Evaluation of Escherichia coli K-12 343/113 and derived strains for microbial mutagenicity assays

Several characteristics of the E. coli K-12 mutagenicity tester strains 343/113 and 343/120 have been investigated for their effects on induced mutagenesis using the arg56 and nad113 genes, and resistance to valine. We found, as have earlier authors, that the nad113 marker is relatively specific for detecting frameshift-inducing mutagens and relatively insensitive to agents that cause point mutations. In contrast, both the Arg and Val markers are primarily specific for reversion (or mutation) induction by point mutagens. In all cases tested, the Arg and Val markers respond to mutagens in a qualitatively similar manner. We have enhanced the sensitivity of this tester system to a wide variety of mutagens by permeabilization of the tester cell population using Tris-EDTA treatment. This treatment prior to mutagen exposure enables the detection of mutagenicity of several compounds that are weakly mutagenic or nonmutagenic in untreated cells. We have also increased the mutagenicity of some chemicals by preincubating with rat-liver S9 at pH values other than 7.4. For diethylnitrosamine, for instance, maximal induction occurred at pH 6.5, and for benzo[a]pyrene, maximal induction was at pH 6.8.     

The use of marine bacteria in mutagenicity assays

Mutagenic pollution of environment is a global and important problem. This includes marine environment. Although many mutagenicity assays have been developed, there are specific problems with testing marine water and sediments for mutagenic contamination. One of them is the fact that most of genetically modified strains used in commonly available microbiological mutagenicity assays, like Escherichia coli or Salmonella, survive relatively poorly in marine waters, especially those of higher salinity. Thus, alternative assays have been developed, in which bacteria occurring naturally in marine habitats are employed. These assays, reviewed in this article, appear to be useful in testing not only marine samples but also can be used in other approaches, which involve detection and estimation of the amount of mutagenic compounds.     

Genotoxicity of zinc in 4 short-term mutagenicity assays

The genotoxicity of zinc was examined in 4 short-term mutagenicity assays. Zinc acetate produced dose-related positive responses in the L5178Y mouse lymphoma assay and an in vitro cytogenetic assay with Chinese hamster ovary cells, but was negative in the Salmonella mutation assay and did not induce unscheduled DNA synthesis in primary cultures of rat hepatocytes. Zinc-2,4-pentanedione produced frameshift mutations in Salmonella tester strains TA1538 and TA98, but did not induce unscheduled DNA synthesis in primary cultures of rat hepatocytes. The effect of ligand binding of zinc in the in vitro test systems is discussed.     

Linking solubility and permeability assays for maximum throughput and reproducibility

Solubility and permeability are intimately linked in drug absorption processes. They have, however, been traditionally assayed separately. To support this linkage, a combined solubility/permeability assay was developed for determining absorption properties of chemical entities. First, solubility is determined at 4 pH values by comparing the concentration of a saturated compound solution to its dilute, known concentration. The filtered, saturated solution from the solubility assay is then used as input material for the membrane permeability determination. The permeability assay is a parallel artificial membrane technique whereby a membrane is created on a solid support parallel artificial membrane permeation assay (PAMPA). The 2 artificial membranes presented here model the gastrointestinal tract and the blood-brain barrier (BBB). Data are presented for control compounds, which are well documented in the literature and exemplify a range of solubility and membrane permeability. The advantages of the combination method are 1) reduction of sample usage and preparation time, 2) elimination of interference from compound precipitation in membrane permeability determination, 3) maximization of input concentration to permeability assay for improved reproducibility, and 4) optimization of sample tracking by streamlining data entry and calculations. BBB permeability ranking of compounds correlates well with literature CNS activity.     

Statistical modeling and analyses of a base-specific Salmonella mutagenicity assay

Statistical features of a base-specific Salmonella mutagenicity assay are considered in detail, following up on a previous report comparing responses of base-specific Salmonella (Ames II) strains with those of traditional tester strains. In addition to using different Salmonella strains, the new procedure also differs in that it is performed as a microwell fluctuation test, as opposed to the standard plate or preincubation test. This report describes the statistical modeling of data obtained from the use of these new strains in the microwell test procedure. We emphasize how to assess any significant interactions between replicate cultures and exposure doses, and how to identify a significant increase in the mutagenic response to a series of concentrations of a test substance.     

Genomic analyses of microbial virulence

Genomic sequencing of bacterial pathogens is providing an increasing wealth of new data. It is, however, still unclear how this information can be used to develop new experimental approaches. Here, we describe recent efforts to complement existing bacterial genetics with genomic methods for the study of pathogenesis.     

The minimum significant ratio: a statistical parameter to characterize the reproducibility of potency estimates from concentration-response assays and estimation by replicate-experiment studies

The authors show by illustration that procedures used to validate the reliability of single-concentration high-throughput screens such as the signal window and Z' factor do not ensure sufficient reliability in potency estimates from concentration response assays. They develop the minimum significant ratio as a statistical parameter to characterize the fold change between 2 compounds run in the same experiment that can be considered a real difference and use this parameter to characterize the reliability of the assay. They adapt methods described by Bland and Altman to develop a simple set of 2 experiments to estimate the minimum significant ratio and show that this protocol can identify assays that lack reproducibility. The methods are then extended to validate the equivalency of the same assay run by multiple laboratories.     

On the statistical evaluation of adherence assays

Parametric (unpaired t-test) and non-parametric (Mann-Whitney U-test) methods have been used in the evaluation of adherence assays on the non-antibiotic antimicrobial agent, Taurolin. In all but one case, where the anti-adherence effect was known to be marginal, both statistical methods gave similar results although there were some minor differences in the levels of significance achieved. The effect of the agent on the deviation of adherence data from normality was quantified by calculation of the skewness coefficient for each data set. A significant anti-adherence effect appears to result in a decrease in the skewness of the adherence assay data. It was concluded that either parametric or non-parametric statistical evaluation of adherence assay data is valid for large numbers of observations. In future studies of this type it is suggested that attention should also be given to the effect of the anti-adherence agent on the deviation of adherence data from normality as denoted by the skewness coefficient.     

On the statistical evaluation of adherence assays

Parametric (unpaired t -test) and non-parametric (Mann-Whitney U-test) methods have been used in the evaluation of adherence assays on the non-antibiotic antimicrobial agent, Taurolin. In all but one case, where the anti-adherence effect was known to be marginal, both statistical methods gave similar results although there were some minor differences in the levels of significance achieved. The effect of the agent on the deviation of adherence data from normality was quantified by calculation of the skewness coefficient for each data set. A significant anti-adherence effect appears to result in a decrease in the skewness of the adherence assay data. It was concluded that either parametric or non-parametric statistical evaluation of adherence assay data is valid for large numbers of observations. In future studies of this type it is suggested that attention should also be given to the effect of the anti-adherence agent on the deviation of adherence data from normality as denoted by the skewness coefficient.     

The statistical reliability of synapomorphic analyses

A statistical test has been developed to ascertain whether a given number of presumptive synapomorphies between one pair of taxa is significantly greater than the number between another pair of taxa. This is shown to be a form of testing the significance of a difference between two proportions. It is necessary first to adjust for common patterns of synapomorphy that raise or lower both numbers. The method has been checked by simulation, and is illustrated by data on the relationships of tetrapods. It proves that Hennigian cladistics has statistical constraints.     

Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches

Cultivation independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. This approach is based on direct extraction of total soil DNA followed by PCR amplification of selected marker genes and subsequent genetic fingerprint analyses. Semi-automated genetic fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA) yield high-resolution patterns of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring, when rapid high throughput screening for differences or changes is more important than phylogenetic identification of organisms affected. Our objective was to perform profound statistical analysis to evaluate the cultivation independent approach and the consistency of results from T-RFLP and RISA. As a model system, we used two different heavy metal treated soils from an open top chamber experiment. Bacterial T-RFLP and RISA profiles of 16S rDNA were converted into numeric data matrices in order to allow for detailed statistical analyses with cluster analysis, Mantel test statistics, Monte Carlo permutation tests and ANOVA. Analyses revealed that soil DNA-contents were significantly correlated with soil microbial biomass in our system. T-RFLP and RISA yielded highly consistent and correlating results and both allowed to distinguish the four treatments with equal significance. While RISA represents a fast and general fingerprinting method of moderate cost and labor intensity, T-RFLP is technically more demanding but offers the advantage of phylogenetic identification of detected soil microorganisms. Therefore, selection of either of these methods should be based on the specific research question under investigation.