• 한국생물공학회:학술대회논문집
• /
• 2003.10a
• /
• pp.391-391
• /
• 2003

• Journal of Animal Reproduction and Biotechnology
• /
• v.39 no.2
• /
• pp.138-144
• /
• 2024

Background: As the number of households raising companion dogs increases, the pet genetic analysis market also continues to grow. However, most studies have focused on specific purposes or native breeds. This study aimed to collect genomic data through single nucleotide polymorphism (SNP) chip analysis of companion dogs in South Korea and perform genetic diversity analysis and SNP annotation. Methods: We collected samples from 95 dogs belonging to 26 breeds, including mixed breeds, in South Korea. The SNP genotypes were obtained for each sample using an Axiom^TM Canine HD Array. Quality control (QC) was performed to enhance the accuracy of the analysis. A genetic diversity analysis was performed for each SNP. Results: QC initially selected SNPs, and after excluding non-diverse ones, 621,672 SNPs were identified. Genetic diversity analysis revealed minor allele frequencies, polymorphism information content, expected heterozygosity, and observed heterozygosity values of 0.220, 0.244, 0.301, and 0.261, respectively. The SNP annotation indicated that most variations had an uncertain or minimal impact on gene function. However, approximately 16,000 non-synonymous SNPs (nsSNPs) have been found to significantly alter gene function or affect exons by changing translated amino acids. Conclusions: This study obtained data on SNP genetic diversity and functional SNPs in companion dogs raised in South Korea. The results suggest that establishing an SNP set for individual identification could enable a gene-based registration system. Furthermore, identifying and researching nsSNPs related to behavior and diseases could improve dog care and prevent abandonment.

• Genomics & Informatics
• /
• v.9 no.2
• /
• pp.89-91
• /
• 2011

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.

• Proceedings of the Korea Society of Environmental Toocicology Conference
• /
• 2003.10a
• /
• pp.173-173
• /
• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• Journal of Sasang Constitutional Medicine
• /
• v.18 no.3
• /
• pp.131-144
• /
• 2006

1. Objectives This research uses the DNA chip, which includes 16,383 gene code, and various statistic prediction way that shows objectification index for the objectification of constitution diagnosis. 2. Methods Drawing blood whose constitution is confirmed, and analyze its gene information by using 1.7k DNA chip to find the gene correlation through multivariate statistical method. 3. Results and Conclusions Distinctive genes such as AK001919, U09384, NM_001805, X99962, NM_004796, AK026738, AL050148, BC002538, AK027074, AK026219, AF087962, AL390142, NM_015372, AL157466, NM_002446, AK024523, NM_014706, NM_014746 and AL137544 were related to Taeumin; AL157448, NM_005957, NM_005656, NM_017548, AK027246, NM_003025, NM_012302 and NM_005905 were represented in Soeumin, while AK026503, AF147325, NM_002076, AF147307, AK001375, NM_003740, NM_005114, AB007890, NM_005505, NM_015900, NM_014936, Z70694, AB023154, U52076, NM_004360, NM_005835, NM_017528, AF087987, NM_014897, AK021720, NM_006420, AJ277915, AK002118 and AK021918 were for Soyangin. This study figured out the possibility to develop the prediction system by sorting each constitution's gene, and research each constitution's distinctive character of manifestation pattern.

• Genomics & Informatics
• /
• v.1 no.2
• /
• pp.94-100
• /
• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• Plant Biotechnology Reports
• /
• v.2 no.4
• /
• pp.233-238
• /
• 2008

Kadainou R-1, an interspecific hybrid grape derived from red (Vitis ficifolia var. ganebu) and white (V. vinifera cv. Muscat of Alexandria) grapes, accumulates high concentrations of anthocyanin in the berry skin. Hence, the expression of uridine 50 -diphosphate (UDP)-glucose:flavonoid 3-O-glucosyltransferase (UFGT), the key enzyme of the anthocyanin pathway, was examined in the berry skin of Kadainou R-1. As information on gene sequences of V. ficifolia var. ganebu and other wild grape species was unavailable, we performed GeneChip hybridization using biotin-labeled genomic deoxyribonucleic acid (DNA) to investigate how the genomic sequences of V. vinifera varieties and that of V. ficifolia var. ganebu differ. The study showed a lower correlation coefficient between V. vinifera cultivars and V. ficifolia var. ganebu than that among V. vinifera cultivars. The sequences of the UFGT gene derived from both parents of the red and white cultivars were sequenced in Kadainou R1 and revealed that both were expressed irrespective of the fact that it was not expressed in the white grape (male parent).

• Tuberculosis and Respiratory Diseases
• /
• v.49 no.5
• /
• pp.546-557
• /
• 2000

Background : Oligonucleotide chip technology has proven to be a very useful tool in the rapid diagnosis of infectious disease. Rifampin resistance is considered as a useful marker of multidrug-resistance in tuberculosis. Mutations in the rpoB gene coding $\beta$ subunit of RNA polymerase represent the main mechanism of rifampin resistance. The purpose of this study was to develop a diagnosis kit using oligonucleotide chip for the rapid and accurate detection of rifampin-resistance in Mycobacterium tuberculosis. Method : The sequence specific probes for mutations in the rpoB gene were designed and spotted onto the glass slide, oligonucleotide chip. 38 clinical isolates of Mycobacterium were tested. A part of rpoB was amplified, labelled, and hybridized on the oligonucleotide chip with probes. Results were analyzed with a laser scanner. Direct sequencing was done to verify the results. Result : The low-density oligonucleotide chip design어 to determine the specific mutations in the rpoB gene of M. tuberculosis accurately detected rifampin resistance associated with mutations in 28 clinical isolates. Mutations at codons 531, 526, and 513 were confirmed by direct sequencing analysis. Conclusion : Mutant detection using oligonucleotide chip technology is a reliable and useful diagnostic tool for the detection of multidrug-resistance in M. tuberculosis.

• Molecular & Cellular Toxicology
• /
• v.3 no.4
• /
• pp.222-230
• /
• 2007

Some drugs may be limited in their clinical application due to their propensity towards their adverse effects. Toxicogenomic technology represents a useful approach for evaluating the toxic properties of new drug candidates early in the drug discovery process. Nitrofurantoin (NF) is clinical chemotherapeutic agent and antimicrobial and used to treatment of urinary tract infections. However, NF has been shown to result in pulmonary toxic effects. In this research, we revealed the changing expression gene profiles in BEAS-2B, human bronchial epithelial cell line, exposed to NF by using human oligonucleotide chip. Through the clustering analysis of gene expression profiles, we identified 136 up-regulated genes and 379 down-regulated genes changed by more than 2-fold by NF. This study identifies several interesting targets and functions in relation to NF-induced toxicity through a gene ontology analysis method including biological process, cellular components, molecular function and KEGG pathway.

• Horticultural Science & Technology
• /
• v.31 no.6
• /
• pp.748-755
• /
• 2013

This study was conducted to find a salt tolerance gene in Brassica rapa. In order to meet this objective, we analyzed data from a KBGP-24K oligo chip [BrEMD (Brassica rapa EST and microarray database)] of the B. rapa ssp. pekinensis 'Chiifu' under salt stress (250 mM NaCl). From the B. rapa KBGP-24K microarray chip analysis, 202 salt-responsive unigenes were primarily selected under salt stress. Of these, a gene with unknown function but known full-length sequence was chosen to closely investigate the gene function. The selected gene was named BrSSR (B. rapa salt stress resistance). BrSSR contains a 285 bp open reading frame encoding a putative 94-amino acid protein, and a DUF581 domain. The pSL94 vector was designed to over-express BrSSR, and was used to transform tobacco plants for salt tolerance analysis. T1 transgenic tobacco plants that over-expressed BrSSR were selected by PCR and DNA blot analyses. Quantitative real-time RT PCR revealed that the expression of BrSSR in transgenic tobacco plants increased by approximately 3.8-fold. Similar results were obtained by RNA blot analysis. Phenotypic characteristics analysis showed that transgenic tobacco plants with over-expressed BrSSR were more salt-tolerant than the wild type control under 250 mM NaCl for 5 days. Based on these results, we hypothesized that the over-expression of BrSSR may be closely related to the enhancement of salt tolerance.