• Asian-Australasian Journal of Animal Sciences
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• v.29 no.10
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• pp.1515-1521
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• 2016

Anethole and garlic have an immune modulatory effects on avian coccidiosis, and these effects are correlated with gene expression changes in intestinal epithelial lymphocytes (IELs). In this study, we integrated gene expression datasets from two independent experiments and investigated gene expression profile changes by anethole and garlic respectively, and identified gene expression signatures, which are common targets of these herbs as they might be used for the evaluation of the effect of plant herbs on immunity toward avian coccidiosis. We identified 4,382 and 371 genes, which were differentially expressed in IELs of chickens supplemented with garlic and anethole respectively. The gene ontology (GO) term of differentially expressed genes (DEGs) from garlic treatment resulted in the biological processes (BPs) related to proteolysis, e.g., "modification-dependent protein catabolic process", "proteolysis involved in cellular protein catabolic process", "cellular protein catabolic process", "protein catabolic process", and "ubiquitin-dependent protein catabolic process". In GO analysis, one BP term, "Proteolysis", was obtained. Among DEGs, 300 genes were differentially regulated in response to both garlic and anethole, and 234 and 59 genes were either up- or down-regulated in supplementation with both herbs. Pathway analysis resulted in enrichment of the pathways related to digestion such as "Starch and sucrose metabolism" and "Insulin signaling pathway". Taken together, the results obtained in the present study could contribute to the effective development of evaluation system of plant herbs based on molecular signatures related with their immunological functions in chicken IELs.

• Journal of the Korea Society of Computer and Information
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• v.20 no.3
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• pp.29-45
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• 2015

This paper proposes an implementation of SPARQL-DL, which is a query language for OWL ontologies, for query-answering over the OWL ontologies virtually generated from existing RDBs. The proposed SPARQL-DL processor internally translates input SPARQL-DL queries into SQL queries and then executes the translated queries. There are two advantages in the query processing method. First, another repository to store OWL ontologies generated from RDBs is not required. Second, a large ABox generated from an RDB instance is able to be served without using Tableau algorithm based reasoners which have a problem in large ABox reasoning. Our algorithm for query rewriting is designed to create one corresponding SQL query from one input SPARQL-DL query to minimize the overhead by establishing connections with RDBs.

• The Korean Journal of Physiology and Pharmacology
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• v.19 no.2
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• pp.141-149
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• 2015

"G protein-coupled receptor 40" (GPR40), a receptor for long-chain fatty acids, mediates the stimulation of glucose-induced insulin secretion. We examined the profiles of differential gene expression in GPR40-activated cells treated with linoleic acid, and finally predicted the integral pathways of the cellular mechanism of GPR40-mediated insulinotropic effects. After constructing a GPR40-overexpressing stable cell line (RIN-40) from the rat pancreatic ${\beta}$-cell line RIN-5f, we determined the gene expression profiles of RIN-5f and RIN-40. In total, 1004 genes, the expression of which was altered at least twofold, were selected in RIN-5f versus RIN-40. Moreover, the differential genetic profiles were investigated in RIN-40 cells treated with $30{\mu}M$ linoleic acid, which resulted in selection of 93 genes in RIN-40 versus RIN-40 treated with linoleic acid. Based on the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG, http://www.genome.jp/kegg/), sets of genes induced differentially by treatment with linoleic acid in RIN-40 cells were found to be related to mitogen-activated protein (MAP) kinase- and neuroactive ligand-receptor interaction pathways. A gene ontology (GO) study revealed that more than 30% of the genes were associated with signal transduction and cell proliferation. Thus, this study elucidated a gene expression pattern relevant to the signal pathways that are regulated by GPR40 activation during the acute period. Together, these findings increase our mechanistic understanding of endogenous molecules associated with GPR40 function, and provide information useful for identification of a target for the management of type 2 diabetes mellitus.

• Genomics & Informatics
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• v.10 no.2
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• pp.123-127
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• 2012

Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.

• The Journal of Internal Korean Medicine
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• v.30 no.3
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• pp.594-603
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• 2009

Objectives : ICH breaks down blood vessels within the brain parenchyma, which finally leads to neuronal loss, drugs to treat ICH have not yet been established. In this experiment, we measured the effect of Woowhangchongshim-won (WWCSW) on intracerebral hemorrhage (ICH) in rat using microarray technology. Methods : We measured the effect of WWCSW on ICH in rat using microarray technology. ICH was induced by injection of collagenase type IV, and total RNA was isolated. Image files of microarray were measured using a ScanArray scanner, and the criteria of the threshold for up- and down-regulation was 2 fold. Hierarchical clustering was implemented using CLUSTER and TREEVIEW program, and for Ontology analysis. GOSTAT program was applied in which p-value was calculated by Chi square or Fisher's exact test based on the total array element. Results : WWCSW-treatment restored the gene expression altered by ICH-induction in brain to the levels of 76.0% and 70.1% for up- and down-regulated genes, respectively. Conclusion : Co-regulated genes by ICH model of rat could be used as molecular targets for therapeutic effects of drug including WWCSW. That is, the presence of co-regulated genes may represent the importance of these genes in ICH in the brain and the change of expression level of these co-regulated genes would also indicate the functional change of brain tissue.

• Journal of Physiology & Pathology in Korean Medicine
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• v.24 no.5
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• pp.831-836
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• 2010

In addition to spice, black pepper (Piper nigrum Linne : PnL) has been used as herbal medicine because of its function in anti-oxidation, anti-inflammation, and anti-carcinogenesis. Recently, it has been reported that piperine, a component of PnL, inhibits adipocyte differentiation by repressing various adipogenic gene expressions. In this study, we determined whether piperine is a major constituent of PnL that confers the anti-adipogenic activity at whole genome level. Differentiation of 3T3-L1 pre-adipocytes was induced in presence of PnL extract or piperine. To compare genes that are regulated by PnL extract or piperine, we performed expression profiling using microarrays (Agilent Mouse 44k 4plex). RNA samples were labeled with Cy3 and Cy5, respectively. Labeled samples were hybridized to the microarrays. Results were filtered and cut off set p<0.05. Genes exhibiting significant differences in expression level were classified into Gene Ontology (GO)-based functional categories (http://www.geneontology.org) and KEGG (http://www.genome.jp/kegg/). Extract of PnL and its component piperine reduced lipid accumulation in 3T3-L1 cells during adipogenesis. Such anti-adipogenic activity appears to result from down-regulation of transcription factor genes involved in adipogenesis, and other genes involved in fatty acid synthesis, transport, triglyceride synthesis, and carbohydrate metabolism. These genome-wide studies lead to conclude that piperine, as a critical component of PnL, plays common role with PnL in anti-adipogenesis.

• The Journal of the Korea Contents Association
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• v.11 no.7
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• pp.9-20
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• 2011

In this paper, we attempt to realize the diversity of human actions in a virtual world in terms of the basic actions. We utilize the comprehensive knowledge structure of ontology to organize the human actions into an action hierarchy, each action being the root action of its associated hierarchy of specialized actions. Each basic action is implemented by composing the primitive motions and each basic action in turn by reusing those basic actions. Our approach to the development of these actions is focused more on their diversity and brevity than on their visual realism. Based on this design we develop a method to grasp virtual humans' characteristics and reflect those characteristics on their respective action patterns. We also present a mechanism for the agents to adapt their motions to diverse qualitative changes in environment. We apply these methods to such basic actions as walk, run and throw to demonstrate their viability.

• Proceedings of the Korean Society of Computer Information Conference
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• 2009.01a
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• pp.19-24
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• 2009

이 논문에서는 메타데이터 레지스트리 (MDR, Metadata Registry) 기반의 웹 온톨로지 생성모델을 제안한다. 메타데이터 레지스트리는 국제 표준(ISO/IEC 11179)으로서 데이터베이스간 상호운용성 향상을 위해 개발되었다. 그러나 데이터 표현과 상호운용성을 위한 컴퓨팅 환경의 변화는 메타데이터 레지스트리의 확장은 물론 메타데이터 레지스트리의 활용 방법의 변화를 요구한다. 이 논문에서의 웹 환경의 변화란 정적인 웹 환경에서 웹 2.0 혹은 시맨틱 웹 이라고 정의하는 차세대 웹 환경으로의 변화를 의미한다. 이러한 환경을 위해서 다양한 기술 개발과 적용 기법에 관한 연구가 필요하다. 특히 차세대 웹을 위해서는 지원에 대한 명확한 의미 정의 및 활용이 요구된다. 이는 웹 온톨로지 스키마를 구성하는 개념들에 대한 보다 일관성 있는 정의 및 사용이 필요하다. 이러한 문제가 해결되지 않을 경우, 또 다시 온톨로지를 구성하는 개념들 간 이질성 문제를 야기한다. 메타데이터 레지스트리는 다양한 표준화 된 개념들을 포함하며, 응용을 위한 데이터를 위한 의미 또한 이 개념들을 이용하여 정의한다. 따라서 이러한 표준 요소를 이용한 웹 온톨로지 스키마 정의 및 활용이 요구되며, 이 논문에서 이와 관련된 기본 개념, 요구 사항을 장의하고 전체적인 모델을 제안한다.

• The KIPS Transactions:PartB
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• v.11B no.4
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• pp.509-516
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• 2004

Semantic interpretation of image is incomplete without some mechanism for understanding semantic content that is not directly visible. For this reason, human assisted content-annotation through natural language is an attachment of textual description to image. However, keyword-based retrieval is in the level of syntactic pattern matching. In other words, dissimilarity computation among terms is usually done by using string matching not concept matching. In this paper, we propose a method for computerized semantic similarity calculation In WordNet space. We consider the edge, depth, link type and density as well as existence of common ancestors. Also, we have introduced method that applied similarity measurement on semantic image retrieval. To combine wi#h the low level features, we use the spatial color distribution model. When tested on a image set of Microsoft's 'Design Gallery Line', proposed method outperforms other approach.

• Biomolecules & Therapeutics
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• v.22 no.2
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• pp.143-148
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• 2014

Marfan syndrome (MFS) is a dominantly inherited connective tissue disorder caused by mutations in the gene encoding fibrillin-1 (FBN1) and is characterized by aortic dilatation and dissection, which is the primary cause of death in untreated MFS patients. However, disease progression-associated changes in gene expression in the aortic lesions of MFS patients remained unknown. Using a mouse model of MFS, FBN1 hypomorphic mouse (mgR/mgR), we characterized the aortic gene expression profiles during the progression of the MFS. Homozygous mgR mice exhibited MFS-like phenotypic features, such as fragmentation of elastic fibers throughout the vessel wall and were graded into mgR1-4 based on the pathological severity in aortic walls. Comparative gene expression profiling of WT and four mgR mice using microarrays revealed that the changes in the transcriptome were a direct reflection of the severity of aortic pathological features. Gene ontology analysis showed that genes related to oxidation/reduction, myofibril assembly, cytoskeleton organization, and cell adhesion were differentially expressed in the mgR mice. Further analysis of differentially expressed genes identified several candidate genes whose known roles were suggestive of their involvement in the progressive destruction of aorta during MFS. This study is the first genome-wide analysis of the aortic gene expression profiles associated with the progression of MFS. Our findings provide valuable information regarding the molecular pathogenesis during MFS progression and contribute to the development of new biomarkers as well as improved therapeutic strategies.