• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• Korean Journal of Agricultural Science
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• v.44 no.4
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• pp.477-486
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• 2017

This review provides an overview of dietary nucleotides as an alternative to in-feed antibiotics for weaning pigs. Dietary nucleotides are composed of DNA or RNA molecules and are normally contained in protein-rich feed ingredient, brewer's yeast, yeast extract, and milk. Weaning pigs are suffering from several stresses, such as environmental challenges (i.e. crowding, transportation, and feeding). Such stressors can damage the intestinal epithelium and cause an invasion by Escherichia coli, secondary inflammatory responses, and post weaning diarrhea. To overcome weaning disorder, people often use antibiotics which reduce symptoms and boost growth performance. However, since antibiotics were banned due to concerns of antibiotic resistant bacteria, researchers are studying alternative materials to antibiotics. Dietary nucleotides are one of the alternative materials for replacing antibiotics and can be used in abnormal conditions, such as weaning diarrhea, low digestibility, and disease condition. Nucleotides have substances that have important roles in cell division and cell growth, affecting growth performance, intestinal condition, and immunological effect at the weaning stage. However, nucleotides' composition is very different between sources and this aspect makes it difficult to utilize nucleotides at the weaning stage. Therefore, this review paper focuses on i) the characteristics and functions of dietary nucleotides and ii) the effect of dietary nucleotides on the growth performance and immune system of pigs.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.97-97
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• 2003

Embryonic stem (ES) cells, derived from preimplantation embryos, are able to differentiate into various types of cells consisting the whole body, or pluripotency. In addition to the plasticity, ES cells are expected to be different from terminally differentiated cells in very many ways, such as patterns of gene expressions, ability and response of the cells in confronting environmental stimulations, metabolism, and growth rate. As a model system to differentiate these two types of cells, human ES (hES, MB03) cells and terminally differentiated cells (HeLa), we examined the ability of these two types of cells in confronting a severe oxidative insult, that is $H_2 O_2$. Ratio of dying cells as determined by the relative amount of dye neutral red entrapped within the cells after the exposures. Cell death rates were not significantly different when either MB03 or HeLa were exposed up to 0.4 mM $H_2 O_2$. However, relative amount of dye entrapped within the cells sharply decreased down to 0.12% in HeLa cells when the cells were exposed to 0.8 mM $H_2 O_2$, while it was approximately 54% in MB03. Pretreatment of cells with BSO (GSH chelator) and measurement of GSH content results suggest that cellular GSH is the major defensive mechanism of hES cells. Induction of apoptosis in hES cell was confirmed by DNA laddering, induction of Bax, and chromatin condensation. In summary, hES cells 1) are extremely resistant to oxidative stress, 2) utilize GSH as a major defensive mechanism. and 3) experience apoptosis upon exposure to oxidative stress.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.275-281
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• 2013

Low temperature is one of the major environmental factors that affect productivity including reduced growth and budding of vines, and changes of metabolic processes in grape (Vitis spp.). To screen the specific expression of abiotic stress-related genes against cold treatment in 'Kyoho' and 'Campbell Early' grapevines, expression of various defense-related genes was investigated by RT-PCR and real-time PCR. Among the 67 genes analyzed by RT-PCR and real-time PCR, 17 and 16 types of cDNA were up-regulated, while 5 and 6 types were down-regulated in cold-treated 'Kyoho' and 'Campbell Early' grapevines, respectively. Genes encoding carotene (Cart3564 and Cart4472), chalcone isomerase (CHI), cytochrome P450 (CYP), flavonol synthase (FLS), endo-${\beta}$-glucanase precursor (Glu), glutathione peroxidase (GPX), glutathione-S-transferase (GST), leucine-rich repeats (LRR), manganese superoxide dismutase (Mn-SOD), phenylalanine ammonia lyase (PAL), polygalacturonase-inhibiting protein (PGIP), proline rich protein 2 (PRP2), small heat shock protein (sHSP), temperature induced lipocalin (TIL), and thaumatin-like protein (TLP) were up-regulated, while those encoding CBF like transcription factor (CBF1), chitinase-like protein (CLP), cold induced protein (CIP), glycerol-3-phosphate acyltransferase (GPAT), and mitogen-activated protein kinase (MAPK) were down-regulated by low temperature treatment in both in 'Kyoho' and 'Campbell Early'.

• The Journal of Internal Korean Medicine
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• v.23 no.2
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• pp.306-312
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• 2002

Systemic Lupus Erythematosus(SLE) is a autoimmune disease characterized by combined symtoms of malar rash, discoid rash, neuropsychiatric disorder, renal disorder, hematologic disorder, photosensitivity immunologic disorder, oral ulcer, anti-nuclear antibody, arthritis, pleuritis and pericarditis, etc. Multiple genetic or environmental causes are supposed to facilitate antiboby production to autoantigen such as ds-DNA, histone, phospholipid, red blood cell, platelet, etc. And defective complementary system fail to remove autoantigen-antibody complex, which deposit in multiple organs and result in inflammatory damages. SLE does not correctly correspond to any specific category of oriental medicine. But, accoring to previous reports, it can be controlled by herb medications used differently patients-to-patients. So we are to report this one SLE case being successfully controlled by classic corticosteroids with herb medications based on oriental diffrential diagnosis of symptoms and signs.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.4
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• pp.205-212
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• 2001

One of the important characteristics of biological systems os their ability to change im-portant properties in response to small environmental signals. The molecular mechanisms that biological molecules utilize to sense and respond provide interesting models for the development of "smart" polymeric biomaterials with biomimetic properties. An important example of this is the protein coat of viruses, which contains peptide units that facilitate the trafficking of the virus into the cell via endocytosis, then out of the endosome into the cytoplasm, and from there into the nucleus, We have designed a family of synthetic polymers whose compositions have been de-signed to mimic specific peptides on viral coats that facilitate endosomal escape. Our biomimetic polymers are responsive to the lowered pH whinin endosomes, leading to distruption of the en-dosomal membrane and release of important biomolecular druges such as DNA, RNA, peptides and proteins to the cytoplasm before they are trafficked to lysosomes and degraded by lysosomal en-zymes. In this article, we review our work on the design, synthesis and action of such smart, pH-sensitive polymers.

• Toxicological Research
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• v.22 no.2
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• pp.95-102
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• 2006

Exposure to soluble nickel compound produces toxic effects on immune system, but the mechanism of action remains to be elucidated. Differential gene expression was studied to understand the potential molecular mechanism responsible for acute toxicity induced by nickel acetate in spleen cells. We exposed mouse spleen cells to nickel acetate with a nontoxic dose ($40{\mu}M$) and then extracted total RNA at 6 h and 12 h after exposure. The RNA was hybridized onto 10K mouse oligonucleotide microarrays, and data were analyzed using GeneSpring 7.1. Nickel had a modest effects on expression of many genes, in the range of 1.3-3 fold. The expression profile showed time-dependent changes in expression levels of differentially expressed genes, including some important genes related to cell cycle, apoptosis and DNA repair. In hierarchical cluster analysis of duplicate experiments, 111 genes were screened out. Out of these, 44 genes showing time- dependent up-regulation (>1.5 fold) and 38 genes showing down-regulation (>1.5 fold) at all time points were chosen for further analysis. The change in the expression of three genes (GPX1, GADD45B and FAIM) after nickel treatment was validated using RT-PCR. As a rule, a number of genes appear to be coordinately regulated between cell survival and cell death from nickel toxicity. In conclusion, changes in the gene profile in the spleen after nickel treatment are complex and genes with diverse functions are modulated. These findings will be contributed to the understanding of the complicated biological effects of nickel.

• Toxicological Research
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• v.17
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• pp.109-115
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• 2001

Abrus agglutinin was purified from the kernels of Abrus precatorius by Sepharose 4B affinity column chromatography followed by Sephadex G-100 gel filtration column chromatography. About 1.25 g of abrus agglutinin was obtained from 1 kg of the kernels. The LD$_{50}$ of abrus agglutinin is 5 mg/kg of body weight, which is less toxic than that of abrin, 20$\mu\textrm{g}$/kg body weight. The amino acid sequence of abrus agglutinin was determined by protein sequencing techniques and deduced from the nucleotide sequence of a cDNA clone encoding full length of abrus agglutinin. There are 258 residues, 2 residues and 267 residues in the A-chain, the linker peptide and the B-chain of abrus agglutinin, respectively. Abrus agglutinin had high homology to abrin-a (77.8%). The 13 amino acid residues involved in catalytic function, which are highly conserved among abrin and ricin, were also conserved within abrus agglutinin. The protein synthesis inhibitory activity of abrus agglutinin ($IC_{50}$/ = 3.5 nM) was weaker than that of abrin-a (0.05 nM). By molecular modeling followed by site-directed mutagenesis showed that Pro199 of abrus agglutinin A-chain located in amphipathic helix H and corresponding to Asn200 of abrin A-chain, can induce bending of helix H. This bending would presumably affect the binding of abrus agglutinin A-chain to its target sequence GpApGpAp, in the tetraloop structure of 285 r-RNA subunit and this could be one of major factors contributing to the relatively weak protein synthesis inhibitory activity and toxicity of abrus agglutinin.n.

• Toxicological Research
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• v.23 no.2
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• pp.135-142
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• 2007

Formononetin is an isoflavonoid phytoestrogen found in certain foodstuffs such as soy and red clover. In this study, we examined the action of formononetin with the carcinogen activation pathway mediated through the aryl hydrocarbon receptor (AhR) in MCF-7 breast carcinoma cells. Treating the cells with formononetin alone caused the accumulation of CYP1A1 mRNA as well as elevation in CYP1A1-specific 7-ethoxyresorufin O-deethylase (EROD) activity in a dose dependent manner. However, a concomitant treatment with 7,12-dimethylbenz[a]anthracene (DMBA) and formononetin markedly reduced both the DMBA-inducible EROD activity and CYP1A1 mRNA level. Under the same conditions, formononetin inhibited the DMBA-induced AhR transactivation, as shown by reporter gene analysis using a xenobiotic responsive element (XRE). Additionally, formononetin inhibited both DMBA-inducible nuclear localization of the aryl hydrocarbon receptor (AhR) and metabolic activation of DMBA, as measured by the formation of the DMBA-DNA adducts. Furthermore, formononetin competed with the prototypical AhR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), for binding to the AhR in an isolated rat cytosol. These results suggest that formononetin might be considered as a natural ligand to bind on AhR and consequently produces a potent protective effect against DMBA-induced genotoxicity. Therefore, that's the potential to act as a chemopreventive agent that is related to its effect on AhR pathway as antagonist/agonist.

• ALGAE
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• v.30 no.3
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• pp.217-222
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• 2015

Pythium species (Pythiales, Oomycetes) are well known as the algal pathogen that causes red rot disease in Pyropia / Porphyra species (Bangiales, Rhodophyta). Accurate species identification of the pathogen is important to finding a scientific solution for the disease and to clarify the host-parasite relationship. In Korea, only Pythium porphyrae has been reported from Pyropia species, with identifications based on culture and genetic analysis of the nuclear internal transcribed spacer (ITS) region. Recent fungal DNA barcoding studies have shown the low taxonomic resolution of the ITS region and suggested the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as an alternative molecular marker to identify Pythium species. In this study, we applied an analysis of both the ITS and cox1 regions to clarify the taxonomic relationships of Korean Pythium species. From the results, the two closely related Pythium species (P. chondricola and P. porphyrae) showed the same ITS sequence, while the cox1 marker successfully discriminated P. chondricola from P. porphyrae. This is the first report of the presence of P. chondricola from the infected blade of Pyropia yezoensis in Asia. This finding of the algal pathogen provides important information for identifying and determining the distribution of Pythium species. Further studies are also needed to confirm whether P. chondricola and P. porphyrae are coexisting as algal pathogens of Pyropia species in Korea.