• Journal of Veterinary Clinics
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• v.16 no.1
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• pp.19-25
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• 1999

A total of 137 strains of Staphylococcus aureus were isolated from dairy cow's milk with subclinical mastitis from 33 herds in 5 provinces and 36 strains of S aureus from clinical mastitis from 4 herds where the mastitis were severe problem. Arbitrary primed polymerase chain reactions with 10 bp oligonucleotide primer were performed and the PCR products were analysed with image analyzer, The S aureus strains were genotyped into 20 distinct DNA fingerprinting profiles. The size of PCR products ranged from 163 to 2,479 bp and PCR products of 506, 770, 784 and 2,479 bp were the most prevailing bands. Genotype 3 was founded in all 5 provinces. The various genotypes were identified in newly founded dairy herds, however, only one or two genotypes were identified in the closed herds. In clinical mastitis, only a limited number of different S aureus genotype was founded in each of the herds in comparision with subclinical mastitis. The results demonstrated that PCR-based DNA fingerprinting analysis of S aureus strain can be used to study epidemiology of mastitis, in addition, common genotype in geographic region can be useful for the development of an effective S aureus bacterin.

• Proceedings of the Korean Society of Crop Science Conference
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• 1998.04a
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• pp.33-34
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• 1998

• Food Engineering Progress
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• v.21 no.2
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• pp.174-179
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• 2017

For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.10
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• pp.1406-1410
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• 2003

The studies were based on the RAPD fingerprinting for the species identification of animals. The genomic DNA samples of ostriches, Taiwan local chickens, Aboracres broilers, Leghorn chickens, quails, doves, emus, Beltville small white turkeys, pheasants, Chinese geese, mule ducks, Holstein cattle and Landrace pigs were amplified with random primers by RAPD-PCR for fingerprinting. The results showed that the varied band patterns of DNA fingerprints were generated from templates depending on the kinds of primers or animal species. The same primer applied to the same breed, all of the main bands are similar, but which were different among species. In order to try to identify the species from the mixture of meat by RAPD fingerprinting, the meat of ostrich and cattle was mixed in different ratios for this study. The results showed that it could be easily and precisely distinguished according to the band distribution of RAPD patterns.

• 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.

• Korean Journal of Food Science and Technology
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• v.37 no.4
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• pp.611-617
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• 2005

Dispersed repetitive DNA elements in genomes of microorganisms differ among and within species. Because distances between repetitive sequences vary depending on bacterial strains, genomic fingerprinting with interspersed repetitive sequence-based probes can be used to distinguish unrelated organisms. Among well-known bacterial repetitive sequences, Repetitive Extragenic Palindromic (REP) sequence has been used to identify environmental bacterial species and strains. We applied REP-PCR to detect and differentiate four major Gram-negative food-borne bacterial pathogens, E. coli, Salmonella, Shigella, and Vibrio. Target DNA fragments of these pathogens were amplified by REP-PCR method. PCR-generated DNA fragments were separated on 1.5% agarose gel. Dendrograms for PCR products of each strain were constructed using photo-documentation system. REP-PCR reactions with primer pairs REP1R-I and REP2-I revealed distinct REP-PCR-derived genomic fingerprinting patterns from E. coli, Salmonella, Shigella, and Vibrio. REP-PCR method provided clear distinctions among different bacterial species containing REP-repetitive elements and can be widely used for typing food-borne Gram-negative strains. Results showed established REP-PCR reaction conditions and generated dendrograms could be used with other supplementary genotyping or phenotyping methods to identify isolates from outbreak and to estimate relative degrees of genetic similarities among isolates from different outbreaks to determine whether they are clonally related.

• Preventive Nutrition and Food Science
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• v.3 no.2
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• pp.198-202
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• 1998

The arbitrary primed polymerase chain reaction (AP-PCR) has been used to detect the genetic alternations in the related species. Simple and reproducible fingerprints of complex genomes can be generated using single arbitrary chosen primers and the PCR. The technique was applied to the Oryza species and characterized the relationship among three cultivars of rice species based on theresult of genomic DNA fingerprints. The results indicated that the polymorphism revealed in rice strains and the differences in the PCR product pattern could be represented for each strainis. There was many variationsin the PCR product pattern between cv. Dongin(japonica type)and cv.Hyangdo (indica type), and our chosen AP-primers can ge as markers for strain identification and verfication.

• Korean Journal of Veterinary Research
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• v.45 no.2
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• pp.199-205
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• 2005

DNA fingerprint patterns of 8 Brucella reference strains and 15 B. abortus field isolates were characterized by repetitive element sequence-based PCR (rep-PCR) using BOX- and ERIC-primers in this study. AMOS PCR differentiated all Brucella field isolates from B. abortus RB51, a vaccine strain by producing a B. abortus-specific 498 bp band. Rep-PCR using BOX-primer produced 13 to 18 bands with sizes of between 230 and 3,300 bp, and discriminated Brucella strains to the species level except B. canis and B. suis. PCR products amplified with ERIC primers were, however, not appropriate for differentiating the Brucella isolates. DNA fingerprint patterns for all B. abortus field isolates were identical among them and were put on one cluster with B. abortus biovar 1 reference strain in the dendrogram, indicating they were highly clonal. These results suggested that rep-PCR using BOX primer might to be a useful tool for calculating genetic relatedness among the Brucella species and for the study of brucellosis epidemiology.

• Journal of Microbiology and Biotechnology
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• v.21 no.12
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• pp.1336-1344
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• 2011

This study details and examines a novel ligation-mediated polymerase chain reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4-base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s) determine a subset of the genomic restriction fragments, which are amplified by PCR. The method permits the differentiation of bacterial species strains on the basis of the different DNA band patterns obtained after electrophoresis in polyacrylamide gels stained with ethidium bromide and visualized in UV light. The usefulness of the LM-PCR/Shifter method for genotyping is analyzed by a comparison with the restriction endonuclease analysis of chromosomal DNA by the pulsed-field gel electrophoresis (REA-PFGE) and PCR melting profile (PCR MP) methods for isolates of clinical origin. The clustering of the LM-PCR/Shifter fingerprinting data matched those of the REA-PFGE and PCR MP methods. We found that the LM-PCR/Shifter is rapid, and offers good discriminatory power and excellent reproducibility, making it a method that may be effectively applied in epidemiological studies.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.599-606
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• 2004

Gram-positive antagonistic bacilli were isolated from agricultural soils for possible use in biocontrol of plant pathogenic fungi, Fusarium oxysporum, Rhizoctonia solani, and/or Pythium ultimum. Among the 65 antagonistic Gram-positive soil isolates, 22 strains were identified as Bacillus species by 16S rDNA sequence analyses. Four strains, including DF14, especially exhibited multiple antagonistic properties against the three damping-off fungi. Genotypic properties of the Bacillus isolates were characterized by rapid molecular fingerprinting methods using repetitive extragenic palindromic-PCR (REP-PCR), ribosomal intergenic spacer-length polymorphisms (RIS-LP), 16S rDNA PCR-restriction fragment length polymorphisms (PCR-RFLP), and strain-specific PCR assays. The results indicated that the REP-PCR method was more valuable than the RIS-LP and 16S rDNA PCR-RFLP analyses as a rapid and reliable approach for bacilli typing and identification. The use of strain-specific primers designed based on 16S rDNA sequence comparisons enabled it to be possible to selectively detect a strain, DF14, which is being used as a biocontrol agent against damping-off fungi.