• Korean Journal of Food Science and Technology
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• v.47 no.1
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• pp.126-131
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• 2015

Pathogenic Escherichia coli is recognized as an important cause of diarrhea, hemorrhagic colitis and hemolytic-uremic syndrome worldwide. This study was conducted to investigate the prevalence E. coli contamination in the Korean traditional food bibimbap. E. coli were isolated from 84 of 1142 (7.3%) bibimbap investigated from 2005 to 2011. Antibiotic resistance profiling demonstrated that 6 of the 84 isolates (7.2%) showed multiple drug resistance. Fifteen virulence genes specific for pathogenic E. coli such as Shiga toxin-producing E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), and enteroaggregative E. coli (EAEC) were examined by multiplex PCR for mixed bacterial cultures derived from bibimbap samples. The EPEC virulence gene (ent) was detected in 5 strains (5.9%), while ETEC, EAEC, and EIEC were not detected. STEC serotypes O103 (1.2%), O91 (1.2%), and O128 (6.0%) were found, but other serogroups such as O26, O157, O145, O111 and O121 were not detecded. Automated Repetitive-Sequence-Based PCR analysis showed different patterns.

• The Korea Journal of Herbology
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• v.22 no.4
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• pp.253-260
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• 2007

Objectives : Intracerebral hemorrhage (ICH) is characterized by breakdown of blood vessels within the brain parenchyma. Fundamental therapeutic strategies for ICH, particularly those aimed at neuroprotection, have to be established. So in this experiment, the effects of Woowhangchongshim-won, a traditional prescription formula for treating Cerebral Apoplexy in Asian countries, were investigated. Methods : After intraperitoneal injection of chloralhydrate, rats were placed in a stereotaxic frame. ICH was induced by injection of 1 U collagenase type IV and drug was administered orally for 10 days. The molecular profile of cerebral hemorrhage in rat brain tissue was measured using micro array technique to identify up- or down- regulated genes in brain tissue. These genes induced by brain damage were mainly concerned with general metabolic process such as primary metabolic process, cellular metabolic process, macromolecule metabolic process, and biosynthetic process. Results : The number of genes increased in control and not-changed in experiment was 374, and decreased in control and not-changed in experiment was 527. We are concerned with genes that can be recovered by treatment with medicine, it is especially interesting to above types of genes. Conclusions : Upon medicine treatment to the rat having cerebral hemorrhage, expressions of some genes were restored to normal level. Further analysis using protein interaction database identified some key molecules that can be used for elucidation of therapeutical mechanism of medicine in future.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.11
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• pp.1649-1656
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• 2015

Gene expression profiling has offered new insights into postmortem molecular changes associated with meat quality. To acquire reliable transcript quantification, high quality RNA is required. The objective of this study was to analyze integrity of RNA isolated from chicken skeletal muscle (pectoralis major) and its capability of serving as the template in quantitative real-time polymerase chain reaction (qPCR) as a function of postmortem intervals representing the end-points of evisceration, carcass chilling and aging stages in chicken abattoirs. Chicken breast muscle was dissected from the carcasses (n = 6) immediately after evisceration, and one-third of each sample was instantly snap-frozen and labeled as 20 min postmortem. The remaining muscle was stored on ice until the next rounds of sample collection (1.5 h and 6 h postmortem). The delayed postmortem duration did not significantly affect $A_{260}/A_{280}$ and $A_{260}/A_{230}$ ($p{\geq}0.05$), suggesting no altered purity of total RNA. Apart from a slight decrease in the 28s:18s ribosomal RNA ratio in 1.5 h samples (p<0.05), the value was not statistically different between 20 min and 6 h samples ($p{\geq}0.05$), indicating intact total RNA up to 6 h. Abundance of reference genes encoding beta-actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), hypoxanthine-guanine phosphoribosyltransferase (HPRT), peptidylprolylisomerase A (PPIA) and TATA box-binding protein (TBP) as well as meat-quality associated genes (insulin-like growth factor 1 (IGF1), pyruvate dehydrogenase kinase isozyme 4 (PDK4), and peroxisome proliferator-activated receptor delta (PPARD) were investigated using qPCR. Transcript abundances of ACTB, GAPDH, HPRT, and PPIA were significantly different among all postmortem time points (p<0.05). Transcript levels of PDK4 and PPARD were significantly reduced in the 6 h samples (p<0.05). The findings suggest an adverse effect of a prolonged postmortem duration on reliability of transcript quantification in chicken skeletal muscle. For the best RNA quality, chicken skeletal muscle should be immediately collected after evisceration or within 20 min postmortem, and rapidly preserved by deep freezing.

• The Korean Journal of Malacology
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• v.32 no.2
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• pp.127-131
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• 2016

The natives of the genus Corbicula have shown worldwide dispersion in recent times, which has caused great ecological and economic impacts on the introduced ecosystems. The species reported from the genus have been consumed as food and explored for medicine with pharmacological activity. Consequently, the demand of Corbicula sp. in the South Korean domestic market has increased and so also it's associated import to the country. However, due to the absence of identification keys of imported Corbicula, the market is facing confronting situations. We hypothesized that the mitochondrial Cytochrome Oxidase I gene (CO-I) based molecular profiling could be a necessary technique for identification of Corbicula sp. in the South Korea domestic market. The genetic analysis identified both Corbicula japonica and Corbicula fluminea from the market foods. C. japonica and C. fluminea are inhabitants in Korea, but C. fluminea production has decreased in Seomjingang river basin. Therefore, C. fluminea identified from this study, is expected to be imported from China and would have a mixed sales in Seomjingang river side basin.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Molecules and Cells
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• v.37 no.12
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• pp.873-880
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• 2014

In our previous study, miRNA-183, a miRNA in the miR-96-182-183 cluster, was significantly over-expressed in esophageal squamous cell carcinoma (ESCC). In the present study, we explored the oncogenic roles of miR-183 in ESCC by gain and loss of function analysis in an esophageal cancer cell line (EC9706). Genome-wide mRNA micro-array was applied to determine the genes that were regulated directly or indirectly by miR-183. 3'UTR luciferase reporter assay, RT-PCR, and Western blot were conducted to verify the target gene of miR-183. Cell culture results showed that miR-183 inhibited apoptosis (p < 0.05), enhanced cell proliferation (p < 0.05), and accelerated G1/S transition (p < 0.05). Moreover, the inhibitory effect of miR-183 on apoptosis was rescued when miR-183 was suppressed via miR-183 inhibitor (p < 0.05). Western blot analysis showed that the expression of programmed cell death 4 (PDCD4), which was predicted as the target gene of miR-183 by microarray profiling and bioinformatics predictions, decreased when miR-183 was over-expressed. The 3'UTR luciferase reporter assay confirmed that miR-183 directly regulated PDCD4 by binding to sequences in the 3'UTR of PDCD4. Pearson correlation analysis further confirmed the significant negative correlation between miR-183 and PDCD4 in both cell lines and in ESCC patients. Our data suggest that miR-183 might play an oncogenic role in ESCC by regulating PDCD4 expression.

• Restorative Dentistry and Endodontics
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• v.35 no.3
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• pp.152-163
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• 2010

This study investigated the changes in gene expression when mineral trioxide aggregate (MTA) was applied in vitro to human dental pulp cells (HDPCs). MTA in a teflon tube (diameter 10 mm, height 2 mm) was applied to HDPCs. Empty tube-applied HDPCs were used as negative control. For microarray analysis, total RNA was extracted at 6, 24, and 72 hrs after MTA application. The results were confirmed selectively by performing reverse transcriptase polymerase chain reaction for genes that showed changes of more than two-fold or less than half. Of the 24,546 genes, 109 genes were up-regulated greater than twofold (e.g., FOSB, THBS1, BHLHB2, EDN1, IL11, FN1, COL10A1, and TUFT1) and 69 genes were down-regulated below 50% (e.g., SMAD6 and DCN). These results suggest that MTA, rather than being a bio-inert material, may have potential to affect the proliferation and differentiation of pulp cells in various ways.

• Molecular & Cellular Toxicology
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• v.3 no.2
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• pp.98-106
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• 2007

Genotoxic stress triggers a variety of biological responses including the transcriptional activation of genes regulating DNA repair, cell survival and cell death. In this study, we investigated to examine gene expression profiles and genotoxic response in TK6 cells treated with DNA damaging agents MNNG (N-methyl-N'-nitrosoguanidine) and hydrogen peroxide $(H_2O_2)$. We extracted total RNA in three independent experiments and hybridized cRNA probes with oligo DNA chip (Applied Biosystems Human Genome Survey Microarray). We analyzed raw signal data with R program and AVADIS software and identified a number of deregulated genes with more than 1.5 log-scale fold change and statistical significancy. We indentified 14 genes including G protein alpha 12 showing deregulation by MNNG. The deregulated genes by MNNG represent the biological pathway regarding MAP kinase signaling pathway. Hydrogen peroxide altered 188 genes including sulfiredoxins. These results show that MNNG and $H_2O_2$ have both uniquely regulated genes that provide the potential to serve as biomarkers of exposure to DNA damaging agents.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.31-38
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• 2015

The bacterial community structures of two marine sponges, Cinachyrella sp. and Plakortis sp., collected from Chuuk in the South Pacific in February 2012 were analyzed by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting. After isolation of the total genomic DNAs from the sponges, the V3 regions of the 16S rRNA genes were amplified and subjected to DGGE profiling. The two species of sponges displayed different DGGE band patterns. The sequences derived from the DGGE bands revealed 85-100% similarities to known bacterial species in the public database. The bacterial community of Cinachyrella sp. was composed of 6 classes: Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria (Alpha-, Gamma-, Delta-). The bacterial community of Plakortis sp. included 7 classes: Actinobacteria, Chloroflexi, Firmicutes, Spirochaetes, and Proteobacteria (Alpha-, Gamma-, Delta-). Though Actinobacteria, Chloroflexi and Proteobacteria were commonly found in both sponges, the predominant bacterial communities differed between the two. Namely, the predominant bacterial groups in Cinachyrella sp. and Plakortis sp. were Proteobacteria and Chloroflexi, respectively. The sponge-associated bacteria are sponge host-specific, as each of the tested sponges from the same geographical location had different predominant bacterial diversity.

• Journal of Life Science
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• v.22 no.11
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• pp.1500-1506
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• 2012

Transforming growth factor (TGF)-${\beta}$-dependent apoptosis is important in the elimination of damaged or abnormal cells from normal tissues, especially in liver, in vivo. To investigate which gene expressions are critical for TGF-${\beta}$-induced apoptosis in hepatocytes, gene expression profiling experiments were performed with TGF-${\beta}$-treated and non-treated mouse hepatocytes AML12 cells. Findings showed that serum and glucocorticoid-inducible protein kinase1 (SGK1) expression is markedly downregulated during TGF-${\beta}$-induced apoptosis. Findings confirmed that expression of SGK1 protein, as well as mRNA, is also markedly decreased with TGF-${\beta}$ treatment. Infection of adenoviral vector encoding constitutively active SGK1 (CA-SGK1), but not kinase dead SGK1 (KD-SGK1), attenuated TGF-${\beta}$-induced apoptosis. All of these results suggest that downregulation of SGK1 expression is critical for TGF-${\beta}$-induced apoptosis in AML12 cells.