Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli.

Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterized the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain - a gene with roles in both quorum sensing and the recycling of methylation products used in E. coli's DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.

UV Induced Mutagenicity in Water: Causes, Detection, Identification and Prevention.

At first it seemed that UV processes for disinfection and advanced oxidation were "harmless", as they didn't involve the addition of "dangerous" chemicals nor seemed to result in the formation of toxic byproducts. However, recently it has become clear that also during UV processes mutagentic/genotoxic byproducts may be formed. It was found that these are nitrogen containing aromatic compounds, which are formed by the reaction of photolysis products of nitrate with (photolysis products of) natural organic matter. Now more has become clear on the formation process of these compounds, it is possible to limit or even prevent their formation during e.g. UV/H2O2 processes. Besides, it appears to be possible to remove such byproducts by means of filtration processes. Thus, UV based processes can safely be applied in water treatment.

2D TCR-pMHC-CD8 kinetics determines T-cell responses in a self-antigen-specific TCR system.

Two-dimensional (2D) kinetic analysis directly measures molecular interactions at cell-cell junctions, thereby incorporating inherent cellular effects. By comparison, three-dimensional (3D) analysis probes the intrinsic physical chemistry of interacting molecules isolated from the cell. To understand how T-cell tumor reactivity relates to 2D and 3D binding parameters and to directly compare them, we performed kinetic analyses of a panel of human T-cell receptors (TCRs) interacting with a melanoma self-antigen peptide (gp100209 -217 ) bound to peptide-major histocompatibility complex in the absence and presence of co-receptor CD8. We found that while 3D parameters are inadequate to predict T-cell function, 2D parameters (that do not correlate with their 3D counterparts) show a far broader dynamic range and significantly improved correlation with T-cell function. Thus, our data support the general notion that 2D parameters of TCR-peptide-major histocompatibility complex-CD8 interactions determine T-cell responsiveness and suggest a potential 2D-based strategy to screen TCRs for tumor immunotherapy.

Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur).

The fluctuation assay remains an important tool for analyzing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria-Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work, extensions to the Luria-Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating were developed. Hence, the novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of the inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates and P values, confidence intervals for an arbitrary function of data (such as fold), and perform power analysis and sample size determination for the likelihood ratio test. The accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments are assessed. Both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea-Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts.

A Modified Fluctuation Assay with a CAN1 Reporter in Yeast.

Understanding the generation of mutations is fundamental to understanding evolution and genetic disease; however, the rarity of such events makes experimentally identifying them difficult. Mutation accumulation (MA) methods have been widely used. MA lines require serial bottlenecks to fix de novo mutations, followed by whole-genome sequencing. While powerful, this method is not suitable for exploring mutation variation among different genotypes due to its poor scalability with cost and labor. Alternatively, fluctuation assays estimate mutation rate in microorganisms by utilizing a reporter gene, in which Loss-of-function (LOF) mutations can be selected for using drugs toxic to cells containing the WT allele. Traditional fluctuation assays can estimate mutation rates but not their base change compositions. Here, we describe a new protocol that adapts traditional fluctuation assay using CAN1 reporter gene in Saccharomyces cerevisiae , followed by pooled sequencing methods, to identify both the rate and spectra of mutations in different strain backgrounds.

Is a liver comparable to a liver? A comparison of different rat-derived S9-fractions with a biotechnological animal-free alternative in the Ames fluctuation assay.

Metabolism has to be considered during the toxicological assessment of chemical and environmental samples because it is an important process in the mammalian liver. It can be assessed in vitro via liver homogenates called S9-fractions, an external metabolic activation system. However, the external metabolic activation systems can vary greatly in their composition due to biological variations among individual animals and animal strains that the S9-fraction are derived as well as the differences in the production treatment. To gain more insight into these variances, three different but commonly used rat-derived S9-fractions were compared in the present study for their variance and performance with a reference compound in the Ames fluctuation assay with Salmonella typhimurium strains TA 98 and TA 100 according to ISO 11350. Severe shortcomings of conventional rat-derived S9-fractions were observed in the present study, such that S9-fractions differed significantly within the same rat strain and for different types of induction procedures in regards to the metabolic capability. An intrinsic mutagenic potential of the three rat-derived S9-fractions were identified in the Ames fluctuation assay with varying S9-fraction concentrations. To address some of the shortcomings of the animal-derived S9-fraction, the present study investigated the use and performance of a biotechnological, animal-free alternative, ewoS9R, in comparison to one of the rat-derived S9-fraction as the others showed a mutagenic potential themselves. Specifically, 12 different chemicals were used as a reference to determine if ewoS9R could serve as an adequate and more consistent replacement of traditional rat-derived metabolic activation systems: 8 pro-mutagenic compounds (i.e., require metabolic activation to show a mutagenic potential), one pro-mutagenic compound but not in the tested strains, one mutagenic compound without metabolic activation and two compounds that are equivocal in the literature. EwoS9R was evaluated as a promising approach in the Ames fluctuation assay with 5 compounds observed to have similar results with both rat-derived S9-fraction and ewoS9R (41%), for 3 compounds ewoS9R was a better metabolization system than the rat-derived S9-fraction (16%). Further research is necessary to determine the full potential of ewoS9R in comparison to rat-derived S9-fractions.

Combining Different In Vitro Bioassays to Evaluate Genotoxicity of Water-Accommodated Fractions from Petroleum Products.

Genotoxicity assessment is of high relevance for crude and refined petroleum products, since oil compounds are known to cause DNA damage with severe consequences for aquatic biota as demonstrated in long-term monitoring studies. This study aimed at the optimization and evaluation of small-scale higher-throughput assays (Ames fluctuation, micronucleus, Nrf2-CALUX®) covering different mechanistic endpoints as first screening tools for genotoxicity assessment of oils. Cells were exposed to native and chemically dispersed water-accommodated fractions (WAFs) of three oil types varying in their processing degree. Independent of an exogenous metabolic activation system, WAF compounds induced neither base exchange nor frame shift mutations in bacterial strains. However, significantly increased chromosomal aberrations in zebrafish liver (ZF-L) cells were observed. Oxidative stress was indicated for some treatments and was not correlated with observed DNA damage. Application of a chemical dispersant increased the genotoxic potential rather by the increased bioavailability of dissolved and particulate oil compounds. Nonetheless, the dispersant induced a clear oxidative stress response, indicating a relevance for general toxic stress. Results showed that the combination of different in vitro assays is important for a reliable genotoxicity assessment. Especially, the ZF-L capable of active metabolism and DNA repair seems to be a promising model for WAF testing.

Integrating bioassays, chemical analysis and in silico techniques to identify genotoxicants in surface water.

Identification of hazardous compounds, as the first step of water protection and regulation, is still challenged by the difficulty to establish a linkage between toxic effects and suspected contaminants. Genotoxic compounds are one type of highly relevant toxicants in surface water, which may attack the DNA and lead to cancer in individual organism, or even damaged germ cells to be passed on to future generations. Thus, the establishment of a linkage between genotoxic effects and genotoxicant is important for environmental toxicologists and chemists. For this purpose, in the present study in silico methods were integrated with bioassays, chemical analysis and literature information to identify genotoxicants in surface water. Large volume water samples from 22 sampling sites of the Danube were collected and subjected to biological and chemical analysis. Samples from the most toxic sites (JDS32, JDS44 and JDS63) induced significant genotoxic effects in the micronucleus assay, and two of them caused mutagenicity in the Ames fluctuation assay. Chemical analysis showed that 68 chemicals were detected in these most toxic samples. Literature findings and in silico techniques using the OECD QSAR Toolbox and the ChemProp software package revealed genotoxic potentials for 29 compounds out of 68 targeted chemicals. To confirm the integrative technical data, the micronucleus assay and the Ames fluctuation assay were applied with artificial mixtures of those compounds and the raw water sample extracts. The results showed that 18 chemicals explained 48.5% of the genotoxicity in the micronucleus assay. This study highlights the capability of in silico techniques in linking adverse biological effect to suspicious hazardous compounds for the identification of toxicity drivers, and demonstrates the genotoxic potential of pollutants in the Danube.

An unbiased attitude is vital to exploring the Beijing genotype of Mycobacterium tuberculosis.

In 2003 Werngren and Hoffner reported the earliest quantitative mutability study comparing Beijing and non-Beijing strains of Mycobacterium tuberculosis. Their null findings appeared to be at odds with the then-popular hypothesis favoring characterization of the Beijing genotype by mutability. Three recent attempts to reexamine the experimental data have resulted in three successively smaller p-values in the literature, each supposedly buttressing a non-null conclusion. In addition to identifying errors responsible for the three misleading p-values, we focus on salutary lessons that will facilitate future research on microbial mutability.

Genotoxicity of three biofuel candidates compared to reference fuels.

Global demand for alternative energy sources increases due to concerns regarding energy security and greenhouse gas emissions. However, little is known regarding the impacts of biofuels to the environment and human health even though the identification of such impacts is important to avoid biofuels leading to undesired effects. In this study mutagenicity and genotoxicity of the three biofuel candidates ethyl levulinate (EL), 2-methyltetrahydrofuran (2-MTHF) and 2-methylfuran (2-MF) were investigated in comparison to two petroleum-derived fuels and a biodiesel. None of the samples induced mutagenicity in the Ames fluctuation test. However, the Micronucleus assay revealed significant effects in Chinese hamster (Cricetulus griseus) V79 cells caused by the potential biofuels. 2-MF revealed the highest toxic potential with significant induction of micronuclei below 20.0 mg/L. EL and 2-MTHF induced micronuclei only at very high concentrations (>1000.0 mg/L). In regard to the genotoxic potential of 2-MF, its usage as biofuel should be critically discussed.

Quantitative Analysis of the Rates for Repeat-Mediated Genome Instability in a Yeast Experimental System.

Instability of repetitive DNA sequences causes numerous hereditary disorders in humans, the majority of which are associated with trinucleotide repeat expansions. Here, we describe a unique system to study instability of triplet repeats in a yeast experimental setting. Using fluctuation assay and the novel program FluCalc we are able to accurately estimate the rates of large-scale expansions, as well as repeat-mediated mutagenesis and gross chromosomal rearrangements for different repeat sequences.

bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis.

Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb.upmc.fr/bzrates.