• Biomedical Science Letters
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• v.9 no.3
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• Molecules and Cells
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• v.25 no.4
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• pp.553-558
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• 2008

Essential aspects of the innate immune response to microbial infection appear to be conserved between insects and mammals. In order to identify new Drosophila melanogaster genes involved in the immune response, we performed gene expression profiling of Drosophila SL2 cells stimulated with bacterial (LPS/PGN) or fungal (curdlan) components using a cDNA microarray that contained 5,405 Drosophila cDNAs. We found that some genes were similarly regulated by LPS/PGN and curdlan. However, a large number, belonging to the functional classes of cell organization, development, signal transduction, morphogenesis, cell cycle, and DNA replication, displayed significant differences in their transcription profiles between the two treatments, demonstrating that bacterial and fungal components induce different immune response even in an in vitro cell system.

• Journal of Ecology and Environment
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• v.41 no.3
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• pp.99-106
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• 2017

Background: Plants over-expressing Arabidopsis ABF3 (abscisic acid-responsive element-binding factor 3) have enhanced tolerance to various environmental stresses, especially drought. Using terminal restriction fragment length polymorphism (T-RFLP) analysis, we compared the rhizosphere-associated structures of microbial communities for transgenic potato containing this gene and conventional "Jopoong" plants. Results: During a 2-year field experiment, fungal richness, evenness, and diversity varied by year, increasing in 2010 when a moderate water deficit occurred. By contrast, the bacterial richness decreased in 2010 while evenness and diversity were similar in both years. No significant difference was observed in any indices for either sampling time or plant line. Although the composition of the microbial communities (defined as T-RF profiles) changed according to year and sampling time, differences were not significant between the transgenic and control plants. Conclusions: The results in this study suggest that the insertion of ABF3 into potato has no detectable (by current T-RFLP technique) effects on rhizosphere communities, and that any possible influences, if any, can be masked by seasonal or yearly variations.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.1013-1017
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• 2020

Mealybugs (Hemiptera: Coccomorpha: Pseudococcidae) harbor diverse microbial symbionts that play essential roles in host physiology, ecology, and evolution. In this study we aimed to reveal microbial communities associated with two different mealybugs, papaya mealybug (Paracoccus marginatus) and two-tailed mealybug (Ferrisia virgata) collected from the same host plant. Comparative analysis of microbial communities associated with these mealybugs revealed differences that appear to stem from phylogenetic associations and different nutritional requirements. This first report on both bacterial and fungal communities associated with these mealybugs provides a preliminary insight on factors affecting the endomicrobial communities.

• Journal of Environmental Science International
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• v.25 no.4
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• pp.525-534
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• 2016

The biological wastewater treatment plant, which uses microbial community to remove organic matter and nutrients in wastewater, is known as its nonlinear behavior and uncertainty to operate. Therefore, operation of the biological wastewater treatment process much depends on observation and knowledge of operators. The manual inspection of human operators is essential to manage the process properly, however, it is impossible to detect a fault promptly so that the process can be exposed to improper condition not securing safe effluent quality. Among various process faults, equipment malfunction is critical to maintain normal operational state. To detect equipment faults automatically, the dynamic time warping was tested using on-line oxidation-reduction potential (ORP) and dissolved oxygen (DO) profiles in a sequencing batch reactor (SBR), which is a type of wastewater treatment process. After one cycle profiles of ORP and DO were measured and stored, they were warped to the template profiles which were prepared already and the distance result, accumulated distance (D) values were calculated. If the D values were increased significantly, some kinds of faults could be detected and an alarm could be sent to the operator. By this way, it seems to be possible to make an early detecting of process faults.

• The Plant Pathology Journal
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• v.30 no.1
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• pp.33-42
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• 2014

Nivalenol (NIV) and deoxynivalenol (DON) are predominant Fusarium-producing mycotoxins found in grains, which are mainly produced by Fusarium asiaticum and F. graminearum. NIV is found in most of cereals grown in Korea, but the genetic basis for NIV production by F. asiaticum has not been extensively explored. In this study, 12 genes belonging to the trichothecene biosynthetic gene cluster were compared at the transcriptional level between two NIV-producing F. asiaticum and four DON-producing F. graminearum strains. Chemical analysis revealed that time-course toxin production patterns over 14 days did not differ between NIV and DON strains, excluding F. asiaticum R308, which was a low NIV producer. Both quantitative real-time polymerase chain reaction and Northern analysis revealed that the majority of TRI gene transcripts peaked at day 2 in both NIV and DON producers, which is 2 days earlier than trichothecene accumulation in liquid medium. Comparison of the gene expression profiles identified an NIV-specific pattern in two transcription factor-encoding TRI genes (TRI6 and TRI10) and TRI101, which showed two gene expression peaks during both the early and late incubation periods. In addition, the amount of trichothecenes produced by both DON and NIV producers were correlated with the expression levels of TRI genes, regardless of the trichothecene chemotypes. Therefore, the reduced production of NIV by R308 compared to NIV or DON by the other strains may be attributable to the significantly lower expression levels of the TRI genes, which showed early expression patterns.

• The Plant Pathology Journal
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• v.32 no.2
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• pp.136-144
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• 2016

Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1352-1359
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• 2018

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (${\text\tiny{L}}-arabinose$, ${\text\tiny{L}}-rhamnose$, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

• Journal of Life Science
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• v.5 no.4
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• pp.211-217
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• 1995

• Food Science of Animal Resources
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• v.29 no.3
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• pp.349-355
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• 2009

The temperature dependence of time temperature integrator (TTI) was investigated in terms of the Arrhenius activation energy (Ea) to determine TTI requirements to accurately predict meat quality during storage. Mathematical simulation was conducted using a numerical analysis. First, using Euler's method and MS Excel VBA, the TTI color change was kinetically modeled and numerically calculated under several storage conditions. From the TTI color variable profiles calculated from the storage time-temperature profiles, $T_{eff}$, which is a constant temperature representing the whole temperature profiles, was calculated. Upon predicting Pseudomonas spp. concentrations (one of the meat qualities) from $T_{eff}$, it was found that if $Ea_{microbial\;spoilage}=Ea_{TTI}$ be true, then Pseudomonas concentrations were calculated to be constant with the same TTI color values, regardless of time-temperature profiles, whereas if $Ea_{microbial\;spoilage}{\neq}Ea_{TTI}$ then Pseudomonas concentrations varied even with the same TTI color values. This indicates that each TTI color value represents its own fixed degree of meat quality, only if $Ea_{meat\;qualities}=Ea_{TTI}$.