Use of factorial designs to optimize animal experiments and reduce animal use

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.

Clever Experimental Designs: Shortcuts for Better iPSC Differentiation

For practical use of pluripotent stem cells (PSCs) for disease modelling, drug screening, and regenerative medicine, the cell differentiation process needs to be properly refined to generate end products with consistent and high quality. To construct and optimize a robust cell-induction process, a myriad of cell culture conditions should be considered. In contrast to inefficient brute-force screening, statistical design of experiments (DOE) approaches, such as factorial design, orthogonal array design, response surface methodology (RSM), definitive screening design (DSD), and mixture design, enable efficient and strategic screening of conditions in smaller experimental runs through multifactorial screening and/or quantitative modeling. Although DOE has become routinely utilized in the bioengineering and pharmaceutical fields, the imminent need of more detailed cell-lineage specification, complex organoid construction, and a stable supply of qualified cell-derived material requires expedition of DOE utilization in stem cell bioprocessing. This review summarizes DOE-based cell culture optimizations of PSCs, mesenchymal stem cells (MSCs), hematopoietic stem cells (HSCs), and Chinese hamster ovary (CHO) cells, which guide effective research and development of PSC-derived materials for academic and industrial applications.

Inter-individual variability in habituation of anxiety-related responses within three mouse inbred strains

Inter-individual variability in behavioral and physiological response has become a well-established phenomenon in animal models of anxiety and other disorders. Such variability is even demonstrated within mouse inbred strains. A recent study showed that adaptive and non-adaptive anxiety phenotypes (measured as habituation and/or sensitization of anxiety responses) may differ within cohorts of 129 mice. This variability was expressed across both anxiety- and activity-related behavioral dimensions. These findings were based however on re-analysis of previously published data. The present study therefore aimed to empirically validate these findings in 129 mice. In addition, we assessed such inter-individuality in two other strains: BALB/c and C57BL/6. Males of three mouse inbred strains (BALB/c, C57BL/6 and 129S2) were behaviorally characterized through repeated exposure to a mild aversive stimulus (modified Hole Board, 4 consecutive trials). Behavioral observations were supplemented with assessment of circulating corticosterone levels. Clustering the individual response trajectories of behavioral and endocrine responses yielded two multidimensional response types of different adaptive value. Interestingly, these response types were displayed by individuals of all three strains. The response types differed significantly on anxiety and activity related behavioral dimensions but not on corticosterone concentrations. This study empirically confirms that adaptive capacities may differ within 129 cohorts. In addition, it extends this inter-individual variability in behavioral profiles to BALB/c and C57BL/6. Whether these two sub-types constitute differential anxiety phenotypes may differ per strain and requires further study.

What is the optimum design for my animal experiment?

Within preclinical research, attention has focused on experimental design and how current practices can lead to poor reproducibility. There are numerous decision points when designing experiments. Ethically, when working with animals we need to conduct a harm-benefit analysis to ensure the animal use is justified for the scientific gain. Experiments should be robust, not use more or fewer animals than necessary, and truly add to the knowledge base of science. Using case studies to explore these decision points, we consider how individual experiments can be designed in several different ways. We use the Experimental Design Assistant (EDA) graphical summary of each experiment to visualise the design differences and then consider the strengths and weaknesses of each design. Through this format, we explore key and topical experimental design issues such as pseudo-replication, blocking, covariates, sex bias, inference space, standardisation fallacy and factorial designs. There are numerous articles discussing these critical issues in the literature, but here we bring together these topics and explore them using real-world examples allowing the implications of the choice of design to be considered. Fundamentally, there is no perfect experiment; choices must be made which will have an impact on the conclusions that can be drawn. We need to understand the limitations of an experiment's design and when we report the experiments, we need to share the caveats that inherently exist.

Biological sex, not reproductive cycle, influences peripheral blood immune cell prevalence in mice

KEY POINTS

Traditionally the female sex, compared with the male sex, has been perceived as having greater variability in many physiological traits, including within the immune system. We investigated effects of biological sex and the female reproductive cycle on numbers of circulating leukocytes in C57BL/6J mice. We show that biological sex, but not female reproductive cyclicity, has a significant effect on peripheral blood immune cell prevalence and variability, and that sex differences were not consistent amongst common inbred laboratory mouse strains. We found that male C57BL/6J mice, compared with female mice, have greater variability in peripheral blood immunophenotype, and that this was influenced by body weight. We created summary tables for researchers to facilitate experiment planning and sample size calculations for peripheral immune cells that consider the effects of biological sex.

ABSTRACT

Immunophenotyping (i.e. quantifying the number and types of circulating leukocytes) is used to characterize immune changes during health and disease, and in response to pharmacological and other interventions. Despite the importance of biological sex in immune function, there is considerable uncertainty amongst researchers as to the extent to which biological sex or the female reproductive cycle influence blood immunophenotype. We quantified circulating leukocytes by multicolour flow cytometry in young C57BL/6J mice and assessed the effects of the reproductive cycle, biological sex, and other experimental and biological factors on data variability. We found that there are no significant effects of the female reproductive cycle on the prevalence of peripheral blood B cells, NK cells, CD4⁺ T cells, CD8⁺ T cells, monocytes, or neutrophils. Immunophenotype composition and variability do not significantly change between stages of the female reproductive cycle. There are, however, sex-specific differences in immune cell prevalence, with fewer monocytes, neutrophils, and NK cells in female mice. Surprisingly, immunophenotype is more variable in male mice, and weight is a significant contributing factor. We provide tools for researchers to perform a priori sample size calculations for two-group and factorial analyses. We show that immunophenotype varies between inbred mouse strains, and that using equal sample sizes of male and female mice is not always appropriate for within-sex evaluations of immune cell populations in peripheral blood.

Challenges and Opportunities for the Veterinary Pathologist in Biomedical Research

Animal models have critical roles in biomedical research in promoting understanding of human disease and facilitating development of new therapies and diagnostic techniques to improve human and animal health. In the study of myriad human conditions, each model requires in-depth characterization of its assets and limitations in order for it to be used to greatest advantage. Veterinary pathology expertise is critical in understanding the relevance and translational validity of animal models to conditions under study, assessing morbidity and mortality, and validating outcomes as relevant or not to the study interventions. Clear communication with investigators and education of research personnel on the use and interpretation of pathology endpoints in animal models are critical to the success of any research program. The veterinary pathologist is underutilized in biomedical research due to many factors including misconceptions about high fiscal costs, lack of perceived value, limited recognition of their expertise, and the generally low number of veterinary pathologists currently employed in biomedical research. As members of the multidisciplinary research team, veterinary pathologists have an important role to educate scientists, ensure accurate interpretation of pathology data, maximize rigor, and ensure reproducibility to provide the most reliable data for animal models in biomedical research.

Krill oil extract inhibits the migration of human colorectal cancer cells and down-regulates EGFR signalling and PD-L1 expression

BACKGROUND

The currently available treatments for colorectal cancer (CRC) are often associated with serious side-effects. Therefore, the development of a novel nutraceutical agent may provide an alternative complementary therapy for CRC. Overexpression of the epidermal growth factor receptor (EGFR) associates with a range of cancers while downregulation of EGFR signalling can inhibit cancer growth. Our previous studies have shown that the free fatty acid extract (FFAE) of krill oil exhibits anti-proliferative and pro-apoptotic properties. This study determines the effects of krill oil extract on the migration of human CRC cells, and its potential role in modulating EGFR signalling pathway and the expression of programmed death ligand 1 (PD-L1).

METHODS

Human CRC cells, DLD-1 and HT-29 were treated with FFAE of KO at 0.03 and 0.12 μL/100 μL for 8 or 24 h. Cell migration was determined by Boyden chamber migration assay. The expression of EGFR, phosphorylated EGFR (pEGFR), protein kinase B (AKT), phosphorylated AKT (pAKT), extracellular signal regulated kinase (ERK1/2), phosphorylated ERK1/2 (pERK1/2) as well as PD-L1 were assessed by western blotting and immunohistochemistry.

RESULTS

The FFAE of krill oil significantly inhibited cell migration compared to ethanol-treated (vehicle control) cells (P < 0.01 to P < 0.001). At the molecular level, krill oil extract reduced the expression of EGFR, pEGFR (P < 0.001 for both) and their downstream signalling, pERK1/2 and pAKT (P < 0.01 to P < 0.001) without altering total ERK 1/2 and AKT levels. In addition, the expression of PD-L1 was reduced by 67 to 72% (P < 0.001) following the treatment with krill oil extract.

CONCLUSION

This study has demonstrated that krill oil may be a potential therapeutic/adjunctive agent for CRC attributed to its anti-migratory effects.. The potential anti-cancer properties of krill oil are likely to be associated with the downregulation of EGFR, pEGFR and their downstream pERK/ERK1/2 and pAKT/AKT signalling pathways along with the downregulation of PD-L1.

Quality of interventional animal experiments in Chinese journals: compliance with ARRIVE guidelines

BACKGROUND

In view of the inadequacy and incompleteness of currently-reported animal experiments and their overall poor quality, we retrospectively evaluated the reporting quality of animal experiments published in Chinese journals adhering to the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines.

RESULTS

The databases CNKI, WanFang, VIP, and CBM were searched from inception until July 2018. Two appropriately-trained reviewers screened and extracted articles independently. The ARRIVE guidelines were used to assess the quality of the published reports of animal experiments. The compliance rate of every item was analyzed relative to their date of publication. A total of 4342 studies were included, of which 73.0% had been cited ≤5 times. Only 29.0% (1261/4342) were published in journals listed in the Chinese Science Citation Database. The results indicate that the compliance rate of approximately half of the sub-items (51.3%, 20/39) was less than 50%, of which 65.0% (13/20) was even less than 10%.

CONCLUSIONS

The reporting quality of animal experiments in Chinese journals is not at a high level. Following publication of the ARRIVE guidelines in 2010, the compliance rate of the majority of its requirements has improved to some extent. However, less attention has been paid to the ethics and welfare of experimental animals, and a number of specific items in the Methods, Results, and Discussion sections continue to not be reported in sufficient detail. Therefore, it is necessary to popularize the ARRIVE guidelines, advocate researchers to adhere to them in the future, and in particular promote the use of the guidelines in specialized journals in order that the design, implementation, and reporting of animal experiments is promoted, to ultimately improve their quality.

Quality of design and reporting of animal research in peritoneal dialysis: A scoping review

The concerns about reproducibility and validity of animal studies are partly related to poor experimental design and reporting. Here, we undertook a scoping review of the literature to determine the extent and quality of reporting of animal studies on peritoneal dialysis (PD). Online databases were searched to identify 567 relevant original articles published between 1979 and 2018. These were analyzed with respect to bibliographic parameters and general aspects of animal experimentation. A subgroup of 120 studies was analyzed in detail in terms of the impact on the reporting quality of the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines for animal studies. The number of animal studies on PD increased continuously over the years with a thematic shift toward long-term preservation of the peritoneum as a dialyzing organ. There were significant deficiencies in research design with the lack of sample size estimation, randomization, and blinding being the commonest shortcomings. The description of animal numbers, housing conditions, use of medication, and statistical analysis was incomplete. The introduction in 2010 of the ARRIVE guidelines produced very little improvement in the completeness of reporting regardless of journal impact factor. The animal studies on PD suffer from deficits in experimental protocols and transparent reporting. These drawbacks need to be corrected to ensure high-quality and much-needed animal research in PD.

Reduction by Well-defined Objectives

Examination of programmes of experimental work involving live animals indicates scope for worthwhile reduction in animal usage by identifying more clearly the objectives of the different stages of a programme. Having a defined first objective for new or transferred methodology as “to optimise the methods”, rather than an exploratory “try it with a few animals and modify” approach, is more likely to obtain the conditions for largest divergence between the effect to be measured and the background variability. Where several experiments will use the same methodology, even small improvements in this “signal to noise” ratio may be worthwhile, as the reduction is cumulative. Subdivision to more precise objectives helps concentrate the animal usage. For example, separating “to determine the time of a distinct peak” from “to determine the size of the peak” avoids using the numbers needed to achieve the latter for every time point at which the peak might occur. Similarly, setting a series of objectives for a programme that lead to clear decision points allows setting of clear criteria for achievement at each stage, as well as for the design and analysis to be the most efficient. This paper gives illustrations of the applicability of these arguments and estimates of potential reduction.

Sex bias in preclinical research and an exploration of how to change the status quo

There has been a revolution within clinical trials to include females in the research pipeline. However, there has been limited change in the preclinical arena; yet the research here lays the ground work for the subsequent clinical trials. Sex bias has been highlighted as one of the contributing factors to the poor translation and replicability issues undermining preclinical research. There have been multiple calls for action, and the funders of biomedical research are actively pushing the inclusion of sex as a biological variable. Here, we consider the current standard practice within the preclinical research setting, why there is a movement to include females and why the imbalance exists. We explore organizational change theory as a tool to shape strategies needed at an individual and institute level to change the status quo. The ultimate goal is to create a scientific environment in which our preclinical research automatically implements sex-sensitive approaches. LINKED ARTICLES: This article is part of a themed section on The Importance of Sex Differences in Pharmacology Research. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.21/issuetoc.

Translational pain assessment: could natural animal models be the missing link?

Failure of analgesic drugs in clinical development is common. Along with the current "reproducibility crisis" in pain research, this has led some to question the use of animal models. Experimental models tend to comprise genetically homogeneous groups of young, male rodents in restricted and unvarying environments, and pain-producing assays that may not closely mimic the natural condition of interest. In addition, typical experimental outcome measures using thresholds or latencies for withdrawal may not adequately reflect clinical pain phenomena pertinent to human patients. It has been suggested that naturally occurring disease in veterinary patients may provide more valid models for the study of painful disease. Many painful conditions in animals resemble those in people. Like humans, veterinary patients are genetically diverse, often live to old age, and enjoy a complex environment, often the same as their owners. There is increasing interest in the development and validation of outcome measures for detecting pain in veterinary patients; these include objective (eg, locomotor activity monitoring, kinetic evaluation, quantitative sensory testing, and bioimaging) and subjective (eg, pain scales and quality of life scales) measures. Veterinary subject diversity, pathophysiological similarities to humans, and diverse outcome measures could yield better generalizability of findings and improved translation potential, potentially benefiting both humans and animals. The Comparative Oncology Trial Consortium in dogs has pawed the way for translational research, surmounting the challenges inherent in veterinary clinical trials. This review describes numerous conditions similarly applicable to pain research, with potential mutual benefits for human and veterinary clinicians, and their respective patients.

Optimisation of ex vivo memory B cell expansion/differentiation for interrogation of rare peripheral memory B cell subset responses

Background: Human memory B cells play a vital role in the long-term protection of the host from pathogenic re-challenge. In recent years the importance of a number of different memory B cell subsets that can be formed in response to vaccination or infection has started to become clear. To study memory B cell responses, cells can be cultured ex vivo, allowing for an increase in cell number and activation of these quiescent cells, providing sufficient quantities of each memory subset to enable full investigation of functionality. However, despite numerous papers being published demonstrating bulk memory B cell culture, we could find no literature on optimised conditions for the study of memory B cell subsets, such as IgM ⁺ memory B cells. Methods: Following a literature review, we carried out a large screen of memory B cell expansion conditions to identify the combination that induced the highest levels of memory B cell expansion. We subsequently used a novel Design of Experiments approach to finely tune the optimal memory B cell expansion and differentiation conditions for human memory B cell subsets. Finally, we characterised the resultant memory B cell subpopulations by IgH sequencing and flow cytometry. Results: The application of specific optimised conditions induce multiple rounds of memory B cell proliferation equally across Ig isotypes, differentiation of memory B cells to antibody secreting cells, and importantly do not alter the Ig genotype of the stimulated cells.  Conclusions: Overall, our data identify a memory B cell culture system that offers a robust platform for investigating the functionality of rare memory B cell subsets to infection and/or vaccination.

Optimisation of ex vivo memory B cell expansion/differentiation for interrogation of rare peripheral memory B cell subset responses

Background:Human memory B cells play a vital role in the long-term protection of the host from pathogenic re-challenge. In recent years the importance of a number of different memory B cell subsets that can be formed in response to vaccination or infection has started to become clear. To study memory B cell responses, cells can be culturedex vivo,allowing for an increase in cell number and activation of these quiescent cells, providing sufficient quantities of each memory subset to enable full investigation of functionality. However, despite numerous papers being published demonstrating bulk memory B cell culture, we could find no literature on optimised conditions for the study of memory B cell subsets, such as IgM+memory B cells.Methods:Following a literature review, we carried out a large screen of memory B cell expansion conditions to identify the combination that induced the highest levels of memory B cell expansion. We subsequently used a novel Design of Experiments approach to finely tune the optimal memory B cell expansion and differentiation conditions for human memory B cell subsets. Finally, we characterised the resultant memory B cell subpopulations by IgH sequencing and flow cytometry.Results:The application of specific optimised conditions induce multiple rounds of memory B cell proliferation equally across Ig isotypes, differentiation of memory B cells to antibody secreting cells, and importantly do not alter the Ig genotype of the stimulated cells. Conclusions:Overall, our data identify a memory B cell culture system that offers a robust platform for investigating the functionality of rare memory B cell subsets to infection and/or vaccination.

The Experimental Design Assistant

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community. It will have an important role in addressing causes of irreproducibility.

Applying the new SABV (sex as a biological variable) policy to research and clinical care

Sex as a biological variable (SABV) is a key part of the new National Institutes of Health (NIH) initiative to enhance reproducibility through rigor and transparency. The SABV policy requires researchers to factor sex into the design, analysis, and reporting of vertebrate animal and human studies. The policy was implemented as it has become increasingly clear that male/female differences extend well beyond reproductive and hormonal issues. Implementation of the policy is also meant to address inattention to sex influences in biomedical research. Sex affects: cell physiology, metabolism, and many other biological functions; symptoms and manifestations of disease; and responses to treatment. For example, sex has profound influences in neuroscience, from circuitry to physiology to pain perception. Extending beyond the robust efforts of NIH to ensure that women are included in clinical trials, the SABV policy also includes rigorous preclinical experimental designs that inform clinical research. Additionally, the NIH has engaged journal editors and publishers to facilitate reproducibility by addressing rigor and promoting transparency through scientifically appropriate sex-specific study results reporting. The Sex And Gender Equity in Research (SAGER) guidelines were developed to assist researchers and journal editors in reporting sex and gender information in publications [1].

Using smartphones to decrease substance use via self-monitoring and recovery support: study protocol for a randomized control trial

Background

Alcohol abuse, other substance use disorders, and risk behaviors associated with the human immunodeficiency virus (HIV) represent three of the top 10 modifiable causes of mortality in the US. Despite evidence that continuing care is effective in sustaining recovery from substance use disorders and associated behaviors, patients rarely receive it. Smartphone applications (apps) have been effective in delivering continuing care to patients almost anywhere and anytime. This study tests the effectiveness of two components of such apps: ongoing self-monitoring through Ecological Momentary Assessments (EMAs) and immediate recovery support through Ecological Momentary Interventions (EMIs).

Methods/design

The target population, adults enrolled in substance use disorder treatment (n = 400), are being recruited from treatment centers in Chicago and randomly assigned to one of four conditions upon discharge in a 2 × 2 factorial design. Participants receive (1) EMAs only, (2) EMIs only, (3) combined EMAs + EMIs, or (4) a control condition without EMA or EMI for 6 months. People in the experimental conditions receive smartphones with the apps (EMA and/or EMI) specific to their condition. Phones alert participants in the EMA and EMA + EMI conditions at five random times per day and present participants with questions about people, places, activities, and feelings that they experienced in the past 30 min and whether these factors make them want to use substances, support their recovery, or have no impact. Those in the EMI and EMA + EMI conditions have continual access to a suite of support services. In the EMA + EMI condition, participants are prompted to use the EMI(s) when responses to the EMA(s) indicate risk. All groups have access to recovery support as usual. The primary outcome is days of abstinence from alcohol and other drugs. Secondary outcomes are number of HIV risk behaviors and whether abstinence mediates the effects of EMA, EMI, or EMA + EMI on HIV risk behaviors.

Discussion

This project will enable the field to learn more about the effects of EMAs and EMIs on substance use disorders and HIV risk behaviors, an understanding that could potentially make treatment and recovery more effective and more widely accessible.

Trial registration

ClinicalTrials.gov, ID: NCT02132481. Registered on 5 May 2014.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-017-2096-z) contains supplementary material, which is available to authorized users.

Factors influencing preclinical in vivo evaluation of mumps vaccine strain immunogenicity

Immunogenicity testing in animals is a necessary preclinical assay for demonstration of vaccine efficacy the results of which are often the basis for the decision whether to proceed or withdraw the further development of the novel vaccine candidate. However, in vivo assays are rarely, if at all, optimized and validated. Here we clearly demonstrate the importance of in vivo assay (mumps virus immunogenicity testing in guinea pigs) optimization for gaining reliable results and the suitability of Fractional factorial design of experiments (DoE) for such a purpose. By the use of DoE with resolution IV (2IV((4-1))) we clearly revealed that the parameters significantly increasing assay sensitivity were interval between animal immunizations followed by the body weight of experimental animals. The quantity (0 versus 2%) of the stabilizer (fetal bovine serum, FBS) in the sample was shown as non-influencing parameter in DoE setup. However, the separate experiment investigating only the FBS influence, and performed under other parameters optimally set, showed that FBS also influences the results of immunogenicity assay. Such finding indicated that (a) factors with strong influence on the measured outcome can hide the effects of parameters with modest/low influence and (b) the matrix of mumps virus samples to be compared for immunogenicity must be identical for reliable virus immunogenicity comparison. Finally the 3 mumps vaccine strains widely used for decades in the licensed vaccines were for the first time compared in an animal model, and results obtained were in line with their reported immunogenicity in human population supporting the predictive power of the optimized in vivo assay.

Studying both sexes: a guiding principle for biomedicine

In May 2014, the U.S. National Institutes of Health (NIH) announced that it will ensure that investigators account for sex as a biological variable (SABV) in NIH-funded preclinical research as part of the agency's rigor and transparency initiative. Herein, I describe in more detail the rationale behind the SABV policy component and provide additional detail about policy goals. In short, studying both sexes is a guiding principle in biomedical research that will expand knowledge toward turning discovery into health. NIH expects that considering SABV in preclinical research will help to build a knowledge base that better informs the design of clinical research and trials in humans. Integrating the practice of studying both sexes in preclinical research will, over time, expand our currently incomplete knowledge base that plays a critical role in informing the development of sex- and gender-appropriate medical care for women and men.

The place of experimental design and statistics in the 3Rs

The 3Rs--replacement, reduction, and refinement--can be applied to any animal experiment by researchers and other bodies seeking to conduct those studies in as humane a manner as possible. Key to the success of this endeavor is an appreciation of the principles of good experimental design and analysis; these need to be considered in concert before any data is collected. Indeed, many of the principles central to helping achieve the objectives of the 3Rs-such as conducting valid, reliable, and efficient experiments; clearly and transparently reporting findings; and ensuring that an appreciation and understanding of animal welfare plays a central role in laboratory practice-are to the betterment of research per se.

Exposure to environmental stressors result in increased viral load and further reduction of production parameters in pigs experimentally infected with PCV2b

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Environmental stress increases viral load of PCV2b in serum and tissue.

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Environmental stress exacerbates PCV2b induced weight loss.

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Environmental stress and PCV2b reduce ADG and impact negatively on FCR.

Porcine circovirus type 2 (PCV2) has been identified as the essential, but not sole, underlying infectious component for PCV-associated diseases (PCVAD). Several co-factors have been suggested to convert an infection with PCV2 into the clinical signs of PCVAD, including co-infection with a secondary pathogen and the genetic background of the pig. In the present study, we investigated the role of environmental stressors in the form of changes in environmental temperature and increased stocking-density on viral load in serum and tissue, average daily weight gain (ADG) and food conversion rate (FCR) of pigs experimentally infected with a defined PCV2b strain over an eight week period. These stressors were identified recently as risk factors leading to the occurrence of severe PCVAD on a farm level. In the current study, PCV2-free pigs were housed in separate, environmentally controlled rooms, and the experiment was performed in a 2 × 2 factorial design. In general, PCV2b infection reduced ADG and increased FCR, and these were further impacted on by the environmental stressors. Furthermore, all stressors led to an increased viral load in serum and tissue as assessed by qPCR, although levels did not reach statistical significance. Our data suggest that there is no need for an additional pathogen to develop PCVAD in conventional status pigs, and growth retardation and clinical signs can be induced in PCV2 infected pigs that are exposed to environmental stressors alone.

Selenium prevents downregulation of antioxidant selenoprotein genes by methylmercury

Selenium (Se) is an essential nutrient required by Se-dependent proteins, termed selenoproteins. The selenoprotein family is small but diverse and includes key proteins in antioxidant, redox signaling, thyroid hormone metabolism, and protein folding pathways. Methylmercury (MeHg) is a toxic environmental contaminant that affects seafood safety. Selenium can reduce MeHg toxicity, but it is unclear how selenoproteins are affected in this interaction. In this study we explored how Se and MeHg interact to affect the mRNA expression of selenoprotein genes in whole zebrafish (Danio rerio) embryos. Embryos were obtained from adult zebrafish fed MeHg with or without elevated Se in a 2×2 factorial design. The embryo mRNA levels of 30 selenoprotein genes were then measured. These genes cover most of the selenoprotein families, including members of the glutathione peroxidase (GPX), thioredoxin reductase, iodothyronine deiodinase, and methionine sulfoxide reductase families, along with selenophosphate synthetase 2 and selenoproteins H, J-P, T, W, sep15, fep15, and fam213aa. GPX enzyme activity and larval locomotor activity were also measured. We found that around one-quarter of the selenoprotein genes were downregulated by elevated MeHg. These downregulated genes were dominated by selenoproteins from antioxidant pathways that are also susceptible to Se-deficiency-induced downregulation. MeHg also decreased GPX activity and induced larval hypoactivity. Elevated Se partially prevented MeHg-induced disruption of selenoprotein gene mRNA levels, GPX activity, and larval locomotor activity. Overall, the MeHg-induced downregulation and subsequent rescue by elevated Se levels of selenogenes regulated by Se status suggest that Se deficiency is a contributing factor to MeHg toxicity.

Selenium and mercury have a synergistic negative effect on fish reproduction

Selenium (Se) can reduce the negative impacts of mercury (Hg) toxicity on growth and survival, but little is known about how these two elements interact in reproduction. In the following study we explored the effects of organic Hg and Se on the growth, survival and reproduction of female zebrafish (Danio rerio). Fish were fed one of four diets from 73 until 226 dpf in a 2 × 2 factorial design, using selenomethionine (SeMet) and methylmercury (MeHg) as the Se and Hg sources, respectively. Each diet contained Se at either requirement (0.7 mg Se/kg DM) or elevated levels (10 mg Se/kgDM), and Hg at either low (0.05 mg Hg/kg DM) or elevated (12 mg Hg/kg DM) levels. Between 151 and 206 dpf the female fish were pairwise crossed against untreated male fish and the mating success, fecundity, embryo survival, and subsequent overall reproductive success were measured. Elevated dietary Se reduced Hg levels in both the adult fish and their eggs. Elevated dietary Hg and Se increased egg Se levels to a greater extent than when dietary Se was elevated alone. At elevated maternal intake levels, egg concentrations of Se and Hg reflected the maternal dietary levels and not the body burdens of the adult fish. Elevated dietary Hg reduced the growth and survival of female fish, but these effects were largely prevented with elevated dietary Se. Elevated dietary Se alone did not affect fish growth or survival. Compared to other treatments, elevated dietary Hg alone increased both mating and overall reproductive success with <100 days of exposure, but decreased these parameters with >100 days exposure. Elevated dietary Se decreased fecundity, embryo survival, and overall reproductive success. The combination of elevated Se and Hg had a synergistic negative effect on all aspects of fish reproduction compared to those groups fed elevated levels of either Se or Hg. Overall the data demonstrate that while increased dietary Se may reduce adverse effects of Hg on the growth and survival in adult fish, it can negatively affect fish reproductive potential, and the effect on reproduction is enhanced in the presence of elevated Hg.

Refinement and reduction through the control of variation

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

Data Mining and Meta-Analysis on DNA Microarray Data

Microarray technology enables high-throughput parallel gene expression analysis, and use has grown exponentially thanks to the development of a variety of applications for expression, genetics and epigenetic studies. A wealth of data is now available from public repositories, providing unprecedented opportunities for meta-analysis approaches, which could generate new biological information, unrelated to the original scope of individual studies. This study provides a guideline for identification of biological significance of the statistically-selected differentially-expressed genes derived from gene expression arrays as well as to suggest further analysis pathways. The authors review the prerequisites for data-mining and meta-analysis, summarize the conceptual methods to derive biological information from microarray data and suggest software for each category of data mining or meta-analysis.

Systematic review of pre-clinical models assessing implant integration in locally compromised sites and/or systemically compromised animals

OBJECTIVE

The aim was to systematically search the dental literature for pre-clinical models assessing implant integration in locally compromised sites (part 1) and systemically compromised animals (part 2), and to evaluate the quality of reporting of included publications.

METHODS

A Medline search (1966-2011) was performed, complimented by additional hand searching. The quality of reporting of the included publications was evaluated using the 20 items of the ARRIVE (Animals in Research In Vivo Experiments) guidelines.

RESULTS

One-hundred and seventy-six (part 1; mean ARRIVE score = 15.6 ± 2.4) and 104 (part 2; 16.2 ± 1.9) studies met the inclusion criteria. The overall mean score for all included studies amounted to 15.8 ± 2.2. Housing (38.3%), allocation of animals (37.9%), numbers analysed (50%) and adverse events (51.4%) of the ARRIVE guidelines were the least reported. Statistically significant differences in mean ARRIVE scores were found depending on the publication date (p < 0.05), with the highest score of 16.7 ± 1.6 for studies published within the last 2 years.

CONCLUSIONS

A large number of studies met the inclusion criteria. The ARRIVE scores revealed heterogeneity and missing information for selected items in more than 50% of the publications. The quality of reporting shifted towards better-reported pre-clinical trials within recent years.

Strategies for the optimisation of in vivo experiments in accordance with the 3Rs philosophy

There are a large number of chemicals in current use for which adequate toxicity data are not available. Whilst there are clear ethical and legal obligations to obtain data from sources other than in vivo experiments wherever possible, in certain cases in vivo assays may be deemed necessary. In such circumstances, it is essential to ensure that the maximum amount of high quality data is obtained from the minimum number of animals, using the most humane procedures, in accordance with the philosophy of reduction, refinement and replacement (3Rs). The aim of this report is to provide a strategy for anyone involved in animal experimentation, for either toxicological or pharmacological purposes, as to how in vivo experiments may be optimised. The impact of generic and endpoint specific sources of variability has been highlighted in a proof-of-principle analysis considering the variation in protocols for assays for four human health endpoints (skin sensitisation, reproductive/developmental toxicity, mutagenicity and carcinogenicity). Other factors such as operator training, experimental/statistical design, use of lower species and use of combined assays are also discussed. Recommendations for optimisation of in vivo assays, in terms of the 3Rs philosophy, applied to performing tests, harvesting data and appropriate reporting are summarised as a checklist of issues to be addressed prior to undertaking such assays.

Pharmacological validation of a telemetric model for the measurement of bronchoconstriction in conscious rats

INTRODUCTION

Telemetric measurement of intra-pleural pressure in conscious animals that are restrained in head-out plethysmography chambers enables determination of airway resistance. Originally proposed over 10 years ago, pharmacological validation of this technique is limited. Here airway resistance in conscious, instrumented rats was compared to measurement in anaesthetised rats via a fluid filled oesophageal catheter following administration of two different pharmacological agents.

METHODS

Male rats were implanted with telemetry devices and were trained to accept the restraint of head-out plethysmography chambers. A separate group of male rats were anaesthetised, placed in a body-enclosed plethysmography chamber and were prepared with a tracheal, oesphageal and jugular vein cannulae. Methacholine or NECA were given intravenously and changes in ventilation and airway resistance were measured.

RESULTS

The pressure signal obtained in the telemetered rats was found to be extremely variable. Variability was confounded by excessive struggling, particularly during the infusion periods. Misplacement of the pressure sensitive catheter tip and prior habituation to the chamber were not factors in signal variability. Consequently, no dose-response relationship to either pharmacological agent was established in this model. Dose-dependent increases in resistance to both methacholine and NECA were measured in anaesthetised rats using body-enclosed plethysmography.

DISCUSSION

Given the variability of the pressure signal within and between rats, the feasibility of a model in conscious rats for the measurement of airway resistance is questioned. Improved restraint methods or alternative models in conscious animals should therefore be explored. In the meantime, assessment of airway resistance is best confined to the anaesthetised rat.

Survey of the quality of experimental design, statistical analysis and reporting of research using animals

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

Design of experiments with multiple independent variables: a resource management perspective on complete and reduced factorial designs

An investigator who plans to conduct an experiment with multiple independent variables must decide whether to use a complete or reduced factorial design. This article advocates a resource management perspective on making this decision, in which the investigator seeks a strategic balance between service to scientific objectives and economy. Considerations in making design decisions include whether research questions are framed as main effects or simple effects; whether and which effects are aliased (confounded) in a particular design; the number of experimental conditions that must be implemented in a particular design and the number of experimental subjects the design requires to maintain the desired level of statistical power; and the costs associated with implementing experimental conditions and obtaining experimental subjects. In this article 4 design options are compared: complete factorial, individual experiments, single factor, and fractional factorial. Complete and fractional factorial designs and single-factor designs are generally more economical than conducting individual experiments on each factor. Although relatively unfamiliar to behavioral scientists, fractional factorial designs merit serious consideration because of their economy and versatility.

An Integrated Decision-tree Testing Strategy for Repeat Dose Toxicity with Respect to the Requirements of the EU REACH Legislation

This paper presents some results of a joint research project conducted by FRAME and Liverpool John Moores University, and sponsored by Defra, on the status of alternatives to animal testing with regard to the European Union REACH (Registration, Evaluation and Authorisation of Chemicals) system for the safety testing and risk assessment of chemicals. The project covered all the main toxicity end-points associated with REACH. This paper focuses on the use of alternative (non-animal) methods (both in vitro and in silico) for repeat dose (sub-acute, sub-chronic and chronic) toxicity testing. It reviews the limited number of in silico and in vitro tests available for this endpoint, and outlines new technologies which could be used in the future, e.g. the use of biomarkers and the ‘omics’ technologies. An integrated testing strategy is proposed, which makes use of as much non-animal data as possible, before any essential in vivo studies are performed. Although none of the non-animal tests are currently undergoing validation, their results could help to reduce the number of animals required for testing for repeat dose toxicity.

An Integrated Decision-tree Testing Strategy for Repeat Dose Toxicity with Respect to the Requirements of the EU REACH Legislation

This paper presents some results of a joint research project conducted by FRAME and Liverpool John Moores University, and sponsored by Defra, on the status of alternatives to animal testing with regard to the European Union REACH (Registration, Evaluation and Authorisation of Chemicals) system for the safety testing and risk assessment of chemicals. The project covered all the main toxicity end-points associated with REACH. This paper focuses on the use of alternative (non-animal) methods (both in vitro and in silico) for repeat dose (sub-acute, sub-chronic and chronic) toxicity testing. It reviews the limited number of in silico and in vitro tests available for this endpoint, and outlines new technologies which could be used in the future, e.g. the use of biomarkers and the ‘omics’ technologies. An integrated testing strategy is proposed, which makes use of as much non-animal data as possible, before any essential in vivo studies are performed. Although none of the non-animal tests are currently undergoing validation, their results could help to reduce the number of animals required for testing for repeat dose toxicity.

Laboratory Animal Science: A Resource to Improve the Quality of Science

The contribution of animal experimentation to biomedical research is of undoubted value, nevertheless the real usefulness of animal models is still being hotly debated. Laboratory Animal Science is a multidisciplinary approach to humane animal experimentation that allows the choice of the correct animal model and the collection of unbiased data. Refinement, Reduction and Replacement, the "3Rs rule", are now widely accepted and have a major influence on animal experimentation procedures. Refinement, namely any decrease in the incidence or severity of inhumane procedures applied to animals, has been today extended to the entire lives of the experimental animals. Reduction of the number of animals used to obtain statistically significant data may be achieved by improving experimental design and statistical analysis of data. Replacement refers to the development of validated alternative methods. A Laboratory Animal Science training program in biomedical degrees can promote the 3Rs and improve the welfare of laboratory animals as well as the quality of science with ethical, scientific and economic advantages complying with the European requirement that "persons who carry out, take part in, or supervise procedures on animals, or take care of animals used in procedures, shall have had appropriate education and training".

Fundamental steps in experimental design for animal studies

Animal studies continue to have a vital role in science development. The aim of this review is to provide to new investigators an overview of the important steps involved in experimental designs and also to suggest some practical information that is commonly associated with this process. Investigators should adhere to the ethical procedure and follow strictly the scientific method. Both the aims and well-formulated hypothesis are essential and practical. In this regard a profound literature search and the aid of an experienced statistician is encouraged. The need of randomization, blinding, and attempting to minimize variation is discussed and recommended. The choosing of good control groups and the employment of pilot studies are useful. Finally, the formulation of new questions to be further responded is expected.

Reduction in laboratory animal use by factorial design

Factorial experimental designs (FEDs) can be used to study the effects of controllable variables, such as an experimental treatment, sex, strain, age, diet and prior treatment of animals, on some defined response. Such designs have been widely used in optimising manufacturing processes, but have rarely been used in optimising animal experiments in drug discovery. FEDs generally provide more information than the alternative "one-variable-at-a-time" approach, because each animal contributes information on the effect of every factor, and because such designs can highlight any interactions among the variables. Although FEDs can have any number of factors and levels of each factor, where many factors are to be explored, it is common to do an initial experiment using two levels of each factor, and in some cases fractional factorial designs can be used to reduce the total number of treatment combinations to manageable levels. These designs have been used successfully at AstraZeneca in the optimisation of in vivo drug screening experiments, where their use has effectively reduced the numbers of animals used in some routine screens.

Sample Power and ExpDesign: tools for improving design of animal experiments

Proper experimental design, involving the correct number of animals, should be a basic skill for any scientist working with animals. The authors describe a university-developed and freely available tutorial program and an interactive computer-assisted learning program, both of which guide students through the steps necessary for designing animal experiments and estimating optimal sample sizes.

Guidelines for the design and statistical analysis of experiments using laboratory animals

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