• Fisheries and Aquatic Sciences
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• v.14 no.1
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• pp.16-21
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• 2011

The genetic diversity and population genetic structure of thread-sail filefish, Stephanolepis cirrhifer (Temminck & Schlegel), were examined with a nucleotide sequence analysis of a 495bp fragment of the 5'-end of the cytochrome b gene in 113 fish collected from five populations from the south and east coasts of the Korean Peninsula. Seventeen variable nucleotide sites and 16 haplotypes were defined. The observed haplotypes had a shallow haplotype genealogy and no geographical association. Most of the populations had high haplotype diversity and low nucleotide diversity, and significant negative values for Fu's $F_S$, suggesting rapid, recent population growth from an ancestral population and sudden population expansion. The estimated pairwise fixation indices ($F_{ST}$) indicate that substantial gene flow occurs among these populations. Thread-sail filefish in the South Sea of Korea and East Sea Korean populations forms a single panmictic population. Thus, thread-sail filefish in these areas should be treated as one management unit.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.170-176
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• 2012

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities ($0.974{\pm}0.029$ to $1.000{\pm}0.076$) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population FST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups ($F_{CT}$ = 0.028, p<0.05), and no genetic variation within groups (0.53%; $F_{SC}$ = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

• Journal of fish pathology
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• v.24 no.3
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• pp.269-278
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• 2011

Gene expression of two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) paralogs was examined during Edwardsiella tarda challenge and heavy metal exposures in mud loach (Misgurnus mizolepis; Cypriniformes) kidney and spleen. Transcription of the two mud loach GAPDH paralogs (mlGAPDH-1 and mlGAPDH-2) was significantly modulated by these stimulatory challenges in an isoform-dependent manner. Based on the real-time RT-PCR analysis, the mlGAPDH-2 transcripts were more preferentially induced by E. tarda challenge, whereas the mlGAPDH-1 transcripts were proven to show more inducibility in response to heavy metal exposure using Cd, Cu, Mn and Zn at $5{\mu}M$. Their isoform-specific response patterns were closely in accordance with the TF binding profiles in promoter and intron-1 of the two mlGAPDH isoforms, in which the mlGAPDH-2 has more binding sites for immune-related transcription factors than mlGAPDH-1 while the mlGAPDH-1 possesses exclusively metal responsive elements in its intron. Collectively, the mlGAPDHs are potentially involved in cellular pathways independent of glycolysis and the two GAPDH paralogs might undergo functional diversification or subfunctionalization at least at the transcription level.

• Animal cells and systems
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• v.15 no.3
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• pp.243-249
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• 2011

The genetic diversity and population history of the Asian shore crab, Hemigrapsus sanguineus, were investigated with a nucleotide sequence analysis of 536 base pairs (bp) of the mitochondrial cytochrome c oxidase subunit I gene (COI) in 111 samples collected from four populations in Korea and one in Japan. In total, 28 haplotypes were defined by 27 variable nucleotide sites in the COI region examined. The observed haplotypes had a shallow haplotype genealogy and no geographical associations. Most of the populations had high haplotype diversity (0.656-0.788) and low nucleotide diversity (0.00165-0.00244), and significant negative values for Fu's $F_S$, suggesting rapid and recent population growth from an ancestral population and sudden population expansion. The pairwise fixation indices ($F_{ST}$) estimated with the exact test and the migration rates indicate that substantial gene flow occurs among these populations as a result of sea currents, except between the Yellow Sea coast of Korea (BUA) and the Pacific Ocean coast of Japan (JPA). These two populations (BUA and JPA) showed significant genetic differentiation and low migration rate.

• Fisheries and Aquatic Sciences
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• v.18 no.1
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• pp.73-80
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• 2015

To examine the interrelationship between transgenic insertion patterns and transgene expression profiles in established transgenic fish lines, four stable transgenic marine medaka Oryzias dancena germlines harboring ${\beta}$-actin regulator-driven RFP reporter constructs were selected. The established transgenic strains were characterized with regard to their transgenic genotypes (insertion pattern, concatemer formation, and transgene copy number based on genomic Southern blot hybridization and qPCR assay) and expression characteristics at the mRNA (qRT-PCR), protein (western blot), and phenotypic (fluorescent appearance) levels. From comparative examinations, it was found that transgenic expression at both the transcription and translation levels could be significantly downregulated in transgenic strains, potentially through methylation-mediated transgene silencing that was particularly associated with the formation of a long tail-to-head tandem concatemer in the chromosomal integration site(s). When this occurred, an inverse relationship between the transgene copy number and fluorescence intensity was observed in the resultant transgenic fish. However, with the other transgenic genotype, transgenic individuals with an identical Southern blot hybridization pattern, containing a tandem concatemer(s), had very different expression levels (highly robust vs. low expression strengths), which was possibly related to the differential epigenetic modifications and/or degrees of methylation. The concatemer-dependent downregulation of transgene activity could be induced in transgenic fish, but the overall pattern was strain-specific. Our data suggest that neither a low (or single) transgene copy number nor tandem transgene concatemerization is indicative of strong or silenced transgene expression in transgenic fish carrying a ubiquitous transgene. Hence, a sufficient number of transgenic lineages, with different genotypes, should be considered to ensure the establishment of the best-performance transgenic line(s) for practical applications.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.6
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• pp.824-828
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• 2017

We investigated the anesthetic effects of MS-222 (tricaine methanesulfonate), clove oil, 2-phenoxyethanol, $NaHCO_3$, lidocaine-HCl and lidocaine-$HCl/NaHCO_3$ in the glass catfish Kryptopterus vitreolus. Based on the efficacy criteria of complete anesthetic induction from 60 s to 120 s, recovery within 300 s, the lowest effective concentrations at $24^{\circ}C$ were determined to be 60 ppm (induction $82.8{\pm}17.6s$, recovery $80.2{\pm}34.7s$) for MS-222, 40 ppm (induction $70.5{\pm}8.2s$, recovery $83.4{\pm}17.7s$) for clove oil, 250 ppm (induction $64.3{\pm}24.0s$, recovery $62.8{\pm}15.6s$) for 2-phenoxyethanol, 300 ppm (induction $127.3{\pm}13.3s$, recovery $107.5{\pm}4.8s$) for lidocaine-HCl and 200/100 ppm (induction $81.2{\pm}17.2s$, recovery $98.3{\pm}19.7s$) for lidocaine-$HCl/NaHCO_3$. Thus, 200/100 ppm of lidocaine-$HCl/NaHCO_3$ was found to be an effective anesthetic agent.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.43 no.5
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• pp.462-473
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• 2010

Inductions of hybrids and reciprocal hybrids between Oryzias dancena and O. javanicus (ODJ and OJD) were conducted and backcross hybrids between female O. dancena and male ODJ were also produced for biological and cytogenetic analysis. Embryonic development of ODJ and OJD were compared with those of their parents. Developmental time was fastest in O. dancena and ODJ, followed by O. javanicus and OJD. Oryzias dancena hatched 11 days (d) after fertilization, ODJ at 13 d, O. javanicus at 14 d and OJD at 15 d. The abnormality of external morphology rate in ODJ was 10.6%; however, OJD showed a high degree of abnormality, over 90%. The proportion of males was 90.0% and 31.3% for ODJ and OJD, respectively. Cytogenetic analysis was conducted to obtain basic information for genetic identification of O. dancena, O. javanicus and their hybrids. The karyotypes of all experimental groups showed 2n=48 chromosomes and the fundamental number (FN) was 48. The first pair carried secondary constrictions near the centromeric regions. Erythrocyte area and volume were $9.8\;{\pm}\;0.5\;{\mu}m^2$ and $18.2\;{\pm}\;1.0\;{\mu}m^3$, respectively, for O. dancena, $8.3\;{\pm}\;0.5\;{\mu}m^2$ and $15.8\;{\pm}\;1.5\;{\mu}m^3$ in O. javanicus, and $18.3\;{\pm}\;0.5\;{\mu}m^2$ and $15.7\;{\pm}\;1.3\;{\mu}m^3$ in ODJ. Erythrocyte area and volume in ODJ were similar to those of O. javanicus. In backcross hybrids between female O. dancena and male ODJ, all embryos failed to develop and died in the late gastrula stage.

• Journal of Aquaculture
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• v.19 no.3
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• pp.157-165
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• 2006

Expression of major antioxidant enzyme (AOE) including Cu/Zn superoxide dismutase (Cu/Zn-SOD), catalase (CAT), glutathione-S-transferase (GST) and 3 glutathione peroxidase isotypes (GPXs) at mRNA levels during heat stress was examined in mud loach (Misgurnus mizolepis) liver. Based on the semi-quantitative RT-PCR, real-time RT-PCR and/or northern dot blot hybridization, the antioxidant enzyme genes were generally up-regulated during elevation of water temperature from $23^{\circ}C$ up to $32^{\circ}C$. GPXs and SOD displayed the most significant elevation of mRNA levels (up to 3 and 2 folds, respectively) while CAT showed the steady-state expression irrespective of thermal conditions. GST represented the relatively moderate response (1.3-fold increase) in its transcription to thermal stress. The transcriptional activation of AOE genes was not significant at the treatment temperature lower than $29^{\circ}C$. Increased mRNA levels of GPX (extracellular form) and SOD genes in the fish exposed to $32^{\circ}C$ was readily detectable 1 day after exposure to heat stress.

• Korean Journal of Agricultural Science
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• v.49 no.4
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• pp.795-807
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• 2022

The development and commercialization of industrial genetically modified (GM) organisms is actively progressing worldwide, highlighting an increased need for improved safety management protocols. We sought to establish an environmental monitoring method, using real-time polymerase chain reaction (PCR) and propidium monoazide (PMA) treatment to develop a quantitative detection protocol for living GM microorganisms. We developed a duplex TaqMan quantitative PCR (qPCR) assay to simultaneously detect the selectable antibiotic gene, ampicillin (AmpR), and the single-copy Escherichia coli taxon-specific gene, D-1-deoxyxylulose 5-phosphate synthase (dxs), using a direct cell suspension culture. We identified viable engineered E. coli cells by performing qPCR on PMA-treated cells. The theoretical cell density (true copy numbers) calculated from mean quantification cycle (Cq) values of PMA-qPCR showed a bias of 7.71% from the colony-forming unit (CFU), which was within ±25% of the acceptance criteria of the European Network of GMO Laboratories (ENGL). PMA-qPCR to detect AmpR and dxs was highly sensitive and was able to detect target genes from a 10,000-fold (10^-4) diluted cell suspension, with a limit of detection at 95% confidence (LOD_95%) of 134 viable E. coli cells. Compared to DNA-based qPCR methods, the cell suspension direct PMA-qPCR analysis provides reliable results and is a quick and accurate method to monitor living GM E. coli cells that can potentially be released into the environment.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2004.05a
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• pp.83-83
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• 2004