• Biomedical Science Letters
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• v.18 no.3
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• pp.313-318
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• 2012

Acanthamoeba is an opportunistic pathogen known to cause granulomatous amoebic encephalitis and amebic keratitis. Acanthamoeba exhibits life cycle consisting of trophozoite and cyst, and the cyst is highly resistant to variable antibiotics and therapeutic agents. To understand the encystation mechanism of Acanthamoeba, the expression profiles of trophozoite and cyst were compared by gene ontology (GO) analysis. Ribosomal proteins and cytoskeletal proteins were highly expressed in trophozoite. In cyst, various protease, and signal transduction - and protein turnover - related proteins were highly expressed. These results correlated with eukaryotic orthologous groups (KOG) assignment and microarray analysis of Acanthamoeba trophozoite and cyst ESTs. The information of differential expression profiles of trophozoite and cyst would provide important clues for research on encystation mechanism of cyst forming protozoa including Acanthamoeba.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.19 no.2
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• pp.77-87
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• 2006

Objectives : We studied Effect of Platycodon grandiflorum on Lung carcinoma Methods : By using cDNA microarray technique, we analyzed the effects of AEPG(aqueous extract of Platycodon grandiflorum) on the gene expression profile. Results : Out of 384 genes screened associated with growth inhibition of carcinoma cell, 9 genes were founded to be affected in their expression levels by more than 1.2-fold after treatment with AEPG. And 67 genes were changed the expression level 0.5 times more than that of reference RNA after treatment of AEPG. Conclusions: These findings suggest that P. grandiflorum has strong potential for development as an agent for prevention and treatment against human lung cancer.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.63-68
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• 2005

Transcription factors regulate gene expression by binding to gene upstream region. Each transcription factor has the specific binding site in promoter region. So the analysis of gene upstream sequence is necessary for understanding regulatory mechanism of genes, under a plausible idea that assumption that DNA sequence motif profiles are closely related to gene expression behaviors of the corresponding genes. Here, we present an effective approach to the analysis of the relation between gene expression profiles and gene upstream sequences on the basis of kernel canonical correlation analysis (kernel CCA). Kernel CCA is a useful method for finding relationships underlying between two different data sets. In the application to a yeast cell cycle data set, it is shown that gene upstream sequence profile is closely related to gene expression patterns in terms of canonical correlation scores. By the further analysis of the contributing values or weights of sequence motifs in the construction of a pair of sequence motif profiles and expression profiles, we show that the proposed method can identify significant DNA sequence motifs involved with some specific gene expression patterns, including some well known motifs and those putative, in the process of the yeast cell cycle.

• Journal of Physiology & Pathology in Korean Medicine
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• v.18 no.5
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• pp.1291-1300
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• 2004

Baicalin, a biologically active flavonoid form the roots of Scutallaria baicalensis (Skullcap), have been reported to not only function as anti-oxidants but also cause anticancer effect. We investigated the mechanism of baicalin-induced cytotoxicity and the macro scale gene expression analysis in leukemia cell line, HL-60 cells. Baicalin (10 μM) were used to treat the cells for 6h, 12h, 24h, 48h and 72h. In a human cDNAchip study of 65,000 genes evaluated 6, 12, 24, 48. 72 hours after treated with Baicalin in HL-60 cells. Hierarchical cluster against the genes which showed expression changes by more than two fold. One hundred one genes were grouped into 6 clusters according to their profile of expression by a hierarchical clustering algorithm. For genes differentially expressed in response to baicalin treatment, we tested functional classes based on Gene Ontology (GO) terms. This study provides the most comprehensive available survey of gene expression changes in response to baicalin treatment in HL-60 cell line.

• Molecular & Cellular Toxicology
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• v.4 no.2
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• pp.113-123
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• 2008

Microglia, which is the primary immune effector cells in the central nervous system, constitutes the first line of defense against infection and injury in the brain. The goal of this study was to determine the protective (anti-inflammation) mechanisms of forsythia suspense (FS) on LPS-induced activation of BV-2 microglial cells. The effects of FS on gene expression profiles in activated BV-2 microglial cells were evaluated using microarray analysis. BV-2 microglial cells were cultured in a 100mm dish $(1{\times}10^7/dish)$ for 24hr and then pretreated with $1{\mu}g/mL$ FS or left untreated for 30 min. Next, $1{\mu}g/mL$ LPS was added to the samples and the cells were reincubated at $37^{\circ}C$ for 30 min, 1hr, and 3hr. The gene expression profiles of the BV-2 microglial cells varied depending on the FS. The oligonucleotide microarray analysis revealed that MAPK pathway-related genes such as Mitogen activated protein kinase 1 (Mapk1), RAS protein activator like 2 (Rasal2), and G-protein coupled receptor 12 (Gpr12) and nitric oxide biosynthesis-related genes such as nitric oxide synthase 1 (neuronal) adaptor protein (Nos1ap), and dimethylarginine dimethylaminohydrolase 1 (Ddah1) were down regulated in FS-treated BV-2 microglial cells. FS can affect the MAPK pathway and nitric oxide biosynthesis in BV-2 microglial cells.

• The Journal of Internal Korean Medicine
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• v.31 no.4
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• pp.706-713
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• 2010

Objectives : The source is from the flower of Carthamus tinctorius L., family Compositae. It is used in clinical medicine to promote blood circulation, remove blood stasis, promote menstruation and alleviate pain. In the present study, we investigated the genome wide analysis of Carthami Flos on the intra-cranial hemorrhage(ICH) model. Methods : ICH in rat was induced by injection of collagenase type IV and Carthami Flos extract(CFe) was administered orally. The molecular profile of cerebral hemorrhage in rat brain tissue was measured using microarray technique to identify up- or down- regulated genes in brain tissue. Results : Expression profile showed that diverse genes were up- or down-regulated by ICH induction. Administration of CFe restored the expression level of some of altered genes by ICH to normal expressional level. Interestingly, these recovered genes by CFe were involved in the same biological pathways which were significantly activated or suppressed by ICH. Conclusion : The above results might explain the therapeutic mechanism of CFe on ICH. Further, by analyzing interaction network, core genes was identified which could be key molecular targets of CFe against ICH.

• BMB Reports
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• v.33 no.1
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• pp.63-68
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• 2000

Most baculoviruses have an ecdysteroid UDP-glucosyltransferase (egt) gene, whose product inactivates ecdysteroid within the infected host. Bomhyx mori larvae infected with BmEGTZ, a mutant B. mori nucleopolyhedrovirus (BmNPV) in which the egt gene has been inactivated, die more rapidly compared to larvae infected with wild-type BmNPV. In this study, the profile of hemolymph proteins, and progression of virus infection in BmEGTZ- and BmNPV-infected B. mori larvae, was analyzed by SDS-PAGE and histochemically. These analyses showed that virus-encoded and virus-induced proteins were expressed quicker in BmEGTZ-infected larvae than in BmNPV-infected larvae. This suggests that the decrease in time to death, following BmEGTZ infection, results from the stimulation of virus-specific protein expression. In order to examine the effect of ecdysteroid on virus transmission, the profile of hemolymph proteins, and progression of virus infection, were analyzed following an ecdysteroid injection of BmEGTZ- or BmNPV-infected larvae. In the BmNPV-infected larvae, ecdysteroid treatment had no apparent effect on hemolymph protein expression. This suggests that the injected ecdysteroid was inactivated by the BmNPV-expressed ecdysteroid UDP-glucosyltransferase. An Ecdysteroid injection into BmEGTZ-infected larvae increased the speed of virus-specific protein expression and virus transmission. These results suggest that ecdysteroid stimulates protein expression, which in tum results in the stimulation of virus transmission.

• Journal of Life Science
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• v.17 no.1 s.81
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• pp.150-161
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• 2007

Acori graminei Rhizomn (AGR) is a perennial herb which has been used clinically as a traditional oriental medicine against stroke, Alzheimer's disease, and vascular dementia. We investigated the effect of AGR on the modulation of gene expression profile in a hypoxic model of cultured rat cortical cells. Rat cerebrocortical cells were grown in Neurobasal medium. On DIV12, cells were treated with AGR $(10ug/m\ell)$, given a hypoxic shock (2% $O_2$, 3 hr) on DIV14, and total RNAs were prepared one day after shock. Microarray analyses indicated that the expression levels of most genes were altered within the global M values +0.5 and -0.5, i.e., 40% increase or decrease. There were 750 genes which were upregulated by < global M +0,2, while 700 genes were downregulated by > global M -0.2. The overall profile of gene expression suggests that AGR suppresses apoptosis (upregulation of anti-apopotic genes such as TEGT, TIEG, Dad, p53, and downregulation of pro-apopotic genes such as DAPK, caspase 2, pdcd8), ROS (upregulation of RARa, AhR), and that AGR has neurotrophic effects (upregulation of Aktl, Akt2). These results provide a platform for investigation of the molecular mechanism of the effect of AGR in neuroprotection.

• Korean Journal of Microbiology
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• v.38 no.3
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• pp.213-220
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• 2002

Inducible expression system for the three structural proteins, capsid (C), precursor membrane (prM/M), and envelop (E) of Japanese encephalitis virus (JEV) was established in BHK-21 cells. Doxycycline, a tetracycline analog, was utilized as an inducer. Transfectants BHK-21/IV (vector only), BHK-21/IC (for C), BHK-21/IP3 (for prM), and BHK-21/IE1 (for E) were selected and cloned in the presence of G4l8 or hygromycin. Transcribed mRNAs for the corresponding genes were observed after doxycycline induction. Effects by the JEV structural gene expression on the transfectants were monitored via cell growth, chromatin condensation, internucleosomal DNA fragmentation, and DNA contents analyses. Clear cell growth retardation and chromatin condensation were observed in all three transfectants while only BHK-2/IC corresponded to the induction status in the DNA fragmentation and DNA content analyses. Combined results, therefore, suggested that JEV capsid protein should be one of the direct and independent factors in apoptotic cell death induced by IEV infection.

• Clinical and Experimental Reproductive Medicine
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• v.34 no.1
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• pp.19-31
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• 2007

Objective: Pathogenesis of the endometriosis is very complex and the etiology is still unclear. Our hypothesis is that there may be some difference in gene expression patterns between eutopic endometriums with or without endometriosis. In this study, we analyzed the difference of gene expression profile with cDNA microarray. Methods: Endometrial tissues were gathered from patients with endometriosis or other benign gynecologic diseases. cDNA microarray technique was applied to screen the different gene expression profiles from early and late secretory phase endometria of those two groups. Each three mRNA samples isolated from early and late secretory phase of endometrial tissues of control were pooled and used as master controls and labeled with Cy3-dUTP. Then the differences of gene expression pattern were screened by comparing eutopic endometria with endometriosis, which were labeled with Cy5-dUTP. Fluorescent labeled probes were hybridized on a microarray of 4,800 human genes. Results: Twelve genes were consistently over-expressed in the endometrium of endometriosis such as ATP synthase H transporting F1 (ATP5B), eukaryotic translation elongation factor 1, isocitrate dehydrogenase 1 (NADP+), mitochondrial ribosomal protein L3, ATP synthase H+ transporting (ATP5C1) and TNF alpha factor. Eleven genes were consistently down-regulated in the endometriosis samples. Many extracellular matrix protein genes (decorin, lumican, EGF-containing fibulin-like extracellular matrix protein 1, fibulin 5, and matrix Gla protein) and protease/protease inhibitors (serine proteinase inhibitor, matrix metalloproteinase 2, tissue inhibitor of metalloproteinase 1), and insulin like growth factor II associated protein were included. Expression patterns of selected eight genes from the cDNA microarray were confirmed by quantitative RT-PCR or real time RT-PCR. Conclusion: The result of this analysis supports the hypothesis that the endometrium from patients with endometriosis has distinct gene expression profile from control endometrium without endometriosis.