• Genes and Genomics
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• v.40 no.11
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• pp.1127-1136
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• 2018

The Greater Sudbury Region has been known as one of the most ecologically disturbed areas in Canada for the past century. Plant adaptation to environmental stressors often results in modifications in gene expression at the transcriptional level. The main objective of the present study was to compare the expression of genes associated with nickel resistance in Acer rubrum and Populus tremuloides growing in areas contaminated and uncontaminated with metals. Primers targeting Nramps4, Nas 3, At2G, MRP4 and alpha-tubulin genes were used to amplify cDNA of both species. The expression of the At2G gene, was $2{\times}$ and $9{\times}$ higher in P. tremuloides than in A. rubrum for St. Charles (uncontaminated site) and Kelly Lake (metal contaminated site), respectively. There was a much smaller difference between the two species for the Nramps 4 gene as its expression was $2.5{\times}$ and $3{\times}$ higher in P. tremuloides compared to A. rubrum from St. Charles and Kelly Lake, respectively. The same trend was observed for the MRP4 gene whose expression was $2{\times}$ and $14{\times}$ higher in P. tremuloides than in A. rubrum from St. Charles and Kelly Lake, respectively. For the Nas 3 gene, the expression was similar in both sites. This gene was upregulated $11{\times}$ and $10{\times}$ in P. tremuloides compared to A. rubrum in samples from St. Charles and Kelly Lake, respectively. In general, no significant difference was observed between the metal contaminated and uncontaminated sites for gene expression. In depth analysis revealed that AT2G and MRP4 genes were significantly down regulated in A. rubrum from the metal contaminated sites compared to those from uncontaminated areas, but environmental factors driving this differential gene expression couldn't be established.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.29-34
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• 2005

DNA microarray becomes a major tool for the investigation of global gene expression in all aspects of cancer and biomedical research. DNA microarray experiment generates enormous amounts of data and they are meaningful only in the context of a detailed description of microarrays, biomaterials, and conditions under which they were generated. MicroArray Gene Expression Data (MGED) society has established microarray standard for structured management of these diverse and large amount data. MGED MAGE-OM (MicroArray Gene Expression Object Model) is an object oriented data model, which attempts to define standard objects for gene expression. To assess the relevance of DNA microarray analysis of cancer research it is required to combine clinical and genomics data. MAGE-OM, however, does not have an appropriate structure to describe clinical information of cancer. For systematic integration of gene expression and clinical data, we create a new model, Cancer Genomics Object Model.

• BMB Reports
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• v.51 no.5
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• pp.211-218
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• 2018

Chromatin is an intelligent building block that can express either external or internal needs through structural changes. To date, three methods to change chromatin structure and regulate gene expression have been well-documented: histone modification, histone exchange, and ATP-dependent chromatin remodeling. Recently, a growing body of literature has suggested that histone tail cleavage is related to various cellular processes including stem cell differentiation, osteoclast differentiation, granulocyte differentiation, mammary gland differentiation, viral infection, aging, and yeast sporulation. Although the underlying mechanisms suggesting how histone cleavage affects gene expression in view of chromatin structure are only beginning to be understood, it is clear that this process is a novel transcriptional epigenetic mechanism involving chromatin dynamics. In this review, we describe the functional properties of the known histone tail cleavage with its proteolytic enzymes, discuss how histone cleavage impacts gene expression, and present future directions for this area of study.

• Genomics & Informatics
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• v.17 no.3
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• pp.30.1-30.4
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• 2019

Neuroblastoma is a major cause of cancer death in early childhood, and its timely and correct diagnosis is critical. Gene expression datasets have recently been considered as a powerful tool for cancer diagnosis and subtype classification. However, no attempts have yet been made to apply deep learning using gene expression to neuroblastoma classification, although deep learning has been applied to cancer diagnosis using image data. Taking the International Neuroblastoma Staging System stages as multiple classes, we designed a deep neural network using the gene expression patterns and stages of neuroblastoma patients. Despite a small patient population (n = 280), stage 1 and 4 patients were well distinguished. If it is possible to replicate this approach in a larger population, deep learning could play an important role in neuroblastoma staging.

• Environmental Mutagens and Carcinogens
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• v.22 no.4
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• pp.274-278
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• 2002

Phthalates, suspected endocrine disruptor, are plasticizer and solvent used in industry, and some phthalates are known as potential carcinogen. Most common human exposure to this compounds may occur with contaminated food. It may migrate into food from plastic wrap or may enter food from general environmental contamination, and it has become widespread environmental pollutants, thus leading to a variety of phthalates that possibly threaten the public health. Dibutyl phthalate (DBP) may playa part of cell proliferator, which mediates changes in gene expression and the metabolism of xenobiotics. An understanding of the role of DBP in modulating gene regulation should provide insight regarding mechanisms of DBP induced xenoestrogenic impact. To elucidate the type of genes that are associated with estrogenic activity induced by DBP at the dose (10$^{-8}$ M) appeared proliferating effects, the pattern of gene expression in MCF7 cells was compared between 17$\beta$-estradiol and DBP exposure in the cDNA microarray. From the results, it showed some differences of gene expression patterns between MCF7 cells treated with 17$\beta$-estradiol and DBP, and also DBP shows estrogenic potential with changes in estrogen-related gene expression levels.

• Proceedings of the Botanical Society of Korea Conference
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• 1999.07a
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• pp.51-56
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• 1999

Plastids, which are organelles unique to plant cells, bear their own genome that is organized into DNA-protein complexes (nucleoids). Regulation of gene expression in the plastid has been extensively investigated because this organelle plays an important role in photosynthesis. Few attempts, however, have been made to characterize the regulation of plastid gene expression at the chromosomal structure, using plastid nucleoids. In this report, we summarize the recent progress in the characterization of DNA-binding proteins in plastids, with special emphasis on CND41, a DNA binding protein, which we recently identified in the choloroplast nucleoids from photomixotrophically cultured tobacco cells. CND41 is a protein of 502 amino acids which consisted of a transit peptide of 120 amino acids and a mature protein of 382 amino acids. The N-terminal of the 'mature' protein has lysine-rich region which is essential for DNA-binding. CNA41 also showed significant identities to some aspartyl proteases. Protease activity of purified CND41 has been recently confirmed and characterized. On the other hand, characterization of accumulation of CND41 both in wild type and transgenic tobacco with reduced amount of CND41 suggests that CND41 is a negative regulator in chloroplast gene expression. Further investigation indicated that gene expression of CND41 is cell-specifically and developmentally regulated as well as sugar-induced expression. The reduction of CND41 expression in transgenic tobacco also brought the stunted plant growth due to the reduced cell length in stem. GA3 treatment on apical meristem reversed the dwarf phenotype in the transformants. Effects of CND41 expression on GA biosynthesis will be discussed.

• Korean Journal of Biological Psychiatry
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• v.8 no.2
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.8
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• pp.372-377
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• 2008

Multiclass cancer classification has been actively investigated based on gene expression profiles, where it determines the type of cancer by analyzing the large amount of gene expression data collected by the DNA microarray technology. Since gene expression data include many genes not related to a target cancer, it is required to select informative genes in order to obtain highly accurate classification. Conventional rank-based gene selection methods often use ideal marker genes basically devised for binary classification, so it is difficult to directly apply them to multiclass classification. In this paper, we propose a novel method for multiclass gene selection, which does not use ideal marker genes but directly analyzes the distribution of gene expression. It measures the class-discriminability by discretizing gene expression levels into several regions and analyzing the frequency of training samples for each region, and then classifies samples by using the naive Bayes classifier. We have demonstrated the usefulness of the proposed method for various representative benchmark datasets of multiclass cancer classification.

• Journal of Periodontal and Implant Science
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• v.30 no.2
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• pp.375-390
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• 2000

The purpose of this study is to evaluate the expression ofIGF-I, considered as the mediator of action of estrogen, and IGF-IA and IGF-IB, alternative slicing form of IGF-I, using $17{\beta}-estradiol$ in MC3T3-E1 cells. We observed the effect on type I collagen and osteopontin gene expression and DNA synthetic activity of MC3T3-E1 cells, added by estrogen, IGF-I and combination and the interactionon proliferation and differentiation of MC3T3-E1 cells. The results were as follows :RT-PCR experiment for observing timedependantIGF-I gene expression patternshowed IGF-IA and IB gene expression in both of control and test group. In these IGF-IA gene expression was appeared predominantly. In control, IGF-I geneexpression level was maintained until 24hr and then decreased gradually. In testgroup, IGF-I gene expression level increased as time goes by. Experiment measuring DNA synthetic activity, as it is added by $17{\beta}-estradiol$, IGF-I and combination, showed that first day , there was the tendency of more increase of synthetic activity in all test group than control but no statical significance(P>0.05), and third day, there was more increase of DNA synthetic activity in $17{\beta}-estradiol$ group and combination group and it was statically significant. (P<0.005) Experiment for observing type I collagen gene expression pattern showed more increase of expression in $17{\beta}-estradiol$ group than control and no significant difference in IGF-I group and combination group. Experiment for observing osteopontin gene expression pattern showed no significant difference in control and test group. In conclusion, $17{\beta}-estradiol$ in MC3T3- E1 cells increased IGF-I gene and DNA synthetic activity simultaneously, therefore it appeared that IGF-I is related to the action of estrogen. Combination treatment of IGF-I and $17{\beta}-estradiol$ has effect on cell proliferation but this effect is lower than IGF-I or $17{\beta}-estradiol$ alone. However, combination treatment has not great effect on type I collagen or osteopontin gene expression thus little effect of cell differentiation.

• Genomics & Informatics
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• v.5 no.1
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• pp.6-9
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• 2007

An RNase P ribozyme library has been developed as a tool for functional genomics studies. Each clone of this library contains a random 18-mer and the sequence of M1 RNA, the catalytic subunit of RNase P. Repression of target gene expression is thus achieved by the complementary binding of mRNA to the random guide sequence and the successive target cleavage via M1 RNA. Cellular expression of the ribozyme expression was confirmed, and EGFP mRNA was used as a model to demonstrate that the RNase P ribozyme expression system can inhibit the target gene expression. The constructed RNase P ribozyme library has a complexity of $1.4\times10^7$. This novel library system should become a useful in functional genomics, to identify novel gene functions in mammalian cells.