Development of a Robust Read-Across Model for the Prediction of Biological Potency of Novel Peroxisome Proliferator-Activated Receptor Delta Agonists.

A robust predictive model was developed using 136 novel peroxisome proliferator-activated receptor delta (PPARδ) agonists, a distinct subtype of lipid-activated transcription factors of the nuclear receptor superfamily that regulate target genes by binding to characteristic sequences of DNA bases. The model employs various structural descriptors and docking calculations and provides predictions of the biological activity of PPARδ agonists, following the criteria of the Organization for Economic Co-operation and Development (OECD) for the development and validation of quantitative structure-activity relationship (QSAR) models. Specifically focused on small molecules, the model facilitates the identification of highly potent and selective PPARδ agonists and offers a read-across concept by providing the chemical neighbours of the compound under study. The model development process was conducted on Isalos Analytics Software (v. 0.1.17) which provides an intuitive environment for machine-learning applications. The final model was released as a user-friendly web tool and can be accessed through the Enalos Cloud platform's graphical user interface (GUI).

Precision Medicine Approaches with Metabolomics and Artificial Intelligence.

Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and machine learning methods, which are fundamental to managing large number of variables and samples. In the present review, we reported and discussed the application of artificial intelligence (AI) strategies for metabolomics data analysis. Particularly, we focused on widely used non-linear machine learning classifiers, such as ANN, random forest, and support vector machine (SVM) algorithms. A discussion of recent studies and research focused on disease classification, biomarker identification and early diagnosis is presented. Challenges in the implementation of metabolomics-AI systems, limitations thereof and recent tools were also discussed.

Reduction of dioxin-like toxicity in effluents by additional wastewater treatment and related effects in fish.

Efficiency of advanced wastewater treatment technologies to reduce micropollutants which mediate dioxin-like toxicity was investigated. Technologies compared included ozonation, powdered activated carbon and granular activated carbon. In addition to chemical analyses in samples of effluents, surface waters, sediments, and fish, (1) dioxin-like potentials were measured in paired samples of effluents, surface waters, and sediments by use of an in vitro biotest (reporter gene assay) and (2) dioxin-like effects were investigated in exposed fish by use of in vivo activity of the mixed-function, monooxygenase enzyme, ethoxyresorufin O-deethylase (EROD) in liver. All advanced technologies studied, based on degradation or adsorption, significantly reduced dioxin-like potentials in samples and resulted in lesser EROD activity in livers of fish. Results of in vitro and in vivo biological responses were not clearly related to quantification of targeted analytes by use of instrumental analyses.

Lipidomic Profiling of Rice Bran after Green Solid-Liquid Extractions for the Development of Circular Economy Approaches.

Rice bran is a rather underutilized by-product of the rice industry that nowadays is far from being valorized. In this study, the lipidomic profile of bran of the Italian rice variety, Roma, has been evaluated through ultra performance liquid chromatography-tandem mass spectrometry. Crude lipid extracts were obtained from rice bran treated with different green solvents (1-butanol, ethanol and methyl tert-butyl ether/methanol mixture) in combination with an ultrasonic pre-treatment, and then compared with extracts obtained with standard solvents (chloroform/methanol mixture). Lipid yield, number and type of lipids and composition of prevalent lipid classes extracted were evaluated in order to provide an exhaustive lipid profile of the rice bran and to identify the most efficient green solvent for solid-liquid extractions. Twelve different lipid classes and a maximum of 276 lipids were identified. Ethanol and methyl tert-butyl ether/methanol solvents provided higher lipid extraction yields, the former being the most effective solvent for the extraction of triglycerides and N-acylethanolamines and the latter the most effective for the extraction of diglycerides, phospholipids and ceramides at 4 °C. Moreover, extraction with ethanol at 20 °C gave similar results as at 4 °C in terms of lipid yield and for most of the classes of lipids extracted. Taken together, our results indicate ethanol and methyl tert-butyl ether/methanol as excellent solvents for lipid extraction from rice bran, with the aim to further valorize this food by-product in the perspective of a circular economy.

Morphological and functional alterations in hemocytes of Mytilus galloprovincialis exposed in high-impact anthropogenic sites.

The work aimed to study the induction of morphological alterations in M. galloprovincialis in the field and its suitability to be integrated into a sensitive, simple, and cost-effective cell-based multimarker approach for the detection of the stress status induced by pollution in coastal marine environments in view of ecotoxicological biomonitoring and assessment application. Cellular morphometric alterations was paralleled by the analysis of standardized biomarkers such as lysosomal membrane destabilization, and genotoxocity biomarkers such as micronuclei and binuclated cells frequencies were investigated. The study was carried out by means of a transplanting experiment in the field, using caged organisms from an initial population exposed in the field in two multi-impacted coastal sites of the central Mediterranean area, Bagnoli in the eastern Tyrrhenian Sea and Augusta-Melilli-Priolo in the western Ionian Sea. Capo Miseno (NA) for the Tyrrhenian area and Brucoli (ME) for the Ionian area were chosen as control sites. Hemocyte enlargement and filopodial elongation increased frequencies were observed in organisms exposed to the impacted sites. These morphometric alterations showed strong agreement with the lysosomal membrane destabilization and biomarkers of genotoxicity, suggesting their usefulness in detecting the pollutant-induced stress syndrome related to genotoxic damage.

Ecotoxicological effects of silver nanoparticles in marine mussels.

As the production of silver nanoparticles (AgNPs) is becoming more prevalent, it is becoming increasingly necessary to understand the toxicological effects they can have on different ecosystems. In the marine bioindicator species M. galloprovincialis Lam we predicted toxicity and bioaccumulation of 5 nm alkane-coated and 50 nm uncoated silver nanoparticles (AgNPs) along with silver nitrate as a function of the actual dose level. We generated a time persistence model of silver in seawater and used the Area Under the Curve (AUC) as independent variable in the hazard assessment. This approach allowed us to evaluate unbiased ecotoxicological endpoints for acute (survival) and chronic toxicity (byssal adhesion). Logistic regression analysis rendered an overall LC5096h values of 0.81 ± 0.07 mg h L-1 irrespectively of the silver form. By contrast, for byssal adhesion regression analysis revealed a much higher toxicological potential of silver nitrate vs AgNPs with EC5024h values respectively of 0.0024 ± 0.0009 vs 0.053 ± 0.016 and 0.063 (no computable error for 50 nm AgNP) mg h L-1, undoubtedly confirming a prevalence of ionic silver effects over AgNPs. Bioaccumulation was more efficient for silver nitrate >5 nm AgNP >50 nm AgNP reflecting a parallel with the preferential uptake route / target organ. Finally, we derived Risk Quotient (RQs) for acute and chronic effects of nanosilver in shellfish and showed that the RQs are far from the Level of Concern (LoC) at current estimated environmental concentrations (EECs). This information can ultimately help researchers, policy makers, and industry professionals decide how to safely regulate and/or dispose of AgNPs.

Carbon nanomaterial functionalization with pesticide-detoxifying carboxylesterase.

Four carbon materials, spent coffee-ground biochar, carbon black, short CNTs, and nitrogen-doped few-layer graphene (N-graphene) were tested for their functionalization with a commercial carboxylesterase. Their robustness to variations in time and key physicochemical parameters (temperature and pH) was analysed. In general, carbon nanomaterials showed better performance than biochar, both in terms of binding capacity and resilience in harsh conditions, at statistically significant levels. Among the tested materials, functionalized N-graphene also showed the highest level of inhibition of carboxylesterase by pesticide exposure. Therefore, N-graphene was selected for biotechnological application of pesticide scavenging toxicity in T. thermophila, a ciliate bioindicator of water quality. While immobilization of the enzyme was not effective in the case of carbaryl, a methyl carbamate, in the case of the organophosphorus dichlorvos, a 1- or 30-min contact time with a water solution containing 5 times the LC100 - 0.5 mM - allowed 50% and 100% rescue of ciliate survival, respectively. These results suggest that functionalization with carboxylesterase may be of additional benefit compared to bare carbon in water clean-up procedures, especially for highly hydrophilic pesticides such as dichlorvos.

Interactions of a pesticide/heavy metal mixture in marine bivalves: a transcriptomic assessment.

BACKGROUND: Mixtures of chemicals present in aquatic environments may elicit toxicity due to additive or synergistic effects among the constituents or, vice versa, the adverse outcome may be reduced by antagonistic interactions. Deviations from additivity should be explained either by the perturbations of toxicokinetic parameters and/or chemical toxicodynamics. We addressed this important question in marine mussels exposed subchronically to a binary mixture made of two wide-spread pollutants: the heavy metal nickel and the organic phosphorus pesticide Chlorpyrifos. To this aim, we carried out in tissues of Mytius galloprovincialis (Lam) a systems approach based on the evaluation and integration of different disciplines, i.e. high throughput gene expression profiling, functional genomics, stress biomakers and toxicokinetics. RESULTS: Cellular and tissue biomarkers, viz. digestive gland lysosomal membrane stability, lysosomal/cytosol volume ratio, neutral lipid content and gill acetylcholinesterase activity were, in general, altered by either the exposure to nickel and Chlorpyrifos. However, their joint action rendered (i) an overall decrease of the stress syndrome level, as evaluated through an expert system integrating biomarkers and (ii) statistically significant antagonistic deviations from the reference model systems to predict mixture toxicity. While toxicokinetic modeling did not explain mixture interactions, gene expression profiling and further Gene Ontology-based functional genomics analysis provided clues that the decrement of toxicity may arise from the development of specific toxicodynamics. Multivariate statistics of microarray data (238 genes in total, representing about 14% of the whole microarray catalogue) showed two separate patterns for the single chemicals: the one belonging to the heavy metal -135 differentially expressed genes (DEGs) was characterized by the modulation of transcript levels involved in nucleic acid metabolism, cell proliferation and lipid metabolic processes. Chlorpyrifos exposure (43 DEGs) yielded a molecular signature which was biased towards carbohydrate catabolism (indeed, chitin metabolism) and developmental processes. The exposure to the mixture (103 DEGs) elicited a composite complex profile which encompassed the core properties of the pesticide but also a relevant set of unique features. Finally, the relative mRNA abundance of twelve genes was followed by Q-PCR to either confirm or complement microarray data. These results, in general, were compatible with those from arrays and indeed confirmed the association of the relative abundance of two GM-2 ganglioside activator genes in the development of the hyperlipidosis syndrome observed in digestive gland lysosomes of single chemical exposed mussels. CONCLUSION: The transcriptomic assessment fitted with biological data to indicate the occurrence of different toxicodynamic events and, in general, a decrease of toxicity, driven by the mitigation or even abolition of lysosomal responses. Furthermore, our results emphasized the importance of the application of mechanistic approaches and the power of systems assessment to study toxicological responses in ecologically relevant organisms.

Mixture toxicity assessment of nickel and chlorpyrifos in the sea bass Dicentrarchus labrax.

The present research work was designed to study Dicentrarchus labrax biotransformation and detoxification responses to acute exposure to nickel (Ni) and chlorpyrifos (CHP). Sexually immature sea bass were treated by intraperitoneal injection of nickel chloride (500 µg kg⁻¹), chlorpyrifos (10 mg kg⁻¹), and their binary mixture for 1, 3, and 7 days. Ni and CHP accumulation was quantified in liver after the exposure periods. The following biological responses were measured: (1) NADPH cytochrome P450 reductase (NCR) activity, as phase I biotransformation parameter; (2) gluthathione S-transferase (GST) activity as a phase II conjugation enzyme, acetylcholinesterase activity, and metallothionein (MT) content. Ni bioaccumulation in the liver resulted in an increasing uptake up to 15.48 µg g⁻¹ wet weight (Ni-treated animals) and 16.73 µg g⁻¹ wet weight (mixture-treated animals) after 7 days of exposure. CHP accumulation showed a distinct pattern in animals exposed to the mixture of chemicals in comparison with CHP-treated animals. NCR activity exhibited a marked activation in CHP and mixture-treated animals. GST activity was significantly increased starting from 1 day exposure in CHP-treated animals and after 3 days in Ni-treated animals. MT accumulation increased in all conditions, with a marked synergetic effect after 7 days of exposure. These data should be carefully considered in view of the biological effects of mixture pollutants, particularly in fish farming conditions.

New Non-Invasive Method for the Authentication of Apple Cultivars.

Food authentication is very important to protect consumers, sellers, and producers from fraud. Although several methods have been developed using a wide range of analytical techniques, most of them require sample destruction and do not allow in situ sampling or analysis, nor reliable quantification of hundreds of molecules at the same time. To overcome these limitations, we have developed and validated a new noninvasive analytical workflow for food authentication. The method uses a functionalized strip to adsorb small molecules from the surface of the food product, followed by gas chromatography-mass spectrometry analysis of the desorbed analytes. We validated the method and applied it to the classification of five different apple varieties. Molecular concentrations obtained from the analysis of 44 apples were used to identify markers for apple cultivars or, in combination with machine learning techniques, to perform cultivar classification. The overall reproducibility of the method was very good, showing a good coefficient of variation for both targeted and untargeted analysis. The approach was able to correctly classify all samples. In addition, the method was also used to detect pesticides and the following molecules were found in almost all samples: chlorpyrifos-methyl, deltamethrin, and malathion. The proposed approach not only showed very good analytical performance, but also proved to be suitable for noninvasive food authentication and pesticide residue analysis.

Processing Adipose Tissue to Make it More Stable When Used for Refilling: A Morphologic and Immunohistochemistry Evaluation.

Breast reconstruction has gained from lipofilling the possibility to recover the aesthetic outcome of anatomical profile in a more natural appearance. However, until today, the long-term graft survival remains unpredictable, and sometimes it does not guarantee a well-adequate aesthetic result. In the present work, the morphological changes, occurring in fat mass used for refilling, harvested by the Coleman's procedure or through the washing/fragmenting procedure were analysed. Adipocyte size; immunohistochemistry against CD8, CD31, CD68 and M2-type macrophages and catalase enzyme, were analysed in vitro on fat mass cultured for 4 weeks. Our observation reveals an increase of connective tissue around the mass and a high number of immune cells occurrence in fat mass harvested by the Coleman's procedure. Instead, the washing/fragmented procedure would reduce the number of immune cells within the fat mass, increase the size of adipocytes, and cause a wider presence of active vessels profile and greater catalase expression. We hypothesize that the fat mass processed by the Coleman's procedure would remain more reactive due to a higher number of immune and macrophages cells, prone to develop cystic formation, leading to a suboptimal integration in the recipient site. On the other hand, the conditions more prone to realize an optimal integration would occur in the fat mass processed by the washing/fragmenting procedure: a reduced number of immune cells, low amount of connective tissue, presence of larger adipocytes. Follow-up monitoring did support our conclusion, as we observed a reduction of re-intervention for refilling procedure in patients treated with the washing/fragmenting procedure.

Effects of mercury on Dictyostelium discoideum: proteomics reveals the molecular mechanisms of physiological adaptation and toxicity.

Dictyostelium discoideum amoebae were exposed to Hg 2 microM corresponding to a sublethal concentration and Hg 10 microM with the first effects on mortality and replication rate. A total of 900 spots were visualized by 2-DE electrophoresis. Two-hundred fifty single proteins were identified by mass spectrometry. Low Hg concentration (2 microM) treatment induced up-regulation of 13 spots, mainly involved in oxidative stress response/detoxification, oxidoreductase activity, and metabolic processes. High Hg concentration (10 microM) treatment showed a different PES with 12 proteins downregulated and only two up-regulated, mainly involved in cellular metabolic processes, metal ion binding, and transferase activity. The analyses for the carbonylation show no changes after 2 microM Hg(2+) treatment and 13 differentially carbonylated proteins after 10 microM Hg(2+) involved in a broad range of cellular processes. Our findings provide insight into the mechanisms of physiological adaptation and toxicity to a low and an high mercury concentration, respectively, of Dictyostelium amoebae.

Uptake and biochemical responses of mussels Mytilus galloprovincialis exposed to sublethal nickel concentrations.

In the present study, mussel (Mytilus galloprovincialis) digestive gland oxidative stress biomarkers and detoxification responses to acute exposure to nickel (Ni) were investigated. Mussels were exposed to two sublethal concentrations of Ni (135 µg/L per animal (2.5 µM) and 770 µg/L per animal (13 µM)) for 24, 48, 72, 96 h and 8 days. Following biological responses were measured: (1) glutathione S-transferase (GST) activity as a phase II conjugation enzyme, (2) catalase activity as antioxidant response, (3) malondialdehyde accumulation (MDA) as lipid peroxydation marker and metallothionein as specific response to metals exposure. The cholinergic system was evaluated using the acetylcholinesterase activity (AChE). Moreover, Ni uptakes during the exposure periods were assessed and the uptake rate constant determined. A correlation matrix (CM) between the investigated biomarkers and a principal component analysis (PCA) were achieved for the two tested concentrations. The Ni-uptake constant was higher in animals exposed to the lowest concentration. The CM and the PCA showed a time-dependent effect of the Ni exposure on the investigated biomarkers being more pronounced in animals exposed to the highest Ni concentration. While AChE showed a significant increase after 48 h and a further return to control values in the lowest concentration, it was drastically maintained inhibited in the highest concentration. Our data provided clues about the occurrence of different toxicokinetics and toxicodynamics of two Ni sublethal concentrations in an ecologically relevant organism.

Radical scavenging abilities of fish MT-A and mussel MT-10 metallothionein isoforms: An ESR study.

Metallothioneins (MTs) are cysteine-rich proteins involved in homeostasis of essential metals, detoxification of toxic metals and scavenging of free radicals. Scavenging of the stable 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical was measured by means of ESR spectroscopy for two recombinant MTs from aquatic species: MT-10 from the sea mussel Mytilus galloprovincialis, and MT-A from the fish Oncorhyncus mykiss. Both the zinc- and the cadmium-loaded forms (Zn(7)-MTs and Cd(7)-MTs) were analysed, using the commercial MT-II (Zn(7)-MT-II and Cd(7)-MT-II, respectively) from rabbit liver as a reference. A decrease in the scavenging ability was observed for all the three MTs passing from the Zn- to the Cd-loaded forms, because of the higher stability of the Cd-mercapto complex. The Zn(7)-MTs from aquatic species were more effective in scavenging DPPH signal than the rabbit Zn(7)-MT-II (2.8 and 4-folds, respectively). Similar results were obtained also for the Cd(7)-MTs, thus confirming the stronger antioxidant power of MTs from aquatic organisms compared with the rabbit MT-II. Moreover, mussel MT-10 was more active in DPPH scavenging than fish MT-A. When the complete release of metals from MTs was obtained by lowering the pH to 3 or, alternatively, by adding the chelating agent diethylenetriaminepentaacetic acid (DTPA), an increase in the scavenging ability of MTs was observed.

Use of highly sensitive sublethal stress responses in the social amoeba Dictyostelium discoideum for an assessment of freshwater quality.

In this work, the sensitivity of a battery of tests on the social amoeba Dictyostelium discoideum has been assessed within a freshwater toxicity study. The results obtained from the evaluation of survival and replication rate of D. discoideum were compared to those derived with a series of widely used tests for freshwater toxicity assessment, i. e. bioassays using Vibrio fischeri, Daphnia magna and Pseudokirchneriella subcapitata. The effects on sublethal endpoints, i.e. lysosomal membrane stability (LMS) and endocytotic rate, were analysed in conjunction with high-level endpoints to verify the potential to make a typical bioassay more sensitive. The field ecotoxicological investigation employing D. discoideum is part of a monitoring study assessing environmental quality of the Bormida River (Italy), subjected until recently to a chronic industrial pollution. The survey was carried out at several stations (upstream and downstream of a chemical factory outlet) in two different periods. In 2002, the results of chemical analyses performed on river water indicated no contamination. The ecotoxicological data obtained in this period showed that no evidence of biological effects was observed using V. fischeri and D. magna bioassays. In spite of the previous classical acute toxicity tests, significant differences in cell viability of D. discoideum were found. By analysing the effects measured on LMS and endocytotic rate, more relevant changes were observed for these sublethal stress biomarkers compared to survival. The chronic toxicity data showed significant changes in cell growth both of P. subcapitata and D. discoideum. Nevertheless, more sensitive and rapid responses were obtained when assessing the effects of exposure on D. discoideum. The chemical and ecotoxicological data obtained in 2006 indicated a full recovery of the quality of the river water (neither contamination nor toxicity found). Altogether, the results reported in this study underline that the use of a battery of biomarkers in conjunction with high-level endpoints may help follow the pollutant-induced stress syndrome in the organisms from early sublethal effects to starting mortality.

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei.

Background: For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions: We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei's genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.

Efects of growth hormone and cadmium on the transcription regulation of two metallothionein isoforms.

The effect of growth hormone (GH) and cadmium (Cd) on metallothionein (MT) expression was investigated in hepatoma cells. In fish the constitutive isoform MT-B and the metal-responsive MT-A are expressed. Real-time RT-PCR revealed that: Cd up-regulates mostly MT-A, GH slightly induces MT-B and the GH/Cd combination induces synergistically both MTs. Perturbations in Ca2+ levels suppressed or reduced the Cd-induction of MTs and abolished the GH/Cd synergy. Similar results were obtained by inhibition of tyrosine kinases. Also the signaling molecules recruited by the GH receptor responded differently to GH and Cd, with ERKs showing a synergistic activation upon GH/Cd. The following conclusions can be drawn: (1) cytosolic Ca2+ is mainly involved in MT-A regulation; (2) both Ca2+ and tyrosine phosphorylation are essential for Cd-induction and GH/Cd synergy on MTs. The synergy could depend on interactions in different signaling pathways, leading to a differential recruitment of MTF-1 and AP-1 transcription factors.

Gene transcription profiling in pollutant exposed mussels (Mytilus spp.) using a new low-density oligonucleotide microarray.

In this study we describe the design and implementation of a novel low-density oligonucleotide microarray (the "Mytox-chip"). It consists of 24 mussel genes involving both normalizing elements and stress response related genes, each represented on the array with one or two different 50 mer oligonucleotide-probe reporters spotted in replicated samples on glass-activated slides. Target genes were selected on the basis of their potential involvement in mechanisms of pollutant and xenobiotic response. They are implicated in both basic and stress related cellular processes such as shock response, biotransformation and excretion, cell-cycle regulation, immune defense, drug metabolism, etc. The microarray was tested on mussels exposed to sublethal concentrations of mercury or a crude North Sea oil mixture. RNA samples were extracted from digestive glands of control and treated mussels for the synthesis of fluorescence labeled cDNAs to be used in dual color hybridizations. Transcription rates of two metallothionein iso-genes (mt10 and mt20), a p53-like gene and actin were quantitatively estimated also by real-time PCR to confirm microarray data. Significant alterations in the gene transcription patterns were seen in response to both treatments.

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.

Assessing the occurrence of a stress syndrome in mussels (Mytilus edulis) using a combined biomarker/gene expression approach.

A combination of biomarkers and gene expression analyses was used to investigate the occurrence of a stress syndrome in mussels (Mytilus edulis) caged along a copper pollution gradient in the Visnes fjord, Norway. The stress level in mussels, as calculated by a novel algorithm (the "Expert System") from a set of seven biomarkers, was compared with gene expression changes utilising a low-density oligonucleotide microarray, employing 24 different genes involved in both cellular homeostasis and stress-related responses. The biomarker battery included lysosomal membrane stability, lysosomal accumulation of neutral lipids and lipofuscin, lysosomal/cytoplasm volume ratio, Ca(2+)-ATPase and catalase activities, and total metallothionein content. Integration of the biomarkers into the Expert System ranked individuals sampled at site 2 as unstressed, mussels sampled at site 3 as being subject to low stress, and those from site 4, which is adjacent to what used to be a copper mine, as being highly stressed, with respect to specimens sampled from the reference site. Microarray analyses demonstrated that at the two innermost and mostly polluted sites, gene expression patterns where severely altered. In particular, some genes exhibited a linear activation response along the copper gradient, e.g. metallothioneins mt 20 and mt 10, and catalase. In addition, stress responsive kinase (krs), glutathione transferase (gst), major vault protein and histones (h1, h2a and h4) were significantly up-regulated at the innermost site. In conclusion, these results demonstrated that sites could be discriminated using both a physiological and a molecular approach. The development of a stress syndrome along the pollution gradient was evidenced with a novel mussel microarray, both in terms of numbers of regulated genes and level of gene response.