• Journal of Plant Biotechnology
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• 제5권4호
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• pp.209-214
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• 2003

Expression of 43 flowering-related genes was examined in two inbred lines of Chinese cabbage, Chiifu and Kenshin, under different photoperiod, vernalization and flower development stages. The floral genes cloned by RT-PCR with degenerated primers showed high homology with Arabidopsis counterparts. Genes in two inbred lines, TOC, CRY1, CO, RGAL and GAl, were highly expressed under all tested conditions. However, expression of three genes was regulated by particular experimental conditions. The expression of LHY gene was predominant in Chiifu under the short-day conditions, whereas the expression of RGAL gene was influenced by vernalization in both inbred lines. Besides, the expression of NAP gene was induced by vernalization only in Chiifu. Most of the flower identity-related genes were expressed during flower development. The transcript level for several genes was not detected in this experiment.

• BMB Reports
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• 제35권6호
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• pp.623-628
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• 2002

The Th1 vs. Th2 balance is critical for the maintenance of immune homeostasis. Therefore, the genes that are selectively-regulated by the Th1 and Th2 cytokines are likely to play an important role in the Th1 and Th2 immune responses. In order to search for and identify the novel target genes that are differentially regulated by the Th1/Th2 cytokines, the human PBMC mRNAs differentially expressed upon the stimulation with IL-4 or IL-12, were screened by employing the differential display-polymerase chain reaction. Among a number of clones selected, DC21 was identified as a novel target gene that is regulated by IL-4 and IL-12. The DC21 gene expression was up-regulated either by IL-4 or IL-12, yet counter-regulated by co-treatment with IL-4 and IL-12. DC21 is a dendritic cell protein with an unknown function. The sequence analysis and conserved-domain search revealed that it has two AU-rich motifs in the 3'UTR, which is a target site for the regulation of mRNA stability by cytokines, and that it belongs to the N-acetyltransferase family. The induction of DC21 by IL-12 peaked around 8-12 h, and lasted until 24 h. LY294002 and SB203580 significantly suppressed the IL-12-induced DC21 gene expression, which implies that PI3K and p38/JNK are involved in the IL-12 signal transduction pathway that leads to the DC21 expression. Furthermore, tissue blot data indicated that DC21 is highly expressed in tissues with specialized-resident macrophages, such as the lung, liver, kidney, and placenta. Together, these data suggest a possible role for DC21 in the differentiation and maturation of dendritic cells regulated by IL-4 and IL-12.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.67.1-67
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• 2003

Phytophthora blight is a devastating disease of pepper and occurs almost anywhere peppers are grown. Phytophthora blight is caused by Phytophthora capsici and this pathogen can infect every part of the plant by moving inoculum in the soil, by infecting water on surface, by aerial dispersal to sporulating lesions. Management of Phytophthora blight currently relies on cultural practices, crop rotation, and use of selective fungicides. Since these treatments are a short-term management, a classical breeding for development of resistant pepper against the Phytophthora is an alternative. So far some of the resistant cultivars have been on the market, but those are limited regionally and commercially. Therefore, ultimately an elite line resistant against this disease should be developed, if possible, by biotechnology. We have set out a series of work recently in order to develop Phytophthora resistant pepper cultivar. For the first time, the cDNA microarray analysis was peformed using an EST chip that holds around 5000 pepper EST clones to identify genes responsive to Phytophthora infection. Total RNA samples were obtained from Capsicum annuum PI201234 after inoculating P. capsici to roots and soil and exposed to the chip. .Around 900 EST clones were up-regulated and down-regulated depending on the two RNA sample tissues, leaf and root. From those, we have found 55 transcription factors that may be involved in gene regulation of the disease defense mechanism. Further and in detail information will be provided in the poster.

• Asian Pacific Journal of Cancer Prevention
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• 제16권7호
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• pp.2793-2800
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• 2015

In molecular-targeted cancer therapy, acquired resistance to gemcitabine is a major clinical problem that reduces its effectiveness, resulting in recurrence and metastasis of cancers. In spite of great efforts to reveal the overall mechanism of acquired gemcitabine resistance, no definitive genetic factors have been identified that are absolutely responsible for the resistance process. Therefore, we performed a cross-platform meta-analysis of three publically available microarray datasets for cancer cell lines with acquired gemcitabine resistance, using the R-based RankProd algorithm, and were able to identify a total of 158 differentially expressed genes (DEGs; 76 up- and 82 down-regulated) that are potentially involved in acquired resistance to gemcitabine. Indeed, the top 20 up- and down-regulated DEGs are largely associated with a common process of carcinogenesis in many cells. For the top 50 up- and down-regulated DEGs, we conducted integrated analyses of a gene regulatory network, a gene co-expression network, and a protein-protein interaction network. The identified DEGs were functionally enriched via Gene Ontology hierarchy and Kyoto Encyclopedia of Genes and Genomes pathway analyses. By systemic combinational analysis of the three molecular networks, we could condense the total number of DEGs to final seven genes. Notably, GJA1, LEF1, and CCND2 were contained within the lists of the top 20 up- or down-regulated DEGs. Our study represents a comprehensive overview of the gene expression patterns associated with acquired gemcitabine resistance and theoretical support for further clinical therapeutic studies.

• Journal of Microbiology and Biotechnology
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• 제23권4호
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• pp.451-458
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• 2013

The human gastric pathogen Helicobacter pylori (Hp) has been considered a microaerophile. However, we recently reported that, when supplied with 10% $CO_2$, Hp growth is stimulated by an atmospheric level of $O_2$, suggesting that Hp is a capnophilic aerobe. In this study, we investigated the effects of aerobic $O_2$ tension on Hp cells by comparing gene expression profiles of cultures grown under microaerobic and aerobic conditions in the presence of 10% $CO_2$. The results showed that overall differences in gene expression in Hp cells grown under the two $O_2$ conditions were predominantly growth-phase-dependent. At 6 h, numerous genes were down-regulated under the aerobic condition, accounting for our previous observation that Hp growth was retarded under this condition. At 36 h, however, diverse groups of genes involved in energy metabolism, cellular processes, transport, and cell envelope synthesis were highly up- or down-regulated under the aerobic condition, indicating a progression of the cultures from the log phase to the stationary phase. The expression of several oxidative stress-associated genes including tagD, katA, and rocF was induced in response to aerobic $O_2$ level, whereas trxA, trxB, and ahpC remained unchanged. Altogether, these data demonstrate that aerobic $O_2$ tension is not detrimental to Hp cells but stimulates Hp growth, supporting our previous finding that Hp may be an aerobic bacterium that requires a high $CO_2$ level for its growth.

• Journal of Applied Biological Chemistry
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• 제42권2호
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• pp.92-96
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• 1999

To study the regulatory mechanism of isoprenoid (carotenoid) biosynthesis, we have compared the expression patterns of nine isoprenoid biosynthetic genes in Korean red pepper (Capsicum. annuum cv. NocKaung). The expression of geranylgeranyl pyrophosphate synthase gene was initially induced at early ripening stage (I1) and was rather slightly decreased during pepper fruit ripening. The ex-pression of phytoene synthase gene was strongly induced at semi-ripening stage (I2) and the phytoene desaturase transcript was maximally induced at the fully ripened stage (R). Our results suggest that genes encoding two 3-hydroxy-3-methylglutaryl-CoA reductase isozymes (HMGR1 and HMGR2) and farnesyl pyrophosphate synthase might be not so critical in pepper carotenoid biosynthesis but three genes encoding geranylgeranyl pyrophosphate synthase, phytoene synthase and phytoene desaturase were induced in a sequential manner and coordinately regulated during the ripening of pepper fruit.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.231-239
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• 2016

담배에서 후성유전관련 유전자의 발현연구를 위해 담배유래 시토신 DNA 탈메틸화 관련 NtROS2a 유전자를 과발현 및 RNAi 식물체를 육성하였다. 이들 형질전환체들은 고염 및 산화 스트레스하에서 내성이 증진되었으며, 다양한 표현형변이를 보였다(Lee et al. 2015). 본연구에서는 선발된 과발현 (OX1), RNAi 식물체(RNAi 13) 및 대조식물체(WT)를 이용하여 Agilent Tobacco 4 X 44K Oligo chip으로 microarray분석을 수행하였다. OX1과 RNAi13 계통을 이용하여 WT과 함께 비교 분석한 결과, 대부분 세포 내 이온 수송, 영양 공급 등과 같은 물질대사와 생물적 비생물적 스트레스 및 methylation과 관련되어 영향을 주는 유전자들에서 up-regulation 되었고, 물질대사관련 유전자와 세포 내 기능유전자의 역할을 담당하는 조효소, 그리고 다양한 스트레스 및 메틸레이션 관련 유전자군에서 또한 down-regulation되었다. 각각의 up-, down-regulation된 유전자들을 WT과 비교하여 qRT-PCR을 수행한 결과, KH domain-containing protein, MADS-box protein 및 Zinc phosphodiesterase ELAC protein 유전자들에서 발현이 높게 나타났으며, 반면에 pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein 및 protein kinase는 0.4 ~ 1.0-fold 발현양이 감소되었다. 따라서 DNA glycosylase를 암호화하는 NtROS2a 유전자는 demethylation과 관련되어 담배 식물체에서 다양한 전사레벨을 조절하는 것으로 판단된다.

• Molecules and Cells
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• 제42권2호
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• 자연과학논문집
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• 제11권1호
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• pp.95-98
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• 1999

$CO_2$ gas 처리가 배추 자가불화합성 타파에 미치는 영향을 조사하고자 배추 inbred line의 암술에서 mRNA를 분리하여 DD-PCR을 수행하였다. $CO_2$ gas를 처리한 암술에서 분리한 mRNA와 처리하지 않은 꽃에서 분리한 암술 mRNA 발현과의 특이적인 차이를 DD-PCR로 조사한 결과 세 가지 각기 다른 anchor primer에 대해 모두 18개의 특이적 증폭 DNA fragment를 얻을 수 있었다. 이 결과로 미루어 보아 $CO_2$ gas 처리에 의한 암술 mRNA발현의 변화가 배추 자가불화합성 타파에 영향을 미치는 것으로 생각된다.

• Journal of Microbiology and Biotechnology
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• 제26권6호
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• pp.1035-1045
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• 2016

To evaluate the effects of lactic acid bacteria (LAB) on Peyer's patch cells, mice were treated with a high dose of kanamycin to disturb the gut microbial environment. The overarching goal was to explore the potential of LAB for use as a dietary probiotic that buffers the negative consequences of antibiotic treatment. In vitro, LAB stimulated the production of immunoglobulin A (IgA) from isolated Peyer's patch cells. Inflammation-related genes (TNF-α, IL-1β, and IL-8) were up-regulated in Caco-2 cells stimulated with lipopolysaccharide (LPS), while tight-junction-related genes (ZO-1 and occludin) were down-regulated; the effects of LPS on inflammatory gene and tight-junction gene expression were reversed by treatment with LAB. Mice treated with a high dose of kanamycin showed increased serum IgE levels and decreases in serum IgA and fecal IgA levels; the number of Peyer's patch cells decreased with kanamycin treatment. However, subsequent LAB treatment was effective in reducing the serum IgE level and recovering the serum IgA and fecal IgA levels, as well as the number of Peyer's patch cells. In addition, ZO-1 and occludin mRNA levels were up-regulated in the ileum tissues of mice receiving LAB treatment. Lactic acid bacteria can enhance the intestinal immune system by improving the integrity of the intestinal barrier and increasing the production of IgA in Peyer's patches. Lactic acid bacteria should be considered a potential probiotic candidate for improving intestinal immunity, particularly in mitigating the negative consequences of antibiotic use.