• BMB Reports
• /
• v.43 no.8
• /
• pp.547-553
• /
• 2010

Biochemical tests such as aspartate aminotransferase (AST) and alanine aminotransferase (ALT) are useful for diagnosing patients with liver disease. In this study, we tested the association between copy number variation and the hepatic biomarkers AST and ALT based on 8,842 samples from population-based cohorts in Korea. We used Affymetrix Genome-Wide Human 5.0 arrays and identified 10,534 CNVs using HelixTree software. Of the CNVs tested using univariate linear regression, 100 CNVs were significant for AST and 16 were significant for ALT (P < 0.05). We identified 39 genes located within the CNV regions. DKK1 and HS3ST3B1 were shown to play roles in heparan sulfate biosynthesis and the Wnt signaling pathway, respectively. NAF1 and NPY1R were associated with glycoprotein processes and neuropeptide Y receptor activity based on GO categories. PTER, SOX14 and TM7SF4 were expressed in liver. DPYS and CTSC were found to be associated with dihydropyrimidinuria and Papillon-Lefevre syndrome phenotypes using OMIM. NPY5R was found to be associated with dyslipidemia using the Genetic Association Database.

• Molecules and Cells
• /
• v.23 no.1
• /
• pp.108-114
• /
• 2007

The mitogen-activated protein kinase (MAPK) signaling cascade is critical for regulating plant defense systems against various kinds of pathogen and environmental stresses. One component of this cascade, the MAP kinase kinases (MAPKK), has not yet been shown to be induced in plants following biotic attacks, such as those by insects and fungi. We describe here a gene coding for a blast (Magnaporthe grisea)- and insect (Nilaparvata lugens)-responsive putative MAPK kinase, OmMKK1 (Oryza minuta MAPKK 1), which was identified in a library of O. minuta expressed sequence tags (ESTs). Two copies of OmMKK1 are present in the O. minuta genome. They encode a predicted protein with molecular mass 39 kDa and pI of 6.2. Transcript patterns following imbibition of plant hormones such as methyl jasmonic acid (MeJA), ethephone, salicylic acid (SA) and abscisic acid (ABA), as well as exposure to methyl viologen (MV), revealed that the expression of OmMKK1 is related to defense response signaling pathways. A comparative analysis of OmMKK1 and its O. sativa ortholog OsMKK1 showed that both were induced by stress-related hormones and biotic stresses, but that the kinetics of their responses differed despite their high amino acid sequence identity (96%).

• Molecules and Cells
• /
• v.25 no.1
• /
• pp.20-29
• /
• 2008

Cytoplasmic male sterility (CMS), one of the most important traits in crop breeding, has been used for commercial seed production by $F_1$ hybrid cultivars of pepper (Capsicum annuum L.). To develop reliable molecular markers for allelic selection of the Restorer-of-fertility (Rf) gene, which is known to be a major determinant of pollen fertility restoration in peppers, a sequence of approximately 10 kb flanking an RAPD fragment closely linked to the Rf locus was obtained by genome walking. A homology search revealed that this sequence contained an LTR retrotransposon and a non-LTR LINE-like retrotransposon. Sequencing of this Rf-linked region to search for polymorphisms between a dominant and recessive allele revealed 98% nucleotide sequence identity between them. A third polymorphic haplotype of the Rf-linked sequence, which has 94-96% nucleotide sequence identity with the two previously isolated haplotypes, was identified among a large number of breeding lines. Utilizing polymorphic sequences in the haplotypes, PCR markers were developed for selection of particular haplotypes and used to examine the distribution of the haplotypes in diverse breeding lines, cultivars, and C. annuum germplasms. Surprisingly, the third haplotype was the predominant type in C. annuum germplasms, while its frequency in $F_1$ hybrid cultivars was relatively low. Meanwhile, analysis of breeding lines whose Rf allele genotypes and male-sterility phenotypes were already known revealed that the third haplotype was mainly present in exotic breeding lines that cause unstable male-sterility when combined with sterile cytoplasms.

• Journal of Microbiology and Biotechnology
• /
• v.10 no.6
• /
• pp.776-783
• /
• 2000

Various alcohol yeast strains have been isolated from main mashes of Korean traditional liquors, and their genetic diversities were previously reported [23]. In this study, the strain SHY111, showing the highest alcohol production, was tested for its fermentation and sporulation characteristics. Additionally, its haploid cells were isolated and tested for their growth and fermentation patterns. The strain was identified as Saccharomyces cerevisiae based on its morphological and physiological characteristics. The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA regions of S. cerevisiae SHY111 were found to be identical to those of S. cerevisiae that was obtained from through the yeast genome project. The maximum fermentation ratio obtained by the strain SHY111 (96.7%) was almost the same as that by S. cerevisiae Balyun No. 1 (96.5%) that was a little higher than that by S. cerevisiae KCCM11215(95.8%). The strain was induced for sporulation in a sporulation liquid medium using log phase cells grown in different types of pre-sporulation media, and its haploid cells were obtained by spore dissection using a micromanipulator. The majority of the spores formed a small colony on a YPD agar plate, and the haploid yeast cells derived from the strain SHY111 showed a variety of growth and alcohol fermentation patterns. It was proposed that the fermentation patterns were related to their growth phenotypes in the most haploid strains, but possible not in some strains.

• Journal of Pharmacopuncture
• /
• v.8 no.1
• /
• pp.31-40
• /
• 2005

Objectives : It has long been known about the osteogenic effect of CTF-HAS on bone tissues. However, it has not been determined the effect of CTF-HAS on cancer cells. The purpose of this study is to screen the CTF-HAS mediated differentially expressed genes in cancer cells such as SNU484 gastric cancer cell lines. Oligonucleotide microarray approach were employed to screen the differential expression genes. Methods : CTF-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CTF-HAS(0.1, 0.5, 1.5, 10, 20mg/ml) for 24 h. Cytotoxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5mg/ml of CTF-HAS. For oligonucleotide microarry assay, total RNA was used for gene expression analysis using oligonucleotide genechip (Human genome U133 Plus 2.0., Affimatrix Co.). Results : It has no cytotoxic effects on HepG2 cells in all concentration (0.1, 0.5, 1.5, 10,20mg/ml). More than twofold up-regulated genes were 5 genes. The number of more than twofold down-regulated genes was 10. Discussion : This study showed the screening of CTF-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray. The screened genes will be used for the better understanding in therapeutic effect of CTF-HAS on cancer field.

• Biomedical Science Letters
• /
• v.10 no.2
• /
• pp.163-169
• /
• 2004

Worldwide, tuberculosis remains one of the leading infectious diseases, accounting for nearly 3 million deaths and more than 8 million new cases annually. DNA typing of Mycobacterium tuberculosis is important for the control of tuberculosis, since it can be used to track transmission route of tuberculosis, source of internal laboratory contaminations, and to answer questions on the nature of tuberculosis infections such as reactivation or exogenous reinfection of disease. At present, IS6110-based RFLP is the choice of method for typing large numbers of clinical isolates of M. tuberculosis, since it has the highest resolution power. However, RFLP requires long time, high cost and qualified experts, so only reference level laboratories can use the RFLP technique. In order to have an optional molecular typing method suitable for the clinical settings, this study evaluated the use of one of PCR-based typing methods, IS6110-based outward PCR for typing clinical isolates of M. tuberculosis. In brief, the results from this study showed that IS6110-based RFLP is useful to discriminate diverse clinical isolates of M. tuberculosis as well as to identify clinical isolates that belong to the same family or cluster groups that have been previously classified by RFLP analysis. In addition, the banding profiles resulted from IS6110-based outward PCR seemed to represent genomic characteristics of M. tuberculosis, since strains belong to the K-family generated unique band that is not present in any other strains but present only in the genome of K-family strains. The IS6110-based outward PCR was also shown to be useful with DNAs isolated directly from liquid cultures indicating this method can be suitable for typing M. tuberculosis in clinical settings.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.18 no.6
• /
• pp.1805-1809
• /
• 2004

In order to validate the use of Radix Curcumae Aromaticae as an anti-inflammatory drug in the traditional Korean medicine, I have investigated the effect of water-soluble extract of Radix Curcumae Aromaticae (ECA) on the expression of inducible heme oxygenase-1 (HO-1), which ha.s anti-inflammatory and cytoprotective effects stimulates, in human umbilical vein endothelial cells (HUVECs) stimulated with a high dose of pro-inflammatory tumor necrosis factor-alpha (TNF-α). The extract protected dose-dependently HUVECs against TNF-α-induced apoptosis, as measured qualitatively by a nuclear staining method using the fluoresoence DAPI and quantitatively by a flow cytometry using fluoresce-enhanced Annexin V antibody, and significantly Increased HO-1 expression, as determined by Western blotting analysis using anti-HO-1 antibody. Biockage of HO-1 activity by a pharmacological inhibitor reversed cytoprotection afforded by the extract, and treatment with carbon monoxide, one of HO-1 metabolites, resulted in cytoprotection comparable to the extract. These results suggest that ECA may have therapeutic potential in the control of endothelial disorders caused by inflammatory cytokines.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.25 no.5
• /
• pp.816-822
• /
• 2011

Kaempferol, a component of Polygonati rhizoma, is one of the herbal flavonoids, which is used in therapeutic agent for anti-hypercholesterol, anti-hypertension and anti-diabetes. And it is also known to be effective in anti-cancer therapy for breast, prostate and other type of cancers. However, the anti-cancer therapeutic mechanisms are pooly understood. To address molecular mechanism underlying kaempferol-induced anti-cancer effects, we determined the effect of kaempferol on cell growth of the lung cancer cell lines, A549, H1299 and H460. From the FACS analysis, measurement of caspase activity, DAPI and tryptophan blue staining, and DNA fragmentation assay, we found that kaempferol induces apoptosis and H460 cells are most sensitive among the tested cell lines. In addition, we performed microarray to identify the genome-wide expression profiling regulated by kaempferol. Lots of cell cycle-related genes were under-expressed, whereas the genes related to TGF-beta/SMAD pathway were over-expressed in kaempferol-treated H460 cells. Additionally, kaempferol also increased expression levels of apoptosis related genes such as death receptors, FAS, TRAIL-R and TNF-R, and casepase-8 and caspase-10. Overall, our results suggest that kaempferol promotes anti-lung cancer therapeutic effects by inducing G1 arrest and apoptosis through TGF-beta/SMAD pathway and death receptors/caspase pathway, respectively.

• The Plant Pathology Journal
• /
• v.27 no.4
• /
• pp.378-384
• /
• 2011

Tomato yellow leaf curl virus (TYLCV), a member of genus Begomovirus, was isolated in Korea in 2008. We sequenced and analyzed the DNA-A of 51 TYLCV isolates from Korea, and 13 of the TYLCV isolates were selected as type representatives of TYLCV from six Korean provinces. The 13 TYLCV isolates were classified into Korea Group 1 (KG1, nine isolates) and Korea Group 2 (KG2, four isolates) based on the results of phylogenetic analysis and genome size (2774 and 2781 nucleotides, respectively). A recombination detection program 3 (RDP3) revealed two recombinations between the TYLCV Korea isolates and other TYLCV isolates [Thailand (AF206674), Iran (AJ132711), and Israel (X76319)]. TYLCV Jeju isolate was characterized by two recombination events (E1 and E2) caused by the presence of E1 in ORF V1 and C3, which may seem to be the mutations of the high nucleotide transversion and transition rate. Collectively, our results suggest that the occurrence of nucleotide transversions and transitions in TYLCV DNA-A might have induced novel recombination events within the TYLCV Korea isolates.

• The Plant Pathology Journal
• /
• v.30 no.4
• /
• pp.384-396
• /
• 2014

Vegetative compatibility groups (VCGs) are determined for many fungi to test for the ability of fungal isolates to undergo heterokaryon formation. In several fungal plant pathogens, isolates belonging to a VCG have been shown to share significantly higher genetic similarity than those of different VCGs. In this study we sought to examine the relationship between VCG and genetic similarity of an important cool season turfgrass pathogen, Sclerotinia homoeocarpa. Twenty-two S. homoeocarpa isolates from the Midwest and Eastern US, which were previously characterized in several studies, were all evaluated for VCG using an improved nit mutant assay. These isolates were also genotyped using 19 microsatellites developed from partial genome sequence of S. homoeocarpa. Additionally, partial sequences of mitochondrial genes cytochrome oxidase II and mitochondrial small subunit (mtSSU) rRNA, and the atp6-rns intergenic spacer, were generated for isolates from each nit mutant VCG to determine if mitochondrial haplotypes differed among VCGs. Of the 22 isolates screened, 15 were amenable to the nit mutant VCG assay and were grouped into six VCGs. The 19 microsatellites gave 57 alleles for this set. Unweighted pair group methods with arithmetic mean (UPGMA) tree of binary microsatellite data were used to produce a dendrogram of the isolate genotypes based on microsatellite alleles, which showed high genetic similarity of nit mutant VCGs. Analysis of molecular variance of microsatellite data demonstrates that the current nit mutant VCGs explain the microsatellite genotypic variation among isolates better than the previous nit mutant VCGs or the conventionally determined VCGs. Mitochondrial sequences were identical among all isolates, suggesting that this marker type may not be informative for US populations of S. homoeocarpa.