• Title/Summary/Keyword: Species-specific PCR

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Detection of Campylobacter jejuni in food and poultry visors using immunomagnetic separation and microtitre hybridization

  • Simard, Ronald-E.
    • Proceedings of the Korean Society of Fisheries Technology Conference
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    • 2000.05a
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    • pp.71-73
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    • 2000
  • Campylobacter jejuni is most frequently identified cause of cause of acute diarrhoeal infections in developeed countries, exceeding rates of illness caused by both salmonella and shigilla(Skirrow, 1990 ; Lior 1994). Previous studies on campylobacter jejuni contamination of commercial broiler carcasses in u.s.(Stern, 1992). Most cases of the disease result from indirect transmission of Campylobactor from animals via milk, water and meat. In addition to Campylobactor jejuni. the closely relates species Campylobactor coli and Campylobactor lari have also been implicated as agents of gastroenteritis in humans. Campylobactor coli represented only approximately 3% of the Campylobactor isolates from patients with Campylobactor enteritis(Griffiths and Park, 1990) whereas Campylobactor coli is mainly isolated from pork(Lmmerding et al., 1988). Campylobactor jejuni has also been isolated from cases of bacteremia, appendicitis and, recently, has been associated with Guillai-Barre syndrome(Allos and Blaser, 1994; von Wulffen et al., 1994; Phillips, 1995). Studies in volunteers indicated that the infectious dose for Campylobactor jejuni is low(about 500 organisms)(Robinson, 1981). The methods traditionally used to detect Campylobactor ssp. in food require at least two days of incubation in an enrichment broth followed by plating and two days of incubation on complex culture media containing many antibiotics(Goossens and Butzler, 1992). Finnaly, several biochemical tests must be done to confirm the indentification at the species level. Therfore, sensitive and specific methods for the detection of small numbers of Campylobactor cells in food are needed. Polymerase chain reaction(PCR) assays targeting specific DNA sequences have been developed for the detection of Campylobactor(Giesendorf and Quint, 1995; Hemandex et al., 1995; Winter and Slavidk, 1995). In most cases, a short enrichment step is needed to enhance the sensitivity of the assay prior to detection by PCR as the number of bacteria in the food products is low in comparison with those found in dinical samples, and because the complex composition of food matrices can hinder the PCR and lower its sensitivity. However, these PCR systems are technically demanding to carry out and cumbersome when processing a large number of samples simutaneously. In this paper, an immunomagnetic method to concentrate Campylobactor cells present in food or clinical samples after an enrichment step is described. To detect specifically the thermophilic Campylobactor. a monoclonal antibody was adsorbed on the surface of the magnetic beads which react against a major porin of 45kDa present on the surface of the cells(Huyer et al., 1986). After this partial purification and concentration step, detection of bound cells was achieved using a simple, inexpensive microtitre plate-based hybridization system. We examined two alternative detection systems, one specific for thermophilic Campylobactor based on the detection of 23S rRNA using an immobilized DNA probe. The second system is less specific but more sensitive because of the high copy number of the rRNA present in bacterial cell($10^3-10^4$). By using specific immunomagnetic beads against thermophilic Campylobactor, it was possible to concentrate these cells from a heterogeneous media and obtain highly specific hybridization reactions with good sensitivity. There are several advantages in using microtitre plates instead of filter membranes or other matrices for hybridization techniques. Microtitre plates are much easier to handle than filter membranes during the adsorption, washing, hybridization and detection steps, and their use faciilitates the simultanuous analysis of multiple sample. Here we report on the use of a very simple detection procedure based on a monoclonal anti-RNA-DNA hybrid antibody(Fliss et al., 1999) for detection of the RNA-DNA hybrids formed in the wells.

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Selective Detection of Salmonella sp. and Salmonella Typhimurium in Meat by Polymerase Chain Reaction (PCR을 이용한 육류 내 Salmonella sp. 및 Salmonella Typhimurium 분리 검출)

  • Joo, Jong-Won;Hong, Kyung-Pyo;Kim, Yong-Hui;Cho, Sang-Buem
    • Journal of the East Asian Society of Dietary Life
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    • v.19 no.2
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    • pp.295-300
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    • 2009
  • The specificity and sensitivity of oligonucleotide primers were examined for the rapid detection of Salmonella in meat samples. The oligonucleotide primers used in this study were designed with the modification of mdh and invA sequence in the chromosome of Salmonella Typhimurium. Through the subsequent analysis of the specificity and sensitivity of the primers, two types of oligonucleotide primers, SLM1 and SLT4 were selected for the detection of Salmonella genus specific and S. Typhimurium species specific, respectively. The lowest detection limit of each primer was represented as 1 cell per reaction when reacted with a prepared DNA solution. The detection efficiency of the two primers was analysed with beef and pork samples intentionally contaminated with a mixture of Salmonella culture, and three preparation methods -, namely direct reaction after extraction, enrichment after extraction, and DNA extraction after enrichment for PCR reaction, - were also compared. No differences were found in the results according to meat sources and preparation methods.

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Molecular Identification and Sequence Analysis of Coat Protein Gene of Ornithogalum mosaic virus Isolated from Iris Plant

  • Yoon, Hye-In;Ryu, Ki-Hyun
    • The Plant Pathology Journal
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    • v.18 no.5
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    • pp.251-258
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    • 2002
  • A potyvirus was isolated from cultivated Iris plants showing leaf streak mosaic symptom. Reverse transcription and polymerase chain reaction (RT-PCR) product of 1 kb long which encoded partial nuclear inclusion B and N-terminal region of viral coat protein (CP) genes for potyviruses was successfully amplified with a set of potyvirus-specific degenerate primers with viral RNA samples from the infected leaves: The RT-PCR product was cloned into the plasmid vector and its nucleotide sequences were determined. The nucleotide sequence of a CDNA clone revealed that the virus was an isolate of Ornithogalum moseic virus (OrMV) based on BLAST search analysis and was denoted as OrMV Korean isolate (OrMV-Ky). To further characterize the CP gene of the virus, a pair of OrMV-specific primers was designed and used for amplification of the entire CP gene of OrMV-Kr, The virus was easily and reliably detected from virus-infected Iris leaves by using the RT-PCR with the set of virus-specific primers. The RT-PCR product of the CP gene of the virus was cloned and its sequences were determined from selected recombinant CDNA clones. Sequence analysis revealed that the CP of OrMV-Kr consisted of 762 nucleotides, which encoded 253 amino acid residues. The CP of OrMV-Ky has 94.1-98.0% amino acid sequence identities (20 amino acid alterations) with that of other three isolates of OrMV, Two NT rich potential N-glycosylation motif sequences, NCTS and NWTM, and a DAC triple box responsible for aphid transmission were conserved in CPs of all the strains of OrMV. The virus has 58.5-86.2% amino acid sequence identities with that of other 16 potyviruses, indicating OrMV to be a distinct species of the genus. OrMV-Ky was the most related with Pterostylia virus Yin the phylogenetic tree analysis of CP at the amino acid level. This is the first report on the occurrence of OrMV in Iris plants in Korea. Data in this study indicate that OrMV is found in cultivated Iris plants, and may have mixed infection of OrMV and Iris severe mosaic virus in Korea.

Identification of Yeasts Isolated from Wild Flowers Collected in Coast Areas of Korea Based on the 26S rDNA Sequences (우리나라 일부 해안 지역 야생화들로부터 분리한 효모들의 분자 생물학적 동정)

  • Min, Jin Hong;Lee, Hyang Burm;Lee, Jong Soo;Kim, Ha Kun
    • The Korean Journal of Mycology
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    • v.41 no.3
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    • pp.185-191
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    • 2013
  • Several yeast colonies were isolated from wild flowers collected from East, West and South coast areas of Korea by plating of flower suspensions on the YPD plates containing antibiotics, streptomycin and ampicillin. Polymerase chain reactions (PCR) were performed for the amplification of D1/D2 region of 26S rDNA for those colonies. PCR-amplified nucleotide sequences were compared using BLAST for their identification. As results, 27 yeast strains belonged to 15 species were isolated from wild flowers collected at Donghae, where is located in eastern coast of Korea. Also, 34 strains belonged to 17 species were isolated from wild flowers of Daecheon, where is located in western coast of Korea. In addition, 22 strains belonged to 13 species were isolated from wild flowers collected at Wando, where is located in southern coast of Korea. Among those 45 species isolated from 3 different collection sites, only 4 species including Cryptococcus laurentii, Metschnikowia koreensis, Pseudozyma rugulosa, and Rhodotorula mucilaginosa were found from all 3 different collection sites. And 5 species including Cryptococcus aureus, Cryptococcus flavus, Hanseniaspora uvarum, Pichia guilliermondii, and Rhodosporidium fluviale were overlapped from the at least 2 different collection sites. Other 23 species were found only in a specific collection sites implying that each area has distinctive yeast flora.

Genomic Polymorphisms of Genome DNA by Polymerase Chain Reaction-RAPD Analysis Using Arbitrary Primers in Rainbow Trout (PCR-RAPD 기법에 의한 무지개송어 Genome DNA 의 다형현상)

  • Yoon, J.M.
    • Korean Journal of Animal Reproduction
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    • v.23 no.4
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    • pp.303-311
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    • 1999
  • Nuclear DNA was isolated from the sperm cells representing genetic characteristics and genomic polymorphisms of rainbow trout by polymerase chain reaction(PCR) amplification of DNA using arbitrary primers. Genomic DNA fingerprints were generated from rainbow trout sperm DNA by polymerase chain reaction amplification using 20 arbitrary decamers as primers. Out of these primers, 4 generated 17 highly reproducible RAPD markers, producing almost six polymorphic bands per primers. Four of 6 primers tested generated amplified fragments which were polymorphic between different individuals. Polymorphic DNA fragments were reproducibly amplified from independent DNA preparations made from individuals. Rainbow trout was distinctly observed 3 specific DNA markers (2. 3, 2.0 and 1.3kb) in bandsharing. Individual fragments generated using the same arbitrary primer, demonstrated that a single primer detected at least three independent genomic polymorphisms in rainbow trout sperm DNA. The RAPD polymorphism generated by this primer may be used as a genetic marker for individual identification The RAPD-PCR technique has been shown to reveal informative polymorphism in many species of fish. The present results demonstrate that RAPD markers are abundant, reproducible and provide a basis for future gene mapping and MAS in these important aquaculture species using RAPD polymorphic markers. It is concluded that RAPD polymorphisms are useful as genetic markers for fish breed differentiation.

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Discovery of a new primer set for detection and quantification of Ilyonectria mors-panacis in soils for ginseng cultivation

  • Farh, Mohamed El-Agamy;Han, Jeong A.;Kim, Yeon-Ju;Kim, Jae Chun;Singh, Priyanka;Yang, Deok-Chun
    • Journal of Ginseng Research
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    • v.43 no.1
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    • pp.1-9
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    • 2019
  • Background: Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. The development of new methods to reveal the existence of the pathogen before cultivation is started is essential. Therefore, a quantitative real-time polymerase chain reaction method was developed to detect and quantify the pathogen in ginseng soils. Methods: In this study, a species-specific histone H3 primer set was developed for the quantification of I. mors-panacis. The primer set was used on DNA from other microbes to evaluate its sensitivity and selectivity for I. mors-panacis DNA. Sterilized soil samples artificially infected with the pathogen at different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. Results: The designed primer set was found to be sensitive and selective for I. mors-panacis DNA. In artificially infected sterilized soil samples, using quantitative real-time polymerase chain reaction the estimated amount of template was positively correlated with the pathogen concentration in soil samples ($R^2=0.95$), disease severity index ($R^2=0.99$), and colony-forming units ($R^2=0.87$). In natural soils, the pathogen was recorded in most fields producing bad yields at a range of $5.82{\pm}2.35pg/g$ to $892.34{\pm}103.70pg/g$ of soil. Conclusion: According to these results, the proposed primer set is applicable for estimating soil quality before ginseng cultivation. This will contribute to disease management and crop protection in the future.

Distribution of Rickettsia spp. in Ticks from Northwestern and Southwestern Provinces, Republic of Korea

  • Jiang, Ju;Choi, Yeon-Joo;Kim, Jeoungyeon;Kim, Heung-Chul;Klein, Terry A;Chong, Sung-Tae;Richards, Allen L.;Park, Hye-Jin;Shin, Sun-Hye;Song, Dayoung;Park, Kyung-Hee;Jang, Won-Jong
    • Parasites, Hosts and Diseases
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    • v.57 no.2
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    • pp.161-166
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    • 2019
  • This study was done to characterize distribution of Rickettsia spp. in ticks in the northwestern and southwestern provinces in the Republic of Korea. A total of 2,814 ticks were collected between May and September 2009. After pooling, 284 tick DNA samples were screened for a gene of Rickettsia-specific 17-kDa protein using nested PCR (nPCR), and produced 88 nPCR positive samples. Of these positives, 75% contained 190-kDa outer membrane protein gene (ompA), 50% 120-kDa outer membrane protein gene (ompB), and 64.7% gene D (sca4). The nPCR products of ompA, ompB, and sca4 genes revealed close relatedness to Rickettsia japonica, R. heilongjiangensis, and R. monacensis. Most Rickettsia species were detected in Haemaphysalis longicornis. This tick was found a dominant vector of rickettsiae in the study regions in the Republic of Korea.

Analysis of Mitochondrial DNA Sequence and Molecular Marker Development for Identification of Panax Species (미토콘드리아 DNA 염기서열 변이를 이용한 인삼 종 판별 연구)

  • Jo, Ick Hyun;Bang, Kyong Hwan;Kim, Young Chang;Kim, Jang Uk;Shin, Mi Ran;Moon, Ji Young;Noh, Bong Soo;Hyun, Dong Yun;Kim, Dong Hwi;Cha, Seon Woo;Kim, Hong Sig
    • Korean Journal of Medicinal Crop Science
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    • v.21 no.2
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    • pp.91-96
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    • 2013
  • This study describes the identification of Panax species using mitochondrial consensus primers. Initially, a total of thirty primers were tested in ten Korean ginseng cultivars and two foreign Panax species, P. quinquefolius and P. notoginseng. In the polymerase chain reaction (PCR) amplification results, three primers (cox1, nad1/2-3 and nad2/1-2) generated co-dominant polymorphic banding patterns discriminating Korean ginseng cultivars from P. quinquefolius and P. notoginseng. However, these primers could not generated polymorphisms among the Korean ginseng cultivars, and simply represented species-specific polymorphisms for P. quinquefolius and P. notoginseng. Primers PQ91 and PN418 were designed from the consensus sequence of nad1/2-3 region. Two banding patterns (A or B) were detected in PQ91. Korean ginseng cultivars and P. notoginseng shared the same banding pattern (A type) and P. quinquefolius was identified another banding pattern (B type). In the case of PN418, two banding patterns (A or B) were detected in the Korean ginseng cultivars and two foreign Panax species. Korean ginseng cultivars and P. quinquefolius shared the same banding pattern (A type) and P. notoginseng was identified another banding pattern (B type). The combination banding patterns of three Panax species, Korean ginseng cultivars (Panax ginseng C. A. Mey.), P. quinquefolius and P. notoginseng, was identified as 'AA', 'BA' and 'AB', respectively. Consequently, PQ91 and PN418 primer sets can be used to distinguish among Panax species.

Detection of Pathogenic Yersinia Enterocolitica in Drinking Water and Vegetables by Mutiplex-PCR (Multiplex-PCR에 의한 먹는샘물 및 야채류로부터의 병원성 Yersinia enterocolitica의 신속검출)

  • 이택수;박부길;오덕환
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.32 no.1
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    • pp.35-41
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    • 2003
  • The study was conducted to develope a rapid method for the detection of Yersinia enterocolitica in spring water and vegetables via multiplex polymerase chain reaction (PCR) technique using ail, yst, uirF and subgenus-specific Y16S primers. Specificity and sensitivity of multiplex PCR and application of best primers for the detection of Y. enterocolitica from spring water and vegetables were investigeted. Y. enterocolitica ATCC 27729 strains gave 356 bP and 200 bp (Y16S) and 134 bp (yst) bands. but Y. enterocolitica ATCC 9610 and ATCC 23715 strains gave 200 bp and 134 bp bands.In the meanwhile, non-pathogenic Yersinia species, such as Y. frederikseni, Y. inter-media, Y. kristenseni and Y. pseudotuberculosis gave only single 200 bp band, and other bacteria including Escherichia coli O157:H7 ATCC 25392, Shigella dysenteri. Staphylococcu aureus ATCC 25923 and Listeria mo-nocytogenes ATCC 19111 did not show any bands. Among primers, yst and Y16S primer showed the best sensitivity. Seven CFU/mL Y. enterocolitica cells could be detected with yst and Y16S primers and the sensitivity was significantly improved by the further 2nd PCR after 38 cycles of first PCR amplication. Spring water, cabbage and mushroom were inoculated with Y. enterocolitica to determine the sensitivity of multiplex-PCR for the rapid detection of Y. enterocolitica. Multiplex-PCR assay could detect 7 or 70 cells in spring water and vegetables using whole cell lysate with repeating PCR amplication.

Development of EvaGreen Based Real-time PCR Assay for Detection and Quantification Toxic Dinoflagellate Pfiesteria Piscicida and Field Applications (유독 와편모조류 Pfiesteria Piscicida 탐지 및 정량 분석을 위한 EvaGreen 기반 Real-time PCR기법 개발과 현장 적용)

  • PARK, BUM SOO;JOO, JAE-HYOUNG;KIM, MYO-KYUNG;KIM, JOO-HWAN;KIM, JIN HO;BAEK, SEUNG HO;HAN, MYUNG-SOO
    • The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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    • v.22 no.1
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    • pp.31-44
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    • 2017
  • Pfiesteria piscicida is one of heterotrophic dinoflagellate having toxic metaboliges, and it is difficult to detect and quantify this dinoflagellate via light microscope due to small size and morphological similarity with Pfiesteria-like dinoflagellate (PLD) species. Alternatively, we developed quantitative real-time PCR assay based on EvaGreen and determined field accessibility throughout the investigation of distribution in the entire Korean coastal waters and population dynamics in Shihwa Lake. The P. piscicida-specific primers based on internal transcribed spacer 1 (ITS 1) were designed and the specificity of primers was confirmed by PCR with other genomic DNAs which have genetic similarity with target species. Through real-time PCR assay, a standard curve which had a significant linear correlation between log cell number and $C_T$ value ($r^2{\geq}0.999$) and one informative melting peak ($88^{\circ}C$) were obtained. These results implies that developed real-time PCR can accurately detect and quantify P. piscicida. Throughout the field applications of real-time PCR assay, P. piscicida was distributed in western (Mokpo and Kimje) and easthern (Gangneng) Korean coastal water even though light microscopy failed to identify P. piscicida. In the investigation of population dynamics in Shihwa Lake, the density of P. piscicida was peaked in June, July and August 2007 at St. 1 where salinity (${\leq}15psu$) was lower than the other 2 sites. In this study, we successed to develop EvaGreen bassed real-time PCR for detection and quantification of P. piscicida in fields, so this developed assay will be useful for various ecological studies in the future.