• Parasites, Hosts and Diseases
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• v.46 no.3
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• pp.157-164
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• 2008

Three Acanthamoeba isolates (KA/E9, KA/E17, and KA/E23) from patients with keratitis were identified as Acanthamoeba triangularis by analysis of their molecular characteristics, a species not previously recognized to be a corneal pathogen. Epidemiologic significance of A. triangularis as a keratopathogen in Korea has been discussed. Morphologic features of Acanthamoeba cysts were examined under a microscope with differential interference contrast (DIC) optics. Mitochondrial DNA (mtDNA) of the ocular isolates KA/E9, KA/E17, and KA/E23 were digested with restriction enzymes, and the restriction patterns were compared with those of reference strains. Complete nuclear 188 and mitochondrial (mt) 16S rDNA sequences were subjected to phylogenetic analysis and species identification. mtDNA RFLP of 3 isolates showed very similar patterns to those of SH621, the type strain of A. triangularis. 16S and 18S rDNA sequence analysis confirmed 3 isolates to be A. triangularis. 18S rDNA sequence differences of the isolates were 1.3% to 1.6% and those of 16S rDNA, 0.4% to 0.9% from A. triangularis SH621. To the best of our knowledge, this is the first report, confirmed by 18S and 16S rDNA sequence analysis, of keratitis caused by A. triangularis of which the type strain was isolated from human feces. Six isolates of A. triangularis had been reported from contaminated contact lens cases in southeastern Korea.

• Journal of Plant Biology
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• v.39 no.1
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• pp.49-55
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• 1996

We have studied the DNA of Allium sativum L. with respect to highly repetitive sequences. Fast reassociated DNA fragments expected to be highly repetitive sequences based on $C_{o}t$ curve were isolated and characterized. Their copy numbers were approximately $10^{5}~10^{7}$ per haploid genome. Nucleotide sequences analysis of six candidates reveals that their G/C content were low, 25-40% and typical patterns of repeating sequences exist. Repeat sequences were used as probes to access restriction fragment length polymorphism (RFLP) of genomic DNAs of four local clones, Tanyang, Mungyong, So san, and Uisong. The hybridization pattern were very similar among these four local clones.clones.

• Journal of Microbiology
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• v.43 no.1
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• pp.1-10
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• 2005

We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of ${\gamma}-Proteobacteria$ (70.3%) and 19 strains of Firmicutes (29.7%). The ${\alpha}-Proteobacteria$ and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The ${\gamma}-Proteobacteria$ group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.51-62
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• 2019

A great variable response was observed when PP-3 and PP-J encumbered with 116 populations of root knot nematode (RKN) at two different temperatures ($25{\pm}2^{\circ}C$ and $30{\pm}2^{\circ}C$) and concentrations ($10^4$ and $10^5$ spores/ml). The PCR reaction amplified intergenic region between cytochrome oxidase subunit II gene (COII) and large subunit of rRNA gene (lrRNA) of the mitochondrial genome of different RKN species. The primer C2F3 and 1108 identified M. incognita with the highest frequency (52.6%) followed by M. javanica (36.8%) and M. arenaria (10.5%). The sizes of PCR products were 1.7 kb for M. incognita and M. javanica populations while populations of M. arenaria produced 1.1 kb fragment. The digestion with Hinf I yielded three different fragment length patterns on 1.5 % agarose gel. From current research it is concluded that intra-Meloidogyne genetic variability exist in RKN populations which have better encumbrance with P. penetrans.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.147.2-148
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• 2003

Complete nucleotide sequence of genome RNA of a Korean isolate of Pepper mottle virus (PepMoV-Vb) from field-collected diseased paprika (Capsicum annuum var grossum) was determined in this study. Symptoms of isolates of PepMoV were divided largely into two groups, vein banding (Vb) and vein clearing (Vc) patterns. PepMoV-Vb RNA consists of 9,640 nucleotides excluding the poly(A) tail. A single open reading frame was identified beginning at nucleotide position 169 encoding a polyprotein of 3024 amino acids which is typical of the Potyvirus genus. The complete nucleotide sequence and coding regions of PepMoV-Vb were compared to that of 11 potyviruses within the genus Potyvirus. The overall nucleotide sequence identity was 94.7 and 94.1％ identical to PepMoV-C and PepMoV-FL, respectively. Full-length cDNAs of PepMoV-Vbl were synthesized from purified viral RNAs by RT-PCR and their genome structure was analysed by RFLP analysis. This is the first report on complete nucleotide sequence of PepMoV isolated from paprika in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.7
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• pp.915-921
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• 2001

IGF-I is involved in the regulation of growth and differentiation in mammals, but its role as a modulator of growth and metabolism in poultry is poorly understood. And, no studies have so far been reported for the comparison between serum IGF-I concentration and body growth in the egg type or the dual purposes (meat and egg type) chicken including the Korean Native Ogol Chicken (KNOC). Therefore, in order to improve the body growth and meat production of the KNOC, this study was conducted for the identification of the polymorphism of IGF-I gene and for its possible association with both body weight and IGF-I concentration. The RFLP patterns for IGF-I gene were identified by the PstI restriction enzyme. The frequencies of +/+, +/-, and -/- genotype were 16.9%, 51.7%, and 31.4%, respectively. Any statistical significance was not observed in all variations except for sex variation (p<0.01) by covariate quadratic model. The significant effect of the IGF-I genotype on body weight by sex indicates that there are different physiological characteristics in gender. Although the body weights of male KNOCs in most ages were not significant, there was a tendency of KNOCs with +/+ IGF-I genotype to be heavier than those with any other genotypes. But all IGF-I genotypes in female did not influence on body weight. The ANOYA revealed no significant effects of IGF-I genotypes on serum IGF-I concentration but sex effect was highly significant on the IGF-I concentration at 20 and 40 weeks (p<0.01). Although the +/+ genotype, in gender, tended to express a higher IGF-I concentration than the other genotypes at all ages in males, a statistical difference among the genotypes was not found except for 60 weeks (p<0.05). Furthermore, since body weight and IGF-I genotypes are associated, it is possible to improve KNOC to a meat type breed if a continuous selection can be made for the body weight and/or IGF-I traits.

• Parasites, Hosts and Diseases
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• v.35 no.4
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• pp.277-282
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• 1997

The only observed morphological difference between Spirometra erinqsei and S. mcnsonoides is the uterine shape of the mature proglottid. Two species of worms are thought to be evolutionarily closely related. Biomolecular colnparison of the ho worms by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was conducted to observe the genetic distance. The 285 rDNA, mitochondrial cytochrome c oxidase subunit I (mCOI), and ribosomal internal transcribed spacer 1 (ITSI) fragments were obtained from the worms by PCR. The PCR products were cleaved by 5 four-base pair restriction enzyme combinations (Msp I, Hae III, Alu I, Cfo I, Rsa I) , electrophoresed and analyzed with PAUP 3.1.1. The fragment Patterns or 285 rDNA and Lni demonstrated that two worms were in identical systematic tree with bootstrap number 94 and 100, respectively As for mCOI, bootstrap number was 74 in a different tree. Above results are indicative of recent common ancestry between S. etinocei and S. mansonoides.

• Toxicological Research
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• v.32 no.1
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• pp.81-87
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• 2016

Aflatoxin B1 (AFB1) is produced by Aspergillus flavus growing in feedstuffs. Early detection of maize contamination by aflatoxigenic fungi is advantageous since aflatoxins exert adverse health effects. In this study, we report the development of an optimized conventional PCR for AFB1 detection and a rapid, sensitive and simple screening Real-time PCR (qPCR) with SYBR Green and two pairs of primers targeting the aflR genes which involved aflatoxin biosynthesis. AFB1 contaminated maize samples were divided into three groups by the toxin concentration. Genomic DNA was extracted from those samples. The target genes for A. flavus were tested by conventional PCR and the PCR products were analyzed by electrophoresis. A conventional PCR was carried out as nested PCR to verify the gene amplicon sizes. PCR-RFLP patterns, obtained with Hinc II and Pvu II enzyme analysis showed the differences to distinguish aflatoxin-producing fungi. However, they are not quantitative and need a separation of the products on gel and their visualization under UV light. On the other hand, qPCR facilitates the monitoring of the reaction as it progresses. It does not require post-PCR handling, which reduces the risk of cross-contamination and handling errors. It results in a much faster throughout. We found that the optimal primer annealing temperature was $65^{\circ}C$. The optimized template and primer concentration were $1.5{\mu}L\;(50ng/{\mu}L)$ and $3{\mu}L\;(10{\mu}M/{\mu}L)$ respectively. SYBR Green qPCR of four genes demonstrated amplification curves and melting peaks for tub1, afIM, afIR, and afID genes are at $88.0^{\circ}C$, $87.5^{\circ}C$, $83.5^{\circ}C$, and $89.5^{\circ}C$ respectively. Consequently, it was found that the four primers had elevated annealing temperatures, nevertheless it is desirable since it enhances the DNA binding specificity of the dye. New qPCR protocol could be employed for the determination of aflatoxin content in feedstuff samples.

• Journal of Wetlands Research
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• v.11 no.1
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• pp.123-130
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• 2009

Hyporheic zone is an area where hydraulic exchanges occur between surface water and ground water. Such transient area is anticipated to facilitate diverse biogeochemical reactions by providing habitats for various microorganism. However, only a few data are available about microbial properties in hyporheic zone, which would be important in better understanding of biogeochemical reactions in whole streams. The study site is Naesung stream, located in the north Kyoung-Sang Province, of which sediment is sandy with little anthropogenic impacts. Soil samples were collected from a transect placed perpendicular to stream flow. The transect includes upland fringe area dominated by Phragmites japonica, bare soil, and soil adjacent to water. In addition, soil samples were also collected from downwelling and upwelling areas in hyporheic zone within the main channel. Soils were collected from 3 depth in each area, and water content, pH, and DOC were measured. Various microbial properties including extracellular enzyme activities ($\beta$-glucosidase, N-acetylglucosaminidase, phosphatase and arylsulfatase), and microbial community structure using T-RFLP were also determined. The results exhibited a positive correlation between water content and DOC, and between extracellular enzyme activities and DOC. Distinctive patterns were observed in soils adjacent to water and hyporheic zone compared with other soils. Overall results of study provided basic information about microbial properties of hyporheic zone, which appeared to be discernable from other locations in the stream corridor.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.386-395
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• 2007

A total of 27 strains of Vibrio parahaemolyticus (18 strains isolated from Korea and 9 strains from Japan) were serotyped and examined for biochemical characteristics, antimicrobial susceptibility patterns, cytotoxicity assay, thermostable direct hemolysin (TDH) production and molecular epidemiology. Using polymerase chain reaction (PCR) method and DNA probe hybridization method, the strains were tested for toxR, tdh, trh and ORF 8 genes. The V. parahaemolyticus isolated from patients were belonged to 8 different serotypes : O3:K6, O1:K38, O3:K57, O4:K9, O4:Kl2, O4:K68, O5:Kl5 and O6:K46. Urease-positive strain possessed the trh gene, and conversely, urease-negative strains lacked the gene, indicating that urease production by V. parahemolyticus strains strongly correlates with the possession of the trh gene. Most strains showed multiple resistant to more than three antibiotics and the antibiogram could be classified into 6 group (I to VI). All of the O3:K6 strains isolated in South Korea and Japan producted TDH at high levels. The TDH titers ranged between 256 and 2.048, and the average titer was 1009. To distinguish the new and increasingly common V. parahaemolyticus strains from clinical isolates, ORF 8 is a useful genetic marker. After Southern hybridization, the HindIII restriction fragment patterns of the tdh gene were grouped one type, respectively. One type showed two bands one of which was 4.3kb and the other was 11.5kb in size. Variation between the O3:K6 serotype are minor when compared to the differences seen with the non O3:K6 strains. The migration patterns of Not I -digested of the total DNA of the O3:K6 strains were similar, and only slight variations were observed between the serotypes. By contrast, the O3:K6 strains and non O3:K6 had markedly different profiles. In conclusion, Random amplified polymorphic DNA (RAPD) profile using appropriate primers was an effective epidemiological marker.