• Journal of Animal Science and Technology
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• 제48권5호
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• pp.637-650
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• 2006

한국의 예산과 당진에서 각각 채취된 붕어 (Carassius auratus)와 떡붕어 (Carassius cuvieri)로부터 genomic DNA를 분리 추출하여 반복해서 PCR로 증폭시켰다. 선택된 7개의 RAPD primer를 이용하여 primer 당 total loci, shared loci by each species, polymorphic 및 specific loci를 얻어냈다. 2종의 붕어로부터 primer와 2지역간에 banding patterns의 복잡성이 두드러지게 나타났다. DNA fragment의 분자적 크기는 150bp에서부터 1,600bp까지 커다란 차이를 나타내었다. 본 연구에서 CCY 붕어 종에서는 458개의 loci가 나타났고, CCD 떡붕어 종에서는 358개의 loci가 확인되었다. 또한 CCY 붕어 종에서는 84개의 polymorphic loci (18.3%)가 확인되었고, CCD떡붕어 종에서는 48개의 polymorphic loci (13.4%)가 확인되었다. CCY 붕어 종에서는 154개의 shared loci가 나타났으며, 이는 primer당 평균적으로 22개의 loci로 확인되었다. 또한 CCD떡붕어 종에서는 187개의 shared loci가 확인되었고, 평균해서 primer 당 26.7개의 loci가 나타났다. CCY붕어 종과 CCD 떡붕어 종의 polymorphic loci는 각각 84개와 48개로 확인되었다. 모든 붕어와 떡붕어 시료의 평균적인 BS value를 기초로 해서 CCY 붕어 종의 similarity matrix를 조사해 본 결과 0.434로부터 0.868까지 나타났고, CCD 떡붕어 종의 값은 0.449로부터 0.924까지 확인되었다. CCY 붕어 종내의 평균적인 BS value는 0.641±0.013이고, CCD 떡붕어 종내의 BS value의 평균값은 0.684±0.013을 나타내었다. 결과적으로 CCD 떡붕어 종내의 개체의 BS value 평균값이 CCY 붕어 종내의 평균값보다 높게 나타났다. 2 붕어와 떡붕어간의 평균적인 BS value은 0.484±0.007 (0.307～0.682)를 나타내었다. 7개의 primer를 사용하여 얻어진 dendrogram은 cluster 1 (AURATUS no. 01～AURATUS no. 11), cluster 2 (CUVIERI no. 12～CUVIERI no. 21) 및cluster 3 (CUVIERI no. 22)와 같이 3개의 유전적 클러스터로 나뉘어졌다. CCY 붕어 종내의 8번째 개체 (AURATUS no. 08)와 9번째 개체 (AURATUS no. 09) 사이가 가장 가까운 유전적 관계 (0.064)를 나타내었다. 또한 CCY붕어 종의 11번째(AURATUS no. 11)와 CCD떡붕어 종의 17번째 (CUVIERI no. 17) 사이가 가장 먼 유전적 거리 (0.477)를 나타내었다. 결과적으로 볼 때 한국 및 대서양산 lobster (0.612), 갈치 (0.708), 동자개(0.714)에 비해서 상대적으로 낮은 유전적 거리를 나타내었다.

• Parasites, Hosts and Diseases
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• 제51권6호
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• pp.689-694
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• 2013

Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at $82.4{\pm}0.09^{\circ}C$ and $85.9{\pm}0.08^{\circ}C$ for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens.

• Parasites, Hosts and Diseases
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• 제60권2호
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• pp.143-147
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• 2022

Acanthamoeba keratitis (AK) is a rare ocular disease, but it is a painful and sight-threatening infectious disease. Early diagnosis and adequate treatment are necessary to prevent serious complications. While AK is frequently diagnosis via several PCR assays or Acanthamoeba-specific antibodies, a more specific and effective diagnostic method is required. This study described the production of a polyclonal peptide antibody against the periplasmic binding protein (PBP) of A. castellanii and investigated its diagnostic potential. Western blot analysis showed that the PBP antibody specifically reacted with the cell lysates of A. castellanii. However, the PBP antibody did not interact with human corneal epithelial (HCE) cells and the other 3 major causative agents of keratitis. Immunocytochemistry (ICC) results revealed the specific detection of A. castellanii trophozoites and cysts by PBP antibodies when A. castellanii were co-cultured with HCE cells. PBP antibody specificity was further confirmed by co-culture of A. castellanii trophozoites with F. solani, S. aureus, and P. aeruginosa via ICC. The PBP antibody specifically reacted with the trophozoites and cysts of A. polyphaga, A. hatchetti, A. culbertsoni, A. royreba, and A. healyi, thus demonstrated its genus-specific nature. These results showed that the PBP polyclonal peptide antibody of A. castellanii could specifically detect several species of Acanthamoeba, contributing to the development of an effective antibody-based AK diagnostics.

• 식물병연구
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• 제7권1호
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• pp.1-7
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• 2001

1998년 수원 근교에서 채집한 전형적인 모자이크 병징을 나타내는 수국(Hydragea macrophylla for. otaksa)으로부터 CMV를 분리하고, Hm-CMV라 명명하였다. 기주실험, 물리적 실험, 혈청학적 성질, RNA와 coat protein의 성질, RT-PCR 및 RAP-PCR 분석을 통하여 Hm-CMV의 특성을 분석하였다. 12종의 CMV 지표식물에서 실시한 기주반응실험의 결과, 지금까지 보고된 CMV 계통들의 반응과 특징적인 차이는 인정되지 않았다. Hm-CMV의 물리적 성질은 내열성에서 6$0^{\circ}C$를 보여 기존 CMV들 보다 낮았다. 혈청학적으로 Hm-CMV는 Y-CMV와 융합하는 subgroup I CMV로 분석되었다. SDS-PAGE로부터에 Hm-CMV의 외피단백질은 28 kDa의 band가 확인되었으며, 4종의 게놈 RNA는 Y-CMV와 같은 분자량을 나타냈으나, 위성 RNA는 존재하지 않았다. 수국의 이병엽에서 분리한 dsRNA의 분석 결과도 Y-CMV와 같은 패턴을 보였다. Hm-CMV의 외피단백질유전자에 대한 RT-PCR 분석 결과, 예상된 분자크기의 DNA 증폭이 인정되었으며, PCR 산물을 이용한 EcoR I 및 Msp I을 처리한 결과는 subgroup I CMV의 특성을 나타냈다. 그런, RAP-PCR의 결과, Hm-CMV는 subgroup I내의 다른 계통들과 구분되었다.

• 한국수산과학회지
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• 제47권5호
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• pp.522-526
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• 2014

Pyropia, economic red algae species, have been cultivated in Korea (referred to as 'gim'), Japan ('nori'), and China ('zicai') for over 300 years. Vegetable seaweed Pyropia species are sold in the public markets in various forms as commercial seafoods. In Korea, two kinds of Pyropia seafood made with species of Pyropia and Ulva (sea lettuce, referred to as 'parae') are also sold. These are referred to as 'parae-gim' (with Pyropia spp. and U. linza) and 'gamtaegim' (with Pyropia spp. and U. prolifera). There is currently no method for identifying the seaweed species that comprise Pyropia seafood products. Therefore, we developed novel molecular markers to identify Ulva species in commercial Pyropia seafoods. Based on rbcL molecular markers, we identified informative characteristics to discriminate U. linza and U. prolifera as seafood ingredients. Moreover, PCR with 3'-end mismatch primers successfully isolated the specific rbcL sequences of U. linza and U. prolifera from Pyropia seafoods. Therefore, our novel molecular markers will be useful for identifying the ingredient species of commercial seafoods.

• 한국동물위생학회지
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• 제33권3호
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• pp.223-231
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• 2010

A total of 191 samples collected from the commercial swine farms located in Chungnam province were investigated by PCR to estimate the prevalence of Lawsonia (L.) intracellularis infection. In the group of the pigs with proliferative enteritis, 14 (93.3%) of 15 intestinal samples and 12 (80.0%) of 15 feces were positive in PCR. In contrast, a relatively low positive rate (18.0%, 29 of 161 samples) was determined in the group of normal healthy pigs. The group of pigs over 120 days showed the highest positive rates (26.8%, 15 of 56 samples). In the comparison of the sequences of 210bp for species specific fragments and 301bp for outer membrane protein, the isolates (L1. L2) showed almost 100% identity with the reference L. intracellularis (L08049, USA). For the sequences of partial 16s rDNA, the homologies among the 5 isolates (L1-L5) were 97.4% to 99.3%, and those of 5 sequences (L1-L5) versus 5 overseas reference strains of L. intracellularis ranged from 98.6% to 99.8%. In the comparison of the nucleotide sequences among 5 isolates and other species in Desulfovibrionales showed 82.4 to 99.5% identities. The 5 isolates shared relatively low identities (76.9% to 84.4%) with the species of alpha-proteobacteria. In phylogenetic analysis based on the 16s rDNA sequences, all of the 5 isolates (L1-L5) were located in the same branch with the strains of L. intracellularis that were previously isolated from the pigs in USA and China. Seven strains of Desulfovibrio sp. were clustered in the neighboring branches, whereas alpha and gamma Proteobacteria showed distant relationship with L. intracellularis strains. The present findings suggest that L. intracellularis infection is endemic in the swine farms in the regions, and that the domestic isolates maintained very limited genetic variation.

• Journal of Microbiology and Biotechnology
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• 제17권5호
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• pp.753-760
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• 2007

The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer(12 and 120 kg/ha). Two cultivars(IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two(FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene(rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars(IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.

• 한국약용작물학회지
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• 제26권4호
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• pp.302-307
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• 2018

Background: A soil-borne pathogenic fungus, Ilyonectria radicicola (Cylindrocarpon destructans) causes root rot on ginseng (Panax ginseng C. A. Meyer) and is known to attack many other plants. The Nectria/Neonectria radicicola complex has been renamed as the I. radicicola complex after analysis of its multi-gene relatedness and morphological characteristics. The fungi in this complex have been reclassified into 16 species under the genus Ilyonectria based on characteristics analysis Methods and Results: To obtain useful data from the Korean ginseng root rot, I. radicicola was isolated from the rhizosphere soils of the chestnut tree. They were identified through a pathogenicity test and a survey of the morphological features. The existence of I. radicicola in soil samples was confirmed by PCR detections using nested PCR with species-specific primer sets. These were subsequenctly isolated on semi-selective media from PCR-positive soils. Genetic analysis of the I. radicicola complex containing these pathogens was done by comparing the DNA sequences of the histone h3 region. These isolates originating from the rhizosphere soils of chestnut constituted a clade with other closely related species or I. radicicola isolates originating from ginseng or other host plants, respectively. Additionally, the pathogenicity tests to analyze the characteristics of these I. radicicola isolates revealed that they caused weakly virulent root rot on ginseng. Conclusions: This is the first study reporting that I. radicicola isolates from chestnut rhizosphere soils can attack ginseng plant in Korea. Thus, these results are expected to provide informations in the selection of suitable fields for ginseng cultivation.

• Journal of Microbiology and Biotechnology
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• 제28권12호
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• pp.1992-1998
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• 2018

In 2015, Bacillus paralicheniformis was separated from B. licheniformis on the basis of phylogenomic and phylogenetic studies, and urease activity was reported as a phenotypic property that differentiates between the two species. Subsequently, we have found that the urease activity of B. paralicheniformis is strain-specific, and does not reliably discriminate between species, as strains having the same urease gene cluster were identified in B. licheniformis and B. sonorensis, the closest relatives of B. paralicheniformis. We developed a multilocus sequence typing scheme using eight housekeeping genes, adk, ccpA, glpF, gmk, ilvD, pur, spo0A, and tpi to clearly identify B. paralicheniformis from closely related Bacillus species and to find a molecular marker for the rapid identification of B. paralicheniformis. The scheme differentiated 33 B. paralicheniformis strains from 90 strains formerly identified as B. licheniformis. Among the eight housekeeping genes, spo0A possesses appropriate polymorphic sites for the design of a B. paralichenofomis-specific PCR primer set. The primer set designed in this study perfectly separated B. paralicheniformis from B. licheniformis and B. sonorensis.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.125.1-125
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• 2003

Pepper anthracnose is one of the major limiting factors in pepper production. Boring last over 10 years, Colletotrichum gloeosporioides has been known as the most prevalent species among five Colletotrichum spp. involved as anthracnose causing agents. Recently, however, the change of major species with pepper anthracnose has been proposed. Identification study was peformed on 12 test isolates collected from anthracnose disease symptoms on pepper during 2001-2002 and 25 reference isolates obtained from several other host plants. The identification of the isolates with morphological observation and IfS region sequence comparison resulted that 11 ones from 12 test isolates colleted from pepper anthracnose during 2001-2002 were identified as C. acutatum. PCR using species-specific primers designed from ITS region sequence suggested a rapid diagnosis method in identifying C. acutatum from C. gloeosporioides.