• Journal of Microbiology and Biotechnology
• /
• v.20 no.1
• /
• pp.169-178
• /
• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• Microbiology and Biotechnology Letters
• /
• v.46 no.2
• /
• pp.162-170
• /
• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• Microbiology and Biotechnology Letters
• /
• v.46 no.2
• /
• pp.135-144
• /
• 2018

The rapid increase in number and diversity of Extended Spectrum ${\beta}$-Lactamases (ESBLs) producing Enterobacteriaceae in natural aquatic environment is a major health concern worldwide. This study investigates abundance and distribution of ESBL producing multidrug resistant Enterobacteriaceae and molecular characterization of ESBL genes among isolates from highly polluted stretch of river Yamuna, India. Water samples were collected from ten different sites distributed across Delhi stretch of river Yamuna, during 2014-15. A total of 506 non duplicate Enterobacteriaceae isolates were obtained. Phenotypic detection of ESBL production and antibiotic sensitivity for 15 different antibiotics were performed according to CLSI guidelines (Clinical and Laboratory Standard Institute, 2015). A subset of ESBL positive Enterobacteriaceae isolates were identified by 16S rRNA gene and screened for ESBL genes, such as $bla_{CTX-M}$, $bla_{TEM}$ and $bla_{OXA}$. Out of 506 non-duplicate bacterial isolates obtained, 175 (34.58%) were positive for ESBL production. Susceptibility pattern for fifteen antibiotics used in this study revealed higher resistance to cefazolin, rifampicin and ampicillin. A high proportion (76.57%) of ESBL positive isolates showed multidrug resistance phenotype, with MAR index of 0.39 at Buddha Vihar and Old Delhi Railway bridge sampling site. Identification and PCR based characterization of ESBL genes revealed the prevalence of $bla_{CTX-M}$ and $bla_{TEM}$ genes to be 88.33% and 61.66%, respectively. Co-occurrence of $bla_{CTX-M}$ and $bla_{TEM}$ genes was detected in 58.33% of the resistant bacteria. The $bla_{OXA}$ gene was not detected in any isolates. This study highlights deteriorating condition of urban aquatic environment due to rising level of ESBL producing Enterobacteriaceae with multidrug resistance phenotype.

• BMB Reports
• /
• v.41 no.6
• /
• pp.415-434
• /
• 2008

Phosphoinositide-specific phospholipase C is an effector molecule in the signal transduction process. It generates two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. Currently, thirteen mammal PLC isozymes have been identified, and they are divided into six groups: PLC-$\beta$, -$\gamma$, -$\delta$, -$\varepsilon$, -$\zeta$ and -$\eta$. Sequence analysis studies demonstrated that each isozyme has more than one alternative splicing variant. PLC isozymes contain the X and Y domains that are responsible for catalytic activity. Several other domains including the PH domain, the C2 domain and EF hand motifs are involved in various biological functions of PLC isozymes as signaling proteins. The distribution of PLC isozymes is tissue and organ specific. Recent studies on isolated cells and knockout mice depleted of PLC isozymes have revealed their distinct phenotypes. Given the specificity in distribution and cellular localization, it is clear that each PLC isozyme bears a unique function in the modulation of physiological responses. In this review, we discuss the structural organization, enzymatic properties and molecular diversity of PLC splicing variants and study functional and physiological roles of each isozyme.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.12
• /
• pp.2141-2147
• /
• 2016

As one of the most complex human-associated microbial habitats, the oral cavity harbors hundreds of bacteria. Halitosis is a prevalent oral condition that is typically caused by bacteria. The aim of this study was to analyze the microbial communities and predict functional profiles in supragingival plaque from healthy individuals and those with halitosis. Ten preschool children were enrolled in this study; five with halitosis and five without. Supragingival plaque was isolated from each participant and 16S rRNA gene pyrosequencing was used to identify the microbes present. Samples were primarily composed of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Candidate phylum TM7. The ${\alpha}$ and ${\beta}$ diversity indices did not differ between healthy and halitosis subjects. Fifteen operational taxonomic units (OTUs) were identified with significantly different relative abundances between healthy and halitosis plaques, and included the phylotypes of Prevotella sp., Leptotrichia sp., Actinomyces sp., Porphyromonas sp., Selenomonas sp., Selenomonas noxia, and Capnocytophaga ochracea. We suggest that these OTUs are candidate halitosis-associated pathogens. Functional profiles were predicted using PICRUSt, and nine level-3 KEGG Orthology groups were significantly different. Hub modules of co-occurrence networks implied that microbes in halitosis dental plaque were more highly conserved than microbes of healthy individuals' plaque. Collectively, our data provide a background for the oral microbiota associated with halitosis from supragingival plaque, and help explain the etiology of halitosis.

• Journal of the Korean Dietetic Association
• /
• v.15 no.2
• /
• pp.128-138
• /
• 2009

The purpose of this study was to assess nutrient intake and dietary quality in female college students according to their coffee consumption. The survey was conducted through questionnaires and 3-day dietary records with 353 students. The subjects were divided into three groups: students who didn't consume coffee (non-coffee group, N=119), students who consumed <250 ml coffee (light-coffee group, N=140), and students who consumed ${\geq}$250 ml coffee (moderate-coffee group, N=94). There were no significant differences in age, weight, height, and BMI among the three groups. The mean daily energy intake was 1800.8 kcal in the non-coffee group, 1724.9 kcal in the light-coffee group, and 1729.7 kcal in the moderate-coffee group. The moderate-coffee group consumed a significantly higher amount of alcohol than the light-coffee group (p<0.05). The average intakes of dietary fiber, vitamin A, ${\beta}$-carotene, and folate in the non-coffee group were significantly higher than those in the light-coffee and moderate-coffee groups. Indexes of Nutritional Quality (INQ) for vitamin A, niacin, and vitamin B6 were significantly higher in the non-coffee group than in the light-coffee group. Also the non-coffee group consumed a significantly higher amount of vegetables compared to the light-coffee group. There was no significant difference in the Dietary Diversity Scores (DDS) among the three groups. These results suggest that coffee consumption affects food and nutrient intake in female college students.

• Journal of Ginseng Research
• /
• v.44 no.2
• /
• pp.215-221
• /
• 2020

Background: Panax ginseng has been used for a variety of medical purposes in eastern countries for more than two thousand years. From the extensive experiences accumulated in its long medication use history and the substantial strong evidence in modern research studies, we know that ginseng has various pharmacological activities, such as antitumor, antidiabetic, antioxidant, and cardiovascular system-protective effects. The active chemical constituents of ginseng, ginsenosides, are rich in structural diversity and exhibit a wide range of biological activities. Methods: Ginsenoside constituents from P. ginseng flower buds were isolated and purified by various chromatographic methods, and their structures were identified by spectroscopic analysis and comparison with the reported data. The 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H- tetrazolium bromide method was used to test their cytotoxic effects on three human cancer cell lines. Results: Six ginsenosides, namely 6'-malonyl formyl ginsenoside F₁ (1), 3β-acetoxyl ginsenoside F₁ (2), ginsenoside Rh₂₄ (6), ginsenoside Rh₂₅ (7), 7β-hydroxyl ginsenoside Rd (8) and ginsenoside Rh₂₆ (10) were isolated and elucidated as new compounds, together with four known compounds (3-5 and 9). In addition, the cytotoxicity of these isolated compounds was shown as half inhibitory concentration values, a tentative structure-activity relationship was also discussed based on the results of our bioassay. Conclusion: The study of chemical constituents was useful for the quality control of P. ginseng flower buds. The study on antitumor activities showed that new Compound 1 exhibited moderate cytotoxic activities against HL-60, MGC80-3 and Hep-G2 with half inhibitory concentration values of 16.74, 29.51 and 20.48 μM, respectively.

• Journal of Plant Biology
• /
• v.25 no.2
• /
• pp.83-99
• /
• 1982

In this study, thirty-two stands in Kwangnung forest located in the central part of Korea were preferentially selected. In each stand, all stems for trees and shrubs were recorded by species and their girths were measured down to 5cm. In addition, several enviromental factors such as field soil pH, field soil moisture, soil compressibility, depth of soil, thickness of litter layer, elevation and basal area were measured. Three soil cores were sampled and various physical and chemcial properties was determined. The vegetational data were subjected to three kinds of multivariate ordination(PO, PCA, RA). The results suggested that Kwangnung forest was consisted of three forest types: coniferous, mixed and broad leaved forest communities. The relation between the stand scores of ordination and several environmental factors were investigated in terms of correlation analysis in order to examine the relationships between the vegetation and certain environmental factors. As a result of this analysis, the amount of sand content in A1 horizon decreased frm the coniferous to broad leaved forest, while maximum field capacity, pore space, exchangeable cations, loss on ignition, soil pH nad the amount of total nitrogen had a tendancy to increase significantly. However, easily soluble phosphorus appeared to have little to do with the forest types. The result of species ordination of centered-standardized PCA suggested that the major successional pathway in Kwangnung forest was; Pinus densifloralongrightarrowQuercus mongolica, Q. serrata, Q. alienalongrightarrowCarpinus laxifloralongrightarrowC. erosa in sequence. This trend is in good agreement with the past studies. In three kinds of ordination (centered PCA, centered-standardized PCA and RA) based on nineteen species and twenty-five stands, the total variances accounted for the first three axes were 77%, 46% and 63% respectively. The estimated beta diversity in Kwangnung forest assumed as a coenocline, was 1.5~1.8 HC. Increasing the effect of the sampling errors on ordination perfermance, this low heterogeneity seems to cause the poor concentration of the total variance. The results from the four kinds of ordination were in good agreement with each other, especially between PO, centered-standardized PCA and RA appeared robust. It seems to be worthy of applying multivariate method for analyzing other forest communities in Korea.

• The Korean Journal of Mycology
• /
• v.46 no.4
• /
• pp.359-367
• /
• 2018

As an effort to explore fungal diversity, fungal survey was undertaken in 2017 in the vicinity of demilitarized zone (DMZ) located in Yeoncheon-gun, Gyeonggi-do, Korea. For the survey, wild plants and soils were sampled and subjected to fungal isolation. A total of 18 genera and 23 species including five unrecorded fungal species, Mortierella sclerotiella, M. sossauensis, M. verticillate, Eupenicillium saturniforme, and Trichoderma hispanicum, were obtained from the survey. This study described their morphological characteristics including colony features formed on media, light microscopic images and molecular characteristics of nucleotide sequences of the internal transcribed spacer (ITS) region, 18S and 28S rDNA, ${\beta}-tubulin$ gene, calmodulin, and translation elongation factor $1{\alpha}$ ($tef1{\alpha}$) nDNA genes.

• Molecules and Cells
• /
• v.42 no.1
• /
• pp.56-66
• /
• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.