Biomedical subjects

Kazuyoshi Yano

Publications and source records attributed to Kazuyoshi Yano.

17 recordsLinked to original sources

PubMed2006

Improving the efficiency of evolutionary de novo peptide design: strategies for probing configuration and parameter settings.

Evolutionary molecular design based on genetic algorithms (GAs) has been demonstrated to be a flexible and efficient optimization approach with potential for locating global optima. Its efficacy and efficiency are largely dependent on the operations and control parameters of the GAs. Accordingly, we have explored new operations and probed good parameter setting through simulations. The findings have been evaluated in a helical peptide design according to "Parameter setting by analogy" strategy; highly helical peptides have been successfully obtained with a population of only 16 peptides and 5 iterative cycles. The results indicate that new operations such as multi-step crossover-mutation are able to improve the explorative efficiency and to reduce the sensitivity to crossover and mutation rates (CR-MR). The efficiency of the peptide design has been furthermore improved by setting the GAs at the good CR-MR setting determined through simulation. These results suggest that probing the operations and parameter settings through simulation in combination with "Parameter setting by analogy" strategy provides an effective framework for improving the efficiency of the approach. Consequently, we conclude that this framework will be useful for contributing to practical peptide design, and gaining a better understanding of evolutionary molecular design.

Algorithms↗

PubMed2006

[Isolation of thermostable direct hemolysin producing Vibrio parahaemolyticus from food using screening by PCR in food-borne outbreaks].

The producibility of thermostable direct hemolysin (TDH) is the most important pathogenic factor in Vibrio parahaemolyticus. TDH (+) V. parahaemolyticus is usually isolated from patients having V. parahaemolyticus food-borne disease. TDH (+) V. parahaemolyticus is, however, very difficult to isolate from food and environmental samples. In the 5 years from 2000 to 2004 in Tokyo, V. parahaemolyticus was isolated from food samples related to 67 of 227 V parahaemolyticus food-borne outbreaks. In these outbreaks, TDH (+) strains were also tried to isolate using PCR as the screening methods. TDH (+) V. parahaemolyticus strains were able to isolate from enrichment broth in which toxR and tdh genes become positive in PCR. TDH (+) strains of the same serotype with patients were able to be isolated from 23 food samples related to 11 outbreaks (16.4%); 3 outbreaks in 2000, 2 in 2001, 2 in 2002, 1 in 2003, and 3 in 2004. The serotypes of V. parahaemolyticus isolated from food were O3 : K6 (10 samples), O3 : K5 (6 samples), O1 : K25 (4 samples), O3 : K29 (2 samples), O4 : K 8 (1 sample), and O4 : K11 (1 sample). The isolation rate of the TDH (+) strain from enrichment broth differed with samples. In several samples TDH (+) strains were isolated easily only by examining 3 colonies, hence no TDH (+) strains were isolated in spite of the examination of 250 colonies. No correlation was seen between the number of V. parahaemolyticus and the isolation rate of TDH (+) strains in food samples. Screening using PCR is very effective method for isolating TDH (+) V. parahaemolyticus from food samples.

Disease Outbreaks↗

PubMed2006

Model comparison for Escherichia coli growth in pouched food.

We recently studied the growth characteristics of Escherichia coli cells in pouched mashed potatoes (Fujikawa et al., J. Food Hyg. Soc. Japan, 47, 95-98 (2006)). Using those experimental data, in the present study, we compared a logistic model newly developed by us with the modified Gompertz and the Baranyi models, which are used as growth models worldwide. Bacterial growth curves at constant temperatures in the range of 12 to 34 degrees C were successfully described with the new logistic model, as well as with the other models. The Baranyi gave the least error in cell number and our model gave the least error in the rate constant and the lag period. For dynamic temperature, our model successfully predicted the bacterial growth, whereas the Baranyi model considerably overestimated it. Also, there was a discrepancy between the growth curves described with the differential equations of the Baranyi model and those obtained with DMfit, a software program for Baranyi model fitting. These results indicate that the new logistic model can be used to predict bacterial growth in pouched food.

Escherichia coli↗

PubMed2006

Novel method for estimating viable Salmonella cell counts using real-time PCR.

A novel method for estimating viable Salmonella Enteritidis cell counts with 5'-nuclease real-time PCR was developed in this study. Our method was based on the increase kinetics of the target DNA region (invA) of the microorganism growing in a food/clinical sample in a culture medium during incubation. The index of increase in the target DNA region studied here was threshold cycle, CT. A test Salmonella strain was grown in buffered peptone water at the optimal temperature (39 degrees C). As Salmonella cells were grown, the value of CT decreased with time, generating a downward sigmoidal curve. The slope of the curve was constant at various initial cell concentrations. With higher initial cell concentration, the CT value evaluated from the slope at a given time was lower. With this relationship, a novel method for estimating the initial viable cell concentration of a sample was developed. Dead Salmonella cells or bacteria other than the target cell caused deviation in the CT curve. Incubation in a selective media suppressed the deviation caused by other bacterial cells. We think that this method could be applied to many other microorganisms cultivable in a suitable medium.

Colony Count, Microbial↗

PubMed2006

[Development of a predictive program for microbial growth under various temperature conditions].

A predictive program for microbial growth under various temperature conditions was developed with a mathematical model. The model was a new logistic model recently developed by us. The program predicts Escherichia coli growth in broth, Staphylococcus aureus growth and its enterotoxin production in milk, and Vibrio parahaemolyticus growth in broth at various temperature patterns. The program, which was built with Microsoft Excel (Visual Basic Application), is user-friendly; users can easily input the temperature history of a test food and obtain the prediction instantly on the computer screen. The predicted growth and toxin production can be important indices to determine whether a food is microbiologically safe or not. This program should be a useful tool to confirm the microbial safety of commercial foods.

Animals↗

PubMed2006

Characteristics and modeling of Escherichia coli growth in pouched food.

Characteristics of the growth kinetics of Escherichia coli cells in pouched mashed potatoes under various conditions were studied with a mathematical model. Bacterial cells were inoculated in sterile mashed potatoes and then sealed in vinyl pouches, in which a very small amount of air was included. The growth curves of cells in the pouched mashed potatoes at constant temperature (12-34 degrees C) were sigmoidal with time on a semi-logarithmic plot and were successfully described with a new logistic model recently developed by us. The rate constant of growth showed a highly linear relationship to the temperature with the square-root model, and the lag period was longer at lower temperatures. The growth curve in glass tubes containing a large volume of air was similar to that in pouches, showing that the rate of growth was not affected by the volume of the surrounding air. The growth curves in pouched mashed potatoes were very similar to those in nutrient broth or on the surface of nutrient agar, which we previously reported. These results suggested that the growth kinetics of the bacterial cells under various conditions of rich nutrition might be almost identical, and can be described with a simple growth model like ours.

Escherichia coli↗

PubMed2006

[Development of effective detection method for Coxiella burnetii in mayonnaise by real-time PCR and investigation of C. burnetii contamination in commercial mayonnaise in Tokyo].

A PCR method for the effective detection of Coxiella burnetii in commercially available mayonnaise was developed. Sample preparations were isolated from 50 g portions of each mayonnaise product by four successive extraction steps in phosphate buffer with 2.0 M NaCl. These extracts were then centrifuged at 20,000 x g for 60 min. DNA was isolated from the solution containing the precipitate with a commercial kit, and amplified quantitatively using real-time PCR that targeted the com1 region of C. burnetii. The recoveries of C. burnetii from 2 kinds of commercial mayonnaise specimens, with a baseline control of 1 x 10(7) particles of the Nine Mile phase II strain, were 85.0 +/- 6.0% and 72.0 +/- 0.4%, respectively. The determination limit of this method was 500 C. burnetii particles per 50 g of mayonnaise. The DNA specimens isolated from 50 different commercial mayonnaise samples sold in Tokyo using this method were amplified using both nested PCR and real-time PCR. No contamination by C. burnetii was detected in any of the mayonnaise samples.

Coxiella burnetii↗

PubMed2005

SNPs (single nucleotide polymorphisms) detection based on the formation of cholic-acid binding DNA aptamer.

Simple and rapid methods for the detection of single nucleotide polymorphisms (SNPs) are required to analyze the genetic information. We have previously isolated DNA aptamers that bind to cholic acid by an in vitro selection method. A common feature of the sequences of the aptamers was that they included a secondary structure, a three-way junction, in which three stems were connected at the junction. It was also revealed that three-way junctions with fully matched three stems bind cholic acid whereas single-base substitutions at the junction lose binding affinity completely. Here we report a new method for the detection of single nucleotide mutations that is based on the formation of fully matched three-way junctions which bind to cholic acid.

Aptamers, Nucleotide↗

PubMed2005

[Investigation of Coxiella burnetii contamination in commercial milk and PCR method for the detection of C. burnetii in egg].

A total of 244 milk samples collected from supermarkets in Tokyo were examined for contamination with Coxiella burnetii. C. burnetii DNA was detected in 131 (53.7%) of the samples by nested PCR. PCR-positive samples were injected into immunosuppressed A/J strain mice. Of the 22 PCR-positive milk samples tested, none resulted in isolation of C. burnetii from the mice. Heat-treatment was sufficient to inactivate C. burnetii in commercial milk. In addition, a PCR detection method for C. burnetii in chicken egg was developed. Egg yolk was added to an equal volume of 1 mol/L of NaCl phosphate buffer and homogenized for removal of protein and lipid. After centrifugal separation, the supernatant was removed, and template DNA in the precipitate was extracted using SDS, proteinase K and NaI. Using such prepared samples, 3.2 x 10(1) C. burnetii particles in 1 g of egg yolk could be detected by nested PCR. All of 200 chicken egg samples collected from supermarkets in Tokyo were negative for C. burnetii by the nested PCR method.

Animals↗

PubMed2004

Single nucleotide polymorphism typing on DNA array with hydrophobic surface fabricated by plasma-polymerization technique.

A DNA array has been fabricated on glass substrates, which enables high-throughput analysis of single-base mismatches. In this work, microfabrication-compatible plasma-polymerization (PP) method was used for immobilizing probe DNAs to study the hybridization behavior by changing surface properties. The immobilization matrix consisting of 35 A of PP layer, applied additionally on the streptavidin absorbed hexamethyldisiloxane (HMDS)-PP layer, was constructed on the substrates to anchor biotinylated DNA probes onto the surface. The hydrophobic immobilization matrix was considered to enhance hybridization accuracy and efficiency, compared with its hydrophilic acetonitrile-PP layers. The oligonucleotide arrays fabricated on HMDS-PP surface were shown to be effective in detection of single nucleotide polymorphisms (SNPs) of ApoE gene.

Apolipoproteins E↗

PubMed2003

Exploration of structural features of monomeric helical peptides designed with a genetic algorithm.

A genetic algorithm (GA)-based strategy to dissect the determinants of peptide folding into alpha-helix was developed. The structural information of helical peptides was obtained with respect to patterns of sequence variability. In many previously reported studies the intrinsic alpha-helical propensities of amino acids although sequence-dependent are apparently independent of the amino acid position. In this research, monomeric helical peptides selected from possible sequences produced by a GA-chemical synthesis were analyzed to identify possible influential structural features. These hexadeca-peptides were obtained after four successive generations. A total of 128 synthetic peptides were evaluated via circular dichroism (CD) measurements in aqueous solution, while the mean ellipticity at 222 nm confirmed the monomeric state of the peptides. The results presented here show that our GA-based strategy may be useful in the design of proteins with increased alpha-helix content.

Algorithms↗

PubMed2003

Electrochemical protein chip with arrayed immunosensors with antibodies immobilized in a plasma-polymerized film.

An electrochemical protein chip was microfabricated. A thin-film three-electrode system, including an array of 36 platinum working electrodes, a set of thin-film Ag/AgCl electrodes, and platinum auxiliary electrodes, was integrated on a glass substrate. Capture antibodies were immobilized in a 4.5-nm-thick double layer of a hexamethyldisiloxane plasma-polymerized film. Because of their highly cross-linked network structure, the capture antibodies could be firmly immobilized. No nonspecific adsorption was observed during a series of procedures to detect target proteins, and electrochemical cross talk between neighboring sites was negligible. The sandwich immunoassay was conducted on a single chip using model proteins, alpha-1-fetoprotein and beta2-microglobulin. A distinct current increase following the oxidation of hydrogen peroxide produced by the enzymatic reaction of glucose oxidase was observed, which indicates that the capture proteins could actually bind the target proteins. Two kinds of protein were detected independently on multiple sites with respective capture antibodies.

Antibodies↗

PubMed2003

Preparation of a whole genome phage library using fragmented Escherichia coli genome and its characterization of protein binding properties by surface plasmon resonance.

A novel phage library has been prepared using the Escherichia coli genome digested with three restriction enzymes. The resulting DNA fragments were ligated to the expression vector pCANTAB5 to obtain the library of recombinant M13 phages displaying relatively long exogenous peptides. The library was screened to isolate recombinant phages with high affinity to alkaline phosphatase (AP) from calf intestine. After four rounds of panning three phages (AP1, AP2 and AP3) were shown to have specific binding properties toward AP by enzyme-linked immunosorbent assay. The phages were further characterized by surface plasmon resonance (SPR). Among the three phages AP3 bound the AP-immobilized sensor chip most and caused the highest resonant angle shift. The sensor response decreased with the decrease of the concentration of AP3 added. Furthermore, displacement of AP3 from the AP-immobilized sensor chip was observed upon injection of AP solution to the SPR system, whereas injection of bovine serum albumin solution led to the great increase of the sensor response. This result indicates the specific binding of AP3 to AP.

Alkaline Phosphatase↗

PubMed2003

Application of plasma-polymerized films for isoelectric focusing of proteins in a capillary electrophoresis chip.

The first use of plasma polymerization technique to modify the surface of a glass chip for capillary isoelectric focusing (cIEF) of different proteins is reported. The electrophoresis separation channel was machined in Tempax glass chips with length 70 mm, 300 microm width and 100 microm depth. Acetonitrile and hexamethyldisiloxane monomers were used for plasma polymerization. In each case 100 nm plasma polymer films were coated onto the chip surface to reduce protein wall adsorption and minimize the electroosmotic flow. Applied voltages of 1000 V, 2000 V and 3000 V were used to separate mixtures of cytochrome c (pI 9.6), hemoglobin (pI 7.0) and phycocyanin (pI 4.65). Reproducible isoelectric focusing of each pI marker protein was observed in different coated capillaries at increasing concentration 2.22-5 microg microL(-1). Modification of the glass capillary with hydrophobic HMDS plasma polymerized films enabled rapid cIEF within 3 min. The separation efficiency of cytochrome c and phycocyanin in both acrylamide and HMDS coated capillaries corresponded to a plate number of 19600 which compares favourably with capillary electrophoresis of neurotransmitters with amperometric detection.

Animals↗

PubMed2003

[Increasing drug resistance in Vibrio cholerae O1 and non-O1 strains isolated from diarrheal cases in Japan].

Drug resistance trends were investigated for 271 Vibrio cholerae O1 (V.c O1) and 401 V. cholerae non-O1 (V.c non-O1) strains isolated from mainly imported diarrheal cases during 1981-2001 in Japan. The results of drug resistance test using 8 drugs (CP, TC, SM, KM, ABPC, ST, NA, and NFLX) showed that 34.7% of the V. c O1 strains and 15.7% of V.c non-O1 strains were multi-drug or mono-drug resistant. The incidence of drug resistant strains has increased since 1991, and it has been remarkable in V.c O1 strains that increased from 1.2% in 1981-1985 to 70.8% in 1996-2001. The drug resistance patterns of the resistant strains classified into 6 types in V.c O1 and 21 types in V.c non-O1. The prevalent patterns recognized were SM (75.5%), CP.TC.SM.ST (10.6%) and CP.SM.ST (8.5%) in V.c O1, and SM (25.4%) and ABPC (25.4%) in V.c non-O1. Ten V.c O1 strains (3.7%) and 10 V.c non-O1 strains (2.5%) were multi-drug resistant including TC. Among those, 13 strains were isolated from travelers who returned to Japan from Thailand. One V.c O1 strain (0.4%) and 6 V.c non-O1 strains (1.5%) were NA high-resistant and fluoroquinolones low-sensitive. Among those, 4 strains were isolated from travelers who returned to Japan from India.

Diarrhea↗

PubMed2002

A flow method with photocatalytic oxidation of dissolved organic matter using a solid-phase (TiO2) reactor followed by amperometric detection of consumed oxygen.

A photocatalytic sensor for the determination of chemical oxygen demand (COD) using titanium dioxide, based on the use of a pair of oxygen electrodes and flow injection analysis, is described. The measuring principle is based on the direct determination of the oxygen concentration change resulting from photocataltic oxidation of organic compounds. One of the two oxygen electrodes, the reference oxygen electrode, was utilized to measure the reference signal responding only to oxygen present in the injected samples. Oxygen consumption due to the TiO2-catalyzed photochemical oxidation of organic compounds in samples was monitored with the working oxygen electrode. The COD value of this sensor was calculated as the difference of the currents at reference and working oxygen electrodes, respectively. The operation characteristics of the sensor are demonstrated using artificially treated wastewater as a substrate. The sensor was also applied to the determination of COD in real water samples from dam reservoirs (n = 20) all over Japan. The results were in good agreement with those from the conventional COD methods (i.e., permanganate and dichromate methods).

Electrochemistry↗

PubMed1998

Cyanide hydrolysis in a cyanide-degrading bacterium, Pseudomonas stutzeri AK61, by cyanidase.

The cyanide-degrading bacterial strain AK61 was isolated from waste water at a metal-plating plant. The isolated strain was characterized by Gram-staining, quinone analysis, fatty acid profile and the API 20NE identification system, and identified as Pseudomonas stutzeri. Whole cells were able to degrade cyanide rapidly in a 1 mM solution containing no organic substances, and produced ammonia as a product. The induction of the cyanide-degrading activity of P. stutzeri AK61 did not depend on the presence of cyanide in the culture medium during growth. The cyanide-degrading enzyme was purified approximately 49-fold from a cell extract of P. stutzeri AK61. The enzyme had a K(m) of 1.7 mM for cyanide and a specific activity of 54.6 mumol ammonia produced min-1. The activity of the enzyme was optimal at 30 degrees C and pH 7.5. The results of SDS-PAGE, gel-filtration chromatography and NH2-terminal amino acid sequence analysis of the enzyme indicated that the functional enzyme was an aggregated protein consisting of a 38 kDa polypeptide. Like cyanidase (cyanide dihydratase), it was shown that the enzyme catalysed the hydrolysis of cyanide to ammonia and formate.

Amino Acid Sequence↗