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

Pebble to the Metal: A Boulder Approach to Enrichment for Danio rerio

Zebrafish are an established and widely used animal model, yet there is limited understanding of their welfare needs. Despite an increasing number of studies on zebrafish enrichment, in-tank environmental enrichment remains unpopular among researchers. This is due to perceived concerns over health/hygiene when it comes to introducing enrichment into the tank, although actual evidence for this is sparse. To accommodate this belief, regardless of veracity, we tested the potential benefits of enrichments presented outside the tank. Thus, we investigated the preferences and physiological stress of zebrafish with pictures of pebbles placed underneath the tank. We hypothesized that zebrafish would show a preference for enriched environments and have lower stress levels than barren housed zebrafish. In our first experiment, we housed zebrafish in a standard rack system and recorded their preference for visual access to a pebble picture, with two positive controls: visual access to conspecifics, and group housing. Using a crossover repeated-measures factorial design, we tested if the preference for visual access to pebbles was as strong as the preference for social contact. Zebrafish showed a strong preference for visual access to pebbles, equivalent to that for conspecifics. Then, in a second experiment, tank water cortisol was measured to assess chronic stress levels of zebrafish housed with or without a pebble picture under their tank, with group housing as a positive control. Cortisol levels were significantly reduced in zebrafish housed with pebble pictures, as were cortisol levels in group housed zebrafish. In fact, single housed zebrafish with pebble pictures showed the same cortisol levels as group housed zebrafish without pebble pictures. Thus, the use of an under-tank pebble picture was as beneficial as being group housed, effectively compensating for the stress of single housing. Pebble picture enrichment had an additive effect with group housing, where group housed zebrafish with pebble pictures had the lowest cortisol levels of any treatment group.

A behavioral roadmap for the development of agency in the rodent

Behavioral interactions within the nuclear family play a pivotal role in the emergence of agency: the capacity to regulate physiological, psychological and social needs. While behaviors may develop over days or weeks in line with nervous system maturation, individual behaviors can occur on sub-second time scales making it challenging to track development in lab studies with brief observation periods, or in field studies with limited temporal precision and animal identification. Here we study development in families of gerbils, a highly social rodent, collecting tens of millions of behavior time points and implementing machine learning methods to track individual subjects. We provided maturing gerbils with a large, undisturbed environment between postnatal day 15 and the age at which they would typically disperse from the family unit (day 30). We identified complex and distinct developmental trajectories for food and water acquisition, solitary exploration, and social behaviors, some of which displayed sex differences and diurnal patterns. Our work supports the emergence of well-delineated autonomous and social behavior phenotypes that correlate with specific periods and loci of neural maturation.

Exploring the similarities between risk factors triggering depression in humans and elevated in-cage "inactive but awake" behavior in laboratory mice

Introduction

Depression is a human mental disorder that can also be inferred in non-human animals. This study explored whether time spent inactive but awake ("IBA") in the home-cage in mice was further triggered by risk factors similar to those increasing vulnerability to depression in humans (early life stress, genetic predispositions, adulthood stress).

Methods

Eighteen DBA/2 J and 18 C57BL/6 J females were tested, of which half underwent as pups a daily maternal separation on post-natal days 2-14 (early-life stress "ELS") (other half left undisturbed). To assess the effect of the procedure, the time the dams from which the 18 subjects were born spent active in the nest (proxy for maternal behavior) was recorded on post-natal days 2, 6, 10 and 14 for 1 h before separation and following reunion (matched times for controls), using live instantaneous scan sampling (total: 96 scans/dam). For each ELS condition, about half of the pups were housed post-weaning (i.e., from 27 days old on average) in either barren (triggering IBA and depression-like symptoms) or larger, highly enriched cages (n = 4-5 per group). Time mice spent IBA post-weaning was observed blind to ELS treatment using live instantaneous scan sampling in two daily 90-min blocks, two days/week, for 6 weeks (total: 192 scans/mouse). Data were analyzed in R using generalized linear mixed models.

Results

The dams were significantly more active in the nest over time (p = 0.016), however with no significant difference between strains (p = 0.18), ELS conditions (p = 0.20) and before/after separation (p = 0.83). As predicted, post-weaning barren cages triggered significantly more time spent IBA in mice than enriched cages (p < 0.0001). However, neither ELS (p = 0.4) nor strain (p = 0.84) significantly influenced time mice spent IBA, with no significant interaction with environmental condition (ELS × environment: p = 0.2861; strain × environment: p = 0.5713).

Discussion

Our results therefore only partly support the hypothesis that greater time spent IBA in mice is triggered by risk factors for human depression. We discuss possible explanations for this and further research directions.

Recommendations for measuring and standardizing light for laboratory mammals to improve welfare and reproducibility in animal research

Light enables vision and exerts widespread effects on physiology and behavior, including regulating circadian rhythms, sleep, hormone synthesis, affective state, and cognitive processes. Appropriate lighting in animal facilities may support welfare and ensure that animals enter experiments in an appropriate physiological and behavioral state. Furthermore, proper consideration of light during experimentation is important both when it is explicitly employed as an independent variable and as a general feature of the environment. This Consensus View discusses metrics to use for the quantification of light appropriate for nonhuman mammals and their application to improve animal welfare and the quality of animal research. It provides methods for measuring these metrics, practical guidance for their implementation in husbandry and experimentation, and quantitative guidance on appropriate light exposure for laboratory mammals. The guidance provided has the potential to improve data quality and contribute to reduction and refinement, helping to ensure more ethical animal use.

Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures

BACKGROUND

Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science.

RESULTS

Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice.

CONCLUSIONS

C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.

Systematic heterogenization revisited: Increasing variation in animal experiments to improve reproducibility?

Life sciences are currently facing a reproducibility crisis. Originally, the crisis was born out of single alarming failures to reproduce findings at different times and locations. Nowadays, systematic studies indicate that the prevalence of irreproducible research does in fact exceed 50%. Viewed from a rather cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. In this respect, animal research has come under particular scrutiny, as the stakes are high in terms of both research ethics and societal impact. To counteract this, it is essential to identify sources of poor reproducibility as well as to iron out these failures. We here review the current debate, briefly discuss potential reasons, and summarize steps that have already been undertaken to improve reproducibility in animal research. By the example of classical behavioural phenotyping studies, we particularly highlight the role strict standardization plays in exacerbating the crisis, and review the concept of systematic heterogenization as an alternative strategy to deal with variation in animal studies. Briefly, we argue that systematic variation rather than strict homogenization of experimental conditions benefits the robustness of research findings, and hence their reproducibility. To this end, we will present concrete examples for systematically heterogenized experiments and provide a practical guide on how to apply systematic heterogenization in experimental practice.

Finding the right power balance: Better study design and collaboration can reduce dependence on statistical power

Power analysis currently dominates sample size determination for experiments, particularly in grant and ethics applications. Yet, this focus could paradoxically result in suboptimal study design because publication biases towards studies with the largest effects can lead to the overestimation of effect sizes. In this Essay, we propose a paradigm shift towards better study designs that focus less on statistical power. We also advocate for (pre)registration and obligatory reporting of all results (regardless of statistical significance), better facilitation of team science and multi-institutional collaboration that incorporates heterogenization, and the use of prospective and living meta-analyses to generate generalizable results. Such changes could make science more effective and, potentially, more equitable, helping to cultivate better collaborations.

Using mice from different breeding sites fails to improve replicability of results from single-laboratory studies

Theoretical and empirical evidence indicates that low external validity due to rigorous standardization of study populations is a cause of poor replicability in animal research. Here we report a multi-laboratory study aimed at investigating whether heterogenization of study populations by using animals from different breeding sites increases the replicability of results from single-laboratory studies. We used male C57BL/6J mice from six different breeding sites to test a standardized against a heterogenized (HET) study design in six independent replicate test laboratories. For the standardized design, each laboratory ordered mice from a single breeding site (each laboratory from a different one), while for the HET design, each laboratory ordered proportionate numbers of mice from the five remaining breeding sites. To test our hypothesis, we assessed 14 outcome variables, including body weight, behavioral measures obtained from a single session on an elevated plus maze, and clinical blood parameters. Both breeding site and test laboratory affected variation in outcome variables, but the effect of test laboratory was more pronounced for most outcome variables. Moreover, heterogenization of study populations by breeding site (HET) did not reduce variation in outcome variables between test laboratories, which was most likely due to the fact that breeding site had only little effect on variation in outcome variables, thereby limiting the scope for HET to reduce between-lab variation. We conclude that heterogenization of study populations by breeding site has limited capacity for improving the replicability of results from single-laboratory animal studies.

Tools for photomotor response assay standardization in ecotoxicological studies: Example of exposure to gentamicin in the freshwater planaria Schmidtea mediterranea

Photomotor response assay (PMR) is very useful in an ecotoxicological context because it allows evaluation of behavioral response to potential toxic compounds. However, a lack of procedure standardization makes results comparison difficult between labs and organisms. Here, we aimed to propose five different tools to standardize the PMR procedure so that it may be applied to all model species, regarding: (1) the minimum total sample size, (2) the acclimation period, (3) the number and duration of light and dark phases alternation, (4) the measured behavior, and (5) the statistical analysis. As an example of procedure application, we analyzed the effect of an exposure to the antibiotic gentamicin on the locomotion behavior during PMR in an invertebrate species: the asexual freshwater planaria Schmidtea mediterranea. We encourage future studies using PMR to follow these five tools to improve data analysis and results comparability.

G × E interactions as a basis for toxicological uncertainty

To transfer toxicological findings from model systems, e.g. animals, to humans, standardized safety factors are applied to account for intra-species and inter-species variabilities. An alternative approach would be to measure and model the actual compound-specific uncertainties. This biological concept assumes that all observed toxicities depend not only on the exposure situation (environment = E), but also on the genetic (G) background of the model (G × E). As a quantitative discipline, toxicology needs to move beyond merely qualitative G × E concepts. Research programs are required that determine the major biological variabilities affecting toxicity and categorize their relative weights and contributions. In a complementary approach, detailed case studies need to explore the role of genetic backgrounds in the adverse effects of defined chemicals. In addition, current understanding of the selection and propagation of adverse outcome pathways (AOP) in different biological environments is very limited. To improve understanding, a particular focus is required on modulatory and counter-regulatory steps. For quantitative approaches to address uncertainties, the concept of "genetic" influence needs a more precise definition. What is usually meant by this term in the context of G × E are the protein functions encoded by the genes. Besides the gene sequence, the regulation of the gene expression and function should also be accounted for. The widened concept of past and present "gene expression" influences is summarized here as Ge. Also, the concept of "environment" needs some re-consideration in situations where exposure timing (Et) is pivotal: prolonged or repeated exposure to the insult (chemical, physical, life style) affects Ge. This implies that it changes the model system. The interaction of Ge with Et might be denoted as Ge × Et. We provide here general explanations and specific examples for this concept and show how it could be applied in the context of New Approach Methodologies (NAM).

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.

The Amphibian Short-Term Assay: Evaluation of a New Ecotoxicological Method for Amphibians Using Two Organophosphate Pesticides Commonly Found in Nature-Assessment of Behavioral Traits

Neurotoxic pesticides are used worldwide to protect crops from insects; they are recognized to impact nontarget organisms that live in areas surrounded by treated crops. Many biochemical and cell-based solutions have been developed for testing insecticide neurotoxicity. Nevertheless, such solutions provide a partial assessment of the impact of neurotoxicity, neglecting important phenotypic components such as behavior. Behavior is the apical endpoint altered by neurotoxicity, and scientists are increasingly recommending including behavioral endpoints in available tests or developing new methods for assessing contaminant-induced behavioral changes. In the present study, we extended an existing protocol (the amphibian short-term assay) with a behavioral test. To this purpose, we developed a homemade device along with an open-source computing solution for tracking trajectories of Xenopus laevis tadpoles exposed to two organophosphates insecticides (OPIs), diazinon (DZN) and chlorpyrifos (CPF). The data resulting from the tracking were then analyzed, and the impact of exposure to DZN and CPF was tested on speed- and direction-related components. Our results demonstrate weak impacts of DZN on the behavioral components, while CPF demonstrated strong effects, notably on speed-related components. Our results also suggest a time-dependent alteration of behavior by CPF, with the highest impacts at day 6 and an absence of impact at day 8. Although only two OPIs were tested, we argue that our solution coupled with biochemical biomarkers is promising for testing the neurotoxicity of this pesticide group on amphibians. Environ Toxicol Chem 2023;42:1595-1606. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

The power of effective study design in animal Experimentation: Exploring the statistical and ethical implications of asking multiple questions of a data set

One of the chief advantages of using highly standardised biological models including model organisms is that multiple variables can be precisely controlled so that the variable of interest is more easily studied. However, such an approach often obscures effects in sub-populations resulting from natural population heterogeneity. Efforts to expand our fundamental understanding of multiple sub-populations are in progress. However, such stratified or personalised approaches require fundamental modifications of our usual study designs that should be implemented in Brain, Behavior and Immunity (BBI) research going forward. Here we explore the statistical feasibility of asking multiple questions (including incorporating sex) within the same experimental cohort using statistical simulations of real data. We illustrate and discuss the large explosion in sample numbers necessary to detect effects with appropriate power for every additional question posed using the same data set. This exploration highlights the strong likelihood of type II errors (false negatives) for standard data and type I errors when dealing with complex genomic data, where studies are too under-powered to appropriately test these interactions. We show this power may differ for males and females in high throughput data sets such as RNA sequencing. We offer a rationale for the use of alternative experimental and statistical strategies based on interdisciplinary insights and discuss the real-world implications of increasing the complexities of our experimental designs, and the implications of not attempting to alter our experimental designs going forward.

Advancing social behavioral neuroscience by integrating ethology and comparative psychology methods through machine learning

Social behavior is naturally occurring in vertebrate species, which holds a strong evolutionary component and is crucial for the normal development and survival of individuals throughout life. Behavioral neuroscience has seen different influential methods for social behavioral phenotyping. The ethological research approach has extensively investigated social behavior in natural habitats, while the comparative psychology approach was developed utilizing standardized and univariate social behavioral tests. The development of advanced and precise tracking tools, together with post-tracking analysis packages, has recently enabled a novel behavioral phenotyping method, that includes the strengths of both approaches. The implementation of such methods will be beneficial for fundamental social behavioral research but will also enable an increased understanding of the influences of many different factors that can influence social behavior, such as stress exposure. Furthermore, future research will increase the number of data modalities, such as sensory, physiological, and neuronal activity data, and will thereby significantly enhance our understanding of the biological basis of social behavior and guide intervention strategies for behavioral abnormalities in psychiatric disorders.

Therapeutic Potential of Microbiota Modulation in Alzheimer's Disease: A Review of Preclinical Studies

Alzheimer's disease (AD) is the most common neurodegenerative disease, yet it currently lacks effective treatment due to its complex etiology. The pathological changes in AD have been linked to the neurotoxic immune responses following aggregation of Aβ and phosphorylated tau. The gut microbiota (GM) is increasingly studied for modulating neuroinflammation in neurodegenerative diseases and in vivo studies emerge for AD. This critical review selected 7 empirical preclinical studies from 2019 onwards assessing therapy approaches targeting GM modulating microglia neuroinflammation in AD mouse models. Results from probiotics, fecal microbiota transplantation, and drugs were compared and contrasted, including for cognition, neuroinflammation, and toxic aggregation of proteins. Studies consistently reported significant amelioration or prevention of cognitive deficits, decrease in microglial activation, and lower levels of pro-inflammatory cytokines, compared to AD mouse models. However, there were differences across papers for the brain regions affected, and changes in astrocytes were inconsistent. Aβ plaques deposition significantly decreased in all papers, apart from Byur dMar Nyer lNga Ril Bu (BdNlRB) treatment. Tau phosphorylation significantly declined in 5 studies. Effects in microbial diversity following treatment varied across studies. Findings are encouraging regarding the efficacy of study but information on the effect size is limited. Potentially, GM reverses GM derived abnormalities, decreasing neuroinflammation, which reduces AD toxic aggregations of proteins in the brain, resulting in cognitive improvements. Results support the hypothesis of AD being a multifactorial disease and the potential synergies through multi-target approaches. The use of AD mice models limits conclusions around effectiveness, as human translation is challenging.

EFFECTS OF LITTER SIZE AND CAGING ON PHYSICAL AND MENTAL DEVELOPMENT IN RATS

As a multidisciplinary field, laboratory animal science promotes or accelerates the emergence of innovative ideas and products. As research has increased, so has the demand for laboratory animals with reliable, standardized characteristics. Thus, the breeding, reproduction, and welfare of laboratory animals are now animals reliable and more. The aim of this study to investigate whether different litter sizes of mothers and different husbandry methods affect the physical and mental development of pups. 30 adults female Wistar Hanover albino rats weighing 200-250 g were used for the study. The weight of the pups was measured once a week from birth until the end of the study, and their physical development was observed. After the pups were weaned, they were randomly divided into cages by sex. The 45 male and 45 female pups were housed in groups of three, five, and seven per cage. When the pups were 12 weeks old, open field test, elevated plus-maze test and Morris water maze behavioral tests were performed every other day, and then plasma corticosterone levels were measured. When the male and female pups in the groups were 14 weeks old, six females were taken from each housing group and mated, and the conception rates and maternal behavior of the pups were observed. During lactation, physical developmental parameters and the body weight of the rats were affected by litter size. Among the post-weaning housing groups, cage density was found to affect weight gain and body weight between groups. It was found that only the sex factor caused significant differences in the behavior of the animals. Females housed with seven rats per cage had higher corticosteroid levels than other females. As a result, it was observed that cages with seven female rats were more physically and psychologically affected than those with three and five rats.

Loss of individualized behavioral trajectories in adult neurogenesis-deficient cyclin D2 knockout mice

There is still limited mechanistic insight into how the interaction of individuals with their environment results in the emergence of individuality in behavior and brain structure. Nevertheless, the idea that personal activity shapes the brain is implicit in strategies for healthy cognitive aging as well as in the idea that individuality is reflected in the brain's connectome. We have shown that even isogenic mice kept in a shared enriched environment (ENR) developed divergent and stable social and exploratory trajectories. As these trajectories-measured as roaming entropy (RE)-positively correlated with adult hippocampal neurogenesis, we hypothesized that a feedback between behavioral activity and adult hippocampal neurogenesis might be a causal factor in brain individualization. We used cyclin D2 knockout mice with constitutively extremely low levels of adult hippocampal neurogenesis and their wild-type littermates. We housed them for 3 months in a novel ENR paradigm, consisting of 70 connected cages equipped with radio frequency identification antennae for longitudinal tracking. Cognitive performance was evaluated in the Morris Water Maze task (MWM). With immunohistochemistry we confirmed that adult neurogenesis correlated with RE in both genotypes and that D2 knockout mice had the expected impaired performance in the reversal phase of the MWM. But whereas the wild-type animals developed stable exploratory trajectories with increasing variance, correlating with adult neurogenesis, this individualizing phenotype was absent in D2 knockout mice. Here the behaviors started out more random and revealed less habituation and low variance. Together, these findings suggest that adult neurogenesis contributes to experience-dependent brain individualization.

A paradigm shift in translational psychiatry through rodent neuroethology

Mental disorders are a significant cause of disability worldwide. They profoundly affect individuals' well-being and impose a substantial financial burden on societies and governments. However, despite decades of extensive research, the effectiveness of current therapeutics for mental disorders is often not satisfactory or well tolerated by the patient. Moreover, most novel therapeutic candidates fail in clinical testing during the most expensive phases (II and III), which results in the withdrawal of pharma companies from investing in the field. It also brings into question the effectiveness of using animal models in preclinical studies to discover new therapeutic agents and predict their potential for treating mental illnesses in humans. Here, we focus on rodents as animal models and propose that they are essential for preclinical investigations of candidate therapeutic agents' mechanisms of action and for testing their safety and efficiency. Nevertheless, we argue that there is a need for a paradigm shift in the methodologies used to measure animal behavior in laboratory settings. Specifically, behavioral readouts obtained from short, highly controlled tests in impoverished environments and social contexts as proxies for complex human behavioral disorders might be of limited face validity. Conversely, animal models that are monitored in more naturalistic environments over long periods display complex and ethologically relevant behaviors that reflect evolutionarily conserved endophenotypes of translational value. We present how semi-natural setups in which groups of mice are individually tagged, and video recorded continuously can be attainable and affordable. Moreover, novel open-source machine-learning techniques for pose estimation enable continuous and automatic tracking of individual body parts in groups of rodents over long periods. The trajectories of each individual animal can further be subjected to supervised machine learning algorithms for automatic detection of specific behaviors (e.g., chasing, biting, or fleeing) or unsupervised automatic detection of behavioral motifs (e.g., stereotypical movements that might be harder to name or label manually). Compared to studies of animals in the wild, semi-natural environments are more compatible with neural and genetic manipulation techniques. As such, they can be used to study the neurobiological mechanisms underlying naturalistic behavior. Hence, we suggest that such a paradigm possesses the best out of classical ethology and the reductive behaviorist approach and may provide a breakthrough in discovering new efficient therapies for mental illnesses.

Advanced methods and implementations for the meta-analyses of animal models: Current practices and future recommendations

Meta-analytic techniques have been widely used to synthesize data from animal models of human diseases and conditions, but these analyses often face two statistical challenges due to complex nature of animal data (e.g., multiple effect sizes and multiple species): statistical dependency and confounding heterogeneity. These challenges can lead to unreliable and less informative evidence, which hinders the translation of findings from animal to human studies. We present a literature survey of meta-analysis using animal models (animal meta-analysis), showing that these issues are not adequately addressed in current practice. To address these challenges, we propose a meta-analytic framework based on multilevel (linear mixed-effects) models. Through conceptualization, formulations, and worked examples, we illustrate how this framework can appropriately address these issues while allowing for testing new questions. Additionally, we introduce other advanced techniques such as multivariate models, robust variance estimation, and meta-analysis of emergent effect sizes, which can deliver robust inferences and novel biological insights. We also provide a tutorial with annotated R code to demonstrate the implementation of these techniques.

Demonstrating a measurement protocol for studying comparative whisker movements with implications for the evolution of behaviour

BACKGROUND

Studying natural, complex behaviours over a range of different species provides insights into the evolution of the brain and behaviour. Whisker movements reveal complex behaviours; however, there does not yet exist a protocol that is able to capture whisker movements and behaviours in a range of different species.

NEW METHOD

We develop a new protocol and make recommendations for measuring comparative whisker movements and behaviours. Using two set-ups - an enclosure camera set-up and a high-speed video set-up - we capture and measure the whisker movements of sixteen different captive mammal species from four different animal collections.

RESULTS

We demonstrate the ability to describe whisker movements and behaviours across a wide range of mammalian species. We describe whisker movements in European hedgehog, Cape porcupine, domestic rabbit, domestic ferret, weasel, European otter and red fox for the first time. We observe whisker movements in all the species we tested, although movement, positions and behaviours vary in a species-specific way.

COMPARISON WITH EXISTING METHOD(S)

The high-speed video set-up is based on the protocols of previous studies. The addition of an enclosure video set-up is entirely new, and allows us to include more species, especially large and shy species that cannot be moved into a high-speed filming arena.

CONCLUSIONS

We make recommendations for comparative whisker behaviour studies, particularly incorporating individual and species-specific considerations. We believe that flexible, comparative behavioural protocols have wide-ranging applications, specifically to better understand links between the brain and complex behaviours.

Recommendations to improve use and reporting of statistics in animal experiments

Flaws in experimental statistics are a major contributor to the poor reproducibility of animal experiments. Informed decisions about whether conclusions are justified requires clear reporting of experimental data and the statistical methods used to analyse them. When data are misinterpreted, manipulated or concealed to generate publications, it creates an illusion that chance observations are robust data which confirm the hypotheses presented. Attempts to reproduce and advance such observations can propagate large areas of irreproducible science. This hinders scientific progress, erodes public support for research, damages reputations and wastes resources. This review analyses and explains recommendations to improve use and reporting of statistics in animal experiments.

Systematic assessment of the replicability and generalizability of preclinical findings: Impact of protocol harmonization across laboratory sites

The influence of protocol standardization between laboratories on their replicability of preclinical results has not been addressed in a systematic way. While standardization is considered good research practice as a means to control for undesired external noise (i.e., highly variable results), some reports suggest that standardized protocols may lead to idiosyncratic results, thus undermining replicability. Through the EQIPD consortium, a multi-lab collaboration between academic and industry partners, we aimed to elucidate parameters that impact the replicability of preclinical animal studies. To this end, 3 experimental protocols were implemented across 7 laboratories. The replicability of results was determined using the distance travelled in an open field after administration of pharmacological compounds known to modulate locomotor activity (MK-801, diazepam, and clozapine) in C57BL/6 mice as a worked example. The goal was to determine whether harmonization of study protocols across laboratories improves the replicability of the results and whether replicability can be further improved by systematic variation (heterogenization) of 2 environmental factors (time of testing and light intensity during testing) within laboratories. Protocols were tested in 3 consecutive stages and differed in the extent of harmonization across laboratories and standardization within laboratories: stage 1, minimally aligned across sites (local protocol); stage 2, fully aligned across sites (harmonized protocol) with and without systematic variation (standardized and heterogenized cohort); and stage 3, fully aligned across sites (standardized protocol) with a different compound. All protocols resulted in consistent treatment effects across laboratories, which were also replicated within laboratories across the different stages. Harmonization of protocols across laboratories reduced between-lab variability substantially compared to each lab using their local protocol. In contrast, the environmental factors chosen to introduce systematic variation within laboratories did not affect the behavioral outcome. Therefore, heterogenization did not reduce between-lab variability further compared to the harmonization of the standardized protocol. Altogether, these findings demonstrate that subtle variations between lab-specific study protocols may introduce variation across independent replicate studies even after protocol harmonization and that systematic heterogenization of environmental factors may not be sufficient to account for such between-lab variation. Differences in replicability of results within and between laboratories highlight the ubiquity of study-specific variation due to between-lab variability, the importance of transparent and fine-grained reporting of methodologies and research protocols, and the importance of independent study replication.

The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level

The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between animal facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multicentre study, whereby inbred C57BL/6J mice from a single breeding cohort were allocated to and reared in 5 different animal facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of the rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that environmental variation among animal facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organisation. We detected changes in chromatin organisation in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity, and regulation of behaviour. Our findings demonstrate that common environmental differences between animal facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and thus argue that study designs should take environmental background into account to increase the robustness and replicability of findings.

The phenotype of an organism results not only from its genotype but also the influence of its environment throughout development. This study shows that common environmental differences between animal facilities can induce substantial variation in the phenotype of mice, thereby highlighting an important limitation of inferences from single-laboratory studies in animal research.

Behavior is movement only but how to interpret it? Problems and pitfalls in translational neuroscience-a 40-year experience

Translational research in behavioral neuroscience seeks causes and remedies for human mental health problems in animals, following leads imposed by clinical research in psychiatry. This endeavor faces several problems because scientists must read and interpret animal movements to represent human perceptions, mood, and memory processes. Yet, it is still not known how mammalian brains bundle all these processes into a highly compressed motor output in the brain stem and spinal cord, but without that knowledge, translational research remains aimless. Based on some four decades of experience in the field, the article identifies sources of interpretation problems and illustrates typical translational pitfalls. (1) The sensory world of mice is different. Smell, hearing, and tactile whisker sensations dominate in rodents, while visual input is comparatively small. In humans, the relations are reversed. (2) Mouse and human brains are equated inappropriately: the association cortex makes up a large portion of the human neocortex, while it is relatively small in rodents. The predominant associative cortex in rodents is the hippocampus itself, orchestrating chiefly inputs from secondary sensorimotor areas and generating species-typical motor patterns that are not easily reconciled with putative human hippocampal functions. (3) Translational interpretation of studies of memory or emotionality often neglects the ecology of mice, an extremely small species surviving by freezing or flight reactions that do not need much cognitive processing. (4) Further misinterpretations arise from confounding neuronal properties with system properties, and from rigid mechanistic thinking unaware that many experimentally induced changes in the brain do partially reflect unpredictable compensatory plasticity. (5) Based on observing hippocampal lesion effects in mice indoors and outdoors, the article offers a simplistic general model of hippocampal functions in relation to hypothalamic input and output, placing hypothalamus and the supraspinal motor system at the top of a cerebral hierarchy. (6) Many translational problems could be avoided by inclusion of simple species-typical behaviors as end-points comparable to human cognitive or executive processing, and to rely more on artificial intelligence for recognizing patterns not classifiable by traditional psychological concepts.

Effects of personality on assessments of anxiety and cognition

Individual variation in responses to commonly used tests of anxiety and spatial memory is often reported. While this variation is frequently considered to be 'noise', evidence suggests that it is, at least partially, related to consistent individual differences in behavioral responses (i.e., personality). The same tests used to assess anxiety are often used to profile personality traits, but personality differences are rarely considered when testing treatment differences in anxiety. Focusing on the rat literature, we describe fundamental principles involved in anxiety and spatial memory tests and we discuss how personality differences and housing conditions can influence behavioral responses in these tests. We propose that an opportunity exists to increase stress resiliency in environmentally sensitive individuals by providing environmental enrichment. We conclude by discussing different approaches to incorporating personality measures into the design and analysis of future studies; given the potential that variation masks research outcomes, we suggest that a strategy which considers the individual and its housing can contribute to improving research reproducibility.

Controlling the uncontrolled variation in the diet induced obese mouse by microbiomic characterization

Group sizes in an animal study are calculated from estimates on variation, effect, power and significance level. Much of the variation in glucose related parameters of the diet-induced obese (DIO) mouse model is due to inter-individual variation in gut microbiota composition. In addition, standard tandem repeats (STRs) in the non-coding DNA shows that inbred mice are not always homogenic. C57BL/6NTac (B6NTac) mice from Taconic and C57BL/6NRj (B6NRj) mice from Janvier Labs were fed a high calorie diet and treated with liraglutide. The fecal microbiota was sequenced before high-calorie feeding (time 1) and after diet-induced obesity instantly before liraglutide treatment (time 2) and mice were divided into clusters on the basis of their microbiota. Although liraglutide in both sub-strains alleviated glucose intolerance and reduced body weight, in a one-way ANOVA a borderline reduction in glycosylated hemoglobin (HbA1c) could only be shown in B6NTac mice. However, if the microbiota clusters from time 1 or time 2 were incorporated in a two-way ANOVA, the HbA1c effect was significant in B6NTac mice in both analyses, while this did not change anything in B6NRj mice. In a one-way ANOVA the estimated group size needed for a significant HbA1c effect in B6NTac mice was 42, but in two-way ANOVAs based upon microbiota clusters of time 1 or time 2 it was reduced to 21 or 12, respectively. The lowering impact on glucose tolerance was also powered by incorporation of microbiota clusters of both times in both sub-strains. B6NRj had up to six, while B6NTac had maximum three alleles in some of their STRs. In B6NRj mice in 28.8% of the STRs the most prevalent allele had a gene frequency less than 90%, while this was only 6.6% in the B6NTac mice. However, incorporation of the STRs with the highest number of alleles or the most even distribution of frequencies in two-way ANOVAs only had little impact on the outcome of data evaluation. It is concluded that the inclusion of microbiota clusters in a two-way ANOVA in the evaluation of the glucose related effects of an intervention in the DIO mouse model might be an efficient tool for increasing power and reducing group sizes in mouse sub-strains, if these have a microbiota, which influences these parameters.

Mice in translational neuroscience: What R we doing?

Animal models play a pivotal role in translational neuroscience but recurrent problems in data collection, analyses, and interpretation, lack of biomarkers, and a tendency to over-reliance on mice have marred neuroscience progress, leading to one of the highest attrition rates in drug translation. Global initiatives to improve reproducibility and model selection are being implemented. Notwithstanding, mice are still the preferred animal species to model human brain disorders even when the translation has been shown to be limited. Non-human primates are better positioned to provide relevant translational information because of their higher brain complexity and homology to humans. Among others, lack of resources and formal training, strict legislation, and ethical issues may impede broad access to large animals. We propose that instead of increasingly restrictive legislation, more resources for training, education, husbandry, and data sharing are urgently needed. The creation of multidisciplinary teams, in which veterinarians need to play a key role, would be critical to improve translational efficiency. Furthermore, it is not usually acknowledged by researchers and regulators the value of comparative studies in lower species, that are instrumental in toxicology, target identification, and mechanistic studies. Overall, we highlight here the need for a conceptual shift in neuroscience research and policies to reach the patients.

Assessing and visualizing fragility of clinical results with binary outcomes in R using the fragility package

With the growing concerns about research reproducibility and replicability, the assessment of scientific results' fragility (or robustness) has been of increasing interest. The fragility index was proposed to quantify the robustness of statistical significance of clinical studies with binary outcomes. It is defined as the minimal event status modifications that can alter statistical significance. It helps clinicians evaluate the reliability of the conclusions. Many factors may affect the fragility index, including the treatment groups in which event status is modified, the statistical methods used for testing for the association between treatments and outcomes, and the pre-specified significance level. In addition to assessing the fragility of individual studies, the fragility index was recently extended to both conventional pairwise meta-analyses and network meta-analyses of multiple treatment comparisons. It is not straightforward for clinicians to calculate these measures and visualize the results. We have developed an R package called "fragility" to offer user-friendly functions for such purposes. This article provides an overview of methods for assessing and visualizing the fragility of individual studies as well as pairwise and network meta-analyses, introduces the usage of the "fragility" package, and illustrates the implementations with several worked examples.

Cross-species discrimination of vocal expression of emotional valence by Equidae and Suidae

BACKGROUND

Discrimination and perception of emotion expression regulate interactions between conspecifics and can lead to emotional contagion (state matching between producer and receiver) or to more complex forms of empathy (e.g., sympathetic concern). Empathy processes are enhanced by familiarity and physical similarity between partners. Since heterospecifics can also be familiar with each other to some extent, discrimination/perception of emotions and, as a result, emotional contagion could also occur between species.

RESULTS

Here, we investigated if four species belonging to two ungulate Families, Equidae (domestic and Przewalski's horses) and Suidae (pigs and wild boars), can discriminate between vocalizations of opposite emotional valence (positive or negative), produced not only by conspecifics, but also closely related heterospecifics and humans. To this aim, we played back to individuals of these four species, which were all habituated to humans, vocalizations from a unique set of recordings for which the valence associated with vocal production was known. We found that domestic and Przewalski's horses, as well as pigs, but not wild boars, reacted more strongly when the first vocalization played was negative compared to positive, regardless of the species broadcasted.

CONCLUSIONS

Domestic horses, Przewalski's horses and pigs thus seem to discriminate between positive and negative vocalizations produced not only by conspecifics, but also by heterospecifics, including humans. In addition, we found an absence of difference between the strength of reaction of the four species to the calls of conspecifics and closely related heterospecifics, which could be related to similarities in the general structure of their vocalization. Overall, our results suggest that phylogeny and domestication have played a role in cross-species discrimination/perception of emotions.

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.

Quantification of fetal organ sparing in maternal low-protein dietary models

Background: Maternal malnutrition can lead to fetal growth restriction. This is often associated with organ sparing and long-lasting physiological dysfunctions during adulthood, although the underlying mechanisms are not yet well understood. Methods: Low protein (LP) dietary models in C57BL/6J mice were used to investigate the proximal effects of maternal malnutrition on fetal organ weights and organ sparing at embryonic day 18.5 (E18.5). Results:  Maternal 8% LP diet induced strikingly different degrees of fetal growth restriction in different animal facilities, but adjustment of dietary protein content allowed similar fetal body masses to be obtained. A maternal LP diet that restricted fetal body mass by 40% did not decrease fetal brain mass to the same extent, reflecting positive growth sparing of this organ. Under these conditions, fetal pancreas and liver mass decreased by 60-70%, indicative of negative organ sparing. A series of dietary swaps between LP and standard diets showed that the liver is capable of efficient catch-up growth from as late as E14.5 whereas, after E10.5, the pancreas is not. Conclusions: This study highlights that the reproducibility of LP fetal growth restriction studies between laboratories can be improved by careful calibration of maternal dietary protein content. LP diets that induce 30-40% restriction of prenatal growth provide a good model for fetal organ sparing. For the liver, recovery of growth following protein restriction is efficient throughout fetal development but, for the pancreas, transient LP exposures spanning the progenitor expansion phase lead to an irreversible fetal growth deficit.

Accounting for Precision Uncertainty of Toxicity Testing: Methods to Define Borderline Ranges and Implications for Hazard Assessment of Chemicals

For hazard classifications of chemicals, continuous data from animal- or nonanimal testing methods are often dichotomized into binary positive/negative outcomes by defining classification thresholds (CT). Experimental data are, however, subject to biological and technical variability. Each test method's precision is limited resulting in uncertainty of the positive/negative outcome if the experimental result is close to the CT. Borderline ranges (BR) around the CT were suggested, which represent ranges in which the study result is ambiguous, that is, positive or negative results are equally likely. The BR reflects a method's precision uncertainty. This article explores and compares different approaches to quantify the BR. Besides using the pooled standard deviation, we determine the BR by means of the median absolute deviation (MAD), with a sequential combination of both methods, and by using nonparametric bootstrapping. Furthermore, we quantify the BR for different hazardous effects, including nonanimal tests for skin corrosion, eye irritation, skin irritation, and skin sensitization as well as for an animal test on skin sensitization (the local lymph node assay, LLNA). Additionally, for one method (direct peptide reactivity assay) the BR was determined experimentally and compared to calculated BRs. Our results demonstrate that (i) the precision of the methods is determining the size of their BRs, (ii) there is no "perfect" method to derive a BR, alas, (iii) a consensus on BR is needed to account for the limited precision of testing methods.

In-Depth Characterization of Somatic and Orofacial Sensitive Dysfunctions and Interfering-Symptoms in a Relapsing-Remitting Experimental Autoimmune Encephalomyelitis Mouse Model

Among the many symptoms (motor, sensory, and cognitive) associated with multiple sclerosis (MS), chronic pain is a common disabling condition. In particular, neuropathic pain symptoms are very prevalent and debilitating, even in early stages of the disease. Unfortunately, chronic pain still lacks efficient therapeutic agents. Progress is needed (i) clinically by better characterizing pain symptoms in MS and understanding the underlying mechanisms, and (ii) preclinically by developing a more closely dedicated model to identify new therapeutic targets and evaluate new drugs. In this setting, new variants of experimental autoimmune encephalomyelitis (EAE) are currently developed in mice to exhibit less severe motor impairments, thereby avoiding confounding factors in assessing pain behaviors over the disease course. Among these, the optimized relapsing-remitting EAE (QuilA-EAE) mouse model, induced using myelin oligodendrocyte glycoprotein peptide fragment (35–55), pertussis toxin, and quillaja bark saponin, seems very promising. Our study sought (i) to better define sensitive dysfunctions and (ii) to extend behavioral characterization to interfering symptoms often associated with pain during MS, such as mood disturbances, fatigue, and cognitive impairment, in this optimized QuilA-EAE model. We made an in-depth characterization of this optimized QuilA-EAE model, describing for the first time somatic thermal hyperalgesia associated with mechanical and cold allodynia. Evaluation of orofacial pain sensitivity showed no mechanical or thermal allodynia. Detailed evaluation of motor behaviors highlighted slight defects in fine motor coordination in the QuilA-EAE mice but without impact on pain evaluation. Finally, no anxiety-related or cognitive impairment was observed during the peak of sensitive symptoms. Pharmacologically, as previously described, we found that pregabalin, a treatment commonly used in neuropathic pain patients, induced an analgesic effect on mechanical allodynia. In addition, we showed an anti-hyperalgesic thermal effect on this model. Our results demonstrate that this QuilA-EAE model is clearly of interest for studying pain symptom development and so could be used to identify and evaluate new therapeutic targets. The presence of interfering symptoms still needs to be further characterized.

Translational science: a survey of US biomedical researchers' perspectives and practices

This national survey aimed to identify how biomedical researchers using vertebrate animals viewed issues of significance for translational science, including oversight and public engagement, and to analyze how researcher characteristics and animal model choice correlate with those views. Responses from 1,187 researchers showed awareness of, and concerns about, problems of translation, reproducibility and rigor. Surveyed scientists were nevertheless optimistic about the value of animal studies, were favorable about research oversight and reported openness with non-scientists in discussing their animal work. Differences in survey responses among researchers also point to diverse perspectives within the animal research community on these matters. Most significant was variability associated with the primary type of animal that surveyed scientists used in their work. Other significant divergence in opinion appeared on the basis of professional role factors, including the type of degree held, workplace setting, type of funding, experience on an institutional animal care and use committee and personal demographic characteristics of age and gender.

Social Factors Influence Behavior in the Novel Object Recognition Task in a Mouse Model of Down Syndrome

The use of mouse models has revolutionized the field of Down syndrome (DS), increasing our knowledge about neuropathology and helping to propose new therapies for cognitive impairment. However, concerns about the reproducibility of results in mice and their translatability to humans have become a major issue, and controlling for moderators of behavior is essential. Social and environmental factors, the experience of the researcher, and the sex and strain of the animals can all have effects on behavior, and their impact on DS mouse models has not been explored. Here we analyzed the influence of a number of social and environmental factors, usually not taken into consideration, on the behavior of male and female wild-type and trisomic mice (the Ts65Dn model) in one of the most used tests for proving drug effects on memory, the novel object recognition (NOR) test. Using principal component analysis and correlation matrices, we show that the ratio of trisomic mice in the cage, the experience of the experimenter, and the timing of the test have a differential impact on male and female and on wild-type and trisomic behavior. We conclude that although the NOR test is quite robust and less susceptible to environmental influences than expected, to obtain useful results, the phenotype expression must be contrasted against the influences of social and environmental factors.

A Good Life for Laboratory Rodents?

Most would agree that animals in research should be spared "unnecessary" harm, pain, or distress, and there is also growing interest in providing animals with some form of environmental enrichment. But is this the standard of care that we should aspire to? We argue that we need to work towards a higher standard-specifically, that providing research animals with a "good life" should be a prerequisite for their use. The aims of this paper are to illustrate our vision of a "good life" for laboratory rats and mice and to provide a roadmap for achieving this vision. We recognize that several research procedures are clearly incompatible with a good life but describe here what we consider to be the minimum day-to-day living conditions to be met when using rodents in research. A good life requires that animals can express a rich behavioral repertoire, use their abilities, and fulfill their potential through active engagement with their environment. In the first section, we describe how animals could be housed for these requirements to be fulfilled, from simple modifications to standard housing through to better cage designs and free-ranging options. In the second section, we review the types of interactions with laboratory rodents that are compatible with a good life. In the third section, we address the potential for the animals to have a life outside of research, including the use of pets in clinical trials (the animal-as-patient model) and the adoption of research animals to new homes when they are no longer needed in research. We conclude with a few suggestions for achieving our vision.

Quantification of fetal organ sparing in maternal low-protein dietary models

Background: Maternal malnutrition can lead to fetal growth restriction. This is often associated with organ sparing and long-lasting physiological dysfunctions during adulthood, although the underlying mechanisms are not yet well understood. Methods: Low protein (LP) dietary models in C57BL/6J mice were used to investigate the proximal effects of maternal malnutrition on fetal organ weights and organ sparing at embryonic day 18.5 (E18.5). Results:  Maternal 8% LP diet induced strikingly different degrees of fetal growth restriction in different animal facilities, but adjustment of dietary protein content allowed similar fetal body masses to be obtained. A maternal LP diet that restricted fetal body mass by 40% did not decrease fetal brain mass to the same extent, reflecting positive growth sparing of this organ. Under these conditions, fetal pancreas and liver mass decreased by 60-70%, indicative of negative organ sparing. A series of dietary swaps between LP and standard diets showed that the liver is capable of efficient catch-up growth from as late as E14.5 whereas, after E10.5, the pancreas is not. Conclusions: This study highlights that the reproducibility of LP fetal growth restriction studies between laboratories can be improved by careful calibration of maternal dietary protein content. LP diets that induce 30-40% restriction of prenatal growth provide a good model for fetal organ sparing. For the liver, recovery of growth following protein restriction is efficient throughout fetal development but, for the pancreas, transient LP exposures spanning the progenitor expansion phase lead to an irreversible fetal growth deficit.

Let's get wild: A review of free-ranging rat assays as context-enriched supplements to traditional laboratory models

More than 24,000 rodent studies are published annually, with the vast majority of these studies focused on genetically undiverse animals in highly-controlled laboratory settings. However, findings from the laboratory have become increasingly unreliable for predicting outcomes in field and clinical settings, leading to a perceived crisis in translational research. One cause of this disparity might be that most human societies, in contrast to laboratory rodents, are genetically diverse and live in super-enriched environments. Methods for importing wild rats into the laboratory, and also exporting laboratory-style chambers into natural environments are not well-known outside their respective disciplines. Therefore, we have reviewed the current status of supplements to the laboratory rodent assay. We progress logically from highly-controlled experiments with natural breeding colonies to purely naturalistic approaches with free-ranging rats. We then highlight a number of approaches that allow genetically-diverse wild rats to be utilized in context-enriched paradigms. While considering the benefits and shortcomings of each available approach, we detail protocols for random sampling, remote-sensing, and deployment of laboratory chambers in the field. As supplements to standardized laboratory trials, some of these assays could offer key insights to help unify outcomes between laboratory and field studies. However, we note several outstanding questions that must be addressed such as: the trade-off between control and context, possible reductions in sample size, ramifications for the 'standardization fallacy', and ethical dilemmas of working with wild animals. Given these challenges, further innovation will be required before supplemental assays can be made broadly-accessible and thus, transferrable across disciplines.

Mapping the discursive dimensions of the reproducibility crisis: A mixed methods analysis

To those involved in discussions about rigor, reproducibility, and replication in science, conversation about the "reproducibility crisis" appear ill-structured. Seemingly very different issues concerning the purity of reagents, accessibility of computational code, or misaligned incentives in academic research writ large are all collected up under this label. Prior work has attempted to address this problem by creating analytical definitions of reproducibility. We take a novel empirical, mixed methods approach to understanding variation in reproducibility discussions, using a combination of grounded theory and correspondence analysis to examine how a variety of authors narrate the story of the reproducibility crisis. Contrary to expectations, this analysis demonstrates that there is a clear thematic core to reproducibility discussions, centered on the incentive structure of science, the transparency of methods and data, and the need to reform academic publishing. However, we also identify three clusters of discussion that are distinct from the main body of articles: one focused on reagents, another on statistical methods, and a final cluster focused on the heterogeneity of the natural world. Although there are discursive differences between scientific and popular articles, we find no strong differences in how scientists and journalists write about the reproducibility crisis. Our findings demonstrate the value of using qualitative methods to identify the bounds and features of reproducibility discourse, and identify distinct vocabularies and constituencies that reformers should engage with to promote change.

Autism-associated biomarkers: test-retest reliability and relationship to quantitative social trait variation in rhesus monkeys

Background

Rhesus monkeys (Macaca mulatta) exhibit pronounced individual differences in social traits as measured by the macaque Social Responsiveness Scale-Revised. The macaque Social Responsiveness Scale was previously adapted from the Social Responsiveness Scale, an instrument designed to assess social and autistic trait variation in humans. To better understand potential biological underpinnings of this behavioral variation, we evaluated the trait-like consistency of several biological measures previously implicated in autism (e.g., arginine vasopressin, oxytocin, and their receptors, as well as ERK1/2, PTEN, and AKT(1–3) from the RAS-MAPK and PI3K-AKT pathways). We also tested which biological measures predicted macaque Social Responsiveness Scale-Revised scores.

Methods

Cerebrospinal fluid and blood samples were collected from N = 76 male monkeys, which, as a sample, showed a continuous distribution on the macaque Social Responsiveness Scale-Revised. In a subset of these subjects (n = 43), samples were collected thrice over a 10-month period. The following statistical tests were used: “Case 2A” intra-class correlation coefficients of consistency, principal component analysis, and general linear modeling.

Results

All biological measures (except AKT) showed significant test–retest reliability within individuals across time points. We next performed principal component analysis on data from monkeys with complete biological measurement sets at the first time point (n = 57), to explore potential correlations between the reliable biological measures and their relationship to macaque Social Responsiveness Scale-Revised score; a three-component solution was found. Follow-up analyses revealed that cerebrospinal fluid arginine vasopressin concentration, but no other biological measure, robustly predicted individual differences in macaque Social Responsiveness Scale-Revised scores, such that monkeys with the lowest cerebrospinal fluid arginine vasopressin concentration exhibited the greatest social impairment. Finally, we confirmed that this result held in the larger study sample (in which cerebrospinal fluid arginine vasopressin values were available from n = 75 of the subjects).

Conclusions

These findings indicate that cerebrospinal fluid arginine vasopressin concentration is a stable trait-like measure and that it is linked to quantitative social trait variation in male rhesus monkeys.

Supplementary information

The online version contains supplementary material available at 10.1186/s13229-021-00442-w.

Functional biology in its natural context: A search for emergent simplicity

The immeasurable complexity at every level of biological organization creates a daunting task for understanding biological function. Here, we highlight the risks of stripping it away at the outset and discuss a possible path toward arriving at emergent simplicity of understanding while still embracing the ever-changing complexity of biotic interactions that we see in nature.

The Pen Is Milder Than the Blade: Identification Marking Mice Using Ink on the Tail Appears More Humane Than Ear-Punching Even with Local Anaesthetic

Simple Summary

Laboratory mice often look identical, so they are commonly marked by cutting the ear via ear-punching, or marking the tail with permanent marker. Ear-punching is permanent but could be painful, and mice could become stressed by weekly tail-marking, so we compared impacts on mice over 5 weeks. We also explored whether local anaesthetic cream could reduce any ear-punching effects. We found that ear-punching, even with anaesthetic, caused mice to be sniffed and groomed by their cagemates for at least 5 min after marking. Mice ear-punched with anaesthetic also groomed themselves and their ears ~5 times more than tail-marked and control mice. Facial grimacing was most common in the unmarked cagemates of tail-marked mice, and possibly in mice ear-punched with anaesthetic. The next day, mice ear-punched with anaesthetic were significantly less likely to eat unfamiliar food in an anxiety test than tail-marked or control mice. Over 5 weeks, ear-punched mice approached the handler significantly less than unmarked mice did, and tail-marked mice showed reduced defecation during re-marking. Other behaviour, bodyweight, and corticosterone showed no treatment effects. This suggests ear-punching caused some signs of pain and anxiety, and anaesthetic did not help. Tail-marking appeared more humane, showing no differences from the controls.

Abstract

Identification marking mice commonly involves ear-punching with or without anaesthetic, or tail-marking with ink. To identify which is most humane, we marked weanling male BALB/c mice using ear-punching (EP), ear-punching with anaesthetic EMLA^TM cream (EP+A), or permanent marker pen (MP). We compared marked mice, unmarked cagemates, and control mice (n = 12–13/group) for 5 weeks, reapplying MP weekly. Treatment-blind observations following marking showed that EP and EP+A mice were allogroomed (p < 0.001) and sniffed (p < 0.001) by their cagemates more than MP and control mice were. EP+A mice groomed themselves (p < 0.001) and their ears (p < 0.001) ~5 times more than most other mice; their cagemates also increased self-grooming (p < 0.001). Unmarked MP cagemates (p = 0.001), and possibly EP+A mice (p = 0.034; a nonsignificant trend), grimaced the most. The following day, half the EP+A mice showed hyponeophagia versus no MP and control mice (p = 0.001). Over the 5 weeks, EP mice approached the handler significantly less than unmarked cagemates did (p < 0.001). Across weeks, defecation during marking of MP mice decreased (p < 0.001). Treatment showed no effects on immediate responses during marking, aggression, bodyweight, plus-maze behaviour or corticosterone. MP mice showed no differences from controls, whilst EP and EP+A mice showed altered behaviour, so ink-marking may be the more humane identification method.

Internal consistency and compatibility of the 3Rs and 3Vs principles for project evaluation of animal research

Using animals for research raises ethical concerns that are addressed in project evaluation by weighing expected harm to animals against expected benefit to society. A harm-benefit analysis (HBA) relies on two preconditions: (a) the study protocol is scientifically suitable and (b) the use of (sentient) animals and harm imposed on them are necessary for achieving the study's aims. The 3Rs (Replace, Reduce and Refine) provide a guiding principle for evaluating whether the use of animals, their number and the harm imposed on them are necessary. A similar guiding principle for evaluating whether a study protocol is scientifically suitable has recently been proposed: the 3Vs principle referring to the three main aspects of scientific validity in animal research (construct, internal and external validity). Here, we analyse the internal consistency and compatibility of these two principles, address conflicts within and between the 3Rs and 3Vs principles and discuss their implications for project evaluation. We show that a few conflicts and trade-offs exist, but that these can be resolved either by appropriate study designs or by ethical deliberation in the HBA. In combination, the 3Vs, 3Rs and the HBA thus offer a coherent framework for a logically structured evaluation procedure to decide about the legitimacy of animal research projects.

Translational Block in Stroke: A Constructive and "Out-of-the-Box" Reappraisal

Why can we still not translate preclinical research to clinical treatments for acute strokes? Despite > 1000 successful preclinical studies, drugs, and concepts for acute stroke, only two have reached clinical translation. This is the translational block. Yet, we continue to routinely model strokes using almost the same concepts we have used for over 30 years. Methodological improvements and criteria from the last decade have shed some light but have not solved the problem. In this conceptual analysis, we review the current status and reappraise it by thinking "out-of-the-box" and over the edges. As such, we query why other scientific fields have also faced the same translational failures, to find common denominators. In parallel, we query how migraine, multiple sclerosis, and hypothermia in hypoxic encephalopathy have achieved significant translation successes. Should we view ischemic stroke as a "chronic, relapsing, vascular" disease, then secondary prevention strategies are also a successful translation. Finally, based on the lessons learned, we propose how stroke should be modeled, and how preclinical and clinical scientists, editors, grant reviewers, and industry should reconsider their routine way of conducting research. Translational success for stroke treatments may eventually require a bold change with solutions that are outside of the box.

Meta-analysis of variation suggests that embracing variability improves both replicability and generalizability in preclinical research

The replicability of research results has been a cause of increasing concern to the scientific community. The long-held belief that experimental standardization begets replicability has also been recently challenged, with the observation that the reduction of variability within studies can lead to idiosyncratic, lab-specific results that cannot be replicated. An alternative approach is to, instead, deliberately introduce heterogeneity, known as "heterogenization" of experimental design. Here, we explore a novel perspective in the heterogenization program in a meta-analysis of variability in observed phenotypic outcomes in both control and experimental animal models of ischemic stroke. First, by quantifying interindividual variability across control groups, we illustrate that the amount of heterogeneity in disease state (infarct volume) differs according to methodological approach, for example, in disease induction methods and disease models. We argue that such methods may improve replicability by creating diverse and representative distribution of baseline disease state in the reference group, against which treatment efficacy is assessed. Second, we illustrate how meta-analysis can be used to simultaneously assess efficacy and stability (i.e., mean effect and among-individual variability). We identify treatments that have efficacy and are generalizable to the population level (i.e., low interindividual variability), as well as those where there is high interindividual variability in response; for these, latter treatments translation to a clinical setting may require nuance. We argue that by embracing rather than seeking to minimize variability in phenotypic outcomes, we can motivate the shift toward heterogenization and improve both the replicability and generalizability of preclinical research.