• 제목/요약/키워드: cDNA Microarray Analysis

검색결과 227건 처리시간 0.025초

모성 및 사회성 분리 백서 모델의 해마에서 유전자 칩을 이용한 유전자 발현 연구 (Microarray Analysis of Gene Expression in Rat Hippocampus of Maternal Social Separation Model)

  • 이희제;손창희;곽형렬;이상현;한윤희;김수영;박종익;전완주;김성수
    • 생물정신의학
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    • 제13권2호
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    • pp.110-116
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    • 2006
  • Objectives : Alteration of hippocampus was demonstrated in the maternal social separation(MSS) pups, separated from dams on postnatal day(pnd) 14 and placed alone. Therefore, to understand the molecular events involved in the MSS, we have initiated a search for gene profiles that are up or down-regulated in the hippocampus of MSS pups. Methods : Analysis of cDNA microarray was performed by using total RNA extracted from the hippocampus of control and MSS pups on pnd 17. Also, passive-avoidance test was demonstrated on pnd 35. Results : Up-regulation of Nedd4a was observed in the hippocampus of MSS pups. Also, MSS rats showed less elongation of latency in passive avoidance test. Conclusion : We suggest that environmental effects of MSS may be altered the neural and/or glial differentiation and synapse formation-related genes which may lead cognitive alterations in MSS rats.

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벼 성숙종자로부터 배상체 캘러스 형성 및 식물체 재분화에 DNA methylation 억제제인 5-azacytidine의 영향 (Effects of 5-azacytidine, a DNA methylation inhibitor, on embryogenic callus formation and shoot regeneration from rice mature seeds)

  • 이연희;이정숙;김수윤;손성한;김둘이;윤인선;권순종;서석철
    • Journal of Plant Biotechnology
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    • 제35권2호
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    • pp.133-140
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    • 2008
  • DNA와 histone 단백질의 변형은 식물 발달에 상당히 중요한 역할을 하는 것으로 알려져 있다. 식물 조직 배양 및 식물 발달 단계에서 methylation의 영향을 알아보고자 벼 종자로부터 캘러스 형성 및 식물체 재분화 단계에서 demethylation 물질인 5-azacytidine을 처리하여 유전자 발현 양상을 분석하였다. 식물체로의 재분화 능력이 있는 벼 배상체 캘러스는 5-azaC가 첨가된 H6A 배지에서는 형성되지 않았으며 갈색을 띠는 캘러스가 형성되었다. 또한 정상적인 캘러스를 5-azaC가 첨가된 MSRA 재분화 배지에서 배양했을 때도 대조구와는 달리 식물체 재분화는 이루어지지 않았다. 이러한 결과는 5-azaC가 정상적인 배상체 캘러스 및 shoot 분화에 부정적인 영향을 미친다는 것을 나타냈으며 따라서 DNA methylation이 식물 조직배양에서의 정상적인 세포 dedifferentiation과 differentiation에 필수 요인이라는 것을 알 수 있었다. 벼 캘러스 형성 및 재분화 과정 동안의 methylation 영향을 알아보고자 각 단계별로 5-azaC를 처리 후 $GeneFishig^{TM}$ DEG와 DNA chip을 사용하여 유전자 발현 양상을 분석하였다. Epigenetic regulation, 전자전달, 핵산대사, 스트레스 반응에 관여하는 일부 유전자들의 발현이 증가하거나 감소하는 것을 알 수 있었다. 발현 차이가 있는 일부 유전자를 클로닝하여 확인하였고 RT-PCR 및 northern 분석으로 각 단계에서의 발현 차이를 할인하였다.

Gene Expression Profile in Iprobenfos Exposed Medaka Fish by Microarray Analysis

  • Woo, Seon-Ock;Son, Sung-Hee;Ryu, Jae-Chun;Yum, Seung-Shic
    • Molecular & Cellular Toxicology
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    • 제4권2호
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    • pp.132-137
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    • 2008
  • Differential gene expression profiling was carried out in the hepatic tissue of medaka fish, Oryzias latipes, after exposure to an organophosphorus pesticide (OPP), Iprobenfos (IBP), a widely used pesticide in agri- and fish-culture, using a medaka cDNA micro array. Twenty six kinds of differentially expressed candidate genes, with 15 and 11 induced and repressed in their gene expressions, respectively, were associated with cytoskeleton (3.8%), development (7.7%), immune (7.7%), metabolism (30.8%), nucleic acid/protein binding (42.3%) and reproduction (7.7%). Of these genes, changes at the transcription level of five were re-evaluated by real-time quantitative PCR (qRT-PCR). Considering the known function of authentic genes, the effects of IBP on the biological activity and pathological aspects in medaka fish were discussed. The identified genes could be used as molecular biomarkers for biological responses to OPPs contamination in an aquatic environment.

Rank-Based Nonlinear Normalization of Oligonucleotide Arrays

  • Park, Peter J.;Kohane, Isaac S.;Kim, Ju Han
    • Genomics & Informatics
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    • 제1권2호
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    • pp.94-100
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    • 2003
  • Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

방기(防己)의 투여가 비만 유발 쥐의 생리기능과 DNA Chip을 통한 유전자 발현에 미치는 영향에 대한 연구 (Effects of Sinomenium acutum Extract on Body Weight Gains and the DNA Chip Expression of Obese Rats.)

  • 조호근;김동일
    • 대한한방부인과학회지
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    • 제20권4호
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    • pp.41-55
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    • 2007
  • Purpose: This study is to examine anti-obesity effect and cytotoxicity of the long-term oral administration of Sinomenium acutum (Bang-gi, SA) Methods: Using diet-induced obesity C57BL/6 mouse model, anti-obesity effect and DNA chip expression and cytotoxicity of the long-term oral administration of this herbal extract were investigated. Results: The herbal extract treated groups were arrested in weight increment only when they were lodged together. Such effects were abolished when they kept individually. SA fed mice behaved very rudely and violently. On the basis of histological studies of liver tissues and also in vitro cytotoxicity tests of the liver and kidney cell lines, no significant toxicity was found by 14 weeks of SA treatments. However, we found significant changes in gene expression profile in SA treated group by micro-array analysis. In case of SA group, up-regulated genes were 1,213 and down-regulated ones were 2,558. Some of lipid metabolism related genes also significantly changed in both treatment groups. Conclusion: SA had effects of increasing the basal metabolic rate by stimulating the sympathetic nervous systems.

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마황(麻黃)의 투여가 비만 유발 쥐의 생리기능과 DNA Chip을 통한 유전자 발현에 미치는 영향에 대한 연구 (Effects of the oral administration of Epedra Sinica Extract on suppression of body weight gains and the DNA chip expression of obese rats.)

  • 조호근;양정민;김동일
    • 대한한방부인과학회지
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    • 제20권3호
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    • pp.65-80
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    • 2007
  • Purpose: This study is to examine anti-obesity effect and cytotoxicity of the long-term oral administration of Ephedra Sinica(Ma-hwang, ES) Methods: Using diet-induced obesity C57BL/6 mouse model, anti-obesity effect and DNA chip expression and cytotoxicity of the long-term oral administration of this herbal extract were investigated. Results: The herbal extract treated groups were arrested in weight increment only when they were lodged together. Such effects were abolished when they kept individually. ES fed mice behaved very rudely and violently. On the basis of histological studies of liver tissues and also in vitro cytotoxicity tests of the liver and kidney cell lines, no significant toxicity was found by 14 weeks of ES treatments. However, we found significant changes in gene expression profile in ES treated group by micro-array analysis. In case of ES group, up-regulated genes were 113 and down-regulated were 120. Some of lipid metabolism related genes also significantly changed in treatment groups. Conclusion: ES had effects of increasing the basal metabolic rate by stimulating the sympathetic nervous systems.

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구강 편평세포암종 세포주에서 Cyclosporin A와 Taxol 투여시 PI-3 kinase/Akt1 Pathway에 의한 세포사멸 병용효과 (APOPTOTIC EFFECT IN COMBINATION OF CYCLOSPORIN A AND TAXOL ON ORAL SQUAMOUS CELL CARCINOMA CELL LINE THROUGH THE PI-3 KINASE/AKT1 PATHWAY)

  • 김규영;이재훈
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • 제33권5호
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    • pp.426-436
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    • 2007
  • Oral cancer take up 2-6% of all carcinomas and squamous cell carcinoma, which is the most common type in oral cancer, has a poor prognosis due to its high metastasis and recurrence rates. In treating oral cancer, chemotherapy to the primary, metastasized and recurrent lesion is a very important and useful treatment, even though its widespread usage is limited due to high general toxicity and local toxicity to other organs. Taxol, a microtubule stabilizing agent, is an anticancer drug that induces cell apoptosis by inhibiting depolymerization of microtubules in between the metaphase and anaphase of the cell mitosis. Recently, its effectiveness and mechanism on various tumor has been reported. However, not much research has been done on the application of Taxol to oral squamous cell carcinoma. Cyclosporin A, which is an immunosuppressant, is being used on cancers and when co-administered with Taxol, effectiveness of Taxol is enhanced by inhibition of Taxol induced multidrug resistance. In this study, Cyclosporin A with different concentration of Taxol was co-administered to HN22, the oral squamous cell carcinomacell line. To observe the cell apoptosis and the mechanisms that take part in this process, mortality evaluation of tumor cell using wortmannin, c-DNA microarray, RT-PCR analysis, cytometry analysis and western blotting were used, and based upon the observation on the effect and mechanism of the agent, the following results were obtained: 1. The HN22 cell line viability was lowest when $100{\mu}M$ of Wortmannin and $5{\mu}g/ml$ of Taxol were co-administered, showing that Taxol participates in P13K-AKT1 pathway. 2. In c-DNA microarray, where $1{\mu}g/ml$ of cyclosporine A and 3mg/ml of Taxol were co-administered, no up regulation of AKT1, PTEN and BAD c-DNA that participate in cell apoptosis was observed. 3. When $1{\mu}g/ml$ of Cyclosporin A was applied alone to HN22 cell line, no difference was found in AKT1, PTEN and BAD mRNA expression. 4. Increased AKT1, mRNA expression was observed when $3{\mu}g/ml$ of Taxol was applied alone to HN22 cell line. 5. When $1{\mu}g/ml$ of Cyclosporin A and Taxol($3{\mu}g/ml\;and\;5{\mu}g/ml$) were co-administered to HN22 cell line, PTEN mRNA expression increased, whereas AKT1 and BAD mRNA decreased. 6. As a result of cytometry analysis, in the group of Cyclosporin A($1{\mu}g/ml$) and Taxol($3{\mu}g/ml$) co-administration, increased Annxin V was observed, which shows that apoptosis occurred by deformation of plasma membrane. However, no significant difference was observed with vary ing concentration. 7. In western blot analysis, no caspase 3 was observed in the group of Cyclosporin A($1{\mu}g/ml$) and Taxol($3{\mu}g/ml$) co-administration. From the results of this study, it can be concluded that synergistic effect can be observed in combination therapy of Taxol and Cyclosporin A on oral squamous cell carcinoma cell line, where decreased activity of the cell line was observed. This resulted in decreased AKT1 and BAD mRNA and increased PTEN mRNA expression and when wortmannin and Taxol were co-administered, the viability decreased which confirms that Taxol decreases the viability of tumor cell line. Hence, when Taxol and cyclosporine A are co-administered, it can be assumed that cell apoptosis occurs through AKt1 pathway.

무지개송어 신장으로부터 EST 발굴 및 연령에 따른 유전자 발현 분석 (Expressed Sequence Tags in Rainbow Trout (Oncorhynchus mykiss) Kidney and Microarray Analysis in Young and Old Kidney)

  • 김순학;신용국;방인철
    • 생명과학회지
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    • 제13권1호
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    • pp.128-135
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    • 2003
  • 무지개 송어(Oncorhynchus mykiss) 신장조직의 유전자 발현 현황을 조사하기 위하여 무지개송어 신장 cDNA library로부터 102개의 ESTs를 조사하였다. 102개의 ESTs 중 57개의 clones 이 NCBI blast 염기서열 검색을 통해 이미 기능이 밝혀진 다른 유전자와의 유사성을 보였고, 그 결과 총 37개의 singleton으로 분류되었다. 나머지 45개의 ESTs는 기존의 밝혀진 유전자와 염기서열 유사성이 전혀 없었고, 상호 염기서열간의 유사성을 통해 40개의 유전자로 밝혀졌다. 또한, 신장조직의 유전자 구성을 기능별로 살펴보기 위하여 기능이 밝혀진 57개의 ESTs를 7개의 functional categories로 분류하였다. 그 결과, 신장조직의 구조에 관여하는 유전자가 14.5%로 가장 높았고, 그 다음으로 유전자 전이/전사에 관여하는 유전자가 11.6%로 판명되었다. 그리고 이들 77개의 유전자를 이용하여 연령에 따른 유전자 발현을 조사하기 위하여 microarray 실험을 하였다. 3개의 replicate를 이용하여 p-value <0.05를 갖는 유전자중 1.5배 이상만 down- 또는 up-regulation되는 유전자만을 조사하였다. 이들 중 2년산 무지개 송어 신장에서 1.5배 이상 감소되는 유전자는 mitochondrion, cytochrome b, rho G, spastin protein, RTK 17, RTK 18과 RTK 60이었다. 반면에 2년산 무지개 송어 신장에 서 1.5배 이상 증가되는 유전자는 calponinl, calcium binding protein, histone deacetyulase 1과 RTK 9 유전자가 유의성 있게 차이가 났다. 이상의 결과, 유전자 발현조사 및 microarray 연구가 무지개송어의 genetic improvemen떼 크게 영향을 미칠 수 있음을 시사하였다.

Acetaminophen Induced Cytotoxicity and Altered Gene Expression in Cultured Cardiomyocytes of $H_9C_2$ Cells

  • Jin, Seon-Mi;Park, Kwang-Sik
    • Environmental Analysis Health and Toxicology
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    • 제27권
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    • pp.11.1-11.8
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    • 2012
  • Objectives: Hepatotoxicity of acetaminophen has been widely studied. However, the adverse effects on the heart have not been sufficiently evaluated. This study was performed to investigate cytotoxicity and alterations of gene expression in cultured cardiomyocytes ($H_9C_2$ cells) after exposure to acetaminophen. Methods: $H_9C_2$ cells were incubated in a 10 mM concentration of acetaminophen for the designated times (6, 12, and 24 hours), and cytotoxicity was determined by the 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. Alteration of gene expression was observed by microarray analysis, and RT-PCR was performed for the three representative oxidative stress-related genes at 24 hours after treatment. Results: It revealed that acetaminophen was toxic to cardiomyocytes, and numerous critical genes were affected. Induced genes included those associated with oxidative stress, DNA damage, and apoptosis. Repressed genes included those associated with cell proliferation, myocardial contraction, and cell shape control. Conclusions: These findings provide the evidences of acetaminophen-induced cytotoxicity and changes in gene expression in cultured cardiomyocytes of $H_9C_2$ cells.

Potentiation of Innate Immunity by β-Glucans

  • Seong, Su-Kyoung;Kim, Ha-Won
    • Mycobiology
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    • 제38권2호
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    • pp.144-148
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    • 2010
  • $\beta$-Glucans have been known to exhibit antitumor activities by potentiating host immunity by an unknown mechanism. The C-type lectin dectin-1, a $\beta$-glucan receptor, is found on the macrophage and can recognize various $\beta$-glucans. Previously, we demonstrated the presence of $\beta$-glucan receptor, dectin-1, on the Raw 264.7 cells as well as on murine mucosal organs, such as the thymus, the lung, and the spleen. In order to investigate immunopotentiation of innate immunity by $\beta$-glucan, we stimulated a murine macrophage Raw 264.7 cell line with $\beta$-glucans from Pleurotus ostreatus, Saccharomyces cerevisiae, and Laminaria digitata. Then, we analyzed cytokines such as tumor necrosis factor (TNF)-$\alpha$ and interleukin (IL)-6 by reverse transcription-polymerase chain reaction (RT-PCR). In addition we analyzed gene expression patterns in $\beta$-glucan-treated Raw 264.7 cells by applying total mRNA to cDNA microarray to investigate the expression of 7,000 known genes. When stimulated with $\beta$-glucans, the macrophage cells increased TNF-$\alpha$ expression. When co-stimulation of the cells with $\beta$-glucan and lipopolysaccharide (LPS), a synergy effect was observed by increased TNF-$\alpha$ expression. In IL-6 expression, any of the $\beta$-glucans tested could not induce IL-6 expression by itself. However, when co-stimulation occurred with $\beta$-glucan and LPS, the cells showed strong synergistic effects by increased IL-6 expression. Chip analysis showed that $\beta$-glucan of P. ostreatus increased gene expressions of immunomodulating gene families such as kinases, lectin associated genes and TNF-related genes in the macrophage cell line. Induction of TNF receptor expression by FACS analysis was synergized only when co-stimulated with $\beta$-glucan and LPS, not with $\beta$-glucan alone. From these data, $\beta$-glucan increased expressions of immunomodulating genes and showed synergistic effect with LPS.