A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions

Of Whales and Genes: Unraveling the Physiological Response to Stressors in Belugas (Delphinapterus leucas) at the Molecular Level

Marine mammals, now more than ever, are exposed to environmental and anthropogenic stressors. A better understanding of stress physiology in marine mammals is warranted in order to assist in conservation efforts. This study screened gene expression profiles (cytokines, stress-response markers) in blood samples collected opportunistically under controlled conditions from aquarium belugas during transport and introduction to a novel environment (T/NEnv), participation in out-of-water examinations (OWE) and from wild belugas during live capture–release health assessments (WLCR). Quantitative-PCR was used to measure gene expression involved in physiological and immune responses at different time scales. Linear mixed models with repeated measures and pairwise comparisons were used for analysis. Overall, a generalized down-regulation of relative gene expression when compared to samples collected under behavioral control from aquarium whales or to pre-assessment samples of wild whales was observed, with genes IFNγ, IL2, TGFβ and Nr3c1 displaying the largest significant (p < 0.05) changes. Significant (p < 0.05) negative associations of inflammatory gene expression with norepinephrine suggest inhibitory effects of catecholamines on the inflammatory response. Overall, this study contributes to our understanding of the physiological response to stressors at the molecular level in belugas, and the genes suggested here can further be utilized as additional tools in beluga health assessments and monitoring.

Transcriptome analysis of cadmium exposure in kidney fibroblast cells of the North Atlantic Right Whale (Eubalaena glacialis)

An 8X15k oligonucleotide microarray was developed consisting of 2334 Eubalaena glacialis probes and 2166 Tursiops truncatus probes and used to measure the effects, at transcriptomic level, of cadmium exposure in right whale kidney fibroblast cells. Cells were exposed to three concentrations (1 μM, 0.1 μM, and 0.01 μM) of cadmium chloride (CdCl₂) for three exposure times (1, 4, and 24 h). Cells exposed to 1 μM CdCl₂ for 4 h and 24 h showed upregulated genes involved in protection from metal toxicity and oxidative stress, protein renaturation, apoptosis inhibition, as well as several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as ubiquitin proteasome system disruption, Ca²⁺ homeostasis interference, mitochondrial membrane potential collapse, reactive oxygen species (ROS) production, and cell cycle arrest. The results also have confirmed the right whale microarray as a reproducible tool in measuring differentiated gene expression that could be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.

IMMUNOMEDIATOR GENE TRANSCRIPTION PROFILING IN BELUGA WHALE (DELPHINAPTERUS LEUCAS) CLINICAL CASES

There is an unmet need for specific diagnostics of immune perturbations and inflammation in beluga whale (Delphinapterus leucas) clinical care. Quantitative real-time polymerase chain reaction (qPCR) has been used to measure immunomediator gene transcription in beluga whales. The study hypothesis was that a qPCR-based immunomediator assay would supplement routine clinical data with specific and sensitive information on immune status. Two beluga whale clinical cases provided an opportunity to test this hypothesis: a whale with a skin laceration and a whale with gastrointestinal inflammation. Mitogen-stimulated immunomediator gene transcription (MSIGT) was compared between the cases and healthy contact whales. In both case studies, mitogens increased transcription of IL1B, PTGS2 (Cox-2), TNF, HIF1A, and IL2 but decreased IL10 transcription in peripheral blood mononuclear cells (PBMC) from the abnormal whale over the control. Correlations were identified between most immunomediators tested and one or more standard blood clinical values. Considering all 15 immunomediators tested, the whale with gastrointestinal inflammation had a more unique MSIGT signature than the whale with a laceration. These results support further elucidation of beluga whale PBMC cytokine profiles for use as immune biomarkers.

Dolphin-derived NETosis results in rapid Toxoplasma gondii tachyzoite ensnarement and different phenotypes of NETs

Toxoplasma gondii is a cosmopolitan zoonotic parasite and nowadays considered as an emerging neozoan pathogen in the marine environment. Cetacean innate immune reactions against T. gondii stages have not yet been investigated. Thus, T. gondii tachyzoites were utilized to trigger neutrophil extracellular traps (NETs) in bottlenose dolphin (Tursiops truncatus) polymorphonuclear neutrophils (PMN). Scanning electron microscopy unveiled T. gondii tachyzoites as potent and rapid inducers of cetacean-derived NETosis. Co-localization of extracellular chromatin with global histones, granulocytic myeloperoxidase and neutrophil elastase confirmed classical characteristics of NETosis. Interestingly, different phenotypes of NETs were induced by tachyzoites resulting in spread, diffuse and aggregated NET formation and moreover, 'anchored' and 'cell free' NETosis was also detected. Current data indicate that cetacean-derived NETosis might represent an early, ancient and well-conserved host innate defense mechanism that not only acts against T. gondii but might also occur in response to other closely related emerging apicomplexan parasites affecting marine cetaceans.

Cytokine expression and lymphocyte proliferative capacity in diseased harbor porpoises (Phocoena phocoena) - Biomarkers for health assessment in wildlife cetaceans

Harbor porpoises (Phocoena phocoena) in the North and Baltic Seas are exposed to anthropogenic influences including acoustic stress and environmental contaminants. In order to evaluate immune responses in healthy and diseased harbor porpoise cells, cytokine expression analyses and lymphocyte proliferation assays, together with toxicological analyses were performed in stranded and bycaught animals as well as in animals kept in permanent human care. Severely diseased harbor porpoises showed a reduced proliferative capacity of peripheral blood lymphocytes together with diminished transcription of transforming growth factor-β and tumor necrosis factor-α compared to healthy controls. Toxicological analyses revealed accumulation of polychlorinated biphenyls (PCBs), dichlorodiphenyldichloroethylene (DDE), and dichlorodiphenyltrichloroethane (DDT) in harbor porpoise blood samples. Correlation analyses between blood organochlorine levels and immune parameters revealed no direct effects of xenobiotics upon lymphocyte proliferation or cytokine transcription, respectively. Results reveal an impaired function of peripheral blood leukocytes in severely diseased harbor porpoises, indicating immune exhaustion and increased disease susceptibility.

On the revolution of cetacean evolution

The order of Cetacea with 88 species including Odontoceti (or toothed whales) and Mysticeti (or baleen whales) is the most specialized and diversified group of mammals. The blue whale with a maximum recorded length of 29.9 m for 173 t of weight is the largest animal known to have ever existed, and any dolphin's brain is most powerful and complex than any other brain in the animal kingdom, second only to primate's. Nevertheless, Cetacea are mammals that re-entered the oceans only a little over 50 million years ago, a relatively short time on the evolutionary scale. During this time cetaceans and humans have developed marked morphological and behavioral differences, yet their genomes show a high level of similarity. This present review is focused on the description and significance of newly accessible cetacean genome tools and information, and their relevance in the study of the evolution of successful phenotypic adaptations associated to mammal's marine existence, and their applicability to the unresolved disease mechanisms in humans.

Molecular footprints of inshore aquatic adaptation in Indo-Pacific humpback dolphin (Sousa chinensis)

The Indo-Pacific humpback dolphin, Sousa chinensis, being a member of cetaceans, had fully adapted to inshore waters. As a threatened marine mammal, little molecular information available for understanding the genetic basis of ecological adaptation. We firstly sequenced and obtained the draft genome map of S. chinensis. Phylogenetic analysis in this study, based on the single copy orthologous genes of the draft genome, is consistent with traditional phylogenetic classification. The comparative genomic analysis indicated that S. chinensis had 494 species-specific gene families, which involved immune, DNA repair and sensory systems associated with the potential adaption mechanism. We also identified the expansion and positive selection genes in S. chinensis lineage to investigate the potential adaptation mechanism. Our study provided the potential insight into the molecular bases of ecological adaptation in Indo-Pacific humpback dolphin and will be also valuable for future understanding the ecological adaptation and evolution of cetaceans at the genomic level.

New Technologies for Monitoring Marine Mammal Health

Omics technologies have been developed in recent decades and applied to different subjects, although the greatest advancements have been achieved in human biology and disease. Genome sequencing and the exploration of its coding and noncoding regions are rapidly yielding meaningful answers to diverse questions, relating genome information to protein activity to environmental changes. In the past, marine mammal genetic and transcriptional studies have been restricted due to the lack of reference genomes. But the advance of high-throughput sequencing is revolutionizing the life sciences technologies. As long-lived organisms, at the top of the food chain, marine mammals play an important role in marine ecosystems and while their protected status is in favor of conservation of the species, it also complicates the researcher's approach to traditional measurements of health. Omics data generated by high-throughput technologies will represent an important key for improving the scientific basis for understanding both marine mammal and environment health.

Bottlenose dolphins (Tursiops truncatus) do also cast neutrophil extracellular traps against the apicomplexan parasite Neospora caninum

Neutrophil extracellular traps (NETs) are web-like structures composed of nuclear DNA decorated with histones and cytoplasmic peptides which antiparasitic properties have not previously been investigated in cetaceans. Polymorphonuclear neutrophils (PMN) were isolated from healthy bottlenose dolphins (Tursiops truncatus), and stimulated with Neospora caninum tachyzoites and the NETs-agonist zymosan. In vitro interactions of PMN with the tachyzoites resulted in rapid extrusion of NETs. For the demonstration and quantification of cetacean NETs, extracellular DNA was stained by using either Sytox Orange® or Pico Green®. Scanning electron microscopy (SEM) and fluorescence analyses demonstrated PMN-derived release of NETs upon exposure to tachyzoites of N. caninum. Co-localization studies of N. caninum induced cetacean NETs proved the presence of DNA adorned with histones (H1, H2A/H2B, H3, H4), neutrophil elastase (NE), myeloperoxidase (MPO) and pentraxin (PTX) confirming the molecular properties of mammalian NETosis. Dolphin-derived N. caninum-NETosis were efficiently suppressed by DNase I and diphenyleneiodonium (DPI) treatments. Our results indicate that cetacean-derived NETs represent an ancient, conserved and relevant defense effector mechanism of the host innate immune system against N. caninum and probably other related neozoan parasites circulating in the marine environment.

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.

A nutrigenomic approach to detect nutritional stress from gene expression in blood samples drawn from Steller sea lions

Gene expression profiles are increasingly being used as biomarkers to detect the physiological responses of a number of species to disease, nutrition, and other stressors. However, little attention has been given to using gene expression to assess the stressors and physiological status of marine mammals. We sought to develop and validate a nutrigenomic approach to quantify nutritional stress in Steller sea lions (Eumetopias jubatus). We subjected 4 female Steller sea lions to 3 feeding regimes over 70-day trials (unrestricted food intake, acute nutritional stress, and chronic nutritional stress), and drew blood samples from each animal at the end of each feeding regime. We then extracted the RNA of white blood cells and measured the response of 8 genes known to react to diet restriction in terrestrial mammals. Overall, we found that the genomic response of Steller sea lions experiencing nutritional stress was consistent with how terrestrial mammals respond to dietary restrictions. Our nutritionally stressed sea lions down-regulated some cellular processes involved in immune response and oxidative stress, and up-regulated pro-inflammatory responses and metabolic processes. Nutrigenomics appears to be a promising means to monitor nutritional status and contribute to mitigation measures needed to assist in the recovery of Steller sea lions and other at-risk species of marine mammals.

Machine learning approaches to investigate the impact of PCBs on the transcriptome of the common bottlenose dolphin (Tursiops truncatus)

As top-level predators, common bottlenose dolphins (Tursiops truncatus) are particularly sensitive to chemical and biological contaminants that accumulate and biomagnify in the marine food chain. This work investigates the potential use of microarray technology and gene expression profile analysis to screen common bottlenose dolphins for exposure to environmental contaminants through the immunological and/or endocrine perturbations associated with these agents. A dolphin microarray representing 24,418 unigene sequences was used to analyze blood samples collected from 47 dolphins during capture-release health assessments from five different US coastal locations (Beaufort, NC, Sarasota Bay, FL, Saint Joseph Bay, FL, Sapelo Island, GA and Brunswick, GA). Organohalogen contaminants including pesticides, polychlorinated biphenyl congeners (PCBs) and polybrominated diphenyl ether congeners were determined in blubber biopsy samples from the same animals. A subset of samples (n = 10, males; n = 8, females) with the highest and the lowest measured values of PCBs in their blubber was used as strata to determine the differential gene expression of the exposure extremes through machine learning classification algorithms. A set of genes associated primarily with nuclear and DNA stability, cell division and apoptosis regulation, intra- and extra-cellular traffic, and immune response activation was selected by the algorithm for identifying the two exposure extremes. In order to test the hypothesis that these gene expression patterns reflect PCB exposure, we next investigated the blood transcriptomes of the remaining dolphin samples using machine-learning approaches, including K-nn and Support Vector Machines classifiers. Using the derived gene sets, the algorithms worked very well (100% success rate) at classifying dolphins according to the contaminant load accumulated in their blubber. These results suggest that gene expression profile analysis may provide a valuable means to screen for indicators of chemical exposure.

Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal

Background

Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals (Arctocephalus gazella) that died of natural causes at Bird Island, South Georgia.

Results

After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog (Canis lupus familiaris) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms.

Conclusions

Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern.

Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers

Next-generation sequencing provides a powerful new approach for developing functional genomic tools for non-model species. This study aims to investigate the spotted seal (Phoca largha) transcriptome by the approach of Illumina paired-end sequencing technology. We obtained a total of 52,146,394 reads for the mixed tissues of liver and spleen from spotted seal. The de novo assemblies yielded 354,014 contigs and 178,466 unigenes. In addition, bioinformatics analysis revealed a total of 4425 simple sequence repeats (SSRs). Fifty SSRs were randomly selected to validate amplification and determine the degree of polymorphism in the genomic DNA pools. Thirty-five primer pairs successfully amplified expected DNA fragments and detected significant polymorphism among 28 spotted seal individuals. These results contribute to the understanding of the genetic makeup of spotted seal transcriptome and provide useful information for functional genomic research in this species.

Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans

Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems.

PCB-associated changes in mRNA expression in killer whales (Orcinus orca) from the NE Pacific Ocean

Killer whales in the NE Pacific Ocean are among the world's most PCB-contaminated marine mammals, raising concerns about implications for their health. Sixteen health-related killer whale mRNA transcripts were analyzed in blubber biopsies collected from 35 free-ranging killer whales in British Columbia using real-time quantitative polymerase chain reaction. We observed PCB-related increases in the expression of five gene targets, including the aryl hydrocarbon receptor (AhR; r(2) = 0.83; p < 0.001), thyroid hormone α receptor (TRα; r(2) = 0.64; p < 0.001), estrogen α receptor (ERα; r(2) = 0.70; p < 0.001), interleukin 10 (IL-10; r(2) = 0.74 and 0.68, males and females, respectively; p < 0.001), and metallothionein 1 (MT1; r(2) = 0.58; p < 0.001). Best-fit models indicated that population (dietary preference), age, and sex were not confounding factors, except for IL-10, where males differed from females. While the population-level consequences are unclear, the PCB-associated alterations in mRNA abundance of such pivotal end points provide compelling evidence of adverse physiological effects of persistent environmental contaminants in these endangered killer whales.

Hematopoietic cell populations in dolphin bone marrow: Analysis of colony formation and differentiation

Bone marrow biopsy is useful for diagnosis of hematopoietic diseases. We have recently reported that bone marrow biopsy from the flipper might be useful for diagnosis of hematopoietic diseases in dolphins. In this study, to demonstrate whether biopsy from the flipper is useful for clinical diagnosis, we investigated the gene expression profiles and proliferation and differentiation of bone marrow mononuclear cell (BMMC) isolated from the humeral bone marrow of bottlenose dolphins. BMMC exhibited gene expression profiles considered to be characteristic of hematopoietic cells. Similarly, a colony forming unit assay showed that dolphin BMMC possessed vigorous colony forming ability. The proliferation of hematopoietic progenitor cells resulted in the formation of three types of colonies, containing neutrophils, monocytes/macrophages and eosinophils with or without megakaryocytes, all of which could be identified based on the morphological characteristics and gene expression profiles typically associated with hematopoietic markers. Thus, dolphin BMMCs from humeral bone marrow contain many hematopoietic progenitor cells, and bone marrow biopsy from the flipper is suggested useful for clinical diagnosis for the dolphins.

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment

Background

The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.

Results

Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation.

Conclusion

In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

Background

Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.

Results

We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) ~84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (≥ 97% identity), only 13% of genes were identified as diverged. While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.

Conclusions

Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.

Immunology of whales and dolphins

The increasing disease susceptibility in different whale and dolphin populations has led to speculation about a possible negative influence of environmental contaminants on the immune system and therefore on the health status of marine mammals. Despite current efforts in the immunology of marine mammals several aspects of immune functions in aquatic mammals remain unknown. However, assays for evaluating cellular immune responses, such as lymphocyte proliferation, respiratory burst as well as phagocytic and cytotoxic activity of leukocytes and humoral immune responses have been established for different cetacean species. Additionally, immunological and molecular techniques enable the detection and quantification of pro- and anti-inflammatory cytokines in lymphoid cells during inflammation or immune responses, respectively. Different T and B cell subsets as well as antigen-presenting cells can be detected by flow cytometry and immunohistochemistry. Despite great homologies between marine and terrestrial mammal lymphoid organs, some unique anatomical structures, particularly the complex lymphoepithelial laryngeal glands in cetaceans represent an adaptation to the marine environment. Additionally, physiological changes, such as age-related thymic atrophy and cystic degeneration of the "anal tonsil" of whales have to be taken into account when investigating these lymphoid structures. Systemic morbillivirus infections lead to fatalities in cetaceans associated with generalized lymphoid depletion. Similarly, chronic diseases and starvation are associated with a loss of functional lymphoid cells and decreased resistance against opportunistic infections. There is growing evidence for an immunotoxic effect of different environmental contaminants in whales and dolphins, as demonstrated in field studies. Furthermore, immunomodulatory properties of different persistent xenobiotics have been confirmed in cetacean lymphoid cells in vitro as well as in animal models in vivo. However, species-specific differences of the immune system and detoxification of xenobiotics between cetaceans and laboratory rodents have to be considered when interpreting these toxicological data for risk assessment in whales and dolphins.

The vitamin D3 transcriptomic response in skin cells derived from the Atlantic bottlenose dolphin

The Atlantic bottlenose dolphin has attracted attention due to the evident impact that environmental stressors have taken on its health. In order to better understand the mechanisms linking environmental health with dolphin health, we have established cell cultures from dolphin skin as in vitro tools for molecular evaluations. The vitamin D3 pathway is one mechanism of interest because of its well established chemopreventative and immunomodulatory properties in terrestrial mammals. On the other hand, little is known of the physiological role of this molecule in aquatic animals. 1,25-dihydroxyvitamin D3 (1,25D3), the bioactive and hormonal form of vitamin D3, exerts its biological function by binding to the vitamin D receptor (VDR), a ligand-activated regulator of gene transcription. Therefore, we investigated the transcriptomic changes induced by 1,25D3 administration in dolphin skin cells. Identification of specific genes activated by 1,25D3 has provided clues to the physiological function of the vitamin D3 pathway in the dolphin. We found that exposure of the cells to 1,25D3 upregulated transactivation of a vitamin D-sensitive promoter. cDNA microarray analysis, using a novel dolphin array, identified specific gene targets within this pathway, and real-time PCR (qPCR) confirmed the enhanced expression of select genes of interest. These transcriptional changes correlated with an increase in VDR levels. This is the first report of the presence and activation of the vitamin D3 pathway in a marine mammal, and our experimental results demonstrate a number of similarities to terrestrial animals. Conservation of this pathway in the Atlantic bottlenose dolphin is consistent with the importance of nonclassic functions of vitamin D3, such as its role in innate immunity, similar to what has been demonstrated in other mammals.

Sampling the skin transcriptome of the North Atlantic right whale

As an initial step in defining the transcriptome of the North Atlantic right whale (Eubalaena glacialis) and developing functional genomic tools to study right whale health at the molecular physiological level, a cDNA library has been constructed from a skin biopsy. 2496 randomly selected clones (expressed sequence tags, ESTs) have been sequenced, and genes identified as important in the response to stress and immune challenges have been cloned by targeted RT-PCR from skin cDNA. The analysis of the EST collection (archived at www.marinegenomics.org and GenBank) showed a 34.79% redundancy, yielding 1578 unigenes and 27 potential microsatellite markers. 96 genes were cloned by targeted PCR; moreover, 52 of these genes are stress and immune function related. A Gene Ontology analysis of the unigene collection indicates that the skin is a rich source of expressed genes with diverse functions, suggesting an important role in multiple physiological processes including those related to immunity and stress response.

Quantitation of leukocyte gene expression in cetaceans

Real-time quantitation of cytokine mRNA is a routine immunologic technique, especially fitting for use in those species for which monoclonal antibodies are not available. Quantitative gene expression assays were developed to assist in the immunologic assessment of three cetacean species including bottlenosed dolphins, Pacific white-sided dolphins and beluga whales. Nine cytokine genes (IL-2, -4, -10, -12, -13, -18, TNFalpha, TGFbeta and IFNgamma) and Cox-2 were selected for analysis. Most mitogen-induced mononuclear leukocyte responses were similar between the three cetacean species with either up- or down-regulation of cytokine genes. IL-10 expression was highly variable between species. No TH/1TH2 polarization was evident. Cytokine gene analysis has the potential to identify immune system perturbations induced by environmental insult as well as providing diagnostic tools for characterizing immune responses to environmental antigens and vaccines.

A transcriptomic analysis of the stress induced by capture-release health assessment studies in wild dolphins (Tursiops truncatus)

The health of wild bottlenose dolphins (Tursiops truncatus) is typically evaluated by the study of animals that are captured and released back into the wild after examination. The impact of such studies on gene expression in peripheral blood cells was investigated using microarray and quantitative polymerase chain reaction methods. Significantly increased expression was observed in two major classes of genes: (i) energy metabolism, and (ii) responsiveness to stress and trauma, the latter effect suggesting the initiation of an acute-phase response. The value of data obtained in capture/release studies may need to be weighed against the potential physiological impacts of such studies.

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.