• Korean Journal of Microbiology
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• v.48 no.4
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• pp.262-269
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• 2012

Seasonal differences of the cultivable bacterial communities associated with the marine sponge, Hymeniacidon sinapium, between spring and summer were analyzed through the Amplified Ribosomal DNA Restriction Analysis (ARDRA). For the cultivation of the bacterial isolates, modified Zobell and MA media were used. The 16S rDNA of individual strains were amplified and fragmented by using two restriction enzymes, HaeIII and MspI. As a result, 23 ARDRA types from the spring sponge and 28 types from the summer sponge were obtained. The partial sequencing result of 1 to 3 selected strains from each types showed over 94% similarities with the known species from the public database. The bacterial communities from the sponge, captured on spring, contained 4 phyla: Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. There were 5 phyla observed from the bacterial communities associated with the sponge, captured on summer: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes. Gammaproteobacteria was predominant group in both spring and summer, accounted for 33.8% of total in spring and 67.4% in summer, showed increase pattern on summer. Because Firmicutes and Actinobacteria participated in 30.2% and 8.3% of the spring sponge while they represented only 6.9% and 0% of the summer sponge, both bacterial groups showed decrease drift on summer. Betaproteobacteria (4.7%) and Bacteroidetes (4.7%) were only observed on the sponge captured on summer. On the sponge, Hymeniacidon sinapium, more diverse bacterial communities were shown on summer than on spring, and even from the same sponge, there were seasonal differences.

• 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.

• Journal of Microbiology
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• v.44 no.3
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• pp.263-268
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• 2006

Pleurotus ostreatus is a widely cultivated white-rot fungus. Owing to its considerable enzymatic versatility p. ostreatus has become the focus of increasing attention for its possible utility in biobleaching and bioremediation applications. Interactions between microorganisms can be an important factor in those processes. In this study, we describe the presence of a bacterial species associated with P. ostreatus strain G2. This bacterial species grew slowly (approximately 30 days) in the liquid and semi-solid media tested. When p. ostreatus was inoculated in solid media containing Tween 80 or Tween 20, bacterial microcolonies were detected proximal to the fungal colonies, and the relevant bacterium was identified via the analysis of a partial 16S rDNA sequence; it was determined to belong to the Burkholderia cepacia complex, but was not closely related to other fungus-isolated Burkholderiaceae. New specific primers were designed, and confirmed the presence of in vitro P. ostreatus cultures. This is the first time that a bacterial species belonging to the B. cepacia complex has been found associated with P. ostreatus.

• Journal of Microbiology and Biotechnology
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• v.17 no.10
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• pp.1607-1615
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• 2007

We investigated the applicability of the TEM-l ${\beta}$-lactamase fragment complementation (BFC) system to develop a strategy for the screening of protein-protein interactions in bacteria. A BFC system containing a human Fas-associated death domain (hFADD) and human Fas death domain (hFasDD) was generated. The hFADD-hFasDD interaction was verified by cell survivability in ampicillin-containing medium and the colorimetric change of nitrocefin. It was also confirmed by His pull-down assay using cell lysates obtained in selection steps. A coiled-coil helix coiled-coil domain-containing protein 5 (CHCH5) was identified as an interacting protein of human uracil DNA glycosylase (hUNG) from the bacterial BFC cDNA library strategy. The interaction between hUNG and CHCH5 was further confirmed with immunoprecipitation using a mammalian expression system. CHCH5 enhanced the DNA glycosylase activity of hUNG to remove uracil from DNA duplexes containing a U/G mismatch pair. These results suggest that the bacterial BFC cDNA library strategy can be effectively used to identify interacting protein pairs.

• The Microorganisms and Industry
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• v.12 no.1
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• pp.23-27
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• 1986

최근까지 후핵세포에 있어서 이러한 불합리 제조합의 예는 상당수가 알려져 있는데 세포분화 과정에 수반되는 체세포 재조합, 효모의 접합형 전환, retroviral DNA의 숙주 DNA로의 삽입, 그리고 여러가지 다양한 종류의 tranposition 현상등이 그것이다. 그러나 비상동 재조합의 분자생물학적 연구는 주로 진핵세포를 대상으로 시작되었는데 그 소재는 주로 bacteriophage의 DNA, 단세포-다형질발현(clonal polymorphism)에 간여하는 유전인자, 그리고 transposable element들이다. 특히 bacterial transposable element는 구조적 특성이 후핵세포의 그것과 상당히 유사하기 때문에 진화의 초기단계에 그 시원을 두고 있으리라 추측되며 넓은 분포, 임상적 중요성, 조작이 용이한 점등의 이유로 많은 연구가 진행되어 왔다.

• Korean Journal of Microbiology
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• v.46 no.2
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• pp.177-182
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• 2010

The bacterial community structure of two marine sponges, Spirastrella abata and Cinachyrella sp. collected from Jeju Island, in April 2009, was analyzed by 16S rDNA-denaturing gradient gel electrophoresis (DGGE). DGGE banding patterns indicated 8 and 7 bands for Spirastrella abata and Cinachyrella sp., respectively. Comparative sequence analysis of variable DGGE bands revealed from 92% to 100% similarity to the known published sequences. The bacterial groups associated with Spirastrella abata were Alphaproteobacteria and Deltaproteobacteria. The bacterial community of Cinachyrella sp. consisted of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria. Alphaproteobacteria was common and predominant in both the sponge species. Deltaproteobacteria was found only in Spirastrella abata while Actinobacteria and Gammaproteobacteria were found only in Cinachyrella sp. The results revealed that though the common bacterial group was found in both the sponges, the bacterial community profiles differed between the two sponge species obtained from the same geographical location.

• BMB Reports
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• v.40 no.5
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• pp.656-661
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• 2007

In this report, we describe an optimized method for generation of ephA8 BAC transgenic mice expressing the lacZ reporter gene under ephA8 regulatory sequences. First, we constructed a targeting vector that carries a 1.2 kb ephA8 DNA upstream of its first exon, a lacZ expression cassette, a kanamycin cassette, and a 0.7 kb ephA8 DNA downstream of its first exon. Second, the targeting vector was electroporated into cells containing the ephA8 BAC and pKOBEGA, in which recombinases induce a homologous recombination between the ephA8 BAC DNA and the targeting vector. Third, the FLP plasmid expressing the Flipase was electroporated into these bacteria to eliminate a kanamycin cassette from the recombinant BAC DNA. The appropriate structures of the modified ephA8 BAC DNA were confirmed by Southern analysis. Finally, BAC transgenic mouse embryos were generated by pronuclear injection of the recombinant BAC DNA. Whole mount X-gal staining revealed that the lacZ reporter expression is restricted to the anterior region of the developing midbrain in each transgenic embryo. These results indicate that the ephA8 BAC DNA contains most, if not all, regulatory sequences to direct temporal and spatial expression of the lacZ gene in vivo.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.236-242
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• 2003

A culture-independent and -dependent survey of the bacterial community structure in the rhizosphere and soil samples from hot pepper plants was conducted using 16S rDNA clone library and FAME analyses. Out of the 78 clones sequenced, 56% belonged to Proteobacteria, 4% to high G+C Gram- positive group, 3% to Cytophyga-Flexibacter-Bacreroides, and 32% could not be grouped with any known taxonomic division. Among the 127 FAME isolates identified, 66% belonged to low G+C Gram-positive bacteria (Baciilus spp.) and 26% to high G+C Gram-positive bacteria. In a cluster analysis, the results for both methods were found to be strikingly dissimilar. The current study is the first comparative study of FAME and 165 rDNA clonal analyses performed on the same set of soil, rhizosphere soil, and root samples.

• International Journal of Oral Biology
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• v.46 no.3
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• pp.140-145
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• 2021

This study aimed to develop Lautropia mirabilis-specific quantitative real-time polymerase chain reaction (qPCR) primers based on the sequence of DNA-directed RNA polymerase subunit beta gene. The PrimerSelect program was used in designing of the qPCR primers, RTLam-F4 and RTLam-R3. The specificity of the qPCR primers were performed by conventional PCR with 37 strains of 37 oral bacterial species, including L. mirabilis. The sensitivity of the primers was determined by qPCR with the serial dilution of purified genomic DNA of L. mirabilis KCOM 3484, ranged from 4 ng to 4 fg. The data showed that the qPCR primers could detect only L. mirabilis strains and as little as 40 fg of genome DNA of L. mirabilis KCOM 3484. These results indicate that this qPCR primer pair (RTLam-F4/RTLam-R3) may be useful for species-specific detection of L. mirabilis in epidemiological studies of oral bacterial infectious diseases such as periodontal disease.

• International Journal of Oral Biology
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• v.44 no.3
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• pp.96-100
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• 2019

The purpose of this study was to develop Peptoniphilus mikwangii-specific quantitative real-time polymerase chain reaction (qPCR) primers based on the 16S ribosomal RNA (16S rDNA) gene. The specificity of the primers was determined by conventional PCR using 29 strains of 27 oral bacterial species including P. mikwangii. The sensitivity of the primers was determined by qPCR using the purified genomic DNA of P. mikwangii KCOM $1628^T$ (40 ng to 4 fg). The data showed that the qPCR primers (RTB134-F4/RTB134-R4) could detect P. mikwangii strains exclusively and as little as 40 fg of the genomic DNA of P. mikwangii KCOM $1628^T$. These results suggest that the developed qPCR primer pair can be useful for detecting P. mikwangii in epidemiological studies of oral bacterial infectious diseases.