Shinji Nagata

Bio: Shinji Nagata is an academic researcher from Kōchi University. The author has contributed to research in topics: Enzyme & Dehydrogenase. The author has an hindex of 22, co-authored 96 publications receiving 1471 citations. Previous affiliations of Shinji Nagata include Kyoto Institute of Technology & Kyoto University.

Rate of emulsion polymerization of styrene

Abstract: In emulsion polymerization, the Smith and Ewart theory gives about two or three times the number of polymer particles obtained by experiment. In this paper, a reaction model is proposed which, from the standpoint of reactor design, can give an adequate explanation of the whole course of an emulsion polymerization of monomer highly insoluble in water. Among other things, the generating process of polymer particles is examined in detail. It is demonstrated experimentally that a new parameter proposed here, which represents the degree of difficulty of monomer initiation in micelles, is indispensable in explaining that process. Also confirmed is that monomer initiation takes place more easily in polymer particles than in micelles. According to the new model, the progress of polymerization, i.e., monomer conversion, the number of the polymer particles, and properties of polymer thus produced can be estimated with satisfactory accuracy. Furthermore, approximate equations are derived for easier estimation.

Gene cloning and sequence determination of leucine dehydrogenase from Bacillus stearothermophilus and structural comparison with other NAD(P)+-dependent dehydrogenases.

Abstract: The gene for leucine dehydrogenase (EC 1419) from Bacillus stearothermophilus was cloned and expressed in Escherichia coli The selection for the cloned gene was based upon activity staining of the replica printed E coli cells A transformant showing high leucine dehydrogenase activity was found to carry an about 9 kilobase pair plasmid, which contained 46 kilobase pairs of B stearothermophilus DNA The nucleotide sequence including the 1287 base pair coding region of the leucine dehydrogenase gene was determined by the dideoxy chain termination method The translated amino acid sequence was confirmed by automated Edman degradation of several peptide fragments produced from the purified enzyme by trypsin digestion The polypeptide contained 429 amino acid residues corresponding to the subunit (Mr 49,000) of the hexameric enzyme Comparison of the amino acid sequence of leucine dehydrogenase with those of other pyridine nucleotide dependent oxidoreductases registered in a protein data bank revealed significant sequence similarity, particularly between leucine and glutamate dehydrogenases, in the regions containing the coenzyme binding domain and certain specific residues with catalytic importance

Effect of stirring on the emulsion polymerization of styrene

Abstract: The purpose of this paper is to clarify the effect of stirring on the course of emulsion polymerization of, for example, styrene. It establishes the existence of an optimum range of stirring speed and three important factors which must be considered in carrying out emulsion polymerization. (1) Stirring significantly affects the course of reaction in the presence of an imperfectly purified nitrogen atmosphere. Consequently, the number of polymer particles produced and the polymerization rate per particle will be affected. (2) At higher stirring speeds, polymer particles coagulate and coalesce. At lower stirring speeds, the reaction rate is controlled by the monomer transport rate from monomer droplets to the aqueous phase. (3) Stirring contributes to the reduction of the number of micelles because emulsifier molecules are adsorbed onto the surfaces of monomer droplets finely dispersed by the stirring. At low emulsifier concentrations near the critical micelle concentration, this effect cannot be neglected.

3-Hydroxyisobutyrate Dehydrogenase from Pseudomonas putida E23: Purification and Characterization

Abstract: The NAD+-dependent 3-hydroxyisobutyrate dehydrogenase [EC 1.1.1.31] was purified to homogeneity from Pseudomonas putida E23. The enzyme was a tetramer (molecular mass, 120kDa) consisted of identical subunits (molecular mass, 30 kDa). The enzyme was specific for NAD+ (Km, 0.44 mm). The maximal activity was obtained at about pH 10. The enzyme was specific for the l-isomer of 3-hydroxyisobutyrate. In addition to l-3-hydroxyisobutyrate, l-serine, 2-methyl-dl-serine, and 3-hydroxypropionate were substrates. The Km for l-3-hydroxyisobutyrate, l-serine, 2-methyl-dl-serine, and 3-hydroxypropionate were 0.12, 18, 44, and 83 mm, respectively. The enzyme was inhibited by p-chloromercuribenzoate, HgCl2, and AgNO3, but not by EDTA, α,α′-dipyridyl, and o-phenanthroline. The N-terminal 26 amino acid sequence was compared with the sequences deduced from the enzyme genes of rat liver and Pseudomonas aeruginosa.

The role of polymer particles in the emulsion polymerization of vinyl acetate

Abstract: The emulsion polymerization of vinyl acetate was carried out at 50°C using sodium lauryl sulfate as an emulsifier and potassium persulfate as an initiator, and the role of the polymer particles produced in this system was studied on the basis of a previous theory. The low value of the average number of radicals per particle obtained in this work, i.e. in the range 0.01 - 0.5, is explained by introducing a mechanism of a rapid escape of monomeric radicals produced by the chain-transfer reaction which occurs dominantly in the polymer particles. Semiempirical equations are proposed for the estimation for the average number of radicals per particle over the whole range of monomer conversion.

Transcriptional Profiling Shows that Gcn4p Is a Master Regulator of Gene Expression during Amino Acid Starvation in Yeast

Abstract: Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments using two different strains derived from S288c revealed that more than 1,000 genes were induced, and a similar number were repressed, by a factor of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Δ strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p target genes. Gcn4p also activates genes involved in glycogen homeostasis, and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcription factors were identified as targets, suggesting that Gcn4p is a master regulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS induced GCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profiling of a gcn4Δ mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.

Cytoplasmic steps of peptidoglycan biosynthesis.

Abstract: The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.

A critical review of dispersion in packed beds

Abstract: The phenomenon of dispersion (transverse and longitudinal) in packed beds is summarized and reviewed for a great deal of information from the literature. Dispersion plays an important part, for example, in contaminant transport in ground water flows, in miscible displacement of oil and gas and in reactant and product transport in packed bed reactors. There are several variables that must be considered, in the analysis of dispersion in packed beds, like the length of the packed column, viscosity and density of the fluid, ratio of column diameter to particle diameter, ratio of column length to particle diameter, particle size distribution, particle shape, effect of fluid velocity and effect of temperature (or Schmidt number). Empirical correlations are presented for the prediction of the dispersion coefficients (D T and D L) over the entire range of practical values of Sc and Pem, and works on transverse and longitudinal dispersion of non-Newtonian fluids in packed beds are also considered.

Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression

Abstract: The network structure and the metabolic fluxes in central carbon metabolism were characterized in aerobically grown cells of Saccharomyces cerevisiae. The cells were grown under both high and low glucose concentrations, i.e., either in a chemostat at steady state with a specific growth rate of 0.1 h−1 or in a batch culture with a specific growth rate of 0.37 h−1. Experiments were carried out using [1-13C]glucose as the limiting substrate, and the resulting summed fractional labelings of intracellular metabolites were measured by gas chromatography coupled to mass spectrometry. The data were used as inputs to a flux estimation routine that involved appropriate mathematical modelling of the central carbon metabolism of S. cerevisiae. The results showed that the analysis is very robust, and it was possible to quantify the fluxes in the central carbon metabolism under both growth conditions. In the batch culture, 16.2 of every 100 molecules of glucose consumed by the cells entered the pentose-phosphate pathway, whereas the same relative flux was 44.2 per 100 molecules in the chemostat. The tricarboxylic acid cycle does not operate as a cycle in batch-growing cells, in contrast to the chemostat condition. Quantitative evidence was also found for threonine aldolase and malic enzyme activities, in accordance with published data. Disruption of the MIG1 gene did not cause changes in the metabolic network structure or in the flux pattern.

Dehydrogenases for the synthesis of chiral compounds

Abstract: Redox reactions are important steps in the metabolism and energy conversion of living cells. Besides the enzymes necessary, a number of coenzymes are involved in such reactions: ferrodoxins, lipoic acid, NAD(H), NADP(H), flavins and cytochromes. The coenzymes differ in their redox potential, in the binding constants and the mode of regeneration [1]. NADH/NADPH are the most frequently encountered coenzymes. In general they dissociate easily and need a second reaction with another metabolite for regeneration. These properties are one of the means by which nature directs the flow of intermediates in response to biosynthetic needs. Because of the spectral properties of the coenzyme moiety, dehydrogenases have been extensively studied in the past [2] and have found widespread applications in clinical and food analysis [3].