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Scientists using laboratory animals are under increasing pressure to justify their sample sizes using a "power analysis". In this paper I review the three methods currently used to determine sample size: "tradition" or "common sense", the "resource equation" and the "power analysis". I explain how, using the "KISS" approach, scientists can make a provisional choice of sample size using any method, and then easily estimate the effect size likely to be detectable according to a power analysis. Should they want to be able to detect a smaller effect they can increase their provisional sample size and recalculate the effect size. This is simple, does not need any software and provides justification for the sample size in the terms used in a power analysis.

There is growing concern about the poor quality and lack of repeatability of many pre-clinical experiments involving laboratory animals. According to one estimate as much as $28 billion is wasted annually in the USA alone in such studies. A decade ago the FDA's "Critical path" white paper noted that "The traditional tools used to assess product safety-animal toxicology and outcomes from human studies-have changed little over many decades and have largely not benefited from recent gains in scientific knowledge. The inability to better assess and predict product safety leads to failures during clinical development and, occasionally, after marketing." Repeat-dose 28-days and 90-days toxicity tests in rodents have been widely used as part of a strategy to assess the safety of drugs and chemicals but their repeatability and power to detect adverse effects have not been formally evaluated.The guidelines (OECD TG 407 and 408) for these tests specify the dose levels and number of animals per dose but do not specify the strain of animals which should be used. In practice, almost all the tests are done using genetically undefined "albino" rats or mice in which the genetic variation, a major cause of inter-individual and strain variability, is unknown and uncontrolled. This chapter suggests that a better strategy would be to use small numbers of animals of several genetically defined strains of mice or rats instead of the undefined animals used at present. Inbred strains are more stable providing more repeatable data than outbred stocks. Importantly their greater phenotypic uniformity should lead to more powerful and repeatable tests. Any observed strain differences would indicate genetic variation in response to the test substance, providing key data. We suggest that the FDA and other regulators and funding organizations should support research to evaluate this alternative.

The results of repeat-dose toxicity tests are usually presented as tables of means and standard deviations (SDs), with an indication of statistical significance for each biomarker. Interpretation is based mainly on the pattern of statistical significance rather than the magnitude of any response. Multiple statistical testing of many biomarkers leads to false-positive results and, with the exception of growth data, few graphical methods for showing the results are available. By converting means and SDs to standardized effect sizes, a range of graphical techniques including dot plots, line plots, box plots, and quantile-quantile plots become available to show the patterns of response. A bootstrap statistical test involving all biomarkers is proposed to compare the magnitudes of the response between treated groups. These methods are proposed as an extension rather than an alternative to current statistical analyses. They can be applied to published work retrospectively, as all that is required is tables of means and SDs. The methods are illustrated using published articles, where the results range from strong positive to completely negative responses to the test substances., (© 2014 by The Author(s).)

The safety of chemicals, drugs, novel foods and genetically modified crops is often tested using repeat-dose sub-acute toxicity tests in rats or mice. It is important to avoid misinterpretations of the results as these tests are used to help determine safe exposure levels in humans. Treated and control groups are compared for a range of haematological, biochemical and other biomarkers which may indicate tissue damage or other adverse effects. However, the statistical analysis and presentation of such data poses problems due to the large number of statistical tests which are involved. Often, it is not clear whether a "statistically significant" effect is real or a false positive (type I error) due to sampling variation. The author's conclusions appear to be reached somewhat subjectively by the pattern of statistical significances, discounting those which they judge to be type I errors and ignoring any biomarker where the p-value is greater than p = 0.05. However, by using standardised effect sizes (SESs) a range of graphical methods and an over-all assessment of the mean absolute response can be made. The approach is an extension, not a replacement of existing methods. It is intended to assist toxicologists and regulators in the interpretation of the results. Here, the SES analysis has been applied to data from nine published sub-acute toxicity tests in order to compare the findings with those of the author's. Line plots, box plots and bar plots show the pattern of response. Dose-response relationships are easily seen. A "bootstrap" test compares the mean absolute differences across dose groups. In four out of seven papers where the no observed adverse effect level (NOAEL) was estimated by the authors, it was set too high according to the bootstrap test, suggesting that possible toxicity is under-estimated.

Inbred strains of mice such as C57BL and BALB/c are more widely used in published work than outbred stocks of mice such as ICR and CD-1. In contrast, outbred stocks of rats such as Wistar and Sprague-Dawley are more widely used than inbred strains such as F344 and LEW. The properties of inbred and outbred mice and rats are briefly reviewed, and it is concluded that, with some exceptions, there is a strong case for using inbred strains in most controlled experiments. This is because they are usually more uniform, so that fewer animals are usually needed to detect a specified response and they are more repeatable, because they are genetically defined (i.e., the strain can be identified using genetic markers) and less liable to genetic change. Yet many scientists continue to use outbred animals. In Daniel Kahneman's book "Thinking Fast and Slow" he explains that we can answer questions in 2 ways: "fast" by intuition or "slow" by analytical reasoning. The former method is instantaneous, requires no thought but is not evidence based. Analytical reasoning is evidence based but requires hard work, which we all avoid. He has found that "… when faced with a difficult question, we often answer an easier one instead, usually without noticing the substitution." The target question of whether to choose outbred or inbred strains in controlled experiments is a difficult one requiring knowledge of the characteristics of these strains and the principles of experimental design. A substitute question, "are humans and outbred stocks both genetically heterogeneous," is easily answered in the affirmative. It is likely that many scientists are intuitively answering the substitute question and are assuming that they have answered the target question. If so they may be using the wrong animals in their research. Nor is the fact that humans and outbred stocks are alike in being genetically heterogeneous a reason for using them. The whole concept of a "model" is that it is similar to the target in some respects but different in others. Rats and mice differ from humans in that we can control their genotype. This is a positive attribute that enormously increases their value in research. Funding organizations should support research in comparing the 2 types in real experiments., (© The Author 2014. Published by Oxford University Press on behalf of the Institute for Laboratory Animal Research. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Animal research has made major contributions to the health and welfare of humans and domestic animals. Immunization, first developed against rabies and anthrax by Pasteur using dogs, sheep, and rabbits, is now used to control many infectious diseases. The first drug, Salvarsan, was developed by Ehrlich using rabbits infected with the organism causing syphilis. This was the forerunner of the many drugs developed by the pharmaceutical industry today. The discovery of vitamins using rats has almost eliminated diseases such as scurvy and rickets; and hormones, such as insulin discovered following work in dogs, have helped to control many metabolic diseases. These and many other advances have enabled physicians to treat a wide range of human diseases. But many diseases continue to cause suffering., (© The Author 2014. Published by Oxford University Press on behalf of the Institute for Laboratory Animal Research. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Randomized block experimental designs have been widely used in agricultural and industrial research for many decades. Usually they are more powerful, have higher external validity, are less subject to bias, and produce more reproducible results than the completely randomized designs typically used in research involving laboratory animals. Reproducibility can be further increased by using time as a blocking factor. These benefits can be achieved at no extra cost. A small experiment investigating the effect of an antioxidant on the activity of a liver enzyme in four inbred mouse strains, which had two replications (blocks) separated by a period of two months, illustrates this approach. The widespread failure to use these designs more widely in research involving laboratory animals has probably led to a substantial waste of animals, money, and scientific resources and slowed down the development of new treatments for human and animal diseases., (© The Author 2014. Published by Oxford University Press on behalf of the Institute for Laboratory Animal Research. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Although rats in various stages of pregnancy are routinely shipped by vendors, the effects of shipping on pregnancy outcomes have not been reported. This study examined the effects of shipping rats 1 day after mating. Two outbred stocks, (Crl:CD(SD), Crl:WI(Han)) and one inbred strain (F344/Crl) of rats (n=300/strain) were mated in a vendor barrier room at 3-month intervals five times, and either shipped the next day (total time in transit ∼24 hr) or held in the room of origin until parturition. The pregnancy status, length of gestation, number of pups born per female, sex ratio of pups born, and neonatal mortality were compared between transported and nontransported rats. These pregnancy and litter parameters were also compared among strains and examined for seasonality; no seasonal effects were observed. Neonatal mortality was negligible at less than 2% in any of the groups. All sex ratios were normal. Transportation affected pregnancy rates only in the F344/Crl, in which 81.8% of the nontransported versus 70% of the transported rats had pups (p=0.025). Overall, slightly fewer transported rats were pregnant, but they had larger litters (10.08 compared with 9.68, p=0.02, pooling across all three strains) so produced the same numbers of pups. A total of 77±8% of transported rats had gestation periods of 22 days or more compared with only 52±10% in the nontransported rats. The reason for larger litters in transported females is unclear. Longer gestation in transported females may be due to facultative embryonic diapause, which might have implications for reproductive toxicology., (© 2013 Wiley Periodicals, Inc.)

Methods of toxicity testing, barely changed for several decades, need to be improved. One way forward would be to use a small battery of inbred strains instead of the single outbred stock currently used in toxicity screening. Inbred strains are more stable, more uniform, more repeatable, and better defined than outbred stocks. Genetic variation would be observed as the difference between strains. Safety could be based on the most susceptible strain. Sometimes it may be possible to identify the genes involved. Mechanisms could be explored using gene expression profiling of susceptible and resistant strains. Two committees of toxicologists have concluded that the use of inbred strains, by controlling interindividual variability, would reduce the number of animals needed in toxicity screening, although both "preferred" outbred stocks. This preference appears to have been based on intuition rather than scientific principles. Data from a previously published study on the response to chloramphenicol in an outbred stock and four inbred strains is used to explain the advantages of the multistrain design. Toxicologists, safety pharmacologists, regulatory authorities, and pharmaceutical companies should take a critical look at the types of animals they use if they want to reduce the attrition rate of new drugs.

According to the US Food and Drugs Administration (Food and Drug Administration (2004) Challenge and opportunity on the critical path to new medical products.) "The inability to better assess and predict product safety leads to failures during clinical development and, occasionally, after marketing". This increases the cost of new drugs as clinical trials are even more expensive than pre-clinical testing.One relatively easy way of improving toxicity testing is to improve the design of animal experiments. A fundamental principle when designing an experiment is to control all variables except the one of interest: the treatment. Toxicologist and pharmacologists have widely ignored this principle by using genetically heterogeneous "outbred" rats and mice, increasing the chance of false-negative results. By using isogenic (inbred or F1 hybrid, see Note 1) rats and mice instead of outbred stocks the signal/noise ratio and the power of the experiments can be increased at little extra cost whilst using no more animals. Moreover, the power of the experiment can be further increased by using more than one strain, as this reduces the chance of selecting one which is resistant to the test chemical. This can also be done without increasing the total number of animals by using a factorial experimental design, e.g. if the ten outbred animals per treatment group in a 28-day toxicity test were replaced by two animals of each of five strains (still ten animals per treatment group) selected to be as genetically diverse as possible, this would increase the signal/noise ratio and power of the experiment. This would allow safety to be assessed using the most sensitive strain.Toxicologists should also consider making more use of the mouse instead of the rat. They are less costly to maintain, use less test substance, there are many inbred and genetically modified strains, and it is easier to identify gene loci controlling variation in response to xenobiotics in this species.We demonstrate here the advantage of using several inbred strains in two parallel studies of the haematological response to chloramphenicol at six dose levels with CD-1 outbred, or using four inbred strains of mice. Toxicity to the white blood cell lineage was easily detected using the inbred strains but not using the outbred stock, clearly showing the advantage of using the multi-inbred strain approach.

Everybody's career depends on many chance factors: the people one meets, the opportunities which are available, or the state of a scientific discipline. Mine is no exception. I started out in agriculture, obtained a PhD in quantitative genetics, and spent most of my career concerned with the use of animals in biomedical research. Soon after I joined the Medical Research Council Laboratory Animals Centre in 1966, as their geneticist in charge of many species and strains of laboratory animals, I was introduced to Russell and Burch's book, The Principles of Humane Experimental Technique. It had a significant effect on my future, which has encompassed two related themes: the need for better experimental design, and the conviction that, in most research, inbred strains of rats and mice should normally be used in preference to genetically undefined outbred stocks. The establishment of the FRAME Reduction Committee has helped me to pursue both of these, although toxicologists continue to ignore basic design principles, by using outbred stocks., (2009 FRAME.)

For scientific, ethical and economic reasons, experiments involving animals should be appropriately designed, correctly analysed and transparently reported. This increases the scientific validity of the results, and maximises the knowledge gained from each experiment. A minimum amount of relevant information must be included in scientific publications to ensure that the methods and results of a study can be reviewed, analysed and repeated. Omitting essential information can raise scientific and ethical concerns. We report the findings of a systematic survey of reporting, experimental design and statistical analysis in published biomedical research using laboratory animals. Medline and EMBASE were searched for studies reporting research on live rats, mice and non-human primates carried out in UK and US publicly funded research establishments. Detailed information was collected from 271 publications, about the objective or hypothesis of the study, the number, sex, age and/or weight of animals used, and experimental and statistical methods. Only 59% of the studies stated the hypothesis or objective of the study and the number and characteristics of the animals used. Appropriate and efficient experimental design is a critical component of high-quality science. Most of the papers surveyed did not use randomisation (87%) or blinding (86%), to reduce bias in animal selection and outcome assessment. Only 70% of the publications that used statistical methods described their methods and presented the results with a measure of error or variability. This survey has identified a number of issues that need to be addressed in order to improve experimental design and reporting in publications describing research using animals. Scientific publication is a powerful and important source of information; the authors of scientific publications therefore have a responsibility to describe their methods and results comprehensively, accurately and transparently, and peer reviewers and journal editors share the responsibility to ensure that published studies fulfil these criteria.

Few data exist regarding the effects of long-term housing of rats and mice in the same secondary enclosure. Historical reproductive and growth data were compared for colonies of mice and rats maintained in open-topped cages in either single-species or dual-species barrier rooms. This analysis included reproductive parameters (litter size at birth, litter size at weaning, and pups missing at weaning) collected from 33 colonies of mice comprising 500 to 38,500 breeding females and 28 colonies of rats totaling 350 to 4,600 breeding females, and representative samples from 28 colonies of each species were analyzed for weight gain from weaning to adulthood. The presence or absence of the other species was not associated with statistically significant differences in weight gain or any of the reproductive parameters. These results suggest that breeding colonies of rats and mice of the same health status can be housed in the same room without a negative effect on the growth and reproduction of either species.

In vivo models of hepatic ischaemia/reperfusion injury (IRI) are widely used to study both the mechanisms of hepatic ischaemic injury and to seek means of hepatic protection. Achieving high-quality reproducible data are essential if the results of multiple studies are to be compared and reconciled. This paper presents our findings concerning the effect of intraoperative thermoregulation upon signal to noise ratios of hepatic IRI experiments in mice. Four experiments were conducted, using three different strategies for core temperature maintenance. Animals underwent hepatic IRI and euthanized 24 h postoperatively for measurement of plasma alanine aminotransferase (ALT). Duration of ischaemia was used to adjust the severity of injury. Experiment 1 utilized a constant output heating system and resulted in rising postoperative ALTs following increasing durations of hepatic ischaemia. Experiment 2, using the same constant output heating system confirmed a difference between ischaemic and sham-operated animals. Experiment 3 used a thermostatically controlled heating system and resulted in highly variable results with a small, but statistically significant correlation between ALT levels and rectal temperature readings. Experiment 4 used a homeothermic warming system and demonstrated highly reproducible data from increasing durations of ischaemia. High-quality data from hepatic ischaemia/reperfusion models are dependent upon careful control of intraoperative temperature. The use of homeothermic warming systems is recommended and conversely, the use of thermostatically controlled warming mats is to be avoided in these models.

The year 2009 is the 100th anniversary of the founding of the first inbred strain of mouse, called DBA. During the last 100 years, inbred strains have proved their value for biomedical research and the number of such strains has mushroomed to over 450, each with different genotypic and phenotypic characteristics and useful for the study of disease and normal function. However, although inbred strains are stable, they are not fixed entities and researchers need to be aware of the phenomena of new mutations and of genetic drift, which occur within all mouse colonies. If the mutations are what we term in this review 'quiet mutations', then they might result in rather unexpected and sometimes tremendously valuable results. Here, we discuss these phenomena and look at how new genomic technologies might help us to detect 'quiet mutations' and use them to our advantage.

Experiments involving neonates should follow the same basic principles as most other experiments. They should be unbiased, be powerful, have a good range of applicability, not be excessively complex, and be statistically analyzable to show the range of uncertainty in the conclusions. However, investigation of growth and development in neonatal multiparous animals poses special problems associated with the choice of "experimental unit" and differences between litters: the "litter effect." Two main types of experiments are described, with recommendations regarding their design and statistical analysis: First, the "between litter design" is used when females or whole litters are assigned to a treatment group. In this case the litter, rather than the individuals within a litter, is the experimental unit and should be the unit for the statistical analysis. Measurements made on individual neonatal animals need to be combined within each litter. Counting each neonate as a separate observation may lead to incorrect conclusions. The number of observations for each outcome ("n") is based on the number of treated females or whole litters. Where litter sizes vary, it may be necessary to use a weighted statistical analysis because means based on more observations are more reliable than those based on a few observations. Second, the more powerful "within-litter design" is used when neonates can be individually assigned to treatment groups so that individuals within a litter can have different treatments. In this case, the individual neonate is the experimental unit, and "n" is based on the number of individual pups, not on the number of whole litters. However, variation in litter size means that it may be difficult to perform balanced experiments with equal numbers of animals in each treatment group within each litter. This increases the complexity of the statistical analysis. A numerical example using a general linear model analysis of variance is provided in the Appendix. The use of isogenic strains should be considered in neonatal research. These strains are like immortal clones of genetically identical individuals (i.e., they are uniform, stable, and repeatable), and their use should result in more powerful experiments. Inbred females mated to males of a different inbred strain will produce F1 hybrid offspring that will be uniform, vigorous, and genetically identical. Different strains may develop at different rates and respond differently to experimental treatments.

Outbred mouse stocks, often used in genetics, toxicology and pharmacology research, have been generated in rather haphazard ways. Understanding the characteristics of these stocks and their advantages and disadvantages is important for experimental design. In many studies these mice are used inappropriately, wasting animals' lives and resources on suboptimal experiments. Recently, however, researchers from the field of complex trait analysis have capitalized on the genetics of outbred stocks to refine the identification of quantitative trait loci. Here we assess the most widely used outbred stocks of mice and present guidelines for their use.

Careful choice of the animal model is essential, if research is to be conducted efficiently, by using the minimum number of animals in order to provide the maximum amount of information. Inbred strains of rodents provide an excellent way of controlling and investigating genetic variation in characters of interest and in response to experimental treatments. Outbred stocks, in which genetic and non-genetic factors are inextricably mixed, are much less suitable, because random and uncontrolled genetic variation tends to obscure any treatment responses. In some cases, the use of inbred strains has led to major advances in scientific understanding. The specific example given here is in the understanding of host-parasite relationships but, more generally, inbred strains have been of critical importance in research which has resulted in the award of at least 17 Nobel prizes. And yet, despite the extensive literature on the properties and scientific value of inbred strains, many scientists continue to use outbred stocks in the mistaken belief that the use of such animals will, in some mysterious way, make their research more applicable to humans. There is really no evidence that this is so, and there is much evidence that the use of inbred strains has been highly successful in many disciplines.

The use of laboratory animals in the year 2002 is essential both to maintain human health and to develop new treatments for the many diseases that still plague humans. The suggestion by Greek and Greek in Sacred Cows and Golden Geese in 2000, that animal experiments are invalid because animals are different from humans, shows clearly that they do not understand the philosophical basis for the use of models in science and every day life. Models only need to resemble the thing being modelled (the target) in a few key respects. A map of Brooklyn Botanic Garden is a useful model, but it differs from the garden in many respects. There are many examples where studies on animals and in vitro alternatives result in accurate predictions of human responses even though the models differ from humans in other ways. In the drug development model, validation is done in clinical trials. Models are also used in the discovery of fundamental processes shared by some, or all, living organisms. The laws of genetics were first discovered by using garden peas, but they are equally applicable to humans. It is because of the ethical, rather than scientific, objections to the use of animals that all scientists are urged to find alternatives according to the principles of reduction, refinement and replacement, laid down by Russell and Burch in 1959.

The key to doing animal experiments efficiently, while using the minimum number of animals without loss of scientific information, lies in good control of random variation, and recognition and control of "fixed effect" variation, such as the sex or strain of the animals. However, many scientists erroneously assume that the use of outbred, genetically heterogeneous animals is justified, because in some way, they more closely model humans. Unfortunately, all this does is to increase the phenotypic variation, which results in less-powerful experiments. If the aim is to model variation in human responses, this can be done by using a small number of animals from several isogenic strains, without increasing the total number of animals. Reducing inter-individual variation, whether caused by genetic or non-genetic causes, will nearly always result in improved experiments. Fixed-effect variation, such as the sex of the animals, can be taken into account, either by restricting the conclusions to the sex actually used, or by assuming that the other sex would respond in the same way, or by including both sexes in the study, by using a factorial design, without increasing the total number of animals.

Surveys of published papers show that there are many errors both in the design of the experiments and in the statistical analysis of the resulting data. This must result in a waste of animals and scientific resources, and it is surely unethical. Scientific quality might be improved, to some extent, by journal editors, but they are constrained by lack of statistical referees and inadequate statistical training of those referees that they do use. Other parties, such as welfare regulators, ethical review committees and individual scientists also have an interest in scientific quality, but they do not seem to be well placed to make the required changes. However, those who fund research would have the power to do something if they could be convinced that it is in their best interests to do so. More examples of the way in which better experimental design has led to improved experiments would be helpful in persuading these funding organisations to take further action.

The United Kingdom Home Office Code of Practice for the housing and care of breeding animals requires that, 'the general well-being of all animals must be checked at least once daily'. However, excessive daily disturbance of rodent breeding colonies could be counter-productive to animal welfare if it increases pre-weaning mortality. An experiment involving 100 breeding cages of BALB/c mice compared daily inspection of the mouse cages, but without disturbing the mice within the nest, with daily inspection in which every individual was studied even if this involved removing the cage lid and disturbing the nest. No statistically significant differences were found between the two groups in breeding performance or pre-weaning mortality, though the disturbed group produced marginally fewer offspring and had slightly higher mortality. Average weaning weight did not differ between the groups, but sexual dimorphism at weaning was significantly increased in the disturbed group. It is concluded that there are unlikely to be any welfare benefits in an inspection regimen that involves disturbance of breeding mice, provided the cage is inspected daily.

Among the actions of 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) in mice is the induction of hepatic porphyria. This is similar to the most common disease of this type in humans, sporadic porphyria cutanea tarda (PCT). Evidence is consistent with the actions of dioxin being mediated through binding to the aryl hydrocarbon receptor (AHR) with different Ahr alleles in mouse strains apparently accounting for differential downstream gene expression and susceptibility. However, studies of dioxin-induced porphyria and liver injury indicate that the mechanisms must involve interactions with other genes, perhaps associated with iron metabolism. We performed a quantitative trait locus (QTL) analysis of an F(2) cross between susceptible C57BL/6J (Ahr(b1) allele) and the highly resistant DBA/2 (Ahr(d) allele) strains after treatment with dioxin and iron. For porphyria we found QTLs on chromosomes 11 and 14 in addition to the Ahr gene (chromosome 12). Studies with C57BL/6.D2 Ahr(d) mice confirmed that the Ahr(d) allele alone did not completely negate the response. SWR mice are syngenic for the Ahr(d) allele with the DBA/2 strain but are susceptible to porphyria after elevation of hepatic iron. Analysis of SWRxD2 F(2) mice treated with iron and dioxin showed a QTL on chromosome 11, as well as finding other loci on chromosomes 1 (and possibly 9), for both porphyria and liver injury. These findings show for the first time the location of genes, other than Ahr, that modulate the mechanism of hepatic porphyria and injury caused by dioxin in mice. Orthologous loci may contribute to the pathogenesis of human sporadic PCT.

For ethical and economic reasons, it is important to design animal experiments well, to analyze the data correctly, and to use the minimum number of animals necessary to achieve the scientific objectives---but not so few as to miss biologically important effects or require unnecessary repetition of experiments. Investigators are urged to consult a statistician at the design stage and are reminded that no experiment should ever be started without a clear idea of how the resulting data are to be analyzed. These guidelines are provided to help biomedical research workers perform their experiments efficiently and analyze their results so that they can extract all useful information from the resulting data. Among the topics discussed are the varying purposes of experiments (e.g., exploratory vs. confirmatory); the experimental unit; the necessity of recording full experimental details (e.g., species, sex, age, microbiological status, strain and source of animals, and husbandry conditions); assigning experimental units to treatments using randomization; other aspects of the experiment (e.g., timing of measurements); using formal experimental designs (e.g., completely randomized and randomized block); estimating the size of the experiment using power and sample size calculations; screening raw data for obvious errors; using the t-test or analysis of variance for parametric analysis; and effective design of graphical data.

Optimization of experiments, such as those used in drug discovery, can lead to useful savings of scientific resources. Factors such as sex, strain, and age of the animals and protocol-specific factors such as timing and methods of administering treatments can have an important influence on the response of animals to experimental treatments. Factorial experimental designs can be used to explore which factors and what levels of these factors will maximize the difference between a vehicle control and a known positive control treatment. This information can then be used to design more efficient experiments, either by reducing the numbers of animals used or by increasing the sensitivity so that smaller biological effects can be detected. A factorial experimental design approach is more effective and efficient than the older approach of varying one factor at a time. Two examples of real factorial experiments reveal how using this approach can potentially lead to a reduction in animal use and savings in financial and scientific resources without loss of scientific validity.

Advancement of cancer prevention and therapy requires clinical development of systemic biomarkers of pharmacological efficacy of the agent under scrutiny. Curcumin, a polyphenol derived from Curcuma spp., has shown wide-ranging chemopreventive activity in preclinical carcinogenic models, in which it inhibits cyclooxygenase (COX)-2 at the transcriptional level. COX-2 has been implicated in the development of many human cancers. To explore the inhibition of COX-2 activity as a systemic biomarker of drug efficacy, a biomarker of potential use in clinical trials of many chemopreventive drugs known to inhibit this enzyme, we measured COX-2 protein induction and prostaglandin E(2) (PGE(2)) production in human blood after incubation with lipopolysaccharide (LPS). When 1 microM curcumin was added in vitro to blood from healthy volunteers, LPS-induced COX-2 protein levels and concomitant PGE(2) production were reduced by 24% and 41%, respectively (P < 0.05 by ANOVA). To test whether effects on COX-2 activity could also be measured after oral dosing in humans, we conducted a dose-escalation pilot study of a standardized formulation of Curcuma extract in 15 patients with advanced colorectal cancer. Basal and LPS-mediated PGE(2) production was measured in blood, twice pretreatment and on days 1, 2, 8, and 29 of treatment. Analysis of basal and LPS-induced PGE(2) production during treatment demonstrated a trend toward dose-dependent inhibition (P < 0.005 by regression analysis), but there was no significant difference compared with values from pretreatment time points. Measurement of leukocyte COX-2 activity should be considered in clinical trials of other agents likely to inhibit this isozyme.

In vitro experiments need to be well designed and correctly analysed if they are to achieve their full potential to replace the use of animals in research. An "experiment" is a procedure for collecting scientific data in order to answer a hypothesis, or to provide material for generating new hypotheses, and differs from a survey because the scientist has control over the treatments that can be applied. Most experiments can be classified into one of a few formal designs, the most common being completely randomised, and randomised block designs. These are quite common with in vitro experiments, which are often replicated in time. Some experiments involve a single independent (treatment) variable, while other "factorial" designs simultaneously vary two or more independent variables, such as drug treatment and cell line. Factorial designs often provide additional information at little extra cost. Experiments need to be carefully planned to avoid bias, be powerful yet simple, provide for a valid statistical analysis and, in some cases, have a wide range of applicability. Virtually all experiments need some sort of statistical analysis in order to take account of biological variation among the experimental subjects. Parametric methods using the t test or analysis of variance are usually more powerful than non-parametric methods, provided the underlying assumptions of normality of the residuals and equal variances are approximately valid. The statistical analyses of data from a completely randomised design, and from a randomised-block design are demonstrated in Appendices 1 and 2, and methods of determining sample size are discussed in Appendix 3. Appendix 4 gives a checklist for authors submitting papers to ATLA.

Background: The evaluation of the safety of drugs and other chemicals is an important aspect of toxicology work. The mouse micronucleus assay is a standard in vivo genotoxicity assay. Chromosomal damage is an indicator of genotoxicity, which manifests in the formation of micronuclei in polychromatic erythrocytes from bone marrow and in peripheral blood erythrocytes. The assay is laborious to perform by manual counting. The laser scanning cytometer allows automated and rapid quantitation of cellular and subcellular fluorescence in monodisperse cell samples on a microscope slide. The object of this study was to evaluate the application of this new technology in the mouse micronucleus genotoxicity assay. Materials and Methods One hundred forty-four mice of various strains were dosed with combinations of carcinogens and antioxidants. Duplicate blood films were prepared 3 days later. One set of slides was stained with acridine orange, and the proportion of micronucleated erythrocytes was counted in 5,000 cells per slide. The duplicates were stained with propidium iodide (40 microg/ml). Five thousand cells per sample were examined using a laser scanning cytometer. The proportion of micronucleated erythrocytes was measured., Results: A coefficient of correlation of 0.96 was found between the data from the two assays. The automation of the assay on the LSC produced a considerable time saving and efficiency gain., Conclusions: We conclude that with further development, laser scanning cytometry is likely to become the preferred modality for the performance of standard genotoxicity assays., (Copyright 2001 Wiley-Liss, Inc.)

Much toxicological research continues to be done using genetically undefined "outbred" stocks of mice and rats, although the case for using isogenic strains has been made repeatedly in the literature over a period of more than two decades. Also, very few studies are conducted using more than one strain, with the result that genetic variation in response is seldom apparent to the investigator. Here we report qualitative and quantitative strain differences in the haematological response to chloramphenicol succinate (CAPS) when administered by gavage at 500-2500 mg/kg for 7 days, to four inbred strains of mouse (C3H/He, CBA/Ca, BALB/c and C57BL/6) and one outbred stock (CD-1). CAPS caused anaemia and reticulocytopenia in all mouse strains, and leucopenia in the inbred strains but not in the outbred CD-1 stock. All four inbred strains showed significant (P<0.01) responses to CAPS at lower dose levels than in CD-1 mice, which were phenotypically more variable than the inbred animals. A simulated experiment, using a sample of records from the present study, showed that the use of two mice at each dose level using CD-1, CBA, BALB/c and C57BL/6 (48 total mice), would have given a more sensitive experiment than the use of 47 CD-1 mice alone, and would also have shown that the response is partly strain dependent. These studies provide additional evidence that inbred strains, because of their greater sensitivity and other valuable properties, should be more widely used in toxicology.

Toxicology is concerned with the interaction between xenobiotics and biological molecules directly or indirectly coded in the DNA, and can be regarded as a branch of genetics. There is genetic variation in these interactions, which has important implications for risk assessment and because it can be used as a tool in studying toxic mechanisms. The genetics of susceptibility can be studied by forward or reverse genetics. Forward genetics involves working from an observed phenotype such as susceptibility to a particular xenobiotic and identifying the susceptibility genes. Often, this involves mapping and identifying quantitative trait loci, as most toxic responses have a polygenic mode of inheritance. The use of inbred strains is almost essential. Reverse genetics involves starting with a known genetic polymorphism and determining its effects on the response to xenobiotics. Studies of 'knockout' animals are a good example, although there are many naturally occurring polymorphisms that may affect toxic responses. In both cases, care has to be taken to ensure that the genetic background is carefully controlled in any comparison between animals thought to be carrying susceptible and resistant alleles.

The tumour suppressor p53 protein regulates many genes involved in cellular responses to DNA damage. To date, a common transcriptionally active DNA-binding site for p53 in vivo has not been identified. The pGL3-Basic vector contains a modified fire-fly luciferase cDNA designated luc+ and is designed for studying putative regulatory sequences as it lacks any known eukaryotic promoter sequences. We report here that the CCCGGG sequence, a Sma I site, in the cloning region of the pGL3-Basic vector can promote p53-dependent transcription of the luc+ gene. We have demonstrated, by electrophoretic mobility shift assay (EMSA), that human p53 is able to bind to the CCCGGG sequence in vitro. These data provide the first demonstration that the CCCGGG sequence is a transcriptionally active DNA-binding site for p53. Thus, the pGL3-Basic vector could be used as an indicator of p53 transcriptional activity, to determine the p53 status of cell lines and to identify DNA damaging agents that initiate the activation of p53. The CCCGGG sequence has been found to be present in a number of promoter regions of p53-regulated genes. This and the present study suggest that the CCCGGG sequence may be a consensus sequence recognized by p53 in vivo and may be used to identify genes whose expression may be controlled by p53., (Copyright 2001 Academic Press.)

The mouse is a prime organism of choice for modelling human disease. Over 450 inbred strains of mice have been described, providing a wealth of different genotypes and phenotypes for genetic and other studies. As new strains are generated and others become extinct, it is useful to review periodically what strains are available and how they are related to each other, particularly in the light of available DNA polymorphism data from microsatellite and other markers. We describe the origins and relationships of inbred mouse strains, 90 years after the generation of the first inbred strain. Given the large collection of inbred strains available, and that published information on these strains is incomplete, we propose that all genealogical and genetic data on inbred strains be submitted to a common electronic database to ensure this valuable information resource is preserved and used efficiently.

We show here that DBA/2 strain mice have a complex mutation/polymorphism in the promoter region of the Trp53 locus (the mouse p53 locus). This region has previously been shown to be essential for p53 expression. We further show that the DBA/2 mutation is associated with approximately fourfold lower p53 levels in thymocytes treated with the DNA-damaging agent etoposide in-vitro, and with relative resistance of these thymocytes to apoptosis induced by the DNA-damaging agent etoposide compared with C57BL/6 mice. When part of the promoter containing this mutation was inserted into a plasmid containing a luciferase reporter gene but lacking eukaryote promoter sequences and transfected into MCF-7 human breast cell line cells, the mean luciferase activity was slightly less with the DBA/2 than with the C57BL/6 promoter-reporter construct (p < 0.01). We found that DBA/2xC57BL/6 F2 hybrid mice with the DBA/2 genotype at the Trp53 locus were relatively resistant to tetrachlorodibenzo-p-dioxin toxicity, and this resistance was additive with resistance associated with the Ahr locus. DBA/2 mice are long-lived and do not have particularly high levels of cancer, suggesting either that they carry other compensatory tumour resistance alleles (such as Ahr(d)), or that, while there may be a p53 protein dosage effect for acute toxicity, lower than normal levels of p53 may still be sufficient to protect against cancer. In evolutionary terms, it may be better to maintain low levels of p53 in order to avoid death from acute toxicity, even at the expense of a higher incidence of cancer in later life.

The Senescence-Accelerated Mouse (SAM) strains constitute a murine model of accelerated senescence originating from the ancestral AKR/J strains and consist of nine senescence-prone (SAMP) strains and four senescence-resistant (SAMR) strains. The chromosomes (Chrs) of the SAM strains were typed with 581 microsatellite markers amplified by PCR, and the fundamental genetic information of the SAM strains was obtained. One-third of the examined markers displayed polymorphism among the strains, and only two alleles were detected in almost all loci among the SAM and AKR/J strains. However, in 12 loci (5.6% of total 215 polymorphic markers), the third allele was detected among the SAM strains. The genetic typing and developmental history suggested that the SAM strains were related inbred strains developed by the accidental crossing between the AKR/J strain and other unknown strain(s). Comparison of the distribution of the loci in the SAMP and the SAMR series revealed notable differences in the four regions on Chrs 4, 14, 16, and 17. This indicated that some of these chromosomal sites might contain the genes responsible for accelerated senescence in the SAMP series.

Genetically heterogeneous (GH) mice and rats continue to be widely used in research even though the case for using isogenic strains has been argued repeatedly. The paper by Miller et al. in this issue appears to be the only one in the last 22 to attempt a scientific justification for the continued use of (a limited subset of) GH stocks. However, although they are to be commended for bravery, they fail to make their case. GH stocks represent poor material for controlled studies because genetic heterogeneity normally leads to phenotypic variability and a decline in experimental sensitivity. To counter this argument, Miller et al. claim that phenotypic variability may actually be smaller in GH animals than in their isogenic parents. Were this so (e.g., all mice being short lived, small, and aggressive), it is difficult to see how the use of such a stock could increase the generality of research results based on it, as claimed by Miller et al. Isogenic strains are a vital, proven, and powerful resource for biomedical research, and should be used in preference to GH stocks by all scientists who use laboratory rodents.

In the control of biologicals, animals are used largely to measure the concentration of a specific substance, rather than as a "model" of humans, so there is considerable scope for the development of replacement alternatives. When animals continue to be be used, a critical analysis of guidelines and regulations has suggested many ways in which the use of animals could be reduced [1]. However, the widespread failure to use genetically and microbiologically defined animals is scientifically questionable and almost certainly results in the use of excessive numbers. International standardisation on a small number of genetically defined F1 hybrid mice should lead to greater precision in individual tests as well as greater comparability among different laboratories.

Four putative quantitative trait loci (QTLs) that influence susceptibility to the induction of lung adenomas by urethane in an F2 cross between A/J and BALB/cOlaHsd have been mapped. Following microsatellite typing of mice with resistant and susceptible phenotypes at 97 microsatellite marker loci, a major locus was identified on chromosome 18 with a lod score of 15. This was responsible for an 8- to 10-fold increase in tumor multiplicity in males and females, respectively, having the AA and CC genotypes at the D18Mit188 marker locus. It mapped close to Dcc (deleted in colorectal cancer). A locus on chromosome 4 (lod score 6.5) had the resistant allele in strain A/J and the susceptible allele in BALB/c, with a 14-fold difference in tumor multiplicity between mice of the AA and CC genotypes. This mapped close to the Cdkn2a (cyclin-dependent kinase inhibitor 2A) locus, which is commonly deleted in mouse lung tumors. Two loci with smaller effects (lod scores 3.03 and 3.25) were identified on chromosomes 1 and 11. There was also significant sexual dimorphism in tumor multiplicity both among 151 F2 hybrids and among 52 mice resulting from a backcross to strain A/J, with males having higher tumor counts than females., (Copyright 1998 Academic Press.)

A locus for mouse pulmonary adenoma susceptibility, Pas-1, has been mapped on distal chromosome 6, where the K-ras gene is located. Allele-specific activation and expression of the K-ras allele from the susceptible parent has been observed in lung tumors from F1 hybrid mice. We report here genetic mapping of lung tumor susceptibility genes in urethane-treated A x B and B x A recombinant inbred (RI) mice using microsatellite markers to seek further evidence for the K-ras gene as candidate for Pas-1. The K-ras genotype differs between the A/J and C57BL/6J progenitors of the RI strains, and distal chromosome 6 contained a major lung tumor susceptibility determinant in the RI mice. Additional evidence that Pas-1 is K-ras involved linkage analysis of (A/JOLaHsd x BALB/ cOLaHsd) F2 intercross mice whose parents shared the same K-ras genotype. In contrast to the results with the A x B and B x A RI strains, no distal chromosome 6 site was significantly associated with tumor development in these F2 mice. In addition to this major locus, linkage analysis of the RI mice revealed additional quantitative trait loci for susceptibility on chromosomes 10, 17, and 19. These loci may serve as modifiers of Pas-1. The relationship between the K-ras genotype and the frequency of K-ras mutations in urethane-induced lung tumors from the RI mice was also explored. All 18 tumor DNAs from RI mice with high susceptibility contained an AT-->TA transversion at the second base of K-ras codon 61. This was also true for DNAs from 27 of 27 (100%) tumors in mice with high intermediate susceptibility. In RI strains with a low intermediate susceptibility, the DNA from 39 of 47 (83%) tumors contained an AT-->TA transversion at codon 61, and only 13 of 21 (62%) tumors had this mutation in the most resistant group. This reflects a positive correlation between the frequency of K-ras mutations in lung tumors of A x B or B x A RI strains and their susceptibility to lung carcinogenesis. Since K-ras appears to be Pas-1, these results suggest that some RI mice that have the resistant K-ras or Pas-1 allele undergo tumor development by a K-ras-independent route.