Prediction of Periodontal Inflammation via Metabolic Profiling of Saliva.

Periodontal disease is characterized by chronic inflammation in subgingival areas, where a vast array of inflammation-associated metabolites are likely produced from tissue breakdown, increased vascular permeability, and microbial metabolism and then eventually show a steady flow into saliva. Thus, prolonged periodontal inflammation is a key feature of disease activity. Although salivary metabolomics has drawn attention for its potential use in diagnosis of periodontal disease, few authors have used that to investigate periodontal inflammation detection. In this pilot study, the authors explored the use of salivary metabolites to reflect periodontal inflammation severity with a recently proposed parameter-periodontal inflamed surface area (PISA)-used to quantify the periodontal inflammatory burden of individual patients with high accuracy. Following PISA determination, whole saliva samples were collected from 19 subjects before and after removal of supragingival plaque and calculus (debridement) with an ultrasonic scaler to assess the influence of the procedure on salivary metabolic profiles. Metabolic profiling of saliva was performed with gas chromatography coupled to time-of-flight mass spectrometry, followed by multivariate regression analysis with orthogonal projections to latent structures (OPLS) to investigate the relationship between PISA and salivary metabolic profiles. Sixty-three metabolites were identified. OPLS analysis showed that postdebridement saliva provided a more refined model for prediction of PISA than did predebridement samples, which indicated that debridement may improve detection of metabolites eluted from subgingival areas in saliva, thus more accurately reflecting the pathophysiology of periodontitis. Based on the variable importance in the projection values obtained via OPLS, 8 metabolites were identified as potential indicators of periodontal inflammation, of which the combination of cadaverine, 5-oxoproline, and histidine yielded satisfactory accuracy (area under the curve = 0.881) for diagnosis of periodontitis. The authors' findings identified potential biomarkers that may be useful for reflecting the severity of periodontal inflammation as part of monitoring disease activity in periodontitis patients.

Monitoring the ripening process of Cheddar cheese based on hydrophilic component profiling using gas chromatography-mass spectrometry.

We proposed an application methodology that combines metabolic profiling with multiple appropriate multivariate analyses and verified it on the industrial scale of the ripening process of Cheddar cheese to make practical use of hydrophilic low-molecular-weight compound profiling using gas chromatography-mass spectrometry to design optimal conditions and quality monitoring of the cheese ripening process. Principal components analysis provided an overview of the effect of sodium chloride content and kind of lactic acid bacteria starter on the metabolic profile in the ripening process of Cheddar cheese and orthogonal partial least squares-discriminant analysis unveiled the difference in characteristic metabolites. When the sodium chloride contents were different (1.6 and 0.2%) but the same lactic acid bacteria starter was used, the 2 cheeses were classified by orthogonal partial least squares-discriminant analysis from their metabolic profiles, but were not given perfect discrimination. Not much difference existed in the metabolic profile between the 2 cheeses. Compounds including lactose, galactose, lactic acid, 4-aminobutyric acid, and phosphate were identified as contents that differed between the 2 cheeses. On the other hand, in the case of the same salt content of 1.6%, but different kinds of lactic acid bacteria starter, an excellent distinctive discrimination model was obtained, which showed that the difference of lactic acid bacteria starter caused an obvious difference in metabolic profiles. Compounds including lactic acid, lactose, urea, 4-aminobutyric acid, galactose, phosphate, proline, isoleucine, glycine, alanine, lysine, leucine, valine, and pyroglutamic acid were identified as contents that differed between the 2 cheeses. Then, a good sensory prediction model for "rich flavor," which was defined as "thick and rich, including umami taste and soy sauce-like flavor," was constructed based on the metabolic profile during ripening using partial least squares regression analysis. The amino acids proline, leucine, valine, isoleucine, pyroglutamic acid, alanine, glutamic acid, glycine, lysine, tyrosine, serine, phenylalanine, methionine, aspartic acid, and ornithine were extracted as ripening process markers. The present study is not limited to Cheddar cheese and can be applied to various maturation-type natural cheeses. This study provides the technical platform for designing optimal conditions and quality monitoring of the cheese ripening process.

Analysis of long-chain polyprenols using supercritical fluid chromatography and matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

The separation of long-chain polyprenols was successfully achieved using supercritical fluid chromatography (SFC). Each 100-mer greater component was separated using tetrahydrofuran as a mobile phase modifier. The molecular mass distributions derived from SFC analyses agreed with the results of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analyses. The number-average molecular mass calculated by MALDI-TOF-MS data were also in accord with the results of quantitative 1H-NMR analysis of terminal groups. A combination of SFC and MALDI-TOF-MS analyses is a powerful tool for the elucidation of the complicated structures of natural polyprenols.

Identification of genes induced by taxol application using a combination of differential display RT-PCR and DNA microarray analysis.

The differential display reverse transcriptional polymerase chain reaction (DD-RT-PCR) was used to hunt for cDNA fragments specifically expressed by taxol treatment of HeLa cells. Forty-eight cDNA clones were differentially displayed through the experiments. The cDNA fragments obtained were separately spotted onto glass slides to prepare a tailor-made DNA chip. The gene expression pattern of differentially displayed cDNA fragments were checked by DNA microarray analysis.

SELEX for tubulin affords specific T-rich DNA aptamers. Systematic evolution of ligands by exponeential enrichment.

We succeeded in acquiring two DNA aptamers that selectively recognize tubulin by the SELEX method. A pool of single-stranded oligo-DNAs including a random region of 59 nucleotides was screened by SELEX for tubulin purified from calf-brain as a target. After 20 repetitions of selection round, the library converged on specific T-rich sequences. The binding activity of T-rich clones was analyzed by the SPR sensor to determine their dissociation constants to be in the order of 10 microM.

Plasma-membrane H+-ATPases are expressed in pitchers of the carnivorous plant Nepenthes alata Blanco.

Nepenthes is a unique genus of carnivorous plants that can capture insects in trapping organs called pitchers and digest them in pitcher fluid. The pitcher fluid includes digestive enzymes and is strongly acidic. We found that the fluid pH decreased when prey accumulates in the pitcher fluid of Nepenthes alata. The pH decrease may be important for prey digestion and the absorption of prey-derived nutrients. To identify the proton pump involved in the acidification of pitcher fluid, plant proton-pump homologs were cloned and their expressions were examined. In the lower part of pitchers with natural prey, expression of one putative plasma-membrane (PM) H+-ATPase gene, NaPHA3, was considerably higher than that of the putative vacuolar H+-ATPase (subunit A) gene, NaVHA1, or the putative vacuolar H+-pyrophosphatase gene, NaV-HP1. Expression of one PM H+-ATPase gene, Na-PHA1, was detected in the head cells of digestive glands in the lower part of pitchers, where proton extrusion may occur. Involvement of the PM H+-ATPase in the acidification of pitcher fluid was also supported by experiments with proton-pump modulators; vanadate inhibited proton extrusion from the inner surface of pitchers, whereas bafilomycin A1 did not, and fusicoccin induced proton extrusion. These results strongly suggest that the PM H+-ATPase is responsible for acidification of the pitcher fluid of Nepenthes.

The occurrence of geometric polyprenol isomers in the rubber-producing plant, Eucommia ulmoides Oliver.

The chain length and geometric isomerism of polyprenols from Eucommia ulmoides Oliver were analyzed using supercritical fluid chromatography. After intensive effort to establish separation conditions for geometric isomers, a phenyl-bonded silica gel-packed column was found that cleanly separated poly-trans and -cis prenols. The presence of long-chain poly-trans prenols (>9 mers) was confirmed for the first time in plants. Trans isomers were found in the leaf, seed coat, and root, but not in the bark and seed. Poly-trans prenols in this plant may act as intermediates for trans-polyisoprene biosynthesis.

In vitro selection of hematoporphyrin binding DNA aptamers.

DNA aptamers that bind to hematoporphyrin IX (HPIX) were isolated using an in vitro selection technique. Most aptamers obtained after the 7th and 10th rounds contained guanine-rich sequences. Binding assay using fluorescence polarization technique and structural analysis by CD spectra revealed that the parallel guanine-quartet structure of the aptamer participates in the recognition of HPIX.

DNA aptamers that bind to chitin.

We have succeeded in the acquisition of DNA aptamers that recognize chitin using in vitro selection. The obtained DNA aptamers have the stem-loop or bulge loop structures with guanine rich loop clusters and the clockwise B-form stems.

Removal of magnesium by Mg-dechelatase is a major step in the chlorophyll-degrading pathway in Ginkgo biloba in the process of autumnal tints.

Autumnal tints are one of the most manifest and fascinating natural phenomena, but the mechanism of chlorophyll (Chl)-breakdown in deciduous trees has not been fully elucidated. In this study, we analyzed the composition of Chl-related compounds and determined the activities of initial Chl-degrading enzymes in Ginkgo leaves at various stages in the process of autumnal coloring. Only pheophytin a (Pheo a, Mg-free Chl a) was detected in yellow leaves by HPLC analysis, and the activity of Mg-dechelatase in yellow leaves was found to be higher than in green leaves. These findings showed that the removal of magnesium from Chl a occurred in advance of dephytylation in the Ginkgo.

Formate dehydrogenase in rice plant: growth stimulation effect of formate in rice plant.

NAD-dependent formate dehydrogenase (FDH, EC 1.2.1.2.) plays a key role in the final step of the catabolism of methanol in methylotrophs. In certain plant species, this enzyme is a mitochondrial and NAD-dependent enzyme. In this study, the complete cDNA sequence of the rice (Oryza sativa cv Hinohikari) FDH gene, which contains an open reading frame (ORF) of 1128 bp, was determined. The sequence corresponds to a protein of 376 amino acids and shows strong homology to the NAD-dependent FDHs from other plants. Our experimental results showed that the expression of the rice cDNA in Escherichia coli induced FDH activity, indicating that the cDNA encodes a functional peptide of FDH. The application of formate to the roots of rice seedlings leads to growth increment both in terms of the length of the aerial part and the fresh weight. The FDH activity and the accumulation of FDH transcripts were strongly enhanced in the root portions of the formate-fed plants. This enhancement indicates that the transcriptional regulation which responds to formate functions in the rice plant, and that formate can act as an effective inducer for FDH activity.

Formate protects photosynthetic machinery from photoinhibition.

In plants, environmental adversity often leads to the formation of reactive oxygen species (ROS) because of excess light energy. We found that incubation of rice leaves under high light intensity together with CO2-depleted air seriously damaged photosynthesis; however, the application of potassium formate (2 mM) before the photoinhibitory treatment protected the photosynthesis of the plant from photoinhibition. Further analysis revealed that formate protects PSII, RuBisCO, and FBPase from photoinhibition. Formate is thought to be involved in endogenous radical scavenging and/or in the supply of CO2, derived from the formate, thereby reducing oxidative damage to the photosystems under photoinhibitory conditions.

An artificial plastic receptor that discriminates axial asymmetry.

An artificial plastic receptor that can discriminate axial asymmetry of optically active binaphthyldiamine derivatives was prepared by the 'molecular imprinting' technique. A light-radical polymerization in the presence of an axially asymmetric compound, (R)-2,2'-bis-methylcarbonylamino-1,1'-binaphthyl (binaphthyldiamine bis-acetamide (BINADA-ac)) as a template molecule with methacrylic acid (MA) as a functional monomer, and ethyleneglycol dimethacrylate (EGDMA) as a crosslinker, at 4 degrees C. The obtained polymer exhibited a superior enantioselectivity to the (R)-enantiomer by HPLC analyses. This plastic receptor should recognize the template molecule with its shape and character of its functional groups. It should be useful in the development of chiral stationary phases for the optical resolutions of axially asymmetric compounds.

Formate dehydrogenase gene of Arabidopsis thaliana is induced by formaldehyde and not by formic acid.

Variability of expression of formate dehydrogenase (FDH) caused by uptake of C-1 compounds was examined by using Arabidopsis thaliana as a model plant. Effects of uptake of several C-1 compounds were evaluated by Northern blot analysis using cDNA of A. thaliana FDH prepared by cloning on the basis of known sequence. As a result, expression of the FDH gene in A. thaliana was not intensely influenced by formic acid, an inherent substrate for FDH, but strongly induced by its reduced form, formaldehyde.

A simple assay for formate dehydrogenase activity by gas chromatography-mass spectrometry.

A new method using GC-MS was devised for the convenient measurement of formate dehydrogenase (FDH) activity in crude tissue samples. FDH activity was detected by measuring headspace 13CO2, which was enzymically converted from [13C]formic acid. This method proved to be sensitive and simple for the estimation of FDH activity without complicated pretreatment.

Lipase-catalyzed kinetic resolution of 2,3-epoxy-1-tridecanol and its application to facile synthesis of (+)-disparlure.

Acylation of (+/-)-2,3-epoxy-1-tridecanol with acetic anhydride in diisopropyl ether by porcine pancreatic lipase yielded (2R, 3S)-2,3-epoxy-1-tridecanol as the remaining substrate with an optical purity of over 99% ee. (+)-Disparlure was synthesized in two steps from this optically active epoxy alcohol.

Structure and expression of genes coding for xylan-degrading enzymes of Bacillus pumilus.

The complete nucleotide sequence of the beta-xylosidase gene (xynB) of Bacillus pumilus IPO and its flanking regions was established. A 1617-bp open reading frame for beta-xylosidase, a homodimer enzyme, was observed. The amino acid sequence of the N-terminal region and the molecular mass 62607 Da) of the beta-xylosidase subunit, deduced from the DNA sequence, agreed with the result obtained with the purified enzyme. The Shine-Dalgarno sequence was found 8 bp upstream of the initiation codon, ATG. The xylanase gene (xynA) of the same strain was 4.6 kbp downstream of the 3' end of xynB, and its DNA sequence was reported in our previous paper [Fukusaki, E., Panbangred, W., Shinmyo, A. & Okada, H. (1984) FEBS Lett. 171, 197-201]. The results of the Northern hybridization suggested that the mRNA of xynA and xynB were produced separately. The 5' and 3' ends of the xynA and xynB gene were mapped with nuclease S1. The '-10' regions for promoter sequences of both genes were similar to the consensus sequence for B. subtilis RNA polymerases, the '-35' regions were different from all the known promoters for B. subtilis RNA polymerases.