PubMed | Kunsan National University and National Institute of Fisheries Science
Type: Journal Article | Journal: Marine drugs | Year: 2016
Antimicrobial peptides are a pivotal component of the invertebrate innate immune system. In this study, we identified a lipopolysaccharide- and -1,3-glucan-binding protein (LGBP) gene from the pacific abalone
PubMed | Chonnam National University, National Institute of Fisheries Science and Gangneung - Wonju National University
Type: | Journal: Parasitology research | Year: 2016
We developed a PCR assay targeting the 28S rDNA of Kudoa iwatai (Multivalvulida: Myxozoa) and investigated the prevalence of infection in rock bream Oplegnathus fasciatus, which is commercially an important aquaculture species in Korea, with this assay. Detection limit of the PCR assay was 2.5fg/l with plasmid DNA and 8.610
Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction
PubMed | Chonnam National University, Asian Institute of Technology, University of Queensland, Korea Research Institute of Bioscience and Biotechnology and 4 more.
Type: Journal Article | Journal: International journal of molecular sciences | Year: 2016
The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the worlds most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.
PubMed | Korea Marine Environment Management Corporation and National Institute of Fisheries Science
Type: Journal Article | Journal: Marine pollution bulletin | Year: 2016
Spatial distributions and temporal variations of trace metals in Korean coastal sediments were investigated by determining seven metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediment collected from 71 stations between 2004 and 2010 (n=491). High metal concentrations were found in the southeastern coast, where there are many cities and industrial complexes, indicating that metal concentrations in Korean coastal sediment are significantly influenced by human activities associated with urbanization and industrialization. However, metal concentrations in sediment did not markedly vary temporally, which was because the coast is managed sustainably and because of the characteristics of the sediment environments. Based on the sediment quality guidelines and geoaccumulation index, Korean coastal sediments are practically unpolluted with Cd, Cr, Cu, Hg, Pb and Zn but moderately polluted with As. More intensive monitoring is required to determine the potential As sources and to understand the As geochemical cycles in Korean coastal sediments.
PubMed | University of Jaffna, Insilicogen Inc., Marine Life Research, Nihon University and National Institute of Fisheries Science
Type: | Journal: Developmental and comparative immunology | Year: 2017
A -galactoside binding lectin, designated as galectin-2, was identified and characterized from rock bream Oplegnathus fasciatus (OfGal-2). The cDNA of OfGal-2 comprised of 692 bp with a coding sequence of 396 bp, encoding a putative polypeptide of 131 amino acids. Gene structure analysis of OfGal-2 revealed a four exon-three intron organization. A single carbohydrate-binding domain containing all seven important residues for carbohydrate binding was located in the third exon, which formed a carbohydrate-binding pocket. Homology screening and sequence analysis demonstrated that OfGal-2 is an evolutionarily conserved proto-type galectin. OfGal-2 transcripts were detected in several healthy fish tissues, with the highest level observed in the intestine, followed by the liver. The expression of OfGal-2 was elevated upon the injection of various mitogenic stimulants and pathogens in a time-dependent manner. Upregulated expression in the liver after tissue injury suggested its role as a damage-associated molecular pattern. Recombinant OfGal-2 protein had hemagglutinating potential and possessed affinity towards lactose and galactose. Moreover, the recombinant protein agglutinated and bound potential pathogenic bacteria and a ciliate. The results of this study indicate that the galectin-2 from rock bream has a potential role in immunity, particularly in the recognition of invading pathogens.
PubMed | Japan National Research Institute of Fisheries Science, Marine Life Research and National Institute of Fisheries Science
Type: | Journal: Comparative biochemistry and physiology. Toxicology & pharmacology : CBP | Year: 2016
Glutathione S-transferases (GSTs, EC 126.96.36.199) are categorized as phase II enzymes, which form an important multifunctional family associated with a wide variety of catalytic activities. GST, GST, and GST are cytosolic GSTs which have been extensively studied in a variety of organisms; however, few studies have focused on teleosts. Those paralogs from black rockfish (Sebastes schlegelii; RfGST, RfGST, and RfGST, respectively) were molecularly, biochemically, and functionally characterized to determine their antioxidant extent and protective aptitudes upon pathogenic stress. RfGST, RfGST, and RfGST, contained open reading frames of 717bp, 678bp, and 720bp respectively, which encoded respective proteins of 239, 226, and 240 amino acids in length. In silico analysis revealed that all RfGSTs possessed characteristic N-terminal domains bearing glutathione (GSH)-binding sites, and C-terminal domains containing substrate-binding sites. Recombinant RfGST (rRfGST) catalyzed the conjugation of GSH to dehydroascorbate (DHA), while rRfGST and rRfGST catalyzed to the model GST substrate 1-Chloro-2,4-dinitrobenzene (CDNB). Kinetic analysis revealed variation in Km and Vmax values for each rRfGST, indicating their different conjugation rates. The optimum conditions (pH and temperature) and inhibition assays of each protein demonstrated different optimal ranges showing their wide range of activity as an assembly. RfGST and RfGST paralogs demonstrated their antioxidant potential towards H2O2 and heavy metals (Cd, Zn, and Cu) in vitro, while RfGST had an antioxidant potential only towards heavy metals (Zn and Cu). Though all the paralogs were ubiquitously expressed in different magnitudes, RfGST was highly expressed in blood, whereas RfGST and RfGST were highly expressed in liver. The mRNA expression of RfGST and RfGST, upon Streptococcus iniae and poly I:C stimulation, revealed a significantly up-regulated expression, whereas RfGST mRNA expression was significantly down-regulated. Collectively, our findings suggest that RfGST, RfGST, and RfGST paralogs are potent in detoxifying xenobiotic toxics, capable of protecting cells from oxidative stress generated by both H2O2 and heavy metals, and finally, yet importantly, stimulated under pathogenic stress signals.
Hwang D.-W.,National Institute of Fisheries Science |
Lee I.-S.,National Institute of Fisheries Science |
Choi M.,National Institute of Fisheries Science |
Kim T.-H.,Jeju National University
Marine Pollution Bulletin | Year: 2016
In order to evaluate the main source of nutrients for maintaining the high production in shellfish farming bay, we have measured 222Rn activities and the concentrations of nutrients in stream water, seawater, and coastal groundwater around Geoje Bay, one of the largest cultivation areas of oyster in the southern sea of Korea in April 2013. Using the 222Rn and Si mass balance model, the residence time of bay seawater was about 5 days and the submarine groundwater discharge (SGD) into the bay was estimated to be approximately 1.8 × 106 m3 d− 1. The SGD-derived nutrient fluxes contributed approximately 54% for DIN, 5% for DIP, and 50% for DSi of total nutrient input entering into the bay. Thus, our results suggest that SGD is the major source of nutrients in Geoje Bay, and SGD-derived nutrients are very important to support the biological production of this shellfish farming bay. © 2016 Elsevier Ltd
PubMed | Jeju National University, Marine Life Research and National Institute of Fisheries Science
Type: | Journal: Fish & shellfish immunology | Year: 2016
Thioredoxin domain-containing protein 12 (TXNDC12) is a small, disulfide-containing protein that belongs to the thioredoxin (TXN) superfamily. In the present study, we identified and characterized a TXNDC12-like gene, designated OfTXNDC12, from rock bream, Oplegnathus fasciatus. OfTXNDC12 consists of seven exons interrupted by six introns. Comparative genomic structural analysis revealed that the TXNDC12 of vertebrates is a structurally conserved gene. The coding sequence of OfTXNDC12 comprises 522 bp, which encodes 173amino acid residues with the conserved thioredoxin active site motif, CGAC, and a probable C-terminal ER retrieval motif, GDEL. Transcriptional analysis of OfTXNDC12 showed the highest concentrations of the mRNA transcript in the liver, implying that it has a significant role in the liver under normal physiological conditions. In comparison, injection of lipopolysaccharide, Edwardsiella tarda, Streptococcus iniae, polyinosinic:polycytidylic acid (poly[I:C]) and rock bream iridovirus mostly triggered greater upregulation of OfTXNDC12 transcript levels in liver than in gill tissue, supporting its potential functional importance in the liver. Insulin disulfide reduction assay showed that the recombinant fusion protein (rOfTXNDC12) possesses significant thioredoxin activity. Treatment of LNCaP cells with the recombinant protein along with H2O2 revealed that rOfTXNDC12 increased the viability of cells and further supported its putative antioxidant capacity. Taken together, the results from our study suggest that OfTXNDC12 encodes for a potent antioxidant involved in redox regulation that shows significant responses to immune stimuli.
PubMed | Jeju National University and National Institute of Fisheries Science
Type: | Journal: Fish & shellfish immunology | Year: 2016
In this study, we describe the identification and characterization of a proto type galectin, galectin-1, from rock bream Oplegnathus fasciatus (OfGal-1). Galectins are evolutionarily conserved carbohydrate binding lectins that show a wide range of functions related to development and immune physiology. They have been identified as pattern recognition receptors of innate immune system that recognize a broad range of microbes. OfGal-1 cDNA comprised of 993 bp with an open reading frame of 408 bp that encodes 135 amino acids. A single carbohydrate recognition domain was present in the OfGal-1 amino acid sequence. The sequence comparison by multiple and pairwise alignments and the phylogenetic tree emphasized the strong evolutionary conservation of Gal-1. The typical -sandwich structure was identified from the predicted tertiary structure. The constitutive expression of mRNA transcripts was detected in a wide range of tissues examined, with the highest expression in the heart. Immune challenges with live bacteria (Edwardsiella tarda and Streptococcus iniae), rock bream irido virus, and mitogens (lipopolysaccharide and poly I:C) modulated the expression of OfGal-1 mRNAs in the gills, head kidney, and liver. The recombinant OfGal-1 (rOfGal-1) strongly agglutinatinated the human erythrocytes, and this hemagglutination was inhibited by lactose and D-galactose. A wide range of bacteria (S. iniae, S. parauberis, Escherichia coli, Edwardsiella tarda, Vibrio anguillarum, Vibrio harveyi, and Vibrio tapetis) and a ciliate (Miamiensis avidus) were also effectively recognized by rOfGal-1. Significant antiviral activity against rock bream irido virus was also demonstrated by rOfGal-1. Collectively, results from the present study indicate that OfGal-1 can recognize a wide range of microbes and is a vital pattern recognition receptor in the innate immune system of rock bream.
Lee J.,National Institute of Fisheries Science
Fisheries and Aquatic Science | Year: 2015
Postprandial ammonia excretion and oxygen consumption in olive flounder Paralichthys olivaceus fed two different feed types, moist pellet (MP) and expanded pellet (EP) diets, to satiation were determined at 12°C, 15°C, 20°C, and 25°C for 48 h. The ammonia excretion and oxygen consumption rates increased with increasing water temperature. However, the postprandial times for the maximum rates of ammonia excretion and oxygen consumption were shortened from 12 h to 6 h after feeding with increasing water temperature. The ammonia excretion and oxygen consumption rates of fish fed EP were significantly higher (P < 0.05) than those fed MP at 12 h post-feeding both for 12°C and 15°C. The highest (P < 0.05) weight-specific ammonia excretion rates at 12°C were observed in fish fed EP and MP at 12.1 mg NH3-N kg-1h-1 and 8.7 mg NH3-N kg-1h-1, respectively, for 12 h and 9 h after feeding. The highest (P < 0.05) weight-specific oxygen consumption rates at 12°C were observed in fish fed EP and MP at 116.4 mg kg-1h-1 and 101.0 mg kg-1h-1, respectively, for 12 h after feeding. The highest ammonia excretion rates at 25°C in fish fed EP and MP increased to 16.9 mg NH3-N kg-1h-1 and 18.3 mg NH3-N kg-1h-1, respectively, for 6 h after feeding. The highest (P < 0.05) weight-specific oxygen consumption rates at 25°C were observed in fish fed EP and MP at 184.3 mg O2 kg-1h-1 and 197.3 mg O2 kg-1h-1, respectively. These data are extremely valuable for the design of biofilters and development of effluent treatment technologies for land-based flounder farms. © 2015 The Korean Society of Fisheries and Aquatic Science.