• Journal of Microbiology and Biotechnology
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• 제25권12호
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• pp.2153-2159
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• 2015

Mycoplasma hyopneumoniae is known to cause porcine enzootic pneumonia (EP), an important disease in swine production. The objective of this study was to examine the effects of sonicated protein fractions of M. hyopneumoniae on inflammatory response and gene expression in the murine alveolar macrophage MH-S cell line. The effects of sonicated protein fractions and intact M. hyopneumoniae on the gene expression of cytokines and iNOS were assessed using RT-PCR. The Annealing Control Primer (ACP)-based PCR method was used to screen differentially expressed genes. Increased transcription of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, COX-2, and iNOS mRNA was observed after exposure to the supernatant (SPT), precipitant (PPT), and intact M. hyopneumoniae protein. A time-dependent analysis of the mRNA expression revealed an upregulation after 4 h for IL-6 and iNOS and after 12 h for IL-1β and TNF-α, for both SPT and PPT; the fold change in COX-2 expression was less. A dose- and time-dependent correlation was observed in nitrite (NO) production for both protein fractions; however, there was no significant difference between the effects of the two protein fractions. In a differential gene analysis, PCR revealed differential expression for nine gene bands after 3 h of stimulation — only one gene was downregulated, while the remaining eight were upregulated. The results of this study provide insights that help improve our understanding of the mechanisms underlying the pathogenesis of and macrophage defenses against M. hyopneumoniae assault, and suggest targets for future studies on therapeutic interventions for M. hyopneumoniae infections.

• 전자공학회논문지CI
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• 제46권6호
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• pp.44-55
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• 2009

최근 활발히 연구가 진행 중인 마이크로어레이로부터 얻어지는 유전자 발현 데이터를 이용한 질병 진단은, 데이터를 직접적으로 분석하기 힘들기 때문에 일반적으로 기계 학습 알고리즘을 사용하여 이루어져왔다. 그러나 유전자 발현 데이터를 분석함에 있어서 유전자들 간의 상호작용을 고려하는 분석이 필요하다는 최근의 연구 결과들은 기존 기계 학습 알고리즘들을 이용한 분석에 한계가 있음을 의미한다고 볼 수 있다. 본 논문에서는 특징들 사이의 고차원 상관관계를 고려 가능한 하이퍼네트워크 모델을 이용하여 유전자 발현 데이터의 분류를 수행하고 기존의 기계 학습 알고리즘들과 분류 성능을 비교한다. 또한 기존 하이퍼네트워크 모델의 단점을 개선 한 모델을 제안하고, 이를 병렬 프로세서 상에서 구현하여 처리 성능을 비교한다. 실험 결과 제안 된 모델은 기존의 기계 학습 방법들과의 비교에서도 경쟁력 있는 분류 성능을 보여주었고, 기존 하이퍼네트워크 모델 보다 안정적이고 향상된 분류 성능을 보여주었다. 또한 이를 병렬 프로세서 상에서 구현 할 경우 처리 성능을 극대화 할 수 있음을 보였다.

• Asian-Australasian Journal of Animal Sciences
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• 제25권8호
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• pp.1102-1116
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• 2012

During embryo implantation in pigs, the uterine endometrium undergoes dramatic morphological and functional changes accompanied with dynamic gene expression. Since the greatest amount of embryonic losses occur during this period, it is essential to understand the expression and function of genes in the uterine endometrium. Although many reports have studied gene expression in the uterine endometrium during the estrous cycle and pregnancy, the pattern of global gene expression in the uterine endometrium in response to the presence of a conceptus (embryo/fetus and associated extraembryonic membranes) has not been completely determined. To better understand the expression of pregnancy-specific genes in the endometrium during the implantation period, we analyzed global gene expression in the endometrium on day (D) 12 and D15 of pregnancy and the estrous cycle using a microarray technique in order to identify differentially expressed endometrial genes between D12 of pregnancy and D12 of the estrous cycle and between D15 of pregnancy and D15 of the estrous cycle. Results showed that the global pattern of gene expression varied with pregnancy status. Among 23,937 genes analyzed, 99 and 213 up-regulated genes and 92 and 231 down-regulated genes were identified as differentially expressed genes (DEGs) in the uterine endometrium on D12 and D15 of pregnancy compared to D12 and D15 of the estrous cycle, respectively. Functional annotation clustering analysis showed that those DEGs included genes involved in immunity, steroidogenesis, cell-to-cell interaction, and tissue remodeling. These findings suggest that the implantation process regulates differential endometrial gene expression to support the establishment of pregnancy in pigs. Further analysis of the genes identified in this study will provide insight into the cellular and molecular bases of the implantation process in pigs.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제34권5호
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• pp.525-531
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• 2008

CDH-13(T-cadherin), which is one of a kind among the 20 cadherins, can be found mainly in wall of aorta, neuron, spleen, blood vessel etc. It is also called H-cadherin. This structural difference can explain that CDH-13 is thought to play a key role in maintaining mutual relation between extra and intra-cellular environment rather than in cell adhesion. The main function of CDH-13 is to participate in blood vessel function. Additionally, it is known to regulate cell growth and cell contact inhibition. When cells are proliferating, cell surface perceives other cells so that substance such as CDH-13 can inhibit their growth or proliferation resulting in homeostasis without endless proliferation or invasion of connective tissue boundaries. However, tumor cell itself appears to be different from normal cells' growth, invasion or transmission. Therefore, it can be diagnosed that these characteristics are closely related to expression of CDH-13 in tumor cells. This study is to investigate expression of CDH-13 in SCC and its correlation with promoter methylation. 20 of tissue species for the study are excised and gathered from 20 patients who are diagnosed as SCC in department of OMS, dental hospital, dankook university. To find development of CDH-13 in each tissue samples, immunohistochemical staining, RT-PCR gene analysis and methylation specific PCR are processed. The results are as follows. 1.Immunohistochemical staining: In normal oral squamous epithelial tissue, strong expression of CDH-13 was found in cell plasma membrane of basal cell layer. On the other hand, in case of low-differentiated oral SCC, development of CDH-13 was hardly seen. 2.The development of CDH-13 gene: In 9 of samples, expression of CDH-13 gene could be seen and 2 of them showed low expression compared to the others. And rest of the 11 samples showed no expression of CDH-13 gene. 3.Methylation of CDH-13 gene: Among 9 samples which expressed CDH-13 gene, 7 of them showed unmethylation. In addition, among 11 samples without CDH-13 gene expression, 10 showed methylation. According to the results stated above, promoter methylation were found in 13 samples(65%) among 20 of oral SCC samples. In low-differentiated SCC, suppression of gene expression could be seen accompanying promoter methylation. These phenomenon of gene expression was proved by immunohistochemical investigation. Finally, for development of oral SCC, conclusions can be made that suppression of CDH-13 played a main role and suppression of gene expression was originated from promoter methylation. Considering this, it is expected that suppression of CDH-13 from promoter methylation to be utilized as a good diagnostic marker of oral SCC.

• Asian-Australasian Journal of Animal Sciences
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• 제30권3호
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• pp.328-337
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• 2017

Objective: An experiment was conducted to determine the relationship between the KAP11.1 and the regulation wool fineness. Methods: In previous work, we constructed a skin cDNA library and isolated a full-length cDNA clone termed KAP11.1. On this basis, we conducted a series of bioinformatics analysis. Tissue distribution of KAP11.1 mRNA was performed using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis. The expression of KAP11.1 mRNA in primary and secondary hair follicles was performed using real-time PCR (real-time polymerase chain reaction) analysis. The expression location of KAP11.1 mRNA in primary and secondary hair follicles was performed using in situ hybridization. Results: Bioinformatics analysis showed that KAP11.1 gene encodes a putative 158 amino acid protein that exhibited a high content of cysteine, serine, threonine, and valine and has a pubertal mammary gland) structural domain. Secondary structure prediction revealed a high proportion of random coils (76.73%). Semi-quantitative RT-PCR showed that KAP11.1 gene was expressed in heart, skin, and liver, but not expressed in spleen, lung and kidney. Real time PCR results showed that the expression of KAP11.1 has a higher expression in catagen than in anagen in the primary hair follicles. However, in the secondary hair follicles, KAP11.1 has a significantly higher expression in anagen than in catagen. Moreover, KAP11.1 gene has a strong expression in inner root sheath, hair matrix, and a lower expression in hair bulb. Conclusion: We conclude that KAP11.1 gene may play an important role in regulating the fiber diameter.

• Genomics & Informatics
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• 제9권4호
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• pp.143-151
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• 2011

In this study, we propose a novel, intuitive method of constructing an expression quantitative trait (eQT) network that is related to the metabolic syndrome using LOD scores and peak loci for selected eQTs, based on the concept of gene-gene interactions. We selected 49 eQTs that were related to insulin resistance. A variance component linkage analysis was performed to explore the expression loci of each of the eQTs. The linkage peak loci were investigated, and the "support zone" was defined within boundaries of an LOD score of 0.5 from the peak. If one gene was located within the "support zone" of the peak loci for the eQT of another gene, the relationship was considered as a potential "directed causal pathway" from the former to the latter gene. SNP markers under the linkage peaks or within the support zone were searched for in the database to identify the genes at the loci. Two groups of gene networks were formed separately around the genes IRS2 and UGCGL2. The findings indicated evidence of networks between genes that were related to the metabolic syndrome. The use of linkage analysis enabled the construction of directed causal networks. This methodology showed that characterizing and locating eQTs can provide an effective means of constructing a genetic network.

• International Journal of Industrial Entomology and Biomaterials
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• 제13권1호
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• pp.23-30
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• 2006

BmCu/Zn SOD was isolated from early embryo of Bombyx mori using microarray analysis. The BmCu/Zn SOD gene was observed during the early embryonic stage with the strongest signal found at the unfertilizaion, fertilization and blastoderm stages. The BmCu/Zn SOD gene encodes a protein of 154 amino acids with a calculated Mr of 15 kDa. The deduced amino acid sequence of BmCu/Zn SOD indicated that the residues that form on the Cu/Zn binding site are conserved and that the sequence is a 60% identity to that of M. domestica. In a phylogenetic tree, Bm SOD was also close to Drosophila SODs rather than other insect SODs. The BmCu/Zn SOD gene exists as a single copy in the genome. Transcripts of BmCu/Zn SOD cDNA were identified by northern blot analysis. The expression of the BmCu/Zn SOD gene was observed weakly in most of larvae, pre-pupae, pupae and adult tissues. Also, the BmCu/Zn SOD gene was observed in early embryonic stage. Although the roles of SODs remains to be further elucidated, the high expression of BmCu/Zn SOD gene at before 24 h post fertilization suggests that this gene is of general importance during early embryogenesis in the Bombyx mod.

• 한국발생생물학회지:발생과생식
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• 제18권4호
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• pp.293-300
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• 2014

Direct cell-cell communication through connexin (Cx) complexes is a way to achieve functional accordance of cells within a tissue or an organ. The initial segment (IS), a part of the epididymis, plays important roles in sperm maturation. Steroid hormones influence on expression of a number of genes in the IS of adult animals. However, developmental effect of sex hormones on the gene expression in the IS has not been examined. In this study, estradiol benzoate (EB, an estrogen agonist) or flutamide (Flu, an androgen antagonist) was exogenously administrated at 1 week of postnatal age, and expressional changes of Cx genes in the IS were determined at 4 months of age by a quantitative real-time PCR analysis. Treatment of EB at $0.015{\mu}g/kg$ body weight (BW) increased expression of Cx30.3, 31.1, and 43 genes. However, treatment of 1.5 mg EB/kg BW resulted in expressional decreases of Cx31, 32, and 45 genes and caused increases of Cx30.3 and 43 gene expression. Significant decreases of Cx31, 31.1, 32, 37, and 45 gene expression were detected with a treatment of $500{\mu}g\;Flu/kg$ BW, while expression of Cx43 gene was significantly increased with a treatment of $500{\mu}g\;Flu/kg$ BW. A treatment of $50{\mu}g\;Flu/kg$ BW led to significant increases of Cx30.3, 32, 37, 40, and 43 gene expression. These findings imply that exogenous exposure of steroidal hormones during the early developmental period would result in aberrant expression of Cx genes in the adult IS.

• 한국미생물·생명공학회지
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• 제35권3호
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• pp.184-190
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• 2007

대략 2 kb의 크기를 가진 Pichia pastoris phosphoglycerate kinase gene (PGK1)의 프로모터부분을 266bp의 작은 크기로 최소화하여 P. pastoris에 있어 episomal의 새로운 항시적 발현벡터를 제조하였다. P. pastoris의 새로운 항시적 발현벡터를 개발하기 위하여 기존의 Pichia발현벡터인 pGABZB의 GAP프로모터부분을 연속적으로 일정 부분이 절단된 PGK1프로모터에 beta-galactosidase유전자가 결합된 부분으로 치환하였다. LacZ유전자를 reporter유전자로 사용하였을 때에 PGK1프로모터의 발현세기는 다른 항시적 프로모터인 GAP프로모터 보다는 낮았지만 TEF1프로모터 보다는 높았다. 본 논문에서 PGK1 프로모터의 불필요한 부분을 제거함으로서 Pichia에서 외래발현을 위한 새로운 episomal발현벡터인 pPGKZ-E를 제조하였으며 이 것은 P. pastoris에 있어 발현세기를 선택할 수 있는 발현벡터선택의 폭을 넓게 하였다.

• BMB Reports
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• 제43권2호
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• pp.115-121
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• 2010

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.