Genome resequencing analysis of Salmonella typhimurium LT-2 strains TA98 and TA100 for the establishment of a next-generation sequencing-based mutagenicity assay.

Next-generation sequencing (NGS) is a potentially useful technology to achieve a more precise evaluation of chemical mutagenicity. To establish NGS-based mutagenicity assays, which enable the direct detection of chemically induced mutations in a whole genome manner, the selection of appropriate biological resources and their precise genome sequences are essential. Here, we performed genome re-sequencing analyses of Salmonella typhimurium LT-2 strains TA98 and TA100, which have been frequently used in mutagenicity assays. We identified several strain-specific mutations including those that were relevant to their known phenotypes (his, ΔuvrB and rfa). The details of rfa mutations were first clarified in this study, which was a frameshift variant in rfaF and a missense variant in rfaC in TA98 and TA100, respectively. The uvrB deletion in TA98 was larger than that in TA100, which suggested differences in defects of lipopolysaccharide synthesis between these strains. The re-sequenced genome data of TA98 and TA100 will help us establish NGS-based bacterial mutagenicity assays and understand the biological events seen in them. Copyright © 2017 John Wiley & Sons, Ltd.

In silico prediction of the mutagenicity of nitroaromatic compounds using correlation weights of fragments of local symmetry.

Most quantitative structure-property/activity relationships (QSPRs/QSARs) techniques involve using different programs separately for generating molecular descriptors and separately for building models based on available descriptors. Here, the capabilities of the CORAL program are evaluated. A user of the program should apply as the basis for models the representation of the molecular structure by means of the simplified molecular input-line entry system (SMILES) as well as experimental data on the endpoint of interest. The local symmetry of SMILES is a novel composition of symmetrically represented symbols, which are three 'xyx', four 'xyyx', or five symbols 'xyzyx'. We updated our CORAL software using this optimal, new flexible descriptor, sensitive to the symmetric composition of a specific part of the molecule. Computational experiments have shown that taking account of these attributes of SMILES can improve the predictive potential of models for the mutagenicity of nitroaromatic compounds. In addition, the above computational experiments have confirmed the advantage of using the index of ideality of correlation (IIC) and the correlation intensity index (CII) for Monte Carlo optimization of the correlation weights for various attributes of SMILES, including the local symmetry. The average value of the coefficient of determination for the validation set (five different models) without fragments of local symmetry is 0.8589 ± 0.025, whereas using fragments of local symmetry improves this criterion of the predictive potential up to 0.9055 ± 0.010.

The enhancement scheme for the predictive ability of QSAR: A case of mutagenicity.

Mutagenicity is one of the most dangerous properties from the point of view of medicine and ecology. Experimental determination of mutagenicity remains a costly process, which makes it attractive to identify new hazardous compounds based on available experimental data through in silico methods or quantitative structure-activity relationships (QSAR). A system for constructing groups of random models is proposed for comparing various molecular features extracted from SMILES and graphs. For mutagenicity (mutagenicity values were expressed by the logarithm of the number of revertants per nanomole assayed by Salmonella typhimurium TA98-S9 microsomal preparation) models, the Morgan connectivity values are more informative than the comparison of quality for different rings in molecules. The resulting models were tested with the previously proposed model self-consistency system. The average determination coefficient for the validation set is 0.8737 ± 0.0312.

Mutagenicity of the Danube River: The contribution of liquid phase and particulate suspended matter.

Bioassays have been used to complement the chemical characterization of aquatic mutagenicity, but the tests sometimes are done only with water liquid phase (LP). Particle-bound mutagens are important because they can be ingested by filtering organisms. Our objective was to evaluate the mutagenicity of organic extracts of the LP and the water suspended particulate matter (SPM) from 13 sites along Danube River with the Salmonella/microsome microsuspension assay using TA98, YG1041, TA1538, and YG5185 strains. A high incidence of mutagenicity was detected, 84% for LP and 92% for SPM samples. The contribution of SPM to the mutagenicity was relatively small when compared with LP however, for five sites SPM was responsible for the whole mutagenicity, highlighting the importance of analyzing SPM when assessing water mutagenicity. YG1041 was the most sensitive strain and should be considered in future water mutagenicity monitoring programs, but it will depend on the main pollution sources.

Mutagenicity as a parameter in surface water monitoring programs-opportunity for water quality improvement.

Effect-based analyses are being recognized as excellent tools to a comprehensive and reliable water quality evaluation to complement physical and chemical parameters. The Salmonella/microsome mutagenicity test was introduced in the São Paulo State water quality-monitoring program in 1999 and waters from 104 sites used to the production of drinking water were analyzed. Samples were tested after organic extraction, using the microsuspension version of the Salmonella/microsome assay with strains TA98 and TA100 with and without S9-mammalian metabolic system. Of the 1720 water samples analyzed in 20 years, 20% were positive; TA98 was the most sensitive strain, detecting alone 99%. Results were presented in hazard categories to facilitate water managers' understanding and general public communication. Hot spots of mutagenicity were identified, and pollution sources investigated. A flow scheme with instructions of how to proceed in case of mutagenic samples was developed and implemented in the monitoring program. Enforcement actions were taken to reduce exposure of humans and aquatic biota to mutagenic compounds. The results presented provide scientific basis for the incorporation of the Salmonella/microsome assay in a regulatory framework, and to guide water-quality managers. The inclusion of a mutagenicity assay using standardized conditions proved to be an opportunity to improve the quality of water, and the strategy presented here could be applied by any environmental agency around the world. Environ. Mol. Mutagen. 61:200-211, 2020. © 2019 Wiley Periodicals, Inc.

The Correlation Contradictions Index (CCI): Building up reliable models of mutagenic potential of silver nanoparticles under different conditions using quasi-SMILES.

The interpretation of the mutagenic potential of silver nanoparticles as a mathematical function of (i) dose; (ii) coating; and (iii) type of mutagenicity (TA98 and TA100) gives quantitative models with good statistical quality. So-called quasi-SMILES are used to represent examined objects (silver nanoparticles under different conditions) for building up models. Simplified molecular input-line entry systems (SMILES) is a well-known sequence of symbols for representation of the molecular structure. Quasi-SMILES is a similar sequence of symbols for representation of experimental conditions. The Correlation Contradiction Index (CCI) calculated with data on the calibration set gives possibility to predict quality of correlation of "experimental vs. calculated values of endpoint" for external validation set.

Evaluation of the genotoxicity of PM2.5 collected by a high-volume air sampler with impactor.

BACKGROUND: The harmful effects of fine particles with an aerodynamic diameter less than 2.5 µm (PM2.5) on respiratory organs are emphasized in pollution studies because PM2.5 have high deposition rates in the respiratory organs and contain various hazardous compounds. In this study, a sampling method combining a high-volume air sampler (HV) with a PM2.5 impactor was developed for collecting large quantities of PM2.5. The concentrations of elemental carbon (EC), organic carbon (OC), inorganic ions, and polycyclic aromatic hydrocarbons (PAHs) were measured in PM2.5 collected by the high-and low-volume air samplers (LV). RESULTS: Similar results were obtained from the HV and LV methods, with respect to inorganic carbon, organic carbon, sodium ions, ammonium ions, and PAHs with more than four rings. Because of the much larger amount of PM2.5 could be collected by the HV method, the trace constituents, that were difficult to detect by the conventional LV method, were readily detected by the HV method. Furthermore, when the microsuspension method that was modified more sensitive Ames mutagenicity test, was used to test the PM2.5 samples at four sites, mutagenic activities were detected by strains TA100 and TA98. Most of the mutagenic activity was associated with the PM2.5 fraction and mutagenic activity in winter was greater than that in summer. CONCLUSIONS: The HV method produced results similar to those from the conventional LV method with respect to the PM2.5 components present in the atmosphere in relatively high concentrations, but its 40-fold greater flow rate enabled the detection of mutagenic compounds present in only trace concentrations.

Mutagenic activities of biochars from pyrolysis.

Biochar production, from pyrolysis of lignocellulosic feedstocks, agricultural residues, and animal and poultry manures are emerging globally as novel industrial and commercial products. It is important to develop and to validate a series of suitable protocols for the ecological monitoring of the qualities and properties of biochars. The highly sensitive Salmonella mutagenicity assays (the Ames test) are used widely by the toxicology community and, via the rat liver extract (S9), can reflect the potential for mammalian metabolic activation. We examined the Ames test for analyses of the mutagenic activities of dimethylsulphoxide (DMSO) extracts of biochars using two bacterial models (S. typhimurium strains TA98 and TA100) in the presence and in the absence of the metabolic activation with the S9-mix. Tester strain TA98 was most sensitive in detecting mutagenic biochar products, and the contribution of S9 was established. Temperature and times of pyrolysis are important. Biochar pyrolysed at 400°C for 10min, from a lignocellulose precursor was mutagenic, but not when formed at 800°C for 60min, or at 600°C for 30min. Biochars from poultry litter, and manures of calves fed on grass had low mutagenicities. Biochar from pig manure had high mutagenicity; biochars from manures of cows fed on a grass plus cereals, those of calves fed on mother's milk, and biochars from solid industrial waste had intermediate mutagenicities. The methods outlined can indicate the need for further studies for screening and detection of the mutagenic residuals in a variety of biochar products.

The mutagenic assessment of an electronic-cigarette and reference cigarette smoke using the Ames assay in strains TA98 and TA100.

Salmonella typhimurium strains TA98 and TA100 were used to assess the mutagenic potential of the aerosol from a commercially available, rechargeable, closed system electronic-cigarette. Results obtained were compared to those for the mainstream smoke from a Kentucky reference (3R4F) cigarette. Two different test matrices were assessed. Aerosol generated from the e-cigarette was trapped on a Cambridge filter pad, eluted in DMSO and compared to cigarette smoke total particulate matter (TPM), which was generated in the same manner for mutagenicity assessment in the Salmonella assay. Fresh e-cigarette and cigarette smoke aerosols were generated on the Vitrocell® VC 10 smoking robot and compared using a modified scaled-down 35mm air agar interface (AAI) methodology. E-cigarette aerosol collected matter (ACM) was found to be non-mutagenic in the 85mm plate incorporation Ames assay in strains TA98 and TA100 conducted in accordance with OECD 471, when tested up to 2400µg/plate. Freshly generated e-cigarette aerosol was also found to be negative in both strains after an AAI aerosol exposure, when tested up to a 1L/min dilution for up to 3h. Positive control responses were observed in both strains, using benzo[a]pyrene, 2-nitrofluorene, sodium azide and 2-aminoanthracene in TA98 and TA100 in the presence and absence of metabolic activation respectively. In contrast, cigarette smoke TPM and aerosol from 3R4F reference cigarettes were found to be mutagenic in both tester strains, under comparable test conditions to that of e-cigarette exposure. Limited information exists on the mutagenic activity of captured e-cigarette particulates and whole aerosol AAI approaches. With the lower toxicant burden of e-cigarette aerosols compared to cigarette smoke, it is clear that a more comprehensive Ames package of data should be generated when assessing e-cigarettes, consisting of the standard OECD-five, TA98, TA100, TA1535, TA1537 (or TA97) and E. coli (or TA102). In addition, TA104 which is more sensitive to the carbonyl based compounds found in e-cigarette aerosols under dry-wicking conditions may also prove a useful addition in a testing battery. Regulatory standard product testing approaches as used in this study will become important when determining whether e-cigarette aerosols are in fact less biologically active than cigarette smoke, as this study suggests. Future studies should be supported by in vitro dosimetry approaches to draw more accurate comparisons between cigarette smoke, e-cigarette aerosol exposure and human use.

Studies on meso-zeaxanthin for potential toxicity and mutagenicity.

The purpose of these studies was to examine the potential toxicity and genotoxicity of meso-zeaxanthin (MZ). Toxicity was assessed by administering MZ daily to rats for 13 weeks followed by a 4-week recovery period. Potential genotoxicity was assessed in separate experiments using the Ames test method. Rats were randomly assigned to four groups to receive corn oil (control) or MZ at dose levels of 2, 20 and 200 mg/kg/day by oral gavage (10/sex/group). Additional rats (five of each sex) in the control and the 200 mg/kg/day groups were retained for the recovery period. No compound-related clinical, biochemical or pathological signs or symptoms were noted and the no-observed-adverse-effect-level (NOAEL) of MZ was >200 mg/kg/day. To investigate genotoxicity, MZ was tested for its ability to induce reverse mutations (±microsomal enzymes) at 2 genomic loci; the histidine locus of 4 strains of Salmonella typhimurium and the tryptophan locus of Escherichia coli strain WP2uvrA. Six doses of MZ ranging from 10 to 5000 µg/plate were tested twice with vehicle and positive controls using 3 plates/dose. MZ did not cause any increase in the mean number of revertants/plate with any bacterial strain, with or without microsomal enzymes, and was therefore unlikely to be mutagenic.

Antimutagenic and Anticarcinogenic Effect of Methanol Extracts of Sweetpotato (Ipomea batata) Leaves.

The present study was conducted to investigate the antimutagenic potential of the methanolic extract from the leaves of sweet potato (Ipomea batatas, IB) with the SOS chromotest (umu test) and Salmonella typhimurium TA 98 and TA 100. The anticarcinogenic effects were also studied by calculation of the IC50 on human cancer cell lines and investigating the function of gap junction in rat liver epithelial cells. The IB extract inhibited dose-dependently the ß-galactosidase activity induced spontaneously at concentration of more than 200 mg/ml in S. typhimurium TA 1535/pSK 1002, and decreased significantly (p < 0.01) the ß-galactosidase activities induced by mutagen 6-chloro-9-[3- (2-chloroethylamino) proylamino]-2-methoxyacridine dihydrochloride (ICR) at dose of more than 0.4 mg/0.1 ml. The IB extract showed no effect on the spontaneous reversions of S. typhimurium TA 98 and 100 but benzo (α) pyrene (BaP) -stimulated reversions were decreased dose-dependently (p < 0.01) at the concentration of more than 100 mg/ml. The IC50 value of stomach cancer cells was lower than that of normal rat liver epithelial cells, but the values of colon and uterine cancer cell lines were similar to those of normal rat liver epithelial cells. The transfer of dye through gap junctions was not affected by treatment of the IB extracts at any concentration during treatment periods. The simultaneously treatment of IB extract and 12-O-tetradecanoylphorbol-13-acetate (TPA) effectively prevented the inhibition of dye transfer induced by TPA 1 hour after treatment at all exposed concentrations. The number of gap junctions was significantly (p < 0.01) increased by the treatment with IB extract at concentrations of more than 40 µg/ml. The inhibition of the expression of gap junction proteins by TPA (0.01 µg/ml) was recovered dose dependently by the simultaneous treatment of IB extracts. Our data suggest that Ipomea batatas has antimutagenic and anticarcionogenic activity in vitro.