National and Local Joint Engineering Laboratory of Ecological Mariculture

Qingdao, China

National and Local Joint Engineering Laboratory of Ecological Mariculture

Qingdao, China
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Li S.,CAS Qingdao Institute of Oceanology | Li S.,National and Local Joint Engineering Laboratory of Ecological Mariculture | Guo S.,CAS Qingdao Institute of Oceanology | Guo S.,University of Chinese Academy of Sciences | And 3 more authors.
Marine Drugs | Year: 2015

Anti-lipopolysaccharide factor (ALF) is a small protein with broad-spectrum antimicrobial activity, which has potential application in the disease control. Previously, we isolated seven ALF isoforms from the Chinese shrimp Fenneropenaeus chinensis. In the present study, their distributions in tissues of shrimp were analyzed and the data showed that different isoforms had different expression profiles, which suggested that they might have different functions. Then, the functions of different isoforms were studied by analyzing the antibacterial and antiviral activities of the functional domain of ALFs, the LPS-binding domain (LBD), which were synthesized by chemical methods. Different ALFs showed distinct antibacterial and antiviral activities, which were consistent with their diverse tissue distribution patterns. Sequence analysis on the LBD domain of different isoforms revealed that an identical lysine residue site was specifically conserved in peptides with anti-WSSV activity. In order to confirm whether this lysine residue is critical to the antiviral activity of the peptide, new peptides were synthesized by changing residues at this site. Changing the lysine residue at the specific site to other amino acid residue, the antiviral activity of the peptide apparently decreased. While replacing other residue with a lysine residue at this site in LBD peptide without anti-WSSV activity, the peptide will obtain the antiviral activity to WSSV. These results not only showed us a comprehensive understanding on the function of ALFs from F. chinensis, but also provided clues for the development of ALFs as potential therapeutic drugs to WSSV. © 2015 by the authors; licensee MDPI.


Hui M.,CAS Qingdao Institute of Oceanology | Song C.,CAS Qingdao Institute of Oceanology | Liu Y.,CAS Qingdao Institute of Oceanology | Li C.,CAS Qingdao Institute of Oceanology | And 3 more authors.
PLoS ONE | Year: 2017

Elucidating the genetic mechanisms of adaptation to the hydrothermal vent in organisms at genomic level is significant for understanding the adaptive evolution process in the extreme environment. We performed RNA-seq on four different tissues of a vent crab species, Austinograea alayseae, producing 725,461 unigenes and 134,489 annotated genes. Genes related to sensory, circadian rhythm, hormone, hypoxia stress, metal detoxification and immunity were identified. It was noted that in the degenerated eyestalk, transcription of phototransduction related genes which are important for retinal function was greatly reduced; three crucial neuropeptide hormones, one molt-inhibiting and two crustacean hyperglycemic hormone precursors were characterized with conserved domains; hypoxia-inducible factor 1 and two novel isoforms of metallothioneins in the vent crabs were discovered. An analysis of 6,932 orthologs among three crabs A. alayseae, Portunus trituberculutus and Eriocheir sinensis revealed 19 positive selected genes (PSGs). Most of the PSGs were involved in immune responses, such as crustins and anti-lipopolysaccharide factor, suggesting their function in the adaptation to environment. The characterization of the first vent crab transcriptome provides abundant resources for genetic and evolutionary studies of this species, and paves the way for further investigation of vent adaptation process in crabs. © 2017 Hui et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Hui M.,CAS Qingdao Institute of Oceanology | Liu Y.,CAS Qingdao Institute of Oceanology | Song C.,CAS Qingdao Institute of Oceanology | Song C.,University of Chinese Academy of Sciences | And 5 more authors.
PLoS ONE | Year: 2014

Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or b-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by aseries of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms. ©2014 Hui et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Song C.,CAS Qingdao Institute of Oceanology | Song C.,University of Chinese Academy of Sciences | Cui Z.,CAS Qingdao Institute of Oceanology | Cui Z.,National and Local Joint Engineering Laboratory of Ecological Mariculture | And 3 more authors.
Comparative Biochemistry and Physiology Part - B: Biochemistry and Molecular Biology | Year: 2015

The FEM-1 protein of Caenorhabditis elegans plays a crucial role in the nematode sex-determination pathway. Here, we reported the characterization of three members of Fem-1 gene family in Eriocheir sinensis (designated EsFem-1a, EsFem-1b, and EsFem-1c), which were homologs of the nematode FEM-1 protein. The amino acid sequences of EsFem-1a, EsFem-1b, and EsFem-1c contained eight, nine, and eight ankyrin repeats, respectively. None of the ankyrin repeats had its own specific signature, and the evolution of ankyrin repeat was not completely independent. The predicted three-dimensional structure of EsFem-1 proteins exhibited highly similar superhelical conformation, especially the N-terminal six contiguous ankyrin repeats, which provided a binding surface for the protein-protein interaction. Phylogenetic tree based on the amino acid sequences revealed that EsFem-1a, EsFem-1b, and EsFem-1c were divided into three obvious separated clades. EsFem-1 genes were highly expressed in fertilized egg, 2-4 cell and blastula stage comparing with larval stage ( P<. 0.01), which suggested they might be maternal genes. They also showed a certain degree of sexually dimorphic expression in some tissues. Notably, the highest expression of EsFem-1a was in the hepatopancreas, with EsFem-1b in testes and EsFem-1c in muscle ( P<. 0.05), which indicated their potential role in a broad array of tissues. In addition, the genes initially involved in sex differentiation were not limited to those specifically expressed in the developing gonad. Taken together, these results suggested that EsFem-1 might function in crab early sex determination and late gonad development. The identification of Fem-1 gene family in E. sinensis provides a new insight into crab sex-determination mechanism. © 2015 Elsevier Inc.


Liu Y.,CAS Qingdao Institute of Oceanology | Hui M.,CAS Qingdao Institute of Oceanology | Cui Z.,CAS Qingdao Institute of Oceanology | Cui Z.,National and Local Joint Engineering Laboratory of Ecological Mariculture | And 6 more authors.
PLoS ONE | Year: 2015

Sex-biased genes are considered to account for most of phenotypic differences between males and females. In order to explore the sex-biased gene expression in crab, we performed the whole-body transcriptome analysis in male and female juveniles of the Chinese mitten crab Eriocheir sinensis using next-generation sequencing technology. Of the 23,349 annotated unigenes, 148 were identified as sex-related genes. A total of 29 candidate genes involved in primary sex determination pathways were detected, indicating the sex determination cascade of the mitten crab might be more complex than previously supposed. Differential expression analysis showed 448 differentially expressed genes (DEGs) between the two transcriptomes. Most of DEGs were involved in processes such as metabolism and immunity, and not associated with obvious sexual function. The pathway predominantly enriched for DEGs were related to lysosome, which might reflect the differences in metabolism between males and females. Of the immune DGEs, 18 up-regulated genes in females were humoral immune factors, and eight up-regulated genes in males were pattern recognition receptors, suggesting sex differences of immune defense might exist in the mitten crab. In addition, two reproduction-related genes, vitellogenin and insulin-like androgenic gland factor, were identified to express in both sexes but with significantly higher level in males. Our research provides the first whole-body RNA sequencing of sex-specific transcriptomes for juvenile E. sinensis and will facilitate further studies on molecular mechanisms of crab sexual dimorphism. © 2015 Liu et al.


Sun Z.,CAS Qingdao Institute of Oceanology | Li S.,CAS Qingdao Institute of Oceanology | Li S.,National and Local Joint Engineering Laboratory of Ecological Mariculture | Li F.,CAS Qingdao Institute of Oceanology | And 2 more authors.
BioMed Research International | Year: 2014

WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC-003225.1) and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into "extracellular region" or "receptor complex" GO-terms. KEGG pathway analysis showed that they were involved in the "ECM-receptor interaction pathway." In the 6 pairs of interacting proteins, an envelope protein called "collagen-like protein" (WSSV-CLP) encoded by an early virus gene "wsv001" in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA), two integrin beta (ITGB), and one syndecan (SDC). Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp. © 2014 Zheng Sun et al.


Sun G.,CAS Qingdao Institute of Oceanology | Sun G.,University of Chinese Academy of Sciences | Sun G.,National and Local Joint Engineering Laboratory of Ecological Mariculture | Li M.,Ocean University of China | And 3 more authors.
Aquaculture Research | Year: 2016

The effects of flow rate on growth and welfare of juvenile turbot (Scophthalmus maximus L.) were investigated in the present study. Fish with same initial weight (102.5 ± 10.6 g) were subjected to four flow rates, equalling to 0.5, 1, 1.5 and 2 tank volumes per hour in twelve 392 L tanks during 80 days. Results showed that specific growth rate of turbots increased (0.40-0.58% day-1) significantly with promoted flow rate (P < 0.05). Total ammonia nitrogen, nitrite nitrogen, unionized ammonia nitrogen, chemical oxygen demand, total bacteria and total vibrio in tanks were affected significantly by flow rate and accumulations were found in low rate (200 L h-1) (P < 0.05). Free carbon dioxide increased significantly with the increased flow rate and ranged between 4.5 and 13.5 mg L-1 (P < 0.05). Both superoxide dismutase activity and lysozyme activity increased significantly with flow rate (P < 0.05), with ranges of 108.51-131.57 U mL-1 and 551.81-869.28 U mL-1. Serum cortisol showed reversed tendency and ranged between 7.39-19.26 ng mL-1. The principal components analysis suggested that increased flow rate promoted fish welfare. It was concluded that increased flow rate promoted the growth of juvenile turbot, possibly explained by fish welfare differences in combination of health, water quality and serum parameters. © 2016 John Wiley & Sons Ltd.


Li Y.,CAS Qingdao Institute of Oceanology | Hui M.,CAS Qingdao Institute of Oceanology | Cui Z.,CAS Qingdao Institute of Oceanology | Cui Z.,National and Local Joint Engineering Laboratory of Ecological Mariculture | And 5 more authors.
Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics | Year: 2014

Within the larval period of Eriocheir sinensis, there is pronounced morphological changes upon the molt from the fifth zoeae (Z5) to megalopae (M), and low survival rate exists during this transition, which is typical in crab species. RNA sequencing was applied to Z5 and M of E. sinensis, resulting in the discovery of 19,186 unigenes and 652 differentially expressed genes (DEGs, 3.40% of the unigenes). The important metabolic pathways that might play roles in the larval development of E. sinensis from Z5 to M were detected to be 'Xenobiotics Biodegradation and Metabolism (8.16%)', 'Metabolism of Cofactors and Vitamins (6.70%)', 'Lipid Metabolism (6.36%)', and 'Amino Acid Metabolism (6.28%)'. Further, 19 DEGs possibly contributing to the morphological and sensory capability changes of the larvae were identified, like multiple copies of cuticle protein genes, retinaldehyde-binding protein 1 (RLBP1), envelope protein (Envelope) and hormone-related gene ecdysteroid-regulated 16 kDa protein (ESR16). Moreover, 62 DEGs were identified to be related to carbohydrate, lipid and protein digestion and metabolism, such as glucose dehydrogenases (GDHs), lipases (LIPs) and serine proteases (SPs). Among these DEGs, more genes related to the substance metabolism were found up-regulated in Z5 than M, suggesting that more energy might be essential to be released for Z5 to complete the transition into M. Characterization of the crucial DEGs by real-time quantitative PCR re-conformed their expression pattern. This study provides the first genome-wide transcriptomic analysis of E. sinensis Z5 and M for studying the molecular basis of the larvae metamorphosis and nutrition metabolism. © 2014 Elsevier Inc.


Liu G.,CAS Qingdao Institute of Oceanology | Liu G.,University of Chinese Academy of Sciences | Huan P.,CAS Qingdao Institute of Oceanology | Liu B.,CAS Qingdao Institute of Oceanology | Liu B.,National and Local Joint Engineering Laboratory of Ecological Mariculture
Development Genes and Evolution | Year: 2015

Shells are one of the most notable features of the majority of mollusks. In addition, the shell is also considered a key characteristic during molluscan evolution and development. However, although the morphological changes during larval shell formation have been well described, the underlying molecular mechanisms remain poorly understood. In this study, we focused on the potential involvement of a GATA gene in shell formation because GATA genes are often downstream genes of BMP (bone morphogenetic protein) signaling pathways, which have been suggested to participate in molluscan shell formation. In the Pacific oyster Crassostrea gigas, we observed that the expression of a GATA2/3 homolog (cgi-gata2/3) was clearly restricted to the edge of the shell field in early larval stages (trochophore and D-veliger). This expression pattern supports the notion that cgi-gata2/3 gene plays conserved roles in bilaterian ectodermal development. It is possible that cgi-gata2/3 is one shell-formation gene under the regulation of BMP signaling pathways. In addition, cgi-gata2/3 was also detected in the ventral side of embryos. The expression of cgi-gata2/3 away from the shell field may be involved in hematopoiesis. Our results provide fundamental support for studies into the molecular mechanisms of larval shell formation and the functions of molluscan GATA genes. © 2015, Springer-Verlag Berlin Heidelberg.


Li S.,CAS Qingdao Institute of Oceanology | Li S.,National and Local Joint Engineering Laboratory of Ecological Mariculture | Wang Z.,CAS Qingdao Institute of Oceanology | Wang Z.,University of Chinese Academy of Sciences | And 3 more authors.
Developmental and Comparative Immunology | Year: 2015

VEGF signaling pathway plays vital roles in many physiological processes including cell proliferation, differentiation, migration, survival, cell-cell communication, vessel permeability and virus-host interaction in mammalian species. However, the VEGF signaling pathway and its biological function are still poorly understood in crustaceans. In the present study, an essential member of VEGF signaling pathway, VEGF receptor (. LvVEGFR), was isolated from Penaeid shrimp Litopenaeus vannamei and its function during virus infection was analyzed. The deduced amino acid sequence of LvVEGFR possessed all common features of VEGFRs reported in other species, including a signal peptide, six IG-like domains, one immunoglobulin subtype 2 domain, a transmembrane domain, a juxtamembrane domain, a protein kinase domain separated by a kinase insert sequence, one ATP binding site and one tyrosine-protein kinase active site. LvVEGFR is mainly expressed in hemocytes and intestine. The transcriptional level of LvVEGFR could be obviously up-regulated in hemocytes and intestine after WSSV infection. Silencing of LvVEGFR gene by double-strand RNA (dsRNA) interference could not only lead to a decrease of virus copy number in WSSV infected shrimp, but also reduce the mortality of shrimp during WSSV infection. These data suggested that VEGF signaling pathway might play an important role during viral infection to shrimp. © 2015 Elsevier Ltd.

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