• Research in Plant Disease
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• v.23 no.1
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• pp.75-81
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• 2017

In May 2016, 24 peach samples showing abnormal and virus like symptoms were collected in one of major peach producing area, Yeongcheon-si, Gyeongsangbuk-do, Korea. We performed RT-PCR diagnosis for confirmation of viral infection. The diagnostic targets are 17 species of viruses and viroids that quarantine and high risk pathogens when it occur. As a results, seven species of viruses and viroids, including an unreported (Apricot pseudo-chlorotic leaf spot virus, APCLSV) and a quarantine (Peach latent mosaic viroid, PLMVd) species in Korea, were detected. For the sequence analysis of unreported virus, APCLSV, the sequence of coat protein gene were amplified and cloned. The sequence showed 97% nucleotide identity with other APCLSV isolates and compared with other seven species of reported Trichoviruses. This virus was classified as APCLSV based on the sequence and phylogenetic analysis. This isolate was named Yeongcheon. As patterns of APCLSV occurrence, all samples that APCLSV detected were co-infected with Apple chlorotic leaf spot virus (ACLSV). As properties of ACLSV, APCLSV has high possibility of wide spread disease in fruit tree farms in Korea. Therefore, it is necessary to do related researches, such as infection route and influence of disease in commercial orchards.

• Microbiology and Biotechnology Letters
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• v.38 no.3
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• pp.322-328
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• 2010

Fermented skate is a traditional Korean food popular in Southwestern area of Korea. It has a characteristic flavor and alkaline pH. In this study we tried to determine the microbial flora in fermented skate using two different approaches. In culture-independent method, we amplified V2 region of 16S rRNA gene by PCR and cloned them into pUC18 plasmid to construct 16S rDNA fragment library. BLAST searches for the sequences obtained from this library revealed that uncultured bacterium clone 054E11.b was the most dominant flora in this fermented fish. In culture-dependent method, we diluted suspension of skate and spreaded on MRS, PCA, and MacConkey plates. We identified colonies grown on those plates by using PCR amplification of V2 region of 16S rRNA and DNA sequencing. BLAST searches of those DNA sequences resulted in totally different species with the observations from the 16S rDNA library analysis. Discrepancies of results obtained from both approaches suggest that the agar plates used in culture-dependent method may be different from the real condition of fermented skate. Therefore, results from culture-independent approach using 16S rDNA fragment library analysis may reflect real microbial flora in fermented skate.

• Journal of Science Criminal Investigation
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• v.11 no.3
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• pp.210-217
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• 2017

In the forensic microbiology laboratories, microorganism analyses from food are requested. There have been several cases of Bacillus cereus isolated from the samples requested to the National Forensic Service. B. cereus is an important pathogenic bacterium which can cause food-borne outbreaks. Therefore, we isolated B. cereus from anchovy aekjeot recently requested for microbial examination and identified using MSId based on the 16S rDNA sequence and real-time PCR method. We also conducted PCR for detection of diarrheal toxin genes and an emetic toxin gene and found the presence of nheABC, bceT and entFM diarrheal toxin genes in the B. cereus isolate. There are several clinically important food-poisoning bacteria that should be noted during inspection. In particular, B. cereus can cause food poisoning even when cooked foods are ingested, because B. cereus forms endo-spore which confers strong environmental resistance and heat resistance to the bacteria, and the bacterial emetic toxin also has heat resistance. Here we highlight the importance to distinguish clinically important bacteria such as B. cereus from food specimens, and we expect this study will provide procedures for identification of B. cereus and detection of the bacterial toxin genes for future cases in the forensic microbiology laboratories.

• Journal of fish pathology
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• v.33 no.2
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• pp.119-125
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• 2020

During the period from 2003 to 2020, a total of 470 Streptococcus species were isolated from farmed flounder in Jeju. Out of 470 isolates, 92 (19.6%) isolates and 378 isolates (80.4%) were identified as Streptococcus iniae and S. parauberis, respectively by multiplex PCR assay. During that period, the percentage of S. iniae decreased from 56.9% in 2003 to 0.0% in 2020 whereas that of S. parauberis increased from 43.1% in 2003 to 100% in 2020. In the PCR assay for serotyping, the isolated S. parauberis showed 3 subserotypes, Ia (34.9%), Ib/Ic (46.3%) and II (18.8%). In 2003 and 2004, serotype II was dominant at 59.1% and 50.0% of isolation rates, however between 2005 and 2009, subserotype Ib/Ic was dominant (57.6%, 86.0%, 84.6%, 57.9%, and 83.3%). After 2010, except for 2015, subserotype Ia was the most dominant one. In the last 3 years (2018 to 2020), subserotype Ia was most abundant (70%), followed by subserotype Ib/Ic (16-30%). Serotype II was not isolated in 2018, but in 2019 and 2020, it showed an increased tendency to 3.4% and 16.7%, respectively. It is believed that continuous monitoring is necessary for research on counter-measures against streptococcosis of flounder.

• Journal of the Korea Organic Resources Recycling Association
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• v.18 no.3
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• pp.31-37
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• 2010

Chitinases (EC 3.2.1.14) hydrolyze the ${\beta}$-1,4-linkages in chitin, the second most abundant polymer of N-acetyl-${\beta}$-D-glucosamine which is a structural component of protective biological matrices such as fungal cell walls and insect exoskeletons. The glycosyl hydrolases 18 family including chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Since earthworms live in the soil with a lot of microbial activities and fungi are supposed to be a major component of the diet of earthworm, it has been reported that there would be appropriate immune system to protect themselves from microorganisms attacks. In this study, the novel chitinase, EaChi, from the midgut of earthworm, Eisenia andrei, were identified and characterized. To obtain full-length cDNA sequence of chitinase, RT-PCR and RACE-PCR analyses were carried out by using the previously identified EST sequence amongst cDNA library established from the midgut of E. andrei. EaChi, a partial chitinase gene, was composed of 927 nucleotides encoding 309 amino acids. By the multiple sequence alignments of amino acids with other different species, it was revealed that EaCHI is a member of glycosyl hydrolases 18 family, which has two highly conserved domains, substrate binding and catalytic domain.

• Restorative Dentistry and Endodontics
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• v.24 no.1
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• pp.13-25
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• 1999

P. endodontalis which was known to be associated with the infected root canals and periapical lesions is very difficult to detect by culture methods or traditional methods. Detection of bacteria using polymerase chain reaction(PCR) for 16S ribosomal DNA(rDNA) is fast, simple, and accurate with relatively small amount of target cells. 16S rDNA consist of conserved regions those are same to all species, and variable regions which represent species specificity. The 16S rDNA sequences of P. endodontalis and P. gingivalis were aligned and two highly variable regions were selected as a pair of species specific oligonucleotide primers for P. endodontalis. And then the pair of primers for PCR amplification was synthesized to identify P. endodontalis. The sequences of the species specific primers for the 16S rDNA of P. endodontalis were as follows ; sense primer[endo1]: 5'-CTATATTCTTCTTTCTCCGCATGGAGGAGG-3' antisense primer[endo2]: 5'-GCATACCTTCGGTCTCCTCTAGCATAT-3' In this study, for the identification of P. endodontalis without culture from the mixed clinical samples, PCR was done with species specific primers for the 16S rDNA sequences of P. endodontalis. The results were as follows : 1. The species specificity of the primers for the 16S rDNA of P. endodntalis was determined by the PCR methods. About 490bp amplicon which was specific only for P. endodntalis was produced with P. endodontalis. No amplicon was produced by PCR with other strains similar to P. endodontalis. 2. The synthesized species specific primers reacted with conventionally identified P. endodontalis which we have in conservative dentistry laboratory. 3. The identification of P. endodontalis using PCR technique with samples collected from infected root canals or periapical lesions was more sensitive than that of culture methods. 4. Seven samples revealed including P. endodontalis by PCR technique. Five of them were related with pains, two of them with sinus tract, three of them with foul odor, and three of them with purulent drainage. P. endodontalis was shown to have great relation with pains.

• The Korean Journal of Mycology
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• v.26 no.4 s.87
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• pp.466-477
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• 1998

Twenty-two Phellinus strains were characterized using colony morphologies and polymerase chain reaction (PCR) to divide into Phellinus linteus. There were some differences in mycelial growth and colony shapes among the strains when they were grown on various media such as PDA, MCM, MEA and YM. Phellinus linteus was slowly growing, formed golden-yellow colony, and produced blue pigment on PDA media. When the regions of internal transcribed spacer (ITS) were amplified from ribosomal RNA (rRNA) coding genes of P. igniarius and P. linteus strains by means of PCR, two types of band (700 bp and 800 bp) were appeared, respectively. For the amplified intergenic region I (IGRI), P. igniarius strains showed a different band among 500, 600, 700 and 800 bp according to the strains, whereas P. linteus strains did one specific band of 700 bp. By polymorphism analysis after digesting the amplified products with 6 different restriction enzymes, a band specific to P. linteus was generated when the products for ITS region were digested with HaeIII, suggesting that the enzyme digestion could provide effective method to distinguish between P. igniarius and P. linteus. And also, the analysis of genetic relationship showed that the genetic similarities were 89% and 95% in P. igniarius and P. linteus strains, respectively. Random amplification polymorphic DNA (RAPD) analysis using multiple primer sets and arbitrarily primed PCR (AP-PCR) with ITS3 primer could also result in a reproducible way to identify P. linteus strains.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.879-883
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• 2005

This study was differentiated between Korea and China arkshells using PCR-aided RFLP method which could identify the variation for inter-and intra-species of arkshell (Scapharca broughtonii Schrenck) at the level of DNA. The DNA fragment patterns were compared after digesting gene of mitochondrial 16S rDNA with 8 kinds of restriction enzymes. A 720 bp DNA fragment corresponding to 16S rDNA gene was amplified by PCR with primers ArkF-3 and ArkR-3. PCR products were cut by restriction enzymes (Pvull, BamHI, Hinfl, HaeIII, EcoRI, RsaI, Ksp221, and BstX21), and RFLP pattern was studied. A unique 275 bp DNA band was observed in the samples from Dukyang, Gamak, Namhae, Jinhae, and Taean in Korea when treated by Hinfl, but Chinese arkshell did not show. Treatment of HaeIII could discriminate the sample of Namhae and Jinhae from Dukyang/Gamak/Taean, as well as Korean and Chinese arkshell based on a 700 bp. However, PuvII, BamHI, EcoRI, RsaI, Ksp221, and BstX21 showed the same of 700 bp band in Korean and Chinese arkshell. The phylogenetic tree inferred from PCR-RFLP pattern comparsion in Korean arkshell was different that the distance between Dukyang/Gamak/Taean and Namhae/Jinhae was approximately 7. In particular, the distance between Korean and Chinese arkshell was 25. Consequently, HinfI and HaeIII played an important role in a reliable molecular tool for rapid discriminating Korean and Chinese arkshell, as well as a intra-species in Korea.

• Journal of Veterinary Clinics
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• v.26 no.4
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• pp.391-394
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• 2009

An Asian water monitor Varanus salvator with physical wound due to bite which was subsequently infected with bacterium resulting to hemorrhage and pus in the skin blisters, abdominal distention and septicemia. Morganella morganii was isolated and identified from the blood and kidney of the reptile, and confirmed by PCR and biochemical tests. The sensitivity of isolated strains to different groups of antibiotics was also evaluated using the disc diffusion method. Pathogenicity test using M. morganii (SNUFPC-MM01) (1.6 ${\times}$ $10^{11}$CFU/mouse) to suckling and adult mice resulted to the death of all mice. This paper describes the first isolation of M. morganii from Asian water monitor in Korea.

• Research in Plant Disease
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• v.14 no.2
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• pp.134-137
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• 2008

A strain of Cucumber mosaic virus(CMV) was isolated newly from sweet pepper(Capsicum annuum var. angulosum) showing necrosis with large necrotic spots on fruits and vein banding with malformation on leaf at Cheongdo area in Gyeongsangbukdo. The new strain was designated as a CMV-NP and the shape of virus particles was isometric of 26 nm in diameter from the sweet pepper fruit by Dip method. The strain of CMV-NP was identified genetically by VC/RT-PCR. CMV-NP could infect systemically on the 9 indicator plants including Cucumis sativus, but it could infect locally on Chenopodim amaranticolor and C. quinoa. CMV-NP induced the specific symptoms of necrotic rings on the inoculated and the upper leaves of N. rustica and Tetragonia expansa. On Cucumis sativus, the large chlorotic ring and vein chlorosis were produced on the upper leaves. CMV-NP had no virulence on Datura stramonium.