• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.337-353
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• 2018

We used Illumina/HiSeq sequencing for analysis of gene expression profiling among four maize seed types (dent, CM3 and CM6; waxy, CM5 and CM19) at 10 DAP (days after pollination). A total of 88,993,000 (CM3), 103,817,340 (CM6), 103,139,640 (CM5), and 66,978,958 (CM19) sequence reads were generated with read lengths of about 0.9, 1.0, 1.0, and 0.7 billion bp, respectively. We obtained 69.1 (CM3), 71.0 (CM6), 71.2 (CM5), and 71.8% (CM19) high quality reads from the raw data and compared them with reference RNA sequences in a public DB (NCBI). It was revealed that mapped reads were 58%, 63%, 62%, and 62% of the EST reference in CM3, CM6, CM5 and CM19, respectively; and more than 51,000 genes were expressed based on RPKM criteria (over 0.25 value) in each CM3, CM6, CM5, and CM19 inbred line. In differentially expressed gene (DEG) analysis, we found that 3,527 genes were differentially expressed by at least two-fold with 1,709 upregulated in the two waxy inbred lines and 1,818 upregulated in the two dent inbred lines. We also detected genes for the sucrose and starch biosynthesis pathways based on BINs, and different expression patterns between waxy and dent inbred lines were shown for the gene set for starch synthesis, such as sh2, bt2, du1, wx1, and ae1. Although some genes were more expressed in dent lines, most genes for starch synthesis were much expressed in waxy lines. Especially, there was greater expression of the sus2 gene in both waxy lines compared with the dent lines.

• Molecular & Cellular Toxicology
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• 제5권4호
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• pp.335-345
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• 2009

A major source of paeoniflorin (PF) which was from the Paeonia lactiflora root, has been used as a herbal medicine in East Asia for its antiallergic, antiinflammatory, and immunoregulatory effects. However, only few details are known about the mechanism of apoptosis induced by this compound. The present study was undertaken to further elucidate the molecular mechanism of apoptosis and the changes of gene expression elicited by PF using DNA microarrays and computational gene-expression analysis tools in human leukemia U937 cells. A comparative global transcription analysis between treatment with PF and anisomycin (AM) that induces apoptosis in U937 cells revealed that c-Jun-$NH_2$-kinase (JNK) pathway related genes were less expressed in PF-treated cells. Elucidation of the mechanisms by which PF conducts its anti-cancer activities through comparative analysis of the gene expression is necessary to provide a solid foundation for its use as a promising agent in prevention and treatment strategies.

• 한국산업보건학회지
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• 제20권1호
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• pp.29-40
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• 2010

This study was aimed at investigating the gene expression profile in basal ganglia of cadmium exposed rat based on cDNA array analysis. For cDNA array analysis, adult Sprague-Dawley male rats (350 ${\pm}$ 25 g) were intraperitoneally injected with 2.0 mg/kg body weight/day of CdCl2 (0.3 ml) for 5 days. For doserelated gene expression analysis rats were intraperitoneally injected with 0.0, 0.1, 0.3, 1.0 mg/kg body weight/day of CdCl$_2$ for 5 days. Control rats were injected with equal volume of saline. Cadmium concentration of brain was analyzed by atomic absorption spectrophotometer. For cDNA array, RNA samples were extracted from basal ganglia and reverse-transcribed in the presence of [${\alpha}$32P]-dATP. Membrane sets of the Atlas Rat 1.2 array II and Toxicology array 1.2 (Clontech, Palo Alto, CA) were hybridized with cDNA probe sets. RT-PCR was employed to validate the relative gene expression patterns obtained from the cDNA array. Northern blot hybridization methods were employed to assess the dose-related gene expression. Among the 2352 cDNAs, 671 genes were detected in both array sets and 63 genes of 38 classes showed significant (more than two fold) changes in expression. Thirty five of these genes were up-regulated and twenty eight were down-regulated in the cadmium exposed group. According to the dose-related gene expression analysis, heat shock 27 kDa protein (HSP27), neurodegeneration-associated protein 1 (Neurodap 1) genes were significantly up-regulated and melatonin receptor 1a (Mel1a), Kinesin family member 3C (KIF3C), novel kinesinrelated protein (KIF1D) genes were significantly downregulated even in the low-dose of cadmium exposed group (0.1 mg/kg body weight/day). Conclusions Sixty three genes detected in this study can give some more useful informations about the cadmium-induced neurotoxicity in the basal ganglia. As well as, HSP27, Neurodap1, Mel1a, KIF3C and KIF1D genes may be useful for the study of the cadmium-induced neurotoxicity because these genes showed dramatic changes of mRNA levels in response to the low dose of cadmium exposure.

• Genomics & Informatics
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• 제4권1호
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• pp.16-22
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• 2006

The KFDA (Korea Food & Drug Administration) has performed a collaborative toxicogenomics project since 2003. Its aim is to construct a toxicology database of 12 compounds administered to mice at initial phase. We chose 6-MP (6-mercaptopurine) which has been used in the treatment of childhood leukemia. It was administered at low (0.224 mg/kg) and at high (2.24 mg/kg) dose (5 mice per group) intraperitonealy to the postnatal 6 weeks mice, then the serum and liver were collected at the indicated time (6, 24 and 72 h) after scarification. Serum biochemical markers for liver toxicity were measured and histopathologic studies also were carried out. The gene expression profiling was carried out by using Applied Biosystems 1700 Full Genome Expression Mouse. By self-organization maps (SOM), we identified groups with unique gene expression patterns, some of them are supposed to be related to 6-MP induced toxicity, including lipid metabolism abnormality, inflammatory response, oxidative stress, ATP depletion and cell death. The potential toxic effects appearing as gene expression changes are dependent of the time of 6-MP but independent of the dosage of it. This study would contribute to establishment of international database as well as national one about hepatotoxicity.

• Toxicological Research
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• 제22권2호
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• pp.103-107
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• 2006

We demonstrate that paclitaxel, an antitumor agent derived from yew tree, inhibits LPS-induced expression of iNOS gene in RAW 264.7 cells. Previously, paclitaxel has been known to induce iNOS gene expression in macrophages. However, in this report we described that the pre-treatment of macrophages with paclitaxel ($0.1{\mu}M$) for 8 h inhibited LPS-induced iNOS gene expression. Pretreatment of RAW 264.7 cells with paclitaxel significantly inhibited LPS-stimulated nitric oxide (NO) production. Western immunoblot of iNOS and RT-PCR analysis showed that the decrease of NO was due to the inhibition of iNOS gene expression in RAW 264.7 cells. Immunocytochemical staining of iNOS further confirmed that pretreatment of macrophages with paclitaxel inhibited macrophage activation. Electrophoretic mobility shift assay showed that paclitaxel inhibited $NF-_{\kappa}/Rel$ DNA binding. Collectively, these series of experiments indicate that paclitaxel inhibits iNOS gene expression by blocking $NF-_{\kappa}B/Rel$ activation.

• Journal of Oral Medicine and Pain
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• 제19권2호
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• pp.57-71
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• 1994

Gingival fibroblasts were cultured and subjected to the test of Northern blot analysis for the demonstration of various mRNA expression in response to the low level laser treatment. For duplication of in vivo. Wound healing process, fibroblasts were pretreated with proinflammatory cytokine interleukin-1$\beta$(IL-1$\beta$) or mitogenic substance phorbol 12-myristate 13-acetate(PMA) prior to laser irradiation. The results were as follows : 1. By the laser irradiation, the gene expression of collagen type I was markedly increased I n gingival fibroblasts, especially in the case of PMA pretreatment. The gene expression of collagen type IV, however, was not only affected by laser irradiation but also by chemical cell stimulation. 2. Oncogene v-myc expression was affected by both laser irradiation and IL-1$\beta$ or PMA stimulation, But v-fos gene expression was not detected in any case of this experimental system. 3. Heat shock gene(Hsp 70)was expressed constiutively, but slightly increased by laser irradiation. 4. mRNA of fibroblast growth factor(FGF) was induced by both laser irradiation and IL-1$\beta$ or PMA treatment.

• Genomics & Informatics
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• 제15권1호
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• pp.38-47
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• 2017

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

• Genomics & Informatics
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• 제15권3호
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• pp.98-107
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• 2017

MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3' untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5'-CAGUCG-3') in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3' UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.

• 한국자원식물학회지
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• 제21권4호
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• pp.249-253
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• 2008

식물의 미토콘드리아에서 eukaryotic 유전자 발현하는 양상을 관찰한다는 것은 매우 중요하게 알여져 왔다. 본 실험에서는 식물의 미토콘드리아에서 발현하는 유전자와 GFP가 미토콘드리아에 발현하는지를 구명하였다. 미토콘드리아(mt)에서 발현 하는 AtBI-1 유전자와 GFP 유전자를 35S promoter를 가진 pBin vector에 재조합한 후, 유전자총을 이용한 형질전환법으로 담배의 잎과 cotyledon에 형질전환하여 재분화 된 shoot를 얻었다. mt에서 그 유전자가 발현 되는 것을 현미경하에서 GFP가 발광하는 것으로 확인하였다. 또한 PCR분석과 Southern분석에서도 미토콘드리아에서 AtBI-1 유전자가 발현함을 확인하였다. 따라서 본 연구의 결과로 mt에 관련된 유전자를 식물의 조직에 형질전환 하여 1개 이상의 유전자가 식물의 mt에 삽입되어 그 유전자의 특성이 발현되는데 이용되어 질수 있을것이라 생각된다.

• 한국발생생물학회지:발생과생식
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• 제17권3호
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• pp.231-240
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• 2013

Olive flounder (Paralichthys olivaceus) is one of the commercial important flatfish species in Korea. The ocular signal transduction pathway is important in newly hatched flounders because it is closely involved in the initial feeding phase thus essential for survival during the juvenile period. However, the study of gene expression during ocular development is incomplete in olive flounder. Therefore we examined the expression analysis of specifically induced genes during the development of the visual system in newly hatched flounders. We searched ocular development-involved gene in the database of expressed sequence tags (ESTs) from olive flounder eye and this gene similar to arrestin with a partial sequence homology. Microscopic observation of retinal formation corresponded with the time of expression of the arrestin gene in the developmental stage. These results suggest that arrestin plays a vital role in the visual signal transduction pathway of the retina during ocular development. The expression of arrestin was strong in the ocular system during the entirety of the development stages. Our findings regarding arrestin have important implications with respect to its biological role and evolution of G-protein coupled receptor (GPCR) signaling in olive flounder. Further studies are required on the GPCR-mediated signaling pathway and to decipher the functional role of arrestin.