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A study of the effect of kHz ultrasound on the mutation rate of Salmonella typhimurium TA102.

Free radicals, induced by ionising radiation or generated by chemical systems, are known to produce DNA damage that may result in mutation. An in vitro study was carried out to discover whether free radicals produced from water using kHz ultrasound increased the mutation rate of Salmonella typhimurium above the spontaneous reversion rate. Results showed that the mutation rate of S. typhimurium did not increase under these conditions. It is concluded that dental ultrasound is not mutagenic to the dental soft tissues under normal conditions of use.

Dental Scaling↗

Pentachlorophenol treatment in vivo elevates point mutation rate in zebrafish p53 gene.

Pentachlorophenol (PCP), a probable human carcinogen, has been heavily used as an aseptic and a biocide throughout the world, and is widely present in the environment. Recent survey in Germany revealed that the average PCP amount in the urine of general German populations was 1.04 microg/L while the peak concentration could reach up to 19.1 microg/L. PCP was reported to cause DNA damage, but whether it can be involved in inducing point mutations in genome is unknown. To determine the genotoxicity of PCP on vertebrate, we first performed acute toxicity test on zebrafish for the effect of PCP exposure. The LC50 values of zebrafish exposed to PCP at 24, 48, 72 and 96 h were determined to be 0.196, 0.130, 0.130 and 0.130 mg/L, respectively. We then treated zebrafish with PCP for 10 days at 0 (control), 0.5, 5 and 50 microg/L, respectively, to determine whether PCP could be involved in inducing point mutations. Employing denaturing high-performance liquid chromatography analysis and DNA sequencing, we demonstrated that exposure of PCP to zebrafish at a concentration as low as 5 microg/L for 10 days elevates point mutation rate in p53 gene in liver cells. This is the first direct evidence revealing that PCP can elevate point mutation rate in the vertebrate genomes. The result implies PCP might be involved in carcinogenesis by elevating point mutation rate in the somatic genomes.

Animals↗

Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes.

We investigate the possibility that differences between synonymous substitution rates of organelle and bacterial genes differing only in copy number may be due to conversion bias. We find that the rather large observed difference in the synonymous rates between genes in the single copy and inverted-repeat regions of chloroplasts can be accounted for by a very small bias against new mutants. More generally, differences in the within-organelle fixation probability result in different apparent mutation rates as measured by the expected rate of appearance of cells homoplasmic for new mutants. Thus, differences in intracellular population parameters rather than molecular mechanisms can account for some variation in the apparent mutation rates of organelle genes, and possibly in other systems with variable numbers of gene copies. On the other hand, our analysis suggests that conversion bias is not a likely explanation for relatively low mutation rates observed near the replication origin of bacterial chromosomes.

Chloroplasts↗

Estimation of mutation rates in cultured mammalian cells.

The factors that affect reliable estimations of mutation rates (mu) in cultured mammalian somatic cell populations by fluctuation analysis are studied experimentally and statistically. We analyze the differential effect of the final cell population size in each culture (Nt) and the number of parallel cultures (C) on the variation in the rate estimates (mu) inferred from the P0 method. The analysis can be made after the derivation of the variance of mu, which is a measure of variation of mu for a given combination of Nt and C in a number of repeat experiments. The variance of mu is inversely proportional to C and to the square of Nt . Nt determines the probability of occurrence of mutations in a cell culture. By influencing the size of P0, Nt also determines whether a rate estimate is obtainable from the experiment. Since Po is estimated from the fraction of cultures containing no mutation in a set of C cultures, C becomes a determining factor for the accuracy of mu. The rate estimated from P0 is biased, but the bias is in general 2 orders of magnitude smaller than mu. By the selection of an appropriate combination of Nt and C for the experiment, this bias can be reduced even further. Based on the notion of comparing two proportions, we propose a test statistic and have applied it to experimental results for a test of equality of mutation rates in different cell lines. This development places the comparison of mutation rates on a statistical basis.

Animals↗

Retroviral mutation rates and A-to-G hypermutations during different stages of retroviral replication.

Retroviruses mutate at a high rate in vivo during viral replication. Mutations may occur during proviral transcription by RNA polymerase II, during minus-strand DNA synthesis (RNA template) by viral reverse transcriptase, or during plus-strand DNA synthesis (DNA template) by reverse transcriptase. To determine the contributions of different stages of replication to the retroviral mutation rates, we developed a spleen necrosis virus-based in vivo system to selectively identify mutations occurring during the early stage (RNA transcription plus minus-strand synthesis) and the late stage (plus-strand synthesis plus DNA repair). A lacZalpha reporter gene was inserted into the long terminal repeat (LTR) of a spleen necrosis virus shuttle vector, and proviruses were recovered from infected cells as plasmids containing either one or both LTRs. Plasmids containing both LTRs generated a mutant phenotype only if the lacZalpha genes in both LTRs were mutated, which is most likely to occur during the early stage. Mutant phenotypes were identified from plasmids containing one LTR regardless of the stage at which the mutations occurred. Thus, mutant frequencies obtained after recovery of plasmids containing both LTRs or one LTR provided early-stage and total mutation rates, respectively. Analysis of 56,409 proviruses suggested that the retroviral mutation rates during the early and late stages of replication were equal or within twofold of each other. In addition, two mutants with A-to-G hypermutations were discovered, suggesting a role for mammalian double-stranded RNA adenosine deaminase enzyme in retroviral mutations. These experiments provide a system to selectively identify mutations in the early stage of retroviral replication and to provide upper and lower limits to the in vivo mutation rates during minus-strand and plus-strand synthesis, respectively.

Animals↗

Mutation rate heterogeneity and the generation of allele diversity at the human minisatellite MS205 (D16S309).

Many tandemly repeated minisatellite loci display extreme levels of length variation as a consequence of high rates of spontaneous germline mutation altering repeat copy number. Direct screening for new allele lengths by small-pool PCR has shown that instability at the human minisatellite locus MS205 (D16S309) is largely germline specific and usually results in the gain or loss of just a few repeat units. Structural analysis of the order of variant repeats has shown that these events occur preferentially at one end of the tandem array and can result in complex rearrangements including the inter-allelic transfer of repeat units. In contrast, putative mutants recovered from somatic DNA occur at a substantially lower rate and are simple and non-polar in nature. Germline mutation rates vary considerably between alleles, consistent with regulation occurring in cis. Although examination of DNA sequence polymorphisms immediately flanking the minisatellite reveals no definitive associations with germline mutation rate variation, differences in rate may be paralleled by changes in mutation spectrum. These findings help to explain the diversity of MS205 allele structures in modern humans and suggest a common mutation pathway with some other minisatellites.

Alleles↗

Ionizing radiation and genetic risks IX. Estimates of the frequencies of mendelian diseases and spontaneous mutation rates in human populations: a 1998 perspective.

This paper is focused on baseline frequencies of mendelian diseases and the conceptual basis for calculating doubling doses both of which are relevant for the doubling dose method of estimating genetic risks of exposure of human populations to ionizing radiation. With this method, the risk per unit dose is obtained as a product of three quantities, namely, the baseline frequency of the disease class under consideration, the relative mutation risk (which is the reciprocal of the doubling dose, which in turn, is calculated as a ratio of spontaneous and induction rates of mutations) and mutation component, i.e., the responsiveness of the disease class to an increase in mutation rate. The estimates of baseline frequencies of mendelian diseases that are currently used in risk estimation date back to the late 1970s. Advances in human genetics during the past two decades now permit an upward revision of these estimates. The revised estimates are 150 per 10(4) livebirths for autosomal dominants (from the earlier estimate of 95 per 10(4)), 75 per 10(4) livebirths for autosomal recessives (from 25 per 10(4)) and to 15 per 10(4) livebirths for X-linked diseases (from 5 per 10(4)). The revised total frequency of mendelian diseases is thus 240 per 10(4) livebirths and is about twice the earlier figure of 125 per 10(4) livebirths. All these estimates, however, pertain primarily to Western European and Western European-derived populations. The fact that in several population isolates or ethnic groups, some of these diseases (especially the autosomal recessives) are more common as a result of founder effects and/or genetic drift is well known and many more recent examples have come to light. These data are reviewed and illustrated with data from studies of the Ashkenazi Jewish, Finnish, French Canadian, Afrikaner and some other populations to highlight the need for caution in extrapolating radiation risks between populations. The doubling dose of 1 Gy that has been used for the past 20 years for risk estimation is based on mouse data for both spontaneous and induction rates of mutations. In extrapolating the mouse-data-based doubling dose to humans, it is assumed that the spontaneous rates in mice and humans are similar. This assumption is incorrect because of the fact that in humans, for several well-studied mendelian diseases, the mutation rate differs between the two sexes and it increases with paternal age. In estimates of spontaneous mutation rates in humans (which represent averages over both sexes), however, paternal age effects are automatically incorporated. In the mouse, these effects are expected to be much less (if they exist at all), but the problem has not been specifically addressed. The complexities and uncertainties associated with assessing the potential impact of spontaneous mutations which arise as germinal mosaics (and which can result in clusters of mutations in the following generation) on mutation rate estimates (in the mouse) and on mutation rate estimates and disease frequencies (in humans) are discussed. In view of (i) the lack of comparability of spontaneous mutation rates in mice and humans and (ii) the fact that these estimates for human genes already include both paternal age effects and correction for clusters (if they had occurred), it is suggested that a prudent procedure now is to base doubling dose calculations on spontaneous mutation rates of human genes (and induction rates of mouse genes, in the absence of a better alternative). This concept, however, is not new and was used by the US National Academy's Committee on the Biological Effects of Ionizing Radiation in its 1972 report.

Genetic Diseases, Inborn↗

Estimation of the mutation rate of hepatitis E virus based on a set of closely related 7.5-year-apart isolates from Sapporo, Japan.

Since hepatitis E virus (HEV) does not persist in infected hosts or in cultured cell lines, it has been difficult to know its spontaneous mutation rate. Recently, we identified an HEV isolate in stored serum from a patient having developed hepatitis E in 1995 (JSM-Sap95), nucleotide sequence of which showed a strong resemblance to those obtained from three patients who contracted hepatitis E in 2000 and 2002 (JKK-Sap00, JYW-Sap02, and JTS-Sap02). The remarkable nucleotide similarity together with the fact that all these patients were residents of the same city, Sapporo, prompted us to hypothesize that JKK-Sap00, JYW-Sap02 and JTS-Sap02 are descendants of JSM-Sap95. Then, the mutation rate of HEV was calculated to be 1.72, 1.41, or [Formula: see text] base substitutions per site per year, from JSM-Sap95 to JKK-Sap00, JYW-Sap02 or JTS-Sap02, respectively. Interestingly, these values were very similar to those ( [Formula: see text] to [Formula: see text] ) reported for hepatitis C virus. Because it remains possible that JSM-Sap95 is not the direct ancestor of the other three isolates but was merely a relative of the true ancestor, HEV mutation rate may be a little lower than [Formula: see text] base substitutions per site per year.

Journal Article↗

Modifiers of mutation rate: a general reduction principle.

A deterministic two-locus population genetic model with random mating is studied. The first locus, with two alleles, is subject to mutation and arbitrary viability selection. The second locus, with an arbitrary number of alleles, controls the mutation at the first locus. A class of viability-analogous Hardy-Weinberg equilibria is analyzed in which the selected gene and the modifier locus are in linkage equilibrium. It is shown that at these equilibria a reduction principle for the success of new mutation-modifying alleles is valid. A new allele at the modifier locus succeeds if its marginal average mutation rate is less than the mean mutation rate of the resident modifier allele evaluated at the equilibrium. Internal stability properties of these equilibria are also described.

Alleles↗

Retinoblastoma: a model for deriving the mutation rate without using any estimate of the size of the population at risk.

Paediatric cancer of the retinae arises from a transient population of stem cells whose growth and decay are responsible for the development of the fully differentiated photo-receptors and nerve cells. A model is described which fits the data on the incidence of bilateral retinoblastoma and gives the somatic mutation rate without using an estimate of the size of the population at risk. It also gives the shape of the retinoblast growth/decay curve. The model has been tested on two independent sets of data from the USA, and given that both sets are representative of the USA as a whole, there seems to have been little change in the somatic mutation rate over the last 30 or so years. For a total retinoblast formation of 4 x 10(6) cells, the average mutation rate is 2.94 x 10(-7) per cell per year.

Age Factors↗

Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line.

An in vivo assay was previously developed for detecting forward mutations in human immunodeficiency virus type 1 (HIV-1) in a single cycle of replication. This system uses the lacZalpha peptide gene as a reporter for mutations, and allows for the rates and types of mutations that occur to be determined. The forward mutation rate for HIV-1 in HeLa cells was found to be 3 x 10(-5) mutations per target base pair per cycle. To test whether the mutation rate was influenced by cell type, the mutation rate of HIV-1 in CEM-A cells, a T lymphoid cell line, was determined. The mutation rate of HIV-1 reverse transcription in CEM-A cells was found to be 4 x 10(-5) mutations per target base pair per cycle. The number and types of mutations observed were similar to that in HeLa cells. Specifically, base substitution mutations predominated, and G-to-A transition mutations were the most common base substitution. G-to-A hypermutants were also characterized. The difference in HIV-1 mutation rate between HeLa and CEM-A cells was not significant, indicating that the accuracy of HIV-1 reverse transcription is comparable in both the HeLa and CEM-A cell lines.

Base Sequence↗

Estimate to mutation rates.

The mathematical methods for estimating the mutation rates of microbes at the level of populations are given in this paper, which are concerned with the estimation of the mixture of two normal distributions. Using the feed forward of livingthing's prior information, the precision of the estimates may be increased and the calculation may be reduced. Finally, an approximate method about the small sample is given in this paper.

Models, Genetic↗

Mutation rates in humans. I. Overall and sex-specific rates obtained from a population study of hemophilia B.

A population-based study of hemophilia B mutations was conducted in the United Kingdom in order to construct a national confidential database of mutations and pedigrees to be used for the provision of carrier and prenatal diagnoses based on mutation detection. This allowed the direct estimate of overall (micro), male (v), and female (u) mutation rates for hemophilia B. The values obtained per gamete per generation and the 95% confidence intervals are micro;=7.73 (6. 29-9.12&parr0;x10-6; v=18.8 (14.5-22.9&parr0;x10-6; and u=2.18 (1. 44-3.16&parr0;x10-6. The ratio of male-to-female mutation rates is 8. 64, with a 95% confidence interval of 5.46-14.5. The higher male rate was not caused by a much higher rate of transition at CpG sites in the male. Attempts to detect evidence of gonadal mosaicism for hemophilia B mutation in suitable families did not detect any instances of ovarian mosaicism in any of 47 available opportunities. This suggests that the risk of a noncarrier mother manifesting as a gonadal mosaic by transmitting the mutation to a second child should be <0.062.

CpG Islands↗

Selection for increased mutation rates with fertility differences between matings.

Previous studies of mutation modification have considered models in which selection is a result of viability differences that are sex symmetric. The results of a numerical study of a model in which selection is a result of fertility differences between mated pairs demonstrate that the type of selection to which a population is subject can have a significant impact on the evolution of various parameters of the genetic system. When the fertility of matings between individuals with different genotypes exceeds the fertility of at least some of the matings between individuals with the same genotype, selection may favor increased rates of mutation, in contrast to the results from all existing constant viability models with random mating and infinite population size. Increased mutation rates are most frequently favored when forward and back mutation occur at approximately equal rates and when the modifying locus is loosely linked to the selected locus. We present one example in which selection favors increased rates of mutation even though the selection scheme is reducible to one of differential viability between the sexes.

Alleles↗

On the power to detect differences between male and female mutation rates for Duchenne muscular dystrophy, using classical segregation analysis and restriction fragment length polymorphisms.

The power to detect departures from the theoretical proportion of new mutants in X-linked lethal disorders has been analyzed for several types of segregation analysis, including methods based on completely linked restriction fragment length polymorphisms. It is shown that all methods require large sample sizes in order to detect even large differences between male and female mutation rates. Ascertainment bias is shown to have a great effect on the outcome of the segregation analysis. All reviewed studies concerning the proportion of new mutants in Duchenne muscular dystrophy, whether they claimed equality or inequality between the male and female mutation rates, give insufficient evidence because of ascertainment bias and a too low power. An ascertainment bias-free method is given, with the advantage that information from many studies can be combined. By doing so, in the long run, even moderate departures from equality in mutation rates (if present) can be detected.

DNA Restriction Enzymes↗

EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster.

Polygenic mutations were induced by treating Drosophila melanogaster adult males with 2.5 mM EMS. The treated second chromosomes, along with untreated controls, were then made homozygous, and five life history, two behavioral, and two morphological traits were measured. EMS mutagenesis led to reduced performance for life history traits. Changes in means and increments in genetic variance were relatively much higher for life history than for morphological traits, implying large differences in mutational target size. Maximum likelihood was used to estimate mutation rates and parameters of distributions of mutation effects, but parameters were strongly confounded with one another. Several traits showed evidence of leptokurtic distributions of effects and mean effects smaller than a few percent of trait means. Distributions of effects for all traits were strongly asymmetrical, and most mutations were deleterious. Correlations between life history mutation effects were positive. Mutation parameters for one generation of spontaneous mutation were predicted by scaling parameter estimates from the EMS experiment, extrapolated to the whole genome. Predicted mutational coefficients of variation were in good agreement with published estimates. Predicted changes in means were up to 0.14% or 0.6% for life history traits, depending on the model of scaling assumed.

Analysis of Variance↗

Modelling germline mosaicism and different new mutation rates simultaneously for appropriate risk calculations in families with Duchenne muscular dystrophy.

For several genetic diseases two biological phenomena have been recognised as important: germline mosaicism; and different new mutation rates in males and females depending on mutation type. Both principles have been investigated separately and their influence on risk estimation in families has been exemplified in the literature. The aim of this paper is to present a general model that includes mosaicism and different new mutation rates. Mosaicism is introduced by defining additional alleles at the disease locus in combination with adapted segregation rules. Taking Duchenne muscular dystrophy as an example, we derive the conditions which have to be fulfilled for a population in mutation selection equilibrium. Our approach describes the model at the population level and not in individual subjects. This has the advantage of being able to use well known algorithms for the calculation of likelihoods in pedigrees, and to include additional diagnostic information such as marker genotypes and carrier deletion test results. We demonstrate the impact of the new model on a typical pedigree. In families where the patient is not available, the distinction between point mutations and deletions is important, since often molecular diagnostic tests for females can only screen for deletions. Negative deletion test results can now be included in the risk calculations.

Female↗

High mutation rate of TPE repeats: a microsatellite in the putative transposase of the hobo element in Drosophila melanogaster.

The hobo transposable element contains a polymorphic microsatellite sequence located in its coding region, the TPE repeats. Previous surveys of natural populations of Drosophila melanogaster have detected at least seven different hobo transposons. These natural populations are geographically structured with regard to TPE polymorphism, and a scenario has been proposed for the invasion process. Natural populations have recently been completely invaded by hobo elements with three TPE repeats. New elements then appeared by mutation, triggering a new stage of invasion by other elements. Since TPE polymorphism appeared over a short period of time, we focused on estimating the mutation rate of these TPE repeats. We used transgenic lines harboring three TPE and/or five TPE hobo elements that had been evolving for at least 16 generations to search for a new TPE repeat polymorphism. We detected three mutants, with four, seven, and eight TPE repeats, respectively. The estimated mutation rate of the TPE repeats is therefore higher than that of neutral microsatellites in D. melanogaster (4.2 x 10-4 versus 6.5 x 10-6). The role of the transposition mechanism and the particular structure of the TPE repeats of the hobo element in this increase in the mutation rate are discussed.

Alleles↗