• Journal of fish pathology
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• v.17 no.3
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• pp.159-169
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• 2004

Bacterial wihte enteritis ocurred by infection of V. ichthyoenteri is a devastating disease in olive flounder (Paralichthys olivaceus) hatcheries in Korea. Since white enteritis has been a problem in aquqtic industries, necessity of a rapid detection method is increased. In an attempt to develop rapid PCR method the detection of V. ichthyoenteri, we examined the 16S-23S rRNA intergenic spacer region(ISR) of V. ichthyoenteri and developed species-specific primer for V. ichthyoenteri. The intergenic spacers were amplified by primers complementary to conserved region of 16S and 23S rRNA genes. The intergenic spacer region between the 16S and 23S rRNA genes of V. ichthoenteri were investigated by PCR fragment length typing and DNA sequencing. Analysis of the ISR sequences showed that V. ichthyoenteri contains one types of polymorphic ISRs. The size of ISRs ranged 348bp length and not contains tRNA genes. Mutiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability, and allowed to design species-specific primer for detection of Vibrio ichthyoenteri. PCR. The specific of the primer was examined using genomic DNA prepared from 19 different Vibrio species, isolated 18group Vibrio species. The results showed that the PCR reaction using species-specific primer designed in this study can be used to detect V. ichthyoenteri.

• Korean Journal of Medicinal Crop Science
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• v.8 no.3
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• pp.266-273
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• 2000

The optimal conditions of PCR components for the random amplification of genomic DNA were $20\;ng/20{\mu}l$ in template DNAs, 250 mM in dNTP, 10 pM in primer $1.0unit/20{\mu}l$ in Taq DNA polymerase respectively with the annealing temperature at $36^{\circ}C$, respectively. Twelve local lines were divided into 3 groups by the coefficients of 107 polymophic bands by Jaccard and Nei. The coefficients value of group I including Chongup # 1, Seochon # 1, Andong # 1, Chinan # 1, and Danyang # 1 ranged from 0.27 to 0.05 and those of group II including Suwon # 2, Chunchon # 1, Japan # 3, Danyang#2 and $F_1$ (Variety Jihwang $1{\times}$ Seohchon) ranged from 0.29 to 0.11. While, Jihwang 1 originated from China and Japan # 1 in group III showed a distant genetic relationship to Korean local lines.

• Journal of Applied Biological Chemistry
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• v.44 no.4
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• pp.163-166
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• 2001

Piezoelectric (PZ) crystal biosensor system was used to detect the DNA of food pathogenic Listeria monocytogenes. L. monocytogenes-specific DNA was multiplied via the polymerase chain reaction using LM1 oligonucleotide (5'-TTACGAATTAAAAAGGAGCG-3') and LM2 oligonucleotide (5'-TTAAATCAGCAGGGGTCTTT-3') as primers. DNA fragment of 161 bp, which was specific only for L. monocytogenes, was observed. To obtain a large amount of single-stranded DNA containing an SH group used for coupling to the gold electrode chemisorptively, LM1 oligonucleotide containing a mercaptohexyl group was utilized as a single strand PCR primer. The PCR product was immobilized onto the gold electrode of PZ crystal, and hybridization was monitored in quartz crystal microbalance (QCM) system by injecting the antisense single-stranded DNA of 161 nucleotides obtained via the single strand PCR using the unmodified LM2 primer. Approximately 70 Hz of frequency drop was observed in the QCM system in the case of two consecutive injections of $5{\mu}g$ of the antisense single-stranded DNA.

• International Journal of Oral Biology
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• v.46 no.3
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• pp.140-145
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• 2021

This study aimed to develop Lautropia mirabilis-specific quantitative real-time polymerase chain reaction (qPCR) primers based on the sequence of DNA-directed RNA polymerase subunit beta gene. The PrimerSelect program was used in designing of the qPCR primers, RTLam-F4 and RTLam-R3. The specificity of the qPCR primers were performed by conventional PCR with 37 strains of 37 oral bacterial species, including L. mirabilis. The sensitivity of the primers was determined by qPCR with the serial dilution of purified genomic DNA of L. mirabilis KCOM 3484, ranged from 4 ng to 4 fg. The data showed that the qPCR primers could detect only L. mirabilis strains and as little as 40 fg of genome DNA of L. mirabilis KCOM 3484. These results indicate that this qPCR primer pair (RTLam-F4/RTLam-R3) may be useful for species-specific detection of L. mirabilis in epidemiological studies of oral bacterial infectious diseases such as periodontal disease.

• The Korean Journal of Mycology
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• v.27 no.5 s.92
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• pp.337-340
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• 1999

The context and upper surface of Phellinus basidiocarp become blackened, rimose and woody. The basidiocarp is sessile, dimidiate and elongate. The basidiospores are pigmented and ovoid to globose. Hymenial setae are $17{\sim}35{\times}6{\sim}8{\mu}m$. Nineteen isolates of Phellinus species, including Phellinus linteus, were used for sequencing of the internal transcribed spacer (ITS) region of the nuclear rDNA. Based on these sequence data, specific primers were designed for identification of Phellinus linteus isolates in Korea. The specific primers were within the ITS1 and ITS2 regions and were nested within the universal primers flanking the spacer regions. A total of four primers (the universal primers ITS-1F and ITS-4, and the specific primers PL-F and PL-R) were used for detection of Phellinus linteus collected in Korea. The length of the four amplification products of Phellinus linteus DNA were 800 bp (ITS-1F/ITS-4), two bands of about 720 bp (ITS-1F/PL-R and PL-F/ITS-4), and 610 bp (PL-F/PL-R). Among 23 isolates of Phellinus species collected in Korea, Thirteen isolates were identified as Phellinus linteus based on the presence of the four bands. The other species produced only the single ITS-1F/ITS-4 product.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.137-141
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• 2002

The SNF2/SW12 family comprises proteins from a variety of species with in vivo functions, such as transcriptional regulation, maintenance of chromosome stability during mitosis, and various types of DNA repair. This study was shown the characterization of hrp2+ gene which was isolated by PCR amplification using the conserved domain of SNF2 motifs. Sequence analysis of hrp2+ gene showed striking evolutionary conservation among the SNF2 family of proteins. The transcript of hrp2+ gene was found to be a 4.7 kb as identified by Northern hybridization. In addition, to determine the transcription initiation site of hrp2+ gene, primer extension analysis was performed. This result showed the band of 64 bp. The transcriptional start point was mapped to a position of 47 base pair from the first ATG codon of translational initiation codon. In order to investigate the inducibility of hrp2+ gene, transcript levels were examined after treating the cells to various DNA damaging agents. The transcripts of hrp2+ were induced by UV-irradiation. But the transcripts were not induced by treatment of 0.25% Methylmethane sulfonate (MMS). These results implied that the effects of damaging agents are complex and different regulatory pathways exist for the induction of this gene.

• Korean Journal of Microbiology
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• v.43 no.1
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• pp.1-6
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• 2007

We describe a multiplex PCR method that can detect and differentiate simultaneously four different kinds of DNA viruses, Epstein-Barr virus (EBV), cytomegalovirus (CMV), hepatitis B virus (HBV) and parvovirus B19 (B19). Primers for the multiplex PCR reaction were designed to amplify specific regions of the EBV (pol), CMV (pol), HBV (pol) and B19 (ns) viral genomes and used to simultaneously detect individual viruses. In order to achieve optimal sensitivity and specificity for multiplex PCR, the thermo-cycling parameters, primer sequences, and concentration of each reaction components were optimized systematically. The sensitivity of the detection method ranged between 5 and 10 copies of viral genome with a mixture of multiple primer pairs. Furthermore, this highly sensitive test showed no cross-reactivity among the four viruses. Thus, the results obtained in this study provide evidence that the assay system is a good tool for supporting the diagnosis of viral infection and contamination.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2000.11a
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• pp.59-75
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• 2000

This study was carried out to develop a DNA marker for identifying between Korean cattle (Hanwoo) and other breeds. First experiment was performed to isolate Hanwoo specific DNA marker at sequence characterized amplified regions (SCARs). Five breeds of cattle including Hanwoo, Holstein, Hereford, Angus and Charolais were represented with the from 8 to 20 individuals. Fourteen primers of 300 arbitrary primers of 10 nucleotides showed reproducible polymorphism across the breeds. An amplified band of 0.9 kb in the primer MG-3 showed the specificity to Holstein breed. And MG-6 and MG-12 detected the Hereford and Hanwoo specific markers at the size of 2.0 kb and 1.0 kb, respectively. A 1.0 kb band of MG-12 was cloned and sequenced. A SCAR primer was designed based on the obtained sequences. It was possible to identify the Hanwoo from Holstein breed. Second experiment was carried out to observe the genotype frequencies of MC1R in 1,044 samples of imported beef and eight different cattle breeds including Hanwoo, Holstein, Angus, Brown-Swiss, Charolais, Limousin, Simmental and Hereford. The primers for the amplification of bovine MC1R gene were designed based on a bovine MC1R gene sequence (GenBank accession no.Y19103). A size of 350 bp was amplified by polymerase chain reaction(PCR), digested with two different restriction enzyme, BsrFI and MspA II, and electrophoresed in 2.5% Metaphore agarose gel for determination of genotypes. Genotype frequencies of Hanwoo were 0.10 in E+e and 0.90 in ee. Allele ED was shown in all of Holstein and Angus breeds tested which have black coat color phenotypes. We suggested that SCAR marker and the bovine MC1R gene could be used as a DNA marker for distinguishing beef between Hanwoo and Holstein.

• Journal of Life Science
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• v.11 no.1
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• pp.65-67
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• 2001

In order to develop a rapid and simple method for testing the purity of radish hybrid seeds using a procedure based on the PCR(Polymerase chain reaction), eighty random primers were screened with the genomic DNA extracted from five day old seedlings of inbred parent lines and their F1 hybrids. Two primers, HRM-02 (5'-GAGACCAGAC-3') and HRM-19(5'-TGAGGCGTGT-3'), generate reproducible unique PCR patterns which can identify each parent lines as well as their hybrids. In actual test of randomly selected hybrid seeds using the two marker primers, the purity tested by one primer was exactly same as that of other primer. It suggests that one marker primer selected in this experiment is enough for the purity test of radish hybrid seeds. We demonstrates the use of RAPD(randomly amplified polymorphic DNAs) markers to identify each of inbred parent lines and hybrids by rapid and simple method.

• Archives of Pharmacal Research
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• v.26 no.8
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• pp.601-605
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• 2003

Traditional taxonomic methods used for the identification and differentiation of ginsengs rely primarily on morphological observations or physiochemical methods, which cannot be used efficiently when only powdered forms or shredded material is available. Randomly amplified polymorphic DNA (RAPD) was used to determine the unique DNA profiles that are characteristic not only of the genus Panax but also of various Panax subgroups collected from five different countries. RAPD results of OP-5A primer showed a specific single band that is characteristic of all ginseng samples. RAPD results of OP-13B primer demonstrated that OP-13B primer could be used as a unique RAPD marker to differentiate Panax species. These results support that this approach could be applied to distinguish Korean Ginseng (Panax ginseng) from others at the molecular level.