka Long-Evans Tokushima Fatty (OLETF) rats lack CCK-A receptor because of a genetic abnormality, we examined whether learning and memory were impaired in these animals using both Morris water maze (MWM) and step-through type passive avoidance (PA) learning test. In the MWM test, memory impairment was observed in OLETF rats. The number of errors was also significantly higher, and that of the correct choices was significantly lower in OLETF rats compared to the controls [Long-Evans Tokushima Otsuka (LETO)] rats. In PA, OLETF rats did not show facilitating response 24 h after training. From these observations, we concluded that a spatial memory was impaired in the OLETF rats.

Animals↗
PubMed2003

Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae.

We studied the effects of cocultivation with either Euglena gracilis (Euglenophyta), Microcystis aeruginosa (Cyanophyta), Chlamydomonas neglecta (Chlorophyta), or Carteria inversa (Chlorophyta) on the production of extracellular plasmid DNA by Escherichia coli LE392(pKZ105). Dot blot hybridization analysis showed a significant release of plasmid DNA by cocultivation with all the algae tested. Further analysis by electrotransformation confirmed the release of transformable plasmid DNA by cocultivation with either E. gracilis, M. aeruginosa, or C. inversa. These results suggest algal involvement in bacterial horizontal gene transfer by stimulating the release of transformable DNA into aquatic environments.

Animals↗