• Title, Summary, Keyword: restriction enzymes

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Identification of promoter sites in Babesia equi ema-l 5' intergenic nucleotide: I. PCR amplification and restriction mapping (Babesia equi ema-l 5' intergenic 뉴클레오타이드의 프로모터 위치 확인: I. PCR 증폭 및 제한효소지도)

  • 곽동미
    • Korean Journal of Veterinary Service
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    • v.27 no.1
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    • pp.103-109
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    • 2004
  • Babesia equi ema-1 5' intergenic(IG) nucleotide was PCR amplified and analyzed for restriction sites in order to identify a promoter region in this IG nucleotide sequence. B equi ema-1 5' IG specific primers identified a 1268 bp PCR product. The sequence had restriction sites for 34 restriction enzymes when analyzed by a computer program. Among them, 26 enzymes had only one restriction site, but the others had more than one sites. When four restriction enzymes (Bgll , HindⅢ, Kpn1 and BamH1) were treated to digest the 1268 bp nucleotide, they had restriction sites as expected by the computer program. Information of restriction sites in the 1268 bp IG nucleotide will be applied to select restriction enzymes for cloning the IG nucleotide to a vector.

Mitochondrial DNA polymorphism in the Cheju horses (제주마의 mitochondrial DNA 다형(多型)의 분석(分析))

  • Han, Bang-keun;Chang, Deuk-jee;Tsuchida, Shuichi;Ikemoto, Shigenori
    • Korean Journal of Veterinary Research
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    • v.34 no.2
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    • pp.243-247
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    • 1994
  • As a result of the detection of mitochondrial DNA(mtDNA) polymorphism to Thoroughbred and Percheron using 14 restriction enzymes, mtDNA polymorphism of Cheju horse observed in the Bam HI and Sac I. Only in both restriction enzymes two types were classified as of A type, which is high expression frequency and B type, which is low expression frequency. In the other 12 restriction enzymes mtDNA polymorphism was not detected. On the basis of this information mtDNA polymorphism of Cheju horse was examined but was not observed the polymorphism and only A type was expressed both Bam HI and Sac I restriction enzymes. Through this study Cheju horse was demonstrated that lower genetic variation was expressed from the detection of mtDNA polymorphism.

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Effects of Total Dietary Restriction on the Contents of Thiobarbituric Acid-Reactive Substance and Antioxidant Enzymes in the Liver and Kidney of Rats (절식이 흰쥐의 간과 신장의 Thiobarbituric Acid-Reactive Substance량 및 항산화효소 활성도에 미치는 영향)

  • 박평심;고춘남;박재윤
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.28 no.2
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    • pp.471-476
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    • 1999
  • The effects of total dietary restriction(100% restriction of energy intake) on thiobarbituric acid reactive substance(TBARS) contents and intracellular antioxidant enzymes activities in the liver and kidney of young male Sprague Dawley rats were studied. The TBARS contents were reduced in both liver and kidney, up to 77% and 79% of the control rats, fed ad libitum, respectively at 7 days after dietary restriction . Superoxide dismutase(SOD) activities in the liver and kidney of rats were increased significantly by total dietary restriction. However, the activity of catalase in kidney was decreased 27% at 6 days after dietary restriction, but this enzyme activity did not change in liver. The changes of glutathione peroxidae(GSHPx) and catalase activities in the liver and kidney of rats with dietary restriction were not significant. These result suggested that dietary restriction reduce the free radical induced by tissue damage, as determined by TBARS content, in both the liver and kidney but the changes of activities of antioxidant enzymes may not be a contributory factor in reducing oxidative damage to tissue.

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Digestion efficiency differences of restriction enzymes frequently used for genotype-by-sequencing technology

  • Chung, Yong Suk;Jun, Taehwan;Kim, Changsoo
    • Korean Journal of Agricultural Science
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    • v.44 no.3
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    • pp.318-324
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    • 2017
  • With the development of next-generation sequencing (NGS), a cutting-edge technology, genotype-by-sequencing (GBS) became available at a low cost per sample. GBS makes it possible to customize the process of library preparation to obtain high-quality single nucleotide polymorphisms (SNPs) in the most efficient way. However, a GBS library is hard to construct due to fine-tuning of concentration of each reagent and set-up. The major reason for this is the presence of undigested genomic DNA (gDNA) owing to the efficiency of different restriction enzymes for different species with unknown reasons. Therefore, this proof-concept study is to demonstrate the unpredictable patterns of enzyme digestion from various plants in order to make the reader aware of the caution needed when choosing restriction enzymes for their GBS library preparations. Indeed, no pattern was found for the digestibility of gDNA samples and restriction enzymes in the current study. We suggest that more data should be accumulated on this matter to help researchers who want to apply GBS technologies in a variety of genetic approaches.

POLYMERASE CHAIN REACTION AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM OF 16S RIBOSOMAL DNA OF STREPTOCOCCI ISOLATED FROM INFECTED ROOT CANALS (감염 근관에서 분리된 연쇄구균의 16S Ribosomal DNA 중합효소 연쇄반응과 제한효소 절단길이 다형성에 관한 연구)

  • Jung, Hee-Il;Im, Mi-Kyung
    • Restorative Dentistry and Endodontics
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    • v.20 no.2
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    • pp.577-609
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    • 1995
  • Bacteria have been regarded as one of the most important factors in pulpal and periapical diseases. Streptococci are frequently isolated facultative anaerobes in infected root canals. Recently molecular biological techniques have been rapidly progressed. This study was designed to apply the molecular biological tools to the identification and classification of streptococci in the endodontic microbiology. Streptococci isolated from infected root canals were identified with both Vitek Systems and API 20 STREP. Identification results were somewhat different in several strains of streptococci. Eighteen streptococci and enterococcal was difficult so to digest plasmid DNA using Hind III and EcoRI to differentiate strains by restriction enzyme analysis of plasmid DNA. 16S rDNA of chromosome was amplified by polymerase chain reaction(PCR) and then restricition fragment length polymorphism(RFLP) using several restriction enzymes was observed. The molecular mass of 16S rDNA of chromosomal DNA was approximately 1.4kb. There were three to five RFLP patterns using eight restriction enzymes. RFLP patterns digested with CfoI which recognizes four base sequences were identical in all stains. Hind III which recognizes six base sequences could not digest the 16S rDNA. Restriction enzymes which recognize five base sequences were suitable for RFLP pattern analysis. At least three different restriction enzymes were needed to compare each strains. 16S rDNA PCR-RFLP was simple and rapid to differentiate and classify strains and could be used in the epidemiological study of root canal infections.

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Differentiation of Vibrio spp. including Core Group Species by PCR-RFLP (PCR-RFLP에 의한 Vibrio core group을 포함한 Vibrio 종의 구분)

  • Park, Jin-Sook
    • Journal of Life Science
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    • v.22 no.2
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    • pp.245-250
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    • 2012
  • The 16S rDNA - RFLP types for six Vibrio species (V. fluvialis, V. proteolyticus, V. vulnificus, V. mimicus) including two core group members, V. alginolyticus and V. parahaemolyticu s, and Grimontia (Vibrio) hollisae were determined using PCR-RFLP analysis. Six tetrameric restriction enzymes (Alu I, Cfo I, Dde I, Hae III, Msp I, and Rsa I) were selected for RFLP analysis. V. alginolyticus, V. parahaemolyticus, and V. proteolyticus showed the same RFLP pattern following digestion with four of the six used restriction enzymes: CfoI, DdeI, MspI, and RsaI. Various restriction enzyme combinations generated digests recognizable as distinct RFLP types for each of the assayed Vibrio species. In particular, AluI single digestion produced species specific band patterns that enabled the differentiation between these Vibrio species. Dendrogram based on restriction patterns showed that two Vibrio core group members, V. alginolyticus and V. parahaemolyticus were closely related having a similarity over 90%. Although the observed RFLP pattern for Grimontia hollisae shared several common bands with other Vibrio spp., G. hollisae results were still clearly distinct from Vibrio spp. RFLP types for all restriction enzymes tested. If restriction enzymes are aptly selected, PCR-RFLP analysis is still a rapid and effective tool for differentiating Vibrio species.

Differentiation of Intraspecific Groups within isolates of Rhizoctonia solani Using PCR-RFLP of Ribosomal DNA (Ribosomal DNA의 PCR-RFLP에 의한 국내산 Rhizoctonia solani 균주들의 종내그룹의 구분)

  • 홍승범;고승주;류진창;김완규;김인수
    • Korean Journal Plant Pathology
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    • v.14 no.2
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    • pp.157-163
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    • 1998
  • Genetic diversity among 27 isolates of Rhizoctonia solani, which were obtained from diseased crops in Korea and classified into 9 intraspecific groups by anastomosis test and cultural characteristics, was studied by PCR-RFLP. Gene regions of nuclear 17S ribosomal DNA and internal transcribed spacers including 5.8S rDNA of the isolates were amplified with polymerase chain reaction and digested with 12 restriction enzymes. Differences of restriction patterns were not shown among isolates within each intraspecific groups, however, each anastomosis group and culturala type sowed unique restriction fragment length polymorphisms by restriction patterns using HaeIII, Cfr13I and MspI. The results suggest that PCR-FRLP of rDNA using three restriction enzymes could be used to differentiate intraspecific groups of Rhizoctonia solani in Korea.

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Genetic Relationships of Cattle Breeds Assessed by PCR-RFLP of the Bovine Mitochondrial DNA D-loop Region

  • Yoon, Du Hak;Lee, Hak Kyo;Oh, Sung Jung;Hong, Ki Chang;Jeon, Gwang Joo;Kong, Hong Sik;Lee, Jun Heon
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.10
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    • pp.1368-1374
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    • 2005
  • To investigate the genetic relationships among various cattle breeds, bovine mtDNA D-loop region was used in 411 animals of 18 cattle breeds, including 8 Asian Bos taurus, 7 European Bos taurus, 1 Asian Bos indicus, and 2 African Bos indicus. The size of amplified PCR products from mtDNA D-loop region was 964 bp and the products were digested by 15 different restriction enzymes. Two different band patterns were identified in eight restriction enzymes (BstXI, Hae III, Msp I, Apa I, Taq I, Alu I, BamH I, EcoN I) and the rest of restriction enzymes showed more than 3 different band patterns among which Apo I and MspR9 resulted in 7 different restriction patterns. The genotypes, number of haplotype, effective number of haplotype, and degree of heterozygosity were analyzed. Based on all the PCR-RFLP data, different haplotypes were constructed and analyzed for calculating genetic distances between these breeds using Nei's unbiased method and constructing a phylogenetic tree.

Restriction Fragment Fingerprint of an Alkaliphilic Micrococcus sp. Y-1 Genome by Pulsed-field Gel Electrophoresis

  • Kim, Cheorl-Ho
    • Journal of Microbiology and Biotechnology
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    • v.5 no.1
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    • pp.1-5
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    • 1995
  • A genomic DNA of alkaliphilic bacterium, Micrococcus sp. Y-l, was analysed using the physical mapping method of pulsed-field gel electrophoresis (PFGE). Five restriction enzymes of Sspl, Hpal, Xbal, Ndel or EcoRI, which recognize the Adenine-Thymine-rich sequences of genomic DNA, were used for the generation of few (7 to 20) distinctly separate fragments, with average sizes in the range of 200~500 kb. However, the sites for Notl and SfiI, 8 base-recognizing enzymes, were highly frequent. The genome size of this strain was determined to be 4 mega base pairs (Mb) from restriction fragments separated by PFGE. This is the first case of restriction mapping in alkaliphilic bacterium.

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restriction Site Polymorphism of mtDNA for differentiating Anopheles quadrimaculatus (Say) Sibling Species (미토콘드리아 DNA 제한효소 절단부위 변이에 의한 Anopheles quadrimaculatus (Say) 모기의 자매종 구별)

  • ;S.K. Narang
    • Korean journal of applied entomology
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    • v.29 no.2
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    • pp.132-135
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    • 1990
  • Three mitochondrial cDNA probes from Aedes albopictus were used to demonstrate restriction site polymorphism in mtDNA of three sibling species of Anopheles quadrimaculatus(Say). It was shown by DNA hybridization to have substantial sequence homology betwen the mtDNA of different genus. The proves reveled local restriction site variation between members of the Anopheles quadrimaculatus sibling species complex. Mitochondrical DNA (mtDNA), isolated from individual mosquitoes was digested by type II restriction enzymes and four enzymes were found to be useful for the purpose. Hind III alone could be used to obtain a diagnostic restriction pattern.

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