• Fisheries and Aquatic Sciences
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• v.11 no.1
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• pp.32-35
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• 2008

The Suminoe oyster, Crassostrea ariakensis, occurs in estuaries where rivers meet seawater. In Korea, it is one of the most popular fisheries resources in the Nam River and Sumjin River. However, the genetic identification of this species has been questioned, because specimens are often mis-identified as other species. To identify the species, we conducted polymerase chain reaction (PCR) amplification of the internal transcribed spacer-1 (ITS-1) region, followed by digestion with the restriction enzyme HaeIII. Restriction profiles for oysters collected from Korea, Japan, and China (north and south) were determined by comparing the PCR-restriction fragment length polymorphism (RFLP) patterns of the ITS-1 regions. Our study verified that the oysters collected from Korea were C. ariakensis based on the PCR-RFLP patterns. These results emphasize the value of molecular markers for identifying morphologically uncertain species.

• The Plant Pathology Journal
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• v.25 no.3
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• pp.236-240
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• 2009

Tylenchulus semipenetrans, citrus nematode is an important phytopathogenic nematode and responsible for serious damage on citrus. However, little information is available about genetic variability of T. semipenetrans among different populations with variation of conventional diagnostic characteristics. In this study, we compared the morphometric and genetic characteristics among different populations. The mature female of T. semipenetrans collected in this study had thicker cuticle than those in the previous studies. In comparative sequence analysis of T. semipenetrans populations obtained from Jeju in Korea, we observed genetic variations within clones generated from single individuals. To determine whether variability among copies of nuclear ribosomal DNA sequences exists in the genome of T. semipenetrans, PCR-RFLP technique from individuals of Korean isolates with MseI and MspI restriction enzymes was used to prove experimentally that all populations have intra-specific variations. Restriction enzyme digestion created several fragments on 3.0% agarose gel corresponding to several haplotypes in all populations, though some populations displayed fragment deletion. The total length of fragments was larger than before digestion, indicating sequence heterogeneity within the genome of T. semipenetrans.

• The Plant Pathology Journal
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• v.17 no.4
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• pp.189-193
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• 2001

The relationships between the phytoplasmas infecting Zizyphus jujuba and Paulownia coreana were investigated by PCR-RELP. The 16S rRNA genes of the phytoplasmas were analyzed and compared with each other after PCR amplification. The amplified bands 1.4 kb in size were analyzed by both restriction digestion and sequencing after cloning into a plasmid vector. In some cases, two different kinds of inserts were observed in the isolates that originated from a single plant. However, many of them appeared to be the amplification products of chloroplastic 16S rRNA gene of host plants. The phytoplasma gene could be differentiated from the chloroplastic gene by restriction digestion of the plasmids carrying the amplification products. Only the recombinant plasmids carrying phytoplasma 16S rRNA gene produced a 1.4 kb band when digested with the enzyme BanII. Of the 52 recombinant plasmids analyzed, 42 appeared to contain inserts that originated from the chloroplastic 16S rRNA gene of the host plants. No variation was detected among 16S rRNA gene of nine phytoplasma isolates infecting Z. jujuba. However, the phytoplasmas infecting Z. jujuba were different from that infecting P. coreana.

• Journal of Microbiology and Biotechnology
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• v.9 no.1
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• pp.78-83
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• 1999

Thirty-six environmental isolates of Vibrio vulnificus obtained from seawater, sediments, and raw seafoods, and 18 clinical isolates from Vibrio septicemia patients were typed by restriction endonuclease digestion profiles (REDP) of genomic DNA with SfiI. The results revealed a high-level of variation in REDPs, indicating a vast genomic diversity among V. vulnificus strains. Genetic relatedness of the strains showed similarities ranging from 10％ to 100％. Different REDPs for isolates from various raw seafoods were obtained, and clustering of strains according to type of seafoods was not observed. In contrast, clinical isolates of V. vulnificus showed higher similarity to one another, and could be subdivided into one separate group. The difference in REDPs of the V. vulnificus isolates from clinical origin and from raw seafoods substantiates the previous observation that only a single type of pathogenic strain was involved in each human infection, despite the numerous genetically polymorphic strains found from implicated oysters.

• 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.

• YAKHAK HOEJI
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• v.34 no.2
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• pp.139-146
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• 1990

Streptococcus sp. TR-1 which has inducible resistance to MLS antibiotics was isolated from soil samples in Korea. Streptococcus sp. TR-1 was cultured in Lysis broth, then a plasmid was isolated by modified Elliker method. Bacillus subtilis UOTO277 was transformed with that plasmid. This result showed that the plasmid has the gene relating with inducible resistance to MLS antibiotics. It was named pMB4 and its size was determined about 2.4 Kb by results of digestion with various restriction enzymes. Restriction endonuclease cleavage site map of pMB4 plasmid was made by double digestion of the plasmid. pMB4 plasmid has different restriction endonuclease site map from the other plasmids that have been discovered in Streptococcus sp. so far. And it could be identified that pMB4 plasmid does not have homology with ermK of Bacillus licheniformis EMR but has homology with ermC of Staphylococcus aureus from the results of Southern hybridization.

• Proceedings of the Ginseng society Conference
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• 1990.06a
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• pp.168-174
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• 1990

This study was focused on the characterization of mitochondrial DNA (mtDNA) for molecular genetically approach of energy Production related mechanism in Panax Ein.fend. The simple and efficient method of mtDNA isolation from ginseng has been developed by modification of recently advanced methods. This procedure can successfully apply to mtDNA isolation of several plants. MtDNA of etiolated shoot and one-year root were digested with restriction endonucleases, but that of 6-year root not Any difference was not observed in the restriction endonuclease digestion patterns among the ginseng variants. Molecular size of ginseng mtDNA was estimated at least 159 kb by the restriction endonuclease fragment analysis. The 4.5 kb extra band at the lane of EcoRll treatment could be observed in restriction patterns digested with the methylation sensitive endonucleases, BstN 1 and EcoRll. For construction of mitochondrial genomic library of ginseng, mtDNA was partially digested with EcoRl, and packaged with EMBL4 phage vector Genomic library was screened and purified for further research including restricttion mapping of ginseng mtDNA, and cloning of the genes. The gene of ATP synthase A subunit was cloned koto the purified EMBL4 library clone No. 16. Now, clone No. 16 is subcloned for structure gene sequence analysis.

• Korean Journal of Oriental Medicine
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• v.1 no.1
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• pp.477-493
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• 1995

In order to facilitate the molecular characterization of the Herpes simplex Virus types 1 and types 2 genome DNAs, a gene library of cloned restriction frtgments have been produced. The Vero cells were infected with HSV-1 and HSV-2. 48 hours after infection, the infected cells Ivere Iysed, and multinucleated giant cells were observed approximately at seventy-two hours postinfection. The multiplication of HSV-1 and HSV-2 was observed in Vero cells using electromicroscopy. The nucleocapsids in nuclei were obseryed, and the assembled virions were budded out through the vacuole, and the virions were released from the cells. HSV-1 and HSV-2 was analyzed by digestion of their genome DANs with restriction ensymes. HSV-1 and HSV-2 genome DNAs were digested with BarnHI, Bgfl respectively. The BarnHI rlestriction fragments of HSV-1 and HSV-2 genome DNAs were twenty-seven fragments and thair molecular sizes were ranging $0.70{\sim}15.08$, $4.4{\sim}31.0$ tilobases. The BglII restriction fragments of HSV-1 and HSV-2 genome DNAs were sixteen, eighteen fragments and thair molecular sizes were ranging $4.8{\sim}30.0$, $1.2{\sim}25.0$ kilobases. And then BglII restriction frgments were cloned in Escherichia coli(E.coil) using the plasmid vector pBacPAK9.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1170-1177
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• 2005

Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to monitor inoculated oil-degrading microorganisms during bioremedial treatability tests. A pair of universal primers, fluorescently labeled 521F and 1392R, was employed to amplify small subunit rDNA in order to simultaneously detect two bacterial strains, Corynebacterium sp. IC10 and Sphingomonas sp. KH3-2, and a yeast strain, Yarrowia lipolytica 180. Digestion of the 5'-end fluorescence/labeled PCR products with HhaI produced specific terminal-restriction fragments (T-RFs) of 185 and 442 bases, corresponding to Corynebacterium sp. IC10 and Y. lipolytica 180, respectively. The enzyme NruI produced a specific T-RF of 338 bases for Sphingomonas sp. KH3-2. The detection limit for oildegrading microorganisms that were inoculated into natural environments was determined to be $0.01\%$ of the total microbial count, regardless of the background environment. When three oil-degrading microorganisms were released into oil-contaminated sand microenvironments, strains IC10 and 180 survived for 35 days after inoculation, whereas strain KH3-2 was detected at 8 days, but not at 35 days. This result implies that T-RFLP could be a useful tool for monitoring the survival and relative abundance of specific microbial strains inoculated into contaminated environments.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.334-339
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• 1999

More innovative molecular markers were investigated for rapid and consistent differentiation of Metarhizium anisopliae var. majus from M. anisopliae var. anisopliae. A total of 28 isolates were obtained from various countries and hosts: 13 isolates of M. anisopliae var. anisopliae, 12 isolates of M. anisopliae var. majus, and 3 isolates of M. anisopliae collected in Korea. This study involved restriction enzyme digestions of a PCR product amplified from nuclear internally transcribed spacer (ITS) and a portion of the 28S rDNA regions. Among 11 different restriction enzymes used in this study, MboⅠ digestion particularly produced a restriction pattern that had characteristics of M. anisopliae var. majus. This restriction pattern was consistent in all isolates of M. anisopliae var. majus regardless of their geographic origins and insect hosts. Mapping experiments revealed that MboⅠ sites of M. anisopliae var. majus are identical to those of M. anisopliae var. anisopliae with an exception for the presence of an additional site in the PCR product. Results from this study provide an additional method for identification and differentiation of isolates of these two varieties of M. anisopliae for use in the field and laboratory experiments.