Genotype-environment interactions in mouse behavior: a way out of the problem

Mouse phenome database: curated data repository with interactive multi-population and multi-trait analyses

The Mouse Phenome Database continues to serve as a curated repository and analysis suite for measured attributes of members of diverse mouse populations. The repository includes annotation to community standard ontologies and guidelines, a database of allelic states for 657 mouse strains, a collection of protocols, and analysis tools for flexible, interactive, user directed analyses that increasingly integrates data across traits and populations. The database has grown from its initial focus on a standard set of inbred strains to include heterogeneous mouse populations such as the Diversity Outbred and mapping crosses and well as Collaborative Cross, Hybrid Mouse Diversity Panel, and recombinant inbred strains. Most recently the system has expanded to include data from the International Mouse Phenotyping Consortium. Collectively these data are accessible by API and provided with an interactive tool suite that enables users' persistent selection, storage, and operation on collections of measures. The tool suite allows basic analyses, advanced functions with dynamic visualization including multi-population meta-analysis, multivariate outlier detection, trait pattern matching, correlation analyses and other functions. The data resources and analysis suite provide users a flexible environment in which to explore the basis of phenotypic variation in health and disease across the lifespan.

Mapping strategies towards improved external validity in preclinical translational research

INTRODUCTION

Translation is about successfully bringing findings from preclinical contexts into the clinic. This transfer is challenging as clinical trials frequently fail despite positive preclinical results. Limited robustness of preclinical research has been marked as one of the drivers of such failures. One suggested solution is to improve the external validity of in vitro and in vivo experiments via a suite of complementary strategies.

AREAS COVERED

In this review, the authors summarize the literature available on different strategies to improve external validity in in vivo, in vitro, or ex vivo experiments; systematic heterogenization; generalizability tests; and multi-batch and multicenter experiments. Articles that tested or discussed sources of variability in systematically heterogenized experiments were identified, and the most prevalent sources of variability are reviewed further. Special considerations in sample size planning, analysis options, and practical feasibility associated with each strategy are also reviewed.

EXPERT OPINION

The strategies reviewed differentially influence variation in experiments. Different research projects, with their unique goals, can leverage the strengths and limitations of each strategy. Applying a combination of these approaches in confirmatory stages of preclinical research putatively increases the chances of success in clinical studies.

Comprehensive ECG reference intervals in C57BL/6N substrains provide a generalizable guide for cardiac electrophysiology studies in mice

Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key elements from the ECG waveform (RR-, PR-, ST-, QT-interval, QT corrected, and QRS complex) demonstrate minimal sexual dimorphism. As expected, anesthesia induces a decrease in heart rate and was shown for both inhalation (isoflurane) and injectable (tribromoethanol) anesthesia. In the absence of pharmacological, environmental, or genetic challenges, we did not observe major age-related ECG changes in C57BL/6N-inbred mice as the differences in the reference ranges of 12-week-old compared to 62-week-old mice were negligible. The generalizability of the C57BL/6N substrain reference ranges was demonstrated by comparison with ECG data from a wide range of non-IMPC studies. The close overlap in data from a wide range of mouse strains suggests that the C57BL/6N-based reference ranges can be used as a robust and comprehensive indicator of normality. We report a unique ECG reference resource of fundamental importance for any experimental study of cardiac function in mice.

A multi-lab experimental assessment reveals that replicability can be improved by using empirical estimates of genotype-by-lab interaction

The utility of mouse and rat studies critically depends on their replicability in other laboratories. A widely advocated approach to improving replicability is through the rigorous control of predefined animal or experimental conditions, known as standardization. However, this approach limits the generalizability of the findings to only to the standardized conditions and is a potential cause rather than solution to what has been called a replicability crisis. Alternative strategies include estimating the heterogeneity of effects across laboratories, either through designs that vary testing conditions, or by direct statistical analysis of laboratory variation. We previously evaluated our statistical approach for estimating the interlaboratory replicability of a single laboratory discovery. Those results, however, were from a well-coordinated, multi-lab phenotyping study and did not extend to the more realistic setting in which laboratories are operating independently of each other. Here, we sought to test our statistical approach as a realistic prospective experiment, in mice, using 152 results from 5 independent published studies deposited in the Mouse Phenome Database (MPD). In independent replication experiments at 3 laboratories, we found that 53 of the results were replicable, so the other 99 were considered non-replicable. Of the 99 non-replicable results, 59 were statistically significant (at 0.05) in their original single-lab analysis, putting the probability that a single-lab statistical discovery was made even though it is non-replicable, at 59.6%. We then introduced the dimensionless "Genotype-by-Laboratory" (GxL) factor-the ratio between the standard deviations of the GxL interaction and the standard deviation within groups. Using the GxL factor reduced the number of single-lab statistical discoveries and alongside reduced the probability of a non-replicable result to be discovered in the single lab to 12.1%. Such reduction naturally leads to reduced power to make replicable discoveries, but this reduction was small (from 87% to 66%), indicating the small price paid for the large improvement in replicability. Tools and data needed for the above GxL adjustment are publicly available at the MPD and will become increasingly useful as the range of assays and testing conditions in this resource increases.

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen

ABSTRACT

Identifying the genetic determinants of pain is a scientific imperative given the magnitude of the global health burden that pain causes. Here, we report a genetic screen for nociception, performed under the auspices of the International Mouse Phenotyping Consortium. A biased set of 110 single-gene knockout mouse strains was screened for 1 or more nociception and hypersensitivity assays, including chemical nociception (formalin) and mechanical and thermal nociception (von Frey filaments and Hargreaves tests, respectively), with or without an inflammatory agent (complete Freund's adjuvant). We identified 13 single-gene knockout strains with altered nocifensive behavior in 1 or more assays. All these novel mouse models are openly available to the scientific community to study gene function. Two of the 13 genes (Gria1 and Htr3a) have been previously reported with nociception-related phenotypes in genetically engineered mouse strains and represent useful benchmarking standards. One of the 13 genes (Cnrip1) is known from human studies to play a role in pain modulation and the knockout mouse reported herein can be used to explore this function further. The remaining 10 genes (Abhd13, Alg6, BC048562, Cgnl1, Cp, Mmp16, Oxa1l, Tecpr2, Trim14, and Trim2) reveal novel pathways involved in nociception and may provide new knowledge to better understand genetic mechanisms of inflammatory pain and to serve as models for therapeutic target validation and drug development.

Do multiple experimenters improve the reproducibility of animal studies?

The credibility of scientific research has been seriously questioned by the widely claimed “reproducibility crisis”. In light of this crisis, there is a growing awareness that the rigorous standardisation of experimental conditions may contribute to poor reproducibility of animal studies. Instead, systematic heterogenisation has been proposed as a tool to enhance reproducibility, but a real-life test across multiple independent laboratories is still pending. The aim of this study was therefore to test whether heterogenisation of experimental conditions by using multiple experimenters improves the reproducibility of research findings compared to standardised conditions with only one experimenter. To this end, we replicated the same animal experiment in 3 independent laboratories, each employing both a heterogenised and a standardised design. Whereas in the standardised design, all animals were tested by a single experimenter; in the heterogenised design, 3 different experimenters were involved in testing the animals. In contrast to our expectation, the inclusion of multiple experimenters in the heterogenised design did not improve the reproducibility of the results across the 3 laboratories. Interestingly, however, a variance component analysis indicated that the variation introduced by the different experimenters was not as high as the variation introduced by the laboratories, probably explaining why this heterogenisation strategy did not bring the anticipated success. Even more interestingly, for the majority of outcome measures, the remaining residual variation was identified as an important source of variance accounting for 41% (CI₉₅ [34%, 49%]) to 72% (CI₉₅ [58%, 88%]) of the observed total variance. Despite some uncertainty surrounding the estimated numbers, these findings argue for systematically including biological variation rather than eliminating it in animal studies and call for future research on effective improvement strategies.

An experimenter heterogenisation was not sufficient to prevent idiosyncratic results in a multi-laboratory setting. Astonishingly, neither the experimenter nor the laboratory accounted for the main portion of the observed variation, but a high amount of residual variation in fact remained unexplained despite strict standardisation regimes.

Challenges of a small world analysis for the continuous monitoring of behavior in mice

Documenting a mouse's "real world" behavior in the "small world" of a laboratory cage with continuous video recordings offers insights into phenotypical expression of mouse genotypes, development and aging, and neurological disease. Nevertheless, there are challenges in the design of a small world, the behavior selected for analysis, and the form of the analysis used. Here we offer insights into small world analyses by describing how acute behavioral procedures can guide continuous behavioral methodology. We show how algorithms can identify behavioral acts including walking and rearing, circadian patterns of action including sleep duration and waking activity, and the organization of patterns of movement into home base activity and excursions, and how they are altered with aging. We additionally describe how specific tests can be incorporated within a mouse's living arrangement. We emphasize how machine learning can condense and organize continuous activity that extends over extended periods of time.

Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data

The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely accessed and highly functional data repository housing primary phenotype data for the laboratory mouse accessible via APIs and providing tools to analyze and visualize those data. Data come from investigators around the world and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD houses rigorously curated per-animal data with detailed protocols. Public ontologies and controlled vocabularies are used for annotation. In addition to phenotype tools, genetic analysis tools enable users to integrate and interpret genome–phenome relations across the database. Strain types and populations include inbred, recombinant inbred, F1 hybrid, transgenic, targeted mutants, chromosome substitution, Collaborative Cross, Diversity Outbred and other mapping populations. Our new analysis tools allow users to apply selected data in an integrated fashion to address problems in trait associations, reproducibility, polygenic syndrome model selection and multi-trait modeling. As we refine these tools and approaches, we will continue to provide users a means to identify consistent, quality studies that have high translational relevance.

Differential navigational strategies during spatial learning in a new modified version of the Oasis maze

During spatial navigation, some typical parameters of learning have been observed, such as latency or path length. However, these parameters are sensitive to patterns of navigation and orientation that are not easily measurable. In the present study, we used a modified version of the Oasis maze and evaluated different parameters of learning, navigation, and orientation in different animal groups. Through a PCA (Principal component analysis) we found different factors such as learning, navigation, speediness, anxiety, orientation, path variability, and turning behavior. Each factor gathers different groups of behavioral variables. ANOVA analysis of those factors demonstrates that some of them are more strongly modulated by trial progression, while others by animal group differences, indicating that each group of variables is better reflecting one of these dimensions. To understand the nature of these navigation differences, we studied orientation strategies between animal conditions and across trials. We found that the main navigational strategy used by the animals consist of locating the target and directing their behaviors towards this area. When testing how this strategy changed after cognitive impairment or enhancement, we found that AβOs treated animals (Amyloid β Oligomers, Alzheimer animal model) have strong orientation difficulties at locating the target at longer distances. While animals with learning enhancement (exercised rat) do not show changes in orientation behaviors. These analyses highlight that experimental manipulations affect learning, but also induced changes in the navigational strategies. We concluded that both dimensions can explain the differences observed in typical learning variables, such as latency or path length, motivating the development of new tools that asses this two-dimension as a separate but, interacting phenomenon.

Knockout and Knock-in Mouse Models to Study Purinergic Signaling

Purinergic signaling involves extracellular purines and pyrimidines acting upon specific cell surface purinoceptors classified into the P1, P2X, and P2Y families for nucleosides and nucleotides. This widespread signaling mechanism is active in all major tissues and influences a range of functions in health and disease. Orthologs to all but one of the human purinoceptors have been found in mouse, making this laboratory animal a useful model to study their function. Indeed, analyses of purinoceptors via knock-in or knockout approaches to produce gain or loss of function phenotypes have revealed several important therapeutic targets. None of the homozygous purinoceptor knockouts proved to be developmentally lethal, which suggest that either these receptors are not involved in key developmental processes or that the large number of receptors in each family allowed for functional compensation. Different models for the same purinoceptor often show compatible phenotypes but there have been examples of significant discrepancies. These revealed unexpected differences in the structure of human and mouse genes and emphasized the importance of the genetic background of different mouse strains. In this chapter, we provide an overview of the current knowledge and new trends in the modifications of purinoceptor genes in vivo. We discuss the resulting phenotypes, their applications and relative merits and limitations of mouse models available to study purinoceptor subtypes.

Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice

The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely used resource that provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD houses individual animal data with detailed, searchable protocols, and makes these data available to other resources via API. MPD provides rigorous curation of experimental data and supporting documentation using relevant ontologies and controlled vocabularies. Most data in MPD are from inbreds and other reproducible strains such that the data are cumulative over time and across laboratories. The resource has been expanded to include the QTL Archive and other primary phenotype data from mapping crosses as well as advanced high-diversity mouse populations including the Collaborative Cross and Diversity Outbred mice. Furthermore, MPD provides a means of assessing replicability and reproducibility across experimental conditions and protocols, benchmarking assays in users’ own laboratories, identifying sensitized backgrounds for making new mouse models with genome editing technologies, analyzing trait co-inheritance, finding the common genetic basis for multiple traits and assessing sex differences and sex-by-genotype interactions.

Determinants of QTL Mapping Power in the Realized Collaborative Cross

The Collaborative Cross (CC) is a mouse genetic reference population whose range of applications includes quantitative trait loci (QTL) mapping. The design of a CC QTL mapping study involves multiple decisions, including which and how many strains to use, and how many replicates per strain to phenotype, all viewed within the context of hypothesized QTL architecture. Until now, these decisions have been informed largely by early power analyses that were based on simulated, hypothetical CC genomes. Now that more than 50 CC strains are available and more than 70 CC genomes have been observed, it is possible to characterize power based on realized CC genomes. We report power analyses from extensive simulations and examine several key considerations: 1) the number of strains and biological replicates, 2) the QTL effect size, 3) the presence of population structure, and 4) the distribution of functionally distinct alleles among the founder strains at the QTL. We also provide general power estimates to aide in the design of future experiments. All analyses were conducted with our R package, SPARCC (Simulated Power Analysis in the Realized Collaborative Cross), developed for performing either large scale power analyses or those tailored to particular CC experiments.

Living inside the box: environmental effects on mouse models of human disease

The impact of the laboratory environment on animal models of human disease, particularly the mouse, has recently come under intense scrutiny regarding both the reproducibility of such environments and their ability to accurately recapitulate elements of human environmental conditions. One common objection to the use of mice in highly controlled facilities is that humans live in much more diverse and stressful environments, which affects the expression and characteristics of disease phenotypes. In this Special Article, we review some of the known effects of the laboratory environment on mouse phenotypes and compare them with environmental effects on humans that modify phenotypes or, in some cases, have driven genetic adaptation. We conclude that the 'boxes' inhabited by mice and humans have much in common, but that, when attempting to tease out the effects of environment on phenotype, a controlled and, importantly, well-characterized environment is essential.

Reproducibility and replicability of rodent phenotyping in preclinical studies

The scientific community is increasingly concerned with the proportion of published “discoveries” that are not replicated in subsequent studies. The field of rodent behavioral phenotyping was one of the first to raise this concern, and to relate it to other methodological issues: the complex interaction between genotype and environment; the definitions of behavioral constructs; and the use of laboratory mice and rats as model species for investigating human health and disease mechanisms. In January 2015, researchers from various disciplines gathered at Tel Aviv University to discuss these issues. The general consensus was that the issue is prevalent and of concern, and should be addressed at the statistical, methodological and policy levels, but is not so severe as to call into question the validity and the usefulness of model organisms as a whole. Well-organized community efforts, coupled with improved data and metadata sharing, have a key role in identifying specific problems and promoting effective solutions. Replicability is closely related to validity, may affect generalizability and translation of findings, and has important ethical implications.

Standardize or Diversify Experimental Conditions in Ecotoxicology? A Case Study on Herbicide Toxicity to Larvae of Two Anuran Amphibians

Despite a steeply increasing number of ecotoxicological studies on the effects of pesticides on nontarget organisms, studies assessing the adequacy and reliability of different experimental approaches have remained scarce. We scrutinized effects of a glyphosate-based herbicide on larvae of two European anuran amphibians by estimating species-specific LC50 values, assessing how an additional stress factor may influence outcomes, and investigating whether replicate experiments yielded qualitatively the same results. We exposed Rana dalmatina and Bufo bufo tadpoles to two predator treatments (no predator vs. predator chemical cues) combined with varying herbicide concentrations, repeated the experiment with a subset of the experimental treatments and partly with slight modifications 1 week later and assessed survival. Our results indicated that the herbicide was moderately toxic to tadpoles. The presence of predator chemical cues did not affect the lethality of the herbicide in either species. The estimated sensitivity of R. dalmatina tadpoles varied considerably across experiments, whereas in case of B. bufo LC50 values remained very similar. Our results suggest that differences in the experimental setup may often have no influence on the measured effects of pesticides, whereas replicated experiments can deliver widely differing results in other cases, perhaps depending on the studied species, the population origin of the tested individuals, or the test conditions. This draws attention to the suggestion that strict standardization may not deliver widely applicable insights into the toxicity of contaminants and, instead, intentionally introducing variation into the design of ecotoxicological experiments and replicating entire experiments may prove highly beneficial.

Refinement of experimental design and conduct in laboratory animal research

The scientific literature of laboratory animal research is replete with papers reporting poor reproducibility of results as well as failure to translate results to clinical trials in humans. This may stem in part from poor experimental design and conduct of animal experiments. Despite widespread recognition of these problems and implementation of guidelines to attenuate them, a review of the literature suggests that experimental design and conduct of laboratory animal research are still in need of refinement. This paper will review and discuss possible sources of biases, highlight advantages and limitations of strategies proposed to alleviate them, and provide a conceptual framework for improving the reproducibility of laboratory animal research.

Ethological concepts enhance the translational value of animal models

The translational value of animal models is an issue of ongoing discussion. We argue that 'Refinement' of animal experiments is needed and this can be achieved by exploiting an ethological approach when setting up and conducting experiments. Ethology aims to assess the functional meaning of behavioral changes, due to experimental manipulation or treatment, in animal models. Although the use of ethological concepts is particularly important for studies involving the measurement of animal behavior (as is the case for most studies on neuro-psychiatric conditions), it will also substantially benefit other disciplines, such as those investigating the immune system or inflammatory response. Using an ethological approach also involves using more optimal testing conditions are employed that have a biological relevance to the animal. Moreover, using a more biological relevant analysis of the data will help to clarify the functional meaning of the modeled readout (e.g. whether it is psychopathological or adaptive in nature). We advocate for instance that more behavioral studies should use animals in group-housed conditions, including the recording of their ultrasonic vocalizations, because (1) social behavior is an essential feature of animal models for human 'social' psychopathologies, such as autism and schizophrenia, and (2) social conditions are indispensable conditions for appropriate behavioral studies in social species, such as the rat. Only when taking these elements into account, the validity of animal experiments and, thus, the translation value of animal models can be enhanced.

Deciding whether follow-up studies have replicated findings in a preliminary large-scale omics study

We propose a formal method to declare that findings from a primary study have been replicated in a follow-up study. Our proposal is appropriate for primary studies that involve large-scale searches for rare true positives (i.e., needles in a haystack). Our proposal assigns an r value to each finding; this is the lowest false discovery rate at which the finding can be called replicated. Examples are given and software is available.

Reproducibility and relevance of future behavioral sciences should benefit from a cross fertilization of past recommendations and today's technology: "Back to the future"

Thanks to the discovery of novel technologies and sophisticated analysis tools we can now 'see' molecules, genes and even patterns of gene expression, which have resulted in major advances in many areas of biology. Recently, similar technologies have been developed for behavioral studies. However, the wide implementation of such technological progress in behavioral research remains behind, as if there are inhibiting factors for accepting and adopting available innovations. The methods of the majority of studies measuring and interpreting behavior of laboratory animals seem to have frozen in time somewhere in the last century. As an example of the so-called classical tests, we will present the history and shortcomings of one of the most frequently used tests, the open field. Similar objections and critical remarks, however, can be made with regard to the elevated plus maze, light-dark box, various other mazes, object recognition tests, etc. Possible solutions and recommendations on how progress in behavioral neuroscience can be achieved and accelerated will be discussed in the second part of this review.

Mining mouse behavior for patterns predicting psychiatric drug classification

RATIONALE

In psychiatric drug discovery, a critical step is predicting the psychopharmacological effect and therapeutic potential of novel (or repurposed) compounds early in the development process. This process is hampered by the need to utilize multiple disorder-specific and labor-intensive behavioral assays.

OBJECTIVES

This study aims to investigate the feasibility of a single high-throughput behavioral assay to classify psychiatric drugs into multiple psychopharmacological classes.

METHODS

Using Pattern Array, a procedure for data mining exploratory behavior in mice, we mined ~100,000 complex movement patterns for those that best predict psychopharmacological class and dose. The best patterns were integrated into a classification model that assigns psychopharmacological compounds to one of six clinically relevant classes--antipsychotic, antidepressant, opioids, psychotomimetic, psychomotor stimulant, and α-adrenergic.

RESULTS

Surprisingly, only a small number of well-chosen behaviors were required for successful class prediction. One of them, a behavior termed "universal drug detector", was dose-dependently decreased by drugs from all classes, thus providing a sensitive index of psychopharmacological activity. In independent validation in a blind fashion, simulating the process of in vivo pre-clinical drug screening, the classification model correctly classified nine out of 11 "unknown" compounds. Interestingly, even "misclassifications" match known alternate therapeutic indications, illustrating drug "repurposing" potential.

CONCLUSIONS

Unlike standard animal models, the discovered classification model can be systematically updated to improve its predictive power and add therapeutic classes and subclasses with each additional diversification of the database. Our study demonstrates the power of data mining approaches for behavior analysis, using multiple measures in parallel for drug screening and behavioral phenotyping.

Enhanced alcohol self-administration and reinstatement in a highly impulsive, inattentive recombinant inbred mouse strain

Deficits in executive control have frequently been associated with alcohol use disorder. Here we investigated to what extent pre-existing genetically encoded levels of impulsive/inattentive behavior associate with motivation to take alcohol and vulnerability to cue-induced reinstatement of alcohol seeking in an operant self-administration paradigm. We took advantage of BXD16, a recombinant inbred strain previously shown to have enhanced impulsivity and poor attentional control. We compared BXD16 with C57BL/6J mice in a simple choice reaction time task (SCRTT) and confirmed its impulsive/inattentive phenotype. BXD16 mice were less active in a novel open field (OF), and were equally active in an automated home cage environment, showing that increased impulsive responding of BXD16 mice could not be explained by enhanced general activity compared to C57BL/6J mice. After training in a sucrose/alcohol fading self-administration procedure, BXD16 showed increased motivation to earn 10% alcohol solution, both under fixed ratio (FR1) and progressive ratio (PR2) schedules of reinforcement. Responding on the active lever readily decreased during extinction training with no apparent differences between strains. However, upon re-exposure to alcohol-associated cues, alcohol seeking was reinstated to a larger extent in BXD16 than in C57BL/6J mice. Although further studies are needed to determine whether impulsivity/inattention and alcohol seeking depend on common or separate genetic loci, these data show that in mice enhanced impulsivity coincides with increased motivation to take alcohol, as well as relapse vulnerability.

Automated home cage assessment shows behavioral changes in a transgenic mouse model of spinocerebellar ataxia type 17

Spinocerebellar Ataxia type 17 (SCA17) is an autosomal dominantly inherited, neurodegenerative disease characterized by ataxia, involuntary movements, and dementia. A novel SCA17 mouse model having a 71 polyglutamine repeat expansion in the TATA-binding protein (TBP) has shown age related motor deficit using a classic motor test, yet concomitant weight increase might be a confounding factor for this measurement. In this study we used an automated home cage system to test several motor readouts for this same model to confirm pathological behavior results and evaluate benefits of automated home cage in behavior phenotyping. Our results confirm motor deficits in the Tbp/Q71 mice and present previously unrecognized behavioral characteristics obtained from the automated home cage, indicating its use for high-throughput screening and testing, e.g. of therapeutic compounds.

Robust and sensitive analysis of mouse knockout phenotypes

A significant challenge of in-vivo studies is the identification of phenotypes with a method that is robust and reliable. The challenge arises from practical issues that lead to experimental designs which are not ideal. Breeding issues, particularly in the presence of fertility or fecundity problems, frequently lead to data being collected in multiple batches. This problem is acute in high throughput phenotyping programs. In addition, in a high throughput environment operational issues lead to controls not being measured on the same day as knockouts. We highlight how application of traditional methods, such as a Student’s t-Test or a 2-way ANOVA, in these situations give flawed results and should not be used. We explore the use of mixed models using worked examples from Sanger Mouse Genome Project focusing on Dual-Energy X-Ray Absorptiometry data for the analysis of mouse knockout data and compare to a reference range approach. We show that mixed model analysis is more sensitive and less prone to artefacts allowing the discovery of subtle quantitative phenotypes essential for correlating a gene’s function to human disease. We demonstrate how a mixed model approach has the additional advantage of being able to include covariates, such as body weight, to separate effect of genotype from these covariates. This is a particular issue in knockout studies, where body weight is a common phenotype and will enhance the precision of assigning phenotypes and the subsequent selection of lines for secondary phenotyping. The use of mixed models with in-vivo studies has value not only in improving the quality and sensitivity of the data analysis but also ethically as a method suitable for small batches which reduces the breeding burden of a colony. This will reduce the use of animals, increase throughput, and decrease cost whilst improving the quality and depth of knowledge gained.

The developmental dynamics of behavioral growth processes in rodent egocentric and allocentric space

In this review I focus on how three methodological principles advocated by Philip Teitelbaum influenced my work to this day: that similar principles of organization should be looked for in ontogeny and recovery of function; that the order of emergence of behavioral components provides a view on the organization of that behavior; and that the components of behavior should be exhibited by the animal itself in relatively pure form. I start by showing how these principles influenced our common work on the developmental dynamics of rodent egocentric space, and then proceed to describe how these principles affected my work with Yoav Benjamini and others on the developmental dynamics of rodent allocentric space. We analyze issues traditionally addressed by physiological psychologists with methods borrowed from ethology, EW (Eshkol-Wachman) movement notation, dynamical systems and exploratory data analysis. Then we show how the natural origins of axes embodied by the behavior of the organism itself, are used by us as the origins of axes for the measurement of the developmental moment-by-moment dynamics of behavior. Using this methodology we expose similar principles of organization across situations, species and preparations, provide a developmental view on the organization of behavior, expose the natural components of behavior in relatively pure form, and reveal how low level primitives generate higher level constructs. Advances in tracking technology should allow us to study how movements in egocentric and allocentric spaces interlace. Tracking of multi-limb coordination, progress in online recording of neural activity in freely moving animals, and the unprecedented accumulation of genetically engineered mouse preparations makes the behavioral ground plan exposed in this review essential for a systematic study of the brain/behavior interface.

Effects of spatial and cognitive enrichment on activity pattern and learning performance in three strains of mice in the IntelliMaze

The IntelliMaze allows automated behavioral analysis of group housed laboratory mice while individually assigned protocols can be applied concomitantly for different operant conditioning components. Here we evaluate the effect of additional component availability (enrichment) on behavioral and cognitive performance of mice in the IntelliCage, by focusing on aspects that had previously been found to consistently differ between three strains, in four European laboratories. Enrichment decreased the activity level in the IntelliCages and enhanced spatial learning performance. However, it did not alter strain differences, except for activity during the initial experimental phase. Our results from non-enriched IntelliCages proved consistent between laboratories, but overall laboratory-consistency for data collected using different IntelliCage set-ups, did not hold for activity levels during the initial adaptation phase. Our results suggest that the multiple conditioning in spatially and cognitively enriched environments are feasible without affecting external validity for a specific task, provided animals have adapted to such an IntelliMaze.

Environmental enrichment of laboratory rodents: the answer depends on the question

Efforts to refine the care and use of animals in research have been ongoing for many years and have led to general standardization of rodent models, particularly with regard to animal housing, genetics, and health status. Concurrently, numerous informal practices and recommendations have been promulgated with the laudable intent of promoting general animal wellbeing through so-called enrichment of the cage environment. However, the variety of housing conditions fostered by efforts at environmental enrichment (EE) complicates the goal of establishing standardized or even defined environments for laboratory rodents. Many studies over the years have sought to determine whether or how various enrichment strategies affect the behavior and physiology of laboratory rodents. The findings, conclusions, and interpretations of these studies are mixed, particularly with regard to their application across rodent species, strains, genders, and ages; whether or how they affect the animals and the science; and, in some cases, whether the effects are positive, negative, or neutral in terms of animal wellbeing. Crucial issues related to the application of EE in research settings include its poorly defined effect on the animals, the potential for increased variability in the data, poor definition across labs and in publications, and potential for animal or scientific harm. The complexities, uncertainties, interpretational conundrums, varying conclusions, and lack of consensus in the EE literature warrant careful assessment of the benefits and liabilities associated with implementing such interventions. Reliance on evidence, professional judgment, and performance standards are crucial in the development of EE strategies.

Reversed light-dark cycle and cage enrichment effects on ethanol-induced deficits in motor coordination assessed in inbred mouse strains with a compact battery of refined tests

The laboratory environment existing outside the test situation itself can have a substantial influence on results of some behavioral tests with mice, and the extent of these influences sometimes depends on genotype. For alcohol research, the principal issue is whether genotype-related ethanol effects will themselves be altered by common variations in the lab environment or instead will be essentially the same across a wide range of lab environments. Data from 20 inbred strains were used to reduce an original battery of seven tests of alcohol intoxication to a compact battery of four tests: the balance beam and grip strength with a 1.25 g/kg ethanol dose and the accelerating rotarod and open-field activation tests with 1.75 g/kg. The abbreviated battery was then used to study eight inbred strains housed under a normal or reversed light-dark cycle, or a standard or enriched home cage environment. The light-dark cycle had no discernable effects on any measure of behavior or response to alcohol. Cage enrichment markedly improved motor coordination in most strains. Ethanol-induced motor coordination deficits were robust; the well-documented strain-dependent effects of ethanol were not altered by cage enrichment.

Quantifying the buildup in extent and complexity of free exploration in mice

To obtain a perspective on an animal's own functional world, we study its behavior in situations that allow the animal to regulate the growth rate of its behavior and provide us with the opportunity to quantify its moment-by-moment developmental dynamics. Thus, we are able to show that mouse exploratory behavior consists of sequences of repeated motion: iterative processes that increase in extent and complexity, whose presumed function is a systematic active management of input acquired during the exploration of a novel environment. We use this study to demonstrate our approach to quantifying behavior: targeting aspects of behavior that are shown to be actively managed by the animal, and using measures that are discriminative across strains and treatments and replicable across laboratories.

Effect of population heterogenization on the reproducibility of mouse behavior: a multi-laboratory study

In animal experiments, animals, husbandry and test procedures are traditionally standardized to maximize test sensitivity and minimize animal use, assuming that this will also guarantee reproducibility. However, by reducing within-experiment variation, standardization may limit inference to the specific experimental conditions. Indeed, we have recently shown in mice that standardization may generate spurious results in behavioral tests, accounting for poor reproducibility, and that this can be avoided by population heterogenization through systematic variation of experimental conditions. Here, we examined whether a simple form of heterogenization effectively improves reproducibility of test results in a multi-laboratory situation. Each of six laboratories independently ordered 64 female mice of two inbred strains (C57BL/6NCrl, DBA/2NCrl) and examined them for strain differences in five commonly used behavioral tests under two different experimental designs. In the standardized design, experimental conditions were standardized as much as possible in each laboratory, while they were systematically varied with respect to the animals' test age and cage enrichment in the heterogenized design. Although heterogenization tended to improve reproducibility by increasing within-experiment variation relative to between-experiment variation, the effect was too weak to account for the large variation between laboratories. However, our findings confirm the potential of systematic heterogenization for improving reproducibility of animal experiments and highlight the need for effective and practicable heterogenization strategies.

Increased striatal injury and behavioral deficits after intracerebral hemorrhage in hemopexin knockout mice

OBJECT

Heme toxicity may contribute to the pathogenesis of intracerebral hemorrhage (ICH). The primary defense against extracellular heme is provided by hemopexin, a serum and neuronal glycoprotein that binds it with very high affinity and mitigates its prooxidant effect. In the present study, the authors tested the hypothesis that hemopexin knockout mice would sustain more injury after experimental ICH than their wild-type counterparts.

METHODS

Striatal ICH was induced by the stereotactic injection of bacterial collagenase or autologous blood. Three days later, striatal protein oxidation was assessed via carbonyl assay. Cell viability was quantified at 8-9 days by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Behavioral deficits were detected with high-resolution digital analysis of 6-hour home cage video recordings and standard testing.

RESULTS

Perihematomal protein oxidation was increased in wild-type collagenase-injected striata by approximately 2.1-fold, as compared with contralateral striata; protein carbonyls were increased 3-fold in knockout mice. Striatal cell viability was reduced by collagenase injection in wild-type mice to 52.9 ± 6.5% of that in the contralateral striata, and to 31.1 ± 3.7% of that in the contralateral striata in knockout mice; similar results were obtained after blood injection. Digital analysis of 6-hour video recordings demonstrated an activity deficit in both models that was significantly exacerbated at 8 days in knockout mice. Striatal heme content 9 days after blood injection was increased approximately 2.7-fold in knockouts as compared with wild-type mice.

CONCLUSIONS

These results suggest that hemopexin has a protective effect against hemorrhagic CNS injuries. Hemopexin deficiency, which is often associated with sickle cell disease, may worsen outcome after ICH.

Consistent behavioral phenotype differences between inbred mouse strains in the IntelliCage

The between-laboratory effects on behavioral phenotypes and spatial learning performance of three strains of laboratory mice known for divergent behavioral phenotypes were evaluated in a fully balanced and synchronized study using a completely automated behavioral phenotyping device (IntelliCage). Activity pattern and spatial conditioning performance differed consistently between strains, i.e. exhibited no interaction with the between-laboratory factor, whereas the gross laboratory effect showed up significantly in the majority of measures. It is argued that overall differences between laboratories may not realistically be preventable, as subtle differences in animal housing and treatment will not be controllable, in practice. However, consistency of strain (or treatment) effects appears to be far more important in behavioral and brain sciences than the absolute overall level of such measures. In this respect, basic behavioral and learning measures proved to be highly consistent in the IntelliCage, therefore providing a valid basis for meaningful research hypothesis testing. Also, potential heterogeneity of behavioral status because of environmental and social enrichment has no detectable negative effect on the consistency of strain effects. We suggest that the absence of human interference during behavioral testing is the most prominent advantage of the IntelliCage and suspect that this is likely responsible for the between-laboratory consistency of findings, although we are aware that this ultimately needs direct testing.

Ten ways to improve the quality of descriptions of whole-animal movement

The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.

The precision of video and photocell tracking systems and the elimination of tracking errors with infrared backlighting

Automated tracking offers a number of advantages over both manual and photocell tracking methodologies, including increased reliability, validity, and flexibility of application. Despite the advantages that video offers, our experience has been that video systems cannot track a mouse consistently when its coat color is in low contrast with the background. Furthermore, the local lab lighting can influence how well results are quantified. To test the effect of lighting, we built devices that provide a known path length for any given trial duration, at a velocity close to the average speed of a mouse in the open-field and the circular water maze. We found that the validity of results from two commercial video tracking systems (ANY-maze and EthoVision XT) depends greatly on the level of contrast and the quality of the lighting. A photocell detection system was immune to lighting problems but yielded a path length that deviated from the true length. Excellent precision was achieved consistently, however, with video tracking using infrared backlighting in both the open field and water maze. A high correlation (r=0.98) between the two software systems was observed when infrared backlighting was used with live mice.

Freedom of movement and the stability of its unfolding in free exploration of mice

Exploration is a central component of human and animal behavior that has been studied in rodents for almost a century. The measures used by neuroscientists to characterize full-blown exploration are limited in exposing the dynamics of the exploratory process, leaving the morphogenesis of its structure and meaning hidden. By unfettering exploration from constraints imposed by hunger, thirst, coercion, and the confines of small cage and short session, using advanced computational tools, we reveal its meaning in the operational world of the mouse. Exploration consists of reiterated roundtrips of increasing amplitude and freedom, involving an increase in the number of independent dimensions along which the mouse moves (macro degrees of freedom). This measurable gradient can serve as a standard reference scale for the developmental dynamics of some aspects of the mouse's emotional-cognitive state and for the study of the interface between behavior and the neurophysiologic and genetic processes mediating it.

A genome-wide panel of congenic mice reveals widespread epistasis of behavior quantitative trait loci

Understanding the genetics of behavioral variation remains a fascinating but difficult problem with considerable theoretical and practical implications. We used the genome-tagged mice (GTM) and an extensive test battery of well-validated behavioral assays to scan the genome for behavioral quantitative trait loci (QTLs). The GTM are a panel of 'speed congenic' mice consisting of over 60 strains spanning the entire autosomal genome. Each strain harbors a small (approximately 23 cM) DBA/2J donor segment on a uniform C57BL/6J background. The panel allows for mapping to regions as small as 5 cM and provides a powerful new tool for increasing mapping power and replicability in the analysis of QTLs. A total of 97 loci were mapped for a variety of complex behavioral traits including hyperactivity, anxiety, prepulse inhibition, avoidance and conditional fear. A larger number of loci were recovered than generally attained from standard mapping crosses. In addition, a surprisingly high proportion of loci, 63%, showed phenotypes unlike either of the parental strains. These data suggest that epistasis decreases sensitivity of locus detection in traditional crosses and demonstrate the utility of the GTM for mapping complex behavioral traits with high sensitivity and precision.

Change in maternal environment induced by cross-fostering alters genetic and epigenetic effects on complex traits in mice

The interaction between maternally provided environment and offspring genotype is a major determinant of offspring development and fitness in many organisms. Recent research has demonstrated that not only genetic effects, but also epigenetic effects may be subject to modifications by the maternal environment. Genomic imprinting resulting in parent-of-origin-dependent gene expression is among the best studied of epigenetic effects. However, very little is known about the degree to which genomic imprinting effects can be modulated by the maternally provided environment, which has important implications for phenotypic plasticity. In this study, we investigated this unresolved question using a cross-fostering design in which mouse pups were nursed by either their own or an unrelated mother. We scanned the entire genome to search for quantitative trait loci whose effects depend on cross-fostering and detected 10 of such loci. Of the 10 loci, 4 showed imprinting by cross-foster interactions. In most cases, the interaction effect was due to the presence of an effect in either cross-fostered or non-cross-fostered animals. Our results demonstrate that genomic imprinting effects may often be modified by the maternal environment and that such interactions can impact key fitness-related traits suggesting a greater plasticity of genomic imprinting than previously assumed.

Environmental standardization: cure or cause of poor reproducibility in animal experiments?

It is widely believed that environmental standardization is the best way to guarantee reproducible results in animal experiments. However, mounting evidence indicates that even subtle differences in laboratory or test conditions can lead to conflicting test outcomes. Because experimental treatments may interact with environmental conditions, experiments conducted under highly standardized conditions may reveal local 'truths' with little external validity. We review this hypothesis here and present a proof of principle based on data from a multilaboratory study on behavioral differences between inbred mouse strains. Our findings suggest that environmental standardization is a cause of, rather than a cure for, poor reproducibility of experimental outcomes. Environmental standardization can contribute to spurious and conflicting findings in the literature and unnecessary animal use. This conclusion calls for research into practicable and effective ways of systematic environmental heterogenization to attenuate these scientific, economic and ethical costs.

Drug discovery in psychiatric illness: mining for gold

The discovery of truly efficacious treatments that lead to full recovery is a daunting task in psychiatric illness. A systems-based orientation to in vivo pharmacology has been suggested as a way to transform psychiatric drug discovery and development. A critical catalyst in the success of recent systems biology efforts has been the incorporation of data mining strategies. Our approach to the drug discovery problem has been to utilize the whole animal to provide a systems response that is subsequently mined for predictive attributes with known psychopharmacological value. Our in vivo data mining approach, termed Pattern Array, establishes a framework for screening novel chemical entities based upon a response that represents the net pharmacological effect on the system of interest, namely the central nervous system (CNS). Large scale screening of small molecules by non-conventional approaches such as this at a systems level may improve the identification of novel chemical entities with psychiatric utility. This type of approach will compliment the more labor-intensive models based upon construct validity. It will take the collective effort of many disciplines and numerous strategies in close association with clinical colleagues to address quality of life issues and breakthrough treatment barriers in psychiatric illness.