• Molecules and Cells
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• v.37 no.8
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• pp.605-612
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• 2014

The p73 gene contains an extrinsic P1 promoter and an intrinsic P2 promoter, controlling the transcription of the pro-apoptotic TAp73 isoform and the anti-apoptotic ${\Delta}Np73$ isoform, respectively. The DNA methylation status of both promoters act equally in the epigenetic transcriptional regulation of their relevant isoforms. The aim of this study was to analyze the different effects of these p73 isoforms in 5-aza-2'-deoxycytidine (5-aza-dC)-induced apoptosis in breast cancer cells. We investigated the effects of the DNA demethylation agent, 5-aza-dC, on the T-47D breast cancer cell line, and evaluated the methylation status of the p73 promoters and expression of TAp73 and ${\Delta}Np73$. Furthermore, we assessed the expression of p53 and p73 isoforms in 5-aza-dC-treated T-47D cells and p53 knockout cells. 5-aza-dC induced significant anti-tumor effects in T-47D cells, including inhibition of cell viability, G1 phase arrest and apoptosis. This was associated with p73 promoter demethylation and a concomitant increase in TAp73 mRNA and protein expression. In contrast, the methylation status of promoter P2 was not associated with ${\Delta}Np73$ mRNA or protein levels. Furthermore, demethylation of P2 failed to inhibit the expression of ${\Delta}Np73$ with 5-aza-dC in the p53 knockdown cell model. Our study suggests that demethylation of the P1 and P2 promoters has opposite effects on the expression of p73 isoforms, namely up-regulation of TAp73 and down-regulation of ${\Delta}Np73$. We also demonstrate that p53 likely contributes to 5-aza-dC-induced ${\Delta}Np73$ transcriptional inactivation in breast cancer cells.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.346-351
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• 1999

Tumor cells may alter the expression of proteins involved in antigen processing and presentation, allowing them to avoid recognition and elimination by cytotoxic T cells. In order to investigate whether the major histocompatibility complex (MHC) class I-mediated antigen processing machinery is preserved in human lung cancer cell lines, we examined the expression of multiple components of the MHC class I antigen processing pathway, including transporter associated with antigen processing (TAP), $\beta_2$-microglobulin, MHC class I molecules, and chaperones which have not been previously examined in this context. Row cytometry analysis showed that the cell surface expression of MHC class I molecules was downregulated in all of the cell lines. While some cell lines showed no detectable expression of MHC class I molecules, pulse-chase experiments showed that MHC class I molecules were synthesized in the other cell lines but not transported from the endoplasmic reticulum to the cell surface. Low or nondetectable levels of TAP1 and/or TAP2 expression were demonstrated by Western blot analysis in all of the cell lines, representing a variety of lung tissue types. In some cases, this was accompanied by loss of tapasin expression. Our findings suggest that downregulation of antigen processing may be one of the strategies used by tumors to escape immune surveillance. This study provides further information for designing the potential therapeutic applications such as immunotherapy and gene therapy against cancers.

• Journal of Microbiology
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• v.45 no.5
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• pp.379-387
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• 2007

A hundred and seventeen antibiotic-resistant Escherichia coli strains were isolated from public tap and spring waters which were polluted by fecal coliforms. There were no significant differences between two water sources as to the coliform pollution level (p> 0.05). All E. coli isolates were detected to be resistant to one or more antibiotics tested. Nearly 42% of the isolates showed multiresistant phenotype. Three (2.5%) of these isolates contained class 1 integron. Sequencing analysis of variable regions of the class 1 integrons showed two gene cassette arrays, dfr1-aadA1 and dhfrA17-aadA5. Resistance to ampicillin, tetracycline or trimethoprim-sulfamethoxazole was transferable according to the results of conjugation experiments. The rate of tetracycline resistance was 15%. tet(A)-mediated tetracycline resistance was widespread among tetracycline-resistant E. coli isolates. Genotyping by BOX-polymerase chain reaction (BOX-PCR) showed that some of the strains were epidemiologically related. This is the first report on the prevalence and characterization of class 1 integron-containing E. coli isolates of environmental origin in Turkey.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.313-318
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• 2005

Estimating the reliability of protein-protein interaction data sets obtained by high-throughput technologies such as yeast two-hybrid assays and mass spectrometry is of great importance. We develop a maximum likelihood estimation method that uses both protein localization and gene expression data to estimate the reliability of protein interaction data sets. By integrating protein localization data and gene expression data, we can obtain more accurate estimates of the reliability of various interaction data sets. We apply the method to protein physical interaction data sets and protein complex data sets. The reliability of the yeast two-hybrid interactions by Ito et al. (2001) is 27%, and that by Uetz et at.(2000) is 68%. The reliability of the protein complex data sets using tandem affinity purification-mass spec-trometry (TAP) by Gavin et at. (2002) is 45%, and that using high-throughput mass spectrometric protein complex identification (HMS-PCI) by Ho et al. (2002) is 20%. The method is general and can be applied to analyze any protein interaction data sets.

• Animal Bioscience
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• v.37 no.6
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• pp.993-1000
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• 2024

Objective: This study was conducted to investigate the differential expression of the major histocompatibility complex (MHC) gene region in Eimeria-infected broiler. Methods: We profiled gene expression of Eimeria-infected and uninfected ceca of broilers sampled at 4, 7, and 21 days post-infection (dpi) using RNA sequencing. Differentially expressed genes (DEGs) between two sample groups were identified at each time point. DEGs located on chicken chromosome 16 were used for further analysis. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was conducted for the functional annotation of DEGs. Results: Fourteen significant (false discovery rate <0.1) DEGs were identified at 4 and 7 dpi and categorized into three groups: MHC-Y class I genes, MHC-B region genes, and non-MHC genes. In Eimeria-infected broilers, MHC-Y class I genes were upregulated at 4 dpi but downregulated at 7 dpi. This result implies that MHC-Y class I genes initially activated an immune response, which was then suppressed by Eimeria. Of the MHC-B region genes, the DMB1 gene was upregulated, and TAP-related genes significantly implemented antigen processing for MHC class I at 4 dpi, which was supported by KEGG pathway analysis. Conclusion: This study is the first to investigate MHC gene responses to coccidia infection in chickens using RNA sequencing. MHC-B and MHC-Y genes showed their immune responses in reaction to Eimeria infection. These findings are valuable for understanding chicken MHC gene function.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.240-246
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• 2021

The Chironomidae is a benthic macroinvertebrate commonly found in freshwater ecosystems, along with Ephemeroptera and Trichoptera, which can be used for environmental health assessments. There are approximately 15,000 species of Chironomidae worldwide, but there are limited studies on species identification of domestic Chironomidae larvae. In the present study, we carried out species classification of the Chironomidae larvae that found in Jeju's tap water purification plants using morphological characteristics and genetic identification based on cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA. Body shape, mentum, antenna, mandible in the head capsule, and claws were observed in the larvae for morphological classification. Analysis of 17 larvae collected from faucets and fire hydrants of domestic tap water purification plants revealed the presence of two species, including 14 Orthocladius tamarutilus and 3 Paratrichocladius tammaater. These results will aid the use of the criteria information about species classification of the Chironomidae for water quality management in water purification plants and diversity monitoring of freshwater environments.

• Parasites, Hosts and Diseases
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• v.60 no.4
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• pp.229-239
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• 2022

The high percentage of Vermamoeba was found in tap water in Korea. This study investigated whether Vermamoeba induced allergic airway inflammation in mice. We selected 2 free-living amoebas (FLAs) isolated from tap water, which included Korean FLA 5 (KFA5; Vermamoeba vermiformis) and 21 (an homolog of Acanthamoeba lugdunensis KA/E2). We axenically cultured KFA5 and KFA21. We applied approximately 1×10⁶ to mice's nasal passages 6 times and investigated their pathogenicity. The airway resistance value was significantly increased after KFA5 and KFA21 treatments. The eosinophil recruitment and goblet cell hyperplasia were concomitantly observed in bronchial alveolar lavage (BAL) fluid and lung tissue in mice infected with KFA5 and KFA21. These infections also activated the Th2-related interleukin 25, thymic stromal lymphopoietin, and thymus and activation-regulated chemokines gene expression in mouse lung epithelial cells. The CD4⁺ interleukin 4⁺ cell population was increased in the lung, and the secretion of Th2-, Th17-, and Th1-associated cytokines were upregulated during KFA5 and KFA21 infection in the spleen, lung-draining lymph nodes, and BAL fluid. The pathogenicity (allergenicity) of KFA5 and KFA21 might not have drastically changed during the long-term in vitro culture. Our results suggested that Vermamoeba could elicit allergic airway inflammation and may be an airway allergen.

• 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.

• Korean Journal of Ecology and Environment
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• v.53 no.3
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• pp.286-294
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• 2020

The Chironomus(Diptera: Chironomidae) is a freshwater benthic invertebrate that is an important indicator organism used for environmental pollution and water quality monitoring. In this study, we performed morphological classification and genetic species identification using the cytochrome c oxidase subunit I (COI) gene on mitochondrial DNA for an accurate species classification of Chironomus larvae found in tap water purification plants in Incheon, Korea. Twenty larvae in six water purification plants consist of four species, including twelve Chironomus kiiensis, six Chironomus flaviplumus, one Chironomus dorsalis, and one Polypedilum yongsanensis (not included Genus Chironomus). Morphological characteristics of each larvae were identified based on the head capsule, the mentum, the mandible, the antenna, and the claw. Based on the COI sequences of 21 individuals of 17 Chironomus species registered in NCBI Genbank, phylogenetic analysis indicated that the 20 individuals investigated in this study consist of the same clade with corresponding species of the high homology (99~100%) including C. kiiensis, C. flaviplumus, C. dorsalis, and P. yongsanensis. These results will be used as main classification indicator for monitoring freshwater ecosystems by providing integrated morphological and genetic information for the species identification of Korean Chironomus.

• Korean Journal of Plant Resources
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• v.17 no.3
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• pp.289-296
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• 2004

A cDNA clone (GenBank accession no. CF924621) homologous to aluminum induced protein gene was isolated and characterized from Codonopsis lanceolata (ClAIP). The ClAIP is 906 nucleotides long and has an open reading frame of 711 bp with a deduced amino acid sequence of 236 residues. The ClAIP shows high homology to A. marina (84%), G. hirsutum(83%), V. radiata (83%), A. thaliana (80%), B. nap us (78%) and T. aestivum (68%). The deduced amino acid sequence of ClAIP also has homology to the N-terminal end of plant Asn synthetase. This region does not contain the active sites of the enzyme and the significance of this conservation is currently not clear. To investigate the expression of ClAIP against several heavy metal stresses, we treated the sliced tap root of C. lanceolata with various heavy metals. The expression of ClAIP was increased by 25 uM $Al_2$(SO$_3$)$_4$ in proportion to incubation time and also increased by 50 uM CdCl$_2$.