• Animal Systematics, Evolution and Diversity
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• v.38 no.4
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• pp.149-156
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• 2022

The magelonid polychaete Magelona parochilis Zhou and Mortimer, 2013 is newly reported from South Korea. The Korean specimens correspond well to the original description of M. parochilis in having prostomium without horn, mucronate chaetae on chaetiger 9, superior dorsal lobes on chaetigers 1-8, ventral neuropodial lobes on chaetiger 9, smooth edged thoracic notopodial lamellae, and unidirectional tridentate hooded hooks on abdominal chaetigers. Partial sequences of cytochrome c oxidase I (COI) and 16S ribosomal DNA (16S rDNA) of the species were determined from Korean specimens. The detailed description and illustrations are provided with partial sequences of COI and 16S rDNA as molecular markers for species identification.

• International Journal of Oral Biology
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• v.31 no.1
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• pp.11-14
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• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus anginosus using species-specific forward and reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene(rDNA). The primer specificity was tested against 12 S. anginosus strains and 6 different species(10 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. anginosus ATCC $33397^T$. The data showed that species-specific amplicons were obtained from all the S. anginosus strains tested, but not in the six other species. The PCR could detect as little as 0.4pg of the chromosomal DNA from S. anginosus. This suggests that the PCR primers are highly sensitive and applicable to the detection and identification of S. anginosus.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• The Journal of the Korean Society for Microbiology
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• v.35 no.1
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• pp.69-76
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• 2000

Members of the genus Acinetobacter are recognized as newer pathogens of the nosocomial infection with an increasing frequency in recent years. Strains that belonged to A. calcoaceticus A. baumannii complex (genomic species 1, 2, 3, and 13TU) were major groups associated with nosocomial infection. Phenotypic identification was unreliable and laborious method to classify Acinetobacter strains into 19 genomic species. Rapid and reliable identification of clinical isolates is essential to diagnosis and epidemiology of Acinetobacter. We investigated the suitability of amplified ribosomal DNA restriction analysis (ARDRA) to identify genomic species of 131 Acinetobacter isolates. The 16S rRNA genes (ribosomal DNA) were enzymatically amplified and the amplified PCR products were restricted independently with the enzymes, AluI, CfoI, and MboI. Genomic species of Acinetobacter was classified by the combinations of restriction patterns. The analysis was showed that restriction profiles were characteristic for each genomic species. One hundred fourteen isolates were identified as A. baumannii, twelve were identified as genomic species 13TU, and one was identified as genomic species 3. Four isolates were found to be unknown organisms. All of the isolates which were identified to A. baumannii by phenotypic tests were completely discriminated into A. baumannii and genomic species 13TU by ARDRA. This study demonstrates that ARDRA is a rapid and simple techniques for the identification of Acinetobacter species according to the genomic species.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.13-24
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• 2012

The genetic diversity of plant growth-promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with the sugarcane (Saccharum officinarum L.) rhizosphere was analyzed. Selected isolates were screened for plant growthpromoting properties including production of indole acetic acid, phosphate solubilization, denitrification ability, and production of antifungal metabolites. Furthermore, 16S rDNA sequence analysis was performed to identify and differentiate these isolates. Based on 16S rDNA sequence similarity, the isolates were designated as Pseudomonas plecoglossicida, P. fluorescens, P. libaniensis, and P. aeruginosa. Differentiation of isolates belonging to the same group was achieved through different genomic DNA fingerprinting techniques, including randomly amplified polymorphic DNA (RAPD), amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC), and bacterial repetitive BOX elements (BOX) analyses. The genetic diversity observed among the isolates and rep-PCR-generated fingerprinting patterns revealed that PGPR fluorescent pseudomonads are associated with the rhizosphere of sugarcane and that P. plecoglossicida is a dominant species. The knowledge obtained herein regarding the genetic and functional diversity of fluorescent pseudomonads associated with the sugarcane rhizosphere is useful for understanding their ecological role and potential utilization in sustainable agriculture.

• Journal of Food Hygiene and Safety
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• v.35 no.1
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• pp.45-50
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• 2020

In this study, seafood products (n=26) sold on sushi buffet restaurants in the city of Wonju were monitored by analyzing sequences of DNA barcode markers (cytochrome c oxidase subunit I and 16S ribosomal RNA genes). NCBI BLAST database was screened with the barcode sequences analyzed as a query for species identification. The BLAST search revealed that fifteen samples (58%) analyzed were consistent with their labeling information; however, the ingredients used in seven samples (27%) were not compliant with their label information. In the case of these mislabeled products, ingredients for sutchi catfish sushi and cherry bass sashimi were identified as Pangasianodon hypophthalmus and Lampris guttatus, respectively. For Japanese flying-fish roe sushi and Pacific herring roe sushi, roe of Mallotus villosus was used as an ingredient. Amphioctopus fangsiao and A. membranaceus were used in octopus sushi and soybean-marinated squid products, respectively. This monitoring result can contribute to the protection of consumer rights and the reduction of fraudulent practices in the food industry.

• Environmental Engineering Research
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• v.14 no.1
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• Journal of Life Science
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• v.19 no.11
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• pp.1522-1528
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• 2009

A marine bacterium was isolated from brown seaweeds for its ability to degrade alginate. Analysis of 16S ribosomal DNA sequence revealed that the strain belongs to Streptomyces like strain ALG-5 which was reported previously. New alginate lyase gene of Streptomyces sp. M3 was cloned by using PCR with the specific primers designed from homologous nucleotide sequences. The consensus sequences of N-terminal YXRSELREM and C-terminal YFKAGXYXQ were conserved in the M3 alginate lyase amino acid sequences. The homology model for the M3 alginate lyase showed a characteristic structure of $\beta$-jelly roll fold main domain like alyPG from Corynebacterium sp. ALY-1. The homogenate of the recombinant E. coli with the alginate lyase gene showed more degrading activity for polyguluronate block than polymannuronate block. The results from the multiple alignments and the homology modeling elucidated in the M3 alginate lyase can be classified into family PL-7.

• International Journal of Oral Biology
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• v.35 no.1
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• pp.21-25
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• 2010

This study was undertaken to develop species-specific forward and universal reverse PCR primers for the detection of Streptococcus sobrinus. These primers target the variable regions of the 16S ribosomal RNA coding gene (rDNA) and their specificity was tested against 10 strains of S. sobrinus strains and 20 different species of oral bacteria using serial dilutions of the purified genomic DNA of S. sobrinus ATCC $33478^T$. Our data show that species-specific amplicons were obtained from all the S. sobrinus strains tested but not from other species. Both direct and nested PCR could detect as little as 400 pg and 4 fg of genomic DNA from S. sobrinus ATCC $33478^T$, respectively. This result suggests that these PCR primers are highly specific and sensitive and applicable to the detection of S. sobrinus.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.319-324
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• 2012

In this study, we investigated molecular divergences and phylogenetic characteristics of the 16S ribosomal RNA (rRNA) and RNA polymerase beta subunit (rpoB) gene sequences from the order Oscillatoriales (Cyanobacteria). The rpoB of Oscillatoriales showed higher genetic divergence when compared with those of 16S rRNA (p-distance: rpoB=0.270, 16S=0.109), and these differences were statistically significant (Student t-test, p<0.001). Phylogenetic trees of 16S rRNA and rpoB were generally compatible; however, rpoB tree clearly separated the compared Oscillatoriales taxa, with higher phylogenetic resolution. In addition, parsimony analyses showed that rpoB gene evolved 2.40-fold faster than 16S rRNA. These results suggest that the rpoB is a useful gene for the molecular phylogenetics and species discrimination in the order Oscillatoriales.