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Raymond Proudlock - One of the best experts on this subject based on the ideXlab platform.
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the micro ames test a direct comparison of the performance and sensitivities of the standard and 24 well plate versions of the Bacterial Mutation test
Environmental and Molecular Mutagenesis, 2016Co-Authors: Raymond Proudlock, Kristie EvansAbstract:“Ames” Bacterial Mutation tests are widely performed for evaluation and registration of new materials including industrial chemicals, agrochemicals, medical devices, pharmaceuticals, pharmaceutical impurities and other materials. Tests are used to predict their potential long-term adverse health effects (including carcinogenicity). Given their importance, pre-screening ‘miniaturized’ versions have been developed which allow higher throughput and use less test material, including the widely-employed 24-well micro-Ames (µAmes) test which uses 20 times less material. However, little quantitative information has been published on the methodology or sensitivity of this system. We describe methods and results used in direct comparisons of the sensitivity of micro and standard systems using the same cultures, formulations, etc. Initial testing utilized the plate incorporation method and, later, the pre-incubation method. In a subsequent phase of testing, a four-way direct comparison was made between the pre-incubation and plate incorporation methods in both systems using some direct-acting mutagens. Tests used only those strain/S9/chemical combinations where a response was expected. Historical control results accumulated during testing are also presented. Spontaneous and induced revertant colony counts for the µAmes system were consistently proportionate and approximately 1/20th those for the standard Ames test. Sensitivities of the two systems were found to be nearly identical in almost all cases for a wide variety of weak and strong inorganic and organic mutagens. Standardized procedures and increased reliability of the estimate of the background revertant frequency in the µAmes system means that the two systems give equivalent results and are expected to be highly predictive of one another. Environ. Mol. Mutagen. 57:687–705, 2016. © 2016 Wiley Periodicals, Inc.
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The micro‐Ames test: A direct comparison of the performance and sensitivities of the standard and 24‐well plate versions of the Bacterial Mutation test
Environmental and molecular mutagenesis, 2016Co-Authors: Raymond Proudlock, Kristie EvansAbstract:"Ames" Bacterial Mutation tests are widely performed for evaluation and registration of new materials including industrial chemicals, agrochemicals, medical devices, pharmaceuticals, pharmaceutical impurities and other materials. Tests are used to predict their potential long-term adverse health effects (including carcinogenicity). Given their importance, pre-screening 'miniaturized' versions have been developed which allow higher throughput and use less test material, including the widely-employed 24-well micro-Ames (µAmes) test which uses 20 times less material. However, little quantitative information has been published on the methodology or sensitivity of this system. We describe methods and results used in direct comparisons of the sensitivity of micro and standard systems using the same cultures, formulations, etc. Initial testing utilized the plate incorporation method and, later, the pre-incubation method. In a subsequent phase of testing, a four-way direct comparison was made between the pre-incubation and plate incorporation methods in both systems using some direct-acting mutagens. Tests used only those strain/S9/chemical combinations where a response was expected. Historical control results accumulated during testing are also presented. Spontaneous and induced revertant colony counts for the µAmes system were consistently proportionate and approximately 1/20th those for the standard Ames test. Sensitivities of the two systems were found to be nearly identical in almost all cases for a wide variety of weak and strong inorganic and organic mutagens. Standardized procedures and increased reliability of the estimate of the background revertant frequency in the µAmes system means that the two systems give equivalent results and are expected to be highly predictive of one another. Environ. Mol. Mutagen. 57:687-705, 2016. © 2016 Wiley Periodicals, Inc.
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Genotoxicity assessment of S-equol in Bacterial Mutation, chromosomal aberration, and rodent bone marrow micronucleus tests
Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 2010Co-Authors: Richard J. Schwen, Richard L. Jackson, Raymond ProudlockAbstract:Intervention studies in man have shown that dietary soy isoflavones may provide certain health benefits. One of the possible reasons for this benefit is that the daidzein contained in soy is converted to S-equol. As part of a drug development program for S-equol, three genotoxicity studies were conducted. The studies comprised Bacterial Mutation, chromosomal aberration, and in vivo bone marrow micronucleus tests conducted according to Good Laboratory Practices (GLP). No evidence of genotoxic activity was observed in the in vitro tests at concentrations up to those associated with cell toxicity. In addition, no evidence of cytotoxicity or genotoxicity was seen in the rat bone marrow micronucleus test in animals dosed at levels up to the standard limit of 2000 mg/kg. It is concluded that S-equol is not active in the standard battery of genotoxicity assays recommended by the International Conference on Harmonisation (ICH) for registration of new pharmaceuticals. The current results support the further development of S-equol.
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Modified Bacterial Mutation test procedures for evaluation of peptides and amino acid-containing material
Mutagenesis, 2005Co-Authors: Crista Thompson, Paul Morley, David Kirkland, Raymond ProudlockAbstract:Biological materials can release amino acids during the course of Bacterial Mutation testing. Low levels of released amino acids from soluble materials can cause moderate increases in the number of revertant colonies on the plate, whereas higher levels lead to overgrowth of the background lawn, making counting of revertant colonies impossible. For poorly soluble material, the released amino acids can be present at high levels in localized spots on the plate, leading to the growth of 'pseudorevertant' colonies. The 'treat and wash' modified preincubation method employed here is an adaptation of the treat and plate method (used for evaluation of antibiotics) and involves washing the bacteria free of test compound after a 90 min exposure prior to plating out on minimal plates. The MC overlay method is a modified version of the standard plate incorporation assay, in which a top overlay containing 4% high viscosity methylcellulose is used in place of agar to stabilize the test compound in solution, preventing precipitation and subsequent localized amino acid release. Both modified methods produce the expected results for negative and positive controls. Peptides [synthetic curtailed analogs of human parathyroid hormone, PTH(1-34) and Ostabolin-C] that produced false positive results or could not be evaluated owing to overgrowth of the background lawn using standard methods, showed no artifacts and no evidence of genotoxicity using the modified methods. It is concluded that the treat and wash and MC overlay methods are valid versions of the Bacterial Mutation test for avoiding complications associated with released amino acids.
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Examination of the potential genotoxicity of pure capsaicin in Bacterial Mutation, chromosome aberration, and rodent micronucleus tests.
Environmental and molecular mutagenesis, 2004Co-Authors: Raymond Proudlock, Crista Thompson, Eric LongstaffAbstract:There is widespread dietary exposure to capsaicin in the form of chili peppers, while capsaicin's analgesic qualities have led to increased use of a topical herbal remedy in various impure forms. Most recently, injection of pure capsaicin has been proposed as a means of relieving a variety of debilitating diseases, in which case tissues would receive relatively high and direct exposure. The purpose of the present study, where a series of standard assays were performed in accordance with the Organisation for Economic Cooperation and Development guidance, was to clarify earlier conflicting reports concerning potential genotoxicity of capsaicin prior to administering it to patients in an injectable form. The results confirm the absence of genotoxic activity of high-purity capsaicin in the Bacterial Mutation and chromosome aberration tests. In addition, no evidence of cytotoxicity or genotoxicity was seen in the rat bone marrow micronucleus test, where systemic exposure to pure capsaicin was achieved using the subcutaneous route and a rising dose toleration protocol. It is concluded that pure capsaicin is not active in the standard battery of genotoxicity assays recommended by the International Conference on Harmonisation for evaluation of new medicines; earlier reported in vitro genotoxic activity is probably associated with mutagenic impurities in commercial grades of the material.
N.e. Nawa - One of the best experts on this subject based on the ideXlab platform.
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Fuzzy system parameters discovery by Bacterial evolutionary algorithm
IEEE Transactions on Fuzzy Systems, 1999Co-Authors: N.e. Nawa, Takahiro FuruhashiAbstract:This paper presents a new method for discovering the parameters of a fuzzy system; namely, the combination of input variables of the rules, the parameters of the membership functions of the variables, and a set of relevant rules from numerical data using the newly proposed Bacterial evolutionary algorithm (BEA). Nawa et al. (1997) proposed the pseudoBacterial genetic algorithm (PBGA) that incorporates a modified Mutation operator called Bacterial Mutation, based on a biological phenomenon of microbial evolution. The BEA has the same features of the PBGA, but introduces a new operation, called gene transfer operation, equally inspired by a microbial evolution phenomenon. While the Bacterial Mutation performs local optimization within the limits of a single chromosome, the gene transfer operation allows the chromosomes to directly transfer information to the other counterparts in the population. The gene transfer is inspired by the phenomenon of transfer of strands of genes in a population of bacteria. By means of this mechanism, one bacterium can rapidly spread its genetic information to other cells. Numerical experiments were performed to show the effectiveness of the BEA. The obtained results show the benefits that can be obtained with this method.
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fuzzy logic controllers generated by pseudo Bacterial genetic algorithm with adaptive operator
Proceedings of International Conference on Neural Networks (ICNN'97), 1997Co-Authors: N.e. Nawa, Tomonori Hashiyama, Takeshi Furuhashi, Yoshiki UchikawaAbstract:This paper presents a new genetic operator called adaptive operator to improve local portions of chromesomes. This new operator is implemented in a pseudo-Bacterial genetic algorithm (PBGA). The PBGA was proposed by the authors as a new approach combining a genetic algorithm (GA) with a local improvement mechanism inspired by a process in Bacterial genetics. The PBGA was applied for the acquisition of fuzzy rules. The aim of the newly introduced adaptive operator is to improve the quality of the generated rules of the fuzzy models, producing blocks of effective rules and more compact models. The new operator adaptively decides the division points of each chromosome for the Bacterial Mutation and the cutting points for the crossover, according to the distribution of degrees of truth values of the rules. In this paper, first, results obtained when using the PBGA with the adaptive operator for a simple fuzzy modeling problem are presented. Second, the PBGA with adaptive operator is used in the design of a fuzzy logic controller for a semi-active suspension system. The results show the benefits obtained with this operator.
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a study on fuzzy rules discovery using pseudo Bacterial genetic algorithm with adaptive operator
IEEE International Conference on Evolutionary Computation, 1997Co-Authors: N.e. Nawa, Tomonori Hashiyama, Takeshi Furuhashi, Yoshiki UchikawaAbstract:This paper presents a new operator called adaptive operator for the Pseudo-Bacterial Genetic Algorithm (PBGA). The PBGA was proposed by the authors as a new approach combining a genetic algorithm (GA) with a local improvement mechanism inspired by a process in Bacterial genetics. The PBGA was applied for the discovery of fuzzy rules. The aim of the newly introduced adaptive operator is to improve the quality of the generated fuzzy rules, producing blocks of effective rules and more compact rule bases. The new operator adaptively decides the division points of each chromosome for the Bacterial Mutation and the cutting points for the crossover. In order to verify the efficiency of the proposed adaptive operator, the PBGA is applied to a simple fuzzy modeling problem. The new operator actuates according to the distribution of degrees of truth values of the rules. The results show the benefits that can be obtained with this operator.
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SMC - Bacterial evolutionary algorithm for fuzzy system design
SMC'98 Conference Proceedings. 1998 IEEE International Conference on Systems Man and Cybernetics (Cat. No.98CH36218), 1Co-Authors: N.e. Nawa, Takeshi FuruhashiAbstract:Presents a method for discovering the parameters of a fuzzy system, namely the combination of input variables of the rules, the parameters of the membership functions of the variables and a set of relevant rules, from numerical data using the newly proposed Bacterial evolutionary algorithm (BEA). In early work, the authors proposed the pseudo-Bacterial genetic algorithm (PBGA) that incorporates a modified Mutation operator called Bacterial Mutation, based on a natural phenomenon of microbial evolution. The BEA has the same features of the PBGA, but introduces a new operator, called gene transfer operation, equally inspired by a microbial evolution phenomenon. While the Bacterial Mutation performs local optimization within the limits of a single chromosome, the gene transfer operation allows the chromosomes to directly transfer information to the other counterparts in the population. The gene transfer is inspired by the natural phenomenon of transfer of strands of genes between bacteria in a population. By means of this mechanism, one bacterium can rapidly spread its genetic information to other cells. Numerical experiments were performed to show the effectiveness of the BEA. The obtained results show the benefits that can be obtained with the newly proposed method.
Angus Buckling - One of the best experts on this subject based on the ideXlab platform.
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the evolution of Bacterial Mutation rates under simultaneous selection by interspecific and social parasitism
Proceedings of The Royal Society B: Biological Sciences, 2013Co-Authors: Siobhan Obrien, Antonio M M Rodrigues, Angus BucklingAbstract:Many Bacterial populations harbour substantial numbers of hypermutable bacteria, in spite of hyperMutation being associated with deleterious Mutations. One reason for the persistence of hypermutators is the provision of novel Mutations, enabling rapid adaptation to continually changing environments, for example coevolving virulent parasites. However, hyperMutation also increases the rate at which intraspecific parasites (social cheats) are generated. Interspecific and intraspecific parasitism are therefore likely to impose conflicting selection pressure on Mutation rate. Here, we combine theory and experiments to investigate how simultaneous selection from inter- and intraspecific parasitism affects the evolution of Bacterial Mutation rates in the plant-colonizing bacterium Pseudomonas fluorescens. Both our theoretical and experimental results suggest that phage presence increases and selection for public goods cooperation (the production of iron-scavenging siderophores) decreases selection for mutator bacteria. Moreover, phages imposed a much greater growth cost than social cheating, and when both selection pressures were imposed simultaneously, selection for cooperation did not affect Mutation rate evolution. Given the ubiquity of infectious phages in the natural environment and clinical infections, our results suggest that phages are likely to be more important than social interactions in determining Mutation rate evolution.
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Coevolution with phages does not influence the evolution of Bacterial Mutation rates in soil.
The ISME journal, 2013Co-Authors: Pedro Gómez, Angus BucklingAbstract:Coevolution with phages drive the evolution of high Bacterial Mutation rates in vitro, but the relevance of this finding to natural populations is unclear. Here, we investigated how coevolution affects Mutation rate evolution in soil, in the presence and absence of the rest of the natural microbial community. Although Mutation rate on average increased threefold, neither coevolving phages nor the rest of natural community significantly affected Mutation rates. Our results suggest that features of the soil over and above directly interacting organisms constrain the evolution of strong mutators, helping to explain their relatively low frequency compared with some laboratory and clinical settings.
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A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated Mutation rates in bacteria
Proceedings of the Royal Society B: Biological Sciences, 2013Co-Authors: Clara Torres-barceló, Angus Buckling, Antonio Oliver, Gabriel Cabot, R. Craig MacleanAbstract:The dominant paradigm for the evolution of mutator alleles in Bacterial populations is that they spread by indirect selection for linked beneficial Mutations when bacteria are poorly adapted. In this paper, we challenge the ubiquity of this paradigm by demonstrating that a clinically important stressor, hydrogen peroxide, generates direct selection for an elevated Mutation rate in the pathogenic bacterium Pseudomonas aeruginosa as a consequence of a trade-off between the fidelity of DNA repair and hydrogen peroxide resistance. We demonstrate that the biochemical mechanism underlying this trade-off in the case of mutS is the elevated secretion of catalase by the mutator strain. Our results provide, to our knowledge, the first experimental evidence that direct selection can favour mutator alleles in Bacterial populations, and pave the way for future studies to understand how Mutation and DNA repair are linked to stress responses and how this affects the evolution of Bacterial Mutation rates.
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IMPACT OF Bacterial Mutation RATE ON COEVOLUTIONARY DYNAMICS BETWEEN BACTERIA AND PHAGES
Evolution, 2010Co-Authors: Andrew D. Morgan, Michael B. Bonsall, Angus BucklingAbstract:Mutator bacteria are frequently found in natural populations of bacteria and although coevolution with parasitic viruses (phages) is thought to be one reason for their persistence, it remains unclear how the presence of mutators affects coevolutionary dynamics. We hypothesized that phages must themselves adapt more rapidly or go extinct, in the face of rapidly evolving mutator bacteria. We compared the coevolutionary dynamics of wild-type Pseudomonas fluorescens SBW25 with a lytic phage to the dynamics of an isogenic mutator of P. fluorescens SBW25 together with the same phage. At the beginning of the experiment both wild-type bacteria and mutator bacteria coevolved with phages. However, mutators rapidly evolved higher levels of sympatric resistance to phages. The phages were unable to "keep-up" with the mutator bacteria, and these rates of coevolution declined to less than the rates of coevolution between the phages and wild-type bacteria. By the end of the experiment, the sympatric resistance of the mutator bacteria was not significantly different to the sympatric resistance of the wild-type bacteria. This suggests that the importance of mutators in the coevolutionary interactions with a particular phage population is likely to be short-lived. More generally, the results demonstrate that coevolving enemies may escape from Red-Queen dynamics
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Coevolution with viruses drives the evolution of Bacterial Mutation rates
Nature, 2007Co-Authors: Csaba Pál, María D. Maciá, Antonio Oliver, Ira Schachar, Angus BucklingAbstract:Bacterial cultures in changing environments sometimes accumulate 'mutator' strains, with elevated Mutation rates, presumably to enhance their potential for adaptive evolution. This can often happen in clinical situations. If they are to persist, mutators need a consistently changing environment. Coevolution with parasites, such as viruses, is a scenario that can provide that. Experiments with Pseudomonas fluorescens now show that coevolution with a naturally occurring bacteriophage significantly increases Bacterial Mutation rates — and results in a higher probability of phage extinction. Targeting phage populations might therefore be a way of weakening selection for mutator bacteria in clinical infections. Bacterial cultures experiencing changes in environmental conditions accumulate mutator strains, presumably to enhance their capability for adaptive evolution. The presence of Bacterial viruses is demonstrated to have a similar effect, as during co-evolution of Pseudomonas fluorescens and its lytic DNA phage, Bacterial Mutation rates significantly increase, resulting in a higher probability of phage extinction. Bacteria with greatly elevated Mutation rates (mutators) are frequently found in natural1,2,3 and laboratory4,5 populations, and are often associated with clinical infections6,7. Although mutators may increase adaptability to novel environmental conditions, they are also prone to the accumulation of deleterious Mutations. The long-term maintenance of high Bacterial Mutation rates is therefore likely to be driven by rapidly changing selection pressures8,9,10,11,12,13,14, in addition to the possible slow transition rate by point Mutation from mutators to non-mutators15. One of the most likely causes of rapidly changing selection pressures is antagonistic coevolution with parasites16,17. Here we show whether coevolution with viral parasites could drive the evolution of Bacterial Mutation rates in laboratory populations of the bacterium Pseudomonas fluorescens18. After fewer than 200 Bacterial generations, 25% of the populations coevolving with phages had evolved 10- to 100-fold increases in Mutation rates owing to Mutations in mismatch-repair genes; no populations evolving in the absence of phages showed any significant change in Mutation rate. Furthermore, mutator populations had a higher probability of driving their phage populations extinct, strongly suggesting that mutators have an advantage against phages in the coevolutionary arms race. Given their ubiquity, bacteriophages may play an important role in the evolution of Bacterial Mutation rates.
Yoshiki Uchikawa - One of the best experts on this subject based on the ideXlab platform.
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fuzzy logic controllers generated by pseudo Bacterial genetic algorithm with adaptive operator
Proceedings of International Conference on Neural Networks (ICNN'97), 1997Co-Authors: N.e. Nawa, Tomonori Hashiyama, Takeshi Furuhashi, Yoshiki UchikawaAbstract:This paper presents a new genetic operator called adaptive operator to improve local portions of chromesomes. This new operator is implemented in a pseudo-Bacterial genetic algorithm (PBGA). The PBGA was proposed by the authors as a new approach combining a genetic algorithm (GA) with a local improvement mechanism inspired by a process in Bacterial genetics. The PBGA was applied for the acquisition of fuzzy rules. The aim of the newly introduced adaptive operator is to improve the quality of the generated rules of the fuzzy models, producing blocks of effective rules and more compact models. The new operator adaptively decides the division points of each chromosome for the Bacterial Mutation and the cutting points for the crossover, according to the distribution of degrees of truth values of the rules. In this paper, first, results obtained when using the PBGA with the adaptive operator for a simple fuzzy modeling problem are presented. Second, the PBGA with adaptive operator is used in the design of a fuzzy logic controller for a semi-active suspension system. The results show the benefits obtained with this operator.
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a study on fuzzy rules discovery using pseudo Bacterial genetic algorithm with adaptive operator
IEEE International Conference on Evolutionary Computation, 1997Co-Authors: N.e. Nawa, Tomonori Hashiyama, Takeshi Furuhashi, Yoshiki UchikawaAbstract:This paper presents a new operator called adaptive operator for the Pseudo-Bacterial Genetic Algorithm (PBGA). The PBGA was proposed by the authors as a new approach combining a genetic algorithm (GA) with a local improvement mechanism inspired by a process in Bacterial genetics. The PBGA was applied for the discovery of fuzzy rules. The aim of the newly introduced adaptive operator is to improve the quality of the generated fuzzy rules, producing blocks of effective rules and more compact rule bases. The new operator adaptively decides the division points of each chromosome for the Bacterial Mutation and the cutting points for the crossover. In order to verify the efficiency of the proposed adaptive operator, the PBGA is applied to a simple fuzzy modeling problem. The new operator actuates according to the distribution of degrees of truth values of the rules. The results show the benefits that can be obtained with this operator.
Paul D. Sniegowski - One of the best experts on this subject based on the ideXlab platform.
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Evolution: Bacterial Mutation in stationary phase.
Current biology : CB, 2004Co-Authors: Paul D. SniegowskiAbstract:A recent study indicates that the genomic Mutation rate of the gut bacterium Escherichia coli is substantially higher in nongrowing than growing cultures. These findings are important in the light of the ongoing controversy over the generality and robustness of stationary phase mutagenesis and its evolutionary implications.