An ancestral molecular response to nanomaterial particulates.

The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.

Ab Initio Studies of Anatase TiO2 (101) Surface-supported Au8 Clusters.

Supported transition metals on TiO2 surfaces have shown exceptional catalytic properties in many important process such as CO oxidation, selective propane oxidation, hydrogenation, water adsorption and other catalytic and photocatalytic oxidation reaction at low-temperature. Among the three polymorphs of TiO2, the anatase crystal is the more photoactive. The anatase (101) surface attracts more attention since it has lower surface energy relative to (001) and (100) surfaces and it is observed to adsorb small molecules on its surface. Using density-functional theory (DFT) with on-site Coulomb interactions corrections, we have computed the structural and electronic properties of selected Au8 clusters interacting with clean and reduced anatase TiO2(101) surfaces. The computed adsorption energies are suggesting that the considered Au8 clusters are only physisorbed onto pristine TiO2(101) surface. Oxygen vacancies are found to enhance the absorption of Au8 on the Ti2(101) surface. Accurate simulations required spin polarized DFT since the ground state of Au8 interacting with defective TiO2(101) shows magnetic solutions. The results show that Au8 clusters are chemically bonded to the surface around the locality of the oxygen vacancy. The surface oxygen vacancy is found to be energetically more favourable than sub-surface oxygen vacancy configuration. These vacancy sites may act as nucleation sites for small Au clusters or Au atoms. Finally, the computed electronic structure of all the Au8/TiO2(101) configurations considered in this work are analysed in the light of available experimental data.

Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance.

Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds).

Evaluation criteria for the quality of published experimental data on nanomaterials and their usefulness for QSAR modelling.

Nowadays nanotechnology is one of the most promising areas of science. The number and quantity of synthesized nanomaterials increase exponentially, therefore it is reasonable to expect that comprehensive risk assessment based only on empirical testing of all novel engineered nanoparticles (NPs) will very soon become impossible. Hence, the development of computational methods complementary to experimentation is very important. Quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) models widely used in pharmaceutical chemistry and environmental science can also be modified and adopted for nanotechnology to predict physico-chemical properties and toxicity of empirically untested nanomaterials. All QSPR/QSAR modelling activities are based on experimentally derived data. It is important that, within a given data set, all values should be consistent, of high quality and measured according to a standardized protocol. Unfortunately, the amount of such data available for engineered nanoparticles in various data sources (i.e. databases and the literature) is very limited and seldom measured with a standardized protocol. Therefore, we have proposed a framework for collecting and evaluating the existing data, with the focus on possible applications for computational evaluation of properties and biological activities of nanomaterials.

Estimating persistence of brominated and chlorinated organic pollutants in air, water, soil, and sediments with the QSPR-based classification scheme.

We have estimated degradation half-lives of both brominated and chlorinated dibenzo-p-dioxins (PBDDs and PCDDs), furans (PBDFs and PCDFs), biphenyls (PBBs and PCBs), naphthalenes (PBNs and PCNs), diphenyl ethers (PBDEs and PCDEs) as well as selected unsubstituted polycyclic aromatic hydrocarbons (PAHs) in air, surface water, surface soil, and sediments (in total of 1,431 compounds in four compartments). Next, we compared the persistence between chloro- (relatively well-studied) and bromo- (less studied) analogs. The predictions have been performed based on the quantitative structure-property relationship (QSPR) scheme with use of k-nearest neighbors (kNN) classifier and the semi-quantitative system of persistence classes. The classification models utilized principal components derived from the principal component analysis of a set of 24 constitutional and quantum mechanical descriptors as input variables. Accuracies of classification (based on an external validation) were 86, 85, 87, and 75% for air, surface water, surface soil, and sediments, respectively. The persistence of all chlorinated species increased with increasing halogenation degree. In the case of brominated organic pollutants (Br-OPs), the trend was the same for air and sediments. However, we noticed that the opposite trend for persistence in surface water and soil. The results suggest that, due to high photoreactivity of C-Br chemical bonds, photolytic processes occurring in surface water and soil are able to play significant role in transforming and removing Br-OPs from these compartments. This contribution is the first attempt of classifying together Br-OPs and Cl-OPs according to their persistence, in particular, environmental compartments.

Application and comparison of different chemometric approaches in QSPR modelling of supercooled liquid vapour pressures for chloronaphthalenes.

Molecular descriptors from calculations at the level of Density Functional Theory (B3LYP/6-311++G**) were effectively applied in QSPR estimation of supercooled liquid vapour pressures (P(L)) for individual chloronaphthalene congeners. The estimated values of log P(L) varied from 1.05 Pa to 5.6 x 10(-5) Pa, depending on the number of chlorine substituents present in the molecule and the substitution pattern. Comparison of the five chemometrical methods of modelling (approaches) led to the final conclusion, that the use of relatively simple PLS combined with one of the variable pre-selection algorithms (UVE or GA) seems to be the optimal choice in such computational studies for persistent organic pollutants. The best GA-PLS model was characterized by the value of root mean square error of prediction RMSEP = 0.108 logarithmic Pascal units.

Octanol/water partition coefficients of chloronaphthalenes.

Computational n-octanol/water partition coefficients data for 75 chloronaphthalene congeners based on the Ghose, Pritchet, and Crippen algorithm; the Moriguchi method; and two QSPR models with principal component regression and partial least-squares (PLS) regression calculations are presented. Chloronaphthalenes log Kow data obtained after PLS are characterized by the lowest root mean square error (RMSEP = 0.0190), whereas results from the Ghose, Pritchet, and Crippen algorithm are characterized by the worst predictive ability (RMSEP = 0.4191). Minimal values of log Kow of chloronaphthalenes ranged between 3.57 and 3.90 for 1-chloronaphthalene, whereas maximal values ranged between 6.36 and 7.19 for octachloronaphthalene.

Computational prediction of 7-ethoxyresorufin-O-diethylase (EROD) and luciferase (luc) inducing potency for 75 congeners of chloronaphthalene.

Based on available toxicological data and matrix of structural descriptors 7-ethoxyresorufin-O-diethylase (EROD) and luciferase (luc) inducing potency for 75 congeners of chloronaphthalene was predicted using quantitative structure-activity relationships (QSAR) strategy. The most active congeners in EROD and luciferase bioassays were CN congeners nos. 75 and 67. Some empirical rules describing toxic PCNs were formulated.

Concentrations and fluxes of chloronaphthalenes in sediment from Lake Kitaura in Japan in past 15 centuries.

The concentrations of 63 congeners of chloronaphthalene (CN; polychlorinated naphthalenes, PCNs) in dated on approximately 500 B.C. to 2000 sediment core from the Lake Kitaura in Japan have been quantified by HRGC/HRMS after double column HPLC fractionation. Sediment from the Lake Kitaura showed a time-dependent pattern in distribution of CNs since the approximately 500 B.C. Starting from the 1910s the total CNs content increased accelerating from the 1960s, and, in parallel, the pattern of CN congeners has changed with a substantial increase in contribution from the penta, hexa, hepta, and octaCN. The total CNs content normalized to dry weight of sediment peaked out in the layer dated on 1984-1985, and next nearly two-fold decreased with further gradually decreasing concentration in 1987-2000. An occurrence of tri and tetraCNs in deep sediment layers corresponded to preindustrial synthesis and use of CNs seems to be connected to relatively greater water solubility and mobility in the pore water of those CN homologue groups. Based on CN congener pattern and results of multivariate analysis three main layers were separated in the sediment core. Starting from 1981 the emission sources related to combustion marker congeners become substantial contributors to flux of annually deposited CNs, while relative significance of the evaporative source marker congeners decreased after 1985. The annual flux of CNs into sediments of the Lake Kitaura was 0.073-0.31 pg/cm2 before 1926, increased to 5.5-14 pg/cm2 in 1963-1970 and next sharply increased to 50-107 pg/ cm2 in 1971-1985, and after that decreased to 17 pg/cm2 in 1997-2000.

Polychlorinated biphenyls (PCBs) and their congener-specific accumulation in edible fish from the Gulf of Gdansk, Baltic Sea.

Concentrations and composition profiles of polychlorinated biphenyls (PCBs) were investigated in composite samples of 10 species of edible fish from the Gulf of Gdansk, in the southern part of the Baltic Sea, Poland, to understand the status of contamination and possible human exposure risk. Apart from the total PCBs, planar non-ortho (IUPAC nos 77, 126, 169) and mono-ortho (nos 105, 114, 118, 123, 156, 157, 167, 189) chlorobiphenyls were also quantified and their dioxin-like toxicity assessed. The absolute total PCB concentrations in fish ranged from 43 to 490 ng g(-1) wet wt (910-11000 ng g(-1) lipids), while of TCDD TEQs of planar members were from 0.15 to 3.1 pg g(-1) wet wt (8.1-81 pg g(-1) lipids). The penta- and hexa-CBs usually comprised 70-80% of the total PCBs and were followed by hepta-, tetra- and tri-CBs, and for a specific site tri- and tetra-CBs comprised as much as 22%. Among the individual CB congeners, nos 118, 153 (+132) and 138 (+160 +163 +164) were the most abundant, while no. 110 comprised between 6.8 and 9.3% of the total PCBs in some species. Principal component analysis (PCA) was applied to examine the interdependences among CB congeners in the factor space. The PCA model and cluster analyses were further used to examine site- and species-specific differences and similarities of PCB composition, and the results are discussed. An assessed daily intake rate of TCDD TEQ of planar PCBs with the fishmeal of the Gulf of Gdansk in the 1990s was between 78 and 96 pg per capita or between 1.3 and 1.6 pg kg(-1) body weight.

Chlorinated cyclodiene pesticide residues in blue mussel, crab, and fish in the Gulf of Gdansk, Baltic Sea.

Chlordane components (CHLs) and their metabolites (heptachlor, cis-heptachlor epoxide, U82, MC4, trans-chlordane, MC5, cis-chlordane, MC7, oxychlordane, MC6- and trans- and cis-nonachlor) and aldrin, dieldrin, endrin, isodrin, endosulfan 1, endosulfan 2, and mirex were quantified in the soft tissues of blue mussel, a whole crab, and whole fishes collected from the spatially different sites in the Gulf of Gdansk. Six to twelve chlordane compounds and metabolites and dieldrin were detected in all organisms examined while aldrin, endrin, isodrin, endosulfans 1 and 2, and mirex were not found above the detection limit of the method. The lipid weight based concentrations in Baltic biota were relatively small and ranged from 12 to 150 and 7.6-77 ng/g, while between 0.16 and 6.8 and 0.10-6.6 ng/g in fresh tissue, respectively. The profile (%) of chlordane compounds was very similar between various fish species with trans-nonachlor (28 +/- 17), cis-chlordane (23 +/- 18), oxychlordane (13 +/- 7), and heptachlor epoxide (11 +/- 5) as major constituents and was totally different in crab with oxychlordane as the most dominating (>65%) compound. Blue mussel, lamprey, and three-spined stickleback exhibited a smallest ability to metabolize CHLs, and such fishes as cod, lesser sand-eel, sand-eel, pikeperch, perch, round goby, flounder, and herring showed a slightly better ability, while crab was able to effectively metabolize most of CHL compounds except trans-nonachlor. A value of the quotient of the trans-nonachlor to cis-chlordane concentrations (N/C quotient) was 1.0 in blue mussel, 3.1 in crab, and between 0.9 and 1.8 in fish. Both the small concentrations of CHLs in all organisms and the values of N/C quotients close to 1 imply on a long-range aerial transport through movement of the air masses from the remote regions of the northern hemisphere as a main source of this pesticide in the Gulf of Gdansk. The interdependences between the CHL profiles for various fish species and between different sampling sites were examined using the principal component analysis (PCA) method. Applying the PCA model the first four significant components explained 90% (43% + 23% + 15% + 8%) of the total variance in the data matrix.