• Journal of Microbiology and Biotechnology
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• 제27권4호
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• pp.709-717
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• 2017

Mucosal tissues are the initial site through which most pathogens invade. As such, vaccines and adjuvants that modulate mucosal immune functions have emerged as important agents for disease prevention. Herein, we investigated the immunomodulatory mechanisms of the B subunit of Escherichia coli heat-labile enterotoxin type IIa ($LT-IIa-B_5$), a potent non-toxic mucosal adjuvant. Alternations in gene expression in response to $LT-IIa-B_5$ were identified using a genome-wide transcriptional microarray that focused on dendritic cells (DC), a type of cell that broadly orchestrates adaptive and innate immune responses. We found that $LT-IIa-B_5$ enhanced the homing capacity of DC into the lymph nodes and selectively regulated transcription of pro-inflammatory cytokines, chemokines, and cytokine receptors. These data are consistent with a model in which directional activation and differentiation of immune cells by $LT-IIa-B_5$ serve as a critical mechanism whereby this potent adjuvant amplifies mucosal immunity to co-administered antigens.

• BMB Reports
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• 제44권8호
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• pp.523-528
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• 2011

To identify novel genes that are regulated by promoter methylation, a combinational approach involving in silico mining followed by molecular assay was performed. From the expression microarray data registered in the European bioinformatics institute (EBI), genes showing downregulation in breast cancer cells were initially screened and then selected by e-Northern analysis using the Unigene database. A series of these in silico methods identified CAMK2B and ARFGEF1 as candidates, and the two genes were revealed to be hypermethylated in breast cancer cell lines and hypomethylated in normal breast cell lines. Additionally, cancer cell lines showed downregulated expression of these genes. Furthermore, treatment of the cancer cell lines with a demethylation agent, 5-Aza-2'-deoxycytidine, recovered expression of CAMK2B and ARFGEF1, implying that hypermethyaltion silenced gene activity in cancer cells. Taken together, promoter methylations of CAMK2B and ARFGEF1 are novel epigenetic markers identified in breast cancer cell lines and can be utilized for the application to clinical cancer tissues.

• Asian Pacific Journal of Cancer Prevention
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• 제16권6호
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• pp.2561-2567
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• 2015

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer death worldwide. Our study aimed to reveal molecular mechanisms. Microarray data of GSE15471 (including 39 matching pairs of pancreatic tumor tissues and patient-matched normal tissues) was downloaded from Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) in PDAC tissues compared with normal tissues by limma package in R language. Then GO and KEGG pathway enrichment analyses were conducted with online DAVID. In addition, principal component analysis was performed and a protein-protein interaction network was constructed to study relationships between the DEGs through database STRING. A total of 532 DEGs were identified in the 38 PDAC tissues compared with 33 normal tissues. The results of principal component analysis of the top 20 DEGs could differentiate the PDAC tissues from normal tissues directly. In the PPI network, 8 of the 20 DEGs were all key genes of the collagen family. Additionally, FN1 (fibronectin 1) was also a hub node in the network. The genes of the collagen family as well as FN1 were significantly enriched in complement and coagulation cascades, ECM-receptor interaction and focal adhesion pathways. Our results suggest that genes of collagen family and FN1 may play an important role in PDAC progression. Meanwhile, these DEGs and enriched pathways, such as complement and coagulation cascades, ECM-receptor interaction and focal adhesion may be important molecular mechanisms involved in the development and progression of PDAC.

• Journal of Acupuncture Research
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• 제21권5호
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• pp.69-78
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• 2004

Objective : This study was undertaken to determine the inhibitory effect of Whallak-tang against Nitric Oxide, the scavenging effect of Whallak-tang on DPPH radical. Methods : Both nitric concentration 1, 3, 6 and 24 hours after treatment with Vit. C and Whallak-tang at 0.1, 1, 10 mg/ml and scavenging effect 10, 20, 30 and 60 minute after treatment with Vit. C and Whallak-tang at 0.1, 1, 10 mg/ml were estimated. Results : The inhibitory effect of Whallak-tang against Nitric Oxide was dose-dependent. The scavenging effect of Whallak-tang on DPPH radical was dose-dependent. Conclusion : These results would provide important basic data on the possibility of the clinical treatment of Whallak-tang in musculoskeletal disease.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.164-164
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• 2017

High throughput transcriptome investigations of immunity in plants highlight the complexity of gene networks leading to incompatible interaction. To identify genes crucial to resistance against Xanthomonas oryzae pv oryzae, functional genetic analysis of selected differentially expressed genes from our microarray data set was carried out. A total of 13 overexpression vector constructs were made using 35S CaMV promoter which drive constitutive expression in rice. Most of the genes are developmentally expressed especially during maximum tillering stage and are commonly highly expressed in the leaves. When screened against Xoo strain K2, the transgenic plants displayed shorter lesion length compared with wild type Dongjin which indicates partial resistance. The levels of ROS continuously magnified after inoculation which indicates robust cellular sensing necessary to initiate cell death. Elevated transcripts levels of several defense-related genes at the downstream of defense signal network also corroborate the phenotype reaction of the transgenic plants. Moreover, expression assays revealed regulation of these genes by cross-communicating signal-transductions pathways mediated by salicylic and jasmonic acid. These collective findings revealed the key immune signaling conduits critical to mount full defense against Xoo.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.13-15
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• 2006

microRNA는 유전자의 전사 후 과정에서 negative regulation을 담당하는 small noncoding RNA의 한 증류이다. 최근까지 330여개의 인간 microRNA가 발견되었지만 그들의 기능이 밝혀진 것은 소수에 불과하다. microRNA의 기능은 3'UTR에 불완전 상보결합을 통해 negative regulation을 받게 되는 유전자의 기능으로부터 유추되는 것이 일반적이다. 특별히 유전체상에 군집화 된 microRNA들은 하나의 전사체로부터 발현되는 것으로 판단되며, 같은 또는 관련된 기능을 하거나 같은 목표 유전자를 조절하기 위한 functional family일 가능성이 높다. 또한 이러한 functional family는 하나의 전사체로부터 발현되기 때문에, 조직별로 조건별로 같은 발현 패턴을 보여야 한다. 본 연구에서는 발현데이터로부터 microRNA functional family를 탐색하기 위해, 5개의 연구 그룹에서 공개한 조직별 microRNA 발현데이터를 표준화 작업을 거친 후 통합하고 k-nearest neighbor 알고리즘을 이용해 결측치를 보정한 후 microRNA 발현사이의 correlation을 계산한다. 이때 데이터 통합에서 생기는 문제에 robust한 결과를 얻기 위해 실제 발현데이터가 아닌 rank 데이터부터 correlation을 측정한다. 계산된 spearman ranked correlation 결과와 microRNA의 genomic coordination 정보로부터 34개의 functional family를 정의할 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제14권4호
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• pp.836-843
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• 2004

Nontypeable H. influenzae (NTHi), a Gram-negative obligate human pathogen, causes pneumonia, chronic bronchitis, and otitis media, and the respiratory epithelium is the first line of defense that copes with the pathogen. In an effort to identify transcriptional responses of human respiratory epithelial cells to infection with NTHi, we examined its differential gene expression using high density cDNA microarrays. BEAS-2B human bronchial epithelial cells were exposed to NTHi for 3 hand 24 h, and the alteration of mRNA expression was analyzed using microarrays consisting of 8,170 human cDNA clones. The results indicated that approximately 2.6% of the genes present on the microarrays increased in expression over 2-fold and 3.8% of the genes decreased during the 24-h infection period. Upregulated genes included cytokines (granulocyte-macrophage colony stimulating factor 2, granulocyte chemotactic protein 2, IL-6, IL-10, IL-8), transcription factors (Kruppel-like factor 7, CCAAT/enhancer binding protein $\beta$, E2F-1, NF-$\kappa$B, cell surface molecules (CD74, ICAM-1, ICAM-2, HLA class I), as well as those involved in signal transduction and cellular transport. Selected genes were further confirmed by reverse-transcription-PCR. These data expand our knowledge of host cellular responses during NTHi infection and should provide a molecular basis for the study of host-NTHi interaction.

• Molecules and Cells
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• 제37권9호
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• pp.685-690
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• 2014

Osteoclasts are large polykaryons that have the unique capacity to degrade bone and are generated by the differentiation of myeloid lineage progenitors. To identify the genes involved in osteoclast development, we performed microarray analysis, and we found that carboxypeptidase E (CPE), a prohormone processing enzyme, was highly upregulated in osteoclasts compared with their precursors, bone marrow-derived macrophages (BMMs). Here, we demonstrate a novel role for CPE in receptor activator of NF-${\kappa}B$ ligand (RANKL)-induced osteoclast differentiation. The overexpression of CPE in BMMs increases the formation of tartrate-resistant acid phosphatase (TRAP)-positive multinuclear osteoclasts and the expression of c-Fos and nuclear factor of activated T cells c1 (NFATc1), which are key regulators in osteoclastogenesis. Furthermore, employing CPE knockout mice, we show that CPE deficiency attenuates osteoclast formation. Together, our data suggest that CPE might be an important modulator of RANKL-induced osteoclast differentiation.

• Molecular & Cellular Toxicology
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• 제3권2호
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• pp.119-126
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• 2007

1, 1-dichloroethylene (DCE) is well known hepatotoxicant as a model acute hepatotoxicity and selectively injure the bile canalicular membrane of centrilobular hepatocytes. In this study, we investigated hepatic gene expression and histopathological changes in response to DCE treatment. DCE was administered once daily at 20 mg/kg up to 14 days via intraperitoneal injection. Five mice were used in each test group and were sacrificed at 1, 7, and 14 days. Serum biochemical and histopathological analysis were performed for evaluation of hepatotoxicity level. Direct bilirubin and total bilirubin activities were slightly elevated in treated group at 7 days. DCE treatment for 7 days resulted in centrilobular hepatocyte hypertrophy and hepatocyte vacuolation, and mild hepatocyte vacuolation and high hepatocyte basophilia were observed in 14 days treated group. One hundred twenty three up-regulated genes and 445 down-regulated genes with over 2-fold changes between treated and control group at each time point were used for pathway analysis. These data may contribute in understanding the molecular mechanism DCE-induced hepatotoxicity.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 추계학술대회 및 정기총회
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• pp.43-43
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• 2014

The rice blast disease caused by of Magnaporthe oryzae is one of the most destructive diseases of rice. By the microarray analysis, we profiled expression changes of genes during conidiation and found out many putative genes that are up-regulated. Among those, we first selected MGG_06399 encoding a dual-specificity tyrosine-regulated protein kinase (DYRK), homologous to YAK1 in yeast. To investigate functional roles of MoYAK1, We made ${\Delta}Moyak1$ mutants by homology dependent gene replacement. The deletion mutant showed a remarkable reduction in conidiation and produced abnormally shaped conidia smaller than those of wild type. The conidia form ${\Delta}Moyak1$ were able to develop a germ tube, but failed to form apppressoria on a hydrophobic coverslip. The ${\Delta}Moyak1$ formed appressria on a hydrophobic cover slip when exogenous cAMP was induced, but the appressoria shape was abnormal. The ${\Delta}Moyak1$ also formed appressoria abberent in shape on onion epidermis and rice sheaths and failed to penetrate the surface of the plants. These data indicate that MoYAK1 is associated with cAMP/PKA pathway and important for conidiation, appressorial formation and pathogenic development in Magnaporthe oryzae. Detailed characterization of MoYAK1 will be presented.