Expression profiling of immune-related genes from Japanese flounder Paralichthys olivaceus kidney cells using cDNA microarrays

Can histology and haematology explain inapparent Streptococcus agalactiae infections and asymptomatic mortalities on Nile tilapia farms?

The aim of this study was to characterise possible histopathological and haemato-immunological changes after subclinical infection by S. agalactiae S13 serotype Ib. One hundred juveniles of Nile tilapia with average weight of 45 g were distributed in ten 90 L experimental units. After the acclimation period 25 fish were euthanised, and fragments of liver, spleen and posterior mid-intestine tissue were sampled to verify the integrity of the organs and blood samples taken to check the haematological profile. Fifty animals were used to verify the optimal dosage for the challenge. The remaining 25 fish were infected with S. agalactiae S13. After 96 h, tissue fragments from the liver, spleen and posterior mid-intestine and blood samples were collected. The analyses revealed that, 96 h after contagion, S. agalactiae S13 serotype Ib caused subclinical lesions in the liver and spleen that are not commonly described as pathognomonic, in addition to haematological alterations. These results allow a better understanding of sudden recurrent mortalities in Brazilian tilapia farms, since the serotype Ib of S. agalactiae causes inapparent infections and can remain lodged in internal organs and cause irreversible lesions and haemato-immunological alterations, therefore compromising physiological functions vital for the health of fish without revealing external clinical signs in the animals.

Zebra Fish Lacking Adaptive Immunity Acquire an Antiviral Alert State Characterized by Upregulated Gene Expression of Apoptosis, Multigene Families, and Interferon-Related Genes

To investigate fish innate immunity, we have conducted organ and cell immune-related transcriptomic as well as immunohistologic analysis in mutant zebra fish (Danio rerio) lacking adaptive immunity (rag1^−/−) at different developmental stages (egg, larvae, and adult), before and after infection with spring viremia carp virus (SVCV). The results revealed that, compared to immunocompetent zebra fish (rag1^+/+), rag1^−/− acquired increased resistance to SVCV with age, correlating with elevated transcript levels of immune genes in skin/fins and lymphoid organs (head kidney and spleen). Gene sets corresponding to apoptotic functions, immune-related multigene families, and interferon-related genes were constitutively upregulated in uninfected adult rag1^−/− zebra fish. Overexpression of activated CASPASE-3 in different tissues before and after infection with SVCV further confirmed increased apoptotic function in rag1^−/− zebra fish. Concurrently, staining of different tissue samples with a pan-leukocyte antibody marker showed abundant leukocyte infiltrations in SVCV-infected rag1^−/− fish, coinciding with increased transcript expression of genes related to NK-cells and macrophages, suggesting that these genes played a key role in the enhanced immune response of rag1^−/− zebra fish to SVCV lethal infection. Overall, we present evidence that indicates that rag1^−/− zebra fish acquire an antiviral alert state while they reach adulthood in the absence of adaptive immunity. This antiviral state was characterized by (i) a more rapid response to viral infection, which resulted in increased survival, (ii) the involvement of NK-cell- and macrophage-mediated transcript responses rather than B- and/or T-cell dependent cells, and (iii) enhanced apoptosis, described here for the first time, as well as the similar modulation of multigene family/interferon-related genes previously associated to fish that survived lethal viral infections. From this and other studies, it might be concluded that some of the characteristics of mammalian trained immunity are present in lower vertebrates.

Characterization and functional analysis of a novel C1q-domain-containing protein in Japanese flounder (Paralichthys olivaceus)

The complement system is important in the innate immune response. C1q-domain-containing proteins have multiple functions and occur extensively in invertebrates and vertebrates. In this study, PoC1ql3 encoding a C1q-domain-containing protein in the Japanese flounder was identified. The 266-amino-acid polypeptide encoded, PoC1ql3, shares high sequence and structural similarity with orthologues in other fish and mammals. PoC1ql3 is abundantly expressed in the brain, but less in the blood, gills, and liver. Transcripts of PoC1ql3 were down-regulated in the spleen and liver 6-24 h after bacterial infection, but were significantly up-regulated after 48 h. Full-length PoC1ql3 (C1ql3-full) and its gC1q domain (C1ql3-part) were both exerted anti-Edwardsiella tarda activity. C1ql3-part bound to lipopolysaccharide and peptidoglycan, and exerted antibacterial effects against E. tarda in vivo, suggesting that C1ql3 functions as a pathogen-recognition receptor. Therefore, PoC1ql3 functions in the innate immune system, which would facilitate the investigation of the immune system in Japanese flounder.

Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production

Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.

A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis

Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production.

Temperature-dependent regulation of gene expression in poly (I:C)-treated Japanese flounder, Paralichthys olivaceus

Gene expression profiling of poly (I:C)-treated Japanese flounder, Paralichthys olivaceus, under different temperatures was investigated using microarray analysis. The response was analyzed in spleen tissue at 3 and 24 h post injection (hpi) at 15 °C and 25 °C. A large number of genes in fish treated with poly (I:C) at 25 °C were expressed at 3 hpi, whereas the expression profiles at 24 hpi appeared to be similar to those of the controls. Cluster analysis of the different expression profiles showed three distinct groups of up-regulated genes in fish reared at 15 °C. These were early (3 hpi), early-to-late (3 and 24 hpi), and late (24 hpi) up-regulated genes. These genes included type I IFN-related genes and inflammatory genes. Among the up-regulated genes, most of the type I IFN-related genes played early-to-late- and late-responding genes at 15 °C but early-responding genes at 25 °C. Thus, several up-regulated genes in these groups from the microarray result were further verified by qPCR. These results indicate that the type I IFN gene expressions of P. olivaceus treated with poly (I:C) can be regulated in a temperature-dependent manner.

De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity

Background

Japanese flounder (Paralichthys olivaceus) is an economically important marine fish in Asia and has suffered from disease outbreaks caused by various pathogens, which requires more information for immune relevant genes on genome background. However, genomic and transcriptomic data for Japanese flounder remain scarce, which limits studies on the immune system of this species. In this study, we characterized the Japanese flounder spleen transcriptome using an Illumina paired-end sequencing platform to identify putative genes involved in immunity.

Methodology/Principal Findings

A cDNA library from the spleen of P. olivaceus was constructed and randomly sequenced using an Illumina technique. The removal of low quality reads generated 12,196,968 trimmed reads, which assembled into 96,627 unigenes. A total of 21,391 unigenes (22.14%) were annotated in the NCBI Nr database, and only 1.1% of the BLASTx top-hits matched P. olivaceus protein sequences. Approximately 12,503 (58.45%) unigenes were categorized into three Gene Ontology groups, 19,547 (91.38%) were classified into 26 Cluster of Orthologous Groups, and 10,649 (49.78%) were assigned to six Kyoto Encyclopedia of Genes and Genomes pathways. Furthermore, 40,928 putative simple sequence repeats and 47, 362 putative single nucleotide polymorphisms were identified. Importantly, we identified 1,563 putative immune-associated unigenes that mapped to 15 immune signaling pathways.

Conclusions/Significance

The P. olivaceus transciptome data provides a rich source to discover and identify new genes, and the immune-relevant sequences identified here will facilitate our understanding of the mechanisms involved in the immune response. Furthermore, the plentiful potential SSRs and SNPs found in this study are important resources with respect to future development of a linkage map or marker assisted breeding programs for the flounder.

Early immune responses in rainbow trout liver upon viral hemorrhagic septicemia virus (VHSV) infection

Among the essential metabolic functions of the liver, in mammals, a role as mediator of systemic and local innate immunity has also been reported. Although the presence of an important leukocyte population in mammalian liver is well documented, the characterization of leukocyte populations in the teleost liver has been only scarcely addressed. In the current work, we have confirmed the presence of IgM⁺, IgD⁺, IgT⁺, CD8α⁺, CD3⁺ cells, and cells expressing major histocompatibility complex (MHC-II) in rainbow trout (Oncorhynchus mykiss) liver by flow cytometry and/or immunohistochemistry analysis. Additionally, the effect of viral hemorrhagic septicemia virus (VHSV) on the liver immune response was assessed. First, we studied the effect of viral intraperitoneal injection on the transcription of a wide selection of immune genes at days 1, 2 and 5 post-infection. These included a group of leukocyte markers genes, pattern recognition receptors (PRRs), chemokines, chemokine receptor genes, and other genes involved in the early immune response and in acute phase reaction. Our results indicate that T lymphocytes play a key role in the initial response to VHSV in the liver, since CD3, CD8, CD4, perforin, Mx and interferon (IFN) transcription levels were up-regulated in response to VHSV. Consequently, flow cytometry analysis of CD8α⁺ cells in liver and spleen at day 5 post-infection revealed a decrease in the number of CD8α⁺ cells in the spleen and an increased population in the liver. No differences were found however in the percentages of B lymphocyte (IgM⁺ or IgD⁺) populations. In addition, a strong up-regulation in the transcription levels of several PRRs and chemokines was observed from the second day of infection, indicating an important role of these factors in the response of the liver to viral infections.

Differential transcriptomic response in the spleen and head kidney following vaccination and infection of Asian seabass with Streptococcus iniae

Vaccination is an important strategy in the protection of aquaculture species from major diseases. However, we still do not have a good understanding of the mechanisms underlying vaccine-induced disease resistance. This is further complicated by the presence of several lymphoid organs that play different roles when mounting an immune response. In this study, we attempt to elucidate some of these mechanisms using a microarray-based approach. Asian seabass (Lates calcarifer) were vaccinated against Streptococcus iniae and the transcriptomic changes within the spleen and head kidney at one and seven days post-vaccination were profiled. We subsequently challenged the seabass at three weeks post-vaccination with live S. iniae and similarly profiled the transcriptomes of the two organs after the challenge. We found that vaccination induced an early, but transient transcriptomic change in the spleens and a delayed response in the head kidneys, which became more similar to one another compared to un-vaccinated ones. When challenged with the pathogen, the spleen, but not the head kidneys, responded transcriptomically at 25-29 hours post-challenge. A unique set of genes, in particular those involved in the activation of NF-κB signaling, was up-regulated in the vaccinated spleens upon pathogen challenge but not in the un-vaccinated spleens. A semi-quantitative PCR detection of S. iniae using metagenomic DNA extracted from the water containing the seabass also revealed that vaccination resulted in reduction of pathogen shedding. This result indicated that vaccination not only led to a successful immune defense against the infection, but also reduced the chances for horizontal transmission of the pathogen. In conclusion, we have provided a transcriptomic analysis of how the teleost spleen and head kidneys responded to vaccination and subsequent infection. The different responses from the two organs are suggestive of their unique roles in establishing a vaccine-induced disease resistance.

Ligand specificities of Toll-like receptors in fish: indications from infection studies

Toll like receptors (TLRs) are present in many different fish families from several different orders, including cyprinid, salmonid, perciform, pleuronectiform and gadiform representatives, with at least some conserved properties among these species. However, low conservation of the leucine-rich repeat ectodomain hinders predictions of ligand specificities of fish TLRs based on sequence information only. We review the presence of a TLR genes, and changes in their gene expression profiles as result of infection, in the context of different fish orders and fish families. The application of RT-qPCR and availability of increasing numbers of fish genomes has led to numerous gene expression studies, including studies on TLR gene expression, providing the most complete dataset to date. Induced changes of gene expression may provide (in)direct evidence for the involvement of a particular TLR in the reaction to a pathogen. Especially when findings are consistent across different studies on the same fish species or consistent across different fish species, up-regulation of TLR gene expression could be a first indication of functional relevance. We discuss TLR1, TLR2, TLR4, TLR5 and TLR9 as presumed sensors of bacterial ligands and discuss as presumed sensors of viral ligands TLR3 and TLR22, TLR7 and TLR8. More functional studies are needed before conclusions on ligands specific to (groups of) fish TLRs can be drawn, certainly true for studies on non-mammalian TLRs. Future studies on the conservation of function of accessory molecules, in conjunction with TLR molecules, may bring new insight into the function of fish TLRs.

Three complement component 1q genes from rock bream, Oplegnathus fasciatus: genome characterization and potential role in immune response against bacterial and viral infections

Complement component 1q (C1q) is a subcomponent of the C1 complex and the key protein that recognizes and binds to a broad range of immune and non-immune ligands to initiate the classical complement pathway. In the present study, we identified and characterized three novel C1q family members from rock bream, Oplegnathus fasciatus. The full-length cDNAs of C1q A-like (RbC1qAL), C1q B-like (RbC1qBL), and C1q C-like (RbC1qCL) consist of 780, 720 and 726 bp of nucleotide sequence encoding polypeptides of 260, 240 and 242 amino acids, respectively. All three RbC1qs possess a leading signal peptide and collagen-like region(s) (CLRs) in the N-terminus, and a C1q domain at the C-terminus. The C1q characteristic Gly-X-Y repeats are present in all three RbC1qs, while the CLR-associated sequence that enhances phagocytic activity is present in RbC1qAL ((49)GEKGEP(54)) and RbC1qCL ((70)GEKGEP(75)). Moreover, the coding region was distributed across six exons in RbCqAL and RbC1qCL, but only five exons in RbC1qBL. Phylogenetic analysis revealed that the three RbC1qs tightly cluster with the fish clade. All three RbC1qs are most highly expressed in the spleen and liver, as indicated by qPCR tissue profiling. In addition, all three are transcriptionally responsive to immune challenge, with liver expression being significantly up-regulated in the early phase of infection with intact, live bacteria (Edwardsiella tarda and Streptococcus iniae) and virus (rock bream iridovirus) and in the late phase of exposure to purified endotoxin (lipopolysaccharide). These data collectively suggest that the RbC1qs may play defense roles as an innate immune response to protect the rock bream from bacterial and viral infections.

Identification of multipath genes differentially expressed in pathway-targeted microarrays in zebrafish infected and surviving spring viremia carp virus (SVCV) suggest preventive drug candidates

Spring viremia carp virus (SVCV) is a rhabdovirus seasonally affecting warm-water cyprinid fish farming causing high impacts in worldwide economy. Because of the lack of effective preventive treatments, the identification of multipath genes involved in SVCV infection might be an alternative to explore the possibilities of using drugs for seasonal prevention of this fish disease. Because the zebrafish (Danio rerio) is a cyprinid susceptible to SVCV and their genetics and genome sequence are well advanced, it has been chosen as a model for SVCV infections. We have used newly designed pathway-targeted microarrays 3-4-fold enriched for immune/infection functional-relevant probes by using zebrafish orthologous to human genes from selected pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). The comparative analysis of differential expression of genes through 20 pathways in 2-day exposed or 30-day survivors of SVCV infection allowed the identification of 16 multipath genes common to more than 6 pathways. In addition, receptors (Toll-like, B-cell, T-cell, RIG1-like) as well as viral RNA infection pathways were identified as the most important human-like pathways targeted by SVCV infection. Furthermore, by using bioinformatic tools to compare the promoter sequences corresponding to up and downregulated multipath gene groups, we identified putative common transcription factors which might be controlling such responses in a coordinated manner. Possible drug candidates to be tested in fish, can be identified now through search of data bases among those associated with the human orthologous to the zebrafish multipath genes. With the use of pathway-targeted microarrays, we identified some of the most important genes and transcription factors which might be implicated in viral shutoff and/or host survival responses after SVCV infection. These results could contribute to develop novel drug-based prevention methods and consolidate the zebrafish/SVCV as a model for vertebrate viral diseases.

Screening and analysis of PoAkirin1 and two related genes in response to immunological stimulants in the Japanese flounder (Paralichthys olivaceus)

A member of the NF-κB signaling pathway, PoAkirin1, was cloned from a full-length cDNA library of Japanese flounder (Paralichthys olivaceus). The full-length cDNA comprises a 5′UTR of 202 bp, an open reading frame of 564 bp encoding a 187-amino-acid polypeptide and a 521-bp 3′UTR with a poly (A) tail. The putative protein has a predicted molecular mass of 21 kDa and an isoelectric point (pI) of 9.22. Amino acid sequence alignments showed that PoAkirin1 was 99% identical to the Scophthalmus maximus Akirin protein (ADK27484). Yeast two-hybrid assays identified two proteins that interact with PoAkirin1: PoHEPN and PoC1q. The cDNA sequences of PoHEPN and PoC1q are 672 bp and 528 bp, respectively. Real-time quantitative reverse-transcriptase polymerase chain reaction analysis showed that bacteria could induce the expressions of PoAkirin1, PoHEPN and PoC1q. However, the responses of PoHEPN and PoC1q to the bacterial challenge were slower than that of PoAkirin1. To further study the function of PoAkirin1, recombinant PoAkirin1 and PoHEPN were expressed in Escherichia coli and would be used to verify the PoAkirin1-PoHEPN binding activity. These results identified two proteins that potentially interact with PoAkirin1 and that bacteria could induce their expression.

Iron-metabolic function and potential antibacterial role of Hepcidin and its correlated genes (Ferroportin 1 and Transferrin Receptor) in turbot (Scophthalmus maximus)

Antimicrobial peptide plays an important role in fish immunity. The small molecular antimicrobial peptide Hepcidin in turbot was studied and reported in this paper. The Ferroportin 1 (FPN1) and Transferrin Receptor (TFR) genes, which are related to Hepcidin, were cloned in turbot. The characteristics of Hepcidin and its related genes were studied, including an analysis of the expression patterns and cloning of the Hepcidin promoter, the relationship between Hepcidin and NF-κB and the regulation of iron-metabolism. The results showed that the promoter of SmHepcidin contains the binding sites of NF-κB, and NF-κB may directly or indirectly receive feedback signals from SmHepcidin. In the liver, spleen and kidney, in which there was an increased SmHepcidin expression level, SmFPN1 dramatically decreased and SmTFR was also either decreased or exhibited no obvious change after bacterial/viral infection and an injection of exogenous Hepcidin protein. RNAi experiments in turbot kidney cells confirmed the expression changes of these gene patterns. Furthermore, the administration of exogenous Hepcidin protein, which regulates the level of chelatable iron in cells, further confirmed the function of Hepcidin in iron metabolism. It is speculated that the rapidly increased expression of SmHepcidin may induce changes in the expression of related genes, and that the in vivo chelatable iron concentration which participates in the antibacterial process was also changed when exogenous pathogens are present in turbot. It is suggested that SmHepcidin plays a defensive role against pathogenic infection.

Microarray-based identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV)

Viral haemorrhagic septicaemia virus (VHSV) is one of the major threats to the development of the aquaculture industry worldwide. The present study was aimed to identify genes differentially expressed in several turbot (Scophthalmus maximus) families showing different mortality rates after VHSV. The expression analysis was conducted through genome-wide expression profiling with an oligo-microarray in the head kidney. A significant proportion of the variation in the gene expression profiles seemed to be explained by the genetic background, indicating that the mechanisms by which particular species and/or populations can resist a pathogen(s) are complex and multifactorial. Before the experimental infections, fish from resistant families (low mortality rates after VHSV infection) showed high expression of different antimicrobial peptides, suggesting that their pre-immune state may be stronger than fish of susceptible families (high mortality rates after VHSV infection). After infection, fish from both high- and low-mortality families showed an up-modulation of the interferon-induced Mx2 gene, the IL-8 gene and the VHSV-induced protein 5 gene compared with control groups. Low levels of several molecules secreted in the mucus were observed in high-mortality families, but different genes involved in viral entrance into target cells were down-regulated in low-mortality families. Moreover, these families also showed a strong down-modulation of marker genes related to VHSV target organs, including biochemical markers of renal dysfunction and myocardial injury. In general, the expression of different genes involved in the metabolism of sugars, lipids and proteins were decreased in both low- and high-mortality families after infection. The present study serves as an initial screen for genes of interest and provides an extensive overview of the genetic basis underlying the differences between families that are resistant or susceptible to VHSV infection.

Identification of surrogates of protection against yersiniosis in immersion vaccinated Atlantic salmon

Simple cost-effective bacterins are the earliest and most successfully used commercial vaccines in fish. In particular, those prepared from Yersinia ruckeri have proven effective at controlling Enteric Red Mouth Disease (ERM) and yersiniosis in rainbow trout and Atlantic salmon, respectively. However, the emergence of outbreaks of ERM caused by atypical biotypes of Y. ruckeri and reports of vaccine failure resulting in mass mortality of hatchery Atlantic salmon has reinvigorated interest in vaccines against fish bacterial diseases. Therefore the objective of this study was to identify surrogates of protection against yersiniosis using cDNA microarray to characterise the response of host genes in the gills of unvaccinated and vaccinated Atlantic salmon challenged with Y. ruckeri. Differentially expressed genes were identified using two-way ANOVA and restricted to those with >2.5-fold change at P<0.05. Using cDNA microarray we identified the expression of 6 genes in response to infection and 4 genes associated with the protective host response to yersiniosis. Analysis by real-time PCR confirmed that three immunologically relevant genes, namely a cathelicidin (47-fold) and a C-type lectin (19-fold) increased in response to yersiniosis. Including collagenase (17-fold increase), an important tissue remodelling and repair enzyme, these genes represent 3 of 6 non-protective and/or pathological responses to yersiniosis. Genes associated with the protective host response included an immunoglobulin gene and a selenoprotein that showed significant fold changes (15-fold increases each), highlighting the importance of antibody-mediated protection against yersiniosis. These findings provide much needed knowledge of the host-pathogen interaction in response to bacterial infection and immunisation in fish. Significantly, we identified a transcriptional biosignature consisting of predominantly immune-relevant genes (14 up and 3 down-regulated) in the gills of Atlantic salmon after immersion vaccination and before bacterial challenge. This biosignature may be used as a surrogate of protection and therefore as a predictor of vaccine success against yersiniosis.

Identification of biomarkers indicative of barotrauma and recovery in black rockfish Sebastes melanops

A Sebastes-specific complementary DNA (cDNA) microarray was developed to identify potential biomarkers involved in the capture stress and recovery of Sebastes species if they are assisted in returning to their original depth of capture following barotrauma. Black rockfish Sebastes melanops were exposed to simulated decompression from 450 kPa (c. 35 m depth) (which resulted in barotrauma) and subsequent recompression. Sebastes melanops were sampled for liver tissue at days 3, 15 and 31 post-barotrauma. Potential candidate genes were identified from the microarray and then quantitative real-time PCR (qrt-PCR) was used to validate expression levels in biological replicates. Six potential biomarkers associated with the innate immune system were identified that were up-regulated in liver tissue at 3 days post-barotrauma: complement C1q-like protein 2, complement component C3, complement regulatory plasma protein, serum amyloid A-5, c-type lysozyme and hepcidin precursor type I. In addition, complement c1q was correlated to the presence of a ruptured swimbladder, providing further support that this gene may be a good biomarker of injury and recovery. Immune genes were no longer up-regulated at day 31 post-barotrauma, a good indication of recovery in S. melanops.

Transglutaminase regulates immune-related genes in shrimp

Transglutaminase (TGase) is known to be involved in blood coagulation, a conserved defence mechanism among invertebrates. Gene silencing of TGase was previously shown to render shrimp susceptible to both bacterial and viral infections suggesting that TGase is an essential component of the shrimp immune system. Here, we examine the effects of the absence of TGase on the transcriptomic profile of kuruma shrimp by microarray analysis, focussing on genes that are involved in shrimp immunity. Total RNAs from shrimp haemocytes injected with dsRNA specific for TGase and control samples were isolated at 3 and 7 days p.i. and analyzed by microarray. Results revealed that TGase silencing affects the expression of genes in shrimp and caused significant down-regulation of the expressions of crustin and lysozyme. Furthermore, TGase-depleted samples were found to have lower haemocyte counts and higher total bacterial counts in their haemolymph. These results suggest that TGase is an important component of the shrimp immune response and is involved in the regulation of some immune-related genes particularly antimicrobial peptides.

PAMPs, PRRs and the genomics of gram negative bacterial recognition in fish

Understanding the mechanisms that underpin pathogen recognition and subsequent orchestration of the immune response in fish is an area of significant importance for both basic research and management of health in aquaculture. In recent years much attention has been given to the identification of pattern recognition receptors (PRRs) in fish, however, characterisation of interactions with specific pathogen-associated molecular patterns (PAMPs) is still incomplete. Microarray studies have significantly contributed to functional studies and early descriptions of PAMP-PRR driven activation of specific response cassettes in the genome have been obtained although much is left to be done. In this review we will address gram negative (G-negative) bacterial recognition in fish addressing contributing factors such as structure-function relationships between G-negative PAMPs, current knowledge of fish PRRs and the input achieved by microarray-based studies ranging from in vivo infection studies to directed in vitro PAMP-cell studies. Finally we revisit the endotoxic recognition paradigm in fish and suggest a series of future perspectives that could contribute toward the further elucidation of G-negative bacterial recognition across the highly diverse group of vertebrates that encompass the fishes.

Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in Japanese flounder Paralichthys olivaceus leucocytes during Edwardsiella tarda and viral hemorrhagic septicemia virus infection

Transcriptional changes in the peripheral blood leucocytes (PBL) of Japanese flounder Paralichthys olivaceus challenged by Edwardsiella tarda and viral hemorrhagic septicemia virus (VHSV) were investigated using suppression subtractive hybridization (SSH) coupled with cDNA microarray analysis. First, we constructed an SSH cDNA library using mRNA samples isolated from PBL of P. olivaceus that had been experimentally infected with E. tarda. We then examined the transcriptional changes occurring in the PBL due to E. tarda and VHSV infection using a cDNA microarray produced using clones produced from the SSH library. A total of 565 and 180 cDNA sequences corresponding to mRNA species that are either up- or down-regulated by E. tarda infection were isolated by SSH. While host gene expression responses in response to E. tarda and VHSV infection share several response elements, distinct patterns of gene expression were also observed. Specifically, E. tarda infection enhanced the expression of cell adhesion molecules while VHSV enhanced the expression of interferon and proteasome-related genes. In challenge trials of the two infectious agents, expression profiles of chemokines were also observed to differ. The results indicated that distinguishing between viral and bacterial infection is possible based on the RNA expression profiles of PBL from infected fish.

A new Akirin1 gene in turbot (Scophthalmus maximus): molecular cloning, characterization and expression analysis in response to bacterial and viral immunological challenge

SmAkirin1, a member of the NF-κB signaling pathway, was isolated from turbot by RACE. Its cDNA was 564 bp and encoded a putative protein of 187 amino acids with a predicted molecular mass of 21 kDa and an isoelectric point (pI) of 9.05. Amino acid sequence alignments showed that SmAkirin1 was 91% identical to the Salvelinus alpinus Akirin1 protein ACV49694. Transient expression of SmAkirin1-GFP in the turbot kidney cell line SMKC revealed a nuclear localization of the protein, and a typical NLS signal was found at the N-terminal region of the SmAkirin1 protein. Trans-activation assay in yeast demonstrated that SmAkirin1 has no transcriptional activation. Transcriptional analysis showed that SmAkirin1 was expressed in all of the tissues examined, with the highest expression in the spleen and brain. Real-time quantitative reverse-transcriptase polymerase chain reaction analysis showed that the SmAkirin1 transcript was induced by bacterial and viral infection.

Genomic resources for flatfish research and their applications

Flatfishes are a group of teleosts of high commercial and environmental interest, whose biology is still poorly understood. The recent rapid development of different 'omic' technologies is, however, enhancing the knowledge of the complex genetic control underlying different physiological processes of flatfishes. This review describes the different functional genomic approaches and resources currently available for flatfish research and summarizes different areas where microarray-based gene expression analysis has been applied. The increase in genome sequencing data has also allowed the construction of genetic linkage maps in different flatfish species; these maps are invaluable for investigating genome organization and identifying genetic traits of commercial interest. Despite the significant progress in this field, the genomic resources currently available for flatfish are still scarce. Further intensive research should be carried out to develop larger genomic sequence databases, high-density microarrays and, more detailed, complete linkage maps, using second-generation sequencing platforms. These tools will be crucial for further expanding the knowledge of flatfish physiology, and it is predicted that they will have important implications for wild fish population management, improved fish welfare and increased productivity in aquaculture.

Zebrafish fin immune responses during high mortality infections with viral haemorrhagic septicemia rhabdovirus. A proteomic and transcriptomic approach

Background

Despite rhabdoviral infections being one of the best known fish diseases, the gene expression changes induced at the surface tissues after the natural route of infection (infection-by-immersion) have not been described yet. This work describes the differential infected versus non-infected expression of proteins and immune-related transcripts in fins and organs of zebrafish Danio rerio shortly after infection-by-immersion with viral haemorrhagic septicemia virus (VHSV).

Results

Two-dimensional differential gel electrophoresis detected variations on the protein levels of the enzymes of the glycolytic pathway and cytoskeleton components but it detected very few immune-related proteins. Differential expression of immune-related gene transcripts estimated by quantitative polymerase chain reaction arrays and hybridization to oligo microarrays showed that while more transcripts increased in fins than in organs (spleen, head kidney and liver), more transcripts decreased in organs than in fins. Increased differential transcript levels in fins detected by both arrays corresponded to previously described infection-related genes such as complement components (c3b, c8 and c9) or class I histocompatibility antigens (mhc1) and to newly described genes such as secreted immunoglobulin domain (sid4), macrophage stimulating factor (mst1) and a cluster differentiation antigen (cd36).

Conclusions

The genes described would contribute to the knowledge of the earliest molecular events occurring in the fish surfaces at the beginning of natural rhabdoviral infections and/or might be new candidates to be tested as adjuvants for fish vaccines.

Microarray technology is an effective tool for identifying genes related to the aquacultural improvement of Japanese flounder, Paralichthys olivaceus

Molecular techniques are now essential for discovering new functional genes for the improvement of cultured marine organisms. Such techniques can be used to obtain expressed sequence tags (EST) and, through the use of microarrays, the entire transcriptome. For example, microarrays can be used to reveal biomarkers of health conditions, nutrient changes and immune response in fish and shellfish. EST-based microarray chips were constructed for cultured fish and shellfish species including Japanese flounder (Paralichthys olivaceus). Using the flounder microarray chip, the efficacy of two DNA vaccines derived from pathogenic viruses [hirame rhabdovirus (HRV) and viral hemorrhagic septicemia virus (VHSV)] was evaluated through gene expression profiles. The results suggest that both DNA vaccines were effective in protecting the flounder from HIRRV and VHSV. The flounder microarray was also used to compare gene expression patterns in fish that are susceptible and resistant to Edwardsiella tarda. At 3days post infection, the gene expression patterns between the two groups were dramatically changed. Thus, microarray analysis is a very powerful tool to understand gene expression profiles in fish.

BCG vaccine confers adaptive immunity against Mycobacterium sp. infection in fish

Mycobacteriosis, caused by Mycobacterium sp., results in severe loss of fish production in Japan's aquaculture industry. In this study, the effects of two vaccine candidates, Bacillus Calmette and Guèrin (BCG, an attenuated strain of Mycobacterium bovis) and formalin-killed cells of Mycobacterium sp. were evaluated in Japanese flounder, Paralichthys olivaceus. In the immediate response and tuberculin response, BCG-vaccinated fish showed higher gene expression levels of inflammatory cytokines such as IL-1beta, IL-6, IFN-gamma and TNFalpha. Furthermore, BCG vaccination conferred protective efficacy against Mycobacterium sp. infection in Japanese flounder. Transcriptome analysis using a Japanese flounder cDNA microarray revealed that BCG vaccination induced not only adaptive immunity against Mycobacterium sp. antigen but also the expression of non-specific bactericidal proteins such as lysozyme. These data suggest that BCG confers immunity to Mycobacterium sp. infection and is a potent vaccine candidate for fish mycobacteriosis.

Stress transcriptomics in fish: a role for genomic cortisol signaling

The physiological responses to stressors, including hormonal profiles and associated tissue responsiveness have been extensively studied in teleosts, but the molecular mechanisms associated with this adaptive response are not well understood. The advent of cDNA microarray technology has transformed the field of functional genomics by revealing global gene expression changes in response to stressor exposures even in non-mammalian vertebrates, including fish. A unifying response in studies related to stressor exposure is activation of the hypothalamus-pituitary-interrenal (HPI) axis in fish, leading to cortisol release into the circulation. Here we will discuss the implications of some of the gene expression changes observed in response to acute stress in fish, while highlighting a role for cortisol in this adaptive stress response. As liver is a key organ for metabolic adjustments to stressors and also is a major target for cortisol action, the genomic studies pertaining to stress and glucocorticoid regulation have focused mainly on this tissue. The studies have identified several genes that are altered transiently after an acute stressor exposure in fish. A number of these stress-responsive genes were also modulated by glucocorticoid receptor activation, suggesting that elevation in cortisol levels during stressor exposure may be a key signal for target tissue molecular programming, essential for stress adaptation. The identification of regulatory gene networks that are stress activated, and modulated by cortisol, both in hepatic and extra-hepatic tissues, including gonads, brain, immune cells and gills, will provide a mechanistic framework to characterize the multifaceted role of cortisol during stress adaptation.

Differential gene expression in black tiger shrimp, Penaeus monodon, following administration of oxytetracycline and oxolinic acid

The intensification of shrimp farming systems has led to the spreading of a variety of bacterial and viral diseases that continue to plague the shrimp industry worldwide. Efforts to combat these pathogenic organisms include the use of immunostimulants, probiotics, vaccines and antibiotics. Although a few studies have already reported on the effects of various stimuli on shrimp, the effect of antibiotics, particularly on the changes in the shrimp transcriptomic profile have yet to be reported. Here we show that injecting shrimp with oxytetracycline and oxolinic acid alters the expression of genes in the black tiger shrimp, Penaeus monodon, lymphoid organ. These antibiotics, especially oxylinic acid, down-regulated the expression of a few immune-related genes, most notably penaeidin, proPO, clotting protein, profilin and whey acidic protein.

Gene expression profile of hemocytes of kuruma shrimp, Marsupenaeus japonicus following peptidoglycan stimulation

Shrimps are believed to lack an adaptive immune system and therefore rely heavily on their innate immune mechanisms to ward off pathogens. Moreover, their innate defense reactions are triggered by bacterial and fungal cell wall components such as lipopolysaccharides, peptidoglycan and beta-glucans. In this study, we used microarray to examine the gene expression profile of kuruma shrimp, Marsupenaeus japonicus, after stimulation with peptidoglycan. Subsequent results show that the number of upregulated genes and percentage of differential expression (21%) was highest at day 1 poststimulation. Differentially expressed genes in day 7 and day 14, on the other hand, were 3.25% and 11.21%, respectively. Sixty-one (61) genes of unknown function were found to have responded outright to peptidoglycan (PG) stimulation. Administration of PG also caused increases in the expressions of crustin, lysozyme, and a few antibacterial peptides, all of which are known to be involved in crustacean immune response. Taken together, our results suggest that innate response in shrimp is triggered instantaneously upon exposure to a bacterial component.

Toxicogenomic analysis of immune system-related genes in Japanese flounder (Paralichthys olivaceus) exposed to heavy oil

Heavy oil contamination is one of the most important environmental issues. Toxicities of polycyclic aromatic hydrocarbons (PAHs), including immune toxicities, are well characterized, however, the immune toxic effects of heavy oil, as a complex mixture of PAHs, have not been investigated. In the present study, we selected Japanese flounder (Paralichthys olivaceus) as a model organism, and observed alteration of immune function by the exposure to heavy oil. To analyze the expression profiles of immune system-related genes, we selected 309 cDNAs from our flounder EST library, and spotted them on a glass slide. Using this cDNA array, alteration of gene expression profiles was analyzed in the kidneys of flounders exposed to heavy oil. Six Japanese flounders (mean body weight: 197 g) were acclimated to laboratory conditions at 19-20 degrees C. Three fish were exposed to heavy oil C (bunker C) at a concentration of 3.8 g/L for 3 days, and the others were kept in seawater without heavy oil and used as the control. After the exposure period, the fish were transferred into control seawater and maintained for 4 days, and then they were dissected and their kidneys were removed. Total RNA was extracted from the kidney samples to use in gene expression analyses. The microarray detected alteration of immune system-related genes in the kidneys of heavy oil-exposed flounders, including down-regulation of immunoglobulin light chain, CD45, major histocompatibility complex class II antigens and macrophage colony-stimulating factor precursor, and up-regulation of interleukin-8 and lysozyme. These results suggest that pathogen resistance may be weakened in heavy oil-exposed fish, causing a subsequent bacterial infection, and then proinflammatory genes may be induced as a defensive response against the infection. Additionally, we found candidate genes for use as biomarkers of heavy oil exposure, such as N-myc downstream regulated gene 1 and heat shock cognate 71 kDa proteins.

Immune-related gene expression profiling of yellowtail (Seriola quinqueradiata) kidney cells stimulated with ConA and LPS using microarray analysis

To better understand the immune system of a commercially important fish (yellowtail, Seriola quinqueradiata), we constructed a cDNA microarray containing 1001 selected genes from yellowtail EST and used this to investigate gene expression of primary cultured kidney cells stimulated with ConA and LPS. The total number of up-regulated genes stimulated by LPS was apparently greater than that of ConA stimulation, whereas down-regulated genes were markedly found in ConA-stimulated group. Of the genes that were up-regulated at 3, 6, and 12h after LPS treatment, 12%, 13% and 12%, respectively, were immune-related. Immune-related genes were sorted into 4 groups based on their differential expression patterns against LPS induction. LPS induced the expression of genes related to inflammation, cytokine activity, antigen presentation and antigen binding such as, IL-1beta, CC chemokine with stalk CK2, MHC class II beta chain and immunoglobulin heavy chain. Amplified fragments of RT-PCR products of IgM, IL-1beta, nephrosin, and beta-actin had signal intensities that were comparable to those obtained with the microarray. Overall, these results show that microarrays are a promising tool for uncovering immune mechanism in teleost fish. cDNA sequences of genes were deposited in the GenBank database at DDBJ with accession numbers BB 996897-BB 997897.

Identification, characterization and expression of a novel cytokine M17 homologue (MSH) in fish

Members of the interleukin 6 (IL6)-cytokine subfamily of proteins are involved in numerous physiological processes including cellular development, inflammatory function, and acute phase and immune responses. Previously, a cytokine-like gene named M17, which is closely associated with the IL6 subfamily, has been identified in fish with no apparent orthologue in higher vertebrates. Here, we cloned a novel cDNA from Japanese flounder, Paralichthys olivaceus, which had significant identity but exhibited contrasting expression with fish M17s, named here as M17 Homologue (MSH). With subsequent in silico search and full annotation of the M17 orthologue in zebrafish (Danio rerio), MSH orthologues in tiger puffer (Takifugu rubripes), green spotted pufferfish (Tetraodon nigroviridis) and stickleback (Gastorosteus aculeatus), as well as structural, synteny comparisons and phylogenetic analysis with known IL6-cytokines, we determined the novelty of the fish MSH. Japanese flounder MSH was observed to be highly expressed in immune-related tissues and are induced by immune stimulants, lipopolysaccharide (LPS), polyI:C and peptidoglycan (PG) in vitro suggesting that it is involved in fish immunity particularly against viral and bacterial agents, a functional feature exhibited by previously reported fish cytokines.

Identification of a novel C-type lectin gene in Japanese flounder, Paralichthys olivaceus

A novel C-type lectin of Japanese flounder (JFCTL) was identified among Japanese flounder liver EST. Of 2083 of Japanese flounder liver ESTs in the GenBank database, 48 were identical to JFCTL, suggesting that JFCTL is abundantly produced in liver. JFCTL cDNA contains an open reading frame of 642 bp encoding 214 amino acids. A C-type lectin domain was conserved in the deduced amino acid sequence. The protein showed homology to transmembrane-type C-type lectin receptors rather than the soluble C-type lectin so far reported, but it was predicted to be a secreted protein. Transcription of JFCTL was restricted to the liver. Although the mRNA was not induced after the treatment of fish with formalin-killed Edwardsiella tarda, expression was higher at 20 degrees C than at 10 degrees C.

Cloning and characterization of the IkappaBalpha gene from Japanese flounder, Paralichthys olivaceus

We identified and characterized the Japanese flounder (Paralichthys olivaceus) inhibitor kappa B alpha (JFIKBA) cDNA. The JFIKBA cDNA contains an open reading frame of 960bp encoding 320 amino acid residues. JFIKBA contains 6 ankyrin repeats in the central coding region. Expression studies by RT-PCR showed constitutive expression of the JFIKBA gene in several Japanese flounder tissues (brain, muscle, gill, heart, kidney, liver, spleen and intestine). Moreover, expression of JFIKBA mRNA was induced in kidney by LPS stimulation. To investigate the role of JFIKBA, we constructed a recombinant plasmid expressing the JFIKBA coding region under the control of the cytomegalovirus (CMV) promoter. Over-expression of the JFIKBA gene in the Japanese flounder cultured cell line derived from kidney, suppressed the expression of the TNF alpha gene with lipopolysaccharide stimulation. These results indicated that JFIKBA has an important role in the innate immune system, especially in the signaling of the cytokine network.

Transcriptional profile of red seabream iridovirus in a fish model as revealed by viral DNA microarrays

Red seabream iridovirus (RSIV) disease is a serious disease of many marine fish species in Japan and elsewhere. For a better understanding of the molecular pathogenic mechanism, we examined the transcriptional profile of RSIV in infected fish using a DNA microarray. Expression of RSIV open reading frames (ORFs) was first detected at about 5 days post-infection (d.p.i.), and accounted for about 45% of total ORFs. Almost all the ORFs (97-99%) were expressed at their maximum levels during 7-9 d.p.i. The expression levels and the number of expressed ORFs started to decrease at 10 d.p.i. These results suggest that pathogenesis of RSIV infection began at around day 5, and continued with high levels of viral multiplication until viral clearance by host antiviral defenses starting from around 10 d.p.i. A comparison of viral gene expressions in the spleen and kidney over the course of the infection suggests that RSIV preferentially targets the spleen. The spleen may thus be the most susceptible organ for diagnosis of iridoviral disease.

Difference in Japanese flounder, Paralichthys olivaceus gene expression profile following hirame rhabdovirus (HIRRV) G and N protein DNA vaccination

The glycoprotein (G protein) gene, but not other genes, of fish rhabdoviruses, when used as a DNA vaccine was previously shown to be highly effective in inducing a protective immune response. In this study we used a DNA microarray to examine differential gene expression in Japanese flounder (Paralichthys olivaceus) in response to a DNA vaccine made from the genes of hirame rhabdovirus (Rhabdovirus olivaceus) (HIRRV) G protein (pHRV-G) and nucleocapsid (N) protein (pHRV-N). A high level of protection against HIRRV infection was observed following vaccination with the pHRV-G but no protection was observed following vaccination with the pHRV-N. Microarray analyses showed that the set of genes induced by pHRV-G was different from the set induced by pHRV-N. Specifically, five genes (Interferon-stimulated gene, 15kDa (ISG15), Interferon-stimulated gene, 56kDa (ISG56), Mx and two unknown genes) were strongly induced after injection by the pHRV-G but not pHRV-N and three of these genes are known as type I IFN-inducible genes. Poly I:C, a known inducer of type I interferon that elicits immune response similar to that elicited by a virus infection, also induced these five genes in kidney cells. These results suggest that in order to be effective and confer protection, vaccines against HIRRV and probably fish rhabdoviruses may need to stimulate the type I IFN system.

Real-time gene expression analysis in carp (Cyprinus carpio L.) skin: inflammatory responses caused by the ectoparasite Ichthyophthirius multifiliis

Real time quantitative PCR (RQ-PCR) assays were developed for the measurement of differential real-time expression of immune-related genes in skin and whole blood from Cyprinus carpio during an infection with the ectoparasite Ichthyophthirius multifiliis. The target genes included the chemokines CXCa and CXCb, the chemokine receptors CXCR1 and CXCR2, the pro-inflammatory cytokines interleukin 1 beta (IL-1beta) and tumour necrosis factor alpha (TNF-alpha) and the enzymes inducible nitric oxide synthase (iNOS) and arginase 2. The strongest up-regulation in skin was observed in the IL-1beta, CXCR1 and iNOS genes at 36-48h post-exposure to theronts. A significant up-regulation of the genes CXCa and TNF-alpha was also observed. An up-regulation of the expression of the genes CXCa, CXCR1, IL-1beta and iNOS was likewise found in blood, although the increase in the expression levels was more moderate and the expression peak was detected earlier in comparison with the skin. In addition, CXCR2 and the arginase 2 genes were specifically induced in blood. Our results confirm the role of CXCR1 and IL-1beta as two prominent molecules involved in the initiation of the inflammatory process in fish in relation to an ectoparasite infection. Moreover, this study confirms the role of carp skin as an important source of pro-inflammatory molecules as well as an active modulator of the local inflammation. Finally, expression and regulation of the evaluated genes in blood confirm the important role of the migrated leucocytes in the immune response against I. multifiliis.

Gene expression of leucocytes in vaccinated Japanese flounder (Paralichthys olivaceus) during the course of experimental infection with Edwardsiella tarda

In this paper, we focused on the detection of differentially expressed genes in peripheral blood leucocytes (PBL) during the course of Edwardsiella tarda infection in vaccinated and non-vaccinated Japanese flounder (Paralichthys olivaceus). cDNA microarray analysis was performed to compare the gene expression patterns of the PBL between the vaccinated and non-vaccinated fish in response to E. tarda inoculation. Fish were vaccinated twice, at a two-week interval and experimentally challenged with E. tarda two weeks after the second vaccination. Among the 1187 analyzed genes, 42 genes were up-regulated during the course of infection either in vaccinated or non-vaccinated fish. These genes included immune-related genes, such as MMP-9, MMP-13, CXC chemokine, CD20 receptor and hepcidin. Some immune-related genes were down-regulated after the E. tarda challenge, i.e. interferon inducible Mx protein, MHC class II-associated invariant chain, MHC class II alpha and MHC class II beta encoding genes, immunoglobulin light chain precursor, immunoglobulin light chain and IgM. These responses are thought to be a common reaction of Japanese flounder PBL in the course of edwardsiellosis, irrespective of immunized condition. Ten genes were significantly up-regulated only in vaccinated fish, and 11 genes were significantly up-regulated only in non-vaccinated fish. These genes may have a correlation with the efficacy of vaccination, although we have no evidence to link the different gene expression patterns and the efficacy of vaccination at present.

Microarray studies of gene expression in fish

The use of microarrays for the study of various aspects of fish physiology has seen a spectacular increase in recent years. From early studies with model species, such as zebrafish, to current studies with commercially important species, such as salmonids, catfish, carp, and flatfish, microarray technology has emerged as a key tool for understanding developmental processes as well as basic physiology. In addition, microarrays are being applied to the fields of ecotoxicology and nutrigenomics. A number of different platforms are now available, ranging from microarrays containing cDNA amplicons to oligomers of various sizes. High-density microarrays containing hundreds of thousands of distinct oligomers have been developed for zebrafish and catfish. As this exciting technology advances, so will our understanding of global gene expression in fish. Furthermore, lessons learned from this experimentally tractable group of organisms can also be applied to more advanced organisms such as humans.

Genome-wide survey of the gene expression response to saprolegniasis in Atlantic salmon

Pathogenic saprolegniaceae species are among the major disease-causing agents in farmed salmonids and in freshwater fish in general. Recent studies have used high-throughput cDNA-based methods to identify new potential actors of fish defence systems against various bacteria and viruses. However, the response of fish to fungal or fungus-like pathogens is still poorly documented. Here, we used a 16,006-gene salmonid cDNA microarray to identify genes which transcription levels are modified in juvenile Atlantic salmon (Salmo salar) affected with saprolegniasis compared to healthy fish from the same families. Our results confirmed the importance of non-specific immunity in the response of fish to saprolegniaceae infections and identified both similarities and differences in their genome-wide transcriptional response to oomycetes compared with their responses to bacterial or viral infections. Moreover, several clones with no known homologues were shown to be over-transcribed in infected fish. These may represent as yet unidentified immune-relevant genes in fish.

Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium

The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APPs) which are synthesized in the liver and function in a wide range of immunity-related activities. Utilizing a new high-density in situ oligonucleotide microarray, we have evaluated the APR in channel catfish liver following infection with Edwardsiella ictaluri, a bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely related blue catfish. The analysis of microarray results using a traditional 2-fold change in gene expression cutoff and a 10% false-discovery rate revealed a well-developed APR in catfish, with particularly high upregulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP genes upregulated greater than 2-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Upregulation of the majority of the complement cascade was observed including the membrane attack complex components and complement inhibitors. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Independent testing of a selection of differentially expressed genes with real-time RT-PCR confirmed microarray results.

Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salar L.): a role for tumor suppressor p53 in AGD pathogenesis?

Neoparamoeba spp. are amphizoic amoebae with the capacity to colonize the gills of some marine fish, causing AGD. Here, the gill tissue transcriptome response of Atlantic salmon (Salmo salar L.) to AGD is described. Tanks housing Atlantic salmon were inoculated with Neoparamoeba spp. and fish sampled at time points up to 8 days postinoculation (pi.). Gill tissues were taken from AGD-affected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-unaffected fish. A total of 206 genes, representing 190 unique transcripts, were reproducibly identified as up- or downregulated in response to Neoparamoeba spp. infection. Informative transcripts having GO biological process identifiers were grouped according to function. Although a number of genes were placed into each category, no distinct patterns were observed. One Atlantic salmon cDNA that was upregulated in infected gill relative to noninfected gill at 114 and 189 h pi. showed significant identity with the Xenopus, mouse, and human anterior gradient-2 (AG-2) homologs. Two Atlantic salmon AG-2 mRNA transcripts, designated asAG-2/1 and asAG-2/2, were cloned, sequenced, and shown to be predominantly expressed in the gill, intestine, and brain of a healthy fish. In AGD-affected fish, differential asAG-2 expression was confirmed in samples used for microarray analyses as well as in AGD-affected gill tissue taken from fish in an independent experiment. The asAG-2 upregulation was restricted to AGD lesions relative to unaffected tissue from the same gill arch, while p53 tumor suppressor protein mRNA was concurrently downregulated in AGD lesions. Differential expression of p53-regulated transcripts, proliferating cell nuclear antigen and growth arrest and DNA damage-inducible gene-45beta (GADD45beta) in AGD lesions, suggests a role for p53 in AGD pathogenesis. Thus AGD may represent a novel model for comparative analysis of p53 and p53-regulated pathways.

Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus

Background

Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide microarray platform based on channel catfish EST sequences. This platform was used to profile gene expression in catfish spleens 2 h, 4 h, 8 h and 24 h after injection of lipopolysaccharide (LPS).

Results

In the spleen samples, 138 genes were significantly induced or repressed greater than 2-fold by LPS treatment. Real-time RT-PCR was used to verify the microarray results for nine selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R² = 0.87) with the results from the microarray.

Conclusion

The first generation channel catfish microarray provided several candidate genes useful for further evaluation of immune response mechanisms in this species. This research will help us to better understand recognition of LPS by host cells and the LPS-signalling pathway in fish.

Transcription program of red sea bream iridovirus as revealed by DNA microarrays

Red sea bream iridovirus (RSIV) has been identified as the causative agent of a serious disease in red sea bream and at least 30 other marine fish species. We developed a viral DNA microarray containing 92 putative open reading frames of RSIV to monitor the viral gene transcription program over the time course of an in vitro infection and to classify RSIV transcripts into temporal kinetic expression classes. The microarray analysis showed that viral genes commenced expression as early as 3 h postinfection (p.i.) and this was followed by a rapid escalation of gene expression from 8 h p.i. onwards. Based on the expression of some enzymes associated with viral DNA replication, the DNA replication of RSIV appeared to begin at around 8 h p.i. in infected cells in vitro. Using a de novo protein synthesis inhibitor (cycloheximide) and a viral DNA replication inhibitor (phosphonoacetic acid), 87 RSIV transcripts could be classified into three temporal kinetic classes: nine immediate-early (IE), 40 early (E), and 38 late (L) transcripts. The gene expression of RSIV occurred in a temporal kinetic cascade with three stages (IE, E, and L). Although the three classes of transcripts were distributed throughout the RSIV genome, E transcripts appeared to cluster in at least six discrete regions and L transcripts appeared to originate from seven discrete regions. The microarray data were statistically confirmed by using a t test, and were also clustered into groups based on similarity in the gene expression patterns by using a cluster program.