• Title/Summary/Keyword: DNA fingerprinting

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DNA FINGERPRINTING AND SEROTYPING OF ACTINOBACILLUS ACTINOMYCETEMCOMITANS ISOLATED FROM PERIODONTAL PATIENTS (Actionbacillus actinomycetemcomitans의 임상분리 혈청형에 따른 유전자 지문 양상에 관한 연구)

  • Heo, Kyung-Kee;Kim, Sung-Jo;Choi, Jeom-Il
    • Journal of Periodontal and Implant Science
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    • v.25 no.1
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    • pp.153-166
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    • 1995
  • 54 clinical isolates of Actinobacillus actinomycetemcomitans showed distinct hybrdization patern(DAN fingerprinting patterns) when the bacterial DNA were hybridized with randomly cloned 4.7 - kb DNA probe. The frequency of the genotypic distribution demonstrated that type C was the most prevalent genotype, the next being D, NT, A, B, and E in the descending order. The most prevalent serotype was serotype c, the next being a, nd, and b in the descending order. It was noted that the one serotype can represent more than two different genotypes and that multiple genotypic variants can also exist in the periodontal pockets within the sam subject.

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Application of Methodology for Microbial Community Analysis to Gas-Phase Biofilters (폐가스 처리용 바이오필터에 미생물 군집 분석 기법의 적용)

  • Lee, Eun-Hee;Park, Hyunjung;Jo, Yun-Seong;Ryu, Hee Wook;Cho, Kyung-Suk
    • Korean Chemical Engineering Research
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    • v.48 no.2
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    • pp.147-156
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    • 2010
  • There are four key factors for gas-phase biofilters; biocatalysts(microorganisms), packing materials, design/operating techniques, and diagnosis/management techniques. Biofilter performance is significantly affected by microbial community structures as well as loading conditions. The microbial studies on biofilters are mostly performed on basis of culture-dependent methods. Recently, advanced methods have been proposed to characterize the microbial community structure in environmental samples. In this study, the physiological, biochemical and molecular methods for profiling microbial communities are reviewed, and their applicability to biofilters is discussed. Community-level physiological profile is based on the utilization capability of carbon substrate by heterotrophic community in environmental samples. Phospholipid fatty acid analysis method is based on the variability of fatty acids present in cell membranes of different microorganisms. Molecular methods using DNA directly extracted from environmental samples can be divided into "partial community DNA analysis" and "whole community DNA analysis" approaches. The former approaches consist in the analysis of PCR-amplified sequence, the genes of ribosomal operon are the most commonly used sequences. These methods include PCR fragment cloning and genetic fingerprinting such as denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism, ribosomal intergenic spacer analysis, and random amplified polymorphic DNA. The whole community DNA analysis methods are total genomic cross-DNA hybridization, thermal denaturation and reassociation of whole extracted DNA and extracted whole DNA fractionation using density gradient.

Genomic Fingerprinting Patterns of Bifidobacteria Isolated from Healthy Koreans Using ERIC-, TAP-, and BOX-PCR (건강한 한국인으로부터 분리된 비피도박테리아의 ERIC-, TAP-, BOX- 중합효소연쇄반응을 이용한 유전자 지문 분석)

  • Lee, Do-Kyung;Kang, Byung-Yong;Chung, Myung-Jun;Lee, Kang-Oh;Kim, Kyung-Jae;Ha, Nam-Joo
    • Environmental Analysis Health and Toxicology
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    • v.23 no.1
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    • pp.1-9
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    • 2008
  • 유산균인 비피도박테리아는 사람과 동물에서 유익한 프로바이오틱 미생물로 알려져 있다. 본 연구에서는 이러한 비피도박테리아 균주의 분류를 위한 repetitive DNA element PCR fingerprinting (ERIC-또는 TAP-PCR)의 사용을 평가하였다. 사람분변으로부터 분리한 알려지지 않은 비피도박테리움 균주와 한국생명공학연구원 생물자원센터로부터 분양받은 표준균주를 가지고 분류 및 동정에 ERIC-PCR과 TAP-PCR을 이용한 RAPD-fingerprinting을 수행하였다. 그 결과 비피도박테리움 균주에 대한 속과 종단위의 분류가 가능하였으며, 실험에 사용된 모든 비피도박테리움 균주는 RAPD-fingerprinting 분석을 통해 유전적 다양성을 확인하였다. 또한 ERIC2와 TAP1 프라이머를 이용한 실험에서는 Bifidobacterium adolescenits 특이 유전자 단편을 확인하였으며 이는 B. adolescenits 균주의 동정에 유용할 것으로 사료된다.

DNA Fingerprinting Analysis of the Genus Phytophthora in Korea

  • Park, Dong-Suk;Kang, Hee-Wan;Lee, Mi-Hee;Park, Young-Jin;Lee, Byoung-Moo;Hahn, Jang-Ho;Go, Seung-Joo
    • Mycobiology
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    • v.31 no.4
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    • pp.235-247
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    • 2003
  • In order to investigate biodiversity and establish identification system for Phytophthora spp. in Korea, a variety of band pattern was produced by using the URP(universal rice primer). The fingerprint patterns of Phytophthora spp. showed many common and variable fragments according to their isolates in distinct genotypes. In particular, P. drechsleri was classified into four distinct types(I to IV). P. drechsleri(KACC 40498 and KACC 40499) and P. cryptogea(KACC 40413) appeared to have almost equal bands despite their being different species. Ninety isolates of Phytophthora spp. were clustered into 13 groups based on UPGMA(unweighted pair group method with arithmetic means) analysis. These DNA fingerprinting data would be helpful for inter- and intra-species identification of Phytophthora species.

Interstrain polymorphisms of isoenzyme profiles and mitochondrial DNA fingerprints among seven strains assigned to Acanthamoeba polyphaga (대식가시아메바(Acmthamoebapokphaga) 일곱 분리주간의 동위효소 profile과 Mitochondria DNA fingerprint의 다양성)

  • Gong, Hyeon-Hui;Park, Jun-Hyeong;Jeong, Dong-Il
    • Parasites, Hosts and Diseases
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    • v.33 no.4
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    • pp.331-340
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    • 1995
  • Interstrain polymorphisms of isoenzyme profiles and mitochondrial (Mt) DNA fingerprints were observed among seven strains of Acnnthnmoeba isolated from different sources and morphologically assigned to A. polvphngn. Mt DNA ringerprints by eight restriction endonucleases (Bgl II, Sca I, Cla I, EcoR I, Xbo I, Kpn I, Sal I, and Sst I) revealed considerable interstrain polymorphisms . Isoenzyme profiles revealed considerable interstrain polymorphisms for acid phosphatase, lactate dehydrogenase, and glucose-6- phosphate dehydrogenase while those for glucose phosphate isomerase , leucine aminopeptidase , and malate dehydrogenase showed similarity Despite of the interstrain polymorphisms, the isoengyme profiles and Mt DNA fingerprints of the strain Ap were found to be identical with those of the strain .tones . Mt DNA fingerprinting was found to be highly applicable for the strain identification, characterization, and differentiation. Key words: Acanthnmoebn polyphcga, interstrain polymorphism, isoenzyme profiles , Mt DNA fingerprints, strain differentiation, strain identification.

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DNA Fingerprinting of Rice Cultivars using AFLP and RAPD Markers

  • Cho, Young-Chan;Shin, Young-Seop;Ahn, Sang-Nag;Gleen B. Gregorio;Kang, Kyong-Ho;Darshan Brar;Moon, Huhn-Pal
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.44 no.1
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    • pp.26-31
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    • 1999
  • This experiment was conducted to evaluate genetic variation in 48 rice accessions (Oryza sativa L.) using AFLP and RAPD markers. For AFLP, a total of 928 bands were generated with 11 primer combinations and 327 bands (35.2%) of them were polymorphic among 48 accessions. In RAPD analyses using 22 random primers 145 bands were produced, and 121 (83.4%) were polymorphic among 48 accessions. Each accession revealed a distinct fingerprint by two DNA marker systems. Cluster analysis using AFLP-based genetic similarity tended to classify rice cultivars into different groups corresponding to their varietal types and breeding pedigrees, but not using RAPD-based genetic similarity. The AFLP marker system was more sensitive than RAPD in fingerprinting of rice cultivars with narrow genetic diversity.

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Application of AFLP Markers to DNA Fingerprinting in Rainbow Trout (Oncorhynchus mykiss)

  • Yoon, Jong-Man;Yoo, Jae-Young;Park, Jae-il
    • Proceedings of the Korean Society of Fisheries Technology Conference
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    • 2003.05a
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    • pp.227-228
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    • 2003
  • The most important of various merits are the capacity to investigate an total genome for polymorphism and AELP is superior to any other systems in terms of the number of sequences amplified per reaction and its reproducibility(Vos et al., 1995). The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of origin o. complexity (Vos et at., 1995). (omitted)

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A Comparison of Bacterial Diversity Associated with the Sponge Spirastrella abata Depending on RFLP and DGGE (RFLP와 DGGE에 따른 해면 Spirastrella abata 공생세균의 다양성 비교)

  • Jeong, Eun-Ji;Im, Choon-Soo;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.46 no.4
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    • pp.366-374
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    • 2010
  • Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.