Function Laboratory for Marine Fisheries Science and Food Production Processes
Function Laboratory for Marine Fisheries Science and Food Production Processes
Ren J.S.,NIWA - National Institute of Water and Atmospheric Research |
Stenton-Dozey J.,NIWA - National Institute of Water and Atmospheric Research |
Zhang J.,Chinese Academy of Fishery Sciences |
Zhang J.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Aquaculture Environment Interactions | Year: 2017
The sea cucumber Apostichopus japonicus is an important aquaculture species in China. As global interest in sustainable aquaculture grows, the species has increasingly been used for co-culture in integrated multitrophic aquaculture (IMTA). To provide a basis for opti - mising stocking density in IMTA systems, we parameterised and validated a standard dynamic energy budget (DEB) model for the sea cucumber. The covariation method was used to estimate parameters of the model with the DEBtool package. The method is based on minimisation of the weighted sum of squared deviation for datasets and model predictions in one single-step pro - cedure. Implementation of the package requires meaningful initial values of parameters, which were estimated using non-linear regression. Parameterisation of the model suggested that the accuracy of the lower (TL) and upper (TH) boundaries of tolerance temperatures are particularly important, as these would trigger the unique behaviour of the sea cucumber for hibernation and aestivation. After parameterisation, the model was validated with datasets from a shellfish aquaculture environment in which sea cucumbers were co-cultured with the scallop Chlamys farreri and Pacific oyster Crassostrea gigas at various combinations of density. The model was also applied to a land-based pond culture environment where the sea cucumber underwent a fast growth period in spring and non-growth periods during winter hibernation and summer aesti - vation. Application of the model to datasets showed that the model is capable of simulating the physiological behaviour of the sea cucumber and responds adequately to the wide range of environmental and culture conditions. © The authors 2017.
Zhong Y.,Ocean University of China |
Fei C.,Ocean University of China |
Tang X.,Ocean University of China |
Zhan W.,Ocean University of China |
And 2 more authors.
Journal of General Virology | Year: 2017
The 27.8 kDa protein in flounder gill (FG) cells was previously proved to be a receptor specific for lymphocystis disease virus (LCDV) entry and infection. In this paper, a 32 kDa viral attachment protein (VAP) of LCDV specifically binding to the 27.8 kDa receptor (27.8R) was found by far-Western blotting coupled with monoclonal antibodies (MAbs) against 27.8R. The 32 kDa protein was confirmed to be encoded by the open reading frame (ORF) 038 gene in LCDV-C, and predicted to contain a putative transmembrane region, multiple N-myristoylation and glycosylation sites and phosphorylation motifs. The expression plasmid of pET-32a-ORF038 was constructed and the recombinant VAP (rVAP) was obtained. Rabbit polyclonal antibodies against the rVAP were prepared and could recognize the rVAP and 32 kDa protein in LCDV. Immunogold electron microscopy showed that the 32 kDa protein was located on the surface of LCDV particles. Immunofluorescence assay demonstrated that the rVAP could bind to the 27.8R on the cell membrane of the FG monolayer and the anti-27.8R MAbs could block the rVAP binding. Pre-incubation of the rVAP with FG cells before LCDV infection, or pre-incubation of LCDV with the antibodies against the rVAP, could significantly decrease the LCDV copy numbers (P<0.05) and delay the emergence of cytopathic effects in FG cells in a dose-dependent manner. These results indicated for the first time that the 32 kDa protein functioned as an attachment protein for the initial attachment and entry of LCDV, and the interaction of the 32 kDa VAP with the 27.8R-initiated LCDV infection. © 2017 The Authors.
Yang X.-L.,Ocean University of China |
Yang C.-J.,Ocean University of China |
Hu C.-Y.,Ocean University of China |
Zhang X.-M.,Ocean University of China |
Zhang X.-M.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Chinese Journal of Applied Ecology | Year: 2017
The relationship between the distribution of halobios and environmental variables has been a focus of present research in marine ecology. Species distribution models (SDMs) have been widely employed to predict the distribution patterns and potential habitat suitability assessments of marine species and provide an efficient approach for marine biodiversity conservation, invasive species prevention, and fishery management. SDMs mainly include habitat suitability index models, mechanism models, and statistical models. In this paper, the theoretical basis of SDMs was firstly concluded and summarized. Next, the exploitation and case-studies of SDMs, especially the statistical models, for predicting potential distribution of marine species were reviewed. Then, comparisons of various methods for variable selection and model validation were made. Conclusions could be drawn that Akaike information criterion showed excellent performance when it came to variable selection, while Kappa coefficient and Area Under receiver operating character Curve (AUC) were widely used in relation to model validation. Finally, problems and prospects of SDMs were discussed. With the development of research on physiological characteristics, using mechanism models to predict potential habitats of halobios would become a trend. © 2017, Science Press. All right reserved.
Teng L.,Chinese Academy of Fishery Sciences |
Fan X.,Chinese Academy of Fishery Sciences |
Xu D.,Chinese Academy of Fishery Sciences |
Zhang X.,Chinese Academy of Fishery Sciences |
And 3 more authors.
Frontiers in Plant Science | Year: 2017
Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS). About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to formsome of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins) involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches. © 2017 Teng, Fan, Xu, Zhang, Mock and Ye.
Shao C.,Chinese Academy of Fishery Sciences |
Shao C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Shao C.,Tokyo University of Marine Science and Technology |
Niu Y.,BGI Shenzhen |
And 14 more authors.
DNA Research | Year: 2015
High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
Shan X.,Chinese Academy of Fishery Sciences |
Shan X.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Quan H.,Fisheries Institute of Mindong |
Dou S.,CAS Qingdao Institute of Oceanology
Fish Physiology and Biochemistry | Year: 2015
A histological method was used to describe the ontogenetic development of the digestive tract of laboratory-reared miiuy croaker (Miichthys miiuy) and to evaluate the effects of short-term food deprivation on the morphology and histology of the digestive tract. Larvae and juveniles were maintained at 24 °C in a thermostatically controlled system. Three starvation experiments were conducted during different developmental stages: 1–7 days after hatching (dah; prior to benthic swimming); 26–35 dah (during settling); and 42–53 dah (after benthic swimming). According to the structural changes in the ontogenetic development of the digestive tract, three stages were observed. The first stage was from hatching to 3 dah; the digestive tract was undifferentiated in newly hatched larvae and then showed remarkable morphological changes and differentiation. During this period, larvae depended on endogenous nutrition. The second stage (4–20 dah) was a critical period in which larvae transitioned from endogenous feeding to exogenous feeding and the digestive tract fully differentiated into the buccopharynx, oesophagus, stomach, anterior intestine and posterior intestine. Goblet cells and vacuoles appeared in the digestive tract, and pharyngeal teeth and taste buds developed. During the third stage (20–36 dah), the gastric glands developed and the stomach differentiated into the fundic, cardiac and pyloric regions. At 25 dah, pyloric caeca developed and mucosal folds and spiral valves were clearly distinguishable. After 30 dah, the digestive tract did not undergo any noticeable differentiation, indicating the complete development of the digestive system. The wet weight and SGR (specific growth rate) of miiuy croaker larvae and juveniles greatly decreased when they were deprived of food, and compensatory growth was observed in re-feeding juveniles. The livers of starved larvae and juveniles were atrophied and dark coloured, the intestines were transparent and thin, and the stomach cubages were reduced. The histological effects of starvation were mainly evident in the degeneration of cells in digestive organs, as seen in the shrinkage and separation of cells and the loss of intercellular substances in the liver, pancreas, intestine and stomach. These changes became more severe with increased duration of starvation. In addition, the histological structure of the digestive tracts of starved larvae and juveniles partly recovered after re-feeding, and the effects of starvation on miiuy croaker were age dependent. © 2015 Springer Science+Business Media Dordrecht
Bai C.,Chinese Academy of Fishery Sciences |
Bai C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Wang C.,Chinese Academy of Fishery Sciences |
Wang C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
And 5 more authors.
Journal of Invertebrate Pathology | Year: 2015
Viral infection caused by Ostreid herpesvirus 1 (OsHV-1) is one of the proximate causes of mass mortalities of cultivated bivalves around the world. The emergence and spread of different variants of OsHV-1 accompanied by different epidemiological characteristics have been reported frequently in different countries around the world. In this paper, we present a study of the detection of OsHV-1 DNA and their variations from 1599 samples over 18 species collected in 27 aquaculture sites and two food markets during 2001-2013 in China. All of the samples were examined by a nested PCR assay targeting the C2/C6 fragment of OsHV-1 followed by sequencing. Our results showed 338 individuals (21.1%) of seven species sampled from 14 (14/27 = 51.9%) sites and the two food markets were positive for viral DNA. Sequencing of 289 PCR products revealed 24 virus types. No shared virus type was found among different countries with 47 types (23 in Japan, 16 in France, 2 in South Korea and 1 in each country of Australia, USA, Ireland, New Zealand, Mexico and China) identified in previous studies. As previously reported, two main phylogenetic groups were identified by phylogenetic analysis based on the 71 virus types; within which 6 separate clades were identified. Our results also demonstrated that two clades were associated with abnormal mortalities of the scallop, Chlamys farrier and the calm, Scapharca broughtonii in China. These findings indicated that cultivated bivalves may face potential threats from OsHV-1 types found in our study. © 2014 Elsevier Inc.
Ren X.,Chinese Academy of Fishery Sciences |
Cui Y.,Chinese Academy of Fishery Sciences |
Gao B.,Chinese Academy of Fishery Sciences |
Liu P.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Li J.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Marine Genomics | Year: 2016
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate gene expression by post-transcriptional repression of mRNAs. The swimming crab Portunus trituberculatus is one of the most important crustacean species for aquaculture in China. However, to date no miRNAs have been reported to for modulating growth in P. trituberculatus. To investigate miRNAs involved in the growth of this species, we constructed six small RNA libraries for big individuals (BIs) and small individuals (SIs) from a highly inbred family. Six mixed RNA pools of five tissues (eyestalk, gill, heart, hepatopancreas, and muscle) were obtained. By aligning sequencing data with those for known miRNAs, a total of 404 miRNAs, including 339 known and 65 novel miRNAs, were identified from the six libraries. MiR-100 and miR-276a-3p were among the most prominent miRNA species. We identified seven differentially expressed miRNAs between the BIs and SIs, which were validated using real-time PCR. Preliminary analyzes of their putative target genes and GO and KEGG pathway analyzes showed that these differentially expressed miRNAs could play important roles in global transcriptional depression and cell differentiation of P. trituberculatus. This study reveals the first miRNA profile related to the body growth of P. trituberculatus, which would be particularly useful for crab breeding programs. © 2016 Elsevier B.V.
Duan Y.,CAS South China Sea Fisheries Research Institute |
Li J.,Chinese Academy of Fishery Sciences |
Li J.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Zhang Z.,CAS South China Sea Fisheries Research Institute |
And 2 more authors.
Fish and Shellfish Immunology | Year: 2016
ADP ribosylation factors (Arf), as highly conserved small guanosine triphosphate (GTP)-binding proteins, participates in intracellular trafficking and organelle structure. In this study, a full-length cDNA of Arf1 (designated EcArf1) was cloned from Exopalaemon carinicauda by using rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of EcArf1 was 1428 bp, which contains an open reading frame (ORF) of 549 bp, encoding a 182 amino-acid polypeptide with the predicted molecular weight of 20.69 kDa and estimated isoelectric point was 7.24. Sequence analysis revealed that the conserved Arf protein family signatures were identified in EcArf1. The deduced amino acid sequence of EcArf1 shared high identity (95%-98%) with that of other species and clustered together with Arf1 of other shrimp in the NJ phylogenetic tree, indicating that EcArf1 should be a member of the Arf1 family. Quantitative real-time RT-qPCR analysis indicated that EcArf1 was expressed in hemocytes, hepatopancreas, gills, muscle, ovary, intestine, stomach and heart, and the most abundant level was in hemocytes and gills, which were also the two main target tissues of pathogen infection and environmental stress. After Vibrio parahaemolyticus challenge, EcArf1 transcripts level significantly increased in hemocytes and hepatopancreas at 3 h and 6 h, respectively. The expression of EcArf1 in hemocytes and hepatopancreas significantly up-regulated at 12 h and 6 h respectively, and down-regulated at 72 h and 48 h, respectively. EcArf1 expression in hepatopancreas and gills both significantly increased at 6 h and decreased at 24 h under ammonia-N stress. The results suggested that EcArf1 might be involved in immune responses to pathogens (V. parahaemolyticus and WSSV) challenge and ammonia-N stress in E. carinicauda. © 2016 Elsevier Ltd.
Wu R.-H.,Ocean University of China |
Tang X.-Q.,Ocean University of China |
Sheng X.-Z.,Ocean University of China |
Zhan W.-B.,Ocean University of China |
Zhan W.-B.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Journal of Comparative Pathology | Year: 2015
Lymphocystis disease virus (LCDV) enters and infects the gill cells of flounder (. Paralichthys olivaceus) via a 27.8 kDa membrane protein receptor. In the present study, immunohistochemistry was performed to locate the tissue distribution of this molecule in healthy flounder and showed that it was widely distributed in the tissues tested. Indirect enzyme-linked immunosorbent assay (ELISA) showed that the expression of the receptor in healthy flounder was highest in the gills and stomach, then in the skin, intestine and liver, followed by the spleen, head kidney, heart, ovary and brain and finally the kidney. On LCDV infection, ELISA indicated that the expression of the receptor, as determined by ELISA, was significantly upregulated in all tissues of LCDV-infected flounder compared with controls, but this expression decreased over the 4 weeks post infection. In contrast, real-time quantitative polymerase chain reaction demonstrated that the copy number of the LCDV gene in the tissues increased with time post infection, and that viral loads were higher in the tissues with higher expressions of the receptor. These results point to a correlation between high expression of the 27.8 kDa receptor and efficient LCDV propagation. The wide tissue distribution of the receptor might be one reason why LCDV can infect various tissues leading to systemic infection. © 2015 Elsevier Ltd.