• Korean Journal of Acupuncture
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• v.23 no.3
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• pp.133-160
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• 2006

Objectives : Scolopendrae Corpus has a broad array of clinical applications in Korean medicine, including treatment of inflammatory conditions such as arthritis. To explore the global gene expression profiles in human Raw cell lines treated with Scolopendrae Corpus herbal-acupuncture solution (SCHAS), cDNA microarray analysis was performed. Methods : The Raw 264.7 cells were treated with lipopolysaccharide (LPS), SCHAS, or both. The primary data was normalized by the total spots of intensity between two groups, and then normalized by the intensity ratio of reference genes such as housekeeping genes in both groups. The expression ratio was converted to log2 ratio. Normalized spot intensities were calculated into gene expression ratios between the control and treatment groups. Greater than 2 fold changes between two groups were considered to be of significance. Results : Of the 8 K genes profiled in this study, with a cut-off level of two-fold change in the expression, 20 genes (BCL2-related protein A1, MARCKS-like 1, etc.) were upregulated and 5 genes (activated RNA polymerase II transcription cofactor 4, calcium binding atopy-related autoantigen 1, etc.) downregulated following LPS treatment. 139 genes (kell blood group precursor (McLeod phenotype), ribosomal protein S7, etc.) were upregulated and 42 genes (anterior gradient 2 homolog (xenopus laevis), phosphodiesterase 8B, etc.) were downregulated following SCHAS treatment. And 10 genes (yeast saccharomyces cerevisiae intergeneic sequence 4-1, mitogen-activated protein kinase 1, etc.) were upregulated and 8 genes (spermatid perinuclear RNA binding protein, nuclear receptor binding protein 2, etc.) were downregulated following co-stimulation of SCHAS and LPS. Discussions : It is thought that microarrays will play an ever-growing role in the advance of our understanding of the pharmacological actions of SCHAS in the treatment of arthritis. But further studies are required to concretely prove the effectiveness of SCHAS.

• The Korea Journal of Herbology
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• v.22 no.4
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• pp.9-19
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• 2007

Objective : The study was done to investigate Scrophularia buergeriana Miquel's effects in the genomic level, by measuring gene expression in hyperthyroid induced rats using cDNA micro array. Methods : Spargue-Dawley rats were separated into three groups(each with 10 rats). Except normal group, the other two groups were treated with Sodium levothyroxine $160{\mu}g$/kg/days for 5 days by oral administration. After 2 hours of the last intake of Sodium levothyroxine on two experimental group, one group was treated Scrophularia buergeriana Miquel extract 1.0g/kg/days for 3 days. The other groups(normal group, administration group) was treated normal saline 1.0g/kg/days for 3 days. Gene expression of hyperthyroid rats were measured after medication of solid extract of Scrophularia buergeriana Miquel with cDNA microarray. Results : In thyroid tissue, the numbers of the genes showed over twice increase and decrease in the control group compared to the normal group were 296, in the Scrophularia buergeriana Miquel administration group compared to the normal group were 859 and in the hypothalamus, the numbers of the genes showed over twice increase and decrease in the control group compared to the normal group were 416, in the Scrophularia buergeriana Miquel administration group compared to the normal group were 391. Conclusion : According to the above results, it is suggested that Scrophulari buergeriana Miquel suppress hyperthyroidism effectively and regulate the gene expression in the thyroid and brain.

• BMB Reports
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• v.38 no.2
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• pp.151-160
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• 2005

By a cDNA array representing 2308 signal transduction related genes, we studied the expression profiles of HeLa cells stably transfected by Hepatitis C virus nonstructural protein 4B (HCV-NS4B). The alterations of the expression of four genes were confirmed by real-time quantitative RT-PCR; and the aldo-keto reductase family 1, member C1 (AKR1C1) enzyme activity was detected in HCV-NS4B transiently transfected HeLa cells and Huh-7, a human hepatoma cell line. Of the 2,308 genes we examined, 34 were up-regulated and 56 were down-regulated. These 90 genes involved oncogenes, tumor suppressors, cell receptors, complements, adhesions, transcription and translation, cytoskeletion and cellular stress. The expression profiling suggested that multiple regulatory pathways were affected by HCV-NS4B directly or indirectly. And since these genes are related to carcinogenesis, host defense system and cell homeostatic mechanism, we can conclude that HCV-NS4B could play some important roles in the pathogenesis mechanism of HCV.

• Journal of Microbiology and Biotechnology
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• v.16 no.12
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• pp.1841-1848
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• 2006

Insights into gene expression have the potential for improvement of antibiotic yield and the development of robust production hosts for use in recombinant biomolecule production. $Cubicin^{TM}$ (daptomycin for injection) is a recently approved antibiotic active against many Gram(+) pathogens, including those resistant to methicillin, vancomycin, and fluoroquinolones. Daptomycin is produced as a secondary metabolite by Streptomyces roseosporus. A 128 kb region of DNA including the daptomycin biosynthetic gene cluster (dpt) has been cloned. and sequenced. Using a selected array of nucleic acid probes representing this region, we compared the expression levels of the dpt genes between S. roseosporus wild-type (WT) and derived S. roseosporus high-producer of daptomycin (HP). We observed that the majority of the biosynthetic genes were upregulated in HP compared with WT; a total of 12 genes, including those encoding daptomycin synthetase, showed consistently and significantly higher expression levels, at least 5-fold, in HP compared with WT. In contrast, some genes, flanking the dpt cluster, were expressed at higher levels in the WT strain. The expression of housekeeping genes such as S. roseosporus rpsL, rpsG, and 16S (positive controls) and presumptive intergenic regions in the dpt cluster (negative control) were identical in the two strains. In addition, we compared transcription during the early, mid-log, and early-stationary phases of growth in the HP strain. The same set of genes was upregulated and downregulated under all conditions examined; housekeeping genes showed no relative change in expression level over the periods of growth tested. Analyses of this type would be of value in studies of strain improvement and also for the identification of gene regulation processes that are important for secondary metabolite production.

• Korean Journal of Oriental Medicine
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• v.8 no.2 s.9
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• pp.95-107
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• 2002

Yukmijihwang-tang(YM) is a noted herbal prescription in Chinese and Korean traditional medicines, and it has been known to reinforce the vital essence and has been widely used for a variety of disease such as stroke, osteoporosis, anti-tumor, and hypothyrodism. Regarding its traditional use, YM has been known to reinforce the Yin (vital essence) of liver and kidney. Also it has been known to reinforce nutrition and biological function in brain. Recently, studies suggested that YM increase antioxidant activities and exert the protective effect against oxidant-induced liver cell injury. We investigated the high-throughput gene expression analysis on the Yukmijihwang-tang administrated in SD rats. Microarray data were validated on a limited number of genes by semiquantitative RT-PCR and Western blot analyses. The recent availability of microarrays provides an attractive strategy for elaborating an unbiased molecular profile of large number of genes in drug discovery This experimental approach offers the potential to identify molecules or cellular pathways not previously associated with herbal medicine. Total RNA from normal control brain and Yukmijihwang-tang administrated brain were hybridized to microarrays containing 10,000 rat genes. The 52 genes were found to be up-regulated(twice or more) excluding EST gene. The nine genes were found to be down-regulated(twice or more) excluding EST gene. Gene array technology was used to identify for the first time many genes expression pathway analysis that arecell cycle pathway, apoptosis pathway, electron transport chain pathway, cytoplasmic ribosomal protein pathway, fatty acid degradation pathway, and TGF-beta signaling pathway. These differentially expressed genes pathway analysis have not previously been iavestigated in the context of herbal medicine efficacy and represent novel factors for further study of the mechanism of herbal medicine efficacy.

• Clinical and Experimental Pediatrics
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• v.59 no.2
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• pp.91-95
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• 2016

We report the case of a 22-month-old boy with a new mosaic partial unbalanced translocation of 1q and 18q. The patient was referred to our Pediatric Department for developmental delay. He showed mild facial dysmorphism, physical growth retardation, a hearing disability, and had a history of patent ductus arteriosus. White matter abnormality on brain magnetic resonance images was also noted. His initial routine chromosomal analysis revealed a normal 46,XY karyotype. In a microarray-based comparative genomic hybridization (aCGH) analysis, subtle copy number changes in 1q32.1-q44 (copy gain) and 18q21.33-18q23 (copy loss) suggested an unbalanced translocation of t(1;18). Repeated chromosomal analysis revealed a low-level mosaic translocation karyotype of 46,XY,der(18)t(1;18) (q32.1;q21.3)[12]/46,XY[152]. Because his parents had normal karyotypes, his translocation was considered to be de novo. The abnormalities observed in aCGH were confirmed by metaphase fluorescent in situ hybridization. We report this patient as a new karyotype presenting developmental delay, facial dysmorphism, cerebral dysmyelination, and other abnormalities.

• Molecular & Cellular Toxicology
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• v.5 no.4
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• pp.310-316
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• 2009

Some environmental chemicals have been shown to cause liver-toxicity as the result of bioaccumulation. Particularly, fungicides have been shown to cause varying degrees of hepatictoxicity and to disrupt steroid hormone homeostasis in in vivo models. The principal objective of this study was to evaluate the liver-toxic responses of environmental chemicals-in this case selected fungicides and parasiticides-in order to determine whether or not this agent differentially affected its toxicogenomic activities in hepatic tumor cell lines. To determine the gene expression profiles of 3 fungicides (triadimefon, myclobutanil, vinclozolin) and 1 parasiticide (dibutyl phthalate), we utilized a modified HazChem human array V2. Additionally, in order to observe the differential alterations in its time-dependent activities, we conducted two time (3 hr, 48 hr) exposures to the respective IC20 values of four chemicals. As a result, we analyzed the expression profiles of a total of 1638 genes, and we identified 70 positive significant genes and 144 negative significant genes using four fungicidic and parasiticidic chemicals, using SAM (Significant Analysis of Microarray) methods (q-value<0.5%). These genes were analyzed and identified as being related to apoptosis, stress responses, germ cell development, cofactor metabolism, and lipid metabolism in GO functions and pathways. Additionally, we found 120 genes among those time-dependently differentially expressed genes, using 1-way ANOVA (P-value<0.05). These genes were related to protein metabolism, stress responses, and positive regulation of apoptosis. These data support the conclusion that the four tested chemicals have common toxicogenomic effects and evidence respectively differential expression profiles according to exposure time.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6347-6350
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• 2013

Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.3197-3203
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• 2013

Background: microRNAs (miRNAs) that regulate proliferation, invasion and metastasis are considered to be the principal molecular basis of tumor heterogeneity. Breast cancer is not a homogeneous tissue. Thus, it is very important to perform microarray-based miRNA screening of tumors at different sites. Methods: Breast tissue samples from the centers and edges of tumors of 30 patients were classified into 5 clinicopathological subtypes. In each group, 6 specimens were examined by microRNA array. All differential miRNAs were analyzed between the edges and centers of the tumors. Results: Seventeen kinds of miRNAs were heterogeneously distributed in the tumors from different clinicopathological subtypes that included 1 kind of miRNA in Luminal A and Luminal B Her2+ subtypes, 4 kinds in Luminal A and Her2 overexpression subtypes, 6 kinds in Luminal B Ki67+ and Luminal B Her2+ subtypes, 2 kinds between Luminal B Ki67+ and triple-negative breast cancer (TNBC) subtypes, 2 kinds between Luminal B Her2+ and TNBC subtypes, and 2 kinds between Luminal B Ki67+, Luminal B Her2+, and TNBC subtypes. Twenty kinds of miRNAs were homogenously distributed in the tumors from different clinicopathological subtypes that included 6 kinds of miRNAs in Luminal B Ki67+ and Luminal B Her2+ subtypes, 1 kind in Luminal B Ki67+ and Her2 overexpression subtypes, 10 kinds between Luminal B Ki67+ and TNBC subtypes, 2 kinds in Luminal B Her2+ and TNBC subtypes, and 1 kind between Luminal B Ki67+, Luminal B Her2+, and TNBC subtypes. Conclusions: A total of 37 miRNAs were significantly distributed in tumors from the centers to edges, and in all clinicopathological subtypes.

• Development and Reproduction
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• v.16 no.1
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• pp.59-67
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• 2012

Previously, we found that $Zap70$ (Zeta-chain-associated protein kinase) expressed in the mouse oocytes and played significant role in completion of meiosis specifically at MI-MII (metaphase I-II) transition. Microinjection of $Zap70$ dsRNA into the cytoplasm of germinal vesicle oocyte resulted in MI arrest, and exhibited abnormalities in their spindles and chromosome configurations. The purpose of this study was to determine the mechanisms of action of $Zap70$ in oocyte maturation by evaluating downstream signal networking after $Zap70$ RNAi (RNA interference). The probe hybridization and data analysis were used by Affymetrix Gene Chip Mouse Genome 430 2.0 array and GenPlex 3.0 (ISTECH, Korea) software, respectively. Total 1,152 genes were up (n=366) and down (n=786) regulated after $Zap70$ RNAi. Among those genes changed, we confirmed the expressional changes of the genes involved in the regulation of actin cytoskeleton and MAPK (mitogen-activated protein kinase) signaling pathway, since the phenotypes of $Zap70$ RNAi in oocytes were found in the changes in the chromosome separation and spindle structures. We confirmed the changes in gene expression in the actin skeletal system as well as in the MAPK signaling pathway, and concluded that these changes are main cause of the aberrant chromosome arrangement and abnormal spindles after $Zap70$ RNAi.