• Clinical and Experimental Reproductive Medicine
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• v.39 no.2
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• pp.87-93
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• 2012

Objective: Lin28 has been known to control the proliferation and pluripotency of embryonic stem cells. The purpose of this study was to determine the downstream effectors of Lin28 in mouse embryonic stem cells (mESCs) by RNA interference and microarray analysis. Methods: The control siRNA and Lin28 siRNA (Dharmacon) were transfected into mESCs. Total RNA was prepared from each type of transfected mESC and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis to confirm the downregulation of Lin28. The RNAs were labeled and hybridized with an Affymetrix Gene-Chip Mouse Genome 430 2.0 array. The data analysis was accomplished by GenPlex 3.0 software. The expression levels of selected genes were confirmed by quantitative real-time RT-PCR. Results: According to the statistical analysis of the cDNA microarray, a total of 500 genes were altered in Lin28-downregulated mESCs (up-regulated, 384; down-regulated, 116). After differentially expressed gene filtering, 31 genes were selected as candidate genes regulated by Lin28 downregulation. Among them, neuropeptide Y5 receptor and oocyte-specific homeobox 5 genes were significantly upregulated in Lin28-downregulated mESCs. We also showed that the families of neuropeptide Y receptor (Npyr) and oocyte-specific homeobox (Obox) genes were upregulated by downregulation of Lin28. Conclusion: Based on the results of this study, we suggest that Lin28 controls the characteristics of mESCs through the regulation of effectors such as the Npyr and Obox families.

• Molecular & Cellular Toxicology
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• v.2 no.2
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• pp.120-125
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• 2006

Phenytoin is an anti-epileptic. It works by slowing down impulses in the brain that cause seizures. The recent microarray technology enables us to understand possible mechanisms of genes related to compounds which have toxicity in biological system. We have studied that the effect of a compound related to hepatotoxin in vitro system using a rat whole genome microarray. In this study, we have used a rat liver epithelial cell line WB-F344 and phenytoin as a hepatotoxin. WB-F344 was treated with phenytoin for 1 to 24 hours. Total RNA was isolated at times 1, 6 and 24h following treatment of phenytoin, and hybridized to the microarray containing about 22,000 rat genes. After analysis with clustering methods, we have identified a total of 1,455 differentially expressed genes during the time course. Interestingly, about 1,049 genes exhibited differential expression pattern in response to phenytoin in early time. Therefore, the identification of genes associated with phenytoin in early response may give important insights into various toxicogenomic studies in vitro system.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4553-4557
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• 2013

Objective: The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. Methods: After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. Results: A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. Conclusion: We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.

• The Korean Journal of Physiology and Pharmacology
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• v.10 no.5
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• pp.263-271
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• 2006

Since astrocytes were shown to play a central role in maintaining neuronal viability both under normal conditions and during stress such as ischemia, studies of the astrocytic response to stress are essential to understand many types of brain pathology. The micro array system permitted screening of large numbers of genes in biological or pathological processes. Therefore, the gene expression patterns in the in vitro model of astrocytes following exposure to oxygen-glucose deprivation (OGD) were evaluated by using the micro array analysis. Primary astrocytic cultures were prepared from postnatal Swiss Webster mice. The cells were exposed to OGD for 4 hrs at $37^{\circ}C$ prior to cell harvesting. From the cultured cells, we isolated mRNA, synthesized cDNA, converted to biotinylated cRNA and then reacted with GeneChips. The data were normalized and analyzed using dChip and GenMAPP tools. After 4 hrs exposure to OGD, 4 genes were increased more than 2 folds and 51 genes were decreased more than 2 folds compared with the control condition. The data suggest that the OGD has general suppressive effect on the gene expression with the exception of some genes which are related with ischemic cell death directly or indirectly. These genes are mainly involved in apoptotic and protein translation pathways and gap junction component. These results suggest that microarray analysis of gene expression may be useful for screening novel molecular mediators of astrocyte response to ischemic injury and making profound understanding of the cellular mechanisms as a whole. Such a screening technique should provide insights into the molecular basis of brain disorders and help to identify potential targets for therapy.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.142-148
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• 2002

Although ionizing radiation (IR) has been used to treat the various human cancers, IR is cytotoxic not only to cancer cells but to the adjacent normal tissue. Since normal tissue complications are the limiting factor of cancer radiotherapy, one of the major concerns of IR therapy is to maximize the cancer cell killing and to minimize the toxic side effects on the adjacent normal tissue. As an attempt to develop a method to monitor the degree of radiation exposure to normal tissues during radiotherapy, we investigated the transcriptional responses of human peripheral blood lymphocytes (PBL) following IR using cDNA microarray chip containing 1,221 (1.2 K) known genes. Since conventional radiotherapy is delivered at about 24 h intervals at 180 to 300 cGy/day, we analyzed the transcriptional responses ex-vivo irradiated human PBL at 200 cGy for 24 h-period. We observed and report on 1) a group of genes transiently induced early after IR at 2 h, 2) of genes induced after IR at 6 h, 3) of genes induced after IR at 24 h and on 4) a group of genes whose expression patters were not changed after IR. Since Biological consequences of IR involve generation of various reactive oxygen species (ROS) and thus oxidative stress induced by the ROS is known to damage normal tissues during radiotherapy, we further tested the temporal expression profiles of genes involved in ROS modulation by RT-PCR. Specific changes of 6 antioxidant genes were identified in irradiated PBL among 9 genes tested. Our results suggest the potential of monitoring post-radiotherapy changes in temporal expression profiles of a specific set of genes as a measure of radiation effects on normal tissues. This type of approach should yield more useful information when validated in in vivo irradiated PBL from the cancer patients.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.845-852
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• 2014

Among various abiotic stress factors, soil salinity decreases the photosynthetic rate, growth, and yield of plants. Recently, many genes have been reported to enhance salt tolerance. The objective of this study was to characterize the Brassica rapa Salt Stress Resistance (BrSSR) gene, of which the function was unclear, although the full-length sequence was known. To characterize the role of BrSSR, a B. rapa Chinese cabbage inbred line ('CT001') was transformed with pSL94 vector containing the full length BrSSR cDNA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression of BrSSR in the transgenic line was 2.59-fold higher than that in the wild type. Analysis of phenotypic characteristics showed that plants overexpressing BrSSR were resistant to salinity stress and showed normal growth. Microarray analysis of BrSSR over-expressing plants confirmed that BrSSR was strongly associated with ERD15 (AT2G41430), a gene encoding a protein containing a PAM2 motif (AT4G14270), and GABA-T (AT3G22200), all of which have been associated with salt tolerance, in the co-expression network of genes related to salt stress. The results of this study indicate that BrSSR plays an important role in plant growth and tolerance to salinity.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.21 no.1
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• pp.55-69
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• 2008

Objective : This study was designed to investigated effects of Gleditsia spina (GS) on human derived melanoma cells Methods : The genetic profile for the effect of medicine on human derived melanoma cells of SK-MEL-2, was measured by using microarray technique, and the functional analysis on these genes was conducted. The network of total protein interactions was measured by using cytoscape program. Results : Total 253 genes were up-regulated and 439 genes down-regulated in cells treated with GS. Genes induced or suppressed by GS were all mainly concerned with metabolic process, regulation of biological process and protein binding. Conclusion : Suggest the possibility of GS as anti-cancer drug and cosmetic agent, and also suggest that related mechanisms are involved in regulation of intra-cellular metabolism in melanoma cells.

• Proceedings of the Korea Information Processing Society Conference
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• 2006.11a
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• pp.69-72
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• 2006

최근 생명 정보학 기술의 발달로 마이크로 단위의 실험조작이 가능해짐에 따라 하나의 chip상에서 전체 genome의 expression pattern을 관찰할 수 있게 되었고, 동시에 수 만개의 유전자들 간의 상호작용도 연구가능하게 되었다. 이처럼 DNA 마이크로어레이 기술은 복잡한 생물체를 이해하는 새로운 방향을 제시해주게 되었다. 따라서 이러한 기술을 통해 얻어진 대량의 유전자 정보들을 효과적으로 분석하는 방법이 시급하다. 본 논문에서는 마이크로어레이 실험에서 다양한 원인에 의해 발생하는 잡음(noise)을 줄이거나 제거하는 과정인 정규화과정을 거쳐 특징 추출방법인 SVM(Support Vector Machine) 방법을 이용하여 데이터를 2개의 클래스로 나누고, 표준화 방법들의 성능 비교를 위해 Adaptive Simulated Annealing 알고리즘으로 정확도를 평가하는 분류 시스템을 설계 구현하였다.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.45-60
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• 2001

. Mediator of transcriptional regulation is the evolutionary conserved coactivator complex that plays He central role in the integration and recruitment of diverse regulatory signals and transcription machinery to certain promoters. In yeast, each Mediator subunit is required for transcriptional regulation of a distinct group of genes. In order to decipher the mechanistic roles of Mediator proteins in regulating developmental specific gene expression, we isolated, and analyzed a multiprotein complex containing Drosophila Mediate. homologs (dMediato.). dMediato. interacts with several sequence-sperific transcription factors and basal transcription machinery, and is critical for activated transcription in response to diverse transcriptional activators. In order to elucidate the function of Mediator in metazoan development, we isolated mutants of a conserved Mediate. subunit, Drosophila Med6 (dMed6). dMed6 null homozygotes failed to pupate and died in the third larval instar. Larval mitotic cells and most imaginal discs showed severe defects in proliferation, but no apparent morphological defect was observed in other larval tissues. Clonal analysis of dMed6 mutant cells revealed that dMed6 is essential for cell viability and proliferation of most adult cell types. Drosophila cDNA microarray, quantitative RT-PCR, and in situ expression analyses of developmentally regulated genes in dMed6 mutants showed that transcriptional activation of a subset of genes involved in neuroblast proliferation in the larval brain were most affected. Our results suggest that dMed6 is required in most for transcriptional regulation of a subset of genes important for cell proliferation and metabolism.

• Tuberculosis and Respiratory Diseases
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• v.50 no.1
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• pp.29-41
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• 2001

Background : The appearance of multiple-drug-resistant Mycobacterium tuberculosis strains has been seriously compromising successful control of tuberculosis. Rifampin-resistance, caused by mutations in the rpoB gene, can be indicative of multiple-drug-resistance, and its detection is of great importance. The present study aimed to develop an oligonucleotide chip for accurate and convenient screening of drug-resistance. Methods : In order to detect point mutations in the rpoB gene, an oligonucleotide chip was prepared by immobilizing specific probe DNA to a microscopic slide glass by a chemical reaction. The probe DNA that was selected from the 81 bp core region of the rpoB gene was designed to have mutation sites at the center. A total of 17 mutant probes related to rifampin-resistance including 8 rifabutin-sensitive mutant probes were used in this study. For accurate determination, wild type probes were prepared for each mutation position with an equal length, which enabled a direct comparison of the hybridization intensities between the mutant and wild type. Results : Mycobacterial genomic DNA from clinical samples was tested with the oligonucleotide chip and the results were compared with those of the drug-susceptibility test in addition to sequencing and INNO-LiPA Rif. TB kit test in some cases. Out of 15 samples, the oligonucleotide chip results of 13 samples showed good agreement with the rifabutin-sensitivity results. The two samples with conflicting result also showed a discrepancy between the other tests, suggesting such possibilities as existence of mixed strains and difference in drug-sensitivity. Further verification of these samples in addition to more case studies are required before the final evaluation of the oligonucleotide chip can be made. Conlcusion : An oligonucleotide chip was developed for the detection of rpoB gene mutations related to drugsusceptibility. The results to date show the potential for using the oligonucleotide chip for accurate and convenient screening of drug-resistance to provide useful information in antituberculosis drug therapy.