• Korean Journal of Animal Reproduction
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• v.27 no.2
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• pp.97-102
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• 2003

This study was carried out to find out PSS(Porcine Stress Syndrome) with the PSE(Pale, Soft, Exudative) in different piglets. These experiments were accomplished with the aid of PCR-RFLP(Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The samples were collected and examined from umbilical cord blood of piglets of Yorkshire, Landrace and Crossbred. And then, the PCR products were digested by restriction enzyme, Hha I. The results obtained were as follows; The PCR products of the blood genomic DNA of ryanodine receptor gene were length of 1 .8kb in umbilical cord blood. Normal type(NN), heterozygous type(Nn) and recessively homozygous type(nn, PSS) as a result of digestion of restriction enzyme, Hha 1, were 90.0%, 10.0% and 0.0% in Yorkshire piglets, 76.2%, 19.0% and 4.8% in Landrace, 69.1%, 23.8% and 7.1% in crossbred, respectively. As already showing the above results, the blood from piglets umbilical cord can be availably used for the determination of genotypes of PSS because of easiness of blood collection without stress in live piglets.

• The Plant Pathology Journal
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• v.27 no.2
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• pp.148-155
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• 2011

Our previous sequence and phylogenetic analyses of the Korean Rice stripe virus (RSV) suggested possible genetic reassortment of RNA segments, but whether this RNA variation contributed to the recent RSV outbreaks in Korea is yet unclear. To further clarify these RSV-RNA segment variations, we developed a reverse transcription-polymerase reaction/restriction enzyme (RT-PCR/RE) analysis-based method. We identified five REs, including DraI, EcoR1, NdeI/AseI, and SpeI, that could differentiate RSV RNA 1-4 subtypes, respectively. Our RT-PCR/RE results provided a clear pattern of RNA reassortment, i.e., different groups of isolates having their RNA segments derived from two to three different RSV ancestors, such as from Eastern and Southwestern Chinese or Japanese M and T isolates. We also found that the migratory small brown planthopper from Eastern China caught by aerial net traps that possesses RSV-RNA3 genotypes corresponds mainly to Eastern China, with a few for Southwestern China based on RT-PCR/RE, sequence and phylogenetic analyses, indicating that RSV populations in Eastern China may also have strong RNA variation. The development of an RE analysisbased method proved a useful epidemiological tool for rapid genotyping and identification of mixed infections by RSV strain and by different subtype.

• Journal of Animal Science and Technology
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• v.50 no.5
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• pp.633-640
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• 2008

With a double mismatch primer set designed for amplifying the modified DNA sequence fragments, bovine melanocortin-1 receptor(MC1R) gene encoded in Extension locus which plays a critical role in coat color development was analyzed using polymerase chain reaction mediated restriction fragment length polymorphism(PCR-RFLP). Amplified PCR fragments were successfully discriminated with combining the MspI- and AluI-RFLP into three major alleles(ED, E+, and e), directly related to bovine coat color phenotypes. The genotyping results showed that Jeju black cattle contained three MC1R alleles, but yellowish-red colored Hanwoo and bridle colored Korean Brindle cattle did not contained the dominant black allele ED. However, two dominant black-colored cattle breeds, Holstein and Angus, contained the ED allele over 96% in frequency. Hanwoo×Holstein F1 and Hanwoo×Angus F1 crossbred calves showed ED/e MC1R genotypes, and uniformly black coat color. the results suggested that this MC1R genotyping method be useful in allele discrimination for bovine MC1R gene which used for breed classification and characterization, as one of the important genetic markers, using combination of MspI- and AluI-RFLP for modified PCR product amplified with a newly designed double mismatch primer set.

• Genomics & Informatics
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• v.18 no.1
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• pp.4.1-4.6
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• 2020

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

• Parasites, Hosts and Diseases
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• v.46 no.2
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• pp.105-108
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• 2008

Although the Korean isolate KI-1 of Toxoplasma gondii has been considered to be a virulent type I lineage because of its virulent clinical manifestations, its genotype is unclear. In the present study, genotyping of the KI-1 was performed by multilocus PCR-RFLP and microsatellite sequencing. For 9 genetic markers (c22-8, c29-2, L358, PK1, SAG2, SAG3, GRA6, BTUB, and Apico), the KI-1 and RH strains exhibited typical PCR-RFLP patterns identical to the type I strains. DNA sequencing of tandem repeats in 5 microsatellite markers (B17, B18, TUB2, W35, and TgM-A) of the KI-1 also revealed patterns characteristic of the type I. These results provide strong genetic evidence that KI-1 is a type I lineage of T. gondii.

• Journal of Microbiology and Biotechnology
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• v.19 no.2
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• pp.121-127
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• 2009

Sequencing analysis of a 5-kb DNA fragment from Streptomyces venezuelae ATCC 15439 revealed the presence of one 3.1-kb open reading frame(ORF), designated as afsR-sv. The deduced product of afsR-sv(1,056 aa) was found to have high homology with the global regulatory protein AfsR. Homology-based analysis showed that aftR-sv represents a transcriptional activator belonging to the Streptomyces antibiotic regulatory protein(SARP) family that includes an N-terminal SARP domain containing a bacterial transcriptional activation domain(BTAD), an NB-ARC domain, and a C-terminal tetratricopeptide repeat domain. Gene expression analysis by reverse transcriptase PCR(RT-PCR) demonstrated the activation of transcription of genes belonging to pikromycin production, when aftR-sv was overexpressed in S. venezuelae. Heterologous expression of the aftR-sv in different Streptomyces strains resulted in increased production of the respective antibiotics, suggesting that afsR-sv is a positive regulator of antibiotics biosynthesis.

• Ocean and Polar Research
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• v.26 no.4
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• pp.551-557
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• 2004

Polymorphism of the lipoprotein lipase (LPL) gene which plays an important role in regulation of lipid deposition was analysed in two red seabream (pagrus major) populations (KF4, cultured KORDI line, n=100 : JPN, imported from Japan, n=100). We amplified a DNA fragment (1,091 bp) including the exon 2 region of the LPL gene, and conducted PCR-RFLP analysis using MspI and AluI. The PCR products were also sequenced. Two alleles (A and B) were found in MspI digestion and Sve alleles (A, B, C, D and E) in AluI digestion. The sequenced data revealed four nucleotide substitutions including one transversion at the MspI recognition site (nt 2,235, $C{\rightarrow}10$) and three transitions at the AluI recognition sites (nt 1,721, $A{\rightarrow}G;$ nt 2,319, $C{\rightarrow}T;$ nt 2,319, $T{\rightarrow}C$). Among them, substitutions at the nt 2,235 and 2,319 sites which are located in the exon 2 were proved to be silent point mutations. MspI polymorphism resulted in 3 genotypes, and the allele frequency was significantly different between the two fish populations, KF4 and JPN. In the case of AluI polymorphism, the 5 alleles (A, B, C, D, E) comprised 12 genotypes of the 5 alleles. KF4 population, alleles D and I were specific to the LPL gene Polymorphisms would be useful DNA markers for red seabream population.

• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.264-266
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• 2000

A new GFP-based T-vector for cloning of PCR products was developed by using a green fluorescent protein (GFP) as a mafker. In order to facilitate the DNA inserts, multiple restriction sites, SP6 and T7 RNA polymerase promoter sites, were introduced close to the PCR DNA insertion site of a pCRGv vector. The XcmI-digested pHNT plasmid can be used to clone a 3' A-overhanged PCR DNA amplified by Taq DNA polymerase. A potential method of easing some difficulties from its use along with its cost savings proveded by this vector are likely to lead to the replacement of other T-vectors for PCR DNA cloning.

• Korean Journal of Veterinary Research
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• v.49 no.2
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• pp.105-111
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• 2009

In this study, occurrence of canine brucellosis was surveyed in kennels, indoor dogs and stray dogs in Korea, and infrequent restriction site-polymerase chain reaction (IRS-PCR) was applied to analyze DNA polymorphism of Brucella canis (B. canis) isolates. Among a total of 501 dogs tested, B. canis antibodies by both rapid screening agglutination with 2-mercaptoethanol (2-ME RSAT) and immunochromatographic assay were detected in only 14.1% of kennel dogs. There were no seropositive cases in indoor dogs and stray dogs. DNA polymorphism was observed in 16 B. canis isolates by the IRS-PCR. Sixteen isolates were tested with primers, PsalA, PsalC, PsalG and PsalT, and different primers produced different DNA patterns. In regard to the IRS-PCR pattern of 16 isolates, 9 (56.3%) belonged to the IRS-PCR type I. The remaining 7 were differentiated as type II, III and IV. An application of the primer PsalC provided discrimination between B. canis isolated in 2005 and others.

• Journal of Microbiology
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• v.39 no.4
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• pp.265-272
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• 2001

Variation within the intergenic spacer(IGS) of the ribosomal DNA gene for twenty-two strains of E. oxysporum and its formae speciales was examined by PCR, couped with RELP analysis. The length of the amplified IGS region was about 2.6 kb in all strains except F.oxysporum f. sp. cucumer-inum from Korea and F. oxysporum f. sp. niveum. Those two strains were 2.5 kb long. Restriction digestion of IGS-RELP regions by Eco RI, NruI, HincII, SAlI, SmaI, BalIi, HindIII, XhoI and KpnI gave rise to nine IGS hapoltypes among all strains. Cluster analysis based on the presence of absence of comigrating restriction reagments show the two groups based on 44% genetic similarity. These results demonstrated that analysis of IGS showed some difference within and between F. oxysporum formae speciales.