• 한방비만학회지
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• 제15권2호
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• pp.111-122
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• 2015

Objectives: Schizandrae fructus (Schizandra chinensis) is one of very common herbs, it is known as natural antioxidants, anti-inflammatory agent. Also some reports show that its extract works to regulate of dyslipidemia. This study was designed to investigate the effects of Schizandrae fructus chloroform fraction (SFCF) on serum lipid levels in dyslipidemic mice. Methods: The levels of total cholesterol, high density lipoprotein-cholesterol, triglyceride, aspartate aminotransferase (AST), alanine aminotransferase (ALT), fasting blood glucose in serum were measured. Histopathological and gene expression changes in liver tissue were also observed. Results: Oral administration of SFCF lowered levels of total cholesterol and triglyceride, which were elevated by high-fat diet. But SFCF did not affect on weight changes and serum AST, ALT levels in dyslipidemic mice. After carrying out gene ontological analysis, large numbers of genes in high-fat diet group were up-(347) or down-regulated (235). In SFCF treated mice, some changed expression of the genes was restored to normal levels, with a recovery rate of 17%. And it seems that fatty acid biosynthesis pathway was one of important key pathways to recovery. Conclusions: SFCF has beneficial effect on dyslipidemia, and could be used to prevent and treat cardiovascular disease.

• International Journal of Industrial Entomology and Biomaterials
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• 제27권2호
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• pp.271-276
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• 2013

The Asian honeybee, Apis cerana, is a native honeybee species in Korea which is important in agriculture for pollination and honey production. For better understanding of the physiology of A. cerana, high-throughput Illumina transcriptome sequencing was performed to analyze the gene expression profiles of queen, worker, and larva. A total of 219,799,682 clean reads corresponding to 22.2 Gb of nucleotide sequences was obtained from the whole body total RNA samples. The Apis mellifera reference mRNA sequence database was used to measure the gene expression level with Bowtie2 and eXpress software, and the Illumina short reads were then mapped to 11,459 out of 11,736 A. mellifera reference genes. Total of 9,221 genes with FPKM value greater than 5 of each sample group were subjected to eggNOG with BLASTX for gene ontology analysis. The differential gene expression between queen and worker, and worker and larva were analyzed to screen the overexpressed genes in each sample group. In the queen and worker sample group, total of 1,766 genes were differentially expressed with 887 and 879 genes overexpressed over two folds in queen and worker, respectively. In the worker and larva sample group, total of 1,410 genes were differentially expressed with 1,009 and 401 genes overexpressed over two folds in worker and larva, respectively.

• 대한본초학회지
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• 제39권3호
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• pp.37-47
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• 2024

Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

• 생명과학회지
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• 제23권11호
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• pp.1325-1335
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• 2013

특수 목적견(구조견, 군견, 안내견 및 탐지견)은 집중력, 소유욕, 대담성 등을 기반으로 한 훈련시험을 통해 선별된다. 최근 특수견으로서의 특수한 능력 및 품성에 대해 유전적인 정보가 중요한 인자로 다뤄지고 있다. 본 연구에서는 특수견으로서의 개의 특수한 능력 및 품성과 관련된 유전자들의 분자적인 특징을 고찰하고자 하였다. 이전 연구에서 보고된 24개의 유전자(AR, BDNF, DAT, DBH, DGCR2, DRD4, MAOA, MAOB, SLC6A4, TH, TPH2, IFT88, KCNA3, TBR2, TRKB, ACE, GNB1, MSTN, PLCL1, SLC25A22, WFIKKN2, APOE, GRIN2B, PIK3CG)를 선택하여 품성, 후각, 운동 및 학습능력 관련 유전자, 네 가지 카테고리로 분류하였다. 본 연구에서는 생물학적인 기법을 이용하여 이 유전자들의 염색체상의 위치, 유전자들 간의 네트워크를 통한 상호관계를 조사하였으며, 어떤 생물학적 기능과 관련이 있는지 Gene Ontology 분석과 데이터베이스를 기반으로 in silico 발현 양상을 살펴보았다. 또한 이전 연구를 통하여 품성 관련 유전자들의 다양한 유전적 다형성에 대한 보고를 조사하였다. 본 연구는 특수 견으로서 주요하게 고려되는 개의 고유한 능력 및 품성 관련된 유전자에 대해 분자적 특징을 제시하고 있다. 이 후보 유전자들은 개의 특수한 표현형과의 관계를 밝힐 수 있는 연구의 기초자료로서 이용될 수 있을 뿐만 아니라 핵심적인 유전인자로 응용되어 신속하고 정확한 특수견 선발에 기여할 수 있을 것으로 전망된다.

• Journal of Animal Science and Technology
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• 제58권4호
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• pp.17.1-17.7
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• 2016

Background: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance. Results: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type ($p{\leq}0.05$). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized. Conclusions: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

• Genomics & Informatics
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• 제6권3호
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• pp.153-156
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• 2008

Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.407-411
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• 2005

KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

• Asian-Australasian Journal of Animal Sciences
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• 제30권4호
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

• 생명과학회지
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• 제22권11호
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• pp.1552-1557
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• 2012

Pipernonaline은 후추나무과에 속하는 필발(Piper longum Linn.)의 유도체로서 전립선 암세포에 대한 항암활성이 보고되고 있다. 하지만 실제 암세포 내에서 생물학적 정보를 가진 수 많은 유전자들에 대한 발현이 어떻게 이루어지고 있는지 알려진 바가 없다. 본 연구에 사용된 microarray 분석은 동시에 수 만개 이상의 유전자 발현양상을 한번에 관찰할 수 있는 기술로서 특정 질병의 유전학적 특성과 기전 연구를 더 광범위하게 연구 할 수 있는 기술이다. 본 연구에서는 전립선 암세포인 PC-3 세포에 pipernonaline을 처리하여 cDNA microarray를 실시하였다. 이후, DAVID database를 이용하여 gene ontology의 Biological Process를 분석하여 세포사멸과 세포주기, 세포성장 및 증식에 관련된 유전자들을 우선적으로 분석하였다. 그 결과, 세포주기관련 256개, 세포사멸관련 197개, 세포성장 및 증식관련에 154개의 유전자가 확인 되었다. 이러한 결과는 pipernonaline은 전립선 암세포 내에 존재하는 생물학적 신호전달체계에 관련된 유전자 발현을 조절함으로써 항암활성을 나타내 것을 알 수 있었고, 이후 이러한 microarray의 추가적인 분석은 암세포 내 새로운 유전자의 탐색 및 메커니즘을 규명하는데 유용하게 사용할 수 있을 것으로 사료된다.

• 한국지능시스템학회논문지
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• 제25권6호
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• pp.529-535
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• 2015

지금까지 생체 네트워크 분석 연구는 정적(static)인 개념으로만 다루어졌다. 그러나 실제 생명현상이 발생하는 세포 내에서는 세포의 상태 및 외부 환경에 따라 일부 단백질과 그 상호작용만이 선택적으로 활성화된다. 따라서 생체 네트워크의 구조가 시간의 흐름에 따라 변화하는 동적(dynamic)인 개념이 적용되어야 하며, 이런 개념은 질병의 진행 추이를 분석하는데 효율적이다. 본 논문에서는 동적인 네트워크 방법을 알츠하이머 질병에 적용하여 질병이 진행되는 단계에 따라 변화하는 단백질 상호작용 네트워크의 구조적, 기능적 특징에 대하여 분석하고자 한다. 우선, 유전자 발현데이터를 기반으로 각 질병의 진행 상태에 따른 부분 네트워크(정상, 초기, 중기, 말기)를 구축하였다. 이를 기반으로, 네트워크의 구조적 특성 분석을 수행하였다. 또한 기능적 특성 분석을 위해 유전자 군집(module)을 탐색하고, 군집별 유전자 기능(Gene Ontology) 분석을 수행했다. 그 결과, 네트워크의 특성들은 각 질병의 단계와 잘 대응되며, 동적 네트워크 분석법이 중요한 생물학적 이벤트를 설명하는데 이용될 수 있음을 보였다. 결론적으로 제안된 연구 방법을 통하여 그동안 알려지지 않았던 질병유발에 관련된 주요 네트워크 변화를 관측할 수 있고, 질병에 관여하는 복잡한 분자 수준의 발생 기작과 진행 과정을 이해하는데 중요한 정보를 획득할 수 있다.