Validation and extension of a similarity-based approach for prediction of acute aquatic toxicity towards Daphnia magna

Quantitative structure–activity relationship (QSAR) models for predicting acute toxicity to Daphnia magna are often associated with poor performances, urging the need for improvement to meet REACH requirements. The aim of this study was to evaluate the accuracy, stability and reliability of a previously published QSAR model by means of further external validation and to optimize its performance by means of extension to new data as well as a consensus approach. The previously published model was validated with a large set of new molecules and then compared with ChemProp model, from which most of the validation data were taken. Results showed better performance of the proposed model in terms of accuracy and percentage of molecules outside the applicability domain. The model was re-calibrated on all the available data to confirm the efficacy of the similarity-based approach. The extended dataset was also used to develop a novel model based on the same similarity approach but using binary fingerprints to describe the chemical structures. The fingerprint-based model gave lower regression statistics, but also less unpredicted compounds. Eventually, consensus modelling was successfully used to enhance the accuracy of the predictions and to halve the percentage of molecules outside the applicability domain.     

Consensus QSAR models estimating acute toxicity to aquatic organisms from different trophic levels: algae,Daphnia and fish

ABSTRACT

We report new consensus models estimating acute toxicity for algae, Daphnia and fish endpoints. We assembled a large collection of 3680 public unique compounds annotated by, at least, one experimental value for the given endpoint. Support Vector Machine models were internally and externally validated following the OECD principles. Reasonable predictive performances were achieved (RMSE_ext = 0.56–0.78) which are in line with those of state-of-the-art models. The known structural alerts are compared with analysis of the atomic contributions to these models obtained using the ISIDA/ColorAtom utility. A benchmarking against existing tools has been carried out on a set of compounds considered more representative and relevant for the chemical space of the current chemical industry. Our model scored one of the best accuracy and data coverage.

Nevertheless, industrial data performances were noticeably lower than those on public data, indicating that existing models fail to meet the industrial needs. Thus, final models were updated with the inclusion of new industrial compounds, extending the applicability domain and relevance for application in an industrial context. Generated models and collected public data are made freely available.     

Comparison of in silico models for prediction of Daphnia magna acute toxicity

Eight in silico modelling packages were evaluated and compared for the prediction of Daphnia magna acute toxicity from the viewpoint of the European legislation on chemicals, REACH. We tested the following models: Discovery Studio (DS) TOPKAT, ACD/Tox Suite, ADMET Predictor?, ECOSAR (Ecological Structure Activity Relationships), TerraQSAR?, T.E.S.T. (Toxicity Estimation Software Tool) and two models implemented in VEGA on 480 industrial compounds for 48-h median lethal concentrations (LC₅₀) to D. magna, matching them with experimental values. The quality of the estimates was compared using a standard statistical review and an additional classification approach in which the hazard predictions were grouped using well-defined regulatory criteria. The regression parameters, correlation coefficient being the most influential, showed that four models (ADMET Predictor?, DS TOPKAT, TerraQSAR? and VEGA DEMETRA) had similar reliability. These performed better than the others, but the coefficient of determination was still low (r² around 0.6), considering that at least half the predicted compounds were inside the training sets. Additionally, we grouped the results in four defined toxicity classes. TerraQSAR? gave 60% of correct classifications, followed by DS TOPKAT, ADMET Predictor? and VEGA DEMETRA, with 56%, 54% and 48%, respectively. These results highlight the challenges associated with developing reliable and easily applied acceptability criteria for the regulatory use of QSAR models to D. magna acute toxicity.     

Development of classification models for predicting chronic toxicity of chemicals to Daphnia magna and Pseudokirchneriella subcapitata

Both the acute toxicity and chronic toxicity data on aquatic organisms are indispensable parameters in the ecological risk assessment priority chemical screening process (e.g. persistent, bioaccumulative and toxic chemicals). However, most of the present modelling actions are focused on developing predictive models for the acute toxicity of chemicals to aquatic organisms. As regards chronic aquatic toxicity, considerable work is needed. The major objective of the present study was to construct in silico models for predicting chronic toxicity data for Daphnia magna and Pseudokirchneriella subcapitata. In the modelling, a set of chronic toxicity data was collected for D. magna (21 days no observed effect concentration (NOEC)) and P. subcapitata (72 h NOEC), respectively. Then, binary classification models were developed for D. magna and P. subcapitata by employing the k-nearest neighbour method (k-NN). The model assessment results indicated that the obtained optimum models had high accuracy, sensitivity and specificity. The model application domain was characterized by the Euclidean distance-based method. In the future, the data gap for other chemicals within the application domain on their chronic toxicity for D. magna and P. subcapitata could be filled using the models developed here.     

QSAR models for biocides: The example of the prediction of Daphnia magna acute toxicity

ABSTRACT

Biocides are multi-component products used to control undesired and harmful organisms able to affect human or animal health or to damage natural and manufactured products. Because of their widespread use, aquatic and terrestrial ecosystems could be contaminated by biocides. The environmental impact of biocides is evaluated through eco-toxicological studies with model organisms of terrestrial and aquatic ecosystems. We focused on the development of in silico models for the evaluation of the acute toxicity (EC₅₀) of a set of biocides collected from different sources on the freshwater crustacean Daphnia magna, one of the most widely used model organisms in aquatic toxicology. Toxicological data specific for biocides are limited, so we developed three models for daphnid toxicity using different strategies (linear regression, random forest, Monte Carlo (CORAL)) to overcome this limitation. All models gave satisfactory results in our datasets: the random forest model showed the best results with a determination coefficient r² = 0.97 and 0.89, respectively, for the training (TS) and the validation sets (VS) while linear regression model and the CORAL model had similar but lower performance (r² = 0.83 and 0.75, respectively, for TS and VS in the linear regression model and r² = 0.74 and 0.75 for the CORAL model).     

External validation of the biodegradability prediction model CATABOL using data sets of existing and new chemicals under the Japanese Chemical Substances Control Law

External validation of the biodegradability prediction model CATABOL was conducted using test data of 338 existing chemicals and 1123 new chemicals under the Japanese Chemical Substances Control Law. CATABOL predicts that 1089 chemicals will have a BOD?<?60% while 925 (85%) actually have an observed BOD<60%. The percentage of chemicals with an observed BOD value <60% tends to increase as the predicted BOD values decrease. In contrast, 340 chemicals were predicted to have a BOD?≥?60% and 234 (69%) actually had an observed BOD?≥?60%. The prediction of poor biodegradability was more accurate than the predictions of high biodegradability. The features of chemical structures affecting CATABOL predictability were also investigated.     

Analysis of polycyclic aromatic hydrocarbons in fish: evaluation of a quick,easy, cheap,effective, rugged,and safe extraction method

QuEChERS method was evaluated for extraction of 16 PAHs from fish samples. For a selective measurement of the compounds, extracts were analysed by LC with fluorescence detection. The overall analytical procedure was validated by systematic recovery experiments at three levels and by using the standard reference material SRM 2977 (mussel tissue). The targeted contaminants, except naphthalene and acenaphthene, were successfully extracted from SRM 2977 with recoveries ranging from 63.5–110.0% with variation coefficients not exceeding 8%. The optimum QuEChERS conditions were the following: 5 g of homogenised fish sample, 10 mL of ACN, agitation performed by vortex during 3 min. Quantification limits ranging from 0.12–1.90 ng/g wet weight (0.30–4.70 μg/L) were obtained. The optimized methodology was applied to assess the safety concerning PAHs contents of horse mackerel (Trachurus trachurus), chub mackerel (Scomber japonicus), sardine (Sardina pilchardus) and farmed seabass (Dicentrarchus labrax). Although benzo(a)pyrene, the marker used for evaluating the carcinogenic risk of PAHs in food, was not detected in the analysed samples (89 individuals corresponding to 27 homogenized samples), the overall mean concentration ranged from 2.52 ± 1.20 ng/g in horse mackerel to 14.6 ± 2.8 ng/g in farmed seabass. Significant differences were found between the mean PAHs concentrations of the four groups.     

Investigation on the coacervation of fish scale gelatin hydrogel with seafood waste hydrolysates for the development of artificial fish bait: Physico-chemical,thermodynamic, and morpho-structural properties

The study dealt with the development of biopolymer based hydrogel artificial fish bait with hydrolysates derived from fish processing wastes. Fish scale gelatin (FSG) was used for the development of a hydrogel to which bioattractants extracted from seafood processing wastes of fish, squid and shrimp were added to prepare composite gels such as FSG-FH, FSG-SH and FSG-SPH, respectively. To understand the homogenesity and cross linking complexation of composite gels, the study aimed at investigating physico-chemical, thermodynamic, molecular and structural properties were analysed. The gel strength, melting point and thermal stability of the composite hydrogels were found to decrease marginally compared to the control gel, FSG. It could be understood that the crystalline structure at 2θ = 23° of the FSG-SH, and FSG-FH were not much altered compared to FSG gel. However, alteration in the crystalline structure in FSG-SPH was evident at 2θ = 27.3°. The TGA and DSC analysis revealed the reduction in the thermal stability of FSG on the addition of protein hydrolysates in the process of coacervation to get hydrogel based fish bait. Further, FESEM and AFM analysis indicated FSG-SH as the composite hydrogel with most compact and smooth surface was evident by Ra and Rq values. Among the composite gels, FSG-SH was found to have higher hydrophobicity due to enhanced gel structure. FTIR spectra of FSG and composite gels exhibitted similarity corresponding to amide-A, B, I, II and III bands. However, NMR analysis revealed the existence of notable difference with respect to chemical shift in the range of 7.0–7.75 ppm expressing the presence of aromatic protons of the amino acid phe and N–H protons of amide in all the composite gels. Further, NMR analysis confirmed the role of imino acids (δ CH₂ & β CH₂ protons) and hydrophobic amino acids (α-CH₂ protons) in decrease the physical and thermal properties of the composite gels. The addition of protein hydrolysates with FSG was found to decrease the physical, thermal and structural properties, however improve the aromatic compounds of the composite gels.     

Development of a volatile amine sensor for the monitoring of fish spoilage

A sensor with potential for the development of a “chemical barcode” for real-time monitoring of fish freshness is described. This on-package sensor contains a pH sensitive dye, bromocresol green, that responds through visible colour change to basic volatile spoilage compounds, such as trimethylamine (TMA), ammonia (NH₃) and dimethylamine (DMA) collectively known as Total Volatile Basic Nitrogen (TVB-N). The sensor characteristics were studied as well as its response with standard ammonia gas. Trials on cod and under-utilised species have verified that the sensor response correlates with bacterial growth patterns in fish samples thus enabling the “real-time” monitoring of spoilage in various fish species. The sensor response can be interrogated with a simple, inexpensive reflectance colorimeter that we have developed based on two light emitting diodes (LEDs) and a photodetector.     

Cold water fish gelatin films: Effects of cross-linking on thermal, mechanical, barrier, and biodegradation properties

Gelatin was extracted from Alaska pollock (Theragra chalcogramma) and Alaska pink salmon (Oncorhynchus gorbuscha) skins and cast into films. The fish gelatin films’ tensile, thermal, water vapor permeability, oxygen permeability, and biodegradation properties were compared to those of bovine and porcine gelatin films. In addition, fish gelatin films were cross-linked with glutaraldehyde. Pollock and salmon gelatin films had comparable tensile properties, but had lower tensile strength and percent elongation than mammalian gelatin films. The lower strength and elongation might have been due to lower structural gelatin levels present in fish gelatin films. The addition of cross-linkers had little effect on tensile properties and melting temperatures of fish gelatin films. Pollock gelatin films had the lowest water vapor and oxygen permeability values, whereas mammalian gelatin films had the highest permeability values. Cross-linking resulted in lower water vapor permeability for salmon gelatin films and higher oxygen permeability for pollock gelatin films. However, all fish gelatin films had better water vapor and oxygen barrier properties than mammalian gelatin films. Also, fish gelatin films degraded faster than mammalian gelatin films.     

Aggregation and dispersion of silver nanoparticles in exposure media for aquatic toxicity tests

Silver nanoparticles (AgNPs) are currently being very widely used in industry, mainly because of their anti-bacterial properties, with applications in many areas. Once released into the environment, the mobility, bioavailability, and toxicity of AgNPs in any ecosystem are dominated by colloidal stability. There have been studies on the stability or the aggregation of various nanoparticles (NPs) under a range of environmental conditions, but there is little information on fully characterised AgNPs in media used in (eco)toxicity studies. In this study, monodisperse 7, 10 and 20 nm citrate-stabilised AgNPs were synthesised, characterised and then fractionated and sized by flow field-flow fractionation (FFF) and measured with dynamic light scattering (DLS) in different dilutions of the media recommended by OECD for Daphnia magna (water flea) toxicity testing. Stability of NPs was assessed over 24 h, and less so over 21 days, similar time periods to the OECD acute and chronic toxicity tests for D. magna. All particles aggregated quickly in the media with high ionic strength (media1), resulting in a loss of colour from the solution. The size of particles could be measured by DLS in most cases after 24h, although a fractogram by FFF could not be obtained due to aggregation and polydispersity of the sample. After diluting the media by a factor of 2, 5 or 10, aggregation was reduced, although the smallest NPs were unstable under all media conditions. Media diluted up to 10-fold in the absence of AgNPs did not induce any loss of mobility or fecundity in D. magna. These results confirm that standard OECD media causes aggregation of AgNPs, which result in changes in organism exposure levels and the nature of the exposed particles compared to exposure to fully dispersed particles. Setting aside questions of dose metrics, significant and substantial reduction in concentration over exposure period suggests that literature data are in the main improperly interpreted and nanoparticles are likely to have far greater biological effects than suggested thus far by poorly controlled exposures. We recommend that the standard OECD media is diluted by a factor of ca. 10 for use with these NPs and this test media, which reduces AgNP aggregation without affecting the viability of the text organism.     

Dual-column GC analysis of mediterranean fish for ten organochlorine pesticides and sixty two chlorobiphenyls

The simultaneous analysis of α-HCH, β-HCH, γ-HCH, HCB, p,p′-DDD, p,p′-DDT, p,p′-DDE, o,p′-DDT, mirex, dieldrin and 62 chlorobiphenyl congeners on two parallel capillary GC columns of different polarity is described for nine Mediterranean fish species. Ten commercially available columns with stationary phases completely characterized in respect of their PCB elution patterns were considered for dual-column GC-ECD analysis. The combination of a 60 m × 0.25 mm i.d. column coated with a 0.25 μm film of 50% diphenyl dimethylsiloxane and a series combination of a 25 m × 0.25 mm i.d. column coated with a 0.25 μm film of 5% diphenyl dimethylsiloxane with a 25 m × 0.22 mm i.d. column coated with a 0.10 μm film of 1, 10-dicarba-closo-dodecarborane dimethylpolysiloxane furnished the highest number of separated chlorobiphenyl congeners (104). The dual-column GC system performed with high stability and reproducibility over a broad concentration range (1–3000 ng/g lipid) of the organochlorine compounds in the investigated fish.     

Multiresidue method for the determination of 13 pesticides in three environmental matrices: water, sediments and fish muscle

Pesticides residues in aquatic ecosystems are an environmental concern which requires efficient analytical methods. In this study, we proposed a generic method for the quantification of 13 pesticides (azoxystrobin, clomazone, diflufenican, dimethachlor, carbendazim, iprodion, isoproturon, mesosulfuron-methyl, metazachlor, napropamid, quizalofop and thifensulfuron-methyl) in three environmental matrices. Pesticides from water were extracted using a solid phase extraction system and a single solid-liquid extraction method was optimized for sediment and fish muscle, followed by a unique analysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Limits of quantification were below 5 ng L⁻¹ for water (except for fluroxypyr and iprodion) and ranged between 0.1 ng g⁻¹ and 57.7 ng g⁻¹ for sediments and regarding fish, were below 1 ng g⁻¹ for 8 molecules and were determined between 5 and 49 ng g⁻¹ for the 5 other compounds. This method was finally used as a new routine practice for environmental research.