Mating-induced mating-type cassette conversion in Saccharomyces cerevisiae

We have previously reported that the HMRa-bearing restriction fragment of a rho degrees sir4-11 strain (HMLalpha-MATalpha-HMRa), which acts as an alpha-mater because of being rho degrees , changes its electrophoretic mobility when the strain mates with a certain group of a-mating strains (HMLalpha-MATa-HMRa). In this study, we found that the sir4-11 strain being rho degrees was not essential for this phenomenon and also that the altered form of the fragment contained HMRalpha in place of HMRa. Furthermore, we observed conversion of HMLa to HMLalpha in the cross in which a sir4-11 HMLa-MATalpha-HMRalpha strain was mated with a representative of the above-mentioned a-mating strain. In addition, when this a-mating strain was mated with a SIR(+) HMLalpha-MATa-HMRalpha strain, the resultant diploid was found to be HMLalpha/HMLalpha MATa/MATalphaHMRa/HMRalpha, indicating that conversion of MATa to MATalpha had taken place in the course of mating. From all these observations, we conclude that there is a group of S. cerevisiae strains that carries factor(s) that induces conversion of a mating-type cassette of the mating partner to alpha mating-type cassette and that this mating type cassette conversion takes place in all three mating type loci, HML, MAT and HMR, if the loci are in the non-silenced condition.     

Prognostic predictor with multiple fuzzy neural models using expression profiles from DNA microarray for metastases of breast cancer

Gene expression profiling data from DNA microarray were analyzed using the fuzzy neural network (FNN) modeling method for predicting the distant metastases of breast cancer. The best model consisting of five genes was able to predict metastases of breast cancer with 94% accuracy. Furthermore, 100% accuracy was achieved by majoritarian decision using only 25 genes from five noninferior models which were constructed independently. From the constructed model, gene expression rules, which may cause distant metastases, were explicitly extracted and 60% of the metastases cases could be explained by this rule. The FNN modeling method described in this paper enables precise extraction of significant biological markers affecting prognosis without prior knowledge.     

Cloning and heterologous expression of a beta-fructofuranosidase gene from Arthrobacter globiformis IFO 3062, and site-directed mutagenesis of the essential aspartic acid and glutamic acid of the active site

We have cloned the gene encoding a beta-fructofuranosidase from Arthrobacter globiformis IFO 3062, and subsequently, the gene was heterologously expressed in Escherichia coli. This beta-fructofuranosidase gene encodes a protein of 548 amino acid residues with a calculated molecular mass of 60,519 Da. We have examined the roles of three residues of A. globiformis IFO 3062 beta-fructofuranosidase by site-directed mutagenesis, and found that aspartic acid 130 and glutamic acid 392, which are two of the apparent catalytic residues, are essential for hydrolase activity. This study provides the first experimental evidence showing that these two amino acid residues of beta-fructofuranosidase play a critical role in hydrolyzing sucrose.     

Effect of a hepatocyte growth factor/heparin-immobilized collagen system on albumin synthesis and spheroid formation by hepatocytes

A hepatocyte growth factor (HGF)/heparin-immobilized collagen system was used as a synthetic extracellular matrix for hepatocyte culture. The albumin synthesis, nucleus numbers and morphology of the hepatocytes were determined separately to evaluate the hepatocyte number and hepatocyte-specific function under this system. The benefits of the HGF/heparin-immobilized collagen system for hepatocyte culture were confirmed by three types of culture methods in vitro, namely 2D film cultures, 2D gel cultures and 3D gel cultures. In 2D collagen film cultures, hepatocytes exhibited the highest albumin synthesis (1.42 μg/well/day) in HGF/heparin-immobilized collagen films at 7 days of culture. Heparin inhibited hepatocyte adhesion while HGF promoted hepatocyte migration, and spheroid formation was easily detected in HGF/heparin-immobilized collagen films. In 2D collagen gel cultures, albumin synthesis of around 15 μg/well/day was detected and maintained for more than 18 days on HGF/heparin-immobilized collagen gels. Similar findings were obtained in 3D HGF/heparin-immobilized collagen gel cultures, which exhibited albumin synthesis of up to 30 μg/well/day. The albumin synthesis by hepatocytes was two-fold higher in 3D gel cultures compared with 2D gel cultures, and was maintained for over 2 weeks compared with 2D film cultures using the HGF/heparin-immobilized collagen system. Taken together, the HGF/heparin-immobilized collagen system was effective for albumin synthesis by hepatocytes in both 2D film cultures and 3D gel cultures, and therefore shows good potential for tissue engineering use.     

Detection of Verotoxigenic Escherichia coli O157 and O26 in food by plating methods and LAMP method: a collaborative study

In order to establish a rapid and sensitive method for the detection of Verotoxigenic Escherichia coli O157 and O26, a collaborative study was conducted focusing on a comparison of the efficiency of loop-mediated amplification (LAMP) assay targeting the Verocytotoxin (also called Shiga toxin) gene, utilizing a direct plating method and a plating method with immunomagnetic separation (IMS-plating method) using various agar media. In combination with enrichment with the modified EC supplemented with novobiocin, E. coli O157 was detected in most samples of ground beef and alfalfa sprouts by LAMP assay, the direct plating method and the IMS-plating method. E. coli O26 was detected in approximately 100% of the food samples by LAMP assay. However, the IMS-plating and direct plating methods recovered 80 and 50% in ground beef samples, respectively. As a result, it was demonstrated the LAMP assay is superior to the IMS-plating method. Based on these results, it appears LAMP assay is effective as a screening assay to detect E. coli O157 and O26 from positive samples.     

Dimethylamine-modified waste paper for the recovery of precious metals

Waste newsprint paper was modified with dimethylamine (DMA) to obtain a tertiary amine type adsorption gel called DMA-paper gel. This new derivative was investigated for adsorption, from hydrochloric acid medium, of gold, palladium, and platinum as well as some base metals. The gel exhibited selectivity only for precious metals with a remarkably high capacity for Au(III), i.e., 4.6 mol/kg dry gel and comparable capacities, i.e., 2.1 and 0.9 mol/kg for Pd(II) and Pt(IV), respectively. Also, Au(III) was reduced to the elemental form during adsorption. Furthermore, column adsorption and subsequent elution of the adsorbed metal ions by acidic thiourea revealed encouraging recoveries (approximately 90%), thus enhancing the scope of the gel for effective preconcentration, separation, and recovery of precious metals. The effectiveness of recovery of precious metals from real industrial liquor was also tested, and it showed highly encouraging results with respect to the stability of the gel in the harsh medium, and selectivity for the targeted metal ions in the presence of excess of other metal ions.     

Occurrence and sources of perfluorinated surfactants in rivers in Japan

We analyzed perfluorinated surfactants (PFSs) in 20 river samples and 5 wastewater secondary effluent samples in Japan to reveal their occurrence and sources. Nine PFS species were determined: perfluorooctanesulfonate (PFOS), perfluorooctane sulfonamide (FOSA), perfluoroheptanoate (PFHpA), perfluorooctanoate (PFOA), perfluorononanoate (PFNA), perfluorodecanoate (PFDA), perfluoroundecanoate (PFUA), perfluorododecanoate (PFDDA), and perfluorotridecanoate (PFTDA). PFSs were detected in all rivers, revealing nationwide contamination of rivers. In particular, 11 out of 20 river samples exceeded New Jersey guidance for PFOA in drinking water (40 ng/L). PFOS, PFHpA, PFOA, and PFNA were major species in Japan. Concentrations of PFOS, PFHpA, and PFNA in rivers were strongly correlated with population density, suggesting that the chemicals were derived from urban activities. PFOA showed a significant but weak correlation. We used crotamiton, a marker of sewage effluent, for further source analysis. Concentrations of PFOS, PFHpA, and PFNAwere strongly correlated with those of crotamiton, and plots of secondary effluents fell near the regression lines of rivers, indicating that the PFOS, PFHpA, and PFNA in rivers were derived from sewage effluent. On the other hand, PFOA was found at remarkably high levels (54-192 ng/L) in seven river samples containing low levels of crotamiton, suggesting that it was derived from nonsewage point sources, as well as sewage effluent. The total fluxes of sewage-derived PFOS, PFHpA, PFOA, and PFNA from Japan were estimated to be 3.6, 2.6, 5.6, and 2.6 t/year, respectively. This is the first report to identify PFOA in several rivers, derived from nonsewage point sources, by using a marker of sewage effluent.     

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.     

Oxygen Self-Diffusion in Single-Crystal Y2O3

Self-diffusion coefficients of the oxygen ion in single-crystal Y₂O₃ were determined by the gas-solid isotope exchange technique. The results in the range 1100° to 1500°C are described by D=7.3 X 10^-6 exp [-19l(kJ/mol)/RT] cm²/s. Comparison of the results with those for oxides with the fluorite-type structure indicates that the regularly arranged vacant anion sites in the C-type structure do not contribute eflectively to oxygen ion diffusion .     

Carbonization properties of carbonaceous substances oxidized by air blowing—I: Carbonization behaviors and chemical structure of residual oils oxidized by air blowing

The carbonization process of oxidized oils was investigated by the successive observation of the cokes at several intermediate stages with particular attention to the cocarbonization compatibility of the components, in order to understand how the medium mosaic texture was developed from the oxidized oils. When the oxidized oil was carbonized, very small anisotropic spheres appeared in the matrix, but, being fixed into the mosaic texture, they formed clusters with limited growth of their diameters. The n-hexane insoluble (nHI) and the n-hexane soluble (nHS) components in the, oxidized oil produced isotropic and flow textures in the cokes, respectively. These components did not allow the smooth growth of the anisotropic spheres because of their poor compatibility. Cocarbonization with some proper additives was found effective both in developing a flow texture from the nHI of the oxidized oil and producing a high coke yield. Chemical analyses of the components were performed in order to explain the compatibility.