• Archives of Pharmacal Research
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• 제29권1호
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• pp.88-95
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• 2006

Analysis of molecular nature of mitochondrial DNA (mtDNA) could be powerful marker for anthropological studies of modern populations. While population genetic studies on mtDNA have been reported for several ethnic groups, no such study has been documented for the Korean population. We surveyed mtDNA polymorphisms in the HVS I of noncoding D-loop region and its upstream region from 430 unrelated healthy Korean population by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing analysis. PCR product with 2,790 bp spanning the specific mtDNA region (mt13715-16504) was subjected to RFLP analysis using 6 restriction enzyme (Hinf I, Hae III, Alu I, Dde I, Mbo I, Rsa I). On the PAUP analysis of PCR-RFLP results, 38 mtDNA haplotypes (Hap 1-38) were detected in the Korean populations, which were classified into 11 haplogroups (Grp 1-11) of related haplotypes encompassing all 38 haplotypes. In comparison of sequencing data with Anderson's reference sequence, the transition type was more prevalent than the transversion type. Insertions or deletions were not found. In addition, three of the polymorphic sites (A16240C, A16351G, G16384A) in HVS-I region are determined newly. The polymorphic sites were distributed randomly in the region, though the frequency at each site was variable. Thus, this research might be required for the genealogical study of Orientals.

• Asian-Australasian Journal of Animal Sciences
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• 제18권7호
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• pp.942-948
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• 2005

New polymorphism of major histocompatibility complex B-G genes was investigated by amplification and digestion of a 401bp fragment including intron 1 and exon 2 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique with two restriction enzymes of Msp I and Tas I in eight breeds of Chinese indigenous chickens and one exotic breed. In the fragment region of the gene, three novel single nucleotide polymorphisms (SNPs) were detected at the two restriction sites. We found the transition of two nucleotides of A294G and T295C occurred at Tas I restriction site, and consequently led to a non-synonymous substitution of asparagine into serine at position 54 within the deduced amino acid sequence of immunoglobulin variable-region-like domain encoded by the exon 2 of B-G gene. It was observed at rare frequency that a single mutation of A294G occurring at the site, also caused an identical substitution of amino acid, asparagine 54-to-serine, to that we described previously. And the transversion of G319C at Msp I site led to a non-synonymous substitution, glutamine 62-to-histidine. The new alleles and allele frequencies identified by the PCR-RFLP method with the two enzymes were characterized, of which the allele A and B frequencies at Msp I and Tas I loci were given disequilibrium distribution either in the eight Chinese local breeds or in the exotic breed. By comparison, allele A at Msp I locus tended to be dominant, while, the allele B at Tas I locus tended to be dominant in all of the breeds analyzed. In Tibetan chickens, the preliminary association analysis revealed that no significant difference was observed between the different genotypes identified at the Msp I and Tas I loci and the laying performance traits, respectively.

• 미생물학회지
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• 제33권2호
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• pp.149-156
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• 1997

Pentachlorophenol(PCP)가 첨가된 혐기성 무기배지에 혐기성 소화조슬럿지와 쓰레기 매립장의 침출수를 각각 접종한 후, 활성을 보이기 전과 후의 각 시료 내에 존재하는 총유전물질로부터 16S rRNA 유전자를 PCR 증폭하여 이들에 대한 restriction fragment length polymorphism(RFLP) 비교분석과 계통수분석을 실시하였다. 3차에 걸친 RFLP 분석 결과 Ala와 Bld로 명명된 두 가지의 FRLP 유형이 두 가지의 활성시료 모두에서 높은 빈도로 발견되었다. 이들 유형에 속하는 모든 클론들의 5'쪽에 해당되는 180개씩의 염기서열분석을 실시하여 계통수 분석을 실시한 결과, 각각의 유형에 속하는 클론들간에는 높은 상동성을 가지는 것으로 확인되었다. 특히 Bld 유형에서는 78%에 해당되는 클론들이 동일한 염기서열을 가지는 것으로 확인되었다. 이들 Ala와 Bld 유형에 속하는 클론들은 PCP에 대한 분해활성의 결과로서 증식된 유사종의 미생물 군집에서 비롯된 것으로 추정된다. 이 두 가지 유형에 속하는 클론들 중 하나씩의 16S rDNA 전체으 염기서열을 분석한 결과 Ala의 클론은 Clostridium ultunae (Genbank No. Z69293)의 염기서열과 89%의 상동성을 보였으며, Bld의 클론은 Thermobacteroides proteolyticus (Genbank No. X69335)의 것과 97%의 상동성을 가지는 것으로 나타났다.

• Animal Bioscience
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• 제36권9호
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• pp.1357-1366
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• 2023

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. Results: The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. Conclusion: The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.

• 대한의생명과학회지
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• 제9권3호
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• BMB Reports
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• 제34권2호
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• pp.114-117
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• 2001

Cervi Parvum Cornu is widely used as a hemopoietic, tonifying, growth-promoting, cardiotonic, and immuno-modulating agent in Korea. In order to develop the quality control method of Cervi Parvum Cornu by the identification of the biological source or origin, the molecular approach was applied using PCR (polymerase chain reaction) and PCR-RFLF (PCR-restriction fragment length polymorphism) analysis. In the PCR analysis of the mitochondrial 12S rRNA gene and cytochrome b gene regions, no distinctive DNA bands from Cervidae (deer) antlers and Rangifer (reindeer) antlers were observed. However, when the amplified products in the mitochondrial cytochrome b gene region were subjected to restriction digestion with TaqI, Cervidae antlers showed an undigested state of 380 by band, differently from two bands of 230 by and 1S0 by from Rangifer antlers. Based on this finding, the base sequences of amplified PCR products in the range of mitochondria) cytochrome b gene from Cervidae antlers and Rangifer antlers were determined and subjected to restriction analysis by various endonucleases. The results showed that antlers from Rangifer species could be simply discriminated with other antlers from 8 Cervidae species (Chinese deer, Russian deer, Hong Kong deer, New Zealand deer, Kazakhstan deer, elk, red deer and Sika deer) by PCR-RFLP analysis using AtuI, HaeIII, HpaII or Sau3AI(MboI) as well as TaqI in the range of the mitochondrial cytochrome b gene.

• The Plant Pathology Journal
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• 제25권1호
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• pp.21-25
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• 2009

Jujube trees infected with phytoplasma exhibit symptoms of typical witches' broom, such as yellowing, abnormally small leaves, short internodes and proliferation of shoots. A 1.2 kb fragment of the 16S rDNA from jujube phytoplasma was generated by R16F2n/R16R2 primer pair from earlier amplified P1/P7 PCR products of cloned jujube witches' broom phytoplasmas. Enzymatic restriction fragment length polymorphism (RFLP) and sequence analysis of 16S rDNA revealed that the jujube tree was infected with 16S rDNA I and V groups of phytoplasmas. Extensive comparative analyses of restriction enzyme profiles from Alu I, Hha I, Msp I, and Rsa I clearly classified the two into different phytoplasma groups. The phylogenie analyses based on 16S rDNA showed that the similarity of the two different clones was 87.5%. This is the first report of a mixed phytoplasmal infection in a single jujube tree.

• The Plant Pathology Journal
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• 제18권1호
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• pp.1-5
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• 2002

The availability of nucleotide sequences of the coat protein gene of Potato leafroll virus (PLRV) permitted the construction of DNA primers that were utilized for cDNA synthesis. Polymerase chain reaction (PCR) products of a 487 bp. and approximately 500 bp DNA fragments were amplified from nucleic acid extracts of PLRV-infected tissue and strawberry mild yellow-edge (SMYE) diseased strawberry tissue, respectively. The amplified DNA fragments were further differentiated by hybridization analysis with a CDNA probe for the coat protein gene of PLRV and restriction fragment length polymorphism (RFLP) analysis. These results suggest that a luteovirus is associated with the SMYE disease.

• Advances in Traditional Medicine
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• 제1권2호
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• pp.52-58
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• 2000

In order to develop convenient and reproducible methods for identification of ginseng drugs at a DNA level, RAPD (randomly amplified polymorphic DNA) and PCR-RFLP (PCR-Restriction fragment length polymorphism) analysis were applied within Panax species. To authenticate Panax ginseng betvyeen Chinese and Korean ginseng population, RAPD analysis were carried out using 20 mer-random primer. The similarity coefficients among the DNA of ginseng plants analyzed were low, ranging from 0.197 to 0.491. In addition, using PCR-RFLP analysis, very different fingerprints were obtained within Korean ginseng plants. These results suggest that these methods are able to authenticate the concerned Panax species. Broader application of this approach to authenticate other morphologically similar medicinal materials is rationalized.

• 미생물학회지
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• 제40권3호
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• pp.244-247
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• 2004

이산화탄소 농도의 증가가 습지토양의 탈질세균 군집구조에 미치는 영향을 살펴보기 위하여 자연농도 (370 ppm)와 고농도 (740 ppm)의 이산화탄소조건의 습지생태계를 조성하여 110일 이상 배양한 후 토양 내 미생물 군집구조의 변화양상을 관찰하였다. 미생물 군집군조 분석은 탈질과정에 관여하는 효소중하나인 nitrite reductase의 유전자인 nirS 유전자를 대상으로 polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) 분석기법을 이용하여 수행하였다. PCR 결과 모든 토양시료에서 nirS 유전자가 검출되었고, RFLP분석을 통해 자연농도의 이산화탄소조건에서 83개, 고농도 조건에서 95개의 phylotype을 획득하여 조성된 습지토양에서 탈질과정이 광범위하게 일어날 수 있음을 확인할 수 있었다. 두 경우 모두 두 종류 (type 1과 type 2)의 phylotype의 우점하고 있었고, 고농도 조건의 탈질세균 군집의 풍부도가 저농도 조건에 비해 더 높고, phylotype의 종류가 현저하게 변화되는 경향을 확인하였다. 본 연구결과는 습지토양의 탈질세균 군집이 매우 다양한 종류로 이루어져 있고, 이산화탄소의 증가에도 큰 영향을 받지 않는 상당히 안정적인 우점 개체군이 존재하고 있는 반면, 전체 phylotype의 약 60％는 이산화탄소 증가에 따라 민감하게 변화함을 보여주었다.