Seungshic Yum

University of California, Berkeley, Berkeley, MO, United States

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Publications (37)41.77 Total impact

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    Seonock Woo, Vianney Denis, Seungshic Yum
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    ABSTRACT: The Javanese medaka, Oryzias javanicus, is a fish highly adaptable to various environmental salinities. Here, we investigated the effects of the environmental pollutant bisphenol A (BPA; an endocrine disrupting chemical) on gene expression levels in this species acclimated to different salinities. Using cDNA microarrays, we detected the induction of differential expression of genes by BPA, and compared the transcriptional changes caused by chemical exposure at different salinities. There were marked transcriptional changes induced by BPA between treatments. While 533 genes were induced by a factor of more than two when O. javanicus was exposed to BPA in seawater, only 215 genes were induced in freshwater. Among those genes, only 78 were shared and changed significantly their expression in both seawater and freshwater. Those genes were mainly involved in cellular processes and signaling pathway. We then categorized by functional group genes specifically induced by BPA exposure in seawater or freshwater. Gene expression changes were further confirmed in O. javanicus exposed to various concentrations of BPA, using quantitative real-time reverse transcription PCR based on primer sets for 28 selected genes.
    Marine Drugs 01/2014; 12(2):983-98. · 3.98 Impact Factor
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    ABSTRACT: Polycyclic aromatic hydrocarbons (PAHs) are the most persistent organic pollutants in worldwide aquatic environments. The extensive isolation of genes responsive to PAH pollution in soft coral (Scleronephthya gracillimum) is described herein. Soft coral colonies were exposed to 100 μg/L of a standard mixture of PAHs. Gene candidates with transcript levels that changed in response to PAH exposure were identified by differential display polymerase chain reaction (DD-PCR). There were 37 types of candidate genes identified, of which 20 were upregulated in expression and 17 were downregulated. The functions of the genes identified included oxidative stress response, ribosomal structure maintenance, molecular chaperone activity, protein kinase activation and tumorigenesis, defense mechanisms, transcription, and other biological responses. mRNA quantification was carried out using real-time quantitative PCR in eight selected genes: cytosolic malate dehydrogenase, protein disulfide isomerase, ribosomal protein L6, ral guanine nucleotide dissociation stimulator-like 1, poly(ADP-ribose) polymerase 4, peptidylglycine α-hydroxylating monooxygenase, a disintegrin and metalloproteinase (ADAM) metallopeptidase protein, and eukaryotic initiation factor 4 gamma 3. Changes in transcript levels were consistent with DD-PCR results. The gene candidates isolated in this study were differentially expressed and therefore have potential as molecular biomarkers for understanding coral responses to environmental stressors.
    Environmental Science and Pollution Research 01/2014; 21(2):901-910. · 2.76 Impact Factor
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    ABSTRACT: Background: In this study, we investigated transcription and enzyme level responses of mussels Mytilus galloprovincialis exposed to hypoxic conditions. Genes for catalase (CAT), cytochrome P450, glutathione S-transferase (GST), metallothionein, superoxide dismutase (SOD), cytochrome c oxidase subunit 1 (COX-1), and NADH dehydrogenase subunit 2 were selected for study. Transcriptional changes were investigated in mussels exposed to hypoxia for 24 and 48 h and were compared to changes in control mussels maintained at normal oxygen levels. Activities of CAT, GST, and SOD enzymes, and lipid peroxidation (LPO) were also investigated in mussels following exposure to hypoxia for 24, 48, and 72 h. Results: Relative to the control group, the CAT activity decreased in all hypoxia treatments, while the activity of GST significantly increased in mussels exposed to hypoxia for 24 and 48 h, but decreased in those exposed for 72 h. The LPO levels were significantly higher in mussels in the 24-and 48-h hypoxia treatments than those in the control mussels, but there was no significant change in the SOD activities among all hypoxia treatments. Messenger RNA levels for the CAT, cytochrome P450, GST, metallothionein, and SOD genes were not significantly affected by hypoxic conditions for 48 h, but the expressions of the COX-1 and NADH dehydrogenase subunit 2 genes were significantly repressed in mussels in both the 24-and 48-h exposure treatments. Conclusions: These results demonstrate the transcriptional stability and changes among several genes related to oxidative stress under oxygen-depletion conditions in M. galloprovincialis and provide useful information about the modulation of antioxidant enzyme activities induced by hypoxia in a marine animal.
    Zoological studies 09/2013; 52:15. · 1.26 Impact Factor
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    ABSTRACT: Differential gene expression profiling was performed using cDNA microarray hybridization on the hepatic tissue of the marine medaka (Oryzias javanicus) after exposure to toxaphene, which is classified as a persistent organic pollutant. Ninety-seven differentially expressed candidate genes were identified; 40 were induced and 57 were repressed (P<0.05). The genes were assembled into 18 groups based mainly on the Eukaryotic Orthologous Groups classification. These isolated gene candidates were differentially expressed and therefore have great potential as molecular biomarkers for identifying environmental stressors and prognosis for the biological effects of the toxicant. Some of the genes were closely related to endocrine disruption, renal and cardiovascular disease, tumorigenesis, immune responses, and detoxification. Our results will allow future studies to assess the molecular mechanisms of toxaphene toxicity and to develop a systems biology approach to environmental stress biology.
    Molecular and Cellular Toxicology 06/2013; 9(2). · 0.72 Impact Factor
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    ABSTRACT: Differential gene expression profiling was carried out using cDNA microarray hybridization on hepatic tissue from marine medaka (Oryzias javanicus) after exposure to benzo[a]pyrene (BaP), a representative polycyclic aromatic hydrocarbon classified as a persistent organic pollutant. Forty-one differentially expressed candidate genes were identified; 18 were induced and 23 were repressed (P/0.05). The genes were assembled into 18 groups based mainly on the Eukaryotic Orthologous Groups classification. These differentially expressed gene candidates could have great potential as molecular biomarkers for identifying environmental stressors and prognosis for the biological effects of BaP. The candidate genes isolated in this study were grouped into endocrine disruption, cardiovascular disease, tumorigenesis, immune response, detoxification, energy production and conversion, and other biological responses. Our results could allow future studies to assess the molecular mechanisms of BaP toxicity and to develop a systems biology approach to environmental stress biology.
    Toxicology and Environmental Health Sciences. 01/2013; 5(3).
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    ABSTRACT: Countless species occur in the marine microalgal domain. Some are used as health functional foods or medical products but many species are harmful such as those that cause the red tide. Therefore, it is necessary to conduct prompt and accurate identification of microalgal species. As it is quite difficult to accurately distinguish all species in terms of morphology, we performed DNA barcoding analysis using molecular markers for more accurate and rapid screening. DNA barcoding analysis, i.e., DNA chip technology, is a powerful method for studies on microalgal taxonomy and biodiversity. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) as a barcoding gene to identify microalgal species. In this study, the diversity and phylogenetic differences among different microalgae were analyzed. Additionally, a microalgal species-specific probe was screened by 21–23 bp and the result was printed on silylated slide for use in a robotic microarrayer. As a result, we performed a DNA chip assay for each of 25 microalgal species and determined that the COI barcode gene was suitable as a marker gene, as it could identify various microalgae from the Korean South Sea by species.
    BioChip journal 12/2012; 6(4). · 0.82 Impact Factor
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    ABSTRACT: Differential gene expression profiling was performed by heterologous hybridization using a medaka cDNA microarray on the hepatic tissue of the marine medaka (Oryzias javanicus) after exposure to Arochlor 1260, a polychlorinated biphenyl (PCB), which is classified as a persistent organic pollutant. Twenty-eight differentially expressed candidate genes were identified; one was induced and 27 were repressed (P<0.01). The genes were assembled into 10 groups based mainly on the Eukaryotic Othologous Groups classification. These isolated gene candidates were differentially expressed and therefore have great potential as molecular biomarkers for identifying environmental stressors. The results obtained in this study will allow future studies to assess the molecular mechanisms of Arochlor 1260 toxicity and to develop a systems biology approach to PCB stress biology.
    Toxicology and Environmental Health Sciences. 06/2012; 4(2).
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    ABSTRACT: We evaluated toxaphene-induced acute toxicity in Hydra magnipapillata. The median lethal concentrations of the animals (LC(50)) were determined to be 34.5 mg/L, 25.0 mg/L and 12.0 mg/L after exposure to toxaphene for 24 h, 48 h and 72 h, respectively. Morphological responses of hydra polyps to a range of toxaphene concentrations suggested that toxaphene negatively affects the nervous system of H. magnipapillata. We used real-time quantitative PCR of RNA extracted from polyps exposed to two concentrations of toxaphene (0.3 mg/L and 3 mg/L) for 24 h to evaluate the differential regulation of levels of transcripts that encode six antioxidant enzymes (CAT, G6PD, GPx, GR, GST and SOD), two proteins involved in detoxification and molecular stress responses (CYP1A and UB), and two proteins involved in neurotransmission and nerve cell differentiation (AChE and Hym-355). Of the genes involved in antioxidant responses, the most striking changes were observed for transcripts that encode GPx, G6PD, SOD, CAT and GST, with no evident change in levels of transcripts encoding GR. Levels of UB and CYP1A transcripts increased in a dose-dependent manner following exposure to toxaphene. Given that toxaphene-induced neurotoxicity was not reflected in the level of AChE transcripts and only slight accumulation of Hym-355 transcript was observed only at the higher of the two doses of toxaphene tested, there remains a need to identify transcriptional biomarkers for toxaphene-mediated neurotoxicity in H. magnipapillata. Transcripts that respond to toxaphene exposure could be valuable biomarkers for stress levels in H. magnipapillata and may be useful for monitoring the pollution of aquatic environments.
    Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology 04/2012; 156(1):37-41. · 2.71 Impact Factor
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    ABSTRACT: Hypoxic events affecting aquatic environments have been reported worldwide and the hypoxia caused by eutrophication is considered one of the serious threats to coastal marine ecosystems. To investigate the molecular-level responses of marine organisms exposed to oxygen depletion stress and to explore the differentially expressed genes induced or repressed by hypoxia, differential display polymerase chain reaction (DD-PCR) was used with mRNAs from the marine mussel, Mytilus galloprovincialis, under oxygen depletion and normal oxygen conditions. In total, 107 cDNA clones were differentially expressed under hypoxic conditions relative to the control mussel group. The differentially expressed genes were analyzed to determine the effects of hypoxia. They were classified into five functional categories: information storage and processing, cellular processes and signaling, metabolism, predicted general function only, and function unknown. The differentially expressed genes were predominantly associated with cellular processing and signaling, and they were particularly related to the signal transduction mechanism, posttranslational modification, and chaperone functions. The observed differences in the DD-PCR of 10 genes (encoding elongation factor 1 alpha, heat shock protein 90, calcium/calmodulin-dependent protein kinase II, GTPase-activating protein, 18S ribosomal RNA, cytochrome oxidase subunit 1, ATP synthase, chitinase, phosphoglycerate/bisphosphoglycerate mutase family protein, and the nicotinic acetylcholine receptor) were confirmed by quantitative RT-PCR and their transcriptional changes in the mussels exposed to hypoxic conditions for 24-72 h were investigated. These results identify biomarker genes for hypoxic stress and provide molecular-level information about the effects of oxygen depletion on marine bivalves.
    Comparative Biochemistry and Physiology Part D Genomics and Proteomics 07/2011; 6(4):348-56. · 2.88 Impact Factor
  • Seonock Woo, Seungshic Yum
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    ABSTRACT: Differential gene expression profiles were established from the head and liver tissues of the marine medaka fish (Oryzias javanicus) after its exposure to toxaphene, a persistent organic pollutant and insecticide, using differential display polymerase chain reaction. Twenty-seven differentially expressed genes were identified, which were associated with the cytoskeleton, development, metabolism, nucleic acid/protein binding, and signal transduction. Among these genes, those encoding molecular biomarkers known to be involved in metabolism, ATP hydrolysis, and protein regulation were strongly induced at the transcription level, and genes encoding one structural protein subunit or involved in lipid metabolism were strongly downregulated. The same trends in gene expression changes were observed with real-time PCR analysis of 12 selected clones. The genes identified could be used as molecular biomarkers of biological responses to polychlorinated camphene contamination in aquatic environments.
    Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology 04/2011; 153(3):355-61. · 2.71 Impact Factor
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    Hyokyoung Won, Seungshic Yum, Seonock Woo
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    ABSTRACT: The construction of a subtractive cDNA library of organisms and the analysis thereof have proven meaningful in the search for clones whose expressions are regulated by exterior changes. The principal objective of this study was to identify the differentially expressed genes of marine medaka fish (Oryzias javanicus) under benzo[a]pyrene exposure conditions. Medaka fish were exposed to 100 μg/L of benzo[a]pyrene for 24 hr and its hepatic RNA was extracted; RNA from the livers of non-exposed medaka fish was also extracted. Both RNAs were employed in the construction of the subtractive cDNA library and the nucleotide sequences of differentially expressed clones were analyzed. Twenty-eight genes of the total differentially expressed clones were considered significant; in particular, the transcription of the cytochrome P450 1A gene was upregulated in a dose-dependent manner under various benzo[a]pyrene concentration exposure conditions. The 28 genes were then divided into 4 categories: (1) information storage and processing, (2) cellular processes and signaling, (3) metabolism, and (4) poorly characterized. The data reported herein provide general information regarding the effects of benzo[a]pyrene contamination on marine organisms, and constitute a primary step in the development of novel biomarkers for marine environmental pollution. KeywordsMarine medaka– Oryzias javanicus –Benzo[a]pyrene–Subtractive cDNA library–Differentially expressed genes
    01/2011; 3(1):39-45.
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    ABSTRACT: Java medaka (Oryzias javanicus) cDNA array was constructed and the microarray platform was used to compare the hepatic expression profiles of Java medaka fish exposed to 17β-estradiol with those of unexposed controls. Data analysis demonstrated that the expression profiles were strongly affected by 17β-estradiol exposure, with 655 genes up- or downregulated after 24 h, and 633 genes after 48 h. The differentially expressed genes were analyzed to determine the effects of 17β-estradiol exposure on the liver tissue and were classified into five functional categories: information storage and processing, cellular processes and signaling, metabolism, general function prediction only, and function unknown. Genes whose expression was upregulated more than 10-fold were predominantly associated with energy production/conversion and reproduction, and 30% of the genes whose expression was downregulated more than 10-fold were associated with carbohydrate transport and metabolism. The observed differences in the expression profiles of 7 genes (encoding apolipoprotein B, cytochrome P450 1A, glucose-6-phosphate dehydrogenase, glutamate dehydrogenase 1b, vitellogenin, selenoprotein M, and transferrin) were confirmed by quantitative RT-PCR, and their transcriptional changes in the livers of Java medaka induced by exposure to 10, 100, and 1,000 μg/L 17β-estradiol were investigated. These results should allow the development of biomarkers for the identification of 17β-estradiol contamination in the environment and provide molecular biological information on the effects of endocrine-disrupting chemical exposure on marine animals. Keywords Oryzias javanicus –Microarray–17β-estradiol–Gene expression–Gene ontology
    Molecular and Cellular Toxicology 01/2011; 7(3):271-281. · 0.72 Impact Factor
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    ABSTRACT: Genes involved in defense mechanisms can be used as efficient biomarkers of physiological changes in organisms caused by both endogenous and exogenous stress. Thus, the expression levels of such genes serve as a critical ‘early warning system’ for the environmental assessment and health of biological organisms. In this study, the transcription levels of Hsp70 and vBPO in Undaria pinnatifida sporophytes were quantitatively compared between two distinct natural populations collected from uncontaminated Mijo (Namhae, Korea) and industrially-polluted Myodo Is. (Yeosu, Korea) in order to verify their potential as biomarker genes and the applicability of this macroalga for assessing the health status of a local marine ecosystem. The results found that the two tested genes were highly expressed in the Myodo population. The results suggest that U. pinnatifida itself and the selected two genes could be applicable to monitoring of marine environments in coastal regions. Keywords Undaria pinnatifida –Brown alga–Differential gene expression– UpiHsp70 – UpivBPO –Real-time quantitative PCR
    01/2011; 3(2):91-96.
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    ABSTRACT: Benzo[k]fluoranthene (B[k]F) is one of numerous polycyclic aromatic hydrocarbons (PAHs) which is a persistent environmental contaminant in air and water. Upon B[k]F exposure, differential gene expression profiling was conducted in marine medaka fish (Oryzias javanicus) using subtractive hybridization. As a result, forty two differentially expressed candidate genes were induced in B[k]F-exposed fish as compared to control group, and the genes were associated with general metabolism, signal transduction, cell cycle, immune response, cytoskeleton, development, nucleotide/protein binding and some were non-categorized. These identified gene candidates have great potential to be developed as biomarkers for the identification of effects of B[k]F exposure in the environment. The results obtained in this study will offer insight to the physiological change induced by B[k]F exposure and will help assess the molecular mechanisms of B[k]F toxicity. Keywords Oryzias javanicus –Marine medaka–Benzo[k]fluoranthene–Differential gene expression
    01/2010; 2(4):231-237.
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    ABSTRACT: Differential gene expression profiling was performed in the hepatic tissue of marine medaka fish (Oryzias javanicus) after exposure to an organophosphorous pesticide (OPP), Iprobenfos (IBP), a widely used pesticide in agri- and fish-culture, by heterologous hybridization using a medaka cDNA microarray. Fifty differentially expressed candidate genes, of which 10 induced and 40 repressed (P<0.01), were identified. The genes were assembled into 19 groups mainly based on Eukaryotic Othologous Groups (KOG) classification. These isolated gene candidates were differentially expressed and therefore have great potential as molecular biomarkers for the identification of environmental stressors. The results obtained in this study will allow future studies to assess the molecular mechanisms of IBP toxicity and the development of a systems biology approach to the stress biology of organophosphorous pesticide. KeywordsMarine medaka– Oryzias javanicus –Heterologous hybridization–Organophosphorus pesticide–Iprobenfos (IBP)–Differential gene expression profile
    01/2010; 2(1):18-24.
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    ABSTRACT: Differential gene expression profiling was performed in the hepatic tissue of marine medaka fish (Oryzias javanicus) after exposure to benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon (PAH), by heterologous hybridization using a medaka cDNA microarray. Thirty-eight differentially expressed candidate genes, of which 23 were induced and 15 repressed (P⁄0.01), were identified and found to be associated with cell cycle, development, endocrine/reproduction, immune, metabolism, nucleic acid/protein binding, signal transduction, or non-categorized. The presumptive physiological changes induced by BaP exposure were identified after considering the biological function of each gene candidate. The results obtained in this study will allow future studies to assess the molecular mechanisms of BaP toxicity and the development of a systems biology approach to the stress biology of organic chemicals.
    Molecular and Cellular Toxicology 12/2009; 5(4):283-290. · 0.72 Impact Factor
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    ABSTRACT: Concentrations of industrial, agricultural and natural chemicals have been increasing in secondary effluents without their combined sub-lethal effects having been elucidated. In this study, two assays (the comet and acetylcholinesterase assays) were combined to evaluate the genotoxic and neurotoxic effects of effluent from the Noksan wastewater treatment plant (WWTP) on two local marine fish species (flounder and sea eel). The fish were exposed to WWTP secondary effluent that had been diluted with filtered seawater to final concentrations of 1%, 10% and 50%. Analysis of fish samples collected 3 and 5 days after exposure showed that DNA damage occurred in flounder exposed to 50% effluent and in sea eels exposed to 10% or 50% effluent. Furthermore, it was found that acetylcholinesterase (EC:3.1.1.7, AChE) activity decreased in both species when exposed to 10% effluent, indicating the presence of large amounts of genotoxic and neurotoxic chemicals in the effluent. Our results indicate that the comet and AChE assays are promising tools for biomonitoring of secondary effluents.
    Molecular and Cellular Toxicology 10/2009; 5(3):265-271. · 0.72 Impact Factor

Publication Stats

150 Citations
41.77 Total Impact Points

Institutions

  • 2010
    • University of California, Berkeley
      • Department of Nutritional Science and Toxicology
      Berkeley, MO, United States
  • 2009
    • Korean Institute of Ocean Science and Technology
      • South Sea Environment Research
      Ansan, Gyeonggi, South Korea