• Title/Summary/Keyword: cDNA microarray analysis

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

  • Lee, Hee Jae;Son, Chang Hee;Kwak, Hyong Ryol;Lee, Sang-Hyun;Han, Yoon Hee;Kim, Soo Young;Park, Jong-Ik;Chun, Wanjoo;Kim, Sung-Soo
    • Korean Journal of Biological Psychiatry
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    • v.13 no.2
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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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Effects of 5-azacytidine, a DNA methylation inhibitor, on embryogenic callus formation and shoot regeneration from rice mature seeds (벼 성숙종자로부터 배상체 캘러스 형성 및 식물체 재분화에 DNA methylation 억제제인 5-azacytidine의 영향)

  • Lee, Yeon-Hee;Lee, Jung-Sook;Kim, Soo-Yun;Sohn, Seong-Han;Kim, Dool-Yi;Yoon, In-Sun;Kweon, Soon-Jong;Suh, Seok-Chul
    • Journal of Plant Biotechnology
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    • v.35 no.2
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    • pp.133-140
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    • 2008
  • The modification of DNA and histone plays an important role for gene expression in plant development. The objective of this research is to observe the effects of methylation on the gene expression during dedifferentiation from rice mature seeds to callus and differentiation from callus to shoots. The embryogenic callus with ability to shoot regeneration was not induced on the N6A medium supplemented with 5-azacytidine and abnormal callus with brown color was formed. When the normal rice callus was placed on the regeneration MSRA medium supplemented with 5-azacytidine, the shoot regeneration was inhibited. The results showed that 5-azacytidine, DNA demethylating agent, had negative effects on normal embryogenic callus formation and shoot regeneration. This suggested that DNA methylation of some genes was required for normal cell dedifferentiation and differentiation in tissue culture. The microarray and $GeneFishig^{TM}$ DEG screening were used to observe the gene transcript profile in callus induction and regeneration on N6A (N6 medium + 5-azaC) and MSRA (MS regeneration medium + 5-azaC). Subsets of genes were up-regulated or down-regulated in response to 5-azaC treatments. The genes related with epigenetic regulation, electron transport, nucleic acid metabolism and response to stress were up and down regulated. The different expression of some genes (germin like protein etc.) during callus induction and shoot regeneration was confirmed using RT-PCR and northern blot analysis.

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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    • v.4 no.2
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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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    • v.1 no.2
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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.

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

  • Joh, Ho-Geun;Kim, Dong-Il
    • The Journal of Korean Obstetrics and Gynecology
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    • v.20 no.4
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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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Effects of the oral administration of Epedra Sinica Extract on suppression of body weight gains and the DNA chip expression of obese rats. (마황(麻黃)의 투여가 비만 유발 쥐의 생리기능과 DNA Chip을 통한 유전자 발현에 미치는 영향에 대한 연구)

  • Joh, Ho-Geun;Yang, Jeong-Min;Kim, Dong-Il
    • The Journal of Korean Obstetrics and Gynecology
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    • v.20 no.3
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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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APOPTOTIC EFFECT IN COMBINATION OF CYCLOSPORIN A AND TAXOL ON ORAL SQUAMOUS CELL CARCINOMA CELL LINE THROUGH THE PI-3 KINASE/AKT1 PATHWAY (구강 편평세포암종 세포주에서 Cyclosporin A와 Taxol 투여시 PI-3 kinase/Akt1 Pathway에 의한 세포사멸 병용효과)

  • Kim, Kyu-Young;Lee, Jae-Hoon
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.33 no.5
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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.

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

  • Kim, Soon-Hag;Shin, Yong-Kook;Bang, In-Chul
    • Journal of Life Science
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    • v.13 no.1
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    • pp.128-135
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    • 2003
  • 102 ESTs (Expressed Sequence Tags) were obtained by sequencing clones from a library of rainbow trout kidney cDNAs. Of the sequences generated, 55.8% of the ESTs were represented by 37 known genes. The 45 clones of unknown gene products potentially represent 40 novel genes. The genes involved in structural function (14.5%) and transcription/translation (11.6%) account for the major gene expression activities in the kidney Microarray experiment was conducted to compare gene expression of the unique ESTs in young and adult rainbow trout kidneys. While mitochondrion, cytochrome b, rho G, spastin protein, and three unknown genes were down-regulated in the mature fish kidney, calponin 1, calcium binding protein, histone deacetylase 1, and an unknown gene were up-regulated in the mature fish kidney. This research demonstrates the feasibility and power of functional genomics in rainbow trout.

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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    • v.27
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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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    • v.38 no.2
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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.