• Korean Journal of Microbiology
• /
• v.52 no.3
• /
• pp.286-297
• /
• 2016

Clostridium perfringens is both a ubiquitous environmental bacterium and a major cause of human gastrointestinal disease, and C. perfringens food poisoning ranks among the most common gastrointestinal diseases in developed countries. 120 isolates of C. perfringens were obtained from food-poisoning outbreaks in 2013~2014, Gyeonggi-do. Using PCR, all 120 isolates were identified as C. perfringens type A. Of the tested isolates, 49 isolates carried the cpe gene, 71 isolates carried the cpb2 gene. The outbreak cases of cpb2 and cpe /cpb2 genes were 7 and 7, whereas the outbreak cases of cpe-gene were 2. The epidemiological relationship between C. perfringens isolates has previously been investigated chiefly by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genetics relatedness of the isolates raged from 53.5-100% and 75 district PFGE type were observed. The PFGE results revealed a wide genetic diversity among the 64 cpb2 carrying isolates (except 7 isolates), while 46 cpe-carrying isolates (except 3 isolates) showed a high genetic similarity. The MLST analysis revealed that 14 cpe isolates (cpe-chromosomal isolates) belong to a distinct cluster that is significantly distant from all the other cpb2 isolates (cpe-plasmid carrying and cpe-negative isolates). The isolates carrying a cpb2 appear to be rarely related, and are more variable than chromosomal cpe isolates. The results suggest that the cpe-positive outbreak isolates showed close genetic relation, whereas the cpb2-positive isolates revealed a wide genetic diversity.

• 한국균학회소식:학술대회논문집
• /
• 2014.10a
• /
• pp.9-9
• /
• 2014

Null mutants generated by targeted gene replacement are frequently used to reveal function of the genes in fungi. However, targeted gene deletions may be difficult to obtain or it may not be applicable, such as in the case of redundant or lethal genes. Constitutive expression system could be an alternative to avoid these difficulties and to provide new platform in fungal functional genomics research. Here we developed a novel platform for functional analysis genes in Magnaporthe oryzae by constitutive expression under a strong promoter. Employing a binary vector (pGOF1), carrying $EF1{\beta}$ promoter, we generated a total of 4,432 transformants by Agrobacterium tumefaciens-mediated transformation. We have analyzed a subset of 54 transformants that have the vector inserted in the promoter region of individual genes, at distances ranging from 44 to 1,479 bp. These transformants showed increased transcript levels of the genes that are found immediately adjacent to the vector, compared to those of wild type. Ten transformants showed higher levels of expression relative to the wild type not only in mycelial stage but also during infection-related development. Two transformants that T-DNA was inserted in the promotor regions of putative lethal genes, MoRPT4 and MoDBP5, showed decreased conidiation and pathogenicity, respectively. We also characterized two transformants that T-DNA was inserted in functionally redundant genes encoding alpha-glucosidase and alpha-mannosidase. These transformants also showed decreased mycelial growth and pathogenicity, implying successful application of this platform in functional analysis of the genes. Our data also demonstrated that comparative phenotypic analysis under over-expression and suppression of gene expression could prove a highly efficient system for functional analysis of the genes. Our over-expressed transformants library would be a valuable resource for functional characterization of the redundant or lethal genes in M. oryzae and this system may be applicable in other fungi.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.39.1-39.15
• /
• 2023

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

• Korean Journal of Ecology and Environment
• /
• v.35 no.4 s.100
• /
• pp.285-294
• /
• 2002

The purpose of this study was to evaluate the relationships between purification characteristics and hydraulic conditions, and to clarify the basic and essential factors required to be considered in the construction and management of artificial wetland system for the improvement of reservoir water quality. The artificial wetland system was composed of a pumping station and six sequential plants beds with five species of macrophytes: Oenanthe javanica, Acorus calamus, Zizania latifolia, Typha angustifolia, and Phragmites australis. The system was operated on free surface-flow system, and operation conditions were $3,444-4,156\; m^3/d$ of inflow rate, 0.5-2.0 hr of HRT, 0.1-0.2 m of water depth, 6.0-9.4 m/d of hydraulic loading, and relatively low nutrients concentration (0.224-2.462 mgN/L, 0.145-0.164 mgP/L) of inflow water. The mean purification efficiencies of TN ranged from 12.1% to 14.3% by showing the highest efficiency at the Phragmites australis bed, and these of TP were 6.3-9.5% by showing the similar ranges of efficiencies among all species. The mean purification efficiencies of SS and Chl-A ranged from 17.4% to 38.5% and from 12.0% to 20.2%, respectively, and the Oenanthe javanica bed showed the highest efficiency with higher concentration of influent than others. The mean purification amount per day of each pollutant were $9.8-4.1\;g{\cdot}m^{-2}{\cdot}d^{-1}$ in BOD, $1.299-2.343\;g{\cdot}m^{-2}{\cdot}d^{-1}$ in TN, $0.085-1.821\;g{\cdot}m^{-2}{\cdot}d^{-1}$ in TP, $17.9-111.6\;g{\cdot}m^{-2}{\cdot}d^{-1}$ in SS and $0.011-0.094\;g{\cdot}m^{-2}{\cdot}d^{-1}$ in Chl-a. The purification amount per day of TN revealed the hi링hest level at the Zizania latifolia bed, and TP showed at the Acrous calamus bed. SS and Chl-a, as particulate materials, revealed the highest purification amount per day at the Oenanthe javanica bed that was high on the whole parameters. It was estimated that the purification amount per day was increased with the high concentration of influent and shoot density of macrophytes, as was shown in the purification efficiency. Correlation coefficients between purification efficiencies and hydraulic conditions (HRT and inflow rate) were 0.016-0.731 of $R^2$ in terms of HRT, and 0.015-0.868 of $R^2$ daily inflow rate. Correlation coefficients of purification amounts per day with hydraulic conditions were 0.173-0.763 of Ra in terms of HRT, and 0.209-0.770 daily inflow rate. Among the correlation coefficients between purification efficiency and hydraulic condition, the percentages of over 0.5 range of $R^2$ were 20% in HRT and in daily inflow rate. However, the percentages of over 0.5 range of correlation coefficients ($R^2$) between purification amount per day and hydraulic conditions were 53% in HRT and 73% in daily inflow rate. The relationships between purificationamount per day and hydraulic condition were more significant than those of purifi-cation efficiency. In this study, high hydraulic conditions (HRT and inflow rate) are not likely to affect significantly the purification efficiency of nutrient. Therefore, the emphasis should be on the purification amounts per day with high hydraulicloadings (HRT and inflow rate) for the improvement of eutrophic reservoir withrelatively low nutrients concentration and large quantity to be treated.