PubMed Health⌕ Search

Biomedical subjects

Yoshio Nakano

Publications and source records attributed to Yoshio Nakano.

At least 19 recordsLinked to original sources
PubMed2006

TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight.

UNLABELLED: TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50 000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser. AVAILABILITY: TRFMA is freely available at http://myamagu.dent.kyushu-u.ac.jp/bioinformatics/trfma/index.html and can be downloaded from the same site.

Algorithms↗
PubMed2006

Identification and molecular characterization of an N-Acetylmuraminidase, Aml, involved in Streptococcus mutans cell separation.

We previously demonstrated Streptococcus mutans produces two bacteriolytic enzymes of 100 kDa and 80 kDa (G. Yoshimura et al. Microbiol. Immunol. 48, 465-469, 2004). Here, we identified the protein sequence of these enzymes and found they come from a single gene product designated as automutanolysin (Aml). Aml has a modular design where the N-terminus contains five 13-amino-acid repeats and a C-terminal enzyme active domain. Aml selectively lyses S. mutans and S. sobrinus but no other oral streptococci. This suggests Aml possesses strong substrate specificity towards cariogenic bacteria present in the human oral cavity. Analysis of S. mutans peptidoglycan fragments released by Aml shows the enzyme is an N-acetylmuraminidase. We found Ca(2+) enhances the activity; and EGTA, EDTA and iodoacetic acid inhibit the activity. The optimum pH range for lytic activity was 6 to 7. Disruption of the aml gene in S. mutans results in the formation of a longer bacterial cell chain length that was dispersed by the addition of a low concentration of Aml. This suggests Aml is involved in S. mutans cell separation.

Amino Acid Sequence↗
PubMed2006

[A case report of autoimmune pancreatitis with Mikulicz' s disease and diabetes mellitus].

A 56-year-old man with bilateral swelling of lacrimal glands was admitted to our hospital. He was diagnosed as autoimmune pancreatitis with Mikulicz' s disease presenting the swelling of lacrimal glands, submandibular glands and the pancreas head and tail. Treatment with systemic prednisolone resulted in improvement of the swelling of these glands and pancreas. On the immunohistochemical examination, infiltration of CD4- and CD8-positive T lymphocytes was detected in the lacrimal gland, the submandibular gland, the gall bladder and the pancreas. Infiltration of IgG4-positive plasma cells was detected in the submandibular gland, the gall bladder and the pancreas. These results may suggest the presence of common etiology between autoimmune pancreatitis and Mikulicz' s disease.

Autoimmune Diseases↗
PubMed2005

Mechanisms of gold recovery from aqueous solutions using a novel tannin gel adsorbent synthesized from natural condensed tannin.

We report a novel recovery system for gold (Au), which is one of the precious metals contained in electronic scrap, utilizing tannin gel particles. Tannin gel particles were prepared by a process of cross-linking of condensed tannin (wattle tannin), which is a ubiquitous and inexpensive natural material having many hydroxyl groups. The adsorption mechanism of gold onto tannin gel particles was elucidated: the adsorption of gold takes place through the reduction of trivalent gold ions to metallic gold on the surface of tannin gel particles, which is accompanied by the simultaneous oxidization of the hydroxyl groups of tannin gel. Additionally, the adsorption capacity of gold was found to be extremely high, 8000 mg-Au/g-dry gel. The outstanding characteristics of tannin gel particles for gold offers the possibility of efficient recovery of other precious metals.

Adsorption↗
PubMed2005

High production of methyl mercaptan by L-methionine-alpha-deamino-gamma-mercaptomethane lyase from Treponema denticola.

Methyl mercaptan is derived from l-methionine by the action of l-methionine-alpha-deamino-gamma-mercaptomethane lyase (METase) and is a major component of oral malodor. This compound is highly toxic and is thought to play an important role in periodontal disease. We found that Treponema denticola, a member of the subgingival biofilm at periodontal disease sites, produced a large amount of methyl mercaptan even at low concentration of l-methionine. METase activity in a cell-free extract from T. denticola was detected by two-dimensional electrophoresis under non-denaturing conditions, and the protein spot that exhibited high METase activity was identified using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The identified gene produced a METase with a K(m) value for l-methionine (0.55mM) that is much lower than those of METases previously identified in the other organisms. This result suggests that T. denticola is an important producer of methyl mercaptan in the subgingival biofilm.

Bacterial Proteins↗
PubMed2005

Adsorption mechanism of palladium by redox within condensed-tannin gel.

Condensed-tannin gel particles with polyhydroxyphenyl groups were synthesized as the adsorbent for the new recovery system of palladium (Pd), which was simple and generated little secondary waste in comparison with the conventional recovery processes. The properties of condensed-tannin gel particles for the Pd adsorption were examined in PdCl2 aqueous solution and it was found that Pd(II) was adsorbed onto the tannin gel particles as a reduced metallic Pd through redox reaction mechanism: chloropalladium(II) species were reduced to Pd(0), while hydroxyl groups of condensed-tannin gel were oxidized during the adsorption. Additionally, it was observed that Pd(II) species containing fewer Cl, such as PdCl2(H2O)2 and PdCl(H2O)3+, were more favorable for the adsorption than PdCl3(H2O)- and PdCl4(2-). By utilizing such characteristics of tannin gel particles, it is expected that they can be applied to recover Pd efficiently and simply with low cost.

Adsorption↗
PubMed2005

Identification and characterization of an autolysin-encoding gene of Streptococcus mutans.

We identified a gene (atlA) encoding autolytic activity from Streptococcus mutans Xc. The AtlA protein predicted to be encoded by atlA is composed of 979 amino acids with a molecular weight of 107,279 and has a conserved beta-1,4-N-acetylmuramidase (lysozyme) domain in the C-terminal portion. Sodium dodecyl sulfate extracts of strain Xc showed two major bacteriolytic bands with molecular masses of 107 and 79 kDa, both of which were absent from a mutant with inactivated atlA. Western blot analysis revealed that the 79-kDa band was derived from the 107-kDa peptide by cleavage of its N-terminal portion. The inactivation of atlA resulted in a marked decrease in autolysis and the formation of very long chains of cells compared to the case for the parent strain. Although both the parent and mutant strains formed biofilms in the presence of sucrose, the biofilms formed by the mutant had a sponge-like architecture with large gaps and contained 30% less biomass than those formed by the parent strain. Furthermore, strain Xc formed glucose-dependent, loose biofilms in the absence of sucrose, but the mutant lost this ability. These results suggest that AtlA may play an important role in biofilm formation by S. mutans. The antibody produced against the C-terminal peptide containing the beta-1,4-N-acetylmuramidase domain drastically inhibited the autolytic activity of strain Xc. This inhibition was specific among the oral streptococci to S. mutans. These results indicate that the catalytic domain of AtlA is located at the C terminus, suggesting that further characterization of this domain may provide a means to control cariogenic dental plaque formation.

Base Sequence↗
PubMed2005

Discrimination of Streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization.

Two oligonucleotide primer sets for the discrimination of Streptococcus pneumoniae from "pneumococcus-like" oral streptococcal isolates by PCR were developed. Genomic subtractive hybridization was performed to search for differences between Streptococcus pneumoniae strain WU2 and the most closely related oral streptococcus, Streptococcus mitis strain 903. We identified 19 clones that contained S. pneumoniae-specific nucleotide fragments that were absent from the chromosomal DNA of typical laboratory strains of S. mitis and other oral bacteria. Subsequently, oligonucleotide PCR primers for the detection of S. pneumoniae were designed from the sequences of the subtracted DNA fragments, and the specificities of the 19 primer sets were evaluated by PCR using chromosomal DNAs extracted from four S. pneumoniae clinical isolates and from 20 atypical organisms classified as S. mitis or S. oralis, which harbored genes encoding the pneumococcal virulence factors autolysin (lytA) or pneumolysin (ply), as templates. Of the 19 primer sets, two (Spn9802 and Spn9828) did not amplify PCR products from any of the pneumococcus-like streptococcal strains that we examined. The genes containing the Spn9802 and Spn9828 sequences encoded proteins of unknown function that did not correspond to any previously described proteins in other bacteria. These new oligonucleotide primers may be very useful for early and correct diagnosis of S. pneumoniae infections.

Bacterial Proteins↗
PubMed2005

Homogeneous enzymatic assay for L-cysteine with betaC-S lyase.

We have developed a new enzymatic assay for determining L-cysteine concentration. The method involves the use of betaC-S lyase from Streptococcus anginosus, which catalyzes the alpha,beta-elimination of L-cysteine to hydrogen sulfide, pyruvate, and ammonia. The production of pyruvate is measured by D-lactate dehydrogenase and NADH. The decrease in NADH was proportional to the L-cysteine concentration up to 1.0 mM. When serum samples were used, within-day and day-to-day coefficient variations were below 4%. This method is simple, and can easily and reliably be used for accurate determination of L-cysteine concentration in serum or other samples.

Calibration↗
PubMed2005

A functional variant in the human betacellulin gene promoter is associated with type 2 diabetes.

Betacellulin (BTC) plays an important role in differentiation, growth, and antiapoptosis of pancreatic beta-cells. We characterized about 2.3 kb of the 5'-flanking region of human BTC gene and identified six polymorphisms (-2159A>G, -1449G>A, -1388C>T, -279C>A, -233G>C, and -226A>G). The G allele in the -226A>G polymorphism was more frequent in type 2 diabetic patients (n = 250) than in nondiabetic subjects (n = 254) (35.6% vs. 27.8%, P = 0.007), and the -2159G, -1449A, and -1388T alleles were in complete linkage disequilibrium with the -226G allele. The frequencies of the -279A and -233C alleles were low (7.0 and 2.0% in diabetic patients), and no significant differences were observed. In the diabetic group, insulin secretion ability, assessed by the serum C-peptide response to intravenous glucagon stimulation, was lower in patients with the -226G allele (G/G, 2.96 +/- 0.16 ng/ml; G/A, 3.65 +/- 0.18 ng/ml; A/A, 3.99 +/- 0.16 ng/ml at 5 min after stimulation; P = 0.008). Furthermore, in vitro functional analyses indicated that both the -226G and the -233C alleles caused an approximately 50% decrease in the promoter activity, but no effects of the -2159A>G, -1449G>A, -1388C>T, and -279C>A polymorphisms were observed. These results suggest that the -226A/G polymorphism of the BTC gene may contribute to the development of diabetes.

5' Untranslated Regions↗
PubMed2005

Quantitative analysis of multi-species oral biofilms by TaqMan Real-Time PCR.

Oral infectious diseases, including dental caries, various forms of periodontitis and oral malodor, are not caused by a single pathogen. The etiology of these diseases is known to be associated with bacterial accumulation and plaque composition on the hard and soft tissues of the oral cavity. Therefore, the quantitative, as well as qualitative, analysis of the microorganisms present in oral biofilms, namely dental plaque, subgingival plaque and tongue debris, is important for diagnosis and rational treatment decisions. The quantitative microbial analysis of oral multi-species biofilms also provides useful information for establishing the etiology of oral infectious diseases. Recently, a 5' fluorogenic, nuclease-based, real-time polymerase chain reaction (PCR) technique has been increasingly employed for the quantitative microbial assessment of the human oral cavity. We review the development and use of TaqMan real-time PCR for quantifying oral bacteria, its role in the diagnosis of oral infectious diseases and their microbial etiology.

Bacteria↗
PubMed2004

A study on pesticide runoff from paddy fields to a river in rural region--1: field survey of pesticide runoff in the Kozakura River, Japan.

Runoff characteristics of nine kinds of herbicides from paddy fields were surveyed in the Kozakura River, that is one of the tributaries flowing into the Lake of Kasumigaura, over a period of 23 April to 30 June (before and after rice transplantation) of year. The flow rates of river water and the concentrations of herbicides in the river water were measured every day in May and every 2 days in April and June at six survey sites along the river. The runoff characteristics of herbicides were elucidated by taking account of the rainfall data, the detailed application data (application date and quantities of herbicides applied to each paddy field in a region), and their physico-chemical properties. The runoff rates (the runoff/application amounts ratio) were calculated for each herbicide, resulting in the range of 8.2-22.4%. The runoff rates were correlated fairly well with octanol-water partition coefficient, logP(ow), rather than with water solubility of herbicides.

Agriculture↗
PubMed2004

A study on pesticide runoff from paddy fields to a river in rural region--2: development and application of a mathematical model.

A mathematical model was developed to predict the runoff of pesticides from paddy fields to a river in a rural region. The model comprises three submodels: (1) submodel for river flow, (2) submodel for pesticide behavior in paddy fields, (3) submodel for pesticide behavior in a river. The tank model was applied to predict the river flow and the paddy water. In order to reproduce the actual behavior of pesticides in paddy fields, the kinetics of the transport and reaction mechanisms of pesticides applied to paddy fields were considered in the model. The model was applied to the Kozakura River Basin where the detailed field survey was conducted. The model reflected well the runoff characteristics of pesticides obtained from the detailed field survey.

Agriculture↗
PubMed2004

Quantitative microbiological study of subgingival plaque by real-time PCR shows correlation between levels of Tannerella forsythensis and Fusobacterium spp.

A TaqMan-based real-time PCR assay was established to quantify the periodontopathic bacteria Tannerella forsythensis and Fusobacterium spp. With this assay, the prevalence and proportion of these bacteria in clinical specimens were evaluated. Our preliminary results suggest a positive colocalization of T. forsythensis and Fusobacterium spp. in periodontal pockets.

Adult↗
PubMed2004

Real-time TaqMan PCR for quantifying oral bacteria during biofilm formation.

A TaqMan PCR was developed for quantifying early colonizer microorganisms in dental biofilms. To design species-specific primers and TaqMan probes, genomic subtractive hybridization was used. This quantitative assay in combination with subtractive hybridization may be of value in the study of microbial ecosystems consisting of related species that are involved in the formation and etiology of biofilms.

Actinomyces↗
PubMed2003

Homocysteine biosynthesis pathways of Streptococcus anginosus.

A gene (cgs) encoding cystathionine gamma-synthase was cloned from Streptococcus anginosus, and its protein was purified and characterized. The cgs gene and the immediately downstream lcd gene were shown to be cotranscribed as an operon. High-performance liquid chromatography analyses showed that the S. anginosus Cgs not only has cystathionine gamma-synthase activity, but also expresses O-acetylhomoserine sulfhydrylase activity. These results suggest that S. anginosus has the capacity to utilize both the transsulfuration and direct sulfhydrylation pathways for homocysteine biosynthesis.

Amino Acid Sequence↗
PubMed2003

Differences in the betaC-S lyase activities of viridans group streptococci.

betaC-S Lyase catalyzes the alpha,beta-elimination of L-cysteine to hydrogen sulfide, which is one of the main causes of oral malodor and is highly toxic to mammalian cells. We evaluated the capacity of six species of oral streptococci to produce hydrogen sulfide. The crude enzyme extract from Streptococcus anginosus had the greatest capacity. However, comparative analysis of amino acid sequences did not detect any meaningful differences in the S. anginosus betaC-S lyase. The capacity of S. anginosus purified betaC-S lyase to degrade L-cysteine was also extremely high, while its capacity to degrade L-cystathionine was unremarkable. These findings suggest that the extremely high capacity of S. anginosus to produce hydrogen sulfide is due to the unique characteristic of betaC-S lyase from that organism.

Base Sequence↗