• Journal of Microbiology
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• v.43 no.6
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• pp.572-576
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• 2005

This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.878-884
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• 2013

Salmonella is a major foodborne pathogen that causes a variety of human diseases. Development of ligands directly and specifically binding to the Salmonella will be crucial for the rapid detection of, and thus for efficient protection from, the virulent bacteria. In this study, we identified a RNA aptamer-based ligand that can specifically recognize Salmonella Typhimurium through SELEX technology. To this end, we isolated and characterized an RNase-resistant RNA aptamer that bound to the OmpC protein of Salmonella Typhimurium with high specificity and affinity ($K_d$ ~ 20 nM). Of note, the selected aptamer was found to specifically bind to Salmonella Typhimurium, but neither to Gram-positive bacteria (Staphylococcus aureus) nor to other Gram-negative bacteria (Escherichia coli O157:H7). This was evinced by aptamer-immobilized ELISA and aptamer-linked precipitation experiments. This Salmonella species-specific aptamer could be useful as a diagnostic ligand against pathogen-caused foodborne sickness.

• 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.

• Bulletin of the Korean Chemical Society
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• v.27 no.4
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• pp.479-483
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• 2006

We developed a microfluidic immunoassay platform for the detection of various analytes such as bacterial pathogen by packing antibody-immobilized glass beads in spatially-isolated microchambers on a microfluidic device. Primary amines of antibody were covalently conjugated to carboxyl-terminated glass beads previously treated with aminosilane followed by glutaraldehyde. Through this covalent binding, up to 905 $\mu$g immunoglobulin G (IgG) per gram of glass beads was immobilized. For application, glass beads attaching antibody specific to Escherichia coli O157:H7, a foodborne pathogen, were packed into a microfluidic device and used for the detection of the serotype. This prototype immunoassay device can be used for the simultaneous detection of multiple analytes by sequentially packing different-sized glass beads attaching different antibody in discrete microchambers on a single microfluidic device.

• Food Science of Animal Resources
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• v.30 no.4
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• pp.590-596
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• 2010

Meat and meat products are a potential source of food-borne pathogens, including Staphylococcus aureus, Salmonella spp., Escherichia coli O157:H7, and Bacillus cereus. A sensitive and specific PCR assay for the detection of these pathogens in meat and meat products was developed in this study, as part of a broader effort to reduce the potential health hazards posed by these pathogens. Initially, PCR conditions were standardized with purified DNA. Under standard conditions, the detection level for PCR was as low as 10 pg of purified bacterial DNA. After overnight growth of bacteria in a broth medium, as few as $10^2$ CFU of bacteria were detected by PCR assay. The primers employed in the PCR assay were found to be highly specific for individual organisms, and evidenced no cross-reactivity with heterologous organisms. Additionally, the multiplex PCR assays also amplified some target genes from the four pathogens, and multiplex amplification was obtained from as little as 10 pg of DNA, thus illustrating the excellent specificity and high sensitivity of the assay. In conclusion, this PCR-based technique provides a sensitive and specific method for the detection of S. aureus, Salmonella spp., E. coli O157:H7, and B. cereus in meat and meat products.

• Journal of Microbiology and Biotechnology
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• v.32 no.1
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• pp.91-98
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• 2022

Tetanus is a potentially fatal public health illness resulted from the neurotoxins generated by Clostridium tetani. C. tetani is not easily culturable and culturing the relevant bacteria from infected wounds has rarely been useful in diagnosis; PCR-based assays can only be conducted at highly sophisticated laboratories. Therefore, a real-time recombinase polymerase amplification assay (Exo-RPA) was constructed to identify the fragments of the neurotoxin gene of C. tetani. Primers and the exo probe targeting the conserved region were designed, and the resulting amplicons could be detected in less than 20 min, with a detection limit of 20 copies/reaction. The RPA assay displayed good selectivity, and there were no cross-reactions with other infectious bacteria common in penetrating wounds. Tests of target-spiked serum and pus extract revealed that RPA is robust to interfering factors and has great potential for further development for biological sample analysis. This method has been confirmed to be reliable for discriminating between toxic and nontoxic C. tetani strains. The RPA assay dramatically improves the diagnostic efficacy with simplified device architecture and is a promising alternative to real-time PCR for tetanus detection.

• KSBB Journal
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• v.21 no.5
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• pp.341-346
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• 2006

This study was carried out to establish the optimum condition for cell disruption with a sonificator in the detection of the gram negative bacteria, E. coli for the purpose of developing automatic fluorometer. The efficiency of sonification on the E. coli disruption was greatly dependent on the diameter of sonificator probe tip. The larger sonificator probe diameter showed greater disruption effect. Sonificator probe of 13 mm diameter was the most efficient one for E. coli when sonificated for 20 seconds. The efficiency of the E. coli disruption differed greatly according to the depth of sonificator probe tip sank in the sample solution. The shorter the distance between probe tip end and the bottom of the container, the higher the disruption efficiency. The detection limit of E. coli was $5{\times}10^5CFU/m{\ell}$ when sample was sonificated for 20 seconds with a sonificator probe of 13 mm diameter.

• KSBB Journal
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• v.21 no.5
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• pp.347-352
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• 2006

This study was carried out to establish the optimum condition for cell disruption with a sonificator in the detection of the gram positive bacteria, Bacillus globigii and Streptococcus epidermidis for the purpose of developing automatic fluorometer. The efficiency of sonificator on the Bacillus globigii and Streptococcus epidermidis disruption differed greatly according to the diameter of sonificator probe tip. The larger sonificator probe diameter showed greater disruption. Bacillus globigii was more disruptive than Streptococcus epidermidis. Sonificator probe of the 13 mm diameter was the most efficient one when sample was sonificated for 20 seconds. The detection limits of Bacillus globigii and Streptococcus epidermidis were $10^5CFU/m{\ell}\;and\;5{\times}10^5CFU/m{\ell}$ respectively when samples were sonificated for 20 seconds with a sonificator probe of 13 mm diameter.

• Journal of The Korean Society of Grassland and Forage Science
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• v.39 no.3
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• pp.132-140
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• 2019

Fermented total mixed ration (TMR) is a novel feed for ruminants in South Korea. The purpose of this study was to evaluate the effects of lactic acid bacteria (LAB) on the quality of TMR and in vitro ruminal fermentation. Strains of three LAB spp. (Lactobacillus plantarum, L. brevis, L. mucosae) were used in fermentation of TMR. Inoculations with the three LAB spp. lowered pH and increased concentrations of lactic acid, acetic acid, and total organic acid compared to non-LAB inoculated control (only addition of an equivalent amount of water) (p<0.05). Bacterial composition indicated that aerobic bacteria and LAB were higher. However, E. coli were lower in the fermented TMR than those in the control treatment (p<0.05). Among the treatments, L. brevis treatment had the highest concentration of total organic acid without fungus detection. Gas production, pH, and ammonia-nitrogen during ruminal in vitro incubation did not differ throughout incubation. However, ruminal total VFA concentration was higher (p<0.05) in the LAB spp. treatments than the control treatment at 48 hours. Overall, the use of L. brevis as an inoculant for fermentation of high moisture. TMR could inhibit fungi growth and promote lactic fermentation, and enhance digestion in the rumen.

• Journal of Korean society of Dental Hygiene
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• v.17 no.2
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• pp.319-330
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• 2017

Objectives: The purpose of this study was to compare SYBR Green qPCR, TaqMan, and bacterial selective medium cultures for accurate quantitative analysis of oral microorganisms. Methods: The SYBR Green method is widely used to analyze the total amount of oral microorganisms in oral saliva. However, in this study, MTR-PCR method based on TaqMan method was performed using newly developed primers and probes. In addition, it was designed to confirm the detection agreement of bacteria among bacteria detection method. Results: As a result of MRT-PCR and SYBR Green qPCR analysis, more than 40 times (0.9-362.9 times) bacterium was detected by MRT-PCR. In addition, more bacteria were detected in saliva in the order of MRT-PCR, SYBR Green qPCR, and bacterium culture, and the results of MRB-PCR and SYBR Green qPCR showed the highest agreement. The agreement between the three methods for detecting P. intermedia was similar between 71.4 and 88.6%, but the agreement between MRT-PCR and SYBR Green qPCR was 80% for S. mutans. Among them, the number of total bacteria, P. intermedia and S. mutans bacteria in saliva was higher than that of SYBR Green qPCR method, and bacterium culture method by MRT-PCR method. P. intermedia and S. mutans in saliva were detected by MRT-PCR and MRT-PCR in 88.6% of cases, followed by the SYBR Green qPCR method (80.0%). Conclusions: The SYBR Green qPCR method is the same molecular biology method, but it can not analyze the germs at the same time. Bacterial culturing takes a lot of time if there is no selective culture medium. Therefore, the MRT-PCR method using newly developed primers and probes is considered to be the best method.