• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8247-8252
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• 2016

Background: The ubiquitin-proteasome system (UPS) degrades a variety of proteins which attach to specific signals. The ubiquitination pathway facilitates degradation of damaged proteins and regulates growth and stress responses. This pathway is altered in various cancers, including acute lymphoblastic leukemia, head and neck squamous cell carcinoma and breast cancer. Recently it has been reported that expression of newly characterized human genes, UBE2Q1 and UBE2Q2, putative members of ubiquitin-conjugating enzyme family (E2), has been also changed in colorectal cancer. Epigenetics is one of the fastest-growing areas of science and nowadays has become a central issue in biological studies of diseases. According to the lack of information about the role of epigenetic changes on gene expression profiling of UBE2Q1 and UBE2Q2, and the presence of CpG islands in the promoter of these two human genes, we decided to evaluate the promoter methylation status of these genes as a first step. Materials and Methods: The promoter methylation status of UBE2Q1 and UBE2Q2 was studied by methylation-specific PCR (MSP) in tumor samples of 60 colorectal cancer patients compared to adjacent normal tissues and 20 non-malignant controls. The frequency of the methylation for each gene was analyzed by chi-square method. Results: MSP results revealed that UBE2Q2 gene promoter were more unmethylated, while a higher level of methylated allele was observed for UBE2Q1 in tumor tissues compared to the adjacent normal tissues and the non malignant controls. Conclusions: UBE2Q1 and UBE2Q2 genes show different methylation profiles in CRC cases.

• Korean Journal of Poultry Science
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• v.28 no.2
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• pp.143-153
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• 2001

Using bioinformatic tools for searching the massive genome databases, it is possible to Identify new genes in few minutes for initial discoveries based on evolutionary conservation, domain homology, and tissue expression patterns, followed by further verification and characterization using the bench-top works. The development of high-density two-dimensional arrays has allowed the analysis of the expression of thousands of genes simultaneously in the humans, mice, rats, yeast, and bacteria to elucidate the genes and pathways involved in physiological processes. In addition, rapid and automated protein identification is being achieved by searching protein and nucleotide sequence databases directly with data generated from mass spectrometry. Recently, analysis at the bio-chemical level such as biochemical screening and metabolic profiling (Biochemical genomics) has been introduced as an additional approach for categorical assignment of gene function. To make advantage of recent achievements in computational approaches for facilitated gene discoveries in the avian model, chicken expression sequence tags (ESTs) have been reported and deposited in the international databases. By searching EST databases, a chicken heparanase gene was identified and functionally confirmed by subsequent experiments. Using combination of sub-tractive hybridization assay and Genbank database searches, a chicken heme -binding protein family (cSOUL/HBP) was isolated in the retina and pineal gland of domestic chicken and verified by Northern blot analysis. Microarrays have identified several host genes whose expression levels are elevated following infection of chicken embryo fibroblasts (CEF) with Marek's disease virus (MDV). The ongoing process of chicken genome projects and new discoveries and breakthroughs in genomics and proteomics will no doubt reveal new and exciting information and advances in the avian research.

• The Korean Journal of Physiology and Pharmacology
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• v.10 no.5
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• pp.263-271
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• 2006

Since astrocytes were shown to play a central role in maintaining neuronal viability both under normal conditions and during stress such as ischemia, studies of the astrocytic response to stress are essential to understand many types of brain pathology. The micro array system permitted screening of large numbers of genes in biological or pathological processes. Therefore, the gene expression patterns in the in vitro model of astrocytes following exposure to oxygen-glucose deprivation (OGD) were evaluated by using the micro array analysis. Primary astrocytic cultures were prepared from postnatal Swiss Webster mice. The cells were exposed to OGD for 4 hrs at $37^{\circ}C$ prior to cell harvesting. From the cultured cells, we isolated mRNA, synthesized cDNA, converted to biotinylated cRNA and then reacted with GeneChips. The data were normalized and analyzed using dChip and GenMAPP tools. After 4 hrs exposure to OGD, 4 genes were increased more than 2 folds and 51 genes were decreased more than 2 folds compared with the control condition. The data suggest that the OGD has general suppressive effect on the gene expression with the exception of some genes which are related with ischemic cell death directly or indirectly. These genes are mainly involved in apoptotic and protein translation pathways and gap junction component. These results suggest that microarray analysis of gene expression may be useful for screening novel molecular mediators of astrocyte response to ischemic injury and making profound understanding of the cellular mechanisms as a whole. Such a screening technique should provide insights into the molecular basis of brain disorders and help to identify potential targets for therapy.

• Molecules and Cells
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• v.24 no.3
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• pp.409-415
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• 2007

The retinoblastoma (Rb) gene is one of the most important genes in cell cycle regulation and tumorigenesis. Homozygosity for a germ-line Rb mutation results in embryonic lethality and evokes developmental defects associated with inappropriate S-phase entry and high levels of apoptosis. Although Rb has been extensively studied, more target genes need to be identified and characterized to unravel the precise mechanism of Rb function. In order to identify Rb-regulated genes, we analyzed the gene expression profile of Rb-deficient mouse embryo fibroblasts (MEFs), and identified an unknown gene, RbEST47, that is transcriptionally upregulated in Rb-deficient MEFs. This gene is conserved from fruitfly to human. It is expressed in brain, lung, kidney, and testis, and is located on mouse chromosome 2. This region is syntenic to human chromosome 9q34.3, which frequently exhibits loss of heterozygosity in neoplastic diseases. RbEST47 was considerably down-regulated in immortalized cells, and showed cell cycle-dependent expression, suggesting important roles in S and/or G2.

• Journal of Microbiology and Biotechnology
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• v.19 no.4
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• pp.403-408
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• 2009

A number of bifidobacterial species of human origin were screened for the presence of cryptic plasmids. One strain, Bifidobacterium longum FI10564, harbored plasmids of approximately 2.2 kb, 3.6 kb, and 4.9 kb in size. The smallest plasmid, pFI2576(2,197 bp), was studied in detail and its complete nucleotide sequence was determined. Computer-assisted analysis of this novel plasmid(G+C content 62%) identified 9 putative open reading frames(orfs), 3 of which were shown to be probable genes. These putative genes are arranged in an operon-like structure, in which the overlapping orfs 1 and 2 encode putative Rep proteins and are highly homologous to the rep genes of the B. longum plasmid pMBI(1,847 bp). The mechanism of replication of pFI2576 was investigated using Southern blot analysis of whole cell lysates, with and without S1 nuclease treatment, and atomic force microscopy(AFM). The results indicate that pFI2576 is likely to use the theta mode of replication.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.29-29
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• 2003

Incompatible plant-pathogen interactions result in the rapid cell death response known as hypersensitive response (HR) and activation of host defense-related genes. To understand the molecular and cellular mechanism controlling defense response better, several approaches including isolation and characterization of novel genes, promoter analysis of those genes, protein-protein interaction analysis and reverse genetic approach etc. By using the yeast two-hybrid system a clone named Tsipl, Tsil -interacting protein 1, was isolated whose translation product apparently interacted with Tsil, an EREBP/AP2 type DNA binding protein. RNA gel blot analysis showed that the expression of Tsipl was increased by treatment with NaCl, ethylene, salicylic acid, or gibberellic acid. Transient expression analysis using a Tsipl::smGFP fusion gene in Arabidopsis protoplasts indicated that the Tsipl protein was targeted to the outer surface of chloroplasts. The targeted Tsipl::smGFP proteins were diffused to the cytoplasm of protoplasts in the presence of salicylic acid (SA) The PEG-mediated co-transfection analysis showed that Tsipl could interact with Tsil in the nucleus. These results suggest that Tsipl-Tsil interaction might serve to regulate defense-related gene expression. Basically the useful promoters are valuable tools for effective control of gene expression related to various developmental and environmental condition.(중략)

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.164-169
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• 2003

In this paper, we propose the integrated Bayesian network framework to reconstruct genetic regulatory networks from genome expression data. The proposed model overcomes the dimensionality problem of multivariate analysis by building coherent sub-networks from confined gene clusters and combining these networks via intermediary points. Gene Shaving algorithm is used to cluster genes that share a common function or co-regulation. Retrieved clusters incorporate prior biological knowledge such as Gene Ontology, pathway, and protein protein interaction information for extracting other related genes. With these extended gene list, system builds genetic sub-networks using Bayesian network with MDL score and Sparse Candidate algorithm. Identifying functional modules of genes is done by not only microarray data itself but also well-proved biological knowledge. This integrated approach can improve there liability of a network in that false relations due to the lack of data can be reduced. Another advantage is the decreased computational complexity by constrained gene sets. To evaluate the proposed system, S. Cerevisiae cell cycle data [1] is applied. The result analysis presents new hypotheses about novel genetic interactions as well as typical relationships known by previous researches [2].

• International Journal of Industrial Entomology and Biomaterials
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• v.17 no.1
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• pp.121-124
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• 2008

The caspase family proteins play an important role in programmed cell death (apoptosis). To date, the expression profiles of the caspase family genes in Bombyx mori (Bm) are poorly known. In this study, we examined the expression profiles of two novel Bm caspase family genes (ice-2 and ice-5), the potential change of the mitochondrial membrane and the morphology in Bm cells after stimulation of ultraviolet (UV) irradiation. The results showed the potential change of the mitochondrial membrane occurred at 5 hours after UV irradiation treatment. Analysis of fluorescent quantitative RT-PCR demonstrated that both the ice-2 and ice-5 might be involved in UV induced apoptosis in Bm cells. Notably, after UV irradiating, expression pattern of ice-2 and ice-5 were remarkably different. The ice-2 gene was highly expressed at two time points, 0.5 and 5 hours after UV stimulating, while the expression level of ice-5 only peaked at 5 hours after UV stimulating. It indicated that apoptosis induced by UV irradiation was involved in the mitochondrial pathway and the two isoforms of Bm ice may act but play different role during the apoptosis of Bm cells.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1169-1176
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• 2007

Genes encoding proteins responsible for limonene catabolism were cloned from a limonene-degrading microorganism, Enterobacter cowanii 6L, which was isolated from citron (Citrus junos) peel. The 8.6, 4.7, and 7.7 kb fragments (CD3, CD4, and CD6) of E. cowanii 6L chromosomal DNA that confer to E. coli the ability to grow on limonene have been cloned and their corresponding DNA sequences were determined. Nine open reading frames (ORFs) were identified, and the four ORFs (921 bp of CD3-2; 1,515 bp of CD4-1; 1,776 bp of CD6-1; and 1,356 bp of CD6-2) that encode limonene hydroxylase were confirmed by independently expressing these genes in E. coli. FAD and NADH were found to stimulate the hydroxylation reaction if added to cell extracts from E. coli recombinants, and multiple compounds (linalool, dihydrolinalool, perillyl alcohol, (${\alpha}-terpineol$, and ${\gamma}-terpineol$) were the principal products observed. Our results suggest that the isolate E. cowanii 6L has a broad metabolic capability including utilization of limonene. This broad metabolic ability was confirmed by identifying four novel limonene hydroxylase functional ORFs in E. cowanii 6L.

• BMB Reports
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• v.46 no.1
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• pp.41-46
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• 2013

Identifying genes indispensable for an organism's life and their characteristics is one of the central questions in current biological research, and hence it would be helpful to develop computational approaches towards the prediction of essential genes. The performance of a predictor is usually measured by the area under the receiver operating characteristic curve (AUC). We propose a novel method by implementing genetic algorithms to maximize the partial AUC that is restricted to a specific interval of lower false positive rate (FPR), the region relevant to follow-up experimental validation. Our predictor uses various features based on sequence information, protein-protein interaction network topology, and gene expression profiles. A feature selection wrapper was developed to alleviate the over-fitting problem and to weigh each feature's relevance to prediction. We evaluated our method using the proteome of budding yeast. Our implementation of genetic algorithms maximizing the partial AUC below 0.05 or 0.10 of FPR outperformed other popular classification methods.