• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.317-320
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• 2003

Genome-wide systematic deletion mutants were generated using a PCR-based targeted mutagenesis of Schizosacchaaromyces pombe. In a drug-sensitivity assay using thiabendazole(TBZ), an inhibitor of microtubule assembly, a heterozygous nda2 mutant ($nda2^+/nda2^-$), deleting one copy of nda2 encoding the microtubule subunit alpha1 demonstrated a distinct sensitivity to TBZ, indicating TBZ-induced haploinsufficiency. This result suggests that profiling drug-induced haploinsufficiency can be exploited to identify target genes for drugs and discover new drugs.

• Journal of dental hygiene science
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• v.19 no.2
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• pp.86-95
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• 2019

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.

• Proceedings of the Korean Society of Crop Science Conference
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• 2020.06a
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• pp.120-120
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• 2020

Based on the simple sequence repeat (SSR) marker, a Korean wheat core collection were established with 616 wheat accessions. Among them, the SNP genotyping for the entire genome was performed using DNA chip array to clarify the whole genome SNP profiles. Consequently, a total of 35,143 SNPs were found and we re-established a mini-core collection with 247 accessions. Population diversity and phylogenetic analysis revealed genetic diversity and relationships from the mini core set. In addition, genome-wide association study (GWAS) was performed on 19 phenotypic traits; ear type, awn length, culm length, ear length, awn color, seed coat color, culm color, ear color, loading, leaf length, leaf width, seeding stand, cold damage, weight, auricle, plant type, heading stage, maturation period, upright habit, and degree of flag leaf. The GWAS was performed using the fixed and random model circulating probability unification (FarmCPU), which identified 14 to 258 SNP loci related to 19 phenotypic traits. Our study indicates that this Korean wheat mini-core collection is a set of germplasm useful for basic and applied research with the aim of understanding and exploiting the genetic diversity of Korean wheat varieties.

• Korean Journal of Biological Psychiatry
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• v.14 no.2
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• pp.115-121
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• 2007

Objetives : Identification of target genes for ethanol in neurons is important for understanding its molecular and cellular mechanism of action and the neuropathological changes seen in alcoholics. The purpose of this study is to identify of altered gene expression after acute treatmet of ethanol in rat gliom cells. Methods : We used high density cDNA microarray chip to measure the expression patterns of multiple genes in cultured rat glioma cells. DNA microarrays allow for the simultaneous measurement of the expression of several hundreds of genes. Results : After comparing hybridized signals between control and ethanol treated groups, we found that treatment with ethanol increased the expression of 15 genes and decreased the expression of 12 genes. Upregulated genes included Orthodenticle(Drosophila) homolog 1, procollagen type II, adenosine A2a receptor, GATA bindning protein 2. Downregulated genes included diacylglycerol kinase beta, PRKC, Protein phosphatase 1, clathrin-associated protein 17, nucleoporin p58, proteasome. Conclusion : The gene changes noted were those related to the regulation of transcription, signal transduction, second messenger systems. modulation of ischemic brain injury, and neurodengeneration. Although some of the genes were previously known to be ethanol responsive, we have for the most part identified novel genes involved in the brain response to ethanol.

• Clinical and Experimental Reproductive Medicine
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• v.34 no.1
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• pp.19-31
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• 2007

Objective: Pathogenesis of the endometriosis is very complex and the etiology is still unclear. Our hypothesis is that there may be some difference in gene expression patterns between eutopic endometriums with or without endometriosis. In this study, we analyzed the difference of gene expression profile with cDNA microarray. Methods: Endometrial tissues were gathered from patients with endometriosis or other benign gynecologic diseases. cDNA microarray technique was applied to screen the different gene expression profiles from early and late secretory phase endometria of those two groups. Each three mRNA samples isolated from early and late secretory phase of endometrial tissues of control were pooled and used as master controls and labeled with Cy3-dUTP. Then the differences of gene expression pattern were screened by comparing eutopic endometria with endometriosis, which were labeled with Cy5-dUTP. Fluorescent labeled probes were hybridized on a microarray of 4,800 human genes. Results: Twelve genes were consistently over-expressed in the endometrium of endometriosis such as ATP synthase H transporting F1 (ATP5B), eukaryotic translation elongation factor 1, isocitrate dehydrogenase 1 (NADP+), mitochondrial ribosomal protein L3, ATP synthase H+ transporting (ATP5C1) and TNF alpha factor. Eleven genes were consistently down-regulated in the endometriosis samples. Many extracellular matrix protein genes (decorin, lumican, EGF-containing fibulin-like extracellular matrix protein 1, fibulin 5, and matrix Gla protein) and protease/protease inhibitors (serine proteinase inhibitor, matrix metalloproteinase 2, tissue inhibitor of metalloproteinase 1), and insulin like growth factor II associated protein were included. Expression patterns of selected eight genes from the cDNA microarray were confirmed by quantitative RT-PCR or real time RT-PCR. Conclusion: The result of this analysis supports the hypothesis that the endometrium from patients with endometriosis has distinct gene expression profile from control endometrium without endometriosis.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.142-148
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• 2002

Although ionizing radiation (IR) has been used to treat the various human cancers, IR is cytotoxic not only to cancer cells but to the adjacent normal tissue. Since normal tissue complications are the limiting factor of cancer radiotherapy, one of the major concerns of IR therapy is to maximize the cancer cell killing and to minimize the toxic side effects on the adjacent normal tissue. As an attempt to develop a method to monitor the degree of radiation exposure to normal tissues during radiotherapy, we investigated the transcriptional responses of human peripheral blood lymphocytes (PBL) following IR using cDNA microarray chip containing 1,221 (1.2 K) known genes. Since conventional radiotherapy is delivered at about 24 h intervals at 180 to 300 cGy/day, we analyzed the transcriptional responses ex-vivo irradiated human PBL at 200 cGy for 24 h-period. We observed and report on 1) a group of genes transiently induced early after IR at 2 h, 2) of genes induced after IR at 6 h, 3) of genes induced after IR at 24 h and on 4) a group of genes whose expression patters were not changed after IR. Since Biological consequences of IR involve generation of various reactive oxygen species (ROS) and thus oxidative stress induced by the ROS is known to damage normal tissues during radiotherapy, we further tested the temporal expression profiles of genes involved in ROS modulation by RT-PCR. Specific changes of 6 antioxidant genes were identified in irradiated PBL among 9 genes tested. Our results suggest the potential of monitoring post-radiotherapy changes in temporal expression profiles of a specific set of genes as a measure of radiation effects on normal tissues. This type of approach should yield more useful information when validated in in vivo irradiated PBL from the cancer patients.

• Journal of KIISE:Computer Systems and Theory
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• v.31 no.9
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• pp.514-526
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• 2004

Microarray is a new technique for gene expression experiment, which has gained biologist's attention for recent years. This technology enables us to obtain hundreds and thousands of expression of gene or genotype at once using microarray Since it requires manual work to analyze patterns of gene expression, we want to develop an effective and automated tools to analyze microarray image. However it is difficult to analyze DNA chip images automatically due to several problems such as the variation of spot position, the irregularity of spot shape and size, and sample contamination. Especially, one of the most difficult problems in microarray analysis is the block and spot addressing, which is performed by manual or semi automated work in all the commercial tools. In this paper we propose a new algorithm to address the position of spot and block using a new concept of regular structure grid searching. In our algorithm, first we construct maximal I-regular sequences from the set of input points. Secondly we calculate the rotational angle and unit distance. Finally, we construct I-regularity graph by allowing pseudo points and then we compute the spot/block address using this graph. Experiment results showed that our algorithm is highly robust and reliable. Supplement information is available on http://jade.cs.pusan.ac.kr/~autogrid.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2003.11a
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• pp.98-98
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• 2003

${\beta}$-(1,3)-D-Glucans have been known to exhibit antitumor and antimicrobial activities. The presence of dectin-1,${\alpha}$, ${\beta}$-glucan receptor of dendritic cell, on macrophage has been controvertial. RT-PCR analysis led to the detection of dectin-1${\alpha}$ and ${\beta}$ in murine macrophage Raw264.7 cell line. Among the various organs of mouse, dectin-1${\alpha}$ and ${\beta}$ were detected in the thymus, lung, spleen, stomach and intestine. To analyze gene expression modulated by ${\beta}$-glucan treated murine Raw264.7 macrophage, total mRNA was applied to cDNA microarray to interrogate the expression of 7,000 known genes. cDNA chip analysis showed that ${\beta}$-glucan of P. osteatus increased gene expressions of immunomodulating genes, membrane antigenic proteins, chemokine ligands, complements, cytokines, various kinases, lectin associated genes and oncogenes in Raw 264.7 cell line. When treated with ${\beta}$-glucan of P. osteatus and LPS, induction of gene expression of TNF-${\alpha}$ and IFN-R1 was confirmed by RT-PCR analysis. Induction of TNF-R type II expression was confirmed by FACS analysis. IL-6 expression was abolished by EDTA in ${\beta}$-glucan and LPS treated Raw264.7 cell line, indicating that ${\beta}$-glucan binds to dectin-l in a Ca$\^$＋＋/ -dependent manner. To increase antitumor efficacy of ${\beta}$-glucan, ginsenoside Rh2 (GRh2) was co-treated with ${\beta}$-glucan in vivo and in vitro tests. IC$\sub$50/ values of GRh2 were 20 and 25 $\mu\textrm{g}$/$m\ell$ in SNU-1 and B16 melanoma F10 cell line, respectively. Co-treatment with ${\beta}$-glucan and GRh2 showed synergistic antitumor activity with cisplatin and mitomycin C both in vitro and in vivo. Single or co-treatment with ${\beta}$-glucan and GRh2 increased tumor bearing mouse life span. Co-treatment with ${\beta}$-glucan and GRh2 showed more increased life span with mitomycin C than that with cisplatin. Antitumor activities were 67% and 72 % by co-injection with ${\beta}$-glucan and GRh2 in the absence or presence of mitomycin C, respectively.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.845-852
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• 2014

Among various abiotic stress factors, soil salinity decreases the photosynthetic rate, growth, and yield of plants. Recently, many genes have been reported to enhance salt tolerance. The objective of this study was to characterize the Brassica rapa Salt Stress Resistance (BrSSR) gene, of which the function was unclear, although the full-length sequence was known. To characterize the role of BrSSR, a B. rapa Chinese cabbage inbred line ('CT001') was transformed with pSL94 vector containing the full length BrSSR cDNA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression of BrSSR in the transgenic line was 2.59-fold higher than that in the wild type. Analysis of phenotypic characteristics showed that plants overexpressing BrSSR were resistant to salinity stress and showed normal growth. Microarray analysis of BrSSR over-expressing plants confirmed that BrSSR was strongly associated with ERD15 (AT2G41430), a gene encoding a protein containing a PAM2 motif (AT4G14270), and GABA-T (AT3G22200), all of which have been associated with salt tolerance, in the co-expression network of genes related to salt stress. The results of this study indicate that BrSSR plays an important role in plant growth and tolerance to salinity.

• Journal of Life Science
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• v.22 no.11
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• pp.1552-1557
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• 2012

It has been reported that pipernonaline isolated from Piper longum Linn. has a wide biochemical and pharmacological effect, including antitumor activity in prostate cancer PC-3 cells. However, its mechanism and expression pattern of many genes involved in biological functions are not clearly understood. To perform the gene expression study in PC-3 cells treated with pipernonaline, a cDNA microarray chip composed of 44,000 human cDNA probes was used. As a result, cell cycle-related genes, apoptosis-related genes, and cell proliferation/growth-related genes have been identified in gene ontology of the DAVID database. These results suggest that pipernonaline has antitumor activity by regulating the expression pattern of genes involved in biological signaling pathway in prostate cancer PC-3 cells. Further, additional analysis of these microarray data can be a useful tool to identify the mechanism and discovery of novel genes in cancer therapy.