Classification of Ilex species based on metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis

The metabolomic analysis of 11 Ilex species, I. argentina, I. brasiliensis, I. brevicuspis, I. dumosavar. dumosa, I. dumosa var. guaranina, I. integerrima, I. microdonta, I. paraguariensis var. paraguariensis, I. pseudobuxus, I. taubertiana, and I. theezans, was carried out by NMR spectroscopy and multivariate data analysis. The analysis using principal component analysis and classification of the (1)H NMR spectra showed a clear discrimination of those samples based on the metabolites present in the organic and aqueous fractions. The major metabolites that contribute to the discrimination are arbutin, caffeine, phenylpropanoids, and theobromine. Among those metabolites, arbutin, which has not been reported yet as a constituent of Ilex species, was found to be a biomarker for I. argentina,I. brasiliensis, I. brevicuspis, I. integerrima, I. microdonta, I. pseudobuxus, I. taubertiana, and I. theezans. This reliable method based on the determination of a large number of metabolites makes the chemotaxonomical analysis of Ilex species possible.     

Color characteristics of monascus pigments derived by fermentation with various amino acids

Various pigment colors were produced by Monascus fermentations with separate addition of 20 amino acids. The color characteristics and structures of the pigment derivatives were investigated. When each amino acid was added to the fermentation broth as a precursor, pigment extracts with different hue and chroma values were obtained depending on the content ratios of yellow, orange, and red colors in the fermentation broth. The yellow and orange pigments were identical regardless of amino acid addition. The red compounds varied on the basis of the type of amino acid added. LC-MS and (1)H and (13)C NMR structural analyses confirmed that the derivative pigments contained the moieties of the added amino acids. L, a, and b values of the CIELAB color system for the derivative pigments were measured. Values of hue and chroma were then calculated. The colors of the derivative pigments were in the range of orangish red to violet red. The hydrophilicities/hydrophobicities of the derivative pigments could be predicted from their log P values, which were estimated using computer programs.     

Effect of far-infrared radiation on the antioxidant activity of rice hulls

After far-infrared (FIR) radiation onto rice hull, a methanolic extract was prepared for the determination of antioxidant ability. After 30 min of FIR treatment, the radical scavenging activity and total phenol contents of rice hull extracts increased from 47.74 to 79.63% and from 0.12 to 0.19 mM, respectively, compared to control. Inhibition of lipid peroxidation in extracts was also increased from 41.07 to 47.96%. According to the GC-MS analysis, more phenolic compounds (p-coumaric acid, 3-vinyl-1-oxybenzene, p-hydroxybenzaldehyde, vanillin, p-hydroxybenzoic acid, and 4,7-dihydroxyvanillic acid) were detected in FIR-irradiated rice hull extract. These results indicated that FIR radiation onto rice hull could liberate and activate covalently bound phenolic compounds that have antioxidant activities.     

Inhibitory effect of a bioactivity-guided fraction from Rheum undulatum on the acid production of Streptococcus mutans biofilms at sub-MIC levels

Rheum undulatum root has been used traditionally in Korea for the treatment of dental diseases. The purpose of this study was to separate a fraction from R. undulatum showing anti-acid production activity against Streptococcus mutans biofilms and identify the main components in that fraction. Methanol extract of R. undulatum root and its fractions were prepared. To select a fraction exhibiting anti-acid production activity, suspension glycolytic pH-drop assay was performed. Among the fractions tested, dichloromethane fraction exhibited the strongest activity in a dose-dependent manner. To examine the effect of the selected fraction on the anti-acid production of S. mutans biofilms, 74 h old S. mutans biofilms were used. The selected fraction reduced the initial rate of acid production of S. mutans biofilms at sub-minimum inhibitory concentration (MIC) levels. HPLC qualitative analysis of the selected fraction indicated that the presence of anthraquinone derivatives, such as aloe-emodin, emodin, chrysophanol and physcion, as main components.     

Management of pine wilt disease in Korea through preventative silvicultural control

Pine wilt disease (PWD) represents a major threat to forest ecosystems worldwide. Although PWD is now better understood, effective control measures for this disease have still not been devised. Here, we report several years of field studies on preventative silvicultural control of PWD. Silvicultural control through preventative clear-cutting and the manual removal of logs was implemented between 2005 and 2009 in 16 Korean districts that had newly PWD-infected stands. Preventative clear-cutting of neighboring asymptomatic pine trees (within a 10-50-m radius of wilt trees) and the removal of felled logs or branches suppressed spread of PWD. Occurrences of PWD wilt pines in districts (city or county) subjected to this silvicultural control method were significantly reduced compared with those in districts using conventional controls (physical or chemical treatment of wilt pine trees). Through silvicultural control, PWD was successfully suppressed in 11 of 16 districts investigated. In contrast, successful control was achieved in only 1 among 18 districts subjected to conventional control. Our results will be of considerable interest to those engaged in the very difficult battle against the global spread of PWD.     

Genetic relationships among cultivated and wild <Emphasis Type="Italic">Vigna angularis</Emphasis> (Willd.) Ohwi et Ohashi and relatives from Korea based on AFLP markers

Genetic variation and relationships among members of the azuki bean complex (Vigna angularis) including wild (V. angularis var. nipponensis), weedy, and cultivated types (V. angularis var. angularis), V. nakashimae, and rice bean (V. umbellata) from Korea were examined using the Amplified fragment length polymorphism (AFLP) method. AFLP analysis of 50 accessions revealed 333 (72.1%) polymorphic fragments out of 462 fragments amplified using seven primer combinations. The number of polymorphic fragments within each species was 70 in the azuki bean complex and 41 in V. nakashimae, but there was no polymorphism in rice bean. The number of shared fragments among species ranges from 142 between the azuki bean complex and V. nakashimae to 166 between the azuki bean complex and rice bean. Within the azuki bean complex, the range of shared bands was from 231 between cultivated and weedy types to 238 between cultivated and wild types. A dendrogram generated from Jaccard’s similarity matrix was divided into three groups, which correspond to V. nakashimae, azuki bean complex, and rice bean. The relationship between azuki bean and rice bean is closer than between azuki bean and V. nakashimae. Phenetic distances averaged 0.502 between the azuki bean complex and V. nakashimae and 0.467 between the azuki bean complex and rice bean. Within the azuki bean complex, the weedy type was more closely related to wild than cultivated types. But UPGMA dendrogram of the azuki bean complex reveals that each type is not clearly isolated. These results will help to understand genetic diversity and evolutionary dynamics of Vigna in Korea.     

Monitoring of Atmospheric Mercury at a Global Atmospheric Watch (GAW) Site on An-Myun Island, Korea

In order to investigate the regional background concentration levels of mercury (Hg), measurements were routinely recorded on An-Myun Island off the coast of Korea (December 2004 to April 2006). The mean concentration of Hg computed from the entire measurement period was 4.61?±?2.21 ng m^?3 with a range of 0.10–25.4 ng m^?3 (N?=?10,485). Using these data, we inspected various aspects of Hg behavior from the relatively remote island of An-Myun in Korea. Inspection of the seasonal patterns of Hg indicated that its concentration levels generally peaked in spring, while reached a minimum in summer. The summertime deficiency of Hg along with the lack of diurnal variation suggests that the environmental behavior of Hg at the study site was strongly suppressed by heavy precipitation during specific period. The diurnal variations of Hg, typically characterized by a relative daytime dominance, are distinguishable between seasons so that such patterns disappear during the summer. The results of our analysis, when inspected in terms of long-range transport of airborne pollutants, imply that Hg concentration levels can be affected intensively by trans-boundary input processes over certain period of time. Its springtime dominance hence suggests the combined effects of various local source processes and the meteorological conditions favorable for the massive air mass transport phenomenon (such as Asian Dust storms) during that time period.     

Ochratoxin A in Korean food commodities: occurrence and safety evaluation

To evaluate the exposure of Koreans to ochratoxin A, we conducted a survey in 2003 for ochratoxin A in various domestic food commodities: 60 polished rices, 22 barleys, 35 wheat flours, 46 beers, and 14 unstrained rice wine (makkolli) samples. They were analyzed for ochratoxin A using immunoaffinity column and high-performance liquid chromatography (HPLC)-fluorescence detection, and the positive samples were confirmed using HPLC-tandem mass spectrometry. By combining results from different surveys on the levels of ochratoxin A in selected foods and the consumption patterns, we obtained the Korean probable daily intakes (PDI) of ochratoxin A. The polished rice commodity had the highest mean levels of ochratoxin A, which ranged from 0.2 (not detected, i.e., ND = 0) to 1.0 ng/g (ND = limit of detection, i.e., LOD). The estimated PDI for all Koreans fell into the range of 0.8-4.1 ng/kg bw/day, while for heavy consumers the estimates ranged from 1.7 to 9.1 ng/kg bw/day, which did not exceed the PTDI value (14 ng/kg bw/day). Staple rice is the major contributor (>90%) to the Korean dietary intake of ochratoxin A. On the basis of these estimates, it may be concluded that there is at present no considerable risk of ochratoxin A exposure for the average Korean consumer.     

Bayesian Semiparametric Model for Pathway-Based Analysis with Zero-Inflated Clinical Outcomes

In this paper, we propose a semiparametric regression approach for identifying pathways related to zero-inflated clinical outcomes, where a pathway is a gene set derived from prior biological knowledge. Our approach is developed by using a Bayesian hierarchical framework. We model the pathway effect nonparametrically into a zero-inflated Poisson hierarchical regression model with an unknown link function. Nonparametric pathway effect was estimated via a kernel machine, and the unknown link function was estimated by transforming a mixture of the beta cumulative density function. Our approach provides flexible nonparametric settings to describe the complicated association between gene expressions and zero-inflated clinical outcomes. The Metropolis-within-Gibbs sampling algorithm and Bayes factor were adopted to make statistical inferences. Our simulation results support that our semiparametric approach is more accurate and flexible than zero-inflated Poisson regression with the canonical link function, which is especially true when the number of genes is large. The usefulness of our approach is demonstrated through its applications to the Canine data set from Enerson et al. (Toxicol Pathol 34:27–32, 2006). Our approach can also be applied to other settings where a large number of highly correlated predictors are present.Supplementary materials accompanying this paper appear on-line.