Calibration Curve for Quantitative Analysis of the Monoclinic-Tetragonal ZrO2 System by X-Ray Diffraction

A nonlinear calibration curve for volume fraction vs integrated intensity ratio was obtained for the monoclinic-tetragonal ZrO² system by using X-ray powder pattern-fitting and pattern-decomposition techniques. The empirical equation agrees well with the theoretical one. By using this equation, the deviation from linearity (6.8% maximum) resulting from the intensity difference of corresponding reflections of the two phases can be estimated quite accurately.     

Family M42 aminopeptidase from the syntrophic bacterium Symbiobacterium thermophilum: characterization using recombinant protein

The chromosomal DNA of the syntrophic thermophile Symbiobacterium thermophilum contains open reading frames of the genes encoding family M42 aminopeptidases, Pep1079, Pep1080, and Pep1081. To characterize these peptidases, the genes were cloned into Escherichia coli and overexpressed. Our experiments using the recombinant proteins confirmed that Pep1079, Pep1080, and Pep1081 are components of arginyl or lysinyl aminopeptidases that require Co2+ for enzymatic activity. Coexistence of Pep1079 and Pep1080 is necessary for expressing high peptidase activity. Pep1081 enhances the activity of Pep1079 and Pep1080.     

Influence of different feeding systems on the growth performance and muscle development of Japanese Black steers

This study investigated the growth performance and gene expression for muscle development between grass hay-fed (GH) and concentrate-fed (CT) steers. Daily gain and energy intake during the fattening period of the GH group were lower than those of the CT group. Analysis of C/EBPα, PPARγ2, myosin heavy chain (MHC), and myostatin gene expressions was performed by real-time PCR. Expressions of C/EBPα and myostatin in semitendinosus and longissimus lumborum (LL) muscles were higher in the CT group than in the GH group at the end of fattening. In LL muscle, MHC expression at the end of fattening was greater in the GH group than in the CT group. These results suggest that regulation of adipogenesis and myogenesis by the expression of genes involved in muscle development might have occurred in the skeletal muscle of the GH group by the feeding of grass hay and/or because of the low energy intakes.     

Cloning and characterization of a β-N-acetylglucosaminidase (BmFDL) from silkworm Bombyx mori

In insects, β-N-acetylglucosaminidase (GlcNAcase) participates in critical physiological processes such as fertilization, metamorphosis, and glycoconjugate degradation. Insects produce glycoproteins carrying paucimannosidic-type N-glycans, the terminal GlcNAc residue of which is cleaved by a GlcNAc-linkage specific GlcNAcase, also known as the fused lobes (FDL) protein. To obtain information on the structure of GlcNAcases and insight into their contribution to physiological processes, we cloned Bombyx mori FDL (BmFDL) from silkworm larvae. The full-length cDNA (1.9 kb) encoded a protein of 633 amino acids with 42% amino acid sequence identity to Drosophila melanogaster FDL (DmFDL). Recombinant BmFDL cleaved only β-1,2-linked GlcNAc residues from the α-1,3 branch of biantennary N-glycan. This substrate specificity was similar to that of DmFDL. Microsomal FDL activity was inhibited by anti-BmFDL antibodies. Taken together, our results suggest that BmFDL is a N-glycan-processing GlcNAcase in B. mori.     

Cloning and characterization of a 4-nitrophenol hydroxylase gene cluster from Rhodococcus sp. PN1

A 4-nitrophenol (4-NP)-degrading bacterium was isolated from activated sludge and identified as a Rhodococcus sp. This bacterium, designated as strain PN1, could utilize 4-NP as a sole carbon, nitrogen and energy source. Degradation tests of 4-NP using cell suspensions of strain PN1 revealed that the degradation was induced by 4-NP and that 4-nitrocatechol (4-NC) was one of the metabolites. A gene library was constructed from the total DNA of strain PN1 and introduced into Rhodococcus rhodochrous ATCC 12674. Two recombinant strains showed 4-NP hydroxylase activity, and a 9.1-kb DNA fragment encoding the activity was isolated from one of the strains. In addition, a 2.4-kb smaller fragment expressing the activity was subcloned from the 9.1-kb fragment and sequenced. The sequence analysis showed that the fragment encodes a two-component 4-NP hydroxylase, the predicted amino acid sequence of which exhibits significant similarity to those of phenol hydroxylases and 4-hydroxyphenylacetate 3-hydroxylases belonging to the two-component flavin diffusible monooxygenase (TC-FDM) family proposed by Galán et al. (J. Bacteriol., 182, 627-636, 2000).     

Preparation of samples for proficiency testing of pesticide residue analysis in processed foods

To conduct proficiency testing for the analysis of pesticide residues in processed foods, fortified samples of retort curry and pancake were examined. In the case of retort curry, heating and mixing were necessary at the time of preparation to provide a homogenous analytical sample. A mixture of 4 carbamates and 11 organophosphorus pesticides was spiked and 14 of them showed consistent results in the samples. In the case of pancake, 10 kinds of pesticides were added to the pastry. The prepared pastry was them cooked. The relative concentrations of most of the pesticides in the pancake were not affected and all the pesticides showed consistent results in the samples. These results showed that the two tested samples were suitable for proficiency testing.     

A motif detection and classification method for peptide sequences using genetic programming

An exploration of common rules (property motifs) in amino acid sequences has been required for the design of novel sequences and elucidation of the interactions between molecules controlled by the structural or physical environment. In the present study, we developed a new method to search property motifs that are common in peptide sequence data. Our method comprises the following two characteristics: (i) the automatic determination of the position and length of common property motifs by calculating the physicochemical similarity of amino acids, and (ii) the quick and effective exploration of motif candidates that discriminates the positives and negatives by the introduction of genetic programming (GP). Our method was evaluated by two types of model data sets. First, the intentionally buried property motifs were searched in the artificially derived peptide data containing intentionally buried property motifs. As a result, the expected property motifs were correctly extracted by our algorithm. Second, the peptide data that interact with MHC class II molecules were analyzed as one of the models of biologically active peptides with buried motifs in various lengths. Twofold MHC class II binding peptides were identified with the rule using our method, compared to the existing scoring matrix method. In conclusion, our GP based motif searching approach enabled to obtain knowledge of functional aspects of the peptides without any prior knowledge.     

Laboratory and field measurements of dry deposition of sulfur dioxide onto Chinese loess surfaces

Laboratory and field measurements were conducted to examine dry deposition of SO2 onto Chinese loess surfaces using native soil sampled in the loess plateau, China. The field tests were employed in Beijing and Lanzhou, China, by directly measuring the dry deposition of SO2 on soil, which uses soil put on a collector as an SO2 passive sampling medium. In the laboratory, a high rate of uptake to SO2 deposition for Chinese soil surfaces due to the highly alkalinity was found. The uptake of SO2 deposition was dependent on the pH soil and relative humidity. Furthermore, we evaluated some factors that affect the measurement precision: response of SO2 uptake, repeatability, recovery factor, and variability associated with the weight and the surface coverage on the collectors. As a result, it was shown that the measurement precision was primarily related to the ratio of the SO2 deposition amount relative to the sulfur content of the original soil. This result was consistent with the field observations. The laboratory and field results indicated an excellent agreement on the SO2 uptake inherent in the results from the soil surfaces in different regions.     

Factors affecting the oxidative activity of laccase towards biphenyl derivatives in homogeneous aqueous-organic systems

Catalytic oxidation of biphenyl derivatives was investigated using laccase in a homogeneous aqueous-organic system. A thermostable laccase from Trametes sp. showed the highest catalytic activity for the oxidation of 4-hydroxybiphenyl (4-HB) at a reaction temperature of 60 degrees C when dimethylsulfoxide (DMSO) was employed as a co-solvent. Furthermore, the catalytic performance was successfully enhanced by the incorporation of a laccase mediator system (LMS) into the aqueous-DMSO media. The catalytic performance strongly depended on the type of mediator, and the highest activity was observed with 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as mediator, suggesting the importance of the selection of a suitable mediator. It was verified that this mediator system is applicable to the oxidation of several biphenyl derivatives with hydroxyl groups.     

Effects of indigenous starter cultures on the microbial and physicochemical characteristics of Urutan, a Balinese fermented sausage

Urutan is a Balinese traditional dry fermented sausage prepared from lean pork and various kinds of spice. Urutan is different from the European sausages, because it is fermented under warm condition with fluctuating temperatures of approximately 25 degrees C at night to 50 degrees C during sun drying. In this study, two of the 71 strains of lactic acid bacteria (LAB) isolated from natural urutan fermentation were used as starter cultures: Lactobacillus plantarum U201, the dominant LAB, and Pediococcus acidilactici U318, a bacteriocin producer. A soft urutan with yellowish brown color was produced using these strains as multiple starters. The starter cultures grew in characteristic succession which reconstructed the natural fermentation process. Lactobacilli were dominant until 48 h fermentation and pediococci dominated at the later stage of fermentation. Proliferation of starter cultures produced lactic acid which resulted in the decrease in pH and coagulation of soluble protein in urutan. Both strains could eliminate the Enterobacteriaceae in urutan after 24 h fermentation, and could suppress and eliminate the occurrence of micrococci at 120 h fermentation. By using a single starter culture, no succession was observed to occur in urutan and the time of elimination of Enterobacteriaceae was delayed. Thus, the strains of L. plantarum U201 and P. acidilactici U318 have great potential for use as multiple starter cultures in urutan fermentation.