• Proceedings of the Korean Society of Toxicology Conference
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• 2000.11a
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• pp.31-41
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• 2000

The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.

• Fisheries and Aquatic Sciences
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• v.15 no.4
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• pp.325-335
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• 2012

The present study characterized the fast skeletal myosin light chain-2 gene (mlc2f) in the euryhaline Javanese ricefish (Oryzias javanicus: Beloniformes). Coding nucleotide and deduced amino acid sequences of Javanese ricefish mlc2f were well conserved in the vertebrate lineage. Javanese ricefish mlc2f showed a typical seven-exon structure, and its promoter exhibited transcription factor binding motifs common to most muscle-specific genes. However, Javanese ricefish mlc2f also displayed tandem duplications of intronic sequences in both intron 1 and intron 3. Based on quantitative reverse transcription-polymerase chain reaction, the mlc2f transcripts were highly predominant in skeletal muscles of adults and were differentially modulated during embryonic development. Microinjection of the mlc2f promoter-driven red fluorescent protein (RFP) reporter construct successfully exhibited heterologous expression of the fluorescent reporter, primarily in muscular areas of hatchlings, although the distribution pattern of RFP signals was not uniform due to the mosaic nature of the introduced transgene. Data from this study indicate that the Javanese ricefish mlc2f gene has undergone "intra-intronic" duplication events in a species-specific manner and that the mlc2f regulator may also be useful in heterologous expression assays of the skeletal muscles of this species.

• Toxicological Research
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• v.18 no.3
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• pp.233-240
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• 2002

In view of the effect of $\beta_2$-Adrenergic receptors ($\beta_2$-AR) as a risk factor for essential hypertension, we investigated the Fnu4HI and MnlI RFLPs of $\beta_2$ -AR gene in the Korean patients with essential hypertension and normal controls. There were no significant differences in the allele and genotype of these polymorphisms between normotensive and essential hypertensive subjects. In ethnic comparison, the allele frequencies of these three sites contained Nde I RFLP reported the association with essential hypertension in Korean population previously, were very different from those of other ethnic populations studied. The significant linkage disequilibrium was detected only in hypertensive group between Nde I and Fnu4HI sites. The Fnu4HI RFLP was also significantly associated with plasma triglyceride (TG) level. Therefore, our results suggest that the significant association between Fnu4HI variation in the human $\beta_2$-AR gene and plasma TG level may reflect the potential role of human $\beta_2$-AR gene as one of the genetic components for cardiovascular risk.

• Fisheries and Aquatic Sciences
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• v.13 no.4
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• pp.263-271
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• 2010

G protein-coupled receptors (GPCR) constitute the largest superfamily of cell membrane receptors, mediating diverse signal-transduction pathways. The melanocortin 4 receptor (MC4R) has been of interest for its physiological role and size, one of the smallest among the GPCRs, which makes it a good model system for the structural study of GPCRs. To study the molecular structure and tissue-specific expression of MC4R in olive flounder (Paralichthys olivaceus), the full-length MC4R gene was obtained using PCR amplification of genomic DNA as well as cDNA synthesis. Sequence analysis of the gene indicates that 978 bp of the MC4R gene encodes 325 amino acids without introns. Sequence alignment with the MC4Rs from other fish shows the highest degree of identity (96%) between Paralichthys olivaceous and Verasper moseri, followed by Takifugu rubripes and Tetraodon nigroviridis (89%). RNA was isolated from various tissues to examine the tissue distribution of MC4R by using RT-PCR. The results showed major expression of MC4R in the liver, brain, and eye, which is consistent with the expression pattern in other fish belonging to the order Pleuronectiformes.

• Journal of Ecology and Environment
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• v.43 no.4
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• pp.421-426
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• 2019

Background: Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results: A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion: Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

• Journal of Microbiology and Biotechnology
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• v.18 no.7
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• pp.1207-1215
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• 2008

To investigate the occurrence and species diversity of mycobacteria in waters, surface water samples were collected monthly from the Han River and tap water samples at the terminal sites of the distribution system. Mycobacteria in each water sample were isolated by decontamination using cetylpyridinium chloride (CPC) and cultivation on Middlebrook 7H10 agar, and then identified by polymerase chain reaction-restriction fragment length polymorphism analysis (PRA) and sequencing of the 65-kDa heat-shock protein gene (hsp65 gene). Mycobacteria were detected in 59% of the surface water samples and 26% of the tap water samples. Over half of the 158 isolates could not be identified by hsp65 PRA and gene sequencing, and several identification discrepancies were observed between the two methods. The most frequently isolated species was Mycobacterium gordonae in surface water and M. lentiflavum in tap water. M. avium complex (MAC), the most important pathogen among environmental mycobacteria, was detected in the surface water samples but not found in the tap water samples. The result demonstrated that water is an important environmental source of mycobacteria and the combined application of hsp65 PRA and sequencing was more reliable than hsp65 PRA alone to accurately identify mycobacteria present in water.

• Research in Plant Disease
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• v.30 no.1
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• pp.50-59
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• 2024

Charcoal rot disease, caused by the fungus Macrophomina phaseolina, is one of the most important diseases of Sesame (Sesamum indicum) all over the world. However, the population biology of M. phaseolina is poorly understood. In this study, M. phaseolina isolates from five different regions of Iran (Khuzestan, Fars, Bushehr, Hormozgan, and Kohgiluyeh & Boyer-Ahmad provinces) (n=200) were analyzed for genetic variation using inter simple sequence repeats marker. In total, 152 unique haplotypes were identified among the 200 M. phaseolina isolates, and gene diversity (H=0.46-0.84) and genotypic diversity were high in each of the regions. The structure analysis clustered five Iranian populations into two distinct groups, the individuals from group 1 were assigned to the Bushehr population and the individuals from Khuzestan, Fars, Hormozgan and Kohgiluyeh & Boyer-Ahmad were aggregated and formed group 2. The results matched with genetic differentiation and gene flow among regions. Analyses of the distribution of gene diversity within and among five Iranian populations were 61% and 39%, respectively. Our results showed that infected seeds are thought to be the dominant mechanism responsible for the spreading of the pathogen in southern parts of Iran. In summary, it is essential to have local quarantine and prevent seed exchanges between geographical populations to restrict the dispersal of pathogen over long distances and provide certified seeds in Iran.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.2
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• pp.443-449
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• 2015

Background: Myeloproliferative disorders (MPDs) are clonal hematologic malignancies originating at the level of the pluripotent hematopoietic stem cell. Matrix metalloproteases (MMPs) are proteolytic enzymes that contribute to all stages of malignancy progression. Genetic variants in the MMP genes may influence the biological function of these enzymes and change their role in carcinogenesis and progression. To our knowledge, this is the first investigation of associations between the -735 C/T and -1562 C/T polymorphisms in the MMP2 and MMP9 genes, respectively, and the risk of essential thrombocytosis (ET), and polycythemia vera (PV). Materials and Methods: The case-control study included JAK2V617F mutation positive 102 ET and PV patients and 111 controls. Polymorphisms were determined by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and electrophoresis. Results: No statistically significant differences were detected between patient (ET+PV) and control groups regarding genotype distribution for MMP2 gene-735 C/T and MMP9 gene -1562 C/T polymorphisms and C/T allele frequency (p>0.050). Statistically borderline significance was observed between PV and control groups regarding genotype distribution for the MMP9 gene -1562 C/T polymorphism (p=0.050, OR=2.26, 95%Cl=0.99-5.16). Conclusions: Consequently this study supported that CC genotype of MMP9 gene -1562 C/T polymorphism may be related with PV even if with borderline significance.

• Korean Journal of Ichthyology
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• v.18 no.1
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• pp.12-19
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• 2006

To examine the relationship of geological distribution and phylogenetic tree of O. latipes in the Far East, we analyzed cytochrome b (cyt b) gene in the mitochondrial genome. In this study we employed the entire sequence of cyt b of 53 samples collected from nine Korean locations and 117 cyt b data retrieved from the GenBank. From 170 Oryzias latipes cyt b sequence data, 142 different haplotypes were identified and phylogenetic relationship was reconstructed based on the dataset. According to the phylogeny, haplotypes were divided into three major haplogroups A, B and C, and their relationships were well correlated to their distributional patterns. Haplogroup A which is widely distribute in the southern part of Korea is separated in the geographical distribution from the haplogroup B which is found from China to the western part of Korea. Haplogroup C is only found in Japan.