Application of SSH and a macroarray to investigate altered gene expression in Mytilus edulis in response to exposure to benzo[a]pyrene

Season influences the transcriptomic effects of dietary exposure to PVP/PEI coated Ag nanoparticles on mussels Mytilus galloprovincialis

Toxicity of AgNPs has been widely studied in waterborne exposed aquatic organisms. However, toxic effects caused by AgNPs ingested through the diet and depending on the season are still unexplored. The first cell response after exposure to xenobiotics occurs at gene transcription level. Thus, the aim of this study was to assess transcription level effects in the digestive gland of female mussels after dietary exposure to AgNPs both in autumn and in spring. Mussels were fed daily for 21 days with Isochrysis galbana microalgae previously exposed for 24 h to a dose close to environmentally relevant concentrations of 1 μg Ag/L PVP/PEI coated 5 nm AgNPs (in spring) and to a higher dose of 10 μg Ag/L of the same AgNPs both in autumn and in spring. After 1 and 21 days, mussels RNA was hybridized in a custom microarray containing 7806 annotated genes. Mussels were more responsive to the high dose compared to the low dose of AgNPs and a higher number of probes were altered in autumn than in spring. In both seasons, significantly regulated genes were involved in the cytoskeleton and lipid transport and metabolism COG categories, among others, while genes involved in carbohydrate transport and metabolism were specifically altered in autumn. Overall, transcription patterns were differently altered depending on the exposure time and season, indicating that season should be considered in ecotoxicological studies of metal nanoparticles in mussels.

Changes in protein expression in mussels Mytilus galloprovincialis dietarily exposed to PVP/PEI coated silver nanoparticles at different seasons

Potential toxic effects of Ag NPs ingested through the food web and depending on the season have not been addressed in marine bivalves. This work aimed to assess differences in protein expression in the digestive gland of female mussels after dietary exposure to Ag NPs in autumn and spring. Mussels were fed daily with microalgae previously exposed for 24 h to 10 μg/L of PVP/PEI coated 5 nm Ag NPs. After 21 days, mussels significantly accumulated Ag in both seasons and Ag NPs were found within digestive gland cells and gills. Two-dimensional electrophoresis distinguished 104 differentially expressed protein spots in autumn and 142 in spring. Among them, chitinase like protein-3, partial and glyceraldehyde-3-phosphate dehydrogenase, that are involved in amino sugar and nucleotide sugar metabolism, carbon metabolism, glycolysis/gluconeogenesis and the biosynthesis of amino acids KEGG pathways, were overexpressed in autumn but underexpressed in spring. In autumn, pyruvate metabolism, citrate cycle, cysteine and methionine metabolism and glyoxylate and dicarboxylate metabolism were altered, while in spring, proteins related to the formation of phagosomes and hydrogen peroxide metabolism were differentially expressed. Overall, protein expression signatures depended on season and Ag NPs exposure, suggesting that season significantly influences responses of mussels to NP exposure.

Gender-Associated Mitochondrial DNA Heteroplasmy in Somatic Tissues of the Endangered Freshwater Mussel Unio crassus (Bivalvia: Unionidae): Implications for Sex Identification and Phylogeographical Studies

Some bivalve species possess two independent mitochondrial DNA lineages: maternally (F-type) and paternally (M-type) inherited. This phenomenon is called doubly uniparental inheritance. It is generally agreed that F-type mtDNA is typically present in female somatic and gonadal tissues as well as in male somatic tissues, whereas the M-type mtDNA occurs only in male germ line and gonadal tissue. In the present study, the mtDNA heteroplasmy (for both F and M genomes) in male somatic tissues of Unio crassus (Philipsson, 1788), species threatened with extinction, has been confirmed. Taking advantage from the presence of Mcox1 marker only in male somatic tissues, we developed a new method of sex identification in this endangered species, using nondestructive tissue sampling. Probability of correct sex identification was estimated at 97.5%. The present study is the first report on gender-associated mitochondrial DNA heteroplasmy in male somatic tissues of thick-shelled river mussel and first approach to U. crassus sex identification at molecular level. Our study also confirmed the utility of paternally inherited Mcox1 gene fragment as a complementary molecular tool for resolving phylogeographical relationships among populations of thick-shelled river mussel.

Transcriptomic responses of Perna viridis embryo to Benzo(a)pyrene exposure elucidated by RNA sequencing

The green mussel Perna viridis is an ideal biomonitor to evaluate marine environmental pollution. Benzo(a)pyrene (BaP) is a typical polycyclic aromatic hydrocarbon (PAH), which is well known for the mutagenic and carcinogenic characteristics. However, the toxicological effects of BaP on Perna viridis embryo are still unclear. In this study, we investigated the embryo transcriptomic profile of Perna viridis treated with BaP via digital gene expression analysis. A total of 92,362,742 reads were produced from two groups (control and BaP exposure) by whole transcriptome sequencing (RNA-Seq). Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis were used on all genes to determine the biological functions and processes. Genes involved in various molecular pathways of toxicological effects were enriched further. The differential expression genes (DEGs) were related to stress response, infectious disease and innate immunity. Quantitative real-time PCR (qRT-PCR) measured expressional levels of six genes confirmed through the DGE analysis. This study reveals that RNA-seq for transcriptome profiling of P. viridis embryo can better understand the embryo toxic effects of BaP. Furthermore, it also suggests that RNA-seq is a superior tool for generating novel and valuable information for revealing the toxic effects caused by BaP at transcriptional level.

Sex determination in blue mussels: Which method to choose?

Sexing methods of blue mussels are mostly based on the presence or absence of gametes, and do not take into account reproductive cycle stages. Exposure effects can be affected by the sex of mussels, thus the aim of this study is to determine an efficient sex determination protocol taking into account the reproductive cycle stage. Eight mussel sexing methods were compared. This study demonstrates that the first step in discerning sex in blue mussels should be assessing the reproductive stage, which can be done by mantle histology. During gametogenesis, histology allows the differentiation of males from females by the observation of gametes. However, when mussels are in sexual rest, the only method that should be used is the sex-specific gene method.

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

It is commonly known that the nature of the diet has diverse consequences on larval performance and longevity, however it is still unclear which genes have critical impacts on bivalve development and which pathways are of particular importance in their vulnerability or resistance. First we show that a diet deficient in essential fatty acid (EFA) produces higher larval mortality rates, a reduced shell growth, and lower postlarval performance, all of which are positively correlated with a decline in arachidonic and eicosapentaenoic acids levels, two EFAs known as eicosanoid precursors. Eicosanoids affect the cell inflammatory reactions and are synthesized from long-chain EFAs. Second, we show for the first time that a deficiency in eicosanoid precursors is associated with a network of 29 genes. Their differential regulation can lead to slower growth and higher mortality of Mytilus edulis larvae. Some of these genes are specific to bivalves and others are implicated at the same time in lipid metabolism and defense. Several genes are expressed only during pre-metamorphosis where they are essential for muscle or neurone development and biomineralization, but only in stress-induced larvae. Finally, we discuss how our networks of differentially expressed genes might dynamically alter the development of marine bivalves, especially under dietary influence.

RNA-Seq-Based Transcriptome Analysis of Changes in Gene Expression Linked to Human Pregnancy Outcome After In Vitro Fertilization-Embryo Transfer

To promote the pregnancy rate of in vitro fertilization-embryo transfer (IVF-ET), we proposed to examine the differentially expressed gene during pregnancy success and failure. We used high-sequencing technology to characterize and compare the gene expression profiles of pregnancy success and pregnancy failure patients during 3 different stages: before IVF-ET (stage I), after ovarian stimulation (stage II), and day 15 after embryo transfer (stage III). Selected data from RNA-sequencing experiments were validated by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 282, 208, and 372 genes in stages I, II, and III, respectively, were differentially expressed between pregnancy success and pregnancy failure, respectively. Through confirmation with qRT-PCR, compared to pregnancy failure, we demonstrated much lower level of major histocompatibility complex, human leukocyte antigen class I A, and an much higher level of human leukocyte antigen, class II DQ α1 (HLA-DQA1) in pregnancy success, although the HLA-DQA1 decreased with development duration of pregnancy. Interleukin 1β increased with the development duration of pregnancy in pregnancy failure group and was much higher than that in pregnancy success group. Hemoglobin δ decreased with the development duration of pregnancy in pregnancy failure women and maintained in a lower level in stage I and II but dramatically increased to a much higher level in stage III in pregnancy success women. Minichromosome maintenance complex component 4 significantly increased in stage III in pregnancy failure but not in pregnancy success women. The altered expression of genes implicated in immune response and inflammation, oocyte meiosis, rhythmic process, and so on. Therefore, the current results provide a strong basis for future research to expound the molecular mechanism coping with pregnancy outcome.

Differential gene expression analysis of benzo(a)pyrene toxicity in the clam, Ruditapes philippinarum

Polycyclic aromatic hydrocarbons (PAHs) are known for their carcinogenic, teratogenic and mutagenic properties. Benzo(a)pyrene (BaP) possesses the greatest carcinogenic potential among the various PAHs. In this study, digital gene expression (DGE) was performed to investigate the digestive gland transcriptome profile of the clam Ruditapes philippinarum exposed to BaP. A total of 10,508,312 and 11,414,297 clean reads were generated respectively, from control and BaP exposure DGE libraries. One hundred and forty-five differentially expressed genes were detected after comparing two libraries with 58 up-regulated and 87 down-regulated genes. GO annotation and KEGG pathway analyses were performed on all genes to understand their biological functions and processes. The results showed that numerous enriched differentially expressed genes are related to growth and development, antioxidant metabolism, apoptosis and detoxification metabolism. Quantitative real-time PCR was performed to verify the expressed genes of DGE. Our results provide evidences that RNA-seq is a powerful tool for toxicology and capable of generating novel and valuable information at the transcriptome level for characterizing deleterious effects caused by BaP.

RNA-seq based on transcriptome reveals differ genetic expressing in Chlamys farreri exposed to carcinogen PAHs

The effects of a mixture of carcinogen polycyclic aromatic hydrocarbons (BaP, BaA, BbF and CHR) on transcriptional responses in the digestive gland of scallop, Chlamys farreri, were investigated by high-throughput RNA-sequencing (RNA-seq) technologies. In total, 209 and 260 genes were identified as significantly up- or down-regulated, respectively. Functional analysis based on gene ontology (GO) classification system and the Kyoto encyclopedia of genes and genomes (KEGG) database revealed that PAHs significantly altered the expression of genes involved in stress response, detoxication, antioxidation which were extensively discussed. In particular, CYP450 2P1 and QO mRNA expression were found to be up-regulated by exposure to PAHs mixture, suggesting that CYP450 2P1 and QO mRNA expression can be a potential marker for prediction of the biological effects of a mixture of PAHs on scallops.

Benzo[a]pyrene modulates the biotransformation, DNA damage and cortisol level of red sea bream challenged with lipopolysaccharide

In animals, biotransformation and the immune system interact with each other, however, knowledge of the toxic mechanism of benzo[a]pyrene (BaP) on these two systems is not well known. The present study investigated the toxic effects of BaP on the biotransformation system, cortisol level and DNA integrity of red sea bream (Pagrus major). The results showed that cortisol level was induced under the challenge of lipopolysaccharide (LPS). Short-term exposure (96 h) of BaP at environmental concentration significantly increased the cortisol level, hepatic EROD activity and CYP1A1 mRNA expression. When P. major was exposed to BaP for 14 d followed by LPS challenge this increased the cortisol level, EROD activity and hepatic DNA damage except CYP1A1 mRNA expression. Combined with our previous data, which showed that BaP exposure can modulate the immunologic response in P. major challenged with LPS, a hypothetical adverse outcome pathway of BaP on fish was suggested.

Benzo[a]pyrene modulation of acute immunologic responses in Red Sea bream pretreated with lipopolysaccharide

The effects of polycyclic aromatic hydrocarbons (PAHs) have been reported to modulate the immune response in aquatic animals, but the collected information of their effects on fish immunity is so far ambiguous. This study demonstrated that Benzo[a]pyrene (BaP) exposure altered the expression pattern of an antimicrobial peptide hepcidin (PM-hepc) gene and the activities of some immune-associated parameters in the lipopolysaccharide (LPS)-challenged red sea bream (Pagrus major). It was observed that LPS could increase respiratory burst, lysozyme and antibacterial activity in P. major. However when the P. major was exposed to different concentrations of BaP (1, 4, or 8 μg L(-1) ) for 14 days and then challenged with LPS there was no significant change in the lysozyme and antibacterial activity. It was further observed that LPS could induce the PM-hepc mRNA expression at 3, 6, and 12-h post-LPS challenge. However, when P. major was exposed first to BaP for 14 days and then challenged with LPS, the expression of PM-hepc mRNA was delayed in the liver until 24 h and not significantly induced until 48 and 96 h. The mRNA expression pattern was completely different from that only with LPS challenge, showing that BaP exposure changed the PM-hepc mRNA expression pattern of fish with LPS challenge. This study demonstrated that BaP exposure can weaken or inhibit the induction of lysozyme and antibacterial activity in the LPS-challenged P. major; conversely BaP exposure could enhance the mRNA expression of PM-hepc gene, indicating that the effect of BaP has different modulatory mechanism on hepcidin genes and immune-associated parameters.

Effects of benzo(a)pyrene on differentially expressed genes and haemocyte parameters of the clam Venerupis philippinarum

In this study a suppression subtractive hybridisation method was employed to identify differentially expressed genes of the clam Venerupis philippinarum exposed to benzo(a)pyrene (BaP). Nineteen known transcripts and seven predicted proteins were found from the subtractive cDNA library of the clam, which could provide more sequence information for further study. Seven of the differentially expressed genes were selected for mRNA expression analysis. Real-time PCR analysis revealed that the expression level of the selected cDNAs of clams was up-regulated to varying degrees by different concentration of BaP. They are suggested as potential molecular biomarkers for polycyclic aromatic hydrocarbons (PAHs) pollution monitoring in aquatic ecosystems. In addition, haemocyte parameters were also measured, and a decrease of total haemocyte counts and suppression of antibacterial and bacteriolytic activities were detected in BaP-stressed clams. We suggest that the modulation of the expression of the selected genes caused by PAHs probably leads to the disturbance of the immune defense of the clam. Meanwhile, the adverse effects of PAHs on haemocyte parameters caused the suppression of the immune defense and susceptibility to infectious diseases. Therefore, it is inferred that PAHs pollutants could interact with components of the immune system and interferes with defense functions of the clam V. philippinarum.

Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.

First evidence of protein profile alteration due to the main cocaine metabolite (benzoylecgonine) in a freshwater biological model

Illicit drugs represent not only a great social problem but are also considered an environmental problem because their use and, often, abuse release large amounts of parent compounds, and especially their metabolites, into freshwaters. One of the most commonly used drugs is cocaine, which is the second most prevalent drug in Europe (accounting for almost 30% of all cocaine users worldwide). Cocaine is rapidly metabolised in humans to benzoylecgonine (35-54%), ecgonine methyl ester (32-49%) and norcocaine (5%), which are eliminated in the urine and are only partially removed by wastewater treatment plants (WWTPs). Because no studies have previously been carried out to evaluate the possible risks due to cocaine and its metabolites in non-target organisms, we applied a multi-disciplinary approach to investigate the possible environmental risk related to benzoylecgonine (BE), the main metabolite of cocaine. Previous studies carried out by means of a biomarker suite and the redox-proteomic approach showed an imbalance of anti-oxidant enzyme activities and several genotoxic effects to be caused by environmental BE concentrations in the freshwater bivalve Zebra mussel (Dreissena polymorpha). This report presents the results obtained in the last step of this study, based on a proteomics analysis. We analysed the protein expression profile in the gills of Zebra mussels exposed to two different concentrations (0.5 and 1 μg/L) of BE for 14 days through 2-DE and mass spectrometry analysis (RP-UPLC ESI-LTQ-Orbitrap). Our results highlight significant changes in some proteins in gill cells whose functions are crucial for overall metabolism. In particular, we detected a probable effect of BE on calcium homeostasis and a consequent imbalance of oxidative stress, as verified for vertebrates.

Construction and characterization of a forward subtracted library of blue mussels Mytilus edulis for the identification of gene transcription signatures and biomarkers of styrene exposure

Transcriptional profiling can elucidate adaptive/toxicity pathways participating in achieving homeostasis or leading to pathogenesis in marine biota exposed to chemical substances. With the aim of analyzing transcriptional responses in the mussel Mytilus edulis exposed to the corrosive and putatively carcinogenic hydrocarbon styrene (3-5 ppm, 3days), a forward subtracted (SSH) cDNA library was produced. Female mussels were selected and digestive gland mRNA was isolated. A library with 1440 clones was produced and a total of 287 clones were sequenced, 53% being identified through BlastN analysis against Mytibase and DeepSeaVent databases. Those genes included GO terms such as 'response to drugs', 'immune defense' and 'cell proliferation'. Furthermore, sequences related to chitin and beta-1-3-glucan metabolism were also up-regulated by styrene. Many of the obtained sequences could not be annotated constituting new mussel sequences. In conclusion, this SSH study reveals novel sequences useful to generate molecular biomarkers of styrene exposure in mussels.

Sequence analysis of a normalized cDNA library of Mytilus edulis hemocytes exposed to Vibrio splendidus LGP32 strain

In the past decades, reports on bivalves' pathogens and associated mortalities have steadily increased. To face pathogenic micro-organisms, bivalves rely on innate defenses established in hemocytes which are essentially based on phagocytosis and cytotoxic reactions. As a step towards a better understanding of the molecular mechanisms involved in the mussel Mytilus edulis innate immune system, we constructed and sequenced a normalized cDNA library specific to M. edulis hemocytes unchallenged (control) and challenged with Vibrio splendidus LGP32 strain for 2, 4 and 6 h. A total of 1,024,708 nucleotide reads have been generated using 454 pyrosequencing. These reads have been assembled and annotated into 19,622 sequences which we believe cover most of the M. edulis hemocytes transcriptome. These sequences were successfully assigned to biological process, cellular component, and molecular function Gene Ontology (GO) categories. Several transcripts related to immunity and stress such as some fibrinogen related proteins and Toll-like receptors, the complement C1qDC, some antioxidant enzymes and antimicrobial peptides have already been identified. In addition, Toll-like receptors signaling pathways and the lysosome and apoptosis mechanisms were compared to KEGG reference pathways. As an attempt for large scale RNA sequencing, this study focuses on identifying and annotating transcripts from M. edulis hemocytes regulated during an in vitro experimental challenge with V. splendidus. The bioinformatic analysis provided a reference transcriptome, which could be used in studies aiming to quantify the level of transcripts using high-throughput analysis such as RNA-Seq.

Annual variation in the levels of transcripts of sex-specific genes in the mantle of the common mussel, Mytilus edulis

Mytilus species are used as sentinels for the assessment of environmental health but sex or stage in the reproduction cycle is rarely considered even though both parameters are likely to influence responses to pollution. We have validated the use of a qPCR assay for sex identification and related the levels of transcripts to the reproductive cycle. A temporal study of mantle of Mytilus edulis found transcripts of male-specific vitelline coat lysin (VCL) and female-specific vitelline envelope receptor for lysin (VERL) could identify sex over a complete year. The levels of VCL/VERL were proportional to the numbers of sperm/ova and are indicative of the stage of the reproductive cycle. Maximal levels of VCL and VERL were found in February 2009 declining to minima between July - August before increasing and re-attaining a peak in February 2010. Water temperature may influence these transitions since they coincide with minimal water temperature in February and maximal temperature in August. An identical pattern of variation was found for a cryptic female-specific transcript (H5) but a very different pattern was observed for oestrogen receptor 2 (ER2). ER2 varied in a sex-specific way with male > female for most of the cycle, with a female maxima in July and a male maxima in December. Using artificially spawned animals, the transcripts for VCL, VERL and H5 were shown to be present in gametes and thus their disappearance from mantle is indicative of spawning. VCL and VERL are present at equivalent levels in February and July-August but during gametogenesis (August to January) and spawning (March to June) VCL is present at lower relative amounts than VERL. This may indicate sex-specific control mechanisms for these processes and highlight a potential pressure point leading to reduced reproductive output if environmental factors cause asynchrony to gamete maturation or release.

Application of SSH and quantitative real time PCR to construction of gene expression profiles from scallop Chlamys farreri in response to exposure to tetrabromobisphenol A

TBBPA-induced genes were identified using suppression subtractive hybridization (SSH) from Chlamys farreri. A total of 203 and 44 clones from SSH forward and reverse library were respectively obtained including cellular process, immune system process, response to stimulus, metabolic process and signaling etc. Differential gene expressions were compared between scallops from control and TBBPA treatment groups (400 μg/L, 15 days) using quantitative real time RT-PCR. For further research, eight significant genes expression from scallops exposed to TBBPA (0; 100; 200; 400 μg/L) sampling at 0, 1, 3, 6 and 15 days, were utilized for Q-RT-PCR. The results revealed that the expression level of most selected cDNAs was dominantly up-regulated or down-regulated in the TBBPA-induced scallops. These findings provide basic genomic information of the bivalve and the selected genes may be the potential molecular biomarkers for TBBPA pollution in aquatic environment.

A new gene, SRP16, differentially expressed in the spermathecae of honeybee queens (Apis mellifera) related with reproduction status

Honey bee queens have the ability to store sperm in spermathecae for fertilizing eggs throughout their life. To investigate mechanisms for sperm storage in Apis mellifera, we employed suppression subtractive hybridization (SSH) to find differentially expressed fragments in spermathecae between virgin queens and newly mated queens. A new gene, named SRP16, was obtained by joining the SSH products with 5'-RACE and 3'-RACE. SRP16 is predicted to encode a 41 kDa protein with 363 amino acid residues. Its expression was found in the spermathecae dominantly in honey bee queens but not in honey bee workers, with the highest expression found in spermathecae of virgin and newly mated queens. SRP16 expression was weak in other tissues of queens other than in the spermathecae and showed no obvious change with reproductive status of queens. The results suggest that SRP16 may play important roles in sperm storage and honey bee reproduction.

Biological effects of the anti-parasitic chemotherapeutant emamectin benzoate on a non-target crustacean, the spot prawn (Pandalus platyceros Brandt, 1851) under laboratory conditions

The potential impact of commercial salmon aquaculture along the coast of British Columbia on the health of non-target marine wildlife is of growing concern. In the current initiative, the biological effects on gene expression within spot prawn (Pandalus platyceros) exposed to the sea lice controlling agent, emamectin benzoate (EB; 0.1-4.8 mg/kg sediment), were investigated. A mean sediment/water partitioning coefficient (K(p)) was determined to be 21.81 and significant levels of EB were detected in the tail muscle tissue in all exposed animals. Animals selected for the experiment did not have eggs and were of similar weight. Significant mortality was observed within 8 days of EB treatment at concentrations between 0.1 and 0.8 mg/kg and there was no effect of EB on molting. Twelve spot prawn cDNA sequences were isolated from the tail muscle either by directed cloning or subtractive hybridization of control versus EB exposed tissues. Three of the transcripts most affected by EB exposure matched sequences encoding the 60S ribosomal protein L22, spliceosome RNA helicase WM6/UAP56, and the intracellular signal mediator histidine triad nucleotide binding protein 1 suggesting that translation, transcription regulation, and apoptosis pathways were impacted. The mRNA encoding the molting enzyme, β-N-acetylglucosaminidase, was not affected by EB treatment. However, the expression of this transcript was extremely variable making it unsuitable for effects assessment. The results suggest that short-term exposure to EB can impact biological processes within this non-target crustacean.

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.

Relationship between mRNA biomarker candidates and location near a marine municipal wastewater outfall in the benthic indicator species Modiolus modiolus (L.)

The deep-sea horse mussel Modiolus modiolus (L.) is a sentinel bivalve species used for the assessment of potential biological exposure to anthropogenic contaminants in benthic environments. Using a combination of endpoints that included gross biological metrics, reproductive status, tissue contaminant load, and mRNA abundance profiles, we characterized variation in the local M. modiolus population situated in different spatial zones relative to a municipal wastewater outfall. Significant differences were observed in reproductive indicators, growth parameters, and abundance of four specific mRNA transcripts representative of stress response or membrane transport (CAT, NET/SCF6, ABCA4 and HSP70) in adductor muscle tissue of animals adjacent to the wastewater outfall. Concentrations of metals and organic chemicals in M. modiolus tissue were generally highest directly at the outfall site with much lower levels at 100-800 m from the outfall. This general pattern did not match the mRNA profiles. HSP70 and ABCA4 mRNA showed increased abundance in all regions adjacent to the municipal outfall compared to the reference site. One site group located within 100-200 m south/south-easterly of the outfall had increased levels of all four transcripts. Some mRNAs showed significant correlations with nickel, arsenic, lead, selenium, copper, and one of thirteen polycyclic aromatic hydrocarbons measured (dibenzo(a,h)-anthracene). Three mRNAs (CAT, NET/SCF6, and ABCA4) were negatively correlated with bis(2-ethylhexyl)phthalate. The data suggest that these benthic organisms are exhibiting biological responses to the outfall and support an alternate interpretation regarding dispersal of contaminants. The potential effects of emerging chemicals of concern entering the receiving environment merits further assessment.

A proteomic study using zebra mussels (D. polymorpha) exposed to benzo(α)pyrene: the role of gender and exposure concentrations

It has recently been established that the use of proteomics can be a useful tool in the field of ecotoxicology. Despite the fact that the mussel Dreissena polymorpha is a valuable bioindicator for freshwater ecosystems, the application of a proteomic approach with this organism has not been deeply investigated. To this end, several zebra mussel specimens were subjected to a 7-day exposure of two different concentrations (0.1 and 2 μg L⁻¹) of the model pollutant benzo[α]pyrene (B[α]P). Changes in protein expression profiles were investigated in gill cytosolic fractions from control/exposed male and female mussels using 2-DE electrophoresis. B[α]P bioaccumulation in mussel soft tissue was also assessed to validate exposure to the selected chemical. We evaluated overall changes in expression profiles for 28 proteins in exposed mussels, 16 and 12 of which were, respectively, over- and under-expressed. Surprisingly, the comparative analysis of protein data sets showed no proteins that varied commonly between the two different B[α]P concentrations. Spots of interest were manually excised and analysed by MALDI-TOF/TOF mass spectrometry. The most significant proteins that were identified as altered were related to oxidative stress, signal transduction, cellular structure and metabolism. This preliminary study indicates the feasibility of a proteomic approach with the freshwater mussel D. polymorpha and provides a starting point for similar investigations. Our results confirm the need to increase the number of invertebrate proteomic studies in order to increase the following: their representation in databases and the successful identification of their most relevant proteins. Finally, additional studies investigating the role of gender and protein modulation are warranted.

Molecular responses of Ostrea edulis haemocytes to an in vitro infection with Bonamia ostreae

Bonamiosis due to the parasite Bonamia ostreae is a disease affecting the flat oyster Ostrea edulis. B. ostreae is a protozoan, affiliated to the order of haplosporidia and to the cercozoan phylum. This parasite is mainly intracellular, infecting haemocytes, cells notably involved in oyster defence mechanisms. Suppression subtractive hybridisation (SSH) was carried out in order to identify oyster genes differentially expressed during an infection of haemocytes with B. ostreae. Forward and reverse banks allowed obtaining 1104 and 1344 clones respectively, among which 391 and 480 clones showed a differential expression between both tested conditions (haemocytes alone versus haemocytes in contact with parasites). ESTs of interest including genes involved in cytoskeleton, respiratory chain, detoxification membrane receptors, and immune system were identified. The open reading frames of two selected genes (galectin and IRF-like) were completely sequenced and characterized. Real time PCR assays were developed to study the relative expression of candidate ESTs during an in vitro infection of haemocytes by live and dead parasites. Haemocyte infection with B. ostreae induced an increased expression of omega glutathione S-transferase (OGST), superoxide dismutase (SOD), tissue inhibitor of metalloproteinase (TIMP), galectin, interferon regulatory factor (IRF-like) and filamin genes.

Gene biomarkers in diatom Thalassiosira pseudonana exposed to polycyclic aromatic hydrocarbons from contaminated marine surface sediments

Marine diatoms have a key role in the global carbon fixation and therefore in the ecosystem. We used Thalassiosira pseudonana as a model organism to assess the effects of exposure to environmental pollutants at the gene expression level. Diatoms were exposed to polycyclic aromatic hydrocarbons mixture (PAH) from surface sediments collected at a highly PAH contaminated area of the Mediterranean Sea (Genoa, Italy), due to intense industrial and harbor activities. The gene expression data for exposure to the sediment-derived PAH mixture was compared with gene expression data for in vitro exposure to specific polycyclic aromatic hydrocarbons. The data shows that genes involved in stress response, silica uptake, and metabolism were regulated both upon exposure to the sediment-derived PAH mixture and to the single component. Complementary monitoring of silica in the diatom cultures provide further evidence of a reduced cellular uptake of silica as an end-point for benzo[a]pyrene exposure that could be linked with the reduced gene and protein expression of the silicon transporter protein. However some genes showed differences in regulation indicating that mixtures of structurally related chemical compounds can elicit a slightly different gene expression response compared to that of a single component. The paper provides indications on the specific pathways affected by PAH exposure and shows that selected genes (silicon transporter, and silaffin 3) involved in silica uptake and metabolism could be suitable molecular biomarkers of exposure to PAHs.

Mediterranean mussel gene expression profile induced by okadaic acid exposure

Seasonal seawater temperature increases define optimal growth conditions for Dinoflagellate species which can reach high concentrations in water column and also in filter-feeding organisms like Mytilus galloprovincialis. Commonly produced by Dinophysis and Prorocentrum spp., okadaic acid (OA) and its analogues are responsible for the Diarrheic Shellfish Poisoning (DSP) syndrome in humans. Closure of shellfishing grounds is therefore recommended by the EU when DSP toxin levels in shellfish exceed 16 μg OA 100 g(-1) flesh. Despite not being responsible for casualties either in humans or mussels, DSP outbreaks are considered natural events causing health and economic issues due to the frequency of their occurrence. Since gene expression studies offer a wide range of different solutions, we used a mussel cDNA microarray to evaluate gene expression changes in the digestive gland of mussels fed for five weeks with OA-contaminated nutrient. Among the differentially expressed genes we observed a general up-regulation of transcripts coding for stress proteins, proteins involved in cellular synthesis, and a few not annotated proteins. Overall, at the first time point analyzed we identified 58 candidate transcripts for OA-induced stress in mussels, half of which have unknown function. In this paper we present the first gene expression analysis performed on Mediterranean mussels exposed to okadaic acid. The characterization of these transcripts could be useful for the identification of an early physiological response to OA exposure.

Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns

Background

Mytilus species are important in marine ecology and in environmental quality assessment, yet their molecular biology is poorly understood. Molecular aspects of their reproduction, hybridisation between species, mitochondrial inheritance, skewed sex ratios of offspring and adaptation to climatic and pollution factors are priority areas.

Methodology/Principal Findings

To start to address this situation, expressed genetic transcripts from M. galloprovincialis were pyrosequenced. Transcripts were isolated from the digestive gland, foot, gill and mantle of both male and female mussels. In total, 175,547 sequences were obtained and for foot and mantle, 90% of the sequences could be assembled into contiguous fragments but this reduced to 75% for the digestive gland and gill. Transcripts relating to protein metabolism and respiration dominated including ribosomal proteins, cytochrome oxidases and NADH dehydrogenase subunits. Tissue specific variation was identified in transcripts associated with mitochondrial energy metabolism, with the digestive gland and gill having the greatest transcript abundance. Using fragment recruitment it was also possible to identify sites of potential small RNAs involved in mitochondrial transcriptional regulation. Sex ratios based on Vitelline Envelop Receptor for Lysin and Vitelline Coat Lysin transcript abundances, indicated that an equal sex distribution was maintained. Taxonomic profiling of the M. galloprovincialis tissues highlighted an abundant microbial flora associated with the digestive gland. Profiling of the tissues for genes involved in intermediary metabolism demonstrated that the gill and digestive gland were more similar to each other than to the other two tissues, and specifically the foot transcriptome was most dissimilar.

Conclusions

Pyrosequencing has provided extensive genomic information for M. galloprovincialis and generated novel observations on expression of different tissues, mitochondria and associated microorganisms. It will also facilitate the much needed production of an oligonucleotide microarray for the organism.

Identification of genes differentially expressed by calorie restriction in the rotifer (Brachionus plicatilis)

A monogonont rotifer Brachionus plicatilis has been widely used as a model organism for physiological, ecological studies and for ecotoxicology. Because of the availability of parthenogenetic mode of reproduction as well as its versatility to be used as live food in aquaculture, the population dynamic studies using the rotifer have become more important and acquired the priority over those using other species. Although many studies have been conducted to identify environmental factors that influence rotifer populations, the molecular mechanisms involved still remain to be elucidated. In this study, gene(s) differentially expressed by calorie restriction in the rotifer was analyzed, where a calorie-restricted group was fed 3 h day(-1) and a well-fed group fed ad libitum. A subtracted cDNA library from the calorie-restricted rotifer was constructed using suppression subtractive hybridization (SSH). One hundred sixty-three expressed sequence tags (ESTs) were identified, which included 109 putative genes with a high identity to known genes in the publicly available database as well as 54 unknown ESTs. After assembling, a total of 38 different genes were obtained among 109 ESTs. Further validation of expression by semi-quantitative reverse transcription-PCR showed that 29 out of the 38 genes obtained by SSH were up regulated by calorie restriction.

Identification of the molecules involved in zebra mussel (Dreissena polymorpha) hemocytes host defense

The invasion of North American waterbodies by the zebra mussel (Dreissena polymorpha) has caused ecological catastrophies in North America. Unfortunately, little is known about this nuisance mollusk and its host defense mechanisms. In this study, 32 expressed sequence tags (ESTs) associated with hemocyte stimulation were obtained from a suppression subtractive hybridization (SSH) cDNA library. This SSH-cDNA library was produced by using a cDNA library of naïve hemocytes as the driver and a cDNA library of hemocytes stimulated with a mixture of microbial antigens namely, lipopolysacchride (LPS), peptidoglycan (PGN), and zymosan (ZYM), as the tester. The driver cDNA was subtracted from the tester to increase the relative abundance of the cDNAs that were induced by stimulations. The putative function of 27 ESTs were obtained by using the homologue searching program BLASTx and BLASTn. Four ESTs encoding the protein product homologous to matrilin (Matrn, AM503947), heat shock protein 70 (HSP70, EU835391), seryl-tRNA synthetase (STS, AM503950), and glycine-rich protein (GRP, AM502279) were selected for a subsequent study using quantitative PCR (qPCR) assays with the RNA extracted from hemocytes stimulated with LPS alone. The results of quantitative PCR with stimulated hemocyte RNA demonstrated that the four candidate genes were upregulated by LPS stimulation. The expression levels of both HSP70 and Matrn genes between naïve and 1-h stimulated hemocyte samples are the most significant with 2.78 and 2.20 fold increases, respectively. The significant changes of GRP and STS genes were observed after 2-h stimulation. The phylogenetic analysis of HSP70 molecule indicated that this protein is phylogenetically close to the HSP70 identified from other mollusks. This study shed light on hemocyte-mediated host defense mechanisms of D. polymorpha.

Hepcidin gene expression induced in the developmental stages of fish upon exposure to Benzo[a]pyrene (BaP)

Hepcidin is known to be expressed in fish with bacterial challenge and iron overload. Here we first report the hepcidin expression induced in the developmental stages from embryo to fry of red sea bream (Pagarus major) and in juvenile black porgy (Acanthopagrus schlegelii B.) upon continuous waterborne exposure to BaP. The gene expression of CYP1A1 and IgL (immunoglobulin light chain) were both measured. Expression of the Pagarus major hepcidin gene (PM-hepc) was increased in post hatch fry at 24 h and 120 h exposure to BaP at concentrations of 0.1, 0.5 and 1.0 microg/l, respectively. The gene expression pattern was comparable to that of CYP1A1 but different from that of IgL. In addition, a high number of AS-hepc2 transcripts (Acanthopagrus schlegelii B. hepcidin gene) were detected in the liver upon exposure to 1.0 microg/l BaP. This study demonstrates that hepcidin gene expression is significantly induced in BaP-exposed red sea bream and black porgy.

Genetic mechanisms of pollution resistance in a marine invertebrate

Pollution is a common stress in the marine environment and one of today's most powerful agents of selection, yet we have little understanding of how anthropogenic toxicants influence mechanisms of adaptation in marine populations. Due to their life history strategies, marine invertebrates are unable to avoid stress and must adapt to variable environments. We examined the genetic basis of pollution resistance across multiple environments using the marine invertebrate, Styela plicata. Gametes were crossed in a quantitative genetic breeding design to enable partitioning of additive genetic variance across a concentration gradient of a common marine pollutant, copper. Hatching success was scored as a measure of stress resistance in copper concentrations of 0, 75, 150, and 350 microg/L. There was a significant genotype x environment interaction in hatching success across copper concentrations. Further analysis using factor analytic modeling confirmed a significant dimension of across-environment genetic variation where the genetic basis of resistance to stress in the first three environments differed from that in the environment of highest copper concentration. A second genetic dimension further differentiated between the genetic basis of resistance to low and high stress environments. These results suggest that marine organisms use different genetic mechanisms to adapt to different levels of pollution and that the level of genetic variation to adapt to intense pollution stresses may be limited.

Comparison of histological, genetic, metabolomics, and lipid-based methods for sex determination in marine mussels

Omics technologies are increasingly being used to monitor organismal responses to environmental stressors. Previous studies have shown that species identification, an appreciation of life history traits, and organism phenotype (e.g., gender) are essential for the accurate interpretation of omics data from field samples. As marine mussels are increasingly being used in ecotoxicogenomics and monitoring, a technique to determine mussel gender throughout their annual reproductive cycle is urgently needed. This study examines four methods for sex determination in the two mussel species found in the United Kingdom, Mytilus edulis and Mytilus galloprovincialis, and their hybrid. Each of these methods-histology, a lipid-based assay, a new reverse transcriptase polymerase chain reaction (RT-PCR) assay, and nuclear magnetic resonance (NMR)-based metabolomics-initially was evaluated using sexually mature ("ripe") mussels whose gender was clearly distinguishable using histology. The methods subsequently were tested on spawned ("spent") mussels. For ripe animals, all techniques yielded high classification accuracies: histology, 100%; RT-PCR, 94.6%; lipid analysis, 90.6%; and metabolomics, 89.5%. The gender of spent animals, however, could not be determined by histology (0%) or lipid analysis (55.6%), but RT-PCR (100%) and metabolomics (88.9%) both proved to be successful. In addition, the RT-PCR, metabolomics, and lipid-based methods identified animals of mixed sex. Our findings highlight the application of a novel RT-PCR method as a robust technique for gender determination of ripe and spent mussels.

Direct sampling of organisms from the field and knowledge of their phenotype: key recommendations for environmental metabolomics

Critical questions must be addressed to evaluate the potential of metabolomics for studying free-living wildlife. First, can metabolomics identify stress-induced phenotypes in animals experiencing a highly variable environment or must animals be stabilized in a controlled laboratory prior to sampling? Second, is knowledge of species and phenotype (gender and age) required to interpret metabolomics data? To address these questions, we characterized the metabolic variability of the mussel and determined if inherent variability masked the metabolic response to an environmental stressor, hypoxia. Specifically, we compared metabolic fingerprints of adductor muscle and mantle from four groups of Mytilus galloprovincialis: animals sampled directly from the field with and without hypoxia and those stabilized in a laboratory for 60 h, also with and without hypoxia. Contrary to expectation, laboratory stabilization increased metabolic variability in adductor muscle, thereby completely masking the response to hypoxia. The principal source of metabolic variability in mantle was shown to be gender-based, highlighting the importance of phenotypic anchoring of samples to known life history traits. We conclude that direct field sampling is recommended for environmental metabolomics since it minimizes metabolic variability and enables stress-induced phenotypic changes to be observed. Furthermore, we recommend that species and phenotype of the study organism must be known for meaningful interpretation of metabolomics data.

Benzo[a]pyrene up-regulates the expression of the proliferating cell nuclear antigen (PCNA) and multixenobiotic resistance polyglycoprotein (P-gp) in Baltic Sea blue mussels (Mytilus edulis L.)

The expression of protein biomarkers in Baltic Sea blue mussels was analyzed after three days exposure to low (2.8 microg/animal/day), intermediate (28 microg/animal/day), or high (280 microg/animal/day) nominal doses of benzo[a]pyrene (BaP). Significant expression changes were found in the animals exposed to the low dose, the lowest reported dose for DNA adduct formation in the gills of Baltic Sea blue mussels. Up-regulated expression of the proliferating cell nuclear antigen (PCNA), quantified from Western blots, and no change in the 5-bromo-deoxyuridine (BrdU) staining pattern, determined by immunocytochemistry, indicated that the observed PCNA response was mainly non-proliferative, and thus possibly due to DNA damage. The expression of the multixenobiotic resistance polyglycoprotein (P-gp) was also up-regulated, proving its usefulness as an exposure marker to planar organic compounds. No effect of the BaP treatment with respect to the retinoblastoma 110 protein or heat shock proteins 60 and 70 was found. The variance in the medium and high dose data was too large to allow for the detection of significant expression changes. We suggest PCNA to be a marker for genotoxic stress derived from the polycyclic aromatic hydrocarbon BaP, irrespective of whether the stress leads to DNA repair or to cell proliferation.

Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution?

Marine bivalves of the genus Mytilus are intertidal filter-feeders commonly used as biosensors of coastal pollution. Mussels adjust their functions to ordinary environmental changes, e.g. temperature fluctuations and emersion-related hypoxia, and react to various contaminants, accumulated from the surrounding water and defining a potential health risk for sea-food consumers. Despite the increasing use of mussels in environmental monitoring, their genome and gene functions are largely unexplored. Hence, we started the systematic identification of expressed sequence tags and prepared a cDNA microarray of Mytilus galloprovincialis including 1714 mussel probes (76% singletons, approximately 50% putatively identified transcripts) plus unrelated controls. To assess the potential use of the gene set represented in MytArray 1.0, we tested different tissues and groups of mussels. The resulting data highlighted the transcriptional specificity of the mussel tissues. Further testing of the most responsive digestive gland allowed correct classification of mussels treated with mixtures of heavy metals or organic contaminants (expression changes of specific genes discriminated the two pollutant cocktails). Similar analyses made a distinction possible between mussels living in the Venice lagoon (Italy) at the petrochemical district and mussels close to the open sea. The suggestive presence of gene markers tracing organic contaminants more than heavy metals in mussels from the industrial district is consistent with reported trends of chemical contamination. Further study is necessary in order to understand how much gene expression profiles can disclose the signatures of pollutants in mussel cells and tissues. Nevertheless, the gene expression patterns described in this paper support a wider characterization of the mussel transcriptome and point to the development of novel environmental metrics.