Identification, mRNA expression and genomic structure of TLR22 and its association with GCRV susceptibility/resistance in grass carp (Ctenopharyngodon idella)

Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila

Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.

Natural selection directing molecular evolution in vertebrate viral sensors

Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.

Comparative Transcriptomics Analysis Reveals Unique Immune Response to Grass Carp Reovirus Infection in Barbel Chub (Squaliobarbus curriculus)

Grass carp (Ctenopharyngodon idella) and barbel chub (Squaliobarbus curriculus)-both Leuciscinae subfamily species-demonstrate differences in grass carp reovirus (GCRV) infection resistance. We infected barbel chubs with type II GCRV and subjected their liver, spleen, head kidney, and trunk kidney samples to investigate anti-GCRV immune mechanisms via RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). We identified 139, 970, 867, and 2374 differentially expressed genes (DEGs) in the liver, spleen, head kidney, and trunk kidney, respectively. Across all four tissues, gene ontology analysis revealed significant immune response-related DEG enrichment, and the Kyoto Encyclopedia of Genes and Genomes analysis revealed pattern recognition receptor (PRR) and cytokine-related pathway enrichment. We noted autophagy pathway enrichment in the spleen, head kidney, and trunk kidney; apoptosis pathway enrichment in the spleen and trunk kidney; and complement- and coagulation-cascade pathway enrichment in only the spleen. Comparative transcriptome analysis between GCRV-infected barbel chubs and uninfected barbel chubs comprehensively revealed that PRR, cytokine-related, complement- and coagulation-cascade, apoptosis, and autophagy pathways are potential key factors influencing barbel chub resistance to GCRV infection. qRT-PCR validation of 11 immune-related DEGs confirmed our RNA-seq data's accuracy. These findings provide a theoretical foundation and empirical evidence for the understanding of GCRV infection resistance in barbel chub and hybrid grass carp-barbel chub breeding.

Comparative Transcriptomic Analysis Revealed Potential Differential Mechanisms of Grass Carp Reovirus Pathogenicity

Grass carp reovirus (GCRV), one of the most serious pathogens threatening grass carp (Ctenopharyngodon idella), can lead to grass carp hemorrhagic disease (GCHD). Currently, GCRV can be divided into three genotypes, but the comparison of their pathogenic mechanisms and the host responses remain unclear. In this study, we utilized the Ctenopharyngodon idella kidney (CIK) model infected with GCRV to conduct comparative studies on the three genotypes. We observed a cytopathic effect (CPE) in the GCRV-I and GCRV-III groups, whereas the GCRV-II group did not show any CPE. Moreover, a consistent trend in the mRNA expression levels of antiviral-related genes across all experimental groups of CIK cells was detected via qPCR and further explored through RNA-seq analysis. Importantly, GO/KEGG enrichment analysis showed that GCRV-I, -II, and -III could all activate the immune response in CIK cells, but GCRV-II induced more intense immune responses. Intriguingly, transcriptomic analysis revealed a widespread down-regulation of metabolism processes such as steroid biosynthesis, butanoate metabolism, and N-Glycan biosynthesis in infected CIK cells. Overall, our results reveal the CIK cells showed unique responses in immunity and metabolism in the three genotypes of GCRV infection. These results provide a theoretical basis for understanding the pathogenesis and prevention and control methods of GCRV.

Understanding the molecular response of non-mammalian toll-like receptor 22 (TLR22) in amphibious air-breathing catfish, Clarias magur (Hamilton, 1822) to bacterial infection or ligand stimulation through molecular cloning and expression profiling

Toll-like receptor (TLR) 22 is a non-mammalian TLR, which is identified initially as a functional substitute of mammalian TLR3 in recognizing cell surface long dsRNA in teleosts. To understand the pathogen surveillance role played by TLR22 in an air-breathing catfish model the full-length cDNA of TLR22 was identified in Clarias magur and found to be consisted of 3597 nucleotides encoding for 966 amino acids. In the deduced amino acid sequence of C. magur TLR22 (CmTLR22) key signature domains such as one signal peptide, 13 LRRs, one transmembrane domain, one LRR_CT domain and an intracellular TIR domain could be identified. The CmTLR22 formed a separate cluster with other catfish TLR22 genes and situated within the TLR22 cluster in the phylogenetic analysis of teleost TLR groups. The CmTLR22 was constitutively expressed in all the 12 tested tissues of healthy C. magur juveniles with the highest transcript abundance in spleen followed by brain, intestine and head kidney. Following induction with the dsRNA viral analogue, poly (I:C), the level of expression of CmTLR22 was up-regulated in tissues such as kidney, spleen and gills. Whereas, in Aeromonas hydrophila-challenged C. magur, the expression levels of CmTLR22 was found to be up-regulated in gills, kidney and spleen, and down-regulated in liver. The findings of the current study suggest that the specific function of TLR22 is evolutionarily conserved in C. magur and might play a key role in mounting immune response by recognizing Gram-negative fish pathogen such as A. hydrophila and aquatic viruses in air-breathing amphibious catfishes.

Effects of Bougainvillea glabra leaf on growth, skin mucosal immune responses, and disease resistance in common carp Cyprinus carpio

This study evaluated the effects of Bougainvillea glabra (BG) leaf as a feed supplement on growth, skin mucosal immune parameters, serum oxidative stress, expression of immune-related genes, and susceptibility to pathogen infection in carp Cyprinus carpio. Diets containing four different BG concentrations (g kg^-1), i.e., 0 g (basal diet), 20 g (BG20), 30 g (BG30), 40 g (BG40), and 50 g (BG50), were fed to the carp (average weight: 14.03 ± 0.81 g) for 8 weeks. Skin mucosal immunological and serum antioxidant parameters were examined 8 weeks post-feeding. Growth performance was significantly higher in BG40. Among the examined skin mucosal immune parameters, lysozyme (33.79 ± 0.98 U mL^-1), protein (6.88 ± 0.37 mg mL^-1), immunoglobulin (IgM; 5.34 ± 0.37 unit-mg mL^-1), and protease activity (3.18 ± 0.36%) were significantly higher in BG40 than in the control; whereas, there was no significant effect on the alkaline phosphatase level. Among serum immune activity, activities of lysozyme, the alternative complement pathway, and IgM were significantly higher in BG40. Phagocytic, and superoxide dismutase (SOD) activities were higher (P < 0.05) in BG30-BG50. Serum ALT, AST, and MDA levels were lower in BG40 than in the control (P < 0.05). Intestinal enzymatic activities were enhanced in BG40 and BG50 (P < 0.05), except for lipase in BG50. Gene expression analysis revealed that the mRNA expressions of antioxidant genes (SOD, GPx, and Nrf2), an anti-inflammatory gene (IL-10), and IκBα were significantly upregulated in BG40. Conversely, the pro-inflammatory gene IL-1β and the signaling molecule NF-κB p65 were downregulated in BG40 and BG50, respectively. BG supplementation had no significant effect on TNF-α, TLR22, or HSP70 mRNA expressions. Moreover, fish in BG40 exhibited the highest relative post-challenge survival (67.74%) against Aeromonas hydrophila infection. These results suggested that dietary supplementation with BG leaves at 40 g/kg can significantly improve the growth performance, immune responses, and disease resistance of C. carpio. BG leaves are a promising food additive for carp in aquaculture.

Impact of dandelion polysaccharides on growth and immunity response in common carp Cyprinus carpio

Natural products have gained considerable attention for improving fish growth performance and immunity to enhance disease resistance. This study evaluated the effect of dandelion polysaccharides (DP) on skin mucosal immune parameters, immune-related gene expression, and susceptibility to pathogen challenge in the Common carp Cyprinus carpio. Diets containing four different concentrations of DP (g Kg^-1):0 g [basal diet], 0.5 g [D1], 1.5 g [D2], 2.5 g [D3], and 4.0 g [D4] were fed to the carp (average weight: 13.92 ± 0.83 g) for eight weeks. Growth parameters were analyzed four and eight weeks after feeding. Immunological, hematological, and antioxidant parameters were examined eight weeks post-feeding. Growth performance was significantly higher on D3, with a final weight gain of 71.48 ± 1.57 g and a specific growth rate of 3.06 ± 0.12. Among hematological parameters examined, erythrocyte^, hematocrit, and mean corpuscular volume (MCV) levels were significantly higher in D3. Skin mucosal immune parameters, such as lysozyme (31.04 ± 1.02 Unit mL^-1), alkaline phosphatase (122.6 ± 3.8 IU L^-1), and protein level (10.6 ± 0.74 mg mL^-1) were significantly higher in D3, while peroxidase activity was higher in D4. Furthermore, SOD activity was higher in D2-D3, whereas catalase activity was higher in D2-D4 (P < 0.05) than in the control. Malondialdehyde level decreased significantly in D3 (5.43 ± 0.36 nmol mL^-1); whereas, serum ALT and AST levels were significantly lower on D2-D4. Intestinal tight-junction-related genes ZO-1 and Claudin 7 were significantly higher in the DP-fed groups; however, DP had no significant effect on claudin 3. Occludin expression was higher (p < 0.05) on D3 only. Pro-inflammatory cytokines (IL-1β and TNF-α) and IFN-γ strongly upregulated in the head kidney at D3. Conversely, the expression of the anti-inflammatory cytokine interleukin-10, HSP70, and TOR were considerably downregulated in D3. Fish from D3 exhibited markedly higher relative post-challenge survival (66.67%) against Aeromonas hydrophila challenge. The results of the present study suggest that dietary supplements of DP at 2.5 g kg^-1 can significantly improve the growth performance, skin mucosal, and serum antioxidant parameters, and strengthen the immunity of C. carpio. Therefore, DP is a promising food additive for carp aquaculture.

Grass Carp Reovirus triggers autophagy enhancing virus replication via the Akt/mTOR pathway

Autophagy impacts the replication cycle of many viruses. Grass Carp Reovirus (GCRV) is an agent that seriously affects the development of the grass carp aquaculture industry. The role of autophagy in GCRV infection is not clearly understood. In this study, we identified that GCRV infection triggered autophagy in CIK cells, which was demonstrated by transmission electron microscopy, the conversion of LC3B I to LC3B II and the level of autophagy substrate p62. Furthermore, we found that GCRV infection activated Akt-mTOR signaling pathway, and the conversion of LC3B I to LC3B II was increased by inhibiting mTOR with rapamycin (Rap) but decreased by activating Akt with insulin. We then assessed the effects of autophagy on GCRV replication. We found that inducing autophagy with Rap promoted GCRV proliferation but inhibiting autophagy with 3 MA or CQ inhibited GCRV replication in CIK cells. Moreover, it was found that enhancing Akt-mTOR activity by insulin, GCRV VP7 protein and viral titers of GCRV were decreased. Collectively, these results indicated that GCRV infection induced autophagy involved in GCRV replication via the Akt-mTOR signal pathway. Thus, new insights into GCRV pathogenesis and antiviral treatment strategies are provided.

Whole-body transcriptome analysis provides insights into the cascade of sequential expression events involved in growth, immunity, and metabolism during the molting cycle in Scylla paramamosain

The molecular mechanisms underlying the dynamic process of crab molting are still poorly understood at the individual level. We investigated global expression changes in the mud crab, Scylla paramamosain, at the transcriptome level and revealed a cascade of sequential expression events for genes involved in various aspects of the molting process using whole-body sequencing of juvenile crabs. RNA-sequencing (RNA-seq) produced 139.49 Gb of clean reads and 20,436 differentially expressed genes (DEGs) among different molting stages. The expression patterns for genes involved in several molecular events critical for molting, such as cuticle reconstruction, cytoskeletal structure remodeling, hormone regulation, immune responses, and metabolism, were characterized and considered as mechanisms underlying molting in S. paramamosain. Among these genes, we identified 10,695 DEGs in adjacent molting stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that significantly enriched pathways included structural constituents of cuticle, binding and chitin metabolic processes, steroid hormone biosynthesis, insulin resistance, and amino sugar metabolic processes. The expression profiles of 12 functional genes detected via RNA-seq were corroborated via real-time RT-PCR assays. The results revealed gene expression profiles across the molting cycle and identified possible activation pathways for future investigation of the underlying molecular mechanisms.

Molecular identification and functional characterization of IRF4 from common carp (Cyprinus carpio. L) in immune response: a negative regulator in the IFN and NF-κB signalling pathways

Background

The interferon (IFN) regulatory factors (IRFs) were originally identified as transcription factors playing critical roles in the regulation of IFN-related genes in the signal pathway. In mammals, IRF4 plays a vital role in both the innate and adaptive immune system. This study aims to reveal the molecular characterization, phylogenetic analysis, expression profiles and the regulatory role in the IFN and NF-κB signalling pathways of IRF4 in common carp (Cyprinus carpio. L) (abbreviation, ccIRF4).

Results

Here, ccIRF4 was identified and characterized, it contained a DNA binding domain (DBD) which possess five tryptophans and an IRF-associated domain (IAD). The predicted protein sequence of the ccIRF4 showed higher identities with grass carp (Ctenopharyngodon idella) and zebrafish (Danio rerio). Phylogenetic analysis suggested that ccIRF4 has the closest relationship with zebrafish IRF4. Quantitative real-time PCR analysis showed that ccIRF4 was constitutively expressed in all investigated tissues with the highest expression level in the gonad. Polyinosinic:polycytidylic acid (poly I:C) stimulation up-regulated the ccIRF4 expressions in the liver, spleen, head kidney, skin, foregut and hindgut. Upon Aeromonas hydrophila injection, the expression level of ccIRF4 was up-regulated in all tissues with the exception of spleen. In addition, ccIRF4 was induced by lipopolysaccharide (LPS), peptidoglycan (PGN) and Flagellin in head kidney leukocytes (HKLs). Overexpression of the ccIRF4 gene in epithelioma papulosum cyprini cells (EPC) down regulated the expressions of IFN-related genes and proinflammatory factors. Dual-luciferase reporter assay revealed that ccIRF4 decreased the activation of NF-κB through MyD88.

Conclusions

These results indicate that ccIRF4 participates in both antiviral and antibacterial immune response and negatively regulates the IFN and NF-κB response. Overall, our study on ccIRF4 provides more new insights into the innate immune system of common carp as well as a theoretical basis for investigating the pathogenesis and prevention of fish disease.

Establishment of a rare minnow (Gobiocypris rarus) model for evaluation of experimental vaccines against a disease induced by grass carp reovirus genotype II

Vaccination is the most effective way to control the grass carp haemorrhagic disease (GCHD) with the primary pathogen grass carp reovirus genotype II (GCRV-II). However, due to the large difference in breeding conditions and unclear genetic background of grass carp, the results of the experiment were not reliable, which further hinders the effective prevention and control of GCHD. The rare minnow (Gobiocypris rarus) is highly sensitive to GCRV. Its small size, easy feeding, transparent egg membrane, and annual spawning are in line with the necessary conditions for an experimental aquatic animals culture object. In this study, immunogenicity and protective effects of attenuated and inactivated viruses for grass carp and rare minnow were evaluated in parallel. The expression of immune-related genes increased statistically significant after immunization. With the rise of specific serum antibody titers, the results of rare minnow and grass carp were consistent. In addition, there was no significant residue of adjuvant observed in both fish species injected with an adjuvanted and inactivated virus. Challenge of immunized grass carp and rare minnow with the isolate HuNan1307 resulted in protection rates of 95.8% and 92.6% for attenuated virus, 81.4% and 77.7% for inactivated virus, respectively, as well as the viral load changed consistently. The results indicated that rare minnow can be used as a model for evaluation of experimental vaccines against GCHD.

TLR22-mediated activation of TNF-α-caspase-1/IL-1β inflammatory axis leads to apoptosis of Aeromonas hydrophila-infected macrophages

Toll-like receptors (TLRs) represent first line of host defence against microbes. Amongst different TLRs, TLR22 is exclusively expressed in non-mammalian vertebrates, including fish. The precise role of TLR22 in fish-immunity remains abstruse. Herein, we used headkidney macrophages (HKM) from Clarias gariepinus and deciphered its role in fish-immunity. Highest tlr22 expression was observed in the immunocompetent organ - headkidney; nonetheless expression in other tissues suggests its possible involvement in non-immune sites also. Aeromonas hydrophila infection up-regulates tlr22 expression in HKM. Our RNAi based study suggested TLR22 restricts intracellular survival of A. hydrophila. Inhibitor and RNAi studies further implicated TLR22 induces pro-inflammatory cytokines TNF-α and IL-1β. We observed heightened caspase-1 activity and our results suggest the role of TLR22 in activating TNF-α/caspase-1/IL-1β cascade leading to caspase-3 mediated apoptosis of A. hydrophila-infected HKM. We conclude, TLR22 plays critical role in immune-surveillance and triggers pro-inflammatory cytokines leading to caspase mediated HKM apoptosis and pathogen clearance.

Challenges and Solutions to Viral Diseases of Finfish in Marine Aquaculture

Aquaculture is the fastest food-producing sector in the world, accounting for one-third of global food production. As is the case with all intensive farming systems, increase in infectious diseases has adversely impacted the growth of marine fish farming worldwide. Viral diseases cause high economic losses in marine aquaculture. We provide an overview of the major challenges limiting the control and prevention of viral diseases in marine fish farming, as well as highlight potential solutions. The major challenges include increase in the number of emerging viral diseases, wild reservoirs, migratory species, anthropogenic activities, limitations in diagnostic tools and expertise, transportation of virus contaminated ballast water, and international trade. The proposed solutions to these problems include developing biosecurity policies at global and national levels, implementation of biosecurity measures, vaccine development, use of antiviral drugs and probiotics to combat viral infections, selective breeding of disease-resistant fish, use of improved diagnostic tools, disease surveillance, as well as promoting the use of good husbandry and management practices. A multifaceted approach combining several control strategies would provide more effective long-lasting solutions to reduction in viral infections in marine aquaculture than using a single disease control approach like vaccination alone.

TLR13, TLR22, TRAF6, and TAK1 in the soiny mullet (Liza haematocheila): Molecular characterization and expression profiling analysis

Toll-like receptors (TLRs) and their associated signaling pathways play pivotal roles in the immune response to invading pathogens. Here, TLR13, TLR22, tumor necrosis factor receptor-associated factor 6 (TRAF6), and transforming growth factor-β-activated kinase1 (TAK1) were characterized in the soiny mullet (Liza haematocheila), representative mugilid species that is widely cultured in Asia. The four mullet genes, which shared characteristic features with their counterparts in other teleosts, were ubiquitously expressed in all of the examined tissues, albeit with different expression patterns. Following Streptococcus dysgalactiae infection, the four genes were upregulated to different degrees in various mullet tissues. These results indicated that the four genes were involved in the mullet immune response to bacterial infection. To the best of our knowledge, this is the first characterization of these four genes in mullet. Our results provide a basis for future studies of TLR signaling pathways in mullet, as well as for similar studies in other mugilids.

Toll-like receptors (TLRs) respond to tributyltin chloride (TBT-Cl) exposure in the river pufferfish (Takifugu obscurus): Evidences for its toxic injury function

Tributyltin chloride (TBT-Cl) residual in water body had become a noticeable ecological problem for aquatic ecosystems. Toll-like receptors (TLRs) are an ancient family of pattern recognition receptors that play key roles in detecting nonself antigens and immune system activation. In this study, we explored the effect of TBT-Cl exposure on four TLRs expression in river pufferfish, Takifugu obscurus. The four T. obscurus Toll-like receptors (To-TLRs) contained different types of domains such as leucine-rich repeats (LRRs), leucine-rich repeats, typical subfamily (LRR_TYP) and other special domains. The To-TLRs mRNA transcripts expressed in all tissues, also To-TLR2 was investigated with higher level in kidney, as well as To-TLR3 in kidney, while To-TLR18 in liver and To-TLR22 in intestine. After the acute and chronic exposure of TBT-Cl, To-TLR2 and To-TLR3 mRNA transcripts were significantly down-regulated in gill. However, To-TLR18 and To-TLR22 were significantly up-regulated in gill and liver. Moreover, the histology and immunohistochemistry (IHC) results showed the different injury degrees of TBT-Cl in liver and gill and implied the cytoplasm reorganization after TBT-Cl stress and the function of immunoregulation for To-TLRs to TBT-Cl exposure. All the results indicated that To-TLRs might involve in sensing and mediating innate immune responses caused by TBT-Cl for keeping detoxification homeostasis.

Thoroughly Remold the Localization and Signaling Pathway of TLR22

TLR22 exists in nearly all the poikilothermic vertebrates and plays a central role in the initiation of innate immunity and activation of adaptive immunity. TLR22 signaling pathway has been characterized in detail in fugu (Takifugu rubripes). Here, we thoroughly remold the localization and signaling pathways of TLR22. We characterized TLR22a and TLR22b in grass carp (Ctenopharyngodon idella), designated as CiTLR22a and CiTLR22b, and explored the ligand(s), adaptor(s), and signaling pathway(s). Results show that both CiTLR22a and CiTLR22b localize to lysosome, acidic compartment. Correspondingly, CiTLR22a and CiTLR22b directly bind and respond to dsRNA analog poly(I:C) at pH 5, but not at pH 7.4, the physiological pH. Moreover, CiTLR22a and CiTLR22b exhibit antagonistic function in signal transmission, wherein CiTLR22a facilitates the protein and phosphorylation levels of IRF7 and enhances the promoter activities of major IFNs and NF-κBs, while CiTLR22b downregulates IRF7 phosphorylation and IRF3 protein level and suppresses the IFN and NF-κB pathways. Further investigations revealed that CiTLR22a restrains grass carp reovirus (GCRV) replication and protects cells from GCRV infection, whereas CiTLR22b plays a negative role in response to GCRV infection. This is the first time to systematically clarify the signaling pathways of two isotype TLR22s; especially, subcellular localization and adaptor are different from previous TLR22 report, which results from technical limitations. The results will serve the antiviral immune mechanisms in poikilothermic vertebrates and evolutionary immunology.

A non-mammalian Toll-like receptor 26 (TLR26)gene mediates innate immune responses in yellow catfish Pelteobagrus fulvidraco

In this study, we identified a fish-specific Toll-like receptor (TLR) in Pelteobagrus fulvidraco, an economically important freshwater fish in China. This TLR, PfTLR26, was shown to be encoded by a 3084 bp open reading frame (ORF), producing a polypeptide 1027 amino acids in length. The PfTLR26 protein contains a signal peptide, eight leucine-rich repeat (LRR) domains, two LRR_TYP domains in the extracellular region, and a Toll/interleukin (IL)-1 receptor (TIR) domain in the cytoplasmic region, consistent with the characteristic TLR domain architecture. This predicted 117.1 kDa protein was highly homologous to those of other fish, with phylogenetic analysis revealing the closest relation to TLR26 of Ictalurus punctatus. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis showed that the PfTLR26 gene was expressed in all tissues tested, with the highest expression levels seen in the head kidney and blood, and the lowest seen in muscle. PfTLR26 exhibited significant upregulation in liver, spleen, head kidney, and blood at different time points following challenge with the common TLR agonists lipopolysaccharide (LPS) and polyriboinosinic polyribocytidylic acid (Poly I:C). Taken together, these results suggest that PfTLR26 may be an important component of the P. fulvidraco innate immune system, participating in the transduction of TLR signaling under pathogen stimulation.

Multiple subtypes of TLR22 molecule from Schizothorax prenanti present the functional diversity in ligand recognition and signal activation

Evolutionary development has increased the diversity of genotypes and the complexity of gene functions in fish. TLR22 has been identified as a teleost-specific gene, but its functions are tremendously different among different fish species. Whether the functional diversity relates to the difference of genotypes remains poorly understand. In this study, we cloned and identified three TLR22 molecules from Schizothorax prenanti (S. prenanti), named as spTLR22-1, spTLR22-2 and spTLR22-3. The full-length coding regions of spTLR22s are 2841 bp, 2805 bp and 2868 bp and coding 946 aa, 934 aa and 955 aa, respectively. All spTLR22s are composed of multiple leucine-rich repeat (LRR) domains, a transmembrane structure and a Toll/IL-1 receptor (TIR) region. The phylogenetic analysis showed that three spTLR22s were close to Cyprinus carpio TLR22-1, TLR22-2 and TLR22-3, respectively. Among the spTLR22s, they presented not close relationship but remained to belong to TLR22 subfamily. All spTLR22s were ubiquitously expressed in all tested tissues, but the expression levels of spTLR22s were dominant in immune-related tissues, such as gill and spleen. The expression levels of spTLR22-1 and spTLR22-3 were significantly increased after treatment with bacteria, LPS and Poly(I:C). However, spTLR22-2 seems like no response to these treatments. The luciferase reporter assay demonstrated that all spTLR22s could activate NF-κB signaling pathway, but only spTLR22-1 and spTLR22-2 could activate IFN-β signaling pathway. Interestingly, in the ligand recognition analysis, spTLR22-1 and spTLR22-3 but not spTLR22-2 had the recognized potential to Poly(I:C), and all spTLR22s could not recognize LPS. Both spTLR22-1 and spTLR22-3 significantly up-regulated the expression of anti-viral-related genes (Mx, IFN and ISG15) and down-regulated the expression of anti-inflammatory factor IL-10 after the overexpression in carp EPC cell line, but spTLR22-2 failed to impact the expression of these genes. Moreover, we found that all spTLR22s localized to the intracellular region. Taken together, our results reveal that spTLR22-1 and spTLR22-3 but not spTLR22-2 may be involved into the anti-viral immune response via IFN-β signaling pathway, and all spTLR22s can activate NF-κB signaling pathway but only spTLR22-1 and spTLR22-3 response to the stimulation of bacteria and LPS.

Effects of bioactive substance from turmeric on growth, skin mucosal immunity and antioxidant factors in common carp, Cyprinus carpio

Present study evaluated the effects of curcumin, the principal curcuminoid of turmeric, on Cyprinus carpio growth, skin mucosal immune parameters, immune-related gene expression, and susceptibility to pathogen challenge. Diets containing four various concentrations of curcumin (g Kg^-1): 0 g [basal diet], 5 g [T5], 10 g [T10], and 15 g [T15] were fed to the carp (average weight: 16.37 g) for 8 weeks. Growth parameters were analysed at 4 and 8 weeks post-feeding. Skin mucosal immune responses and expression were examined in 8 weeks post-feeding. Growth performance was significantly higher in T10 and T15, with final weight gain of 102.26 ± 2.31 g and specific growth rate of 3.24 ± 0.37, respectively. The lowest feed conversion ratio (2.35 ± 0.16) was recorded in T15 than in the control (P < 0.05). Among the skin mucosal immune parameters examined, lysozyme (36.8 ± 4.03 U mL^-1), total immunoglobulin (6.74 ± 0.5 mg mL^-1), protein level (18.7 ± 1.62 mg mL^-1), alkaline phosphatase (96.37 ± 6.3 IU L^-1), and protease activity (9.47 ± 0.82%) were significantly higher in T15, while the peroxidase activity was higher in T10 (10.24 ± 0.9 U mg^-1 protein). Further, lysozyme, superoxide dismutase (SOD) and catalase (CAT) activities were measured in serum and found to be higher in T10 or T15 than in the control (P < 0.05). However, malondialdehyde level decreased significantly in T10 and T15. Furthermore, antioxidant genes (SOD, CAT, nuclear factor erythroid 2-related factor 2) and anti-inflammatory cytokine Interleukin-10 were upregulated in the head kidney, intestine, and hepatopancreas of fish in T10 and T15. Conversely, expression of pro-inflammatory cytokines (IL-1β, tumour necrosis factor-alpha), signalling molecule NF-κBp65 were down-regulated in the tested tissues of T10 and T15. Expression of Toll-like receptor 22 (TLR22) was down regulated in head-kidney and intestine of T15. Fish from T15 exhibited significantly higher relative post-challenge survival (69.70%) against Aeromonas hydrophila challenge. Results of the present study suggest that dietary supplements of curcumin at 15 g Kg^-1can significantly improve the growth performance, skin mucosal and serum antioxidant parameters, and strengthen the immunity of C. carpio. Therefore, curcumin represents a promising food additive for carps in aquaculture.

Transcriptome analysis of rare minnow (Gobiocypris rarus) infected by the grass carp reovirus

Grass carp shares the largest portion of the aquaculture production in China, but hemorrhagic disease caused by grass carp reovirus (GCRV) often results in tremendous loss of fingerlings and yearlings, causing significant economic damages. However, it is difficult to study antiviral mechanisms in grass carp in vivo due to its large size and long reproductive cycle. Therefore, a small cyprinid species named rare minnow with high sensitivity to GCRV, is regarded as a useful model to study the mechanisms of this disease. In this study, rare minnows were infected with the type-IIGCRV (GCRV-HZ08), and pathogenesis was investigated by BGISEQ-500 transcriptome sequencing of four cDNA libraries, hepatopancreas, gills, head-kidney and spleen, and real time quantitative PCR (qRT-PCR). We obtained 51.22 Gb bases in total, and de novo assembled 107,756 unigenes with an average length of 1,441 bp. GO analysis revealed that the differentially expressed genes (DEGs) involved in the defense mechanisms were the most enriched GO terms in all four tissues. KEGG analysis revealed that the most enriched pathways were "Influenza A", "Herpes simplex infection", "Transcriptional misregulation in cancer" and "Metabolic" pathways. We also performed a comparative transcriptomic study between GCRV-infected rare minnow and grass carp data. This revealed that "IL-17 signaling pathway", "NF-kappa B signaling pathway" and "Influenza A" pathways are conserved (important) in the regulation of anti-GCRV infection in both species, and need to be further investigated. Furthermore, a total of four immune-related DEGs were selected for qRT-PCR validation, and the results confirmed the RNA-seq data. These results enhance our understanding of the antiviral responses of cyprinid fish infected by GCRV.

Antiviral defense in salmonids - Mission made possible?

Viral diseases represent one of the major threats for salmonid aquaculture. Survival from viral infections are highly dependent on host innate antiviral immune defense, where interferons are of crucial importance. Neutralizing antibodies and T cell effector mechanisms mediate long-term antiviral protection. Despite an immune cell repertoire comparable to higher vertebrates, farmed fish often fail to mount optimal antiviral protection. In the quest to multiply and spread, viruses utilize a variety of strategies to evade or escape the host immune system. Understanding the specific interplay between viruses and host immunity at depth is crucial for developing successful vaccination and treatment strategies in mammals. However, this knowledge base is still limited for pathogenic fish viruses. Here, we have focused on five RNA viruses with major impact on salmonid aquaculture: Salmonid alphavirus, Infectious salmon anemia virus, Infectious pancreatic necrosis virus, Piscine orthoreovirus and Piscine myocarditis virus. This review explore the protective immune responses that salmonids mount to these viruses and the existing knowledge on how the viruses counteract and/or bypass the immune response, including their IFN antagonizing effects and their mechanisms to establish persisting infections.

Cyprinid viral diseases and vaccine development

In the past decades, global freshwater fish production has been rapidly growing, while cyprinid takes the largest portion. Along with the rapid rise of novel forms of intensive aquaculture, increased global aquatic animal movement and various anthropogenic stress to aquatic ecosystems during the past century, freshwater fish farming industry encounter the emergence and breakout of many diseases, especially viral diseases. Because of the ability to safely and effectively prevent aquaculture diseases, vaccines have become the mainstream technology for prevention and control of aquatic diseases in the world. In this review, authors summarized six major cyprinid viral diseases, including koi herpesvirus disease (KHVD), spring viraemia of carp (SVC), grass carp hemorrhagic disease (GCHD), koi sleepy disease (KSD), carp pox disease (CPD) and herpesviral haematopoietic necrosis (HPHN). The present review described the characteristics of these diseases from epidemiology, pathology, etiology and diagnostics. Furthermore, the development of specific vaccines respective to these diseases is stated according to preparation methods and immunization approaches. It is hoped that the review could contribute to aquaculture in prevention and controlling of cyprinid viral diseases, and serve the healthy and sustainable development of aquaculture industry.

Characterization of the TLR Family in Branchiostoma lanceolatum and Discovery of a Novel TLR22-Like Involved in dsRNA Recognition in Amphioxus

Toll-like receptors (TLRs) are important for raising innate immune responses in both invertebrates and vertebrates. Amphioxus belongs to an ancient chordate lineage which shares key features with vertebrates. The genomic research on TLR genes in Branchiostoma floridae and Branchiostoma belcheri reveals the expansion of TLRs in amphioxus. However, the repertoire of TLRs in Branchiostoma lanceolatum has not been studied and the functionality of amphioxus TLRs has not been reported. We have identified from transcriptomic data 30 new putative TLRs in B. lanceolatum and all of them are transcribed in adult amphioxus. Phylogenetic analysis showed that the repertoire of TLRs consists of both non-vertebrate and vertebrate-like TLRs. It also indicated a lineage-specific expansion in orthologous clusters of the vertebrate TLR11 family. We did not detect any representatives of the vertebrate TLR1, TLR3, TLR4, TLR5 and TLR7 families. To gain insight into these TLRs, we studied in depth a particular TLR highly similar to a B. belcheri gene annotated as bbtTLR1. The phylogenetic analysis of this novel BlTLR showed that it clusters with the vertebrate TLR11 family and it might be more related to TLR13 subfamily according to similar domain architecture. Transient and stable expression in HEK293 cells showed that the BlTLR localizes on the plasma membrane, but it did not respond to the most common mammalian TLR ligands. However, when the ectodomain of BlTLR is fused to the TIR domain of human TLR2, the chimeric protein could indeed induce NF-κB transactivation in response to the viral ligand Poly I:C, also indicating that in amphioxus, specific accessory proteins are needed for downstream activation. Based on the phylogenetic, subcellular localization and functional analysis, we propose that the novel BlTLR might be classified as an antiviral receptor sharing at least partly the functions performed by vertebrate TLR22. TLR22 is thought to be viral teleost-specific TLR but here we demonstrate that teleosts and amphioxus TLR22-like probably shared a common ancestor. Additional functional studies with other lancelet TLR genes will enrich our understanding of the immune response in amphioxus and will provide a unique perspective on the evolution of the immune system.

Characterization of grass carp CD40 and CD154 genes and the association between their polymorphisms and resistance to grass carp reovirus

In bony fish, CD40 and CD154 are two very important costimulatory molecules involved in T and B cell cooperation in thymus-dependent antibody production. In the current study, we identified the cDNAs of CD40 and CD154 and analyzed their genomic structures in grass carp. Quantitative real-time PCR indicated that the CD40 and CD154 were mainly expressed in immune organs. After challenge with grass carp reovirus (GCRV), these two genes were up-regulated at 72 h in head kidney and spleen. Moreover, seven and five single nucleotide polymorphisms (SNPs) were identified in the CD40 and CD154 respectively. Statistical analysis indicated that three SNPs in the coding region of the CD40 were significantly associated with the resistance of grass carp against GCRV. These results indicated that CD40 and CD154 play important roles in the responses to GCRV in grass carp. The SNP markers in the CD40 associated with the resistance to GCRV may facilitate the disease-resistant breeding of grass carp.

Genomic structure, expression pattern and polymorphisms of GILT in golden pompano Trachinotus ovatus (Linnaeus 1758)

The interferon-g-inducible lysosomal thiol reductase (GILT) plays a significant character in the processing and presentation of MHC class II restricted antigen (Ag) by catalyzing disulfide bond reduction in mammals. To explore the function of GILT in the immune system of fish, we cloned a GILT gene homologue from Trachinotus ovatus, the full-length cDNA of GILT, which consisted of 2, 747 bp with a 771 bp open reading frame, encoding a protein of 256 amino acids. Moreover, similar to other species GILT gene, 7 exons and 6 introns were identified in T. ovatus, the deduced protein also possessed a representative characteristic of known GILT proteins. The result of real-time quantitative PCR showed that GILT mRNA was dramatically expressed in immune-associated tissues, such as spleen (p < 0.01) and kidney (p < 0.05). Bacterial challenge revealed that GILT mRNA level remarkably up-regulation in liver, spleen, kidney and intestine after induction with Photobacterium damsela. Furthermore, based on cloned sequences and genome BLAST, only one SNP site (ToGILT-S1-g.148C>G) was identified, and the allele C was significantly associated with high-susceptibility (HS) group, nevertheless, the allele G was dramatically associated with high-resistance (HR) group, indicating potential application for disease resistant breeding selection in T. ovatus.

Teleosts Genomics: Progress and Prospects in Disease Prevention and Control

Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for the control and prevention of fish diseases. Metagenomics has emerged to be an important tool used to identify emerging infectious diseases for the timely design of rational disease control strategies, determining microbial compositions in different aquatic environments used for fish farming and the use of host microbiota to monitor the health status of fish. Expounding the use of antimicrobial peptides (AMPs) as therapeutic agents against different pathogens as well as elucidating their role in tissue regeneration is another vital aspect of genomics studies that had taken precedent in recent years. In vaccine development, prospects made include the identification of highly immunogenic proteins for use in recombinant vaccine designs as well as identifying gene signatures that correlate with protective immunity for use as benchmarks in optimizing vaccine efficacy. Progress in quantitative trait loci (QTL) mapping is beginning to yield considerable success in identifying resistant traits against some of the highly infectious diseases that have previously ravaged the aquaculture industry. Altogether, the synopsis put forth shows that genomics studies are beginning to yield positive contribution in the prevention and control of fish diseases in aquaculture.

Toll-like receptor (TLR) 22, a non-mammalian TLR in Asian seabass, Lates calcarifer: Characterisation, ontogeny and inductive expression upon exposure with bacteria and ligands

Toll-like receptor (TLR) 22 is a non-mammalian TLR found mostly in teleosts and characterized initially as a cell surface surveillance receptor for detecting extracellular long dsRNA. In the current study, the full-length cDNA sequence consisting of 3312 nucleotides encoding for 960 amino acids in Asian seabass (Lates calcarifer) TLR22 (AsTLR22) was identified. From the putative protein sequence, signature TLR domains such as 18 LRR domains, two transmembrane domains, a single LRR_CT domain and an intracellular TIR domain could be predicted. Phylogenetic analysis showed that AsTLR22 is clustered with other teleost TLR22 and is distinctly different from the other TLR groups. The transcript of AsTLR22 was ubiquitously expressed in all the tissues tested of healthy juveniles with the highest expression in gill followed by hindgut, spleen and skin. The AsTLR22 mRNA transcript was also detected in all the developmental stages as early as unfertilized eggs with higher expression in later stages such as neurula and early embryo. The dsRNA viral analogue, poly (I:C) and Gram-negative bacterium, Vibrio alginolyticus, were found to modulate the AsTLR22 expression in different tissues with the highest expression in kidney and liver. Gram-positive bacterium, Staphylococcus aureus, was also found to regulate the AsTLR22 expression at certain time-points with the highest expression in gill. Similarly, noticeable change in AsTLR22 expression was detected in SISK cell line induced with different ligands such as poly (I:C), LPS and PGN. The findings indicate that AsTLR22 responds in transcript level towards bacteria-borne PAMPs and extracellular dsRNA in the euryhaline teleost Asian seabass. Further, this might act as an important pathogen surveillance receptor during early developmental stages.

Complement component Bf/C2b gene mediates immune responses against Aeromonas hydrophila in grass carp Ctenopharyngodon idella

The complement system is a significant component of innate immunity. Here, we identified a Bf/C2 homolog (gcBf/C2b) in grass carp. gcBf/C2b shares a high similarity with Bf/C2b counterparts in other teleosts. gcBf/C2b transcription was widely distributed in different tissues, induced by Aeromonas hydrophila in vivo and in vitro, and affected by lipopolysaccharide and flagellin stimulation in vitro. In cells over-expressing gcBf/C2b, transcript levels of all components except gcC5 were significantly enhanced, and gcBf/C2b, gcIL1β, gcTNF-α, gcIFN, gcCD59, gcC5aR1, and gcITGβ-2 were significantly upregulated after A. hydrophila challenge or stimulation with bacterial pathogen-associated molecular patterns (PAMPs). However, gcBf/C2b in interference cells down-regulated the transcript levels after A. hydrophila challenge, and gcBf/C2b induced NF-κB signaling. These findings indicate the vital role of gcBf/C2b in innate immunity in grass carp.

SNPs in the Toll1 receptor of Litopenaeus vannamei are associated with immune response

Tolls and Toll-like receptors (TLRs) are important regulators in the innate immune system and their genetic variations usually affect the host's susceptibility/resistance to pathogen infections. In this study, we report on the single nucleotide polymorphisms (SNPs) of Toll1 in Litopenaeus vannamei (LvToll1) and how this is associated with immune response. PCR-DGGE analysis revealed genetic polymorphisms in LvToll1 at both the genomic DNA (gDNA) and cDNA levels. Using high-throughput sequencing, 223 SNPs were identified at the gDNA level, of which 145 were non-synonymous SNP (nsSNP), with 3 nsSNPs having frequency over 1%. On the other hand, 60 SNPs were identified at the cDNA level including 38 nsSNPs and 4 nsSNPs with frequency over 1%. Upon challenging shrimps with Streptococcus iniae, Vibrio parahaemolyticus and white spot syndrome virus (WSSV), LvToll1 was shown to generate 6, 4 and 4 novel bands, respectively when analyzed with PCR-DGGE. Sequencing analysis of these bands showed that they contained 6, 4 and 2 nsSNPs, respectively. Moreover, the nsSNP C1526T was detected in S. iniae-resistant but not in susceptible shrimps. Most significantly, the C1526T mutation could shorten the α-helix of the LRR domain and was predicted to affect the function of LvToll1, indicating that SNP C1526T might be associated with shrimp's resistance to pathogen infections. In sum, our findings here reveal that the genetic polymorphisms of Toll receptor are linked with the immune response to pathogen infections in L. vannamei.

Mannose-binding lectin and its roles in immune responses in grass carp (Ctenopharyngodon idella) against Aeromonas hydrophila

The complement system is a crucial component of the innate immune system that links innate and adaptive immunity via four pathways. Mannose-binding lectin (MBL), the initiating molecule of the lectin pathway, plays a significant role in the innate immune system in mammals and fish. Herein, we identified an MBL homolog (gcMBL) in grass carp (Ctenopharyngodon idella). The full-length 948 bp gcMBL cDNA includes a 741 bp open reading frame encoding a 246 amino acid protein with a signal peptide, collagen triple helix repeat domain, and a C-type lectin-like/link domain. The gcMBL protein shares low similarity with MBL counterparts in other species, and is most closely related to Cyprinus carpio MBL. Transcription of gcMBL was widely distributed in different tissues, and was induced by Aeromonas hydrophila in vivo and in vitro. Expression of gcMBL was also affected by LPS and flagellin stimulation in vitro. In cells over-expressing gcMBL, transcripts of almost all components except gcC5 were up-regulated, and gcMBL, gcIL1β, gcTNF-α, gcIFN, gcCD59, gcC5aR and gcITGβ-2 were significantly up-regulated following exposure to A. hydrophila or stimulation by bacterial PAMPs. Meanwhile, gcMBL deficiency achieved by RNAi down-regulated transcript levels following A. hydrophila challenge, and gcMBL induced NF-κB signalling. These findings indicate a vital role of gcMBL in innate immunity in grass carp.

Development of HyBeacon® probes for specific mRNA detection using body fluids as a model system

HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods. The work presented here details the development of a single-step one-tube RT-PCR assay to detect the presence of body fluids of forensic interest (saliva, blood, seminal fluid, vaginal fluid and menstrual blood) using HyBeacon^® probes and melt curve analysis. Each assay shows a high degree of specificity to the target body fluid mRNA suggesting there is no requirement to remove genomic DNA prior to analysis. Of the five assays developed, four were able to detect between 10 and 100 copies of target cDNA, the fifth 1000 copies of target. The results presented here demonstrate that such an approach can be optimised for non-expert users and further areas of work are discussed.

Pattern recognition receptors in grass carp Ctenopharyngodon idella: I. Organization and expression analysis of TLRs and RLRs

Pattern recognition receptors (PRRs) play indispensable roles in the immune responses against invading pathogens. In the present study, we systematically identified and characterized Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) as well as their adaptors in grass carp (Ctenopharyngodon idella). A comprehensive analysis of BLAST and other bioinformatics methods showed that C. idella TLR family consist of 21 members and their adaptors contain four members. Phylogenetic analyses confirmed the existence of six TLR subfamilies (TLR1, 3, 4, 5, 7 and 11 subfamily) in C. idella and revealed their homologous relationships with other species. Most C. idella TLRs possess three typical structural features of TLR protein family: LRR, TM and TIR domains. Meanwhile, RLR family consist of three conserved members (RIG-I, MDA5 and LGP2) as well as two adaptors (IPS-1 and STING) in C. idella. mRNA expression analyses of TLRs, RLRs and their adaptors indicated that most members are sustainably expressed in multiple tissues before and after grass carp reovirus (GCRV) or Aeromonas hydrophila infection, while TLR9, TLR20a/b, TLR25, TIRAP, SARM1 and STING are transiently expressed in specific tissues. TLRs are transmembrane receptors with few introns, while RLRs are cytoplasmic receptors with plenty of introns. TLRs and RLRs interact with adaptors to perform their functions via various signaling pathways. In conclusion, this study systematically explores the characteristics of TLRs and RLRs in C. idella and provides evidence for the response patterns after viral and/or bacterial infection in vivo. These results contribute to studying the regulation mechanisms of TLR and RLR signaling pathways, and deeply understanding fish immune responses against pathogen infection.

The polymorphism of chicken-type lysozyme gene in Japanese flounder (Paralichthys olivaceus) and its association with resistance/susceptibility to Listonella anguillarum

Lysozyme is a crucially spread hydrolase in organisms that can defend against bacterial infection in innate immunity. In this study, we successfully sequenced the coding region of chicken-type lysozyme gene (PoLysC) in Paralichthys olivaceus and identified nine single nucleotide polymorphisms (SNPs). We then amplified the 2500 bp promoter region of lysozyme and identified the eight sites of polymorphisms. All SNPs were genotyped between susceptible and resistance groups after Listonella anguillarum challenge. One of these SNP sites in the codon of PoLysC was genotyped and determined to be a significant marker by analyzing its distribution in the susceptible and resistant groups. As a nonsynonymous mutation, the frequency of 140G/C genotype in the resistant group was higher (67.74%) than that in the susceptible group (32.26%). The linkage between SNP140 and polymorphisms in the promoter region was also studied. Results revealed that the frequency of haplotype CC_-536/CC_-1200/GG₁₄₀ in the resistance group was significantly higher than that in the susceptible group. The quantitative expression of lysozyme gene in the resistant group was also higher than that in the susceptible group. This finding indicated that the linkage between polymorphism -536 and -1200 sites in promoter and SNP140 in codon sequence was associated with the resistance of P. olivaceus to L. anguillarum. All these results suggest that the mutations in promoter and coding region were related to changes in PoLysC for resisting L. anguillarum. The haplotype CC_-536/CC_-1200/GG₁₄₀ was a potential marker and can thus be applied to selective breeding for the disease resistance of P. olivaceus.

Mannan-binding lectin-associated serine protease-1 (MASP-1) mediates immune responses against Aeromonas hydrophila in vitro and in vivo in grass carp

The mannan-binding lectin-associated serine protease-1 (MASP-1) gene is a crucial component of the lectin pathway in the complement and coagulation cascade. Although MASP-1 has been found in the immune system of teleosts, its immune functions in response to bacterial infection are unclear. In this study, we identified a MASP-1 homolog (gcMASP-1) in the grass carp (Ctenopharyngodon idella). The full-length 3308-bp gcMASP-1 cDNA includes a 2160-bp open reading frame encoding a protein composed of 719 amino acids with epidermal growth factor-like, complement control protein, and trypsin-like domains. gcMASP-1 shares a high similarity with MASP-1 counterparts in other species, and it is most closely related to Cyprinus carpio MASP-1 and Sinocyclocheilus anshuiensis MASP-1. Transcription of gcMASP-1 was widely distributed in different tissues and induced by Aeromonas hydrophila in vivo and in vitro. Expression of gcMASP-1 was also affected by lipopolysaccharide and flagellin stimulation in vitro. In cells over-expressing gcMASP-1, transcript levels of almost all components, except gcMBL and gcC5, were significantly enhanced, and gcIL1β, gcTNF-α, gcIFN, gcCD59, gcC5aR1, and gcITGβ-2 were significantly upregulated after exposure to A. hydrophila; gcMASP-1 interference downregulated the transcript levels after A. hydrophila challenge. In addition, gcMASP-1 activated NF-κB signaling. These findings indicate the vital role of gcMASP-1 in innate immunity in C. idella.

Tissue specific expression profile of some immune related genes in Labeo rohita to Edwardsiella tarda infection

Rohu (Labeo rohita), an Indian Major Carp (IMC) is an economically important aquaculture species in India. Inspite of the technological advances, infectious diseases caused by viruses, bacteria and parasites have been a major limiting factor in the development and profitability of fish farms. At present, information regarding the immune status of the Indian major carps is limited. This lack of knowledge is a major impediment for establishment of effective preventive measures against broad spectrum of infectious agents. The present study was undertaken to examine the modulation of few immune-regulatory genes: IgHC, NOD 1, TLR 22, iNOS and IL-1β during experimental infection of E. tarda in L. rohita to understand their role in pathogenesis. Rohu fingerlings were intra-peritoneally injected with Edwardsiella tarda (LD₅₀ dose of 8.7 × 10⁴ CFU/fish) and sampled for three immunologically important organs (kidney, liver and spleen) at different time intervals (zero hour or pre-challenge and 6 h, 12 h, 24 h, 48 h and 96 h post challenge). For absolute quantification of genes by real time RT-PCR, all the genes transcript were amplified from Poly I:C induced rohu lymphocytes and cloned in pTZ57R/T plasmid. Standard curves for each gene was generated from serially diluted plasmid bearing respective genes. Evaluation of copy number of different genes present in the tissue showed that the expression of IgHC, iNOS and IL-1β was highest in kidney followed by spleen and least in liver. While for NOD 1 and TLR 22 gene, liver showed higher expression than kidney and spleen. Further, the expression of IgHC, INOS, TLR 22, NOD 1 and IL-1β genes significantly differed (P < 0.05) in the E. tarda challenged fish when compared with pre-challenged control fish. Among the five genes we studied, the basal expression of TLR 22 gene was highest. The result also depicts that iNOS and NOD 1 are immediate responsive genes as their expression reached maximum level at 6-24 h post infection (hpi) after which the expression declined. In contrast, TLR 22 and IgHC gene transcript showed enhanced expression during the late phase of with maximum expression observed after 48 hpi and 96 hpi respectively. IL-1β, being the exception, showed high expression both at 24 hpi and 96 hpi. From this study, we conclude that these five immune genes have a definite role to play in the defense mechanism of host (L. rohita) against E. tarda.

Molecular characterization and expression analysis of toll-like receptors 5 and 22 from natural triploid Carassius auratus

Innate immunity, as the most primitive and universal host defense in fish, constitutes an efficient first line of defense to combat invading microbes. Toll-like receptors (TLRs) play essential roles in the innate immunity, and TLR5 and TLR22 are two important TLRs that can recognize flagellin and double stranded RNA (dsRNA), respectively. In this study, we identified and characterized two TLRs genes of Qihe crucian carp (Carassius auratus) (designated as CaTLR5 and CaTLR22). The full-length cDNA sequence of CaTLR5 was cloned with 2972 bp including a 140 bp 5'-terminal untranslated region (UTR), a 183 bp 3'-UTR, and a 2649 bp open reading frame (ORF) encoding a deduced protein with 882 amino acids. The full-length cDNA of CaTLR22 was identified to be 3613 bp, consisting of a 228 bp 5'-UTR, a 547 bp 3'-UTR, and a 2838 bp ORF encoding a predicted protein of 945 amino acids. A typical TLR structure (an extracellular leucine-rich repeat domain, a transmembrane domain, and an intracellular Toll/IL-1 receptor domain) was found in CaTLR5 and CaTLR22. For either CaTLR5 or CaTLR22 gene, the mRNA expression levels varied in the different periods during the early stages of development. It was suggested that expression changes of gene CaTLR5 and CaTLR22 at mRNA levels were involved in developmental regulation in the early stages, and it was postulated that CaTLR5 and CaTLR22 play the important roles in immune defense in the early development stages of fish. Quantitative Real-Time PCR (qRT-PCR) revealed that CaTLR5 and CaTLR22 were constitutively expressed in all eleven tissues examined, although the mRNA expression level varied considerably among the different tissues. Following exposure to polyI:C, flagellin, and Aeromonas hydrophila, CaTLR5 and CaTLR22 were up-regulated in different tissues, and it was suggested that CaTLR5 and CaTLR22 were involved in the immune response of Qihe crucian carp against pathogenic invasions. The present findings will provide the valuable information for understanding the structure, function, expression, and the immune defense process of CaTLR5 and CaTLR22 in Qihe crucian carp, and provide new insights for developing the new strategies of disease control to protect fish against pathogens infection.

Molecular characterization of a fish-specific toll-like receptor 22 (TLR22) gene from common carp (Cyprinus carpio L.): Evolutionary relationship and induced expression upon immune stimulants

In the host innate immune system, various pattern recognition receptors (PRRs) recognize conserved pathogens-associated molecular patterns (PAMPs), and represent an efficient first line of defense against invading pathogens. TLR22 is one of the fish-specific Toll-like receptors (TLRs), identified in a variety of fish species. In this study, we report the cloning and identification of a TLR22 cDNA from the gills of common carp (Cyprinus carpio L.). The full-length CcTLR22 cDNA was 3301 bp long, including a 32 bp 5'-untranslated region (UTR), an open reading frame (ORF) of 2838 bp and a 432 bp 3'-UTR.The CcTLR22 protein was found to comprise a signal peptide, 16 LRR domains, a LRRCT domain in the extracellular region and a TIR domain in the cytoplasmic region, which fits with the characteristic TLR domain architecture. The genomic organization of CcTLR22 was identified, which was encoded by an uninterrupted exon. Sequence alignment and phylogenetic analysis showed that all known teleost TLR22 members were clustered into an independent clade of the TLR22 family, and showed high amino acid identities with other fish TLRs. Real-time PCR assay showed that CcTLR22 mRNA was expressed in almost all tissues examined, while the levels obviously varied among different tissues. When challenged with poly(I:C) (a viral model) or A. hydrophila bacteria, the expression level of CcTLR22 was up-regulated in a variety of common carp tissues. These results indicate that CcTLR22 plays a significant role in systemic as well as mucosal defence after viral or bacterial stimulation or infection.

Magnolol and honokiol from Magnolia officinalis enhanced antiviral immune responses against grass carp reovirus in Ctenopharyngodon idella kidney cells

Medicinal plants have been widely used for a long history. Exploration of pharmacologically active compounds from medicinal plants present a broad prevalent of application. By examining viral mRNA expression in GCRV-infected Ctenopharyngodon idella kidney (CIK) cells treated with thirty kinds of plant extracts, we identified Magnolia officinalis Rehd et Wils. was able to preferably suppress viral replication. Further studies demonstrated that the main ingredients of magnolia bark, namely, magnolol and honokiol presented protective pharmacological function when treated GCRV-infected CIK cells with a concentration of 2.00 μg/ml and 1.25 μg/ml, respectively. Furthermore, reverse transcript quantitative polymerase chain reaction (RT-qPCR) and western blot showed that both magnolol and honokiol were efficient to restrain the replication of GCRV in CIK cells at non-toxic concentration (2.51 ± 0.51 μg/ml for magnolol, and 3.18 ± 0.61 μg/ml for honokiol). Moreover, it was found that magnolol and honokiol promoted the expression of immune-related genes. Magnolol obviously significantly increased the expression of interferon (IFN) regulatory factor (IRF)7 rather than that of IRF3 in the GCRV-infected cells, leading to the activation of type I IFN (IFN-I). Simultaneously, magnolol drastically facilitated the expression of interleukin (IL)-1β, but failed to induce the molecules in nuclear factor (NF)-κB pathways. Differently, honokiol strikingly motivated not only the expression of IL-1β, but also those of tumor necrosis factor α (TNFα) and NF-κB. Interestingly, though honokiol motivated the expression of IFN-β promoter stimulator 1 (IPS-1), IRF3 and IRF7, it failed to up-regulate the expression of IFN-I, indicating that honokiol enhanced the host innate antiviral response to GCRV infection via NF-κB pathways. Collectively, the present study revealed that magnolol and honokiol facilitated the expression of innate immune-related genes to strengthen the innate immune signaling responses to resist GCRV infection, which contributed to understanding the mechanisms by which small-molecule drugs possessed antiviral activities. In addition, these results lay a foundation for the development of broad-spectrum antiviral compounds in aquaculture industry.

Expression analysis of nine Toll-like receptors in yellow catfish (Pelteobagrus fulvidraco) responding to Aeromonas hydrophila challenge

Toll-like receptors (TLRs) are important components of pattern recognition receptors (PRRs), which play significant roles in innate immunity to defense against pathogen invasion. Many TLRs have been found in teleosts, but there are no reports about cloning and expression of TLR genes in yellow catfish (Pelteobagrus fulvidraco). In this study, we analyzed the sequence characters and the relative mRNA expression levels of nine TLRs (TLR1, TLR2, TLR3, TLR4-1, TLR5, TLR7, TLR8-2, TLR9 and TLR22) in different tissues of yellow catfish. The results showed that all nine TLR genes are highly expressed in head kidney, trunk kidney, spleen and liver, all of which are related to host immunity. Subsequently we used Aeromonas hydrophila as a stimulating agent to detect the expression profiles of these nine TLRs in the liver, spleen, trunk kidney and head kidney of yellow catfish at different time points after injection with killed Aeromonas hydrophila. All nine TLRs responded to A. hydrophila challenge with tissue-specific patterns in different immune tissues. The kinetics of up- or down-regulation of these nine TLRs exhibited a similar trend, rising to an elevated level at first and then falling to the basal level, but the peak value differed at different time points in different tissues. The expression levels of the TLR3, TLR4-1, TLR9 and TLR22 genes were significantly up-regulated after bacterial challenge in the liver, spleen, head kidney and trunk kidney. The relatively high expression of TLR genes in the immune tissues in response to the A. hydrophila challenge indicated that TLRs may play important roles in the innate immune response against gram-negative bacteria in yellow catfish.

Characterization and expression of Megalobrama amblycephala toll-like receptor 22 involved in the response to Aeromonas hydrophila

The toll-like receptors (TLR) tlr22 was identified and characterized for the first time in one of the economically most important freshwater fish species in China, Megalobrama amblycephala. The full-length cDNA (4039 bp) of M. amblycephala tlr22 contains an open reading frame of 2706 bp, encoding a 901 amino-acid long polypeptide. The putative polypeptide contains 16 leucine-rich repeat (LRR) motifs, an LRR C-terminal, a transmembrane region and a cytoplasmic toll-interleukin-1 receptor (TIR) domain. Phylogenetic analyses revealed that M. amblycephala Tlr22 shared the closest relationship with a grass carp ortholog. tlr22 was constitutively expressed in nine tissues and during 10 developmental stages studied, albeit with varying expression levels. Along with many pathological changes observed after Aeromonas hydrophila bacterium infection, tlr22 and myd88 mRNA were significantly upregulated in blood, head kidney, spleen and intestine, indicating that tlr22 is involved in the immune response. These results provide an insight into tlr22 regulation mechanisms in the innate immune response to bacterial infection.

Characterization of Toll-like receptor gene expression in goldfish (Carassius auratus) during Dactylogyrus intermedius infection

Toll-like receptors (TLRs), the first and best understood innate immune receptors, play a notable role in the innate immune system by sensing pathogenic agents and initiating appropriate immune responses. However, studies about the roles of fish TLRs in response to the infection of the ectoparasitic monogenean Dactylogyrus intermedius have been surprisingly vacant. In the present study, cDNA fragments of five members of TLRs family in goldfish (Carassius auratus) were cloned and the expression patterns of nine TLRs in five tissues at different time points during D. intermedius infection were subsequently investigated. We found that the expressions of TLR4, TLR5, TLR20 and TLR22 were significantly elevated after infection at some time points, of which the transcription of TLR5 was progressively increased nearly in all tissues, whereas the mRNA levels of other TLRs (TLR2, 3, 7, 9 and 21) were down-regulated or showed no significant change compared with the control at most time points. Additionally, this paper was also conducted to explore the expression of above TLRs after re-infected with D. intermedius. The results showed a significant upregulation of TLR4, TLR5 and TLR22 in all tested tissues at these two time points, especially the levels of TLR4 and TLR22 expression, were even higher comparing with the first infection. Besides, tissue-specific expression analysis revealed that spleen featured the highest expressions of almost all the TLR-encoding genes among detected tissues. The informations obtained here could be helpful towards understanding the functions of TLRs in response to parasitic infection in goldfish and provide new insights for the development of preventive and therapeutic approaches against D. intermedius infection.

Immunity to nervous necrosis virus infections of orange-spotted grouper (Epinephelus coioides) by vaccination with virus-like particles

Nervous necrosis virus (NNV) is a kind of the betanodaviruses, which can cause viral nervous necrosis (VNN) and massive mortality in larval and juvenile stages of orange-spotted grouper (Epinephelus coioides). Due to the lack of viral genomes, virus-like particles (VLPs) are considered as one of the most promising candidates in vaccine study to control this disease. In this study, a type of VLPs, which was engineered on the basis of orange-spotted grouper nervous necrosis virus (OGNNV), was produced from prokaryotes. They possessed the similar structure and size to the native NNV. In addition, synthetic oligodeoxynucleotide (ODN) containing CpG motif was added in vaccines, and the expression patterns of several genes were analyzed after injecting with VLP and VLP with adjuvant (VA) to assess the regulation effect of vaccine for inducing immune responses. RT-PCR assays showed that six related genes in healthy tissues were ubiquitously expressed in all nine tested tissues. The vaccine alone was able to enhance the expression of genes, including MHCIa, MyD88, TLR3, TLR9 and TLR22 after vaccination, indicating that the vaccine was able to induce immune response in grouper. In liver, spleen and kidney, the gene expressions of VA group were all significantly higher than that of VLP group at 72 h post-stimulation, showing that the fish of VA challenge group obtained the longer-lasting protective immunity and resistance to pathogen challenge than that of VLP group. The data indicated that the efficacy of vaccine could be further enhanced by CpG ODN after vaccination and provided the reference for the development of future viral vaccine in grouper.

Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila

The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.

Moroxydine hydrochloride inhibits grass carp reovirus replication and suppresses apoptosis in Ctenopharyngodon idella kidney cells

Moroxydine hydrochloride (Mor) is known to have multi-antiviral activities against DNA and RNA viruses but very little information exists on its pharmacology. The paper was undertaken to explore the antiviral response and antiapoptotic mechanism of Mor against grass carp reovirus (GCRV) in Ctenopharyngodon idella kidney (CIK) cells. The results showed that exposing GCRV-infected cell to 6.3 μg mL(-1) of Mor for 96 h avoid ca. 50% apoptosis. Meanwhile, Mor had lower cytotoxicity than ribavirin (Rib) as the value of safe concentration was threefold higher than effective concentration and the compound could ensure sufficient into and out of cells within 4 h when tested at the maximal safe concentration. Mor blocked the GCRV-induced cytopathic effects and eliminated nucleocapsids in CIK cells to keep the normal morphological structure. Moreover, the expressions of viral protein genes were significantly inhibited especially the guanylyl transferase and RNA-dependent RNA polymerase related expression. Furthermore, GCRV caused Bcl-2 down-regulation and Bax mitochondrial translocation was prevented by treatment of CIK cells with Mor. The downstream effector, caspase activity was also significantly inhibited in Mor treated cells. The potential mechanism might be that mitochondrial apoptotic signals were not activated by the intervention of Mor for targeting viral gene expression. Taken together, Mor showed high anti-GCRV activity and had been proved as a secure and promising agent in viral controlling in aquaculture industry.

Transcriptome profiling of grass carp (Ctenopharyngodon idellus) infected with Aeromonas hydrophila

Aeromonas hydrophila is the causative pathogen of intestinal hemorrhage which has caused great economic loss in grass carp aquaculture. In order to understand the immunological response of grass carp to infection by A. hydrophila, the transcriptomic profiles of the spleens from infected and non-infected grass carp groups were obtained using HiSeq™ 2500 (Illumina). An average of 63 million clean reads per library was obtained, and approximately 80% of these genes were successfully mapped to the reference genome. A total of 1591 up-regulated and 530 down-regulated genes were identified. Eight immune-related categories involving 105 differently expressed genes were scrutinized. 16 of the differently expressed genes involving immune response were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of grass carp defense against A. hydrophila invasion.